Superconducting state parameters of monovalent and polyvalent amorphous

NASA Astrophysics Data System (ADS)

Sonvane, Y. A.; Patel, H. P.; Thakor, P. B.

2015-08-01

In the present study deals, we have calculated superconducting state parameter (SSP) like electron-phonon coupling strength λ, coulomb pseudo potential, μ*, transition temperature Tc, isotope effect exponent α and effective interaction strength N0V of monovalent (Li), divalent (Zn), trivalent (In) and tetravalent (Pb) amorphous. To carry out this work we have used our newly constructed model pseudo potential to describe electron ion interaction along with three different local field correction functions like Hartree, Taylor and Sarkar et al. The present results are found in good agreement with other available theoretical as well as experimental data.

Interaction Potentials for Br(2P) + Ar, Kr, Xe (1S) by the Crossed Molecular Beams Method.

DTIC Science & Technology

1981-03-01

recombination was significantly affected by eBr-RG" In their study, the interaction potential between Br and RG was assumed to be of the Lennard ... Jones (L-J) form with the following parameters: RG=Ar, c=1.0 kcal/mole, a=3.0 A; RG=Xe, e-1.0 kcal/mole, a=3.5 A. A slightly shallower Br-Ar potential ...AOA-A00 002 CALIFORNIA UNIV BERKELEY LAWRENCE BERKELEY LAB F/6 20/7 INTERACTION POTENTIALS FOR BR2P) + AR. KR. XE (IS) BY THE CROS--ETCfIU MAR 81 P

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Study on superconducting state parameters of Cu1-xZrx metallic glasses using model potentials

NASA Astrophysics Data System (ADS)

Jambusarwala, Tasneem S.; Gajjar, P. N.

2018-05-01

The superconducting state parameters (SSP) of Cu1-xZrx metallic glasses over the full range of concentration x of Zr have been investigated to study influence of various local pseudopotentials. The study includes the computation of electron-phonon coupling strength (λ), transition temperature (TC), isotope effect exponent (α) and effective interaction strength (N0V) using fourteen different forms of local model potentials. The local field correction function proposed by Taylor (T) is used. The influence of model potential on various parameters is ranging from 6% to 83% for pure Zr and 28% to 84% for pure Cu. The present study confirms that the identification of model potential is vital in studying Superconducting State Parameters.

Constraints on the dark matter and dark energy interactions from weak lensing bispectrum tomography

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

An, Rui; Feng, Chang; Wang, Bin, E-mail: an_rui@sjtu.edu.cn, E-mail: chang.feng@uci.edu, E-mail: wang_b@sjtu.edu.cn

We estimate uncertainties of cosmological parameters for phenomenological interacting dark energy models using weak lensing convergence power spectrum and bispectrum. We focus on the bispectrum tomography and examine how well the weak lensing bispectrum with tomography can constrain the interactions between dark sectors, as well as other cosmological parameters. Employing the Fisher matrix analysis, we forecast parameter uncertainties derived from weak lensing bispectra with a two-bin tomography and place upper bounds on strength of the interactions between the dark sectors. The cosmic shear will be measured from upcoming weak lensing surveys with high sensitivity, thus it enables us to usemore » the higher order correlation functions of weak lensing to constrain the interaction between dark sectors and will potentially provide more stringent results with other observations combined.« less

Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies.

PubMed

Beste, A; Harrison, R J; Yanai, T

2006-08-21

Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (cf. thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a nongeometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as the constraint on the orbitals to be orthogonal.

Factorial experimental design for the culture of human embryonic stem cells as aggregates in stirred suspension bioreactors reveals the potential for interaction effects between bioprocess parameters.

PubMed

Hunt, Megan M; Meng, Guoliang; Rancourt, Derrick E; Gates, Ian D; Kallos, Michael S

2014-01-01

Traditional optimization of culture parameters for the large-scale culture of human embryonic stem cells (ESCs) as aggregates is carried out in a stepwise manner whereby the effect of varying each culture parameter is investigated individually. However, as evidenced by the wide range of published protocols and culture performance indicators (growth rates, pluripotency marker expression, etc.), there is a lack of systematic investigation into the true effect of varying culture parameters especially with respect to potential interactions between culture variables. Here we describe the design and execution of a two-parameter, three-level (3(2)) factorial experiment resulting in nine conditions that were run in duplicate 125-mL stirred suspension bioreactors. The two parameters investigated here were inoculation density and agitation rate, which are easily controlled, but currently, poorly characterized. Cell readouts analyzed included fold expansion, maximum density, and exponential growth rate. Our results reveal that the choice of best case culture parameters was dependent on which cell property was chosen as the primary output variable. Subsequent statistical analyses via two-way analysis of variance indicated significant interaction effects between inoculation density and agitation rate specifically in the case of exponential growth rates. Results indicate that stepwise optimization has the potential to miss out on the true optimal case. In addition, choosing an optimum condition for a culture output of interest from the factorial design yielded similar results when repeated with the same cell line indicating reproducibility. We finally validated that human ESCs remain pluripotent in suspension culture as aggregates under our optimal conditions and maintain their differentiation capabilities as well as a stable karyotype and strong expression levels of specific human ESC markers over several passages in suspension bioreactors.

Refined potentials for rare gas atom adsorption on rare gas and alkali-halide surfaces

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1985-01-01

The utilization of models of interatomic potential for physical interaction to estimate the long range attractive potential for rare gases and ions is discussed. The long range attractive force is calculated in terms of the atomic dispersion properties. A data base of atomic dispersion parameters for rare gas atoms, alkali ion, and halogen ions is applied to the study of the repulsive core; the procedure for evaluating the repulsive core of ion interactions is described. The interaction of rare gas atoms on ideal rare gas solid and alkali-halide surfaces is analyzed; zero coverage absorption potentials are derived.

Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.

PubMed

Dubinets, Nikita; Slipchenko, Lyudmila V

2017-07-20

Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.

On the interatomic potentials for noble gas mixtures

NASA Astrophysics Data System (ADS)

Watanabe, Kyoko; Allnatt, A. R.; Meath, William J.

1982-07-01

Recently, a relatively simple scheme for the construction of isotropic intermolecular potentials has been proposed and tested for the like species interactions involving He, Ne, Ar, Kr and H 2. The model potential has an adjustable parameter which controls the balance between its exchange and Coulomb energy components. The representation of the Coulomb energy contains a damped multipolar dispersion energy series (which is truncated through O( R-10) and provides additional flexibility through adjustment of the dispersion energy coefficients, particularly C8 and C10, within conservative error estimates. In this paper the scheme is tested further by application to interactions involving unlike noble gas atoms where the parameters in the potential model are determined by fitting mixed second virial coefficient data as a function of temperature. Generally the approach leads to potential of accuracy comparable to the best available literature potentials which are usually determined using a large base of experimental and theoretical input data. Our results also strongly indicate the need of high quality virial data.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases

NASA Astrophysics Data System (ADS)

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-01

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.

Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis

PubMed Central

Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

2016-01-01

A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement. PMID:26799483

Assessment of the Potential Impacts of Wheat Plant Traits across Environments by Combining Crop Modeling and Global Sensitivity Analysis.

PubMed

Casadebaig, Pierre; Zheng, Bangyou; Chapman, Scott; Huth, Neil; Faivre, Robert; Chenu, Karine

2016-01-01

A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites × 125 years), management practices (3 sowing dates × 3 nitrogen fertilization levels) and CO2 (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait × environment × management landscape (∼ 82 million individual simulations in total). The patterns of parameter × environment × management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference cultivar. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identification of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement.

Automated optimization of water-water interaction parameters for a coarse-grained model.

PubMed

Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

2014-02-13

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.

Novel design of interactive multimodal biofeedback system for neurorehabilitation.

PubMed

Huang, He; Chen, Y; Xu, W; Sundaram, H; Olson, L; Ingalls, T; Rikakis, T; He, Jiping

2006-01-01

A previous design of a biofeedback system for Neurorehabilitation in an interactive multimodal environment has demonstrated the potential of engaging stroke patients in task-oriented neuromotor rehabilitation. This report explores the new concept and alternative designs of multimedia based biofeedback systems. In this system, the new interactive multimodal environment was constructed with abstract presentation of movement parameters. Scenery images or pictures and their clarity and orientation are used to reflect the arm movement and relative position to the target instead of the animated arm. The multiple biofeedback parameters were classified into different hierarchical levels w.r.t. importance of each movement parameter to performance. A new quantified measurement for these parameters were developed to assess the patient's performance both real-time and offline. These parameters were represented by combined visual and auditory presentations with various distinct music instruments. Overall, the objective of newly designed system is to explore what information and how to feedback information in interactive virtual environment could enhance the sensorimotor integration that may facilitate the efficient design and application of virtual environment based therapeutic intervention.

Prediction of binary nanoparticle superlattices from soft potentials

DOE PAGES

Horst, Nathan; Travesset, Alex

2016-01-07

Driven by the hypothesis that a sufficiently continuous short-ranged potential is able to account for shell flexibility and phonon modes and therefore provides a more realistic description of nanoparticle interactions than a hard sphere model, we compute the solid phase diagram of particles of different radii interacting with an inverse power law potential. From a pool of 24 candidate lattices, the free energy is optimized with respect to additional internal parameters and the p-exponent, determining the short-range properties of the potential, is varied between p = 12 and p = 6. The phase diagrams contain the phases found in ongoingmore » self-assembly experiments, including DNA programmable self-assembly and nanoparticles with capping ligands assembled by evaporation from an organic solvent. Thus, the resulting phase diagrams can be mapped quantitatively to existing experiments as a function of only two parameters: Nanoparticle radius ratio (γ) and softness asymmetry.« less

Prediction of Binary Nanoparticle Superlattices from Soft Potentials

NASA Astrophysics Data System (ADS)

Horst, Nathan; Travesset, Alex

Driven by the hypothesis that a sufficiently continuous short-ranged potential is able to account for shell flexibility and phonon modes and therefore provides a more realistic description of nanoparticle interactions than a hard sphere model, we compute the solid phase diagram of particles of different radii interacting with an inverse power law potential. We explore 24 candidate lattices where the p-exponent, determining the short-range properties of the potential, is varied between p=12 and p=6, and optimize the free energy with respect to additional internal parameters. The phase diagrams contain the phases found in ongoing self-assembly experiments, including DNA programmable self-assembly and nanoparticles with capping ligands assembled by evaporation from an organic solvent. The resulting phase diagrams can be mapped quantitatively to existing experiments as a function of only two parameters: nanoparticle radius ratio (γ) and softness asymmetry (SA). Supported by DOE under Contract Number DE-AC02-07CH11358.

Prediction of binary nanoparticle superlattices from soft potentials

NASA Astrophysics Data System (ADS)

Horst, Nathan; Travesset, Alex

2016-01-01

Driven by the hypothesis that a sufficiently continuous short-ranged potential is able to account for shell flexibility and phonon modes and therefore provides a more realistic description of nanoparticle interactions than a hard sphere model, we compute the solid phase diagram of particles of different radii interacting with an inverse power law potential. From a pool of 24 candidate lattices, the free energy is optimized with respect to additional internal parameters and the p-exponent, determining the short-range properties of the potential, is varied between p = 12 and p = 6. The phase diagrams contain the phases found in ongoing self-assembly experiments, including DNA programmable self-assembly and nanoparticles with capping ligands assembled by evaporation from an organic solvent. The resulting phase diagrams can be mapped quantitatively to existing experiments as a function of only two parameters: Nanoparticle radius ratio (γ) and softness asymmetry.

Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

NASA Astrophysics Data System (ADS)

Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

2018-03-01

Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

PROBLEMS OF THE OPTICAL MODEL FOR DEUTERONS. II. EXPERIMENTS FOR DETERMINATION OF THE PARAMETERS OF THE OPTICAL POTENTIAL FOR DEUTERONS (in Polish)

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

Grotowski, K.

1963-01-01

An experiment for determination of the parameters of the optical potential for deuterons is presented. Total reaction cross sections for the interaction of deuterons with nuclei were determined by evaluating the cross sections for the emission of charged particles and neutrons. The angular distributions for the elastic scattering of deuterons were also measured. (auth)

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Critical evaluation of dipolar, acid-base and charge interactions I. Electron displacement within and between molecules, liquids and semiconductors.

PubMed

Rosenholm, Jarl B

2017-09-01

Specific dipolar, acid-base and charge interactions involve electron displacements. For atoms, single bonds and molecules electron displacement is characterized by electronic potential, absolute hardness, electronegativity and electron gap. In addition, dissociation, bonding, atomization, formation, ionization, affinity and lattice enthalpies are required to quantify the electron displacement in solids. Semiconductors are characterized by valence and conduction band energies, electron gaps and average Fermi energies which in turn determine Galvani potentials of the bulk, space charge layer and surface states. Electron displacement due to interaction between (probe) molecules, liquids and solids are characterized by parameters such as Hamaker constant, solubility parameter, exchange energy density, surface tension, work of adhesion and immersion. They are determined from permittivity, refractive index, enthalpy of vaporization, molar volume, surface pressure and contact angle. Moreover, acidic and basic probes may form adducts which are adsorbed on target substrates in order to establish an indirect measure of polarity, acidity, basicity or hydrogen bonding. Acidic acceptor numbers (AN), basic donor numbers (DN), acidic and basic "electrostatic" (E) and "covalent" (C) parameters determined by enthalpy of adduct formation are considered as general acid-base scales. However, the formal grounds for assignments as dispersive, Lifshitz-van der Waals, polar, acid, base and hydrogen bond interactions are inconsistent. Although correlations are found no of the parameters are mutually fully compatible and moreover the enthalpies of acid-base interaction do not correspond to free energies. In this review the foundations of different acid-base parameters relating to electron displacement within and between (probe) molecules, liquids and (semiconducting) solids are thoroughly investigated and their mutual relationships are evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

SENSITIVE PARAMETER EVALUATION FOR A VADOSE ZONE FATE AND TRANSPORT MODEL

EPA Science Inventory

This report presents information pertaining to quantitative evaluation of the potential impact of selected parameters on output of vadose zone transport and fate models used to describe the behavior of hazardous chemicals in soil. The Vadose 2one Interactive Processes (VIP) model...

Autoresonant excitation of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Batalov, S. V.; Shagalov, A. G.; Friedland, L.

2018-03-01

Controlling the state of a Bose-Einstein condensate driven by a chirped frequency perturbation in a one-dimensional anharmonic trapping potential is discussed. By identifying four characteristic time scales in this chirped-driven problem, three dimensionless parameters P1 ,2 ,3 are defined describing the driving strength, the anharmonicity of the trapping potential, and the strength of the particles interaction, respectively. As the driving frequency passes the linear resonance in the problem, and depending on the location in the P1 ,2 ,3 parameter space, the system may exhibit two very different evolutions, i.e., the quantum energy ladder climbing (LC) and the classical autoresonance (AR). These regimes are analyzed both in theory and simulations with the emphasis on the effect of the interaction parameter P3. In particular, the transition thresholds on the driving parameter P1 and their width in P1 in both the AR and LC regimes are discussed. Different driving protocols are also illustrated, showing efficient control of excitation and deexcitation of the condensate.

Adsorbed molecules in external fields: Effect of confining potential

NASA Astrophysics Data System (ADS)

Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

2016-12-01

We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials.

A Global Sensitivity Analysis Method on Maximum Tsunami Wave Heights to Potential Seismic Source Parameters

NASA Astrophysics Data System (ADS)

Ren, Luchuan

2015-04-01

A Global Sensitivity Analysis Method on Maximum Tsunami Wave Heights to Potential Seismic Source Parameters Luchuan Ren, Jianwei Tian, Mingli Hong Institute of Disaster Prevention, Sanhe, Heibei Province, 065201, P.R. China It is obvious that the uncertainties of the maximum tsunami wave heights in offshore area are partly from uncertainties of the potential seismic tsunami source parameters. A global sensitivity analysis method on the maximum tsunami wave heights to the potential seismic source parameters is put forward in this paper. The tsunami wave heights are calculated by COMCOT ( the Cornell Multi-grid Coupled Tsunami Model), on the assumption that an earthquake with magnitude MW8.0 occurred at the northern fault segment along the Manila Trench and triggered a tsunami in the South China Sea. We select the simulated results of maximum tsunami wave heights at specific sites in offshore area to verify the validity of the method proposed in this paper. For ranking importance order of the uncertainties of potential seismic source parameters (the earthquake's magnitude, the focal depth, the strike angle, dip angle and slip angle etc..) in generating uncertainties of the maximum tsunami wave heights, we chose Morris method to analyze the sensitivity of the maximum tsunami wave heights to the aforementioned parameters, and give several qualitative descriptions of nonlinear or linear effects of them on the maximum tsunami wave heights. We quantitatively analyze the sensitivity of the maximum tsunami wave heights to these parameters and the interaction effects among these parameters on the maximum tsunami wave heights by means of the extended FAST method afterward. The results shows that the maximum tsunami wave heights are very sensitive to the earthquake magnitude, followed successively by the epicenter location, the strike angle and dip angle, the interactions effect between the sensitive parameters are very obvious at specific site in offshore area, and there exist differences in importance order in generating uncertainties of the maximum tsunami wave heights for same group parameters at different specific sites in offshore area. These results are helpful to deeply understand the relationship between the tsunami wave heights and the seismic tsunami source parameters. Keywords: Global sensitivity analysis; Tsunami wave height; Potential seismic tsunami source parameter; Morris method; Extended FAST method

Long-range interacting systems in the unconstrained ensemble.

PubMed

Latella, Ivan; Pérez-Madrid, Agustín; Campa, Alessandro; Casetti, Lapo; Ruffo, Stefano

2017-01-01

Completely open systems can exchange heat, work, and matter with the environment. While energy, volume, and number of particles fluctuate under completely open conditions, the equilibrium states of the system, if they exist, can be specified using the temperature, pressure, and chemical potential as control parameters. The unconstrained ensemble is the statistical ensemble describing completely open systems and the replica energy is the appropriate free energy for these control parameters from which the thermodynamics must be derived. It turns out that macroscopic systems with short-range interactions cannot attain equilibrium configurations in the unconstrained ensemble, since temperature, pressure, and chemical potential cannot be taken as a set of independent variables in this case. In contrast, we show that systems with long-range interactions can reach states of thermodynamic equilibrium in the unconstrained ensemble. To illustrate this fact, we consider a modification of the Thirring model and compare the unconstrained ensemble with the canonical and grand-canonical ones: The more the ensemble is constrained by fixing the volume or number of particles, the larger the space of parameters defining the equilibrium configurations.

Optical-model potential for electron and positron elastic scattering by atoms

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

Salvat, Francesc

2003-07-01

An optical-model potential for systematic calculations of elastic scattering of electrons and positrons by atoms and positive ions is proposed. The electrostatic interaction is determined from the Dirac-Hartree-Fock self-consistent atomic electron density. In the case of electron projectiles, the exchange interaction is described by means of the local-approximation of Furness and McCarthy. The correlation-polarization potential is obtained by combining the correlation potential derived from the local density approximation with a long-range polarization interaction, which is represented by means of a Buckingham potential with an empirical energy-dependent cutoff parameter. The absorption potential is obtained from the local-density approximation, using the Born-Ochkurmore » approximation and the Lindhard dielectric function to describe the binary collisions with a free-electron gas. The strength of the absorption potential is adjusted by means of an empirical parameter, which has been determined by fitting available absolute elastic differential cross-section data for noble gases and mercury. The Dirac partial-wave analysis with this optical-model potential provides a realistic description of elastic scattering of electrons and positrons with energies in the range from {approx}100 eV up to {approx}5 keV. At higher energies, correlation-polarization and absorption corrections are small and the usual static-exchange approximation is sufficiently accurate for most practical purposes.« less

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

Low energy peripheral scaling in nucleon-nucleon scattering and uncertainty quantification

NASA Astrophysics Data System (ADS)

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

2018-03-01

We analyze the peripheral structure of the nucleon-nucleon interaction for LAB energies below 350 MeV. To this end we transform the scattering matrix into the impact parameter representation by analyzing the scaled phase shifts (L + 1/2) δ JLS (p) and the scaled mixing parameters (L + 1/2)ɛ JLS (p) in terms of the impact parameter b = (L + 1/2)/p. According to the eikonal approximation, at large angular momentum L these functions should become an universal function of b, independent on L. This allows to discuss in a rather transparent way the role of statistical and systematic uncertainties in the different long range components of the two-body potential. Implications for peripheral waves obtained in chiral perturbation theory interactions to fifth order (N5LO) or from the large body of NN data considered in the SAID partial wave analysis are also drawn from comparing them with other phenomenological high-quality interactions, constructed to fit scattering data as well. We find that both N5LO and SAID peripheral waves disagree more than 5σ with the Granada-2013 statistical analysis, more than 2σ with the 6 statistically equivalent potentials fitting the Granada-2013 database and about 1σ with the historical set of 13 high-quality potentials developed since the 1993 Nijmegen analysis.

Zero-range effective field theory for resonant wino dark matter. Part III. Annihilation effects

NASA Astrophysics Data System (ADS)

Braaten, Eric; Johnson, Evan; Zhang, Hong

2018-05-01

Near a critical value of the wino mass where there is a zero-energy S-wave resonance at the neutral-wino-pair threshold, low-energy winos can be described by a zero-range effective field theory (ZREFT) in which the winos interact nonperturbatively through a contact interaction and through Coulomb interactions. The effects of wino-pair annihilation into electroweak gauge bosons are taken into account through the analytic continuation of the real parameters for the contact interaction to complex values. The parameters of ZREFT can be determined by matching wino-wino scattering amplitudes calculated by solving the Schrödinger equation for winos interacting through a real potential due to the exchange of electroweak gauge bosons and an imaginary potential due to wino-pair annihilation into electroweak gauge bosons. ZREFT at leading order gives an accurate analytic description of low-energy wino-wino scattering, inclusive wino-pair annihilation, and a wino-pair bound state. ZREFT can also be applied to partial annihilation rates, such as the Sommerfeld enhancement of the annihilation rate of wino pairs into monochromatic photons.

A convenient and accurate wide-range parameter relationship between Buckingham and Morse potential energy functions

NASA Astrophysics Data System (ADS)

Lim, Teik-Cheng; Dawson, James Alexander

2018-05-01

This study explores the close-range, short-range and long-range relationships between the parameters of the Morse and Buckingham potential energy functions. The results show that the close-range and short-range relationships are valid for bond compression and for very small changes in bond length, respectively, while the long-range relationship is valid for bond stretching. A wide-range relationship is proposed to combine the comparative advantages of the close-range, short-range and long-range parameter relationships. The wide-range relationship is useful for replacing the close-range, short-range and long-range parameter relationships, thereby preventing the undesired effects of potential energy jumps resulting from functional switching between the close-range, short-range and long-range interaction energies.

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

Xantheas, Sotiris S.; Werhahn, Jasper C.

Based on the formulation of the analytical expression of the potential V(r) describing intermolecular interactions in terms of the dimensionless variables r*=r/rm and !*=V/!, where rm is the separation at the minimum and ! the well depth, we propose more generalized scalable forms for the commonly used Lennard-Jones, Mie, Morse and Buckingham exponential-6 potential energy functions (PEFs). These new generalized forms have an additional parameter from and revert to the original ones for some choice of that parameter. In this respect, the original forms can be considered as special cases of the more general forms that are introduced. We alsomore » propose a scalable, but nonrevertible to the original one, 4-parameter extended Morse potential.« less

Antagonistic and synergistic interactions among predators.

PubMed

Huxel, Gary R

2007-08-01

The structure and dynamics of food webs are largely dependent upon interactions among consumers and their resources. However, interspecific interactions such as intraguild predation and interference competition can also play a significant role in the stability of communities. The role of antagonistic/synergistic interactions among predators has been largely ignored in food web theory. These mechanisms influence predation rates, which is one of the key factors regulating food web structure and dynamics, thus ignoring them can potentially limit understanding of food webs. Using nonlinear models, it is shown that critical aspects of multiple predator food web dynamics are antagonistic/synergistic interactions among predators. The influence of antagonistic/synergistic interactions on coexistence of predators depended largely upon the parameter set used and the degree of feeding niche differentiation. In all cases when there was no effect of antagonism or synergism (a ( ij )=1.00), the predators coexisted. Using the stable parameter set, coexistence occurred across the range of antagonism/synergism used. However, using the chaotic parameter strong antagonism resulted in the extinction of one or both species, while strong synergism tended to coexistence. Whereas using the limit cycle parameter set, coexistence was strongly dependent on the degree of feeding niche overlap. Additionally increasing the degree of feeding specialization of the predators on the two prey species increased the amount of parameter space in which coexistence of the two predators occurred. Bifurcation analyses supported the general pattern of increased stability when the predator interaction was synergistic and decreased stability when it was antagonistic. Thus, synergistic interactions should be more common than antagonistic interactions in ecological systems.

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

PubMed Central

Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

2007-01-01

Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. PMID:17919319

The role of electrostatics in protein-protein interactions of a monoclonal antibody.

PubMed

Roberts, D; Keeling, R; Tracka, M; van der Walle, C F; Uddin, S; Warwicker, J; Curtis, R

2014-07-07

Understanding how protein-protein interactions depend on the choice of buffer, salt, ionic strength, and pH is needed to have better control over protein solution behavior. Here, we have characterized the pH and ionic strength dependence of protein-protein interactions in terms of an interaction parameter kD obtained from dynamic light scattering and the osmotic second virial coefficient B22 measured by static light scattering. A simplified protein-protein interaction model based on a Baxter adhesive potential and an electric double layer force is used to separate out the contributions of longer-ranged electrostatic interactions from short-ranged attractive forces. The ionic strength dependence of protein-protein interactions for solutions at pH 6.5 and below can be accurately captured using a Deryaguin-Landau-Verwey-Overbeek (DLVO) potential to describe the double layer forces. In solutions at pH 9, attractive electrostatics occur over the ionic strength range of 5-275 mM. At intermediate pH values (7.25 to 8.5), there is a crossover effect characterized by a nonmonotonic ionic strength dependence of protein-protein interactions, which can be rationalized by the competing effects of long-ranged repulsive double layer forces at low ionic strength and a shorter ranged electrostatic attraction, which dominates above a critical ionic strength. The change of interactions from repulsive to attractive indicates a concomitant change in the angular dependence of protein-protein interaction from isotropic to anisotropic. In the second part of the paper, we show how the Baxter adhesive potential can be used to predict values of kD from fitting to B22 measurements, thus providing a molecular basis for the linear correlation between the two protein-protein interaction parameters.

Adsorbed molecules in external fields: Effect of confining potential.

PubMed

Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

2016-12-05

We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials. Copyright © 2016 Elsevier B.V. All rights reserved.

Two-parameter double-oscillator model of Mathews-Lakshmanan type: Series solutions and supersymmetric partners

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

Schulze-Halberg, Axel, E-mail: axgeschu@iun.edu, E-mail: xbataxel@gmail.com; Wang, Jie, E-mail: wangjie@iun.edu

2015-07-15

We obtain series solutions, the discrete spectrum, and supersymmetric partners for a quantum double-oscillator system. Its potential features a superposition of the one-parameter Mathews-Lakshmanan interaction and a one-parameter harmonic or inverse harmonic oscillator contribution. Furthermore, our results are transferred to a generalized Pöschl-Teller model that is isospectral to the double-oscillator system.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases.

PubMed

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-15

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases. Copyright © 2015 Elsevier B.V. All rights reserved.

The interacting correlated fragments model for weak interactions, basis set superposition error, and the helium dimer potential

NASA Astrophysics Data System (ADS)

Liu, B.; McLean, A. D.

1989-08-01

We report the LM-2 helium dimer interaction potential, from helium separations of 1.6 Å to dissociation, obtained by careful convergence studies with respect to configuration space, through a sequence of interacting correlated fragment (ICF) wave functions, and with respect to the primitive Slater-type basis used for orbital expansion. Parameters of the LM-2 potential are re=2.969 Å, rm=2.642 Å, and De=10.94 K, in near complete agreement with those of the best experimental potential of Aziz, McCourt, and Wong [Mol. Phys. 61, 1487 (1987)], which are re=2.963 Å, rm=2.637 Å, and De=10.95 K. The computationally estimated accuracy of each point on the potential is given; at re it is 0.03 K. Extrapolation procedures used to produce the LM-2 potential make use of the orbital basis inconsistency (OBI) and configuration base inconsistency (CBI) adjustments to separated fragment energies when computing the interaction energy. These components of basis set superposition error (BSSE) are given a full discussion.

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Structural characterization, surface characteristics and non covalent interactions of a heterocyclic Schiff base: Evaluation of antioxidant potential by UV-visible spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Chithiraikumar, S.; Gandhimathi, S.; Neelakantan, M. A.

2017-06-01

A heterocyclic Schiff base, (E)-4-(1-((pyridin-2-ylmethyl)imino)ethyl)benzene-1,3-diol (L) was synthesized and isolated as single crystals. Its structure was characterized by FT-IR, UV, 1H and 13C NMR, and further confirmed by X-ray crystallography. Qualitatively and quantitatively the various interactions in the crystal structure of L has been analyzed by Hirshfeld surfaces and 2D fingerprint plots. Non covalent interactions have been studied by electron localization function (ELF) and mapped with reduced density gradient (RDG) analysis. The molecular structure was studied computationally by DFT-B3LYP/6-311G(d,p) calculations. HOMO-LUMO energy levels, chemical reactivity descriptors and thermodynamic parameters have been investigated at the same level of theory. The antioxidant potential of L was evaluated experimentally by measuring DPPH free radical scavenging effect using UV-visible spectroscopy and theoretically by DFT. Theoretical parameters, such as bond dissociation enthalpy (BDE) and spin density calculated suggests that antioxidant potential of L is due to H atom abstraction from the sbnd OH group.

Adaptive Monte Carlo methods

NASA Astrophysics Data System (ADS)

Fasnacht, Marc

We develop adaptive Monte Carlo methods for the calculation of the free energy as a function of a parameter of interest. The methods presented are particularly well-suited for systems with complex energy landscapes, where standard sampling techniques have difficulties. The Adaptive Histogram Method uses a biasing potential derived from histograms recorded during the simulation to achieve uniform sampling in the parameter of interest. The Adaptive Integration method directly calculates an estimate of the free energy from the average derivative of the Hamiltonian with respect to the parameter of interest and uses it as a biasing potential. We compare both methods to a state of the art method, and demonstrate that they compare favorably for the calculation of potentials of mean force of dense Lennard-Jones fluids. We use the Adaptive Integration Method to calculate accurate potentials of mean force for different types of simple particles in a Lennard-Jones fluid. Our approach allows us to separate the contributions of the solvent to the potential of mean force from the effect of the direct interaction between the particles. With contributions of the solvent determined, we can find the potential of mean force directly for any other direct interaction without additional simulations. We also test the accuracy of the Adaptive Integration Method on a thermodynamic cycle, which allows us to perform a consistency check between potentials of mean force and chemical potentials calculated using the Adaptive Integration Method. The results demonstrate a high degree of consistency of the method.

Development of a gluten-free rice noodle by utilizing protein-polyphenol interaction between soy protein isolate and extract of Acanthopanax sessiliflorus.

PubMed

Lee, Da-Som; Kim, Yang; Song, Youngwoon; Lee, Ji-Hye; Lee, Suyong; Yoo, Sang-Ho

2016-02-01

The potential of the protein-polyphenol interaction was applied to crosslinking reinforced protein networks in gluten-free rice noodles. Specifically, inter-component interaction between soy protein isolate and extract of Acanthopanax sessiliflorus fruit (ogaja) was examined with a view to improving its quality. In a components-interacting model system, a mixture of soy protein isolate (SPI) and ogaja extract (OE) induced a drastic increase in absorbance at 660 nm by haze formation, while the major anthocyanin of ogaja, cyanidin-3-O-sambubioside, sparsely interacted with SPI or gelatin. Individual or combined treatment of SPI and OE on rice dough decreased all the viscosity parameters in rapid visco analysis. However, SPI-OE treatment significantly increased all the texture parameters of rice dough derived from Mixolab(®) analysis (P < 0.05). Incorporation of SPI in rice dough significantly reduced endothermic ΔH, and SPI-OE treatment further decreased this value. SPI-OE interaction significantly increased the tensile properties of cooked noodle and decreased 53.7% of cooking loss compared to the untreated rice noodle. SPI-OE treatment caused a considerable reinforcement of the network as shown by reducing cooking loss and suggested the potential for utilizing protein-polyphenol interaction for gluten-free rice noodle production. © 2015 Society of Chemical Industry.

Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

PubMed

Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

2014-03-01

Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Chronology: An Important (and Potentially Accessible) Parameter in Understanding Europa Surface-Subsurface Material Interchange, Burial, and Resurfacing Processes

NASA Technical Reports Server (NTRS)

Swindle, T. D.

2001-01-01

Time is an important parameter in understanding the interaction of the surface and subsurface of Europa. It should be possible to determine potassium-argon and cosmic ray exposure ages in situ on the surface of Europa. Additional information is contained in the original extended abstract.

Analytical interatomic potential for modeling nonequilibrium processes in the W-C-H system

NASA Astrophysics Data System (ADS)

Juslin, N.; Erhart, P.; Träskelin, P.; Nord, J.; Henriksson, K. O. E.; Nordlund, K.; Salonen, E.; Albe, K.

2005-12-01

A reactive interatomic potential based on an analytical bond-order scheme is developed for the ternary system W-C-H. The model combines Brenner's hydrocarbon potential with parameter sets for W-W, W-C, and W-H interactions and is adjusted to materials properties of reference structures with different local atomic coordinations including tungsten carbide, W-H molecules, as well as H dissolved in bulk W. The potential has been tested in various scenarios, such as surface, defect, and melting properties, none of which were considered in the fitting. The intended area of application is simulations of hydrogen and hydrocarbon interactions with tungsten, which have a crucial role in fusion reactor plasma-wall interactions. Furthermore, this study shows that the angular-dependent bond-order scheme can be extended to second nearest-neighbor interactions, which are relevant in body-centered-cubic metals. Moreover, it provides a possibly general route for modeling metal carbides.

Phase diagram of the Shastry-Sutherland Kondo lattice model with classical localized spins: a variational calculation study

NASA Astrophysics Data System (ADS)

Shahzad, Munir; Sengupta, Pinaki

2017-08-01

We study the Shastry-Sutherland Kondo lattice model with additional Dzyaloshinskii-Moriya (DM) interactions, exploring the possible magnetic phases in its multi-dimensional parameter space. Treating the local moments as classical spins and using a variational ansatz, we identify the parameter ranges over which various common magnetic orderings are potentially stabilized. Our results reveal that the competing interactions result in a heightened susceptibility towards a wide range of spin configurations including longitudinal ferromagnetic and antiferromagnetic order, coplanar flux configurations and most interestingly, multiple non-coplanar configurations including a novel canted-flux state as the different Hamiltonian parameters like electron density, interaction strengths and degree of frustration are varied. The non-coplanar and non-collinear magnetic ordering of localized spins behave like emergent electromagnetic fields and drive unusual transport and electronic phenomena.

Reconstructed historical land cover and biophysical parameters for studies of land-atmosphere interactions within the eastern United States

USGS Publications Warehouse

Steyaert, Louis T.; Knox, R.G.

2008-01-01

Over the past 350 years, the eastern half of the United States experienced extensive land cover changes. These began with land clearing in the 1600s, continued with widespread deforestation, wetland drainage, and intensive land use by 1920, and then evolved to the present-day landscape of forest regrowth, intensive agriculture, urban expansion, and landscape fragmentation. Such changes alter biophysical properties that are key determinants of land-atmosphere interactions (water, energy, and carbon exchanges). To understand the potential implications of these land use transformations, we developed and analyzed 20-km land cover and biophysical parameter data sets for the eastern United States at 1650, 1850, 1920, and 1992 time slices. Our approach combined potential vegetation, county-level census data, soils data, resource statistics, a Landsat-derived land cover classification, and published historical information on land cover and land use. We reconstructed land use intensity maps for each time slice and characterized the land cover condition. We combined these land use data with a mutually consistent set of biophysical parameter classes, to characterize the historical diversity and distribution of land surface properties. Time series maps of land surface albedo, leaf area index, a deciduousness index, canopy height, surface roughness, and potential saturated soils in 1650, 1850, 1920, and 1992 illustrate the profound effects of land use change on biophysical properties of the land surface. Although much of the eastern forest has returned, the average biophysical parameters for recent landscapes remain markedly different from those of earlier periods. Understanding the consequences of these historical changes will require land-atmosphere interactions modeling experiments.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Gravity, antigravity and gravitational shielding in (2+1) dimensions

NASA Astrophysics Data System (ADS)

Accioly, Antonio; Helayël-Neto, José; Lobo, Matheus

2009-07-01

Higher-derivative terms are introduced into three-dimensional gravity, thereby allowing for a dynamical theory. The resulting system, viewed as a classical field model, is endowed with a novel and peculiar feature: its nonrelativistic potential describes three gravitational regimes. Depending on the choice of the parameters in the action functional, one obtains gravity, antigravity or gravitational shielding. Interesting enough, this potential is very similar, mutatis mutandis, to the potential for the interaction of two superconducting vortices. Furthermore, the gravitational deflection angle of a light ray, unlike that of Einstein gravity in (2+1) dimensions, is dependent on the impact parameter.

Distinguishing boson stars from black holes and neutron stars from tidal interactions in inspiraling binary systems

NASA Astrophysics Data System (ADS)

Sennett, Noah; Hinderer, Tanja; Steinhoff, Jan; Buonanno, Alessandra; Ossokine, Serguei

2017-07-01

Binary systems containing boson stars—self-gravitating configurations of a complex scalar field—can potentially mimic black holes or neutron stars as gravitational-wave sources. We investigate the extent to which tidal effects in the gravitational-wave signal can be used to discriminate between these standard sources and boson stars. We consider spherically symmetric boson stars within two classes of scalar self-interactions: an effective-field-theoretically motivated quartic potential and a solitonic potential constructed to produce very compact stars. We compute the tidal deformability parameter characterizing the dominant tidal imprint in the gravitational-wave signals for a large span of the parameter space of each boson star model, covering the entire space in the quartic case, and an extensive portion of interest in the solitonic case. We find that the tidal deformability for boson stars with a quartic self-interaction is bounded below by Λmin≈280 and for those with a solitonic interaction by Λmin≈1.3 . We summarize our results as ready-to-use fits for practical applications. Employing a Fisher matrix analysis, we estimate the precision with which Advanced LIGO and third-generation detectors can measure these tidal parameters using the inspiral portion of the signal. We discuss a novel strategy to improve the distinguishability between black holes/neutrons stars and boson stars by combining tidal deformability measurements of each compact object in a binary system, thereby eliminating the scaling ambiguities in each boson star model. Our analysis shows that current-generation detectors can potentially distinguish boson stars with quartic potentials from black holes, as well as from neutron-star binaries if they have either a large total mass or a large (asymmetric) mass ratio. Discriminating solitonic boson stars from black holes using only tidal effects during the inspiral will be difficult with Advanced LIGO, but third-generation detectors should be able to distinguish between binary black holes and these binary boson stars.

Higgs-portal assisted Higgs inflation with a sizeable tensor-to-scalar ratio

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

Kim, Jinsu; Ko, Pyungwon; Park, Wan-Il, E-mail: kimjinsu@kias.re.kr, E-mail: pko@kias.re.kr, E-mail: Wanil.Park@uv.es

We show that the Higgs portal interactions involving extra dark Higgs field can save generically the original Higgs inflation of the standard model (SM) from the problem of a deep non-SM vacuum in the SM Higgs potential. Specifically, we show that such interactions disconnect the top quark pole mass from inflationary observables and allow multi-dimensional parameter space to save the Higgs inflation, thanks to the additional parameters (the dark Higgs boson mass m {sub φ}, the mixing angle α between the SM Higgs H and dark Higgs Φ, and the mixed quartic coupling) affecting RG-running of the Higgs quartic coupling.more » The effect of Higgs portal interactions may lead to a larger tensor-to-scalar ratio, 0.08 ∼< r ∼< 0.1, by adjusting relevant parameters in wide ranges of α and m {sub φ}, some region of which can be probed at future colliders. Performing a numerical analysis we find an allowed region of parameters, matching the latest Planck data.« less

A Workflow for Global Sensitivity Analysis of PBPK Models

PubMed Central

McNally, Kevin; Cotton, Richard; Loizou, George D.

2011-01-01

Physiologically based pharmacokinetic (PBPK) models have a potentially significant role in the development of a reliable predictive toxicity testing strategy. The structure of PBPK models are ideal frameworks into which disparate in vitro and in vivo data can be integrated and utilized to translate information generated, using alternative to animal measures of toxicity and human biological monitoring data, into plausible corresponding exposures. However, these models invariably include the description of well known non-linear biological processes such as, enzyme saturation and interactions between parameters such as, organ mass and body mass. Therefore, an appropriate sensitivity analysis (SA) technique is required which can quantify the influences associated with individual parameters, interactions between parameters and any non-linear processes. In this report we have defined the elements of a workflow for SA of PBPK models that is computationally feasible, accounts for interactions between parameters, and can be displayed in the form of a bar chart and cumulative sum line (Lowry plot), which we believe is intuitive and appropriate for toxicologists, risk assessors, and regulators. PMID:21772819

Asymptotic Normalization Coefficients in a Potential Model Involving Forbidden States

NASA Astrophysics Data System (ADS)

Blokhintsev, L. D.; Savin, D. A.

2018-03-01

It is shown that values obtained for asymptotic normalization coefficients by means of a potential fitted to experimental data on elastic scattering depend substantially on the presence and the number n of possible forbidden states in the fitted potential. The present analysis was performed within exactly solvable potential models for various nuclear systems and various potentials without and with allowance for Coulomb interaction. Various methods for changing the number n that are based on the use of various versions of the change in the parameters of the potential model were studied. A compact analytic expression for the asymptotic normalization coefficients was derived for the case of the Hulthén potential. Specifically, the d + α and α + 12C systems, which are of importance for astrophysics, were examined. It was concluded that an incorrect choice of n could lead to a substantial errors in determining the asymptotic normalization coefficients. From the results of our calculations, it also follows that, for systems with a low binding energy and, as a consequence, with a large value of the Coulomb parameter, the inclusion of the Coulomb interaction may radically change the asymptotic normalization coefficients, increasing them sharply.

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

Stiegler, Thomas; Sadus, Richard J., E-mail: rsadus@swin.edu.au

General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic propertiesmore » predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.« less

Full-Potential Modeling of Blade-Vortex Interactions. Degree awarded by George Washington Univ., Feb. 1987

NASA Technical Reports Server (NTRS)

Jones, Henry E.

1997-01-01

A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.

Convergent Cross Mapping: Basic concept, influence of estimation parameters and practical application.

PubMed

Schiecke, Karin; Pester, Britta; Feucht, Martha; Leistritz, Lutz; Witte, Herbert

2015-01-01

In neuroscience, data are typically generated from neural network activity. Complex interactions between measured time series are involved, and nothing or only little is known about the underlying dynamic system. Convergent Cross Mapping (CCM) provides the possibility to investigate nonlinear causal interactions between time series by using nonlinear state space reconstruction. Aim of this study is to investigate the general applicability, and to show potentials and limitation of CCM. Influence of estimation parameters could be demonstrated by means of simulated data, whereas interval-based application of CCM on real data could be adapted for the investigation of interactions between heart rate and specific EEG components of children with temporal lobe epilepsy.

Hydrodynamic interactions induce movement against an external load in a ratchet dimer Brownian motor.

PubMed

Fornés, José A

2010-01-15

We use the Brownian dynamics with hydrodynamic interactions simulation in order to describe the movement of a elastically coupled dimer Brownian motor in a ratchet potential. The only external forces considered in our system were the load, the random thermal noise and an unbiased thermal fluctuation. For a given set of parameters we observe direct movement against the load force if hydrodynamic interactions were considered.

Meson-nucleus potentials and the search for meson-nucleus bound states

NASA Astrophysics Data System (ADS)

Metag, V.; Nanova, M.; Paryev, E. Ya.

2017-11-01

Recent experiments studying the meson-nucleus interaction to extract meson-nucleus potentials are reviewed. The real part of the potentials quantifies whether the interaction is attractive or repulsive while the imaginary part describes the meson absorption in nuclei. The review is focused on mesons which are sufficiently long-lived to potentially form meson-nucleus quasi-bound states. The presentation is confined to meson production off nuclei in photon-, pion-, proton-, and light-ion induced reactions and heavy-ion collisions at energies near the production threshold. Tools to extract the potential parameters are presented. In most cases, the real part of the potential is determined by comparing measured meson momentum distributions or excitation functions with collision model or transport model calculations. The imaginary part is extracted from transparency ratio measurements. Results on K+ ,K0 ,K- , η ,η‧ , ω, and ϕ mesons are presented and compared with theoretical predictions. The interaction of K+ and K0 mesons with nuclei is found to be weakly repulsive, while the K- , η ,η‧ , ω and ϕ meson-nucleus potentials are attractive, however, with widely different strengths. Because of meson absorption in the nuclear medium the imaginary parts of the meson-nucleus potentials are all negative, again with a large spread. An outlook on planned experiments in the charm sector is given. In view of the determined potential parameters, the criteria and chances for experimentally observing meson-nucleus quasi-bound states are discussed. The most promising candidates appear to be the η and η‧ mesons.

The minimal number of parameters in triclinic crystal-field potentials

NASA Astrophysics Data System (ADS)

Mulak, J.

2003-09-01

The optimal parametrization schemes of the crystal-field (CF) potential in fitting procedures are those based on the smallest numbers of parameters. The surplus parametrizations usually lead to artificial and non-physical solutions. Therefore, the symmetry adapted reference systems are commonly used. Instead of them, however, the coordinate systems with the z-axis directed along the principal axes of the CF multipoles (2 k-poles) can be applied successfully, particularly for triclinic CF potentials. Due to the irreducibility of the D(k) representations such a choice can reduce the number of the k-order parameters by 2 k: from 2 k+1 (in the most general case) to only 1 (the axial one). Unfortunately, in general, the numbers of other order CF parameters stay then unrestricted. In this way, the number of parameters for the k-even triclinic CF potentials can be reduced by 4, 8 or 12, for k=2,4 or 6, respectively. Hence, the parametrization schemes based on maximum 14 parameters can be in use solely. For higher point symmetries this number is usually greater than that for the symmetry adapted systems. Nonetheless, many instructive correlations between the multipole contributions to the CF interaction are attainable in this way.

Novel nonlinear knowledge-based mean force potentials based on machine learning.

PubMed

Dong, Qiwen; Zhou, Shuigeng

2011-01-01

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge-based mean force potentials. The nonlinear potentials can be widely used for ab initio protein structure prediction, model quality assessment, protein docking, and other challenging problems in computational biology.

Analysis of airframe/engine interactions - An integrated control perspective

NASA Technical Reports Server (NTRS)

Schmidt, David K.; Schierman, John D.; Garg, Sanjay

1990-01-01

Techniques for the analysis of the dynamic interactions between airframe/engine dynamical systems are presented. Critical coupling terms are developed that determine the significance of these interactions with regard to the closed loop stability and performance of the feedback systems. A conceptual model is first used to indicate the potential sources of the coupling, how the coupling manifests itself, and how the magnitudes of these critical coupling terms are used to quantify the effects of the airframe/engine interactions. A case study is also presented involving an unstable airframe with thrust vectoring for attitude control. It is shown for this system with classical, decentralized control laws that there is little airframe/engine interaction, and the stability and performance with those control laws is not affected. Implications of parameter uncertainty in the coupling dynamics is also discussed, and effects of these parameter variations are also demonstrated to be small for this vehicle configuration.

Lattice dynamics of solid N2 with an ab initio intermolecular potential

NASA Astrophysics Data System (ADS)

Luty, T.; van der Avoird, A.; Berns, R. M.

1980-11-01

We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

PubMed Central

Keskin, O.; Bahar, I.; Badretdinov, A. Y.; Ptitsyn, O. B.; Jernigan, R. L.

1998-01-01

Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study, the interfacial regions of protein-protein complexes are examined to extract inter-molecular inter-residue potentials, using the same statistical methods as those previously adopted for intra-molecular residue pairs. Two sets of energy parameters are derived, corresponding to solvent-mediation and "average residue" mediation. The former set is shown to be highly correlated (correlation coefficient 0.89) with that previously obtained for inter-residue interactions within single chain monomers, while the latter exhibits a weaker correlation (0.69) with its intra-molecular counterpart. In addition to the close similarity of intra- and inter-molecular solvent-mediated potentials, they are shown to be significantly more residue-specific and thereby discriminative compared to the residue-mediated ones, indicating that solvent-mediation plays a major role in controlling the effective inter-residue interactions, either at interfaces, or within single monomers. Based on this observation, a reduced set of energy parameters comprising 20 one-body and 3 two-body terms is proposed (as opposed to the 20 x 20 tables of inter-residue potentials), which reproduces the conventional 20 x 20 tables with a correlation coefficient of 0.99. PMID:9865952

Temperature dependences of the time of electron-electron interactions in two-dimensional heterojunction

NASA Astrophysics Data System (ADS)

Bukhenskyy, K. V.; Dubois, A. B.; Kucheryavyy, S. I.; Mashnina, S. N.; Safoshkin, A. S.; Baukov, A. A.; Shchigorev, E. Yu

2017-12-01

The article discusses the joint solution of the Schrödinger and Poisson equations for two-dimensional semiconductor heterojunction. The application of a triangular potential of well approximation for the calculation of the electron-electron interaction is offered in the paper. The influence of the parameters of the selected approximation was analyzed.

Monopole-antimonopole interaction potential

NASA Astrophysics Data System (ADS)

Saurabh, Ayush; Vachaspati, Tanmay

2017-11-01

We numerically study the interactions of twisted monopole-antimonopole pairs in the 't Hooft-Polyakov model for a range of values of the scalar to vector mass ratio. We also recover the sphaleron solution at maximum twist discovered by Taubes [Commun. Math. Phys. 86, 257 (1982), 10.1007/BF01206014] and map out its energy and size as functions of parameters.

Thermodynamic model of a solid with RKKY interaction and magnetoelastic coupling

NASA Astrophysics Data System (ADS)

Balcerzak, T.; Szałowski, K.; Jaščur, M.

2018-04-01

Thermodynamic description of a model system with magnetoelastic coupling is presented. The elastic, vibrational, electronic and magnetic energy contributions are taken into account. The long-range RKKY interaction is considered together with the nearest-neighbour direct exchange. The generalized Gibbs potential and the set of equations of state are derived, from which all thermodynamic functions are self-consistently obtained. Thermodynamic properties are calculated numerically for FCC structure for arbitrary external pressure, magnetic field and temperature, and widely discussed. In particular, for some parameters of interaction potential and electron concentration corresponding to antiferromagnetic phase, the existence of negative thermal expansion coefficient is predicted.

Microscopic description of a drop on a solid surface.

PubMed

Ruckenstein, Eli; Berim, Gersh O

2010-06-14

Two approaches recently suggested for the treatment of macro- or nanodrops on smooth or rough, planar or curved, solid surfaces, based on fluid-fluid and fluid-solid interaction potentials are reviewed. The first one employs the minimization of the total potential energy of a drop by assuming that the drop has a well defined profile and a constant liquid density in its entire volume with the exception of the monolayer nearest to the surface where the density has a different value. As a result, a differential equation for the drop profile as well as the necessary boundary conditions are derived which involve the parameters of the interaction potentials and do not contain such macroscopic characteristics as the surface tensions. As a consequence, the macroscopic and microscopic contact angles which the drop profile makes with the surface can be calculated. The macroscopic angle is obtained via the extrapolation of the circular part of the drop profile valid at some distance from the surface up to the solid surface. The microscopic angle is formed at the intersection of the real profile (which is not circular near the surface) with the surface. The theory provides a relation between these two angles. The ranges of the microscopic parameters of the interaction potentials for which (i) the drop can have any height (volume), (ii) the drop can have a restricted height but unrestricted volume, and (iii) a drop cannot be formed on the surface were identified. The theory was also extended to the description of a drop on a rough surface. The second approach is based on a nonlocal density functional theory (DFT), which accounts for the inhomogeneity of the liquid density and temperature effects, features which are missing in the first approach. Although the computational difficulties restrict its application to drops of only several nanometers, the theory can be applied indirectly to macrodrops by calculating the surface tensions and using the Young equation to determine the contact angle. Employing the canonical ensemble version of the DFT, nanodrops on smooth and rough solid surfaces could be investigated and their characteristics, such as the drop profile, contact angle, as well as the fluid density distribution inside the drop can be determined as functions of the parameters of the interaction potentials and temperature. It was found that the contact angle of the drop has a simple (quasi)universal dependence on the energy parameter epsilon(fs) of the fluid-solid interaction potential and temperature. The main feature of this dependence is the existence of a fixed value theta(0) of the contact angle theta which separates the solid substrates (characterized by the energy parameter epsilon(fs) of the fluid-solid interaction potential) into two classes with respect to their temperature dependence. For theta>theta(0) the contact angle monotonously increases and for theta

Families of one-point interactions resulting from the squeezing limit of the sum of two- and three-delta-like potentials

NASA Astrophysics Data System (ADS)

Zolotaryuk, A. V.

2017-06-01

Several families of one-point interactions are derived from the system consisting of two and three δ-potentials which are regularized by piecewise constant functions. In physical terms such an approximating system represents two or three extremely thin layers separated by some distance. The two-scale squeezing of this heterostructure to one point as both the width of δ-approximating functions and the distance between these functions simultaneously tend to zero is studied using the power parameterization through a squeezing parameter \\varepsilon \\to 0 , so that the intensity of each δ-potential is cj =aj \\varepsilon1-μ , aj \\in {R} , j  =  1, 2, 3, the width of each layer l =\\varepsilon and the distance between the layers r = c\\varepsilon^τ , c  >  0. It is shown that at some values of the intensities a 1, a 2 and a 3, the transmission across the limit point potentials is non-zero, whereas outside these (resonance) values the one-point interactions are opaque splitting the system at the point of singularity into two independent subsystems. Within the interval 1 < μ < 2 , the resonance sets consist of two curves on the (a_1, a_2) -plane and three surfaces in the (a_1, a_2, a_3) -space. As the parameter μ approaches the value μ =2 , three types of splitting the one-point interactions into countable families are observed.

Free cooling phase-diagram of hard-spheres with short- and long-range interactions

NASA Astrophysics Data System (ADS)

Gonzalez, S.; Thornton, A. R.; Luding, S.

2014-10-01

We study the stability, the clustering and the phase-diagram of free cooling granular gases. The systems consist of mono-disperse particles with additional non-contact (long-range) interactions, and are simulated here by the event-driven molecular dynamics algorithm with discrete (short-range shoulders or wells) potentials (in both 2D and 3D). Astonishingly good agreement is found with a mean field theory, where only the energy dissipation term is modified to account for both repulsive or attractive non-contact interactions. Attractive potentials enhance cooling and structure formation (clustering), whereas repulsive potentials reduce it, as intuition suggests. The system evolution is controlled by a single parameter: the non-contact potential strength scaled by the fluctuation kinetic energy (granular temperature). When this is small, as expected, the classical homogeneous cooling state is found. However, if the effective dissipation is strong enough, structure formation proceeds, before (in the repulsive case) non-contact forces get strong enough to undo the clustering (due to the ongoing dissipation of granular temperature). For both repulsive and attractive potentials, in the homogeneous regime, the cooling shows a universal behaviour when the (inverse) control parameter is used as evolution variable instead of time. The transition to a non-homogeneous regime, as predicted by stability analysis, is affected by both dissipation and potential strength. This can be cast into a phase diagram where the system changes with time, which leaves open many challenges for future research.

Observational constraints on holographic tachyonic dark energy in interaction with dark matter

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

Micheletti, Sandro M. R., E-mail: smrm@fma.if.usp.br

2010-05-01

We discuss an interacting tachyonic dark energy model in the context of the holographic principle. The potential of the holographic tachyon field in interaction with dark matter is constructed. The model results are compared with CMB shift parameter, baryonic acoustic oscilations, lookback time and the Constitution supernovae sample. The coupling constant of the model is compatible with zero, but dark energy is not given by a cosmological constant.

Possible Experiment for the Demonstration of Neutron Waves Interaction with Spatially Oscillating Potential

NASA Astrophysics Data System (ADS)

Miloi, Mădălina Mihaela; Goryunov, Semyon; Kulin, German

2018-04-01

A wide range of problems in neutron optics is well described by a theory based on application of the effective potential model. It was assumed that the concept of the effective potential in neutron optics have a limited region of validity and ceases to be correct in the case of the giant acceleration of a matter. To test this hypothesis a new Ultra Cold neutron experiment for the observation neutron interaction with potential structure oscillating in space was proposed. The report is focused on the model calculations of the topography of sample surface that oscillate in space. These calculations are necessary to find an optimal parameters and geometry of the planned experiment.

Whole Protein Native Fitness Potentials

NASA Astrophysics Data System (ADS)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

Protein structure prediction can be separated into two tasks: sample the configuration space of the protein chain, and assign a fitness between these hypothetical models and the native structure of the protein. One of the more promising developments in this area is that of knowledge based energy functions. However, standard approaches using pair-wise interactions have shown shortcomings demonstrated by the superiority of multi-body-potentials. These shortcomings are due to residue pair-wise interaction being dependent on other residues along the chain. We developed a method that uses whole protein information filtered through machine learners to score protein models based on their likeness to native structures. For all models we calculated parameters associated with the distance to the solvent and with distances between residues. These parameters, in addition to energy estimates obtained by using a four-body-potential, DFIRE, and RWPlus were used as training for machine learners to predict the fitness of the models. Testing on CASP 9 targets showed that our method is superior to DFIRE, RWPlus, and the four-body potential, which are considered standards in the field.

Effective intermolecular potential and critical point for C60 molecule

NASA Astrophysics Data System (ADS)

Ramos, J. Eloy

2017-07-01

The approximate nonconformal (ANC) theory is applied to the C60 molecule. A new binary potential function is developed for C60, which has three parameters only and is obtained by averaging the site-site carbon interactions on the surface of two C60 molecules. It is shown that the C60 molecule follows, to a good approximation, the corresponding states principle with n-C8H18, n-C4F10 and n-C5F12. The critical point of C60 is estimated in two ways: first by applying the corresponding states principle under the framework of the ANC theory, and then by using previous computer simulations. The critical parameters obtained by applying the corresponding states principle, although very different from those reported in the literature, are consistent with the previous results of the ANC theory. It is shown that the Girifalco potential does not correspond to an average of the site-site carbon-carbon interaction.

Thermodynamic scaling of glassy dynamics and dynamic heterogeneities in metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Hu, Yuan-Chao; Shang, Bao-Shuang; Guan, Peng-Fei; Yang, Yong; Bai, Hai-Yang; Wang, Wei-Hua

2016-09-01

A ternary metallic glass-forming liquid is found to be not strongly correlating thermodynamically, but its average dynamics, dynamic heterogeneities including the high order dynamic correlation length, and static structure are still well described by thermodynamic scaling with the same scaling exponent γ. This may indicate that the metallic liquid could be treated as a single-parameter liquid. As an intrinsic material constant stemming from the fundamental interatomic interactions, γ is theoretically predicted from the thermodynamic fluctuations of the potential energy and the virial. Although γ is conventionally understood merely from the repulsive part of the inter-particle potentials, the strong correlation between γ and the Grüneisen parameter up to the accuracy of the Dulong-Petit approximation demonstrates the important roles of anharmonicity and attractive force of the interatomic potential in governing glass transition of metallic glassformers. These findings may shed light on how to understand metallic glass formation from the fundamental interatomic interactions.

Kinklike structures in models of the Dirac-Born-Infeld type

NASA Astrophysics Data System (ADS)

Bazeia, D.; Lima, Elisama E. M.; Losano, L.

2018-01-01

The present work investigates several models of a single real scalar field, engendering kinetic term of the Dirac-Born- Infeld type. Such theories introduce nonlinearities to the kinetic part of the Lagrangian, which presents a square root restricting the field evolution and including additional powers in derivatives of the scalar field, controlled by a real parameter. In order to obtain topological solutions analytically, we propose a first-order framework that simplifies the equation of motion ensuring solutions that are linearly stable. This is implemented using the deformation method, and we introduce examples presenting two categories of potentials, one having polynomial interactions and the other with nonpolynomial interactions. We also explore how the Dirac-Born-Infeld kinetic term affects the properties of the solutions. In particular, we note that the kinklike solutions are similar to the ones obtained through models with standard kinetic term and canonical potential, but their energy densities and stability potentials vary according to the parameter introduced to control the new models.

A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

PubMed

Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

2015-04-14

One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions.

Density functional theory and phytochemical study of 8-hydroxyisodiospyrin

NASA Astrophysics Data System (ADS)

Ullah, Zakir; Ata-ur-Rahman; Fazl-i-Sattar; Rauf, Abdur; Yaseen, Muhammad; Hassan, Waseem; Tariq, Muhammad; Ayub, Khurshid; Tahir, Asif Ali; Ullah, Habib

2015-09-01

Comprehensive theoretical and experimental studies of a natural product, 8-hydroxyisodiospyrin (HDO) have been carried out. Based on the correlation of experimental and theoretical data, an appropriate computational model was developed for obtaining the electronic, spectroscopic, and thermodynamic parameters of HDO. First of all, the exact structure of HDO is confirmed from the nice correlation of theory and experiment, prior to determination of its electroactive nature. Hybrid density functional theory (DFT) is employed for all theoretical simulations. The experimental and predicted IR and UV-vis spectra [B3LYP/6-31+G(d,p) level of theory] have excellent correlation. Inter-molecular non-covalent interaction of HDO with different gases such as NH3, CO2, CO, H2O is investigated through geometrical counterpoise (gCP) i.e., B3LYP-gCP-D3/6-31G∗ method. Furthermore, the inter-molecular interaction is also supported by geometrical parameters, electronic properties, thermodynamic parameters and charge analysis. All these characterizations have corroborated each other and confirmed the electroactive nature (non-covalent interaction ability) of HDO for the studied gases. Electronic properties such as Ionization Potential (IP), Electron Affinities (EA), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap of HDO have been estimated for the first time theoretically.

Semimicroscopic, Lane-consistent nucleon-nucleus optical model potential up to 200 MeV

NASA Astrophysics Data System (ADS)

Bauge, Eric; Delaroche, Jean-Paul; Girod, Michel

2000-10-01

Our semimicroscopic optical model potential (E. Bauge et al., Phys. Rev. C 58), 1118 (1998). is re-evaluated in order to obtain a Lane-consistent description of (p,p), (n,n) and (p,n IAS) elastic scattering and reaction observables. The re-assessed nuclear matter interaction (which includes sizable renormalizations of the isovector potentials) is folded with microscopic HFB nuclear densities, producing OMPs that are free of adjustable parameters for nuclei with A >= 40. With Lane-consistency of the interaction, and the predictive nature of our HFB calculations, this scheme can be used to calculate observables for nuclei far from the stability line with good predictivity.

On the use of interaction error potentials for adaptive brain computer interfaces.

PubMed

Llera, A; van Gerven, M A J; Gómez, V; Jensen, O; Kappen, H J

2011-12-01

We propose an adaptive classification method for the Brain Computer Interfaces (BCI) which uses Interaction Error Potentials (IErrPs) as a reinforcement signal and adapts the classifier parameters when an error is detected. We analyze the quality of the proposed approach in relation to the misclassification of the IErrPs. In addition we compare static versus adaptive classification performance using artificial and MEG data. We show that the proposed adaptive framework significantly improves the static classification methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

On ballistic parameters of less lethal projectiles influencing the severity of thoracic blunt impacts.

PubMed

Pavier, Julien; Langlet, André; Eches, Nicolas; Jacquet, Jean-François

2015-01-01

The development and safety certification of less lethal projectiles require an understanding of the influence of projectile parameters on projectile-chest interaction and on the resulting terminal effect. Several energy-based criteria have been developed for chest injury assessment. Many studies consider kinetic energy (KE) or energy density as the only projectile parameter influencing terminal effect. In a common KE range (100-160 J), analysis of the firing tests of two 40 mm projectiles of different masses on animal surrogates has been made in order to investigate the severity of the injuries in the thoracic region. Experimental results have shown that KE and calibre are not sufficient to discriminate between the two projectiles as regards their injury potential. Parameters, such as momentum, shape and impedance, influence the projectile-chest interaction and terminal effect. A simplified finite element model of projectile-structure interaction confirms the experimental tendencies. Within the range of ballistic parameters used, it has been demonstrated that maximum thoracic deflection is a useful parameter to predict the skeletal level of injury, and it largely depends on the projectile pre-impact momentum. However, numerical simulations show that these results are merely valid for the experimental conditions used and cannot be generalised. Nevertheless, the transmitted impulse seems to be a more general factor governing the thorax deflection.

Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Chae, Kyungchan; Violi, Angela

2011-01-01

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green-Kubo formula. The computed results were compared with the values obtained using the Chapman-Enskog (C-E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C-E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500-1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter σ _{12}, and potential energy well depth \\varepsilon _{12} of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.

Nonperturbative derivation of the interaction potential of static nucleons

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

Izmailov, A.F.; Kessel', A.R.; Fainberg, V.Y.

1989-05-01

A new approach is used to calculate the interaction potential of nucleons which describes virtual processes of exchange of scalar and pseudoscalar mesons in all orders in the nucleon{endash}meson local coupling constant. The theory contains a natural parameter---a limiting momentum {ital p}{sub {ital m}}. The nucleon{endash}nucleon potential of scalar mesodynamics for various values of {ital p}{sub {ital m}} reproduces accurately the well known phenomenological potentials, such as the Hamada{endash}Johnston potential, the Reid soft-core potential, and the de Toureil{endash}Sprung supersoft-core potential.{sup 15} In pseudoscalar mesodynamics, it has been possible to reproduce completely the behavior of the empirical tensor potential. The shapemore » of the central potential at all distances is reproduced in the states {tau}=0, {sigma}=0 and {tau}=0, {sigma}=1, and at intermediate and large distances in the states {tau}=1, {sigma}=0 and {tau}=1, {sigma}=1.« less

Bayesian approach to inverse statistical mechanics.

PubMed

Habeck, Michael

2014-05-01

Inverse statistical mechanics aims to determine particle interactions from ensemble properties. This article looks at this inverse problem from a Bayesian perspective and discusses several statistical estimators to solve it. In addition, a sequential Monte Carlo algorithm is proposed that draws the interaction parameters from their posterior probability distribution. The posterior probability involves an intractable partition function that is estimated along with the interactions. The method is illustrated for inverse problems of varying complexity, including the estimation of a temperature, the inverse Ising problem, maximum entropy fitting, and the reconstruction of molecular interaction potentials.

Bayesian approach to inverse statistical mechanics

NASA Astrophysics Data System (ADS)

Habeck, Michael

2014-05-01

Inverse statistical mechanics aims to determine particle interactions from ensemble properties. This article looks at this inverse problem from a Bayesian perspective and discusses several statistical estimators to solve it. In addition, a sequential Monte Carlo algorithm is proposed that draws the interaction parameters from their posterior probability distribution. The posterior probability involves an intractable partition function that is estimated along with the interactions. The method is illustrated for inverse problems of varying complexity, including the estimation of a temperature, the inverse Ising problem, maximum entropy fitting, and the reconstruction of molecular interaction potentials.

Herb–drug interaction prediction based on the high specific inhibition of andrographolide derivatives towards UDP-glucuronosyltransferase (UGT) 2B7

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

Ma, Hai-Ying, E-mail: cmu4h-mhy@126.com; Sun, Dong-Xue; Cao, Yun-Feng

2014-05-15

Herb–drug interaction strongly limits the clinical application of herbs and drugs, and the inhibition of herbal components towards important drug-metabolizing enzymes (DMEs) has been regarded as one of the most important reasons. The present study aims to investigate the inhibition potential of andrographolide derivatives towards one of the most important phase II DMEs UDP-glucuronosyltransferases (UGTs). Recombinant UGT isoforms (except UGT1A4)-catalyzed 4-methylumbelliferone (4-MU) glucuronidation reaction and UGT1A4-catalyzed trifluoperazine (TFP) glucuronidation were employed to firstly screen the andrographolide derivatives' inhibition potential. High specific inhibition of andrographolide derivatives towards UGT2B7 was observed. The inhibition type and parameters (K{sub i}) were determined for themore » compounds exhibiting strong inhibition capability towards UGT2B7, and human liver microsome (HLMs)-catalyzed zidovudine (AZT) glucuronidation probe reaction was used to furtherly confirm the inhibition behavior. In combination of inhibition parameters (K{sub i}) and in vivo concentration of andrographolide and dehydroandrographolide, the potential in vivo inhibition magnitude was predicted. Additionally, both the in vitro inhibition data and computational modeling results provide important information for the modification of andrographolide derivatives as selective inhibitors of UGT2B7. Taken together, data obtained from the present study indicated the potential herb–drug interaction between Andrographis paniculata and the drugs mainly undergoing UGT2B7-catalyzed metabolic elimination, and the andrographolide derivatives as potential candidates for the selective inhibitors of UGT2B7. - Highlights: • Specific inhibition of andrographolide derivatives towards UGT2B7. • Herb-drug interaction related withAndrographis paniculata. • Guidance for design of UGT2B7 specific inhibitors.« less

Electrostatic potential calculation for biomolecules--creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures.

PubMed

Rocchia, W; Neshich, G

2007-10-05

STING and Java Protein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and Java Protein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.

Potential for geophysical experiments in large scale tests.

USGS Publications Warehouse

Dieterich, J.H.

1981-01-01

Potential research applications for large-specimen geophysical experiments include measurements of scale dependence of physical parameters and examination of interactions with heterogeneities, especially flaws such as cracks. In addition, increased specimen size provides opportunities for improved recording resolution and greater control of experimental variables. Large-scale experiments using a special purpose low stress (100MPa).-Author

Summary Report for the CONSET Program at AEDC

DTIC Science & Technology

1980-09-01

the Lennard - Jones 12-6 intermolecular potential function, reduced onset pressures (P;) and temperatures (T;) have been determined using (lo) 16 AEDC...different, and this illustrates the inadequacy of the two-parameter Lennard - Jones potential for describing the interaction of polar molecules. As is well...molecules well described by the 12-6 Lennard - Jones potential will have common onset loci depending upon the specific heat ratio. However, polar molecules

Multiple regimes of robust patterns between network structure and biodiversity

NASA Astrophysics Data System (ADS)

Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

2015-12-01

Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities.

Multiple regimes of robust patterns between network structure and biodiversity

PubMed Central

Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

2015-01-01

Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities. PMID:26632996

Atomistic modeling of metallic thin films by modified embedded atom method

NASA Astrophysics Data System (ADS)

Hao, Huali; Lau, Denvid

2017-11-01

Molecular dynamics simulation is applied to investigate the deposition process of metallic thin films. Eight metals, titanium, vanadium, iron, cobalt, nickel, copper, tungsten, and gold, are chosen to be deposited on the aluminum substrate. The second nearest-neighbor modified embedded atom method potential is adopted to predict their thermal and mechanical properties. When quantifying the screening parameters of the potential, the error for Young's modulus and coefficient of thermal expansion between the simulated results and the experimental measurements is less than 15%, demonstrating the reliability of the potential to predict metallic behaviors related to thermal and mechanical properties. A set of potential parameters which governs the interactions between aluminum and other metals in a binary system is also generated from ab initio calculation. The details of interfacial structures between the chosen films and substrate are successfully simulated with the help of these parameters. Our results indicate that the preferred orientation of film growth depends on the film crystal structure, and the inter-diffusion at the interface is correlated the cohesive energy parameter of potential for the binary system. Such finding provides an important basis to further understand the interfacial science, which contributes to the improvement of the mechanical properties, reliability and durability of films.

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

PubMed

Park, Jungkap; Saitou, Kazuhiro

2014-09-18

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.

Theory of polyelectrolytes in solvents.

PubMed

Chitanvis, Shirish M

2003-12-01

Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

A Study of the Vacancy-Impurity Interaction in Dilute Nickel Alloys by Core Electron Annihilation

NASA Astrophysics Data System (ADS)

Arbuzov, V. L.; Danilov, S. E.; Druzhkov, A. P.

1997-08-01

It is shown that the angular correlation of annihilation radiation can be used to identify vacancy-impurity complexes in dilute alloys. Annihilation of trapped positrons with core electrons bears information about the chemical environment of a vacancy defect. The method is especially effective for d-matrices doped with sp-impurities since annihilation parameters of positrons with d- and sp-shell electrons differ considerably. The potentialities of the method of core-electron annihilation of positrons are demonstrated taking electron-irradiated dilute Ni-P and Ni-Si alloys as an example. It is shown that the interaction between the vacancies, which migrate at the III stage of annealing, and P atoms in Ni-P causes a considerable change in the annihilation parameters of positrons with core electrons compared to pure Ni. In Ni-Si alloys the annihilation parameters of trapped positrons with core electrons do not differ from those in Ni. This fact is an evidence that Si atoms do not interact with vacancies in Ni.

Influence of structure properties on protein-protein interactions-QSAR modeling of changes in diffusion coefficients.

PubMed

Bauer, Katharina Christin; Hämmerling, Frank; Kittelmann, Jörg; Dürr, Cathrin; Görlich, Fabian; Hubbuch, Jürgen

2017-04-01

Information about protein-protein interactions provides valuable knowledge about the phase behavior of protein solutions during the biopharmaceutical production process. Up to date it is possible to capture their overall impact by an experimentally determined potential of mean force. For the description of this potential, the second virial coefficient B22, the diffusion interaction parameter kD, the storage modulus G', or the diffusion coefficient D is applied. In silico methods do not only have the potential to predict these parameters, but also to provide deeper understanding of the molecular origin of the protein-protein interactions by correlating the data to the protein's three-dimensional structure. This methodology furthermore allows a lower sample consumption and less experimental effort. Of all in silico methods, QSAR modeling, which correlates the properties of the molecule's structure with the experimental behavior, seems to be particularly suitable for this purpose. To verify this, the study reported here dealt with the determination of a QSAR model for the diffusion coefficient of proteins. This model consisted of diffusion coefficients for six different model proteins at various pH values and NaCl concentrations. The generated QSAR model showed a good correlation between experimental and predicted data with a coefficient of determination R2 = 0.9 and a good predictability for an external test set with R2 = 0.91. The information about the properties affecting protein-protein interactions present in solution was in agreement with experiment and theory. Furthermore, the model was able to give a more detailed picture of the protein properties influencing the diffusion coefficient and the acting protein-protein interactions. Biotechnol. Bioeng. 2017;114: 821-831. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

How CMB and large-scale structure constrain chameleon interacting dark energy

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

Boriero, Daniel; Das, Subinoy; Wong, Yvonne Y.Y., E-mail: boriero@physik.uni-bielefeld.de, E-mail: subinoy@iiap.res.in, E-mail: yvonne.y.wong@unsw.edu.au

2015-07-01

We explore a chameleon type of interacting dark matter-dark energy scenario in which a scalar field adiabatically traces the minimum of an effective potential sourced by the dark matter density. We discuss extensively the effect of this coupling on cosmological observables, especially the parameter degeneracies expected to arise between the model parameters and other cosmological parameters, and then test the model against observations of the cosmic microwave background (CMB) anisotropies and other cosmological probes. We find that the chameleon parameters α and β, which determine respectively the slope of the scalar field potential and the dark matter-dark energy coupling strength,more » can be constrained to α < 0.17 and β < 0.19 using CMB data and measurements of baryon acoustic oscillations. The latter parameter in particular is constrained only by the late Integrated Sachs-Wolfe effect. Adding measurements of the local Hubble expansion rate H{sub 0} tightens the bound on α by a factor of two, although this apparent improvement is arguably an artefact of the tension between the local measurement and the H{sub 0} value inferred from Planck data in the minimal ΛCDM model. The same argument also precludes chameleon models from mimicking a dark radiation component, despite a passing similarity between the two scenarios in that they both delay the epoch of matter-radiation equality. Based on the derived parameter constraints, we discuss possible signatures of the model for ongoing and future large-scale structure surveys.« less

Multiscale Asymptotics for the Skeleton of the Madden-Julian Oscillation and Tropical-Extratropical Interactions (Open Access)

DTIC Science & Technology

2015-11-30

equatorial baroclinic dynamics, and (iii) the interactive effects of moisture and convection. More specifically, the model integrates the dry...interactions 5 Par. Derivation Dim. val. Description β 2.3× 10−11 m−1s−1 Variation of Coriolis parameter with latitude θ0 300 K Potential temperature...tropical Coriolis force, and x and y denote the zonal and meridional coordinates. Without the moisture q and convection envelope a, system (1) is the two

Exchange repulsive potential adaptable for electronic structure changes during chemical reactions

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

Yokogawa, D., E-mail: d.yokogawa@chem.nagoya-u.ac.jp

2015-04-28

Hybrid methods combining quantum mechanical (QM) and classical calculations are becoming important tools in chemistry. The popular approach to calculate the interaction between QM and classical calculations employs interatomic potentials. In most cases, the interatomic potential is constructed of an electrostatic (ES) potential and a non-ES potential. Because QM treatment is employed in the calculation of the ES potential, the electronic change can be considered in this ES potential. However, QM treatment of the non-ES potential is difficult because of high computational cost. To overcome this difficulty of evaluating the non-ES potential, we proposed an exchange repulsive potential as themore » main part of the non-ES potential on the basis of a QM approach. This potential is independent of empirical parameters and adaptable for electronic structure. We combined this potential with the reference interaction site model self-consistent field explicitly including spatial electron density distribution and successfully applied it to the chemical reactions in aqueous phase.« less

Molecular theory of smectic ordering in liquid crystals with nanoscale segregation of different molecular fragments

NASA Astrophysics Data System (ADS)

Gorkunov, M. V.; Osipov, M. A.; Kapernaum, N.; Nonnenmacher, D.; Giesselmann, F.

2011-11-01

A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure.

Dissipative particle dynamics study of velocity autocorrelation function and self-diffusion coefficient in terms of interaction potential strength

NASA Astrophysics Data System (ADS)

Zohravi, Elnaz; Shirani, Ebrahim; Pishevar, Ahmadreza; Karimpour, Hossein

2018-07-01

This research focuses on numerically investigating the self-diffusion coefficient and velocity autocorrelation function (VACF) of a dissipative particle dynamics (DPD) fluid as a function of the conservative interaction strength. Analytic solutions to VACF and self-diffusion coefficients in DPD were obtained by many researchers in some restricted cases including ideal gases, without the account of conservative force. As departure from the ideal gas conditions are accentuated with increasing the relative proportion of conservative force, it is anticipated that the VACF should gradually deviate from its normally expected exponentially decay. This trend is confirmed through numerical simulations and an expression in terms of the conservative force parameter, density and temperature is proposed for the self-diffusion coefficient. As it concerned the VACF, the equivalent Langevin equation describing Brownian motion of particles with a harmonic potential is adapted to the problem and reveals an exponentially decaying oscillatory pattern influenced by the conservative force parameter, dissipative parameter and temperature. Although the proposed model for obtaining the self-diffusion coefficient with consideration of the conservative force could not be verified due to computational complexities, nonetheless the Arrhenius dependency of the self-diffusion coefficient to temperature and pressure permits to certify our model over a definite range of DPD parameters.

Thomas-Fermi simulations of dense plasmas without pseudopotentials

NASA Astrophysics Data System (ADS)

Starrett, C. E.

2017-07-01

The Thomas-Fermi model for warm and hot dense matter is widely used to predict material properties such as the equation of state. However, for practical reasons current implementations use pseudopotentials for the electron-nucleus interaction instead of the bare Coulomb potential. This complicates the calculation and quantities such as free energy cannot be converged with respect to the pseudopotential parameters. We present a method that retains the bare Coulomb potential for the electron-nucleus interaction and does not use pseudopotentials. We demonstrate that accurate free energies are obtained by checking variational consistency. Examples for aluminum and iron plasmas are presented.

webPIPSA: a web server for the comparison of protein interaction properties

PubMed Central

Richter, Stefan; Wenzel, Anne; Stein, Matthias; Gabdoulline, Razif R.; Wade, Rebecca C.

2008-01-01

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org. PMID:18420653

Visual exploration of parameter influence on phylogenetic trees.

PubMed

Hess, Martin; Bremm, Sebastian; Weissgraeber, Stephanie; Hamacher, Kay; Goesele, Michael; Wiemeyer, Josef; von Landesberger, Tatiana

2014-01-01

Evolutionary relationships between organisms are frequently derived as phylogenetic trees inferred from multiple sequence alignments (MSAs). The MSA parameter space is exponentially large, so tens of thousands of potential trees can emerge for each dataset. A proposed visual-analytics approach can reveal the parameters' impact on the trees. Given input trees created with different parameter settings, it hierarchically clusters the trees according to their structural similarity. The most important clusters of similar trees are shown together with their parameters. This view offers interactive parameter exploration and automatic identification of relevant parameters. Biologists applied this approach to real data of 16S ribosomal RNA and protein sequences of ion channels. It revealed which parameters affected the tree structures. This led to a more reliable selection of the best trees.

Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

NASA Astrophysics Data System (ADS)

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F.; Ingrosso, Francesca

2014-07-01

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

Therapeutic peptides for cancer therapy. Part I - peptide inhibitors of signal transduction cascades.

PubMed

Bidwell, Gene L; Raucher, Drazen

2009-10-01

Therapeutic peptides have great potential as anticancer agents owing to their ease of rational design and target specificity. However, their utility in vivo is limited by low stability and poor tumor penetration. The authors review the development of peptide inhibitors with potential for cancer therapy. Peptides that inhibit signal transduction cascades are discussed. The authors searched Medline for articles concerning the development of therapeutic peptides and their delivery. Given our current knowledge of protein sequences, structures and interaction interfaces, therapeutic peptides that inhibit interactions of interest are easily designed. These peptides are advantageous because they are highly specific for the interaction of interest, and they are much more easily developed than small molecule inhibitors of the same interactions. The main hurdle to application of peptides for cancer therapy is their poor pharmacokinetic and biodistribution parameters. Therefore, successful development of peptide delivery vectors could potentially make possible the use of this new and very promising class of anticancer agents.

Non-additive simple potentials for pre-programmed self-assembly

NASA Astrophysics Data System (ADS)

Mendoza, Carlos

2015-03-01

A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts are currently concentrated in the development of the so called ``patchy'' particles. Here we follow a completely different approach and introduce a very accessible model to produce a large variety of pre-programmed two-dimensional (2D) complex structures. Our model consists of a binary mixture of particles that interact through isotropic interactions that is able to self-assemble into targeted lattices by the appropriate choice of a small number of geometrical parameters and interaction strengths. We study the system using Monte Carlo computer simulations and, despite its simplicity, we are able to self assemble potentially useful structures such as chains, stripes, Kagomé, twisted Kagomé, honeycomb, square, Archimedean and quasicrystalline tilings. Our model is designed such that it may be implemented using discotic particles or, alternatively, using exclusively spherical particles interacting isotropically. Thus, it represents a promising strategy for bottom-up nano-fabrication. Partial Financial Support: DGAPA IN-110613.

Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

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

Noy, A

2004-05-04

Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNAmore » duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.« less

Applicability of effective pair potentials for active Brownian particles.

PubMed

Rein, Markus; Speck, Thomas

2016-09-01

We have performed a case study investigating a recently proposed scheme to obtain an effective pair potential for active Brownian particles (Farage et al., Phys. Rev. E 91, 042310 (2015)). Applying this scheme to the Lennard-Jones potential, numerical simulations of active Brownian particles are compared to simulations of passive Brownian particles interacting by the effective pair potential. Analyzing the static pair correlations, our results indicate a limited range of activity parameters (speed and orientational correlation time) for which we obtain quantitative, or even qualitative, agreement. Moreover, we find a qualitatively different behavior for the virial pressure even for small propulsion speeds. Combining these findings we conclude that beyond linear response active particles exhibit genuine non-equilibrium properties that cannot be captured by effective pair interaction alone.

Oscillon in Einstein-scalar system with double well potential and its properties.

NASA Astrophysics Data System (ADS)

Ikeda, Taishi; Yoo, Chul-Moon; Cardoso, Vitor

2018-01-01

The dynamical evolution of self-interacting scalar field has many nontrivial behaviors, which tell us many lessons in a nonlinear dynamics. On Minkowski spacetime, the scalar field with double well potential has localized, non-singular, time-dependent, long-lived solutions, which are called oscillons. The lifetime of the oscillon depends on the initial conditions. Furthermore, when the initial parameter is fine-tuned, oscillons can be infinitely, and type I critical behavior is observed. Here, we investigate the Einstein-scalar system with double well potential. We show that oscillons exist in this system, and discuss the behavior when the initial parameter is fine-tuned. Our results suggests that a new type of critical behavior appears in this theory.

Relationship of the Williams-Poulios and Manning-Rosen Potential Energy Models for Diatomic Molecules

NASA Astrophysics Data System (ADS)

Jia, Chun-Sheng; Liang, Guang-Chuan; Peng, Xiao-Long; Tang, Hong-Ming; Zhang, Lie-Hui

2014-06-01

By employing the dissociation energy and the equilibrium bond length for a diatomic molecule as explicit parameters, we generate an improved form of the Williams-Poulios potential energy model. It is found that the negative Williams-Poulios potential model is equivalent to the Manning-Rosen potential model for diatomic molecules. We observe that the Manning-Rosen potential is superior to the Morse potential in reproducing the interaction potential energy curves for the {{a}3 Σu+} state of the 6Li2 molecule and the {{X}1 sum+} state of the SiF+ molecule.

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

Two competing species in super-diffusive dynamical regimes

NASA Astrophysics Data System (ADS)

La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.

2010-09-01

The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.

Development of MCAERO wing design panel method with interactive graphics module

NASA Technical Reports Server (NTRS)

Hawk, J. D.; Bristow, D. R.

1984-01-01

A reliable and efficient iterative method has been developed for designing wing section contours corresponding to a prescribed subcritical pressure distribution. The design process is initialized by using MCAERO (MCAIR 3-D Subsonic Potential Flow Analysis Code) to analyze a baseline configuration. A second program DMCAERO is then used to calculate a matrix containing the partial derivative of potential at each control point with respect to each unknown geometry parameter by applying a first-order expansion to the baseline equations in MCAERO. This matrix is calculated only once but is used in each iteration cycle to calculate the geometry perturbation and to analyze the perturbed geometry. The potential on the new geometry is calculated by linear extrapolation from the baseline solution. This extrapolated potential is converted to velocity by numerical differentiation, and velocity is converted to pressure by using Bernoulli's equation. There is an interactive graphics option which allows the user to graphically display the results of the design process and to interactively change either the geometry or the prescribed pressure distribution.

Common misconceptions about the dynamical theory of crystal lattices: Cauchy relations, lattice potentials and infinite crystals

NASA Astrophysics Data System (ADS)

Elcoro, Luis; Etxebarria, Jesús

2011-01-01

The requirement of rotational invariance for lattice potential energies is investigated. Starting from this condition, it is shown that the Cauchy relations for the elastic constants are fulfilled if the lattice potential is built from pair interactions or when the first-neighbour approximation is adopted. This is seldom recognized in widely used solid-state textbooks. Frequently, pair interaction is even considered to be the most general situation. In addition, it is shown that the demand of rotational invariance in an infinite crystal leads to inconsistencies in the symmetry of the elastic tensor. However, for finite crystals, no problems arise, and the Huang conditions are deduced using exclusively a microscopic approach for the elasticity theory, without making any reference to macroscopic parameters. This work may be useful in both undergraduate and graduate level courses to point out the crudeness of the pair-potential interaction and to explore the limits of the infinite-crystal approximation.

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

Marion, Antoine; Monard, Gérald; Ruiz-López, Manuel F., E-mail: Manuel.Ruiz@univ-lorraine.fr

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering themore » potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.« less

pynoddy 1.0: an experimental platform for automated 3-D kinematic and potential field modelling

NASA Astrophysics Data System (ADS)

Florian Wellmann, J.; Thiele, Sam T.; Lindsay, Mark D.; Jessell, Mark W.

2016-03-01

We present a novel methodology for performing experiments with subsurface structural models using a set of flexible and extensible Python modules. We utilize the ability of kinematic modelling techniques to describe major deformational, tectonic, and magmatic events at low computational cost to develop experiments testing the interactions between multiple kinematic events, effect of uncertainty regarding event timing, and kinematic properties. These tests are simple to implement and perform, as they are automated within the Python scripting language, allowing the encapsulation of entire kinematic experiments within high-level class definitions and fully reproducible results. In addition, we provide a link to geophysical potential-field simulations to evaluate the effect of parameter uncertainties on maps of gravity and magnetics. We provide relevant fundamental information on kinematic modelling and our implementation, and showcase the application of our novel methods to investigate the interaction of multiple tectonic events on a pre-defined stratigraphy, the effect of changing kinematic parameters on simulated geophysical potential fields, and the distribution of uncertain areas in a full 3-D kinematic model, based on estimated uncertainties in kinematic input parameters. Additional possibilities for linking kinematic modelling to subsequent process simulations are discussed, as well as additional aspects of future research. Our modules are freely available on github, including documentation and tutorial examples, and we encourage the contribution to this project.

pynoddy 1.0: an experimental platform for automated 3-D kinematic and potential field modelling

NASA Astrophysics Data System (ADS)

Wellmann, J. F.; Thiele, S. T.; Lindsay, M. D.; Jessell, M. W.

2015-11-01

We present a novel methodology for performing experiments with subsurface structural models using a set of flexible and extensible Python modules. We utilise the ability of kinematic modelling techniques to describe major deformational, tectonic, and magmatic events at low computational cost to develop experiments testing the interactions between multiple kinematic events, effect of uncertainty regarding event timing, and kinematic properties. These tests are simple to implement and perform, as they are automated within the Python scripting language, allowing the encapsulation of entire kinematic experiments within high-level class definitions and fully reproducible results. In addition, we provide a~link to geophysical potential-field simulations to evaluate the effect of parameter uncertainties on maps of gravity and magnetics. We provide relevant fundamental information on kinematic modelling and our implementation, and showcase the application of our novel methods to investigate the interaction of multiple tectonic events on a pre-defined stratigraphy, the effect of changing kinematic parameters on simulated geophysical potential-fields, and the distribution of uncertain areas in a full 3-D kinematic model, based on estimated uncertainties in kinematic input parameters. Additional possibilities for linking kinematic modelling to subsequent process simulations are discussed, as well as additional aspects of future research. Our modules are freely available on github, including documentation and tutorial examples, and we encourage the contribution to this project.

Two-ball Newton's cradle

NASA Astrophysics Data System (ADS)

Glendinning, Paul

2011-12-01

Newton's cradle for two balls with Hertzian interactions is considered as a hybrid system, and this makes it possible to derive return maps for the motion between collisions in an exact form despite the fact that the three-halves interaction law cannot be solved in closed form. The return maps depend on a constant whose value can only be determined numerically, but solutions can be written down explicitly in terms of this parameter, and we compare this with the results of simulations. The results are in fact independent of the details of the interaction potential.

A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

PubMed Central

Hu, Zhineng; Lu, Wei; Han, Bing

2015-01-01

This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

PubMed Central

Christensen, Anders S.; Elstner, Marcus; Cui, Qiang

2015-01-01

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets. PMID:26328834

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

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

Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Elstner, Marcus

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculatedmore » at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.« less

SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.

PubMed

Bueno, Marta; Camacho, Carlos J; Sancho, Javier

2007-09-01

The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. 2007 Wiley-Liss, Inc.

Laser-driven two-electron quantum dot in plasmas

NASA Astrophysics Data System (ADS)

Bahar, M. K.; Soylu, A.

2018-06-01

We have investigated the energies of two-electron parabolic quantum dots (TEPQdots) embedded in plasmas characterized by more general exponential cosine screened Coulomb (MGECSC) potential under the action of a monochromatic, linearly polarized laser field by solving the corresponding Schrödinger equation numerically via the asymptotic iteration method. The four different cases of the MGECSC potential constituted by various sets of the potential parameters are reckoned in modeling of the interactions in the plasma environments which are Debye and quantum plasmas. The plasma environment is a remarkable experimental argument for the quantum dots and the interactions in plasma environments are different compared to the interactions in an environment without plasma and the screening specifications of the plasmas can be controlled through the plasma parameters. These findings constitute our major motivation in consideration of the plasma environments. An appreciable confinement effect is made up by implementing the laser field on the TEPQdot. The influences of the laser field on the system are included by using the Ehlotzky approximation, and then Kramers-Henneberger transformation is carried out for the corresponding Schrödinger equation. The influences of the ponderomotive force on two-electron quantum dots embedded in plasmas are investigated. The behaviours, the similarities and the functionalities of the laser field, the plasma environment, and the quantum dot confinement are also scrutinized. In addition, the role of the plasma environments in the mentioned analysis is also discussed in detail.

Bayesian parameter estimation for chiral effective field theory

NASA Astrophysics Data System (ADS)

Wesolowski, Sarah; Furnstahl, Richard; Phillips, Daniel; Klco, Natalie

2016-09-01

The low-energy constants (LECs) of a chiral effective field theory (EFT) interaction in the two-body sector are fit to observable data using a Bayesian parameter estimation framework. By using Bayesian prior probability distributions (pdfs), we quantify relevant physical expectations such as LEC naturalness and include them in the parameter estimation procedure. The final result is a posterior pdf for the LECs, which can be used to propagate uncertainty resulting from the fit to data to the final observable predictions. The posterior pdf also allows an empirical test of operator redundancy and other features of the potential. We compare results of our framework with other fitting procedures, interpreting the underlying assumptions in Bayesian probabilistic language. We also compare results from fitting all partial waves of the interaction simultaneously to cross section data compared to fitting to extracted phase shifts, appropriately accounting for correlations in the data. Supported in part by the NSF and DOE.

Conditions where random phase approximation becomes exact in the high-density limit

NASA Astrophysics Data System (ADS)

Morawetz, Klaus; Ashokan, Vinod; Bala, Renu; Pathak, Kare Narain

2018-04-01

It is shown that, in d -dimensional systems, the vertex corrections beyond the random phase approximation (RPA) or G W approximation scales with the power d -β -α of the Fermi momentum if the relation between Fermi energy and Fermi momentum is ɛf˜pfβ and the interacting potential possesses a momentum power law of ˜p-α . The condition d -β -α <0 specifies systems where RPA is exact in the high-density limit. The one-dimensional structure factor is found to be the interaction-free one in the high-density limit for contact interaction. A cancellation of RPA and vertex corrections render this result valid up to second order in contact interaction. For finite-range potentials of cylindrical wires a large-scale cancellation appears and is found to be independent of the width parameter of the wire. The proposed high-density expansion agrees with the quantum Monte Carlo simulations.

Measurement of Anisotropic Particle Interactions with Nonuniform ac Electric Fields.

PubMed

Rupp, Bradley; Torres-Díaz, Isaac; Hua, Xiaoqing; Bevan, Michael A

2018-02-20

Optical microscopy measurements are reported for single anisotropic polymer particles interacting with nonuniform ac electric fields. The present study is limited to conditions where gravity confines particles with their long axis parallel to the substrate such that particles can be treated using quasi-2D analysis. Field parameters are investigated that result in particles residing at either electric field maxima or minima and with long axes oriented either parallel or perpendicular to the electric field direction. By nonintrusively observing thermally sampled positions and orientations at different field frequencies and amplitudes, a Boltzmann inversion of the time-averaged probability of states yields kT-scale energy landscapes (including dipole-field, particle-substrate, and gravitational potentials). The measured energy landscapes show agreement with theoretical potentials using particle conductivity as the sole adjustable material property. Understanding anisotropic particle-field energy landscapes vs field parameters enables quantitative control of local forces and torques on single anisotropic particles to manipulate their position and orientation within nonuniform fields.

Atomic interaction of the MEAM type for the study of intermetallics in the Al-U alloy

NASA Astrophysics Data System (ADS)

Pascuet, M. I.; Fernández, J. R.

2015-12-01

Interaction for both pure Al and Al-U alloys of the MEAM type are developed. The obtained Al interatomic potential assures its compatibility with the details of the framework presently adopted. The Al-U interaction fits various properties of the Al2U, Al3U and Al4U intermetallics. The potential verifies the stability of the intermetallic structures in a temperature range compatible with that observed in the phase diagram, and also takes into account the greater stability of these structures relative to others that are competitive in energy. The intermetallics are characterized by calculating elastic and thermal properties and point defect parameters. Molecular dynamics simulations show a growth of the Al3U intermetallic in the Al/U interface in agreement with experimental evidence.

Effect of spin-orbit and on-site Coulomb interactions on the electronic structure and lattice dynamics of uranium monocarbide

NASA Astrophysics Data System (ADS)

Wdowik, U. D.; Piekarz, P.; Legut, D.; Jagło, G.

2016-08-01

Uranium monocarbide, a potential fuel material for the generation IV reactors, is investigated within density functional theory. Its electronic, magnetic, elastic, and phonon properties are analyzed and discussed in terms of spin-orbit interaction and localized versus itinerant behavior of the 5 f electrons. The localization of the 5 f states is tuned by varying the local Coulomb repulsion interaction parameter. We demonstrate that the theoretical electronic structure, elastic constants, phonon dispersions, and their densities of states can reproduce accurately the results of x-ray photoemission and bremsstrahlung isochromat measurements as well as inelastic neutron scattering experiments only when the 5 f states experience the spin-orbit interaction and simultaneously remain partially localized. The partial localization of the 5 f electrons could be represented by a moderate value of the on-site Coulomb interaction parameter of about 2 eV. The results of the present studies indicate that both strong electron correlations and spin-orbit effects are crucial for realistic theoretical description of the ground-state properties of uranium carbide.

Low testosterone levels are related to oxidative stress, mitochondrial dysfunction and altered subclinical atherosclerotic markers in type 2 diabetic male patients.

PubMed

Rovira-Llopis, Susana; Bañuls, Celia; de Marañon, Aranzazu M; Diaz-Morales, Noelia; Jover, Ana; Garzon, Sandra; Rocha, Milagros; Victor, Victor M; Hernandez-Mijares, Antonio

2017-07-01

Low testosterone levels in men are associated with type 2 diabetes and cardiovascular risk. However, the role of testosterone in mitochondrial function and leukocyte-endothelium interactions is unknown. Our aim was to evaluate the relationship between testosterone levels, metabolic parameters, oxidative stress, mitochondrial function, inflammation and leukocyte-endothelium interactions in type 2 diabetic patients. The study was performed in 280 male type 2 diabetic patients and 50 control subjects. Anthropometric and metabolic parameters, testosterone levels, reactive oxygen species (ROS) production, mitochondrial membrane potential, TNFα, adhesion molecules and leukocyte-endothelium cell interactions were evaluated. Testosterone levels were lower in diabetic patients. Total and mitochondrial ROS were increased and mitochondrial membrane potential, SOD and GSR expression levels were reduced in diabetic patients. TNFα, ICAM-1 and VCAM-1 levels, leukocyte rolling flux and adhesion were all enhanced in diabetic patients, while rolling velocity was reduced. Testosterone levels correlated negatively with glucose, HOMA-IR, HbA1c, triglycerides, nonHDL-c, ApoB, hs-CRP and AIP, and positively with HDL-c and ApoA1. The multivariable regression model showed that HDL-c, HOMA-IR and age were independently associated with testosterone. Furthermore, testosterone levels correlated positively with membrane potential and rolling velocity and negatively with ROS production, VCAM-1, rolling flux and adhesion. Our data highlight that low testosterone levels in diabetic men are related to impaired metabolic profile and mitochondrial function and enhanced inflammation and leukocyte-endothelium cell interaction, which leaves said patients at risk of cardiovascular events. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamics of nonautonomous discrete rogue wave solutions for an Ablowitz-Musslimani equation with PT-symmetric potential.

PubMed

Yu, Fajun

2017-02-01

Starting from a discrete spectral problem, we derive a hierarchy of nonlinear discrete equations which include the Ablowitz-Ladik (AL) equation. We analytically study the discrete rogue-wave (DRW) solutions of AL equation with three free parameters. The trajectories of peaks and depressions of profiles for the first- and second-order DRWs are produced by means of analytical and numerical methods. In particular, we study the solutions with dispersion in parity-time ( PT) symmetric potential for Ablowitz-Musslimani equation. And we consider the non-autonomous DRW solutions, parameters controlling and their interactions with variable coefficients, and predict the long-living rogue wave solutions. Our results might provide useful information for potential applications of synthetic PT symmetric systems in nonlinear optics and condensed matter physics.

The triel bond: a potential force for tuning anion-π interactions

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2018-02-01

Using ab-initio calculations, the mutual influence between anion-π and B···N or B···C triel bond interactions is investigated in some model complexes. The properties of these complexes are studied by molecular electrostatic potential, noncovalent interaction index, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. According to the results, the formation of B···N or B···C triel bond interactions in the multi-component systems makes a significant shortening of anion-π distance. Such remarkable variation in the anion-π distances has not been reported previously. The strengthening of the anion-π bonding in the multi-component systems depend significantly on the nature of the anion, and it becomes larger in the order Br- > Cl- > F-. The parameters derived from the QTAIM and NBO methodologies are used to study the mechanism of the cooperativity between the anion-π and triel bond interactions in the multi-component complexes.

Quality of traffic flow on urban arterial streets and its relationship with safety.

PubMed

Dixit, Vinayak V; Pande, Anurag; Abdel-Aty, Mohamed; Das, Abhishek; Radwan, Essam

2011-09-01

The two-fluid model for vehicular traffic flow explains the traffic on arterials as a mix of stopped and running vehicles. It describes the relationship between the vehicles' running speed and the fraction of running vehicles. The two parameters of the model essentially represent 'free flow' travel time and level of interaction among vehicles, and may be used to evaluate urban roadway networks and urban corridors with partially limited access. These parameters are influenced by not only the roadway characteristics but also by behavioral aspects of driver population, e.g., aggressiveness. Two-fluid models are estimated for eight arterial corridors in Orlando, FL for this study. The parameters of the two-fluid model were used to evaluate corridor level operations and the correlations of these parameters' with rates of crashes having different types/severity. Significant correlations were found between two-fluid parameters and rear-end and angle crash rates. Rate of severe crashes was also found to be significantly correlated with the model parameter signifying inter-vehicle interactions. While there is need for further analysis, the findings suggest that the two-fluid model parameters may have potential as surrogate measures for traffic safety on urban arterial streets. Copyright © 2011 Elsevier Ltd. All rights reserved.

Combination Rules for Morse-Based van der Waals Force Fields.

PubMed

Yang, Li; Sun, Lei; Deng, Wei-Qiao

2018-02-15

In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.

Bond lifetime and diffusion coefficient in colloids with short-range interactions.

PubMed

Ndong Mintsa, E; Germain, Ph; Amokrane, S

2015-03-01

We use molecular dynamics simulations to study the influence of short-range structures in the interaction potential between hard-sphere-like colloidal particles. Starting from model potentials and effective potentials in binary mixtures computed from the Ornstein-Zernike equations, we investigate the influence of the range and strength of a possible tail beyond the usual core repulsion or the presence of repulsive barriers. The diffusion coefficient and mean "bond" lifetimes are used as indicators of the effect of this structure on the dynamics. The existence of correlations between the variations of these quantities with the physical parameters is discussed to assess the interpretation of dynamics slowing down in terms of long-lived bonds. We also discuss the question of a universal behaviour determined by the second virial coefficient B ((2)) and the interplay of attraction and repulsion. While the diffusion coefficient follows the B ((2)) law for purely attractive tails, this is no longer true in the presence of repulsive barriers. Furthermore, the bond lifetime shows a dependence on the physical parameters that differs from that of the diffusion coefficient. This raises the question of the precise role of bonds on the dynamics slowing down in colloidal gels.

Influence of Plasma Environment on K-Line Emission in Highly Ionized Iron Atoms Evaluated Using a Debye-Huckel Model

NASA Technical Reports Server (NTRS)

Deprince, J.; Fritzsche, S.; Kallman, T. R.; Palmeri, P.; Quinet, P.

2017-01-01

The influence of plasma environment on the atomic parameters associated with the K-vacancy states has been investigated theoretically for several iron ions. To do this, a time-averaged Debye-Huckel potential for both the electron-nucleus and electron-electron interactions has been considered in the framework of relativistic multiconfiguration Dirac-Fock computations. More particularly, the plasma screening effects on ionization potentials, K-thresholds, transition energies, and radiative rates have been estimated in the astrophysical context of accretion disks around black holes. In the present paper, we describe the behavior of those atomic parameters for Ne-, Na-, Ar-, and K-like iron ions.

Measurements of Sheath Currents and Equilibrium Potential on the Explorer VIII Satellite (1960 xi)

NASA Technical Reports Server (NTRS)

Bourdeau, R. E.; Donley, J. L.; Serbu, G. P.; Whipple, E. C., Jr.

1961-01-01

Experimental data were obtained from the Explorer VIII satellite on five parameters pertinent to the problem of the interaction of space vehicles with an ionized atmosphere. The five parameters are: photoemission current due to electrons emitted from the satellite surfaces as a result of solar radiation; electron and positive ion currents due to the diffusion of charged particles from the medium to the spacecraft; the vehicle potential relative to the medium, and the ambient electron temperature. Included in the experimental data is the aspect dependence of the photoemission and diffusion currents. On the basis of the observations, certain characteristics of the satellite's plasma sheath are postulated.

Structural properties of liquid lanthanides using charge hard sphere reference system

NASA Astrophysics Data System (ADS)

Thakora, P. B.; Sonvane, Y. A.; Patel, H. P.; Gajjar, P. N.; Jani, A. R.

2012-06-01

In the present paper Charge Hard Sphere (CHS) system is employed to investigate the structural properties like long wavelength limit S(0), isothermal compressibility (χT) and coordination number n for some liquid lanthanides viz.: La, Ce, Pr, Nd, Eu, Gd, Tb, Dy, Ho, Er, Yb and Lu. Our well established parameter free model potential is used to describe the electron-ion interaction alongwith sarkar et al. dielectric function. From the present results, it is seen that good agreement between present results and available experimental data have been achieved. At last, we establish the applicability of our parameter free model potential and CHS method to account such structural properties.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions.

PubMed

Abraham, Alex; Chatterji, Apratim

2018-04-21

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

NASA Astrophysics Data System (ADS)

Abraham, Alex; Chatterji, Apratim

2018-04-01

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Effects of laser radiation field on energies of hydrogen atom in plasmas

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

Bahar, M. K., E-mail: mussiv58@gmail.com

2015-09-15

In this study, for the first time, the Schrödinger equation with more general exponential cosine screened Coulomb (MGECSC) potential is solved numerically in the presence of laser radiation field within the Ehlotzky approximation using the asymptotic iteration method. The MGECSC potential includes four different potential forms in consideration of different sets of the parameters in the potential. By applying laser field, the total interaction potential of hydrogen atom embedded in plasmas converts to double well-type potential. The plasma screening effects under the influence of laser field as well as confinement effects of laser field on hydrogen atom in Debye andmore » quantum plasmas are investigated by solving the Schrödinger equation with the laser-dressed MGECSC potential. It is resulted that since applying a monochromatic laser field on hydrogen atom embedded in a Debye and quantum plasma causes to shift in the profile of the total interaction potential, the confinement effects of laser field on hydrogen atom in plasmas modeled by the MGECSC potential change localizations of energy states.« less

Population of computational rabbit-specific ventricular action potential models for investigating sources of variability in cellular repolarisation.

PubMed

Gemmell, Philip; Burrage, Kevin; Rodriguez, Blanca; Quinn, T Alexander

2014-01-01

Variability is observed at all levels of cardiac electrophysiology. Yet, the underlying causes and importance of this variability are generally unknown, and difficult to investigate with current experimental techniques. The aim of the present study was to generate populations of computational ventricular action potential models that reproduce experimentally observed intercellular variability of repolarisation (represented by action potential duration) and to identify its potential causes. A systematic exploration of the effects of simultaneously varying the magnitude of six transmembrane current conductances (transient outward, rapid and slow delayed rectifier K(+), inward rectifying K(+), L-type Ca(2+), and Na(+)/K(+) pump currents) in two rabbit-specific ventricular action potential models (Shannon et al. and Mahajan et al.) at multiple cycle lengths (400, 600, 1,000 ms) was performed. This was accomplished with distributed computing software specialised for multi-dimensional parameter sweeps and grid execution. An initial population of 15,625 parameter sets was generated for both models at each cycle length. Action potential durations of these populations were compared to experimentally derived ranges for rabbit ventricular myocytes. 1,352 parameter sets for the Shannon model and 779 parameter sets for the Mahajan model yielded action potential duration within the experimental range, demonstrating that a wide array of ionic conductance values can be used to simulate a physiological rabbit ventricular action potential. Furthermore, by using clutter-based dimension reordering, a technique that allows visualisation of multi-dimensional spaces in two dimensions, the interaction of current conductances and their relative importance to the ventricular action potential at different cycle lengths were revealed. Overall, this work represents an important step towards a better understanding of the role that variability in current conductances may play in experimentally observed intercellular variability of rabbit ventricular action potential repolarisation.

Population of Computational Rabbit-Specific Ventricular Action Potential Models for Investigating Sources of Variability in Cellular Repolarisation

PubMed Central

Gemmell, Philip; Burrage, Kevin; Rodriguez, Blanca; Quinn, T. Alexander

2014-01-01

Variability is observed at all levels of cardiac electrophysiology. Yet, the underlying causes and importance of this variability are generally unknown, and difficult to investigate with current experimental techniques. The aim of the present study was to generate populations of computational ventricular action potential models that reproduce experimentally observed intercellular variability of repolarisation (represented by action potential duration) and to identify its potential causes. A systematic exploration of the effects of simultaneously varying the magnitude of six transmembrane current conductances (transient outward, rapid and slow delayed rectifier K+, inward rectifying K+, L-type Ca2+, and Na+/K+ pump currents) in two rabbit-specific ventricular action potential models (Shannon et al. and Mahajan et al.) at multiple cycle lengths (400, 600, 1,000 ms) was performed. This was accomplished with distributed computing software specialised for multi-dimensional parameter sweeps and grid execution. An initial population of 15,625 parameter sets was generated for both models at each cycle length. Action potential durations of these populations were compared to experimentally derived ranges for rabbit ventricular myocytes. 1,352 parameter sets for the Shannon model and 779 parameter sets for the Mahajan model yielded action potential duration within the experimental range, demonstrating that a wide array of ionic conductance values can be used to simulate a physiological rabbit ventricular action potential. Furthermore, by using clutter-based dimension reordering, a technique that allows visualisation of multi-dimensional spaces in two dimensions, the interaction of current conductances and their relative importance to the ventricular action potential at different cycle lengths were revealed. Overall, this work represents an important step towards a better understanding of the role that variability in current conductances may play in experimentally observed intercellular variability of rabbit ventricular action potential repolarisation. PMID:24587229

Influence of the inter-ion interaction on the phase diagrams of the 1D Falicov-Kimball system

NASA Astrophysics Data System (ADS)

Gajek, Z.; Lemański, R.

2004-05-01

A model of itinerant, spinless electrons interacting with ions via the on-site Coulomb potential U, modified by the inter-ionic nearest-neighbour interaction V, is studied on the one-dimensional infinite lattice. Only periodical configurations of the ions with a limited number of lattice sites in a unit cell and their mixtures are taken into account. Phases whose energies reach minimum values for given electron and ion chemical potentials are selected and depicted for a set of model parameters. Then the results are translated into the ion density-electron density canonical phase diagrams and summarized in the electrondensity-U plane. The diagrams clearly show how various kinds of charge ordering evolve with V, starting from V=0 case, that represents the standard Falicov-Kimball model discussed previously.

Electrostatic and hydrodynamics effects in a sedimented magnetorheological suspension.

PubMed

Domínguez-García, P; Pastor, J M; Melle, Sonia; Rubio, Miguel A

2009-08-01

We present experimental results on the equilibrium microstructure of a sedimented magnetorheological suspension, namely, an aqueous suspension of micron-sized superparamagnetic particles. We develop a study of the electrical interactions on the suspension by processing video-microscopy images of the sedimented particles. We calculate the pair distribution function, g(r), which yields the electrostatic pair potential u(r), showing an anomalous attractive interaction for distances on the order of twice the particle diameter, with characteristic parameters whose values show a dependence with the two-dimensional concentration of particles. The repulsive body of the potential is adjusted to a DLVO expression in order to calculate the Debye screening length and the effective surface charge density. Influence of confinement and variations on the Boltzmann sedimentation profile because of the electrostatic interactions appear to be essential for the interpretation of experimental results.

Effect of Anharmonicity on the Kondo Phenomena of a Magnetic Ion Vibrating in a Confinement Potential

NASA Astrophysics Data System (ADS)

Yashiki, Satoshi; Ueda, Kazuo

2011-08-01

Effect of anharmonicity of a cage potential for a magnetic ion vibrating in a metal is investigated by the numerical renormalization group method. The cage potential is assumed to be one-dimensional and of the double-well type. In the absence of the Coulomb interaction, we find continuous crossover among the three limiting cases: Yu--Anderson-type Kondo regime, the double-well-type Kondo one, and the renormalized Fermi chain one. In the entire parameter space of the double-well potential, the ground state is described by a local Fermi liquid. In the Yu--Anderson-type Kondo regime, a quantum phase transition to the ground state with odd parity takes place passing through the two-channel Kondo fixed point when the Coulomb interaction increases. Therefore, the vibration of a magnetic ion in an oversized cage structure is a promising route to the two-channel Kondo effect.

Time-dependent local potential in a Tomonaga-Luttinger liquid

NASA Astrophysics Data System (ADS)

Kamar, Naushad Ahmad; Giamarchi, Thierry

2017-12-01

We study the energy deposition in a one-dimensional interacting quantum system with a pointlike potential modulated in amplitude. The pointlike potential at position x =0 has a constant part and a small oscillation in time with a frequency ω . We use bosonization, renormalization group, and linear response theory to calculate the corresponding energy deposition. It exhibits a power law behavior as a function of the frequency that reflects the Tomonaga-Luttinger liquid (TLL) nature of the system. Depending on the interactions in the system, characterized by the TLL parameter K of the system, a crossover between weak and strong coupling for the backscattering due to the potential is possible. We compute the frequency scale ω*, at which such crossover exists. We find that the energy deposition due to the backscattering shows different exponents for K >1 and K <1 . We discuss possible experimental consequences, in the context of cold atomic gases, of our theoretical results.

Classification of hydrological parameter sensitivity and evaluation of parameter transferability across 431 US MOPEX basins

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

Ren, Huiying; Hou, Zhangshuan; Huang, Maoyi

The Community Land Model (CLM) represents physical, chemical, and biological processes of the terrestrial ecosystems that interact with climate across a range of spatial and temporal scales. As CLM includes numerous sub-models and associated parameters, the high-dimensional parameter space presents a formidable challenge for quantifying uncertainty and improving Earth system predictions needed to assess environmental changes and risks. This study aims to evaluate the potential of transferring hydrologic model parameters in CLM through sensitivity analyses and classification across watersheds from the Model Parameter Estimation Experiment (MOPEX) in the United States. The sensitivity of CLM-simulated water and energy fluxes to hydrologicalmore » parameters across 431 MOPEX basins are first examined using an efficient stochastic sampling-based sensitivity analysis approach. Linear, interaction, and high-order nonlinear impacts are all identified via statistical tests and stepwise backward removal parameter screening. The basins are then classified accordingly to their parameter sensitivity patterns (internal attributes), as well as their hydrologic indices/attributes (external hydrologic factors) separately, using a Principal component analyses (PCA) and expectation-maximization (EM) –based clustering approach. Similarities and differences among the parameter sensitivity-based classification system (S-Class), the hydrologic indices-based classification (H-Class), and the Koppen climate classification systems (K-Class) are discussed. Within each S-class with similar parameter sensitivity characteristics, similar inversion modeling setups can be used for parameter calibration, and the parameters and their contribution or significance to water and energy cycling may also be more transferrable. This classification study provides guidance on identifiable parameters, and on parameterization and inverse model design for CLM but the methodology is applicable to other models. Inverting parameters at representative sites belonging to the same class can significantly reduce parameter calibration efforts.« less

Scalar field as a Bose-Einstein condensate?

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

Castellanos, Elías; Escamilla-Rivera, Celia; Macías, Alfredo

We discuss the analogy between a classical scalar field with a self-interacting potential, in a curved spacetime described by a quasi-bounded state, and a trapped Bose-Einstein condensate. In this context, we compare the Klein-Gordon equation with the Gross-Pitaevskii equation. Moreover, the introduction of a curved background spacetime endows, in a natural way, an equivalence to the Gross-Pitaevskii equation with an explicit confinement potential. The curvature also induces a position dependent self-interaction parameter. We exploit this analogy by means of the Thomas-Fermi approximation, commonly used to describe the Bose-Einstein condensate, in order to analyze the quasi bound scalar field distribution surroundingmore » a black hole.« less

Social Anxiety, Acute Social Stress, and Reward Parameters Interact to Predict Risky Decision-Making among Adolescents

PubMed Central

Richards, Jessica M.; Patel, Nilam; Daniele, Teresa; MacPherson, Laura; Lejuez, C.W.; Ernst, Monique

2014-01-01

Risk-taking behavior increases during adolescence, leading to potentially disastrous consequences. Social anxiety emerges in adolescence and may compound risk-taking propensity, particularly during stress and when reward potential is high. However, the manner in which social anxiety, stress, and reward parameters interact to impact adolescent risk-taking is unclear. To clarify this question, a community sample of 35 adolescents (15 to 18 yo), characterized as having high or low social anxiety, participated in a 2-day study, during each of which they were exposed to either a social stress or a control condition, while performing a risky decision-making task. The task manipulated, orthogonally, reward magnitude and probability across trials. Three findings emerged. First, reward magnitude had a greater impact on the rate of risky decisions in high social anxiety (HSA) than low social anxiety (LSA) adolescents. Second, reaction times (RTs) were similar during the social stress and the control conditions for the HSA group, whereas the LSA group’s RTs differed between conditions. Third, HSA adolescents showed the longest RTs on the most negative trials. These findings suggest that risk-taking in adolescents is modulated by context and reward parameters differentially as a function of social anxiety. PMID:25465884

Evaluation of photosynthetic efficacy and CO2 removal of microalgae grown in an enriched bicarbonate medium.

PubMed

Abinandan, S; Shanthakumar, S

2016-06-01

Bicarbonate species in the aqueous phase is the primary source for CO 2 for the growth of microalgae. The potential of carbon dioxide (CO 2 ) fixation by Chlorella pyrenoidosa in enriched bicarbonate medium was evaluated. In the present study, effects of parameters such as pH, sodium bicarbonate concentration and inoculum size were assessed for the removal of CO 2 by C. pyrenoidosa under mixotrophic condition. Central composite design tool from response surface methodology was used to validate statistical methods in order to study the influence of these parameters. The obtained results reveal that the maximum removal of CO 2 was attained at pH 8 with sodium bicarbonate concentration of 3.33 g/l, and inoculum size of 30 %. The experimental results were statistically significant with R 2 value of 0.9527 and 0.960 for CO 2 removal and accumulation of chlorophyll content, respectively. Among the various interactions, interactive effects between the parameters pH and inoculum size was statistically significant (P < 0.05) for CO 2 removal and chlorophyll accumulation. Based on the studies, the application of C. pyrenoidosa as a potential source for carbon dioxide removal at alkaline pH from bicarbonate source is highlighted.

Soft-Rotator Coupled Channels Global Optical Potential for A=24-122 Mass Region Nuclides up to 200-MeV Incident Nucleon Energies

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

Soukhovitski, Efrem Sh.; Chiba, Satoshi; Lee, Jeong-Yeon

2005-05-24

A coupled-channels optical model with a coupling scheme based on nuclear wave functions of the soft-rotator model was applied to analyze experimental nucleon-nucleus interaction data for even-even nuclides with mass number A=24-122. We found that all the available data (total cross sections, angular distributions of elastically and inelastically scattered nucleons, and reaction cross sections) for these nuclides can be described to a good accuracy using an optical potential having smooth dependencies of potential values, radii, and diffuseness on the mass number. The individual properties of the target nuclides are accounted for by individuality of the nuclear Hamiltonian parameters, adjusted tomore » reproduce the low-lying collective level structure, Fermi energies, and deformation parameters.« less

Dynamical stabilization of grazing systems: An interplay among plant-water interaction, overgrazing and a threshold management policy.

PubMed

Costa, Michel Iskin da Silveira; Meza, Magno Enrique Mendoza

2006-12-01

In a plant-herbivore system, a management strategy called threshold policy is proposed to control grazing intensity where the vegetation dynamics is described by a plant-water interaction model. It is shown that this policy can lead the vegetation density to a previously chosen level under an overgrazing regime. This result is obtained despite both the potential occurrence of vegetation collapse due to overgrazing and the possibility of complex dynamics sensitive to vegetation initial densities and parameter uncertainties.

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

PubMed Central

Neshich, Goran; Rocchia, Walter; Mancini, Adauto L.; Yamagishi, Michel E. B.; Kuser, Paula R.; Fileto, Renato; Baudet, Christian; Pinto, Ivan P.; Montagner, Arnaldo J.; Palandrani, Juliana F.; Krauchenco, Joao N.; Torres, Renato C.; Souza, Savio; Togawa, Roberto C.; Higa, Roberto H.

2004-01-01

JavaProtein Dossier (JPD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide new insights into the sequence–structure–function relationship. In JPD, residue selection can be performed according to multiple criteria. JPD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures. In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology with its exceptional level of interactivity. JPD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: JavaProtein Dossier). PMID:15215458

A molecular scale perspective: Monte Carlo simulation for rupturing of ultra thin polymer film melts

NASA Astrophysics Data System (ADS)

Singh, Satya Pal

2017-04-01

Monte Carlo simulation has been performed to study the rupturing process of thin polymer film under strong confinement. The change in mean square displacement; pair correlation function; density distribution; average bond length and microscopic viscosity are sampled by varying the molecular interaction parameters such as the strength and the equilibrium positions of the bonding, non-bonding potentials and the sizes of the beads. The variation in mean square angular displacement χθ = [ < Δθ2 > - < Δθ>2 ] fits very well to a function of type y (t) = A + B *e-t/τ. This may help to study the viscous properties of the films and its dependence on different parameters. The ultra thin film annealed at high temperature gets ruptured and holes are created in the film mimicking spinodal dewetting. The pair correlation function and density profile reveal rich information about the equilibrium structure of the film. The strength and equilibrium bond length of finite extensible non-linear elastic potential (FENE) and non-bonding Morse potential have clear impact on microscopic rupturing of the film. The beads show Rouse or repetition motion forming rim like structures near the holes created inside the film. The higher order interaction as dipole-quadrupole may get prominence under strong confinement. The enhanced excluded volume interaction under strong confinement may overlap with the molecular dispersion forces. It can work to reorganize the molecules at the bottom of the scale and can imprint its signature in complex patterns evolved.

Investigation of the Dirac Equation by Using the Conformable Fractional Derivative

NASA Astrophysics Data System (ADS)

Mozaffari, F. S.; Hassanabadi, H.; Sobhani, H.; Chung, W. S.

2018-05-01

In this paper,the Dirac equation is constructed using the conformable fractional derivative so that in its limit for the fractional parameter, the normal version is recovered. Then, the Cornell potential is considered as the interaction of the system. In this case, the wave function and the energy eigenvalue equation are derived with the aim of the bi-confluent Heun functions. use of the conformable fractional derivative is proven to lead to a branching treatment for the energy of the system. Such a treatment is obvious for small values of the fractional parameter, and a united value as the fractional parameter approaches unity.

Towards robust quantification and reduction of uncertainty in hydrologic predictions: Integration of particle Markov chain Monte Carlo and factorial polynomial chaos expansion

NASA Astrophysics Data System (ADS)

Wang, S.; Huang, G. H.; Baetz, B. W.; Ancell, B. C.

2017-05-01

The particle filtering techniques have been receiving increasing attention from the hydrologic community due to its ability to properly estimate model parameters and states of nonlinear and non-Gaussian systems. To facilitate a robust quantification of uncertainty in hydrologic predictions, it is necessary to explicitly examine the forward propagation and evolution of parameter uncertainties and their interactions that affect the predictive performance. This paper presents a unified probabilistic framework that merges the strengths of particle Markov chain Monte Carlo (PMCMC) and factorial polynomial chaos expansion (FPCE) algorithms to robustly quantify and reduce uncertainties in hydrologic predictions. A Gaussian anamorphosis technique is used to establish a seamless bridge between the data assimilation using the PMCMC and the uncertainty propagation using the FPCE through a straightforward transformation of posterior distributions of model parameters. The unified probabilistic framework is applied to the Xiangxi River watershed of the Three Gorges Reservoir (TGR) region in China to demonstrate its validity and applicability. Results reveal that the degree of spatial variability of soil moisture capacity is the most identifiable model parameter with the fastest convergence through the streamflow assimilation process. The potential interaction between the spatial variability in soil moisture conditions and the maximum soil moisture capacity has the most significant effect on the performance of streamflow predictions. In addition, parameter sensitivities and interactions vary in magnitude and direction over time due to temporal and spatial dynamics of hydrologic processes.

Unbinding transition from fluid membranes with associated polymers.

PubMed

Benhamou, M; Kaidi, H

2013-10-01

We consider two neighboring fluid membranes that are associated with long flexible polymers (proteins or other macromolecules). We are interested in two physical systems consisting of i) two adjacent membranes with end-grafted (or adsorbed) polymers (system I), or ii) two membranes confining a polymer solution (system II). In addition to the pure interactions between membranes, the presence of polymers gives rise to new induced mediated interactions, which are repulsive, for system I, and attractive, for system II. In fact, repulsive induced interactions are caused by the excluded-volume forces between grafted polymers, while attractive ones, by entropy loss, due to free motion of polymers between membranes. The main goal is a quantitative study of the unbinding transition thermodynamics that is drastically affected by the associated polymers. For system I, the repulsive polymer-mediated force delays this transition that can happen at low temperature. To investigate the unbinding phenomenon, we first present an exact mathematical analysis of the total potential that is the sum of the primitive and induced potentials. This mathematical study enables us to classify the total interaction potentials, in terms of all parameters of the problem. Second, use is made of the standard variational method to calculate the first moments of the membrane separation. Special attention is paid to the determination of the unbinding temperature. In particular, we discuss its dependence on the extra parameters related to the associated polymers, which are the surface coverage and the polymer layer thickness on each membrane (for system I) or the polymer density and the gyration radius of coils (for system II). Third, we compute the disjoining pressure upon membrane separation. Finally, we emphasize that the presence of polymers may be a mechanism to delay or to accentuate the appearance of the unbinding transition between fluid membranes.

Nonstandard neutrino interactions in supernovae

NASA Astrophysics Data System (ADS)

Stapleford, Charles J.; Väänänen, Daavid J.; Kneller, James P.; McLaughlin, Gail C.; Shapiro, Brandon T.

2016-11-01

Nonstandard interactions (NSI) of neutrinos with matter can significantly alter neutrino flavor evolution in supernovae with the potential to impact explosion dynamics, nucleosynthesis, and the neutrinos signal. In this paper, we explore, both numerically and analytically, the landscape of neutrino flavor transformation effects in supernovae due to NSI and find a new, heretofore unseen transformation processes can occur. These new transformations can take place with NSI strengths well below current experimental limits. Within a broad swath of NSI parameter space, we observe symmetric and standard matter-neutrino resonances for supernovae neutrinos, a transformation effect previously only seen in compact object merger scenarios; in another region of the parameter space we find the NSI can induce neutrino collective effects in scenarios where none would appear with only the standard case of neutrino oscillation physics; and in a third region the NSI can lead to the disappearance of the high density Mikheyev-Smirnov-Wolfenstein resonance. Using a variety of analytical tools, we are able to describe quantitatively the numerical results allowing us to partition the NSI parameter according to the transformation processes observed. Our results indicate nonstandard interactions of supernova neutrinos provide a sensitive probe of beyond the Standard Model physics complementary to present and future terrestrial experiments.

A new parameter-free soft-core potential for silica and its application to simulation of silica anomalies

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

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2015-12-28

A core-softening of the effective interaction between oxygen atoms in water and silica systems and its role in developing anomalous thermodynamic, transport, and structural properties have been extensively debated. For silica, the progress with addressing these issues has been hampered by a lack of effective interaction models with explicit core-softening. In this work, we present an extension of a two-body soft-core interatomic force field for silica recently reported by us [S. Izvekov and B. M. Rice, J. Chem. Phys. 136(13), 134508 (2012)] to include three-body forces. Similar to two-body interaction terms, the three-body terms are derived using parameter-free force-matching ofmore » the interactions from ab initio MD simulations of liquid silica. The derived shape of the O–Si–O three-body potential term affirms the existence of repulsion softening between oxygen atoms at short separations. The new model shows a good performance in simulating liquid, amorphous, and crystalline silica. By comparing the soft-core model and a similar model with the soft-core suppressed, we demonstrate that the topology reorganization within the local tetrahedral network and the O–O core-softening are two competitive mechanisms responsible for anomalous thermodynamic and kinetic behaviors observed in liquid and amorphous silica. The studied anomalies include the temperature of density maximum locus and anomalous diffusivity in liquid silica, and irreversible densification of amorphous silica. We show that the O–O core-softened interaction enhances the observed anomalies primarily through two mechanisms: facilitating the defect driven structural rearrangements of the silica tetrahedral network and modifying the tetrahedral ordering induced interactions toward multiple characteristic scales, the feature which underlies the thermodynamic anomalies.« less

Influences of the third and fourth nearest neighbouring interactions on the surface anisotropy of face-centred-cubic metals

NASA Astrophysics Data System (ADS)

Luo, Yongkun; Qin, Rongshan

2014-06-01

The structure and the anisotropic properties of the surfaces of face-centred-cubic (FCC) metals have been studied using the broken-bond model while considering the third and fourth nearest neighbouring (3rd and 4th NN) interactions. The pair potential expressions are obtained using the Rose-Vinet universal potential equation. The model is suitable for calculation of the property of a surface with arbitrary crystallographic orientations and can provide absolute unrelaxed surface energy values using three input parameters, namely the lattice constant, bulk modulus and cohesive energy. These parameters are available for the majority of FCC metals. The numerical results for 7 FCC metals have been obtained and compared with these obtained from ab initio calculations and experimental measurements. Good agreement is observed between the two. Taking into account up to the 4th NN interactions, the overall surface energy anisotropy for FCC metals was found to be between 12% to 16%, and the ratio between the surface energies at (100) and (111) planes was found to be 1.05. These values are less than those reported by conventional calculations but more similar to experimental measurements. It is found that the strength of 3rd and 4th NN interactions differs from one element to another, the Ni and Cu interactions being the most significant while the Au, Pt and Pb interactions are the least significant. This suggests that the polar diagrams of the surface energy of Ni and Cu are different from those of Au, Pt and Pb by showing cusps of the unconventional {110} and high-index {210}, {311} and possibly {135} poles. This provides explanations to the recent experimental observations of the {110}, {210}, {311} and {135} facets in equilibrated Ni and Cu crystallines.

Effects of medium on nuclear properties in multifragmentation

NASA Astrophysics Data System (ADS)

De, J. N.; Samaddar, S. K.; Viñas, X.; Centelles, M.; Mishustin, I. N.; Greiner, W.

2012-08-01

In multifragmentation of hot nuclear matter, properties of fragments embedded in a soup of nucleonic gas and other fragments should be modified as compared with isolated nuclei. Such modifications are studied within a simple model where only nucleons and one kind of heavy nuclei are considered. The interaction between different species is described with a momentum-dependent two-body potential whose parameters are fitted to reproduce properties of cold isolated nuclei. The internal energy of heavy fragments is parametrized according to a liquid-drop model with density- and temperature-dependent parameters. Calculations are carried out for several subnuclear densities and moderate temperatures, for isospin-symmetric and asymmetric systems. We find that the fragments get stretched due to interactions with the medium and their binding energies decrease with increasing temperature and density of nuclear matter.

Midi-maxi computer interaction in the interpretation of nuclear medicine procedures

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

Schlapper, G.A.

1977-01-01

A study of renal function with an Anger Gamma Camera coupled with a Digital Equipment Corporation Gamma-11 System and an IBM System 370 demonstrates the potential of quantitative determinations of physiological function through the application of midi-maxi computer interaction in the interpretation of nuclear medicine procedures. It is shown that radiotracers can provide an opportunity to assess physiological processes of renal function by noninvasively following the path of a tracer as a function of time. Time-activity relationships obtained over seven anatomically defined regions are related to parameters of a seven compartment model employed to describe the renal clearance process. Themore » values obtained for clinically significant parameters agree with known renal pathophysiology. Differentiation of failure of acute, chronic, and obstructive forms is indicated.« less

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

PubMed

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-03-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Massive neutron star with strangeness in a relativistic mean-field model with a high-density cutoff

NASA Astrophysics Data System (ADS)

Zhang, Ying; Hu, Jinniu; Liu, Peng

2018-01-01

The properties of neutron stars with the strangeness degree of freedom are studied in the relativistic mean-field (RMF) model via including a logarithmic interaction as a function of the scalar meson field. This interaction, named the σ -cut potential, can largely reduce the attractive contributions of the scalar meson field at high density without any influence on the properties of nuclear structure around the normal saturation density. In this work, the TM1 parameter set is chosen as the RMF interaction, while the strengths of σ -cut potential are constrained by the properties of finite nuclei so that we can obtain a reasonable effective nucleon-nucleon interaction. The hyperons Λ ,Σ , and Ξ are considered in neutron stars within this framework, whose coupling constants with mesons are determined by the latest hyperon-nucleon and Λ -Λ potentials extracted from the available experimental data of hypernuclei. The maximum mass of neutron star can be larger than 2 M⊙ with these hyperons in the present framework. Furthermore, the nucleon mass at high density will be saturated due to this additional σ -cut potential, which is consistent with the conclusions obtained by other calculations such as Brueckner-Hartree-Fock theory and quark mean-field model.

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

Modeling strategic behavior in human-automation interaction - Why an 'aid' can (and should) go unused

NASA Technical Reports Server (NTRS)

Kirlik, Alex

1993-01-01

Task-offload aids (e.g., an autopilot, an 'intelligent' assistant) can be selectively engaged by the human operator to dynamically delegate tasks to automation. Introducing such aids eliminates some task demands but creates new ones associated with programming, engaging, and disengaging the aiding device via an interface. The burdens associated with managing automation can sometimes outweigh the potential benefits of automation to improved system performance. Aid design parameters and features of the overall multitask context combine to determine whether or not a task-offload aid will effectively support the operator. A modeling and sensitivity analysis approach is presented that identifies effective strategies for human-automation interaction as a function of three task-context parameters and three aid design parameters. The analysis and modeling approaches provide resources for predicting how a well-adapted operator will use a given task-offload aid, and for specifying aid design features that ensure that automation will provide effective operator support in a multitask environment.

Growth rate in the dynamical dark energy models.

PubMed

Avsajanishvili, Olga; Arkhipova, Natalia A; Samushia, Lado; Kahniashvili, Tina

Dark energy models with a slowly rolling cosmological scalar field provide a popular alternative to the standard, time-independent cosmological constant model. We study the simultaneous evolution of background expansion and growth in the scalar field model with the Ratra-Peebles self-interaction potential. We use recent measurements of the linear growth rate and the baryon acoustic oscillation peak positions to constrain the model parameter [Formula: see text] that describes the steepness of the scalar field potential.

Semilocal momentum-space regularized chiral two-nucleon potentials up to fifth order

NASA Astrophysics Data System (ADS)

Reinert, P.; Krebs, H.; Epelbaum, E.

2018-05-01

We introduce new semilocal two-nucleon potentials up to fifth order in the chiral expansion. We employ a simple regularization approach for the pion exchange contributions which i) maintains the long-range part of the interaction, ii) is implemented in momentum space and iii) can be straightforwardly applied to regularize many-body forces and current operators. We discuss in detail the two-nucleon contact interactions at fourth order and demonstrate that three terms out of fifteen used in previous calculations can be eliminated via suitably chosen unitary transformations. The removal of the redundant contact terms results in a drastic simplification of the fits to scattering data and leads to interactions which are much softer ( i.e., more perturbative) than our recent semilocal coordinate-space regularized potentials. Using the pion-nucleon low-energy constants from matching pion-nucleon Roy-Steiner equations to chiral perturbation theory, we perform a comprehensive analysis of nucleon-nucleon scattering and the deuteron properties up to fifth chiral order and study the impact of the leading F-wave two-nucleon contact interactions which appear at sixth order. The resulting chiral potentials at fifth order lead to an outstanding description of the proton-proton and neutron-proton scattering data from the self-consistent Granada-2013 database below the pion production threshold, which is significantly better than for any other chiral potential. For the first time, the chiral potentials match in precision and even outperform the available high-precision phenomenological potentials, while the number of adjustable parameters is, at the same time, reduced by about ˜ 40%. Last but not least, we perform a detailed error analysis and, in particular, quantify for the first time the statistical uncertainties of the fourth- and the considered sixth-order contact interactions.

Effect of attractive interactions on the water-like anomalies of a core-softened model potential.

PubMed

Pant, Shashank; Gera, Tarun; Choudhury, Niharendu

2013-12-28

It is now well established that water-like anomalies can be reproduced by a spherically symmetric potential with two length scales, popularly known as core-softened potential. In the present study we aim to investigate the effect of attractive interactions among the particles in a model fluid interacting with core-softened potential on the existence and location of various water-like anomalies in the temperature-pressure plane. We employ extensive molecular dynamic simulations to study anomalous nature of various order parameters and properties under isothermal compression. Order map analyses have also been done for all the potentials. We observe that all the systems with varying depth of attractive wells show structural, dynamic, and thermodynamic anomalies. As many of the previous studies involving model water and a class of core softened potentials have concluded that the structural anomaly region encloses the diffusion anomaly region, which in turn, encloses the density anomaly region, the same pattern has also been observed in the present study for the systems with less depth of attractive well. For the systems with deeper attractive well, we observe that the diffusion anomaly region shifts toward higher densities and is not always enclosed by the structural anomaly region. Also, density anomaly region is not completely enclosed by diffusion anomaly region in this case.

Nucleon-deuteron scattering with the JISP16 potential

NASA Astrophysics Data System (ADS)

Skibiński, R.; Golak, J.; Topolnicki, K.; Witała, H.; Volkotrub, Yu.; Kamada, H.; Shirokov, A. M.; Okamoto, R.; Suzuki, K.; Vary, J. P.

2018-01-01

The nucleon-nucleon J -matrix inverse scattering potential JISP16 is applied to elastic nucleon-deuteron scattering and the deuteron breakup process at the laboratory nucleon energies up to 135 MeV. The formalism of the Faddeev equations is used to obtain three-nucleon scattering states. We compare predictions based on the JISP16 force with data and with results based on various two-body interactions, including the CD Bonn, the Argonne AV18, the chiral force with the semilocal regularization at the fifth order of the chiral expansion and with low-momentum interactions obtained from the CD Bonn force as well as with the predictions from the combination of the AV18 NN interaction and the Urbana IX 3 N force. JISP16 provides a satisfactory description of some observables at low energies but strong deviations from data as well as from standard and chiral potential predictions with increasing energy. However, there are also polarization observables at low energies for which the JISP16 predictions differ from those based on the other forces by a factor of two. The reason for such a behavior can be traced back to the P -wave components of the JISP16 force. At higher energies the deviations can be enhanced by an interference with higher partial waves and by the properties of the JISP16 deuteron wave function. In addition, we compare the energy and angular dependence of predictions based on the JISP16 force with the results of the low-momentum interactions obtained with different values of the momentum cutoff parameter. We found that such low-momentum forces can be employed to interpret the nucleon-deuteron elastic scattering data only below some specific energy which depends on the cutoff parameter. Since JISP16 is defined in a finite oscillator basis, it has properties similar to low momentum interactions and its application to the description of nucleon-deuteron scattering data is limited to a low momentum transfer region.

s -wave scattering length of a Gaussian potential

NASA Astrophysics Data System (ADS)

Jeszenszki, Peter; Cherny, Alexander Yu.; Brand, Joachim

2018-04-01

We provide accurate expressions for the s -wave scattering length for a Gaussian potential well in one, two, and three spatial dimensions. The Gaussian potential is widely used as a pseudopotential in the theoretical description of ultracold-atomic gases, where the s -wave scattering length is a physically relevant parameter. We first describe a numerical procedure to compute the value of the s -wave scattering length from the parameters of the Gaussian, but find that its accuracy is limited in the vicinity of singularities that result from the formation of new bound states. We then derive simple analytical expressions that capture the correct asymptotic behavior of the s -wave scattering length near the bound states. Expressions that are increasingly accurate in wide parameter regimes are found by a hierarchy of approximations that capture an increasing number of bound states. The small number of numerical coefficients that enter these expressions is determined from accurate numerical calculations. The approximate formulas combine the advantages of the numerical and approximate expressions, yielding an accurate and simple description from the weakly to the strongly interacting limit.

Substitution effect on a hydroxylated chalcone: Conformational, topological and theoretical studies

NASA Astrophysics Data System (ADS)

Custodio, Jean M. F.; Vaz, Wesley F.; de Andrade, Fabiano M.; Camargo, Ademir J.; Oliveira, Guilherme R.; Napolitano, Hamilton B.

2017-05-01

The effect of substituents on two hydroxylated chalcones was studied in this work. The first chalcone, with a dimethylamine group (HY-DAC) and the second, with three methoxy groups (HY-TRI) were synthesized and crystallized from ethanol on centrosymmetric space group P21/c. The geometric parameters and supramolecular arrangement for both structures obtained from single crystal X-ray diffraction data were analyzed. The intermolecular interactions were investigated by Hirshfeld surfaces with their respective 2D plot for quantification of each type of contact. Additionally, the observed interactions were characterized by QTAIM analysis, and DFT calculations were applied for theoretical vibrational spectra, localization and quantification of frontier orbitals and potential electrostatic map. The flatness of both structures was affected by the substituents, which led to different monoclinic crystalline packing. The calculated harmonic vibrational frequencies and homo-lumo gap confirmed the stability of the structures, while intermolecular interactions were confirmed by potential electrostatic map and QTAIM analysis.

N-Ω Interaction from High-Energy Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Morita, Kenji; Ohnishi, Akira; Hatsuda, Tetsuo

We discuss possible observation of the N-Ω interaction from intensity correlation function in high energy heavy ion collisions. Recently a lattice QCD simulation by the HAL QCD collaboration predicts the existence of a N-Ω bound state in the 5S2 channel. We adopt the N-Ω interaction potential obtained by the lattice simulation and use it to calculate the N-Ω correlation function. We also study the variation of the correlation function with respect to the change of the binding energy and scattering parameters. Our result indicates that heavy ion collisions at RHIC and LHC may provide information on the possible existence of the N-Ω dibaryon.

Accurate potential energy curves, spectroscopic parameters, transition dipole moments, and transition probabilities of 21 low-lying states of the CO+ cation

NASA Astrophysics Data System (ADS)

Xing, Wei; Shi, Deheng; Zhang, Jicai; Sun, Jinfeng; Zhu, Zunlue

2018-05-01

This paper calculates the potential energy curves of 21 Λ-S and 42 Ω states, which arise from the first two dissociation asymptotes of the CO+ cation. The calculations are conducted using the complete active space self-consistent field method, which is followed by the valence internally contracted multireference configuration interaction approach with the Davidson correction. To improve the reliability and accuracy of the potential energy curves, core-valence correlation and scalar relativistic corrections, as well as the extrapolation of potential energies to the complete basis set limit are taken into account. The spectroscopic parameters and vibrational levels are determined. The spin-orbit coupling effect on the spectroscopic parameters and vibrational levels is evaluated. To better study the transition probabilities, the transition dipole moments are computed. The Franck-Condon factors and Einstein coefficients of some emissions are calculated. The radiative lifetimes are determined for a number of vibrational levels of several states. The transitions between different Λ-S states are evaluated. Spectroscopic routines for observing these states are proposed. The spectroscopic parameters, vibrational levels, transition dipole moments, and transition probabilities reported in this paper can be considered to be very reliable and can be used as guidelines for detecting these states in an appropriate spectroscopy experiment, especially for the states that were very difficult to observe or were not detected in previous experiments.

Charge independence, charge symmetry breaking in the S-wave nucleon-nucleon interaction, and renormalization

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

Alvaro Calle Cordon,Manuel Pavon Valderrama,Enrique Ruiz Arriola

2012-02-01

We study the interplay between charge symmetry breaking and renormalization in the NN system for S-waves. We find a set of universality relations which disentangle explicitly the known long distance dynamics from low energy parameters and extend them to the Coulomb case. We analyze within such an approach the One-Boson-Exchange potential and the theoretical conditions which allow to relate the proton-neutron, proton-proton and neutron-neutron scattering observables without the introduction of extra new parameters and providing good phenomenological success.

A Pipeline for Constructing a Catalog of Multi-method Models of Interacting Galaxies

NASA Astrophysics Data System (ADS)

Holincheck, Anthony

Galaxies represent a fundamental unit of matter for describing the large-scale structure of the universe. One of the major processes affecting the formation and evolution of galaxies are mutual interactions. These interactions can including gravitational tidal distortion, mass transfer, and even mergers. In any hierarchical model, mergers are the key mechanism in galaxy formation and evolution. Computer simulations of interacting galaxies have evolved in the last four decades from simple restricted three-body algorithms to full n-body gravity models. These codes often included sophisticated physical mechanisms such as gas dynamics, supernova feedback, and central blackholes. As the level of complexity, and perhaps realism, increases so does the amount of computational resources needed. These advanced simulations are often used in parameter studies of interactions. They are usually only employed in an ad hoc fashion to recreate the dynamical history of specific sets of interacting galaxies. These specific models are often created with only a few dozen or at most few hundred sets of simulation parameters being attempted. This dissertation presents a prototype pipeline for modeling specific pairs of interacting galaxies in bulk. The process begins with a simple image of the current disturbed morphology and an estimate of distance to the system and mass of the galaxies. With the use of an updated restricted three-body simulation code and the help of Citizen Scientists, the pipeline is able to sample hundreds of thousands of points in parameter space for each system. Through the use of a convenient interface and innovative scoring algorithm, the pipeline aids researchers in identifying the best set of simulation parameters. This dissertation demonstrates a successful recreation of the disturbed morphologies of 62 pairs of interacting galaxies. The pipeline also provides for examining the level of convergence and uniqueness of the dynamical properties of each system. By creating a population of models for actual systems, the current research is able to compare simulation-based and observational values on a larger scale than previous efforts. Several potential relationships between star formation rate and dynamical time since closest approach are presented.

Effective Hubbard model for Helium atoms adsorbed on a graphite

NASA Astrophysics Data System (ADS)

Motoyama, Yuichi; Masaki-Kato, Akiko; Kawashima, Naoki

Helium atoms adsorbed on a graphite is a two-dimensional strongly correlated quantum system and it has been an attractive subject of research for a long time. A helium atom feels Lennard-Jones like potential (Aziz potential) from another one and corrugated potential from the graphite. Therefore, this system may be described by a hardcore Bose Hubbard model with the nearest neighbor repulsion on the triangular lattice, which is the dual lattice of the honeycomb lattice formed by carbons. A Hubbard model is easier to simulate than the original problem in continuous space, but we need to know the model parameters of the effective model, hopping constant t and interaction V. In this presentation, we will present an estimation of the model parameters from ab initio quantum Monte Carlo calculation in continuous space in addition to results of quantum Monte Carlo simulation for an obtained discrete model.

Modeling of Hydraulic Fracturing on the Basis of the Particle Method

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Gabsalikova, N. F.; Izotov, V. G.; Miheev, V. V.

2018-01-01

A technique of calculating the deformation of the soil environment when it interacts with a liquid on the basis of the particle method a is realized. To describe the behavior of the solid and liquid phases of the soil, a classical two-parameter Lennard-Jones interaction potential and its modified version proposed by the authors were chosen. The model problem of deformation and partial destruction of a soil massif under strong pressure from the liquid pumped into it is solved. Analysis of the results shows that the use of the modified Lennard-Jones potential for describing the solid phase of the soil environment makes it possible to describe the process of formation of cracks in the soil during hydraulic fracturing of the formation.

Ground state atoms confined in a real Rydberg and complex Rydberg-Scarf II potential

NASA Astrophysics Data System (ADS)

Mansoori Kermani, Maryam

2017-12-01

In this work, a system of two ground state atoms confined in a one-dimensional real Rydberg potential was modeled. The atom-atom interaction was considered as a nonlocal separable potential (NLSP) of rank one. This potential was assumed because it leads to an analytical solution of the Lippmann-Schwinger equation. The NLSPs are useful in the few body problems that the many-body potential at each point is replaced by a projective two-body nonlocal potential operator. Analytical expressions for the confined particle resolvent were calculated as a key function in this study. The contributions of the bound and virtual states in the complex energy plane were obtained via the derived transition matrix. Since the low energy quantum scattering problems scattering length is an important quantity, the behavior of this parameter was described versus the reduced energy considering various values of potential parameters. In a one-dimensional model, the total cross section in units of the area is not a meaningful property; however, the reflectance coefficient has a similar role. Therefore the reflectance probability and its behavior were investigated. Then a new confined potential via combining the complex absorbing Scarf II potential with the real Rydberg potential, called the Rydberg-Scarf II potential, was introduced to construct a non-Hermitian Hamiltonian. In order to investigate the effect of the complex potential, the scattering length and reflectance coefficient were calculated. It was concluded that in addition to the competition between the repulsive and attractive parts of both potentials, the imaginary part of the complex potential has an important effect on the properties of the system. The complex potential also reduces the reflectance probability via increasing the absorption probability. For all numerical computations, the parameters of a system including argon gas confined in graphite were considered.

Thermodynamical properties of liquid lanthanides-A variational approach

NASA Astrophysics Data System (ADS)

Patel, H. P.; Thakor, P. B.; Sonvane, Y. A.

2015-06-01

Thermodynamical properties like Entropy (S), Internal energy (E) and Helmholtz free energy (F) of liquid lanthanides using a variation principle based on the Gibbs-Bogoliubuv (GB) inequality with Percus Yevick hard sphere reference system have been reported in the present investigation. To describe electron-ion interaction we have used our newly constructed parameter free model potential along with Sarkar et al. local field correction function. Lastly, we conclude that our newly constructed model potential is capable to explain the thermodynamical properties of liquid lanthanides.

Thermodynamical properties of liquid lanthanides-A variational approach

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

Patel, H. P.; Department of Applied Physics, S. V. National Institute of Technology, Surat 395 007, Gujarat; Thakor, P. B., E-mail: pbthakor@rediffmail.com

2015-06-24

Thermodynamical properties like Entropy (S), Internal energy (E) and Helmholtz free energy (F) of liquid lanthanides using a variation principle based on the Gibbs-Bogoliubuv (GB) inequality with Percus Yevick hard sphere reference system have been reported in the present investigation. To describe electron-ion interaction we have used our newly constructed parameter free model potential along with Sarkar et al. local field correction function. Lastly, we conclude that our newly constructed model potential is capable to explain the thermodynamical properties of liquid lanthanides.

Detection of Volatile Organic Compounds by Self-assembled Monolayer Coated Sensor Array with Concentration-independent Fingerprints

PubMed Central

Chang, Ye; Tang, Ning; Qu, Hemi; Liu, Jing; Zhang, Daihua; Zhang, Hao; Pang, Wei; Duan, Xuexin

2016-01-01

In this paper, we have modeled and analyzed affinities and kinetics of volatile organic compounds (VOCs) adsorption (and desorption) on various surface chemical groups using multiple self-assembled monolayers (SAMs) functionalized film bulk acoustic resonator (FBAR) array. The high-frequency and micro-scale resonator provides improved sensitivity in the detections of VOCs at trace levels. With the study of affinities and kinetics, three concentration-independent intrinsic parameters (monolayer adsorption capacity, adsorption energy constant and desorption rate) of gas-surface interactions are obtained to contribute to a multi-parameter fingerprint library of VOC analytes. Effects of functional group’s properties on gas-surface interactions are also discussed. The proposed sensor array with concentration-independent fingerprint library shows potential as a portable electronic nose (e-nose) system for VOCs discrimination and gas-sensitive materials selections. PMID:27045012

Cross-section analysis of the Magnum-PSI plasma beam using a 2D multi-probe system

NASA Astrophysics Data System (ADS)

Costin, C.; Anita, V.; Ghiorghiu, F.; Popa, G.; De Temmerman, G.; van den Berg, M. A.; Scholten, J.; Brons, S.

2015-02-01

The linear plasma generator Magnum-PSI was designed for the study of plasma-surface interactions under relevant conditions of fusion devices. A key factor for such studies is the knowledge of a set of parameters that characterize the plasma interacting with the solid surface. This paper reports on the electrical diagnosis of the plasma beam in Magnum-PSI using a multi-probe system consisting of 64 probes arranged in a 2D square matrix. Cross-section distributions of floating potential and ion current intensity were registered for a hydrogen plasma beam under various discharge currents (80-175 A) and magnetic field strengths (0.47-1.41 T in the middle of the coils). Probe measurements revealed a high level of flexibility of plasma beam parameters with respect to the operating conditions.

Model-independent description of quartet nd scattering at low energies

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

Grinyuk, B.E.; Simenog, I.V.; Sitnichenko, A.I.

1984-02-01

Asymptotic expansions are obtained for the scattering length a/sub 3//sub ///sub 2/ and the effective range r/sub 3//sub ///sub 2/ for the quartet state of three nucleons in the form of series in powers of the two-nucleon triplet effective range r/sub 0t/. This allows a model-independent description of these parameters and of the quartet phase shift of nd scattering in the effective-range approximation. Correlations between the parameters of three- and two-nucleon scattering are proposed and explained; these correlations allow the systematization of numerical calculations of a/sub 3//sub ///sub 2/ and r/sub 3//sub ///sub 2/ for different forms of interaction potentials.more » The influence of the energy dependence of the interaction on a/sub 3//sub ///sub 2/ is also considered.« less

Acute effect of Vagus nerve stimulation parameters on cardiac chronotropic, inotropic, and dromotropic responses

NASA Astrophysics Data System (ADS)

Ojeda, David; Le Rolle, Virginie; Romero-Ugalde, Hector M.; Gallet, Clément; Bonnet, Jean-Luc; Henry, Christine; Bel, Alain; Mabo, Philippe; Carrault, Guy; Hernández, Alfredo I.

2017-11-01

Vagus nerve stimulation (VNS) is an established therapy for drug-resistant epilepsy and depression, and is considered as a potential therapy for other pathologies, including Heart Failure (HF) or inflammatory diseases. In the case of HF, several experimental studies on animals have shown an improvement in the cardiac function and a reverse remodeling of the cardiac cavity when VNS is applied. However, recent clinical trials have not been able to reproduce the same response in humans. One of the hypothesis to explain this lack of response is related to the way in which stimulation parameters are defined. The combined effect of VNS parameters is still poorly-known, especially in the case of VNS synchronously delivered with cardiac activity. In this paper, we propose a methodology to analyze the acute cardiovascular effects of VNS parameters individually, as well as their interactive effects. A Latin hypercube sampling method was applied to design a uniform experimental plan. Data gathered from this experimental plan was used to produce a Gaussian process regression (GPR) model in order to estimate unobserved VNS sequences. Finally, a Morris screening sensitivity analysis method was applied to each obtained GPR model. Results highlight dominant effects of pulse current, pulse width and number of pulses over frequency and delay and, more importantly, the degree of interactions between these parameters on the most important acute cardiovascular responses. In particular, high interacting effects between current and pulse width were found. Similar sensitivity profiles were observed for chronotropic, dromotropic and inotropic effects. These findings are of primary importance for the future development of closed-loop, personalized neuromodulator technologies.

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST)

PubMed Central

Xu, Chonggang; Gertner, George

2013-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements. PMID:24143037

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST).

PubMed

Xu, Chonggang; Gertner, George

2011-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements.

Potential Energy Curves and Transport Properties for the Interaction of He with Other Ground-state Atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Stallcop, James R.; Levin, Eugene; Arnold, Jim (Technical Monitor)

2001-01-01

The interactions of a He atom with a heavier atom are examined for 26 different elements, which are consecutive members selected from three rows (Li - Ne, Na - Ar, and K,Ca, Ga - Kr) and column 12 (Zn,Cd) of the periodic table. Interaction energies are determined wing high-quality ab initio calculations for the states of the molecule that would be formed from each pair of atoms in their ground states. Potential energies are tabulated for a broad range of Interatomic separation distances. The results show, for example, that the energy of an alkali interaction at small separations is nearly the same as that of a rare-gas interaction with the same electron configuration for the dosed shells. Furthermore, the repulsive-range parameter for this region is very short compared to its length for the repulsion dominated by the alkali-valence electron at large separations (beyond about 3-4 a(sub 0)). The potential energies in the region of the van der Waals minimum agree well with the most accurate results available. The ab initio energies are applied to calculate scattering cross sections and obtain the collision integrals that are needed to determine transport properties to second order. The theoretical values of Li-He total scattering cross sections and the rare-gas atom-He transport properties agree well (to within about 1%) with the corresponding measured data. Effective potential energies are constructed from the ab initio energies; the results have been shown to reproduce known transport data and can be readily applied to predict unknown transport properties for like-atom interactions.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Parametric Studies of Square Solar Sails Using Finite Element Analysis

NASA Technical Reports Server (NTRS)

Sleight, David W.; Muheim, Danniella M.

2004-01-01

Parametric studies are performed on two generic square solar sail designs to identify parameters of interest. The studies are performed on systems-level models of full-scale solar sails, and include geometric nonlinearity and inertia relief, and use a Newton-Raphson scheme to apply sail pre-tensioning and solar pressure. Computational strategies and difficulties encountered during the analyses are also addressed. The purpose of this paper is not to compare the benefits of one sail design over the other. Instead, the results of the parametric studies may be used to identify general response trends, and areas of potential nonlinear structural interactions for future studies. The effects of sail size, sail membrane pre-stress, sail membrane thickness, and boom stiffness on the sail membrane and boom deformations, boom loads, and vibration frequencies are studied. Over the range of parameters studied, the maximum sail deflection and boom deformations are a nonlinear function of the sail properties. In general, the vibration frequencies and modes are closely spaced. For some vibration mode shapes, local deformation patterns that dominate the response are identified. These localized patterns are attributed to the presence of negative stresses in the sail membrane that are artifacts of the assumption of ignoring the effects of wrinkling in the modeling process, and are not believed to be physically meaningful. Over the range of parameters studied, several regions of potential nonlinear modal interaction are identified.

Problem of the Optical Model for Deuterons; ZAGADNIENIA MODELU OPTYCZNEGO DLA DEUTERONOW

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

Grotowski, K.

1963-01-01

Problems concerning parameters of the optical potential for deuterons are presented. Total cross-sections for the interaction of deuterons with nuclei were determined by the evaluation of the cross-sections for the emission of charged particles and neutrons. The angular distributions for the elastic scattering of deuterons were also measured, 47 references. (auth)

Strength of the interatomic potential derived from angular scans in LEIS

NASA Astrophysics Data System (ADS)

Primetzhofer, D.; Markin, S. N.; Draxler, M.; Beikler, R.; Taglauer, E.; Bauer, P.

2008-09-01

Angular scans were performed for a Cu(1 0 0) single crystal and He + ions. The results were compared to MARLOWE, KALYPSO and FAN simulations to obtain information on the interaction potential. The influence of the used evaluation procedure on the deduced scattering potential was investigated. The scattering potential is found to be weaker than what is predicted by an uncorrected TFM potential. It was found that the use of a single screening correction factor is applicable in a wide range of impact parameters. It is further shown that selection of single scattering trajectories and a limitation of information depth to the surface layers is possible for neutral and charge integrated spectra.

Elastic and inelastic collisions of swarms

NASA Astrophysics Data System (ADS)

Armbruster, Dieter; Martin, Stephan; Thatcher, Andrea

2017-04-01

Scattering interactions of swarms in potentials that are generated by an attraction-repulsion model are studied. In free space, swarms in this model form a well-defined steady state describing the translation of a stable formation of the particles whose shape depends on the interaction potential. Thus, the collision between a swarm and a boundary or between two swarms can be treated as (quasi)-particle scattering. Such scattering experiments result in internal excitations of the swarm or in bound states, respectively. In addition, varying a parameter linked to the relative importance of damping and potential forces drives transitions between elastic and inelastic scattering of the particles. By tracking the swarm's center of mass, a refraction rule is derived via simulations relating the incoming and outgoing directions of a swarm hitting the wall. Iterating the map derived from the refraction law allows us to predict and understand the dynamics and bifurcations of swarms in square boxes and in channels.

Scattering of charged particles on two spatially separated time-periodic optical fields

NASA Astrophysics Data System (ADS)

Szabó, Lóránt Zs.; Benedict, Mihály G.; Földi, Péter

2017-12-01

We consider a monoenergetic beam of moving charged particles interacting with two separated oscillating electric fields. Time-periodic linear potential is assumed to model the light-particle interaction using a nonrelativistic, quantum mechanical description based on Gordon-Volkov states. Applying Floquet theory, we calculate transmission probabilities as a function of the laser field parameters. The transmission resonances in this Ramsey-like setup are interpreted as if they originated from a corresponding static double-potential barrier with heights equal to the ponderomotive potential resulting from the oscillating field. Due to the opening of new "Floquet channels," the resonances are repeated at input energies when the corresponding frequency is shifted by an integer multiple of the exciting frequency. These narrow resonances can be used as precise energy filters. The fine structure of the transmission spectra is determined by the phase difference between the two oscillating light fields, allowing for the optical control of the transmission.

Classical Molecular Dynamics Simulation of Nuclear Fuel

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

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a varietymore » of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.« less

Interacting parametrized post-Friedmann method

NASA Astrophysics Data System (ADS)

Richarte, Martín G.; Xu, Lixin

2016-04-01

We apply the interacting parametrized post-Friedmann (IPPF) method to coupled dark energy models where the interaction is proportional to dark matter density at background level. In the first case, the dark components are treated as fluids and the growth of dark matter perturbations only feel the interaction via the modification of background quantities provided dark matter follows geodesic. We also perform a Markov Chain Monte-Carlo analysis which combines several cosmological probes including the cosmic microwave background (WMAP9+Planck) data, baryon acoustic oscillation (BAO) measurements, JLA sample of supernovae, Hubble constant (HST), and redshift-space distortion (RSD) measurements through the fσ 8(z) data points. The joint observational analysis of Planck+WP+JLA+BAO+HST+ RSD data leads to a coupling parameter, ξ c=0.00140_{-0.00080}^{+0.00079} at 1σ level for vanishing momentum transfer potential. On the other hand, we deal with a coupled quintessence model which exhibits a violation of the equivalence principle coming form a coupling term in the modified Euler equation; as a result of that the local Hubble expansion rate and the effective gravitational coupling are both enhanced. Provided that the interaction is parallel to scalar field velocity the momentum transfer potential is switched on, leading to a lower interaction coupling ξ c=0.00136_{-0.00073}^{+0.00080} at 1σ level when Planck+WP+JLA+BAO+HST+RSD data are combined. Besides, the CMB power spectrum shows up a correlation between the coupling parameter ξ c and the position of acoustic peaks or their amplitudes. The first peak's height increases when ξ c takes larger values and its position is shifted. We also obtain the matter power spectrum may be affected by the strength of interaction coupling over scales bigger than 10^{-2} h Mpc^{-1}, reducing its amplitude in relation to the vanilla model.

Optimal aluminum/zirconium: Protein interactions for predicting antiperspirant efficacy using zeta potential measurements.

PubMed

Yuan, Shaotang; Vaughn, John; Pappas, Iraklis; Fitzgerald, Michael; Masters, James G; Pan, Long

2015-01-01

The interactions between commercial antiperspirant (AP) salts [aluminum chlorohydrate (ACH), activated ACH, aluminum sesquichlorohydrate (ASCH), zirconium aluminum glycine (ZAG), activated ZAG), pure aluminum polyoxocations (Al13-mer, Al30-mer), and the zirconium(IV)-glycine complex Zr6 (O)4 (OH)4 (H2O)8 (Gly)8]12+(-) (CP-2 or ZG) with Bovine serum albumin (BSA) were studied using zeta potential and turbidity measurements. The maximal turbidity, which revealed the optimal interactions between protein and metal salts, for all protein-metal salt samples was observed at the isoelectric point (IEP), where the zeta potential of the solution was zero. Efficacy of AP salts was determined via three parameters: the amount of salt required to flocculate BSA to reach IEP, the turbidity of solution at the IEP, and the pH range over which the turbidity of the solution remains sufficiently high. By comparing active salt performance from this work to traditional prescreening methods, this methodology was able to provide a consistent efficacy assessment for metal actives in APs or in water treatment.

PBEQ-Solver for online visualization of electrostatic potential of biomolecules.

PubMed

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil

2008-07-01

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 A before and 1 A after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.

Nuclear symmetry energy in terms of single-nucleon potential and its effect on the proton fraction of β-stable npeμ matter

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

Sahoo, Babita, E-mail: patra-babita@rediffmail.com; Chakraborty, Suparna, E-mail: banerjee.suparna@hotmail.com; Sahoo, Sukadev, E-mail: sukadevsahoo@yahoo.com

2016-01-15

Momentum and density dependence of single-nucleon potential u{sub τ} (k, ρ, β) is analyzed using a density dependent finite range effective interaction of the Yukawa form. Depending on the choice of the strength parameters of exchange interaction, two different trends of the momentum dependence of nuclear symmetry potential are noticed which lead to two opposite types of neutron and proton effective mass splitting. The 2nd-order and 4th-order symmetry energy of isospin asymmetric nuclear matter are expressed analytically in terms of the single-nucleon potential. Two distinct behavior of the density dependence of 2nd-order and 4th-order symmetry energy are observed depending onmore » neutron and proton effective mass splitting. It is also found that the 4th-order symmetry energy has a significant contribution towards the proton fraction of β-stable npeμ matter at high densities.« less

Binding analysis of carbon nanoparticles to human immunoglobulin G: Elucidation of the cytotoxicity of CNPs and perturbation of immunoglobulin conformations

NASA Astrophysics Data System (ADS)

Zhang, Shengrui; Yang, Haitao; Ji, Xiaohui; Wang, Qin

2016-02-01

The chemical compositions, sizes and fluorescent properties of synthesized carbon nanoparticles (CNPs) were characterized. Escherichia coli (E. coli) cells were used as a model to study the cytotoxicity of CNPs, and the results of the cellular uptake of CNPs yielded excellent results: the CNPs demonstrated good biocompatibility and were non-toxic to the growth of the E. coli cells. Moreover, to assess the potential toxicity of CNPs to human health, the binding behavior of CNPs with human immunoglobulin G (HIgG) was examined by fluorescence quenching spectroscopy, synchronous fluorescence spectroscopy and circular dichroism spectroscopy under physiological conditions. The fluorescence quenching constants and parameters for the interaction at different temperatures had been calculated according to Scatchard. The thermodynamic parameters, such as enthalpy change (ΔH), entropy change (ΔS) and free energy change (ΔG), were calculated, and the results indicated strong static quenching and showed that van der Waals forces, hydrogen bonds and hydrophobic interactions were the predominant intermolecular forces stabilizing the CNP-HIgG complex. Synchronous fluorescence and circular dichroism spectra provided information regarding the conformational alteration of HIgG in the presence of CNPs. These findings help to characterize the interactions between CNPs and HIgG, which may clarify the potential risks and undesirable health effects of CNPs, as well as the related cellular trafficking and systemic translocation.

Regular and Chaotic Spatial Distribution of Bose-Einstein Condensed Atoms in a Ratchet Potential

NASA Astrophysics Data System (ADS)

Li, Fei; Xu, Lan; Li, Wenwu

2018-02-01

We study the regular and chaotic spatial distribution of Bose-Einstein condensed atoms with a space-dependent nonlinear interaction in a ratchet potential. There exists in the system a space-dependent atomic current that can be tuned via Feshbach resonance technique. In the presence of the space-dependent atomic current and a weak ratchet potential, the Smale-horseshoe chaos is studied and the Melnikov chaotic criterion is obtained. Numerical simulations show that the ratio between the intensities of optical potentials forming the ratchet potential, the wave vector of the laser producing the ratchet potential or the wave vector of the modulating laser can be chosen as the controlling parameters to result in or avoid chaotic spatial distributional states.

Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

PubMed

Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

2015-10-26

We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

NASA Astrophysics Data System (ADS)

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

2015-11-01

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.

PubMed

Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

2015-11-07

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

Contact interaction in an unitary ultracold Fermi gas

DOE PAGES

Pessoa, Renato; Gandolfi, Stefano; Vitiello, S. A.; ...

2015-12-16

An ultracold Fermi atomic gas at unitarity presents universal properties that in the dilute limit can be well described by a contact interaction. By employing a guiding function with correct boundary conditions and making simple modifications to the sampling procedure we are able to calculate the properties of a true contact interaction with the diffusion Monte Carlo method. The results are obtained with small variances. Our calculations for the Bertsch and contact parameters are in excellent agreement with published experiments. The possibility of using a more faithful description of ultracold atomic gases can help uncover additional features of ultracold atomicmore » gases. In addition, this work paves the way to perform quantum Monte Carlo calculations for other systems interacting with contact interactions, where the description using potentials with finite effective range might not be accurate.« less

Computer simulation of liquid-vapor coexistence of confined quantum fluids

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

Trejos, Víctor M.; Gil-Villegas, Alejandro, E-mail: gil@fisica.ugto.mx; Martinez, Alejandro

2013-11-14

The liquid-vapor coexistence (LV) of bulk and confined quantum fluids has been studied by Monte Carlo computer simulation for particles interacting via a semiclassical effective pair potential V{sub eff}(r) = V{sub LJ} + V{sub Q}, where V{sub LJ} is the Lennard-Jones 12-6 potential (LJ) and V{sub Q} is the first-order Wigner-Kirkwood (WK-1) quantum potential, that depends on β = 1/kT and de Boer's quantumness parameter Λ=h/σ√(mε), where k and h are the Boltzmann's and Planck's constants, respectively, m is the particle's mass, T is the temperature of the system, and σ and ε are the LJ potential parameters. The non-conformalmore » properties of the system of particles interacting via the effective pair potential V{sub eff}(r) are due to Λ, since the LV phase diagram is modified by varying Λ. We found that the WK-1 system gives an accurate description of the LV coexistence for bulk phases of several quantum fluids, obtained by the Gibbs Ensemble Monte Carlo method (GEMC). Confinement effects were introduced using the Canonical Ensemble (NVT) to simulate quantum fluids contained within parallel hard walls separated by a distance L{sub p}, within the range 2σ ⩽ L{sub p} ⩽ 6σ. The critical temperature of the system is reduced by decreasing L{sub p} and increasing Λ, and the liquid-vapor transition is not longer observed for L{sub p}/σ < 2, in contrast to what has been observed for the classical system.« less

Construction of drug-polymer thermodynamic phase diagrams using Flory-Huggins interaction theory: identifying the relevance of temperature and drug weight fraction to phase separation within solid dispersions.

PubMed

Tian, Yiwei; Booth, Jonathan; Meehan, Elizabeth; Jones, David S; Li, Shu; Andrews, Gavin P

2013-01-07

Amorphous drug-polymer solid dispersions have the potential to enhance the dissolution performance and thus bioavailability of BCS class II drug compounds. The principle drawback of this approach is the limited physical stability of amorphous drug within the dispersion. Accurate determination of the solubility and miscibility of drug in the polymer matrix is the key to the successful design and development of such systems. In this paper, we propose a novel method, based on Flory-Huggins theory, to predict and compare the solubility and miscibility of drug in polymeric systems. The systems chosen for this study are (1) hydroxypropyl methylcellulose acetate succinate HF grade (HPMCAS-HF)-felodipine (FD) and (2) Soluplus (a graft copolymer of polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol)-FD. Samples containing different drug compositions were mixed, ball milled, and then analyzed by differential scanning calorimetry (DSC). The value of the drug-polymer interaction parameter χ was calculated from the crystalline drug melting depression data and extrapolated to lower temperatures. The interaction parameter χ was also calculated at 25 °C for both systems using the van Krevelen solubility parameter method. The rank order of interaction parameters of the two systems obtained at this temperature was comparable. Diagrams of drug-polymer temperature-composition and free energy of mixing (ΔG(mix)) were constructed for both systems. The maximum crystalline drug solubility and amorphous drug miscibility may be predicted based on the phase diagrams. Hyper-DSC was used to assess the validity of constructed phase diagrams by annealing solid dispersions at specific drug loadings. Three different samples for each polymer were selected to represent different regions within the phase diagram.

Retrospective use of PBPK modelling to understand a clinical drug-drug interaction between dextromethorphan and GSK1034702.

PubMed

Hobbs, Michael J; Bloomer, Jackie; Dear, Gordon

2017-08-01

1. In a clinical trial, a strong drug-drug interaction (DDI) was observed between dextromethorphan (DM, the object or victim drug) and GSK1034702 (the precipitant or perpetrator drug), following single and repeat doses. This study determined the inhibition parameters of GSK1034702 in vitro and applied PBPK modelling approaches to simulate the clinical observations and provide mechanistic hypotheses to understand the DDI. 2. In vitro assays were conducted to determine the inhibition parameters of human CYP2D6 by GSK1034702. PBPK models were populated with the in vitro parameters and DDI simulations conducted and compared to the observed data from a clinical study with DM and GSK1034702. 3. GSK1034702 was a potent direct and metabolism-dependent inhibitor of human CYP2D6, with inhibition parameters of: IC 50  =   1.6 μM, K inact  = 3.7 h -1 and K I  = 0.8 μM. Incorporating these data into PBPK models predicted a DDI after repeat, but not single, 5 mg doses of GSK1034702. 4. The DDI observed with repeat administration of GSK1034702 (5 mg) can be attributed to metabolism-dependent inhibition of CYP2D6. Further, in vitro data were generated and several potential mechanisms proposed to explain the interaction observed following a single dose of GSK1034702.

Extended Bose Hubbard model of interacting bosonic atoms in optical lattices: From superfluidity to density waves

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

Mazzarella, G.; Giampaolo, S. M.; Illuminati, F.

2006-01-15

For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zeromore » and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters.« less

Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

NASA Astrophysics Data System (ADS)

Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

2016-09-01

Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

Interactions between silica particles in the presence of multivalent coions.

PubMed

Uzelac, Biljana; Valmacco, Valentina; Trefalt, Gregor

2017-08-30

Forces between charged silica particles in solutions of multivalent coions are measured with colloidal probe technique based on atomic force microscopy. The concentration of 1 : z electrolytes is systematically varied to understand the behavior of electrostatic interactions and double-layer properties in these systems. Although the coions are multivalent the Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory perfectly describes the measured force profiles. The diffuse-layer potentials and regulation properties are extracted from the forces profiles by using the DLVO theory. The dependencies of the diffuse-layer potential and regulation parameter shift to lower concentration with increasing coion valence when plotted as a function of concentration of 1 : z salt. Interestingly, these profiles collapse to a master curve if plotted as a function of monovalent counterion concentration.

The crystal acceleration effect for cold neutrons

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

Braginetz, Yu. P., E-mail: aiver@pnpi.spb.ru; Berdnikov, Ya. A.; Fedorov, V. V., E-mail: vfedorov@pnpi.spb.ru

A new mechanism of neutron acceleration is discussed and studied experimentally in detail for cold neutrons passing through the accelerated perfect crystal with the energies close to the Bragg one. The effect arises due to the following reason. The crystal refraction index (neutron-crystal interaction potential) for neutron in the vicinity of the Bragg resonance sharply depends on the parameter of deviation from the exact Bragg condition, i.e. on the crystal-neutron relative velocity. Therefore the neutrons enter into accelerated crystal with one neutron-crystal interaction potential and exit with the other. Neutron kinetic energy cannot vary inside the crystal due to itsmore » homogeneity. So after passage through such a crystal neutrons will be accelerated or decelerated because of the different energy change at the entrance and exit crystal boundaries.« less

Dapoxetine has no pharmacokinetic or cognitive interactions with ethanol in healthy male volunteers.

PubMed

Modi, Nishit B; Dresser, Mark; Desai, Dhaval; Edgar, Christopher; Wesnes, Keith

2007-03-01

Dapoxetine is being investigated for the treatment of premature ejaculation. This study evaluated the potential pharmacokinetic and cognitive interactions of dapoxetine 60 mg with ethanol 0.5 g/kg in a single-center, double-blind, randomized, placebo-controlled crossover study in healthy adult male participants (n = 24). Dapoxetine was rapidly absorbed and eliminated; peak concentrations were noted 1.47 hours after administration and decreased with an alpha half-life of 1.33 hours and a terminal half-life of 15.6 hours. Pharmacokinetic parameters (C(max), AUC(infinity), t((1/2)), and t(max)) of dapoxetine were not altered with concurrent ethanol consumption. Furthermore, coadministration of dapoxetine did not affect the pharmacokinetics of ethanol or potentiate the cognitive and subjective effects of ethanol.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Farm water budgets for semiarid irrigated floodplains of northern New Mexico: characterizing the surface water-groundwater interactions

NASA Astrophysics Data System (ADS)

Gutierrez, K. Y.; Fernald, A.; Ochoa, C. G.; Guldan, S. J.

2013-12-01

KEY WORDS - Hydrology, Water budget, Deep percolation, Surface water-Groundwater interactions. With the recent projections for water scarcity, water balances have become an indispensable water management tool. In irrigated floodplains, deep percolation from irrigation can represent one of the main aquifer recharge sources. A better understanding of surface water and groundwater interactions in irrigated valleys is needed for properly assessing the water balances in these systems and estimating potential aquifer recharge. We conducted a study to quantify the parameters and calculate the water budgets in three flood irrigated hay fields with relatively low, intermediate and, high water availability in northern New Mexico. We monitored different hydrologic parameters including total amount of water applied, change in soil moisture, drainage below the effective root zone, and shallow water level fluctuations in response to irrigation. Evapotranspiration was calculated from weather station data collected in-situ using the Samani-Hargreaves. Previous studies in the region have estimated deep percolation as a residual parameter of the water balance equation. In this study, we used both, the water balance method and actual measurements of deep percolation using passive lysimeters. Preliminary analyses for the three fields show a relatively rapid movement of water through the upper 50 cm of the vadose zone and a quick response of the shallow aquifer under flood irrigation. Further results from this study will provide a better understanding of surface water-groundwater interactions in flood irrigated valleys in northern New Mexico.

Investigating the nature of chiral near-field interactions

NASA Astrophysics Data System (ADS)

Barr, Lauren E.; Horsley, Simon A. R.; Hooper, Ian R.; Eager, Jake K.; Gallagher, Cameron P.; Hornett, Samuel M.; Hibbins, Alastair P.; Hendry, Euan

2018-04-01

In recent years, there have been reports of enhanced chiroptical interactions in the near-fields of antennas, postulated to be mediated by high spatial gradients in the electromagnetic fields. Here, using gigahertz experimentation, we investigate the nature of the chiral near-field generated by an array of staggered-rod antennas through its interaction with an array of aligned, subwavelength metallic helices. This allows us to eliminate many potential origins of enhancements, such as those associated with plasmon-exciton interactions, and search solely for enhancements due to the high spatial gradients in the chirality of the fields around chiral antennas (so-called `superchiral fields'). By comparing the strength of the chiral interaction with our helices to that of a homogeneous chiral layer with effective material parameters, we find that the strength of this chiral interaction can be predicted using a completely local effective medium approximation. This suggests no obvious enhancement in the chiral interaction in the near-field and indicates that nonlocal interactions are negligible in this system.

A network-based approach to disturbance transmission through microbial interactions

PubMed Central

Hunt, Dana E.; Ward, Christopher S.

2015-01-01

Microbes numerically dominate aquatic ecosystems and play key roles in the biogeochemistry and the health of these environments. Due to their short generations times and high diversity, microbial communities are among the first responders to environmental changes, including natural and anthropogenic disturbances such as storms, pollutant releases, and upwelling. These disturbances affect members of the microbial communities both directly and indirectly through interactions with impacted community members. Thus, interactions can influence disturbance propagation through the microbial community by either expanding the range of organisms affected or buffering the influence of disturbance. For example, interactions may expand the number of disturbance-affected taxa by favoring a competitor or buffer the impacts of disturbance when a potentially disturbance-responsive clade’s growth is limited by an essential microbial partner. Here, we discuss the potential to use inferred ecological association networks to examine how disturbances propagate through microbial communities focusing on a case study of a coastal community’s response to a storm. This approach will offer greater insight into how disturbances can produce community-wide impacts on aquatic environments following transient changes in environmental parameters. PMID:26579091

Research requirements for development of improved helicopter rotor efficiency

NASA Technical Reports Server (NTRS)

Davis, S. J.

1976-01-01

The research requirements for developing an improved-efficiency rotor for a civil helicopter are documented. The various design parameters affecting the hover and cruise efficiency of a rotor are surveyed, and the parameters capable of producing the greatest potential improvement are identified. Research and development programs to achieve these improvements are defined, and estimated costs and schedules are presented. Interaction of the improved efficiency rotor with other technological goals for an advanced civil helicopter is noted, including its impact on engine noise, hover and cruise performance, one-engine-inoperative hover capability, and maintenance and reliability.

Interfacial energetics of two-dimensional colloidal clusters generated with a tunable anharmonic interaction potential

NASA Astrophysics Data System (ADS)

Hilou, Elaa; Du, Di; Kuei, Steve; Biswal, Sibani Lisa

2018-02-01

Interfacial characteristics are critical to various properties of two-dimensional (2D) materials such as band alignment at a heterojunction and nucleation kinetics in a 2D crystal. Despite the desire to harness these enhanced interfacial properties for engineering new materials, unexpected phase transitions and defects, unique to the 2D morphology, have left a number of open questions. In particular, the effects of configurational anisotropy, which are difficult to isolate experimentally, and their influence on interfacial properties are not well understood. In this work, we begin to probe this structure-thermodynamic relationship, using a rotating magnetic field to generate an anharmonic interaction potential in a 2D system of paramagnetic particles. At low magnetic field strengths, weakly interacting colloidal particles form non-close-packed, fluidlike droplets, whereas, at higher field strengths, crystallites with hexagonal ordering are observed. We examine spatial and interfacial properties of these 2D colloidal clusters by measuring the local bond orientation order parameter and interfacial stiffness as a function of the interaction strength. To our knowledge, this is the first study to measure the tunable interfacial stiffness of a 2D colloidal cluster by controlling particle interactions using external fields.

Effect of breed and sperm concentration on the changes in structural, functional and motility parameters of ram-lamb spermatozoa during storage at 4 degrees C.

PubMed

Kasimanickam, Ramanathan; Kasimanickam, Vanmathy; Pelzer, Kevin D; Dascanio, John J

2007-09-01

The objectives of this study were (1) to determine the changes in structural, functional and motility parameters of ram-lamb semen stored at two different concentrations at 4 degrees C for 8 days in egg-yolk based extender and (2) to determine the effect of breed of ram-lambs on the changes in structural, functional and motility parameters of ram-lamb semen from different breeds stored at two different concentrations at 4 degrees C for 8 days in egg-yolk based extender. Two different concentrations suitable for laparoscopic and cervical insemination were employed in this experiment. A total of 14 ram-lambs (Polled Dorset-5, Suffolk-5, Katahdin-4) with satisfactory breeding potential were selected. Semen samples were collected by electro-ejaculation. Semen samples were extended to 50 and 200 million sperm per ml with a commercial egg yolk based extender (Triladyl, Minitube of America, Verona, WI, USA) at room temperature and were stored at 4 degrees C. The sperm DNA fragmentation index (DFI), percentages of high mitochondrial membrane potential (hMMP) and plasma membrane integrity (PMI) were assessed using flow cytometry as part of structural and functional parameters on Days 0, 1, 4, 6, and 8. A computer assisted sperm analyser (HTM-IVOS, Version 10.8, Hamilton Thorne Research, Beverly, MA, USA) was used to assess the sperm motility parameters on Days 0, 1, 4, 6, and 8. PROC MIXED procedure was used to determine the effect of days of storage, concentration and breed. The concentration and days of storage significantly affected the sperm structural, functional and motility parameters (P<0.0001). Significant concentration x days of storage interaction was found for all structural and functional parameters. There was a significant concentration x days of storage interaction for average path velocity, curvilinear velocity, straightness and linearity. Overall changes in the sperm structural, functional and sperm motility parameters over the storage period were less dramatic in the 200 x 10(6) ml(-1) concentration when compared to 50 x 10(6) ml(-1) concentration. The hMMP and total progressive motility were influenced by breed. In conclusion, the quality of structural, functional and motility parameters declined as days of storage were increased and the magnitude of changes in the parameters was less dramatic at the higher concentration.

A Computational Study of Rare Gas Clusters: Stepping Stones to the Solid State

ERIC Educational Resources Information Center

Glendening, Eric D.; Halpern, Arthur M.

2012-01-01

An upper-level undergraduate or beginning graduate project is described in which students obtain the Lennard-Jones 6-12 potential parameters for Ne[subscript 2] and Ar[subscript 2] from ab initio calculations and use the results to express pairwise interactions between the atoms in clusters containing up to N = 60 atoms. The students use simulated…

Group contribution methodology based on the statistical associating fluid theory for heteronuclear molecules formed from Mie segments.

PubMed

Papaioannou, Vasileios; Lafitte, Thomas; Avendaño, Carlos; Adjiman, Claire S; Jackson, George; Müller, Erich A; Galindo, Amparo

2014-02-07

A generalization of the recent version of the statistical associating fluid theory for variable range Mie potentials [Lafitte et al., J. Chem. Phys. 139, 154504 (2013)] is formulated within the framework of a group contribution approach (SAFT-γ Mie). Molecules are represented as comprising distinct functional (chemical) groups based on a fused heteronuclear molecular model, where the interactions between segments are described with the Mie (generalized Lennard-Jonesium) potential of variable attractive and repulsive range. A key feature of the new theory is the accurate description of the monomeric group-group interactions by application of a high-temperature perturbation expansion up to third order. The capabilities of the SAFT-γ Mie approach are exemplified by studying the thermodynamic properties of two chemical families, the n-alkanes and the n-alkyl esters, by developing parameters for the methyl, methylene, and carboxylate functional groups (CH3, CH2, and COO). The approach is shown to describe accurately the fluid-phase behavior of the compounds considered with absolute average deviations of 1.20% and 0.42% for the vapor pressure and saturated liquid density, respectively, which represents a clear improvement over other existing SAFT-based group contribution approaches. The use of Mie potentials to describe the group-group interaction is shown to allow accurate simultaneous descriptions of the fluid-phase behavior and second-order thermodynamic derivative properties of the pure fluids based on a single set of group parameters. Furthermore, the application of the perturbation expansion to third order for the description of the reference monomeric fluid improves the predictions of the theory for the fluid-phase behavior of pure components in the near-critical region. The predictive capabilities of the approach stem from its formulation within a group-contribution formalism: predictions of the fluid-phase behavior and thermodynamic derivative properties of compounds not included in the development of group parameters are demonstrated. The performance of the theory is also critically assessed with predictions of the fluid-phase behavior (vapor-liquid and liquid-liquid equilibria) and excess thermodynamic properties of a variety of binary mixtures, including polymer solutions, where very good agreement with the experimental data is seen, without the need for adjustable mixture parameters.

Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction

NASA Astrophysics Data System (ADS)

Hansen, Matthew; Everett, Logan; Singh, Larry; Hannenhalli, Sridhar

Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation. Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in a (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on three biological cases in cow and in yeast. While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.

The effects of transverse magnetic field and local electronic interaction on thermoelectric properties of monolayer graphene

NASA Astrophysics Data System (ADS)

Rezania, Hamed; Azizi, Farshad

2018-02-01

We study the effects of a transverse magnetic field and electron doping on the thermoelectric properties of monolayer graphene in the context of Hubbard model at the antiferromagnetic sector. In particular, the temperature dependence of thermal conductivity and Seebeck coefficient has been investigated. Mean field approximation has been employed in order to obtain the electronic spectrum of the system in the presence of local electron-electron interaction. Our results show the peak in thermal conductivity moves to higher temperatures with increase of both chemical potential and Hubbard parameter. Moreover the increase of magnetic field leads to shift of peak in temperature dependence of thermal conductivity to higher temperatures. Finally the behavior of Seebeck coefficient in terms of temperature has been studied and the effects of magnetic field and Hubbard parameter on this coefficient have been investigated in details.

Kinetic theory of a two-dimensional magnetized plasma. II - Balescu-Lenard limit.

NASA Technical Reports Server (NTRS)

Vahala, G.

1972-01-01

The kinetic theory of a two-dimensional one-species plasma in a uniform dc magnetic field is investigated in the small plasma parameter limit. The plasma consists of charged rods interacting through the logarithmic Coulomb potential. Vahala and Montgomery earlier (1971) derived a Fokker-Planck equation for this system, but it contained a divergent integral, which had to be cut off on physical grounds. This cutoff is compared to the standard cutoff introduced in the two-dimensional unmagnetized Fokker-Planck equation. In the small plasma parameter limit, it is shown that the Balescu-Lenard collision term is zero in the long time average limit if only two-body interactions are considered. The energy transfer from a test particle to an equilibrium plasma is discussed and is also shown to be zero in the long time average limit. This supports the unexpected result of zero Balescu-Lenard collision term.

Dynamics in multiple-well Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Nigro, M.; Capuzzi, P.; Cataldo, H. M.; Jezek, D. M.

2018-01-01

We study the dynamics of three-dimensional weakly linked Bose-Einstein condensates using a multimode model with an effective interaction parameter. The system is confined by a ring-shaped four-well trapping potential. By constructing a two-mode Hamiltonian in a reduced highly symmetric phase space, we examine the periodic orbits and calculate their time periods both in the self-trapping and Josephson regimes. The dynamics in the vicinity of the reduced phase space is investigated by means of a Floquet multiplier analysis, finding regions of different linear stability and analyzing their implications on the exact dynamics. The numerical exploration in an extended region of the phase space demonstrates that two-mode tools can also be useful for performing a partition of the space in different regimes. Comparisons with Gross-Pitaevskii simulations confirm these findings and emphasize the importance of properly determining the effective on-site interaction parameter governing the multimode dynamics.

Astrophysical neutrinos flavored with beyond the Standard Model physics

NASA Astrophysics Data System (ADS)

Rasmussen, Rasmus W.; Lechner, Lukas; Ackermann, Markus; Kowalski, Marek; Winter, Walter

2017-10-01

We systematically study the allowed parameter space for the flavor composition of astrophysical neutrinos measured at Earth, including beyond the Standard Model theories at production, during propagation, and at detection. One motivation is to illustrate the discrimination power of the next-generation neutrino telescopes such as IceCube-Gen2. We identify several examples that lead to potential deviations from the standard neutrino mixing expectation such as significant sterile neutrino production at the source, effective operators modifying the neutrino propagation at high energies, dark matter interactions in neutrino propagation, or nonstandard interactions in Earth matter. IceCube-Gen2 can exclude about 90% of the allowed parameter space in these cases, and hence will allow us to efficiently test and discriminate between models. More detailed information can be obtained from additional observables such as the energy dependence of the effect, fraction of electron antineutrinos at the Glashow resonance, or number of tau neutrino events.

Uncertainty Quantification in Aeroelasticity

NASA Astrophysics Data System (ADS)

Beran, Philip; Stanford, Bret; Schrock, Christopher

2017-01-01

Physical interactions between a fluid and structure, potentially manifested as self-sustained or divergent oscillations, can be sensitive to many parameters whose values are uncertain. Of interest here are aircraft aeroelastic interactions, which must be accounted for in aircraft certification and design. Deterministic prediction of these aeroelastic behaviors can be difficult owing to physical and computational complexity. New challenges are introduced when physical parameters and elements of the modeling process are uncertain. By viewing aeroelasticity through a nondeterministic prism, where key quantities are assumed stochastic, one may gain insights into how to reduce system uncertainty, increase system robustness, and maintain aeroelastic safety. This article reviews uncertainty quantification in aeroelasticity using traditional analytical techniques not reliant on computational fluid dynamics; compares and contrasts this work with emerging methods based on computational fluid dynamics, which target richer physics; and reviews the state of the art in aeroelastic optimization under uncertainty. Barriers to continued progress, for example, the so-called curse of dimensionality, are discussed.

Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

NASA Astrophysics Data System (ADS)

Cui, Jie; Li, Zhiying; Krems, Roman V.

2015-10-01

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A-H to make predictions of the dynamical properties for another molecule related to A-H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A-X. We assume that the effect of the -H →-X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can be used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C6H5CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C6H6 collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C6H5CN with He.

Fixed-node diffusion Monte Carlo potential energy curve of the fluorine molecule F{sub 2} using selected configuration interaction trial wavefunctions

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

Giner, Emmanuel; Scemama, Anthony; Caffarel, Michel

2015-01-28

The potential energy curve of the F{sub 2} molecule is calculated with Fixed-Node Diffusion Monte Carlo (FN-DMC) using Configuration Interaction (CI)-type trial wavefunctions. To keep the number of determinants reasonable and thus make FN-DMC calculations feasible in practice, the CI expansion is restricted to those determinants that contribute the most to the total energy. The selection of the determinants is made using the CIPSI approach (Configuration Interaction using a Perturbative Selection made Iteratively). The trial wavefunction used in FN-DMC is directly issued from the deterministic CI program; no Jastrow factor is used and no preliminary multi-parameter stochastic optimization of themore » trial wavefunction is performed. The nodes of CIPSI wavefunctions are found to reduce significantly the fixed-node error and to be systematically improved upon increasing the number of selected determinants. To reduce the non-parallelism error of the potential energy curve, a scheme based on the use of a R-dependent number of determinants is introduced. Using Dunning’s cc-pVDZ basis set, the FN-DMC energy curve of F{sub 2} is found to be of a quality similar to that obtained with full configuration interaction/cc-pVQZ.« less

Dynamics of atoms in strong laser fields I: A quasi analytical model in momentum space based on a Sturmian expansion of the interacting nonlocal Coulomb potential

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

Ongonwou, F., E-mail: fred.ongonwou@gmail.com; Tetchou Nganso, H.M., E-mail: htetchou@yahoo.com; Ekogo, T.B., E-mail: tekogo@yahoo.fr

In this study we present a model that we have formulated in the momentum space to describe atoms interacting with intense laser fields. As a further step, it follows our recent theoretical approach in which the kernel of the reciprocal-space time-dependent Schrödinger equation (TDSE) is replaced by a finite sum of separable potentials, each of them supporting one bound state of atomic hydrogen (Tetchou Nganso et al. 2013). The key point of the model is that the nonlocal interacting Coulomb potential is expanded in a Coulomb Sturmian basis set derived itself from a Sturmian representation of Bessel functions of the firstmore » kind in the position space. As a result, this decomposition allows a simple spectral treatment of the TDSE in the momentum space. In order to illustrate the credibility of the model, we have considered the test case of atomic hydrogen driven by a linearly polarized laser pulse, and have evaluated analytically matrix elements of the atomic Hamiltonian and dipole coupling interaction. For various regimes of the laser parameters used in computations our results are in very good agreement with data obtained from other time-dependent calculations.« less

Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

NASA Astrophysics Data System (ADS)

Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

2017-05-01

We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6. We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

Effect of Ion Streaming on Diffusion of Dust Grains in Dissipative System

NASA Astrophysics Data System (ADS)

Begum, M.; Das, N.

2018-01-01

The presence of strong electric fields in the sheath region of laboratory complex plasma induces an ion drift and perturbs the field around dust grains. The downstream focusing of ions leads to the formation of oscillatory kind of attractive wake potential which superimpose with the normal Debye-Hückel (DH) potential. The structural properties of complex plasma and diffusion coefficient of dust grains in the presence of such a wake potential have been investigated using Langevin dynamics simulation in the subsonic regime of ion flow. The study reveals that the diffusion of dust grains is strongly affected by the ion flow, so that the diffusion changes its character in the wake potential to the DH potential dominant regimes. The dependence of the diffusion coefficient on the parameters, such as the neutral pressure, dust grain size, ion flow velocity, and Coulomb coupling parameter, have been calculated for the subsonic regime by using the Green-Kubo expression, which is based on the integrated velocity autocorrelation function. It is found that the diffusion and the structural property of the system is intimately connected with the interaction potential and significantly get affected in the presence of ion flow in the subsonic regime.

A trap potential model investigation of the optical activity induced in dye-DNA intercalation complexes

NASA Astrophysics Data System (ADS)

Kamiya, Mamoru

1988-02-01

The fundamental features of the optical activity induced in dye-DNA intercalation complexes are studied by application of the trap potential model which is useful to evaluate the induced rotational strength without reference to detailed geometrical information about the intercalation complexes. The specific effect of the potential depth upon the induced optical activity is explained in terms of the relative magnitudes of the wave-phase and helix-phase variations in the path of an electron moving on a restricted helical segment just like an exciton trapped around the dye intercalation site. The parallel and perpendicular components of the induced rotational strength well reflect basic properties of the helicity effects about the longitudinal and tangential axes of the DNA helical cylinder. The trap potential model is applied to optimize the potential parameters so as to reproduce the ionic strength effect upon the optical activity induced to proflavine-DNA intercalation complexes. From relationships between the optimized potential parameters and ionic strengths, it is inferred that increase in the ionic strength contributes to the optical activity induced by the nearest-neighbour interaction between intercalated proflavine and DNA base pairs.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

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

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel; Fita, Ignacio

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothingmore » effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.« less

Thermal motion in proteins: Large effects on the time-averaged interaction energies

NASA Astrophysics Data System (ADS)

Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

2016-03-01

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

Colloids exposed to random potential energy landscapes: From particle number density to particle-potential and particle-particle interactions

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

Bewerunge, Jörg; Capellmann, Ronja F.; Platten, Florian

2016-07-28

Colloidal particles were exposed to a random potential energy landscape that has been created optically via a speckle pattern. The mean particle density as well as the potential roughness, i.e., the disorder strength, were varied. The local probability density of the particles as well as its main characteristics were determined. For the first time, the disorder-averaged pair density correlation function g{sup (1)}(r) and an analogue of the Edwards-Anderson order parameter g{sup (2)}(r), which quantifies the correlation of the mean local density among disorder realisations, were measured experimentally and shown to be consistent with replica liquid state theory results.

Elastic and inelastic scattering for the 10B+58Ni system at near-barrier energies

NASA Astrophysics Data System (ADS)

Scarduelli, V.; Crema, E.; Guimarães, V.; Abriola, D.; Arazi, A.; de Barbará, E.; Capurro, O. A.; Cardona, M. A.; Gallardo, J.; Hojman, D.; Martí, G. V.; Pacheco, A. J.; Rodrígues, D.; Yang, Y. Y.; Deshmukh, N. N.; Paes, B.; Lubian, J.; Mendes Junior, D. R.; Morcelle, V.; Monteiro, D. S.

2017-11-01

Full angular distributions of the 10B elastically and inelastically scattered by 58Ni have been measured at different energies around the Coulomb barrier. The elastic and inelastic scattering of 10B on a medium mass target has been measured for the first time. The obtained angular distributions have been analyzed in terms of large-scale coupled reaction channel calculations, where several inelastic transitions of the projectile and the target, as well as the most relevant one- and two-step transfer reactions have been included in the coupling matrix. The roles of the spin reorientation, the spin-orbit interaction, and the large ground-state deformation of the 10B, in the reaction mechanism, were also investigated. The real part of the interaction potential between projectile and target was represented by a parameter-free double-folding potential, whereas no imaginary potential at the surface was considered. In this sense, the theoretical calculations were parameter free and their results were compared to experimental data to investigate the relative importance of the different reaction channels. A striking influence of the ground-state spin reorientation of the 10B nucleus was found, while all transfer reactions investigated had a minimum contribution to the dynamics of the system. Finally, the large static deformation of the 10B and the spin-orbit coupling can also play an important role in the system studied.

Revisiting CMB constraints on warm inflation

NASA Astrophysics Data System (ADS)

Arya, Richa; Dasgupta, Arnab; Goswami, Gaurav; Prasad, Jayanti; Rangarajan, Raghavan

2018-02-01

We revisit the constraints that Planck 2015 temperature, polarization and lensing data impose on the parameters of warm inflation. To this end, we study warm inflation driven by a single scalar field with a quartic self interaction potential in the weak dissipative regime. We analyse the effect of the parameters of warm inflation, namely, the inflaton self coupling λ and the inflaton dissipation parameter QP on the CMB angular power spectrum. We constrain λ and QP for 50 and 60 number of e-foldings with the full Planck 2015 data (TT, TE, EE + lowP and lensing) by performing a Markov-Chain Monte Carlo analysis using the publicly available code CosmoMC and obtain the joint as well as marginalized distributions of those parameters. We present our results in the form of mean and 68 % confidence limits on the parameters and also highlight the degeneracy between λ and QP in our analysis. From this analysis we show how warm inflation parameters can be well constrained using the Planck 2015 data.

Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

PubMed

Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

2015-01-12

Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coarse grained modeling of directed assembly to form functional nanoporous films

NASA Astrophysics Data System (ADS)

Al Khatib, Amir

A coarse-grained (CG) simulation of polyethylene glycol (PEG) and Polymethylsilsesquixane nanoparticle (PMSSQ) referred to as (NP) at different sizes and concentrations were done using the Martini coarse-grained (CG) force field. The interactions between CG PEG and CG NP were parameterized from the chemical compound of each molecule and based on Martini force field. NP particles migrates to the surface of the substrate in an agreement with the experimental output at high temperature of 800K. This demonstration of nanoparticles-polymer film to direct it to self-assemble a systematically spatial pattern using the substrate surface energy as the key gating parameter. Validation of the model comparing molecular dynamics simulations with experimental data collected from previous study. NP interaction with the substrate at low interactions energy using Lennard-Johns potential were able to direct the NP to self-assemble in a hexagonal shape up to 4 layers above the substrate. This thesis established that substrate surface energy is a key gating parameter to direct the collective behavior of functional nanoparticles to form thin nanoporous films with spatially predetermined optical/dielectric constants.

Looking for the WIMP next door

NASA Astrophysics Data System (ADS)

Evans, Jared A.; Gori, Stefania; Shelton, Jessie

2018-02-01

We comprehensively study experimental constraints and prospects for a class of minimal hidden sector dark matter (DM) models, highlighting how the cosmological history of these models informs the experimental signals. We study simple `secluded' models, where the DM freezes out into unstable dark mediator states, and consider the minimal cosmic history of this dark sector, where coupling of the dark mediator to the SM was sufficient to keep the two sectors in thermal equilibrium at early times. In the well-motivated case where the dark mediators couple to the Standard Model (SM) via renormalizable interactions, the requirement of thermal equilibrium provides a minimal, UV-insensitive, and predictive cosmology for hidden sector dark matter. We call DM that freezes out of a dark radiation bath in thermal equilibrium with the SM a WIMP next door, and demonstrate that the parameter space for such WIMPs next door is sharply defined, bounded, and in large part potentially accessible. This parameter space, and the corresponding signals, depend on the leading interaction between the SM and the dark mediator; we establish it for both Higgs and vector portal interactions. In particular, there is a cosmological lower bound on the portal coupling strength necessary to thermalize the two sectors in the early universe. We determine this thermalization floor as a function of equilibration temperature for the first time. We demonstrate that direct detection experiments are currently probing this cosmological lower bound in some regions of parameter space, while indirect detection signals and terrestrial searches for the mediator cut further into the viable parameter space. We present regions of interest for both direct detection and dark mediator searches, including motivated parameter space for the direct detection of sub-GeV DM.

Social dilemmas in multistrategy evolutionary potential games

NASA Astrophysics Data System (ADS)

Szabó, György; Bunth, Gergely

2018-01-01

The nature of social dilemmas is studied in n -strategy evolutionary potential games on a square lattice with nearest-neighbor interactions and the logit rule. For symmetric games with symmetric payoff matrices there are no dilemmas because of the coincidence of individual and common interests. The dilemmas are caused by the antisymmetric parts of the self- and cross-dependent payoff components if it modifies the preferred Nash equilibrium. The contentment of players and the emergence of dilemmas in the preferred Nash equilibria are illustrated on some two-dimensional cross sections of the parameter space.

Sonic horizon formation for oscillating Bose-Einstein condensates in isotropic harmonic potential

PubMed Central

Wang, Ying; Zhou, Yu; Zhou, Shuyu

2016-01-01

We study the sonic horizon phenomena of the oscillating Bose-Einstein condensates in isotropic harmonic potential. Based on the Gross-Pitaevskii equation model and variational method, we derive the original analytical formula for the criteria and lifetime of the formation of the sonic horizon, demonstrating pictorially the interaction parameter dependence for the occur- rence of the sonic horizon and damping effect of the system distribution width. Our analytical results corroborate quantitatively the particular features of the sonic horizon reported in previous numerical study. PMID:27922129

Thermophysical properties of liquid rare earth metals

NASA Astrophysics Data System (ADS)

Thakor, P. B.; Sonvane, Y. A.; Patel, H. P.; Jani, A. R.

2013-06-01

The thermodynamical properties like long wavelength limit S(0), iso-thermal compressibility (χT), thermal expansion coefficient (αV), thermal pressure coefficient (γV), specific heat at constant volume (CV) and specific heat at constant pressure (CP) are calculated for liquid rare earth metals. Our newly constructed parameter free model potential is used to describe the electron ion interaction due to Sarkar et al (S) local field correction function. Lastly, we conclude that our newly constructed model potential is capable to explain the thermophysical properties of liquid rare earth metals.

Four classes of interactions for evolutionary games.

PubMed

Szabó, György; Bodó, Kinga S; Allen, Benjamin; Nowak, Martin A

2015-08-01

The symmetric four-strategy games are decomposed into a linear combination of 16 basis games represented by orthogonal matrices. Among these basis games four classes can be distinguished as it is already found for the three-strategy games. The games with self-dependent (cross-dependent) payoffs are characterized by matrices consisting of uniform rows (columns). Six of 16 basis games describe coordination-type interactions among the strategy pairs and three basis games span the parameter space of the cyclic components that are analogous to the rock-paper-scissors games. In the absence of cyclic components the game is a potential game and the potential matrix is evaluated. The main features of the four classes of games are discussed separately and we illustrate some characteristic strategy distributions on a square lattice in the low noise limit if logit rule controls the strategy evolution. Analysis of the general properties indicates similar types of interactions at larger number of strategies for the symmetric matrix games.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Electric-field-induced modification in Curie temperature of Co monolayer on Pt(111)

NASA Astrophysics Data System (ADS)

Nakamura, Kohji; Oba, Mikito; Akiyama, Toru; Ito, Tomonori; Weinert, Michael

2015-03-01

Magnetism induced by an external electric field (E-field) has received much attention as a potential approach for controlling magnetism at the nano-scale with the promise of ultra-low energy power consumption. Here, the E-field-induced modification of the Curie temperature for a prototypical transition-metal thin layer of a Co monolayer on Pt(111) is investigated by first-principles calculations by using the full-potential linearized augmented plane wave method that treats spin-spiral structures in an E-field. An applied E-field modifies the magnon (spin-spiral formation) energies by a few meV, which leads to a modification of the exchange pair interaction parameters within the classical Heisenberg model. With inclusion of the spin-orbit coupling (SOC), the magnetocrystalline anisotropy and the Dzyaloshinskii-Morita interaction are obtained by the second variation SOC method. An E-field-induced modification of the Curie temperature is demonstrated by Monte Carlo simulations, in which a change in the exchange interaction is found to play a key role.

Magnon-induced superconductivity in a topological insulator coupled to ferromagnetic and antiferromagnetic insulators

NASA Astrophysics Data System (ADS)

Hugdal, Henning G.; Rex, Stefan; Nogueira, Flavio S.; Sudbø, Asle

2018-05-01

We study the effective interactions between Dirac fermions on the surface of a three-dimensional topological insulator due to the proximity coupling to the magnetic fluctuations in a ferromagnetic or antiferromagnetic insulator. Our results show that the magnetic fluctuations can mediate attractive interactions between Dirac fermions of both Amperean and BCS types. In the ferromagnetic case, we find pairing between fermions with parallel momenta, so-called Amperean pairing, whenever the effective Lagrangian for the magnetic fluctuations does not contain a quadratic term. The pairing interaction also increases with increasing Fermi momentum and is in agreement with previous studies in the limit of high chemical potential. If a quadratic term is present, the pairing is instead of BCS type above a certain chemical potential. In the antiferromagnetic case, BCS pairing occurs when the ferromagnetic coupling between magnons on the same sublattice exceeds the antiferromagnetic coupling between magnons on different sublattices. Outside this region in parameter space, we again find that Amperean pairing is realized.

Gap Solitons of Superfluid Fermi Gas in FS Optical Lattices

NASA Astrophysics Data System (ADS)

Chen, Yan; Zhang, Ke-Zhi; He, Yong-Lin; Liu, Zhen-Lai; Zhu, Liao

2018-01-01

By employing the mean-field theory and hydrodynamic scheme, we study the gap solitons of superfluid Fermi gas in Fourier-Synthesized(FS) optical lattices. By means of numerical methods and variational approximation, the atomic interaction, the chemical potential, the potential depth of the lattice and relative phase of the Fermi system are derived along the Bose-Enstein condensation(BEC)side to the Bardeen-Cooper-Schrieffer (BCS)side. It means that the condition exciting gap solitons is obtained. Moreover, we analyze the fundamental gap soltions of the superfluid Fermi gas. It is found that the relative phase α impacts greatly on the properties of fundamental gap solitons for superfluid Fermi gas. Especially, the nonlinearity interaction term g decreases with α. Add, due to Fermi pressure, curvature changes of g in the BEC limit( γ = 1, here, γ is a function of an interaction parameter) is larger than that at unitary ( γ = 2/3). Spatial distribution of gap solitons exhibit very obvious different when the system transit from the BEC side to BCS side.

Enhanced effect of temporal variation of the fine structure constant and the strong interaction in 229Th.

PubMed

Flambaum, V V

2006-09-01

The relative effects of the variation of the fine structure constant alpha = e2/variant Planck's over 2pi c and the dimensionless strong interaction parameter m(q)/LambdaQCD are enhanced by 5-6 orders of magnitude in a very narrow ultraviolet transition between the ground and the first excited states in the 229Th nucleus. It may be possible to investigate this transition with laser spectroscopy. Such an experiment would have the potential of improving the sensitivity to temporal variation of the fundamental constants by many orders of magnitude.

Cell and Particle Interactions and Aggregation During Electrophoretic Motion

NASA Technical Reports Server (NTRS)

Wang, Hua; Zeng, Shulin; Loewenberg, Michael; Todd, Paul; Davis, Robert H.

1996-01-01

The stability and pairwise aggregation rates of small spherical particles under the collective effects of buoyancy-driven motion and electrophoretic migration are analyzed. The particles are assumed to be non-Brownian, with thin double-layers and different zeta potentials. The particle aggregation rates may be enhanced or reduced, respectively, by parallel and antiparallel alignments of the buoyancy-driven and electrophoretic velocities. For antiparallel alignments, with the buoyancy-driven relative velocity exceeding the electrophoretic relative velocity between two widely-separated particles, there is a 'collision-forbidden region' in parameter space due to hydrodynamic interactions; thus, the suspension becomes stable against aggregation.

Path integrals with higher order actions: Application to realistic chemical systems

NASA Astrophysics Data System (ADS)

Lindoy, Lachlan P.; Huang, Gavin S.; Jordan, Meredith J. T.

2018-02-01

Quantum thermodynamic parameters can be determined using path integral Monte Carlo (PIMC) simulations. These simulations, however, become computationally demanding as the quantum nature of the system increases, although their efficiency can be improved by using higher order approximations to the thermal density matrix, specifically the action. Here we compare the standard, primitive approximation to the action (PA) and three higher order approximations, the Takahashi-Imada action (TIA), the Suzuki-Chin action (SCA) and the Chin action (CA). The resulting PIMC methods are applied to two realistic potential energy surfaces, for H2O and HCN-HNC, both of which are spectroscopically accurate and contain three-body interactions. We further numerically optimise, for each potential, the SCA parameter and the two free parameters in the CA, obtaining more significant improvements in efficiency than seen previously in the literature. For both H2O and HCN-HNC, accounting for all required potential and force evaluations, the optimised CA formalism is approximately twice as efficient as the TIA formalism and approximately an order of magnitude more efficient than the PA. The optimised SCA formalism shows similar efficiency gains to the CA for HCN-HNC but has similar efficiency to the TIA for H2O at low temperature. In H2O and HCN-HNC systems, the optimal value of the a1 CA parameter is approximately 1/3 , corresponding to an equal weighting of all force terms in the thermal density matrix, and similar to previous studies, the optimal α parameter in the SCA was ˜0.31. Importantly, poor choice of parameter significantly degrades the performance of the SCA and CA methods. In particular, for the CA, setting a1 = 0 is not efficient: the reduction in convergence efficiency is not offset by the lower number of force evaluations. We also find that the harmonic approximation to the CA parameters, whilst providing a fourth order approximation to the action, is not optimal for these realistic potentials: numerical optimisation leads to better approximate cancellation of the fifth order terms, with deviation between the harmonic and numerically optimised parameters more marked in the more quantum H2O system. This suggests that numerically optimising the CA or SCA parameters, which can be done at high temperature, will be important in fully realising the efficiency gains of these formalisms for realistic potentials.

Spectroscopic properties of the molecular ions BeX+ (X=Na, K, Rb): forming cold molecular ions from an ion-atom mixture by stimulated Raman adiabatic process

NASA Astrophysics Data System (ADS)

Ladjimi, Hela; Sardar, Dibyendu; Farjallah, Mohamed; Alharzali, Nisrin; Naskar, Somnath; Mlika, Rym; Berriche, Hamid; Deb, Bimalendu

2018-07-01

In this theoretical work, we calculate potential energy curves, spectroscopic parameters and transition dipole moments of molecular ions BeX+ (X=Na, K, Rb) composed of alkaline ion Be and alkali atom X with a quantum chemistry approach based on the pseudopotential model, Gaussian basis sets, effective core polarisation potentials and full configuration interaction. We study in detail collisions of the alkaline ion and alkali atom in quantum regime. Besides, we study the possibility of the formation of molecular ions from the ion-atom colliding systems by stimulated Raman adiabatic process and discuss the parameters regime under which the population transfer is feasible. Our results are important for ion-atom cold collisions and experimental realisation of cold molecular ion formation.

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination

PubMed Central

González-Ramírez, Laura R.; Ahmed, Omar J.; Cash, Sydney S.; Wayne, C. Eugene; Kramer, Mark A.

2015-01-01

Epilepsy—the condition of recurrent, unprovoked seizures—manifests in brain voltage activity with characteristic spatiotemporal patterns. These patterns include stereotyped semi-rhythmic activity produced by aggregate neuronal populations, and organized spatiotemporal phenomena, including waves. To assess these spatiotemporal patterns, we develop a mathematical model consistent with the observed neuronal population activity and determine analytically the parameter configurations that support traveling wave solutions. We then utilize high-density local field potential data recorded in vivo from human cortex preceding seizure termination from three patients to constrain the model parameters, and propose basic mechanisms that contribute to the observed traveling waves. We conclude that a relatively simple and abstract mathematical model consisting of localized interactions between excitatory cells with slow adaptation captures the quantitative features of wave propagation observed in the human local field potential preceding seizure termination. PMID:25689136

Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

ERIC Educational Resources Information Center

Chen, Cheng-Te; Wang, Wen-Chung

2007-01-01

This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

Effects of two successive parity-invariant point interactions on one-dimensional quantum transmission: Resonance conditions for the parameter space

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

Konno, Kohkichi, E-mail: kohkichi@tomakomai-ct.ac.jp; Nagasawa, Tomoaki, E-mail: nagasawa@tomakomai-ct.ac.jp; Takahashi, Rohta, E-mail: takahashi@tomakomai-ct.ac.jp

We consider the scattering of a quantum particle by two independent, successive parity-invariant point interactions in one dimension. The parameter space for the two point interactions is given by the direct product of two tori, which is described by four parameters. By investigating the effects of the two point interactions on the transmission probability of plane wave, we obtain the conditions for the parameter space under which perfect resonant transmission occur. The resonance conditions are found to be described by symmetric and anti-symmetric relations between the parameters.

Self-interaction effects on charge-transfer collisions

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Andrade, Xavier; ...

2017-04-27

In this article, we investigate the role of the self-interaction error in the simulation of collisions using time-dependent density functional theory (TDDFT) and Ehrenfest dynamics. In addition, we compare many different approximations of the exchange and correlation potential, using as a test system the collision of H + + CH 4 at 30 eV. We find that semilocal approximations, like the Perdew-Burke- Ernzerhof (PBE), and even hybrid functionals, such as the Becke, 3-parameter, Lee-Yang-Parr (B3LYP), produce qualitatively incorrect predictions for the scattering of the proton. This discrepancy appears because the self-interaction error allows the electrons to jump too easily tomore » the proton, leading to radically different forces with respect to the non-self-interacting case. Lastly, from our results, we conclude that using a functional that is self-interaction free is essential to properly describing charge-transfer collisions between ions and molecules in TDDFT.« less

Influence of Coulomb interaction of tunable shapes on the collective transport of ultradilute two-dimensional holes.

PubMed

Huang, Jian; Pfeiffer, L N; West, K W

2014-01-24

In high quality updoped GaAs field-effect transistors, the two-dimensional charge carrier concentrations can be tuned to very low values similar to the density of electrons on helium surfaces. An important interaction effect, screening of the Coulomb interaction by the gate, rises as a result of the large charge spacing comparable to the distance between the channel and the gate. Based on the results of the temperature (T) dependence of the resistivity from measuring four different samples, a power-law characteristic is found for charge densities ≤2×10(9)  cm(-2). Moreover, the exponent exhibits a universal dependence on a single dimensionless parameter, the ratio between the mean carrier separation and the distance to the metallic gate that screens the Coulomb interaction. Thus, the electronic properties are tuned through varying the shape of the interaction potential.

Exponential 6 parameterization for the JCZ3-EOS

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

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

1998-07-01

A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium for detonation and expansion states of energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. All product species are characterized by r*, the radius of the minimum pair potential energy, and {var_epsilon}/k, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) EOS database describing 750 gases (including all the gases in the JANNAF tables), and have been obtained by using Lennard-Jones potential parameters, a corresponding states theory, pure liquid shockmore » Hugoniot data, and fit values using an empirical EOS. This database can be used with the CHEETAH 1.40 or CHEETAH 2.0 interface to the TIGER computer program that predicts the equilibrium state of gas- and condensed-phase product species. The large JCZS-EOS database permits intermolecular potential based equilibrium calculations of energetic materials with complex elemental composition.« less

Halogenation of Hydraulic Fracturing Additives in the Shale Well Parameter Space

NASA Astrophysics Data System (ADS)

Sumner, A. J.; Plata, D.

2017-12-01

Horizontal Drilling and Hydraulic fracturing (HDHF) involves the deep-well injection of a `fracking fluid' composed of diverse and numerous chemical additives designed to facilitate the release and collection of natural gas from shale plays. The potential impacts of HDHF operations on water resources and ecosystems are numerous, and analyses of flowback samples revealed organic compounds from both geogenic and anthropogenic sources. Furthermore, halogenated chemicals were also detected, and these compounds are rarely disclosed, suggesting the in situ halogenation of reactive additives. To test this transformation hypothesis, we designed and operated a novel high pressure and temperature reactor system to simulate the shale well parameter space and investigate the chemical reactivity of twelve commonly disclosed and functionally diverse HDHF additives. Early results revealed an unanticipated halogenation pathway of α-β unsaturated aldehyde, Cinnamaldehyde, in the presence of oxidant and concentrated brine. Ongoing experiments over a range of parameters informed a proposed mechanism, demonstrating the role of various shale-well specific parameters in enabling the demonstrated halogenation pathway. Ultimately, these results will inform a host of potentially unintended interactions of HDHF additives during the extreme conditions down-bore of a shale well during HDHF activities.

Analysis of ISS Plasma Interaction

NASA Technical Reports Server (NTRS)

Reddell, Brandon; Alred, John; Kramer, Leonard; Mikatarian, Ron; Minow, Joe; Koontz, Steve

2006-01-01

To date, the International Space Station (ISS) has been one of the largest objects flown in lower earth orbit (LEO). The ISS utilizes high voltage solar arrays (160V) that are negatively grounded leading to pressurized elements that can float negatively with respect to the plasma. Because laboratory measurements indicate a dielectric breakdown potential difference of 80V, arcing could occur on the ISS structure. To overcome the possibility of arcing and clamp the potential of the structure, two Plasma Contactor Units (PCUs) were designed, built, and flown. Also a limited amount of measurements of the floating potential for the present ISS configuration were made by a Floating Potential Probe (FPP), indicating a minimum potential of 24 Volts at the measurement location. A predictive tool, the ISS Plasma Interaction Model (PIM) has been developed accounting for the solar array electron collection, solar array mast wire and effective conductive area on the structure. The model has been used for predictions of the present ISS configuration. The conductive area has been inferred based on available floating potential measurements. Analysis of FPP and PCU data indicated distribution of the conductive area along the Russian segment of the ISS structure. A significant input to PIM is the plasma environment. The International Reference Ionosphere (IRI 2001) was initially used to obtain plasma temperature and density values. However, IRI provides mean parameters, leading to difficulties in interpretation of on-orbit data, especially at eclipse exit where maximum charging can occur. This limits our predicative capability. Satellite and Incoherent Scatter Radar (ISR) data of plasma parameters have also been collected. Approximately 130,000 electron temperature (Te) and density (Ne) pairs for typical ISS eclipse exit conditions have been extracted from the reduced Langmuir probe data flown aboard the NASA DE-2 satellite. Additionally, another 18,000 Te and Ne pairs of ISR data from several radar locations around the globe were used to assure consistency of the satellite data. PIM predictions for ISS charging made with this data correlated very well with FPP data, indicating that the general physics of spacecraft charging with high voltage solar arrays have been captured. The predictions also provided the probabilities of occurrences for ISS charging. These probabilities give a numerical measure of the number of times when the ISS will approach or exceed the vehicle plasma hazard conditions for each configuration. In this paper we shall present the interaction mechanisms between the ISS and the surrounding plasma and give an overview of the PIM components. PIM predictions are compared with available data followed by a discussion of the variability of plasma parameters and the conductive area on the ISS. The ISS PIM will be further tested and verified as data from the Floating Potential Measurement Unit become available, and construction of the ISS continues.

Nonstandard neutrino interactions at DUNE, T2HK and T2HKK

DOE PAGES

Liao, Jiajun; Marfatia, Danny; Whisnant, Kerry

2017-01-17

Here, we study the matter effect caused by nonstandard neutrino interactions (NSI) in the next generation long-baseline neutrino experiments, DUNE, T2HK and T2HKK. If multiple NSI parameters are nonzero, the potential of these experiments to detect CP violation, determine the mass hierarchy and constrain NSI is severely impaired by degeneracies between the NSI parameters and by the generalized mass hierarchy degeneracy. In particular, a cancellation between leading order terms in the appearance channels when ϵ eτ= cot θ 23ϵ eμ, strongly affects the sensitivities to these two NSI parameters at T2HK and T2HKK. We also study the dependence of themore » sensitivities on the true CP phase and the true mass hierarchy, and find that overall DUNE has the best sensitivity to the magnitude of the NSI parameters, while T2HKK has the best sensitivity to CP violation whether or not there are NSI. Furthermore, for T2HKK a smaller off-axis angle for the Korean detector is better overall. We find that due to the structure of the leading order terms in the appearance channel probabilities, the NSI sensitivities in a given experiment are similar for both mass hierarchies, modulo the phase change δ→δ + 180°.« less

Nonstandard neutrino interactions at DUNE, T2HK and T2HKK

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

Liao, Jiajun; Marfatia, Danny; Whisnant, Kerry

Here, we study the matter effect caused by nonstandard neutrino interactions (NSI) in the next generation long-baseline neutrino experiments, DUNE, T2HK and T2HKK. If multiple NSI parameters are nonzero, the potential of these experiments to detect CP violation, determine the mass hierarchy and constrain NSI is severely impaired by degeneracies between the NSI parameters and by the generalized mass hierarchy degeneracy. In particular, a cancellation between leading order terms in the appearance channels when ϵ eτ= cot θ 23ϵ eμ, strongly affects the sensitivities to these two NSI parameters at T2HK and T2HKK. We also study the dependence of themore » sensitivities on the true CP phase and the true mass hierarchy, and find that overall DUNE has the best sensitivity to the magnitude of the NSI parameters, while T2HKK has the best sensitivity to CP violation whether or not there are NSI. Furthermore, for T2HKK a smaller off-axis angle for the Korean detector is better overall. We find that due to the structure of the leading order terms in the appearance channel probabilities, the NSI sensitivities in a given experiment are similar for both mass hierarchies, modulo the phase change δ→δ + 180°.« less

Quantifying Parameter Sensitivity, Interaction and Transferability in Hydrologically Enhanced Versions of Noah-LSM over Transition Zones

NASA Technical Reports Server (NTRS)

Rosero, Enrique; Yang, Zong-Liang; Wagener, Thorsten; Gulden, Lindsey E.; Yatheendradas, Soni; Niu, Guo-Yue

2009-01-01

We use sensitivity analysis to identify the parameters that are most responsible for shaping land surface model (LSM) simulations and to understand the complex interactions in three versions of the Noah LSM: the standard version (STD), a version enhanced with a simple groundwater module (GW), and version augmented by a dynamic phenology module (DV). We use warm season, high-frequency, near-surface states and turbulent fluxes collected over nine sites in the US Southern Great Plains. We quantify changes in the pattern of sensitive parameters, the amount and nature of the interaction between parameters, and the covariance structure of the distribution of behavioral parameter sets. Using Sobol s total and first-order sensitivity indexes, we show that very few parameters directly control the variance of the model output. Significant parameter interaction occurs so that not only the optimal parameter values differ between models, but the relationships between parameters change. GW decreases parameter interaction and appears to improve model realism, especially at wetter sites. DV increases parameter interaction and decreases identifiability, implying it is overparameterized and/or underconstrained. A case study at a wet site shows GW has two functional modes: one that mimics STD and a second in which GW improves model function by decoupling direct evaporation and baseflow. Unsupervised classification of the posterior distributions of behavioral parameter sets cannot group similar sites based solely on soil or vegetation type, helping to explain why transferability between sites and models is not straightforward. This evidence suggests a priori assignment of parameters should also consider climatic differences.

Application of an Optical Model to the Interaction of the $pi$ Meson with the Nucleus in the $pi$ Mesic Atom (thesis); APPLICATION D'UN MODELE OPTIQUE POUR L'INTERACTION DU MESON $pi$ MESIQUE (THESE)

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

Berthet, M.

1963-01-01

The energy levels and their displacement DELTA E with respect to that of a meson placed in a coulomb potential are determined and compared with the experimental values. This comparison permits the selection of values for the parameters introduced by the hypothesis of the optical model. The absorption in the nucleus is studied using the hamiltonian of the nucleon- pi meson interaction and not th optical model. The results are compared with experimen values. As an introduction, the exact form of the interac tion of mesons with nuclei is defined by adopting the opti model. (J.S.R.)

Investigation of Carbohydrate Recognition via Computer Simulation

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

Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

Investigation of Carbohydrate Recognition via Computer Simulation

DOE PAGES

Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; ...

2015-04-28

Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

Theoretical and experimental investigation of drug-polymer interaction and miscibility and its impact on drug supersaturation in aqueous medium.

PubMed

Baghel, Shrawan; Cathcart, Helen; O'Reilly, Niall J

2016-10-01

Amorphous solid dispersions (ASDs) have the potential to offer higher apparent solubility and bioavailability of BCS class II drugs. Knowledge of the solid state drug-polymer solubility/miscibility and their mutual interaction are fundamental requirements for the effective design and development of such systems. To this end, we have carried out a comprehensive investigation of various ASD systems of dipyridamole and cinnarizine in polyvinylpyrrolidone (PVP) and polyacrylic acid (PAA) at different drug loadings. Theoretical and experimental examinations (by implementing binary and ternary Flory-Huggins (F-H) theory) related to drug-polymer interaction/miscibility including solubility parameter approach, melting point depression method, phase diagram, drug-polymer interaction in the presence of moisture and the effect of drug loading on interaction parameter were performed. The information obtained from this study was used to predict the stability of ASDs at different drug loadings and under different thermal and moisture conditions. Thermal and moisture sorption analysis not only provided the composition-dependent interaction parameter but also predicted the composition dependent miscibility. DPM-PVP, DPM-PAA and CNZ-PAA systems have shown molecular level mixing over the complete range of drug loading. For CNZ-PVP, the presence of a single Tg at lower drug loadings (10, 20 and 35%w/w) indicates the formation of solid solution. However, drug recrystallization was observed for samples with higher drug weight fractions (50 and 65%w/w). Finally, the role of polymer in maintaining drug supersaturation has also been explored. It has been found that drug-polymer combinations capable of hydrogen-bonding in the solution state (DPM-PVP, DPM-PAA and CNZ-PAA) are more effective in preventing drug crystallization compared to the drug-polymer systems without such interaction (CNZ-PVP). The DPM-PAA system outperformed all other ASDs in various stability conditions (dry-state, in the presence of moisture and in solution state), which was attributed to the drug's low crystallization tendency, the strong DPM-PAA interaction, the robustness of this interaction against moisture or water and the ability of PAA in maintaining DPM supersaturation. Copyright © 2016 Elsevier B.V. All rights reserved.

Dark-dark-soliton dynamics in two density-coupled Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Morera, I.; Mateo, A. Muñoz; Polls, A.; Juliá-Díaz, B.

2018-04-01

We study the one-dimensional dynamics of dark-dark solitons in the miscible regime of two density-coupled Bose-Einstein condensates having repulsive interparticle interactions within each condensate (g >0 ). By using an adiabatic perturbation theory in the parameter g12/g , we show that, contrary to the case of two solitons in scalar condensates, the interactions between solitons are attractive when the interparticle interactions between condensates are repulsive g12>0 . As a result, the relative motion of dark solitons with equal chemical potential μ is well approximated by harmonic oscillations of angular frequency wr=(μ /ℏ ) √{(8 /15 ) g12/g } . We also show that, in finite systems, the resonance of this anomalous excitation mode with the spin-density mode of lowest energy gives rise to alternating dynamical instability and stability fringes as a function of the perturbative parameter. In the presence of harmonic trapping (with angular frequency Ω ) the solitons are driven by the superposition of two harmonic motions at a frequency given by w2=(Ω/√{2 }) 2+wr2 . When g12<0 , these two oscillators compete to give rise to an overall effective potential that can be either single well or double well through a pitchfork bifurcation. All our theoretical results are compared with numerical solutions of the Gross-Pitaevskii equation for the dynamics and the Bogoliubov equations for the linear stability. A good agreement is found between them.

Analysis of the interactions between He + ions and transition metal surfaces using co-axial impact collision ion scattering spectroscopy

NASA Astrophysics Data System (ADS)

Walker, M.; Brown, M. G.; Draxler, M.; Fishwick, L.; Dowsett, M. G.; McConville, C. F.

2011-01-01

The interactions between low energy He + ions and a series of transition metal surfaces have been studied using co-axial impact collision ion scattering spectroscopy (CAICISS). Experimental data were collected from the Ni(110), Cu(100), Pd(111), Pt(111) and Au(111) surfaces using ion beams with primary energies between 1.5 keV and 4.0 keV. The shadow cone radii deduced from the experimental surface peak positions were found to closely match theoretical predictions. Data analysis was performed using both the FAN and Kalypso simulation codes, revealing a consistent requirement for a reduction of 0.252 in the screening length correction in the Molière approximation within the Thomas-Fermi (TFM) interaction potential. The adjustments of the screening length in the TFM potential, predicted by O'Connor, and the uncorrected Ziegler-Biersack-Littmark (ZBL) potential both yielded inaccurate results for all of the surfaces and incident energies studied. We also provide evidence that, despite their different computational methodologies, the FAN and Kalypso simulation codes generate similar results given identical input parameters for the analysis of 180° backscattering spectra.

Diffusion mechanism of non-interacting Brownian particles through a deformed substrate

NASA Astrophysics Data System (ADS)

Arfa, Lahcen; Ouahmane, Mehdi; El Arroum, Lahcen

2018-02-01

We study the diffusion mechanism of non-interacting Brownian particles through a deformed substrate. The study is done at low temperature for different values of the friction. The deformed substrate is represented by a periodic Remoissenet-Peyrard potential with deformability parameter s. In this potential, the particles (impurity, adatoms…) can diffuse. We ignore the interactions between these mobile particles consider them merely as non-interacting Brownian particles and this system is described by a Fokker-Planck equation. We solve this equation numerically using the matrix continued fraction method to calculate the dynamic structure factor S(q , ω) . From S(q , ω) some relevant correlation functions are also calculated. In particular, we determine the half-width line λ(q) of the peak of the quasi-elastic dynamic structure factor S(q , ω) and the diffusion coefficient D. Our numerical results show that the diffusion mechanism is described, depending on the structure of the potential, either by a simple jump diffusion process with jump length close to the lattice constant a or by a combination of a jump diffusion model with jump length close to lattice constant a and a liquid-like motion inside the unit cell. It shows also that, for different friction regimes and various potential shapes, the friction attenuates the diffusion mechanism. It is found that, in the high friction regime, the diffusion process is more important through a deformed substrate than through a non-deformed one.

Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density-functional theory.

PubMed

Likos, Christos N; Mladek, Bianca M; Gottwald, Dieter; Kahl, Gerhard

2007-06-14

We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive pair potentials with oscillating Fourier transforms. Subsequently, we prove the validity of a bilinear, random-phase density functional for arbitrary inhomogeneous phases of the same systems. On the basis of this functional, we calculate analytically the freezing parameters of the latter. We demonstrate explicitly that the stable crystals feature a lattice constant that is independent of density and whose value is dictated by the position of the negative minimum of the Fourier transform of the pair potential. This property is equivalent with the existence of clusters, whose population scales proportionally to the density. We establish that regardless of the form of the interaction potential and of the location on the freezing line, all cluster crystals have a universal Lindemann ratio Lf=0.189 at freezing. We further make an explicit link between the aforementioned density functional and the harmonic theory of crystals. This allows us to establish an equivalence between the emergence of clusters and the existence of negative Fourier components of the interaction potential. Finally, we make a connection between the class of models at hand and the system of infinite-dimensional hard spheres, when the limits of interaction steepness and space dimension are both taken to infinity in a particularly described fashion.

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties.

PubMed

Wennberg, Christian L; Murtola, Teemu; Hess, Berk; Lindahl, Erik

2013-08-13

The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

Potential energy function for CH3+CH3 ⇆ C2H6: Attributes of the minimum energy path

NASA Astrophysics Data System (ADS)

Robertson, S. H.; Wardlaw, D. M.; Hirst, D. M.

1993-11-01

The region of the potential energy surface for the title reaction in the vicinity of its minimum energy path has been predicted from the analysis of ab initio electronic energy calculations. The ab initio procedure employs a 6-31G** basis set and a configuration interaction calculation which uses the orbitals obtained in a generalized valence bond calculation. Calculated equilibrium properties of ethane and of isolated methyl radical are compared to existing theoretical and experimental results. The reaction coordinate is represented by the carbon-carbon interatomic distance. The following attributes are reported as a function of this distance and fit to functional forms which smoothly interpolate between reactant and product values of each attribute: the minimum energy path potential, the minimum energy path geometry, normal mode frequencies for vibrational motion orthogonal to the reaction coordinate, a torsional potential, and a fundamental anharmonic frequency for local mode, out-of-plane CH3 bending (umbrella motion). The best representation is provided by a three-parameter modified Morse function for the minimum energy path potential and a two-parameter hyperbolic tangent switching function for all other attributes. A poorer but simpler representation, which may be satisfactory for selected applications, is provided by a standard Morse function and a one-parameter exponential switching function. Previous applications of the exponential switching function to estimate the reaction coordinate dependence of the frequencies and geometry of this system have assumed the same value of the range parameter α for each property and have taken α to be less than or equal to the ``standard'' value of 1.0 Å-1. Based on the present analysis this is incorrect: The α values depend on the property and range from ˜1.2 to ˜1.8 Å-1.

Measurement of redox potential in nanoecotoxicological investigations.

PubMed

Tantra, Ratna; Cackett, Alex; Peck, Roger; Gohil, Dipak; Snowden, Jacqueline

2012-01-01

Redox potential has been identified by the Organisation for Economic Co-operation and Development (OECD) as one of the parameters that should be investigated for the testing of manufactured nanomaterials. There is still some ambiguity concerning this parameter, i.e., as to what and how to measure, particularly when in a nanoecotoxicological context. In this study the redox potentials of six nanomaterials (either zinc oxide (ZnO) or cerium oxide (CeO(2))) dispersions were measured using an oxidation-reduction potential (ORP) electrode probe. The particles under testing differed in terms of their particle size and dispersion stability in deionised water and in various ecotox media. The ORP values of the various dispersions and how they fluctuate relative to each other are discussed. Results show that the ORP values are mainly governed by the type of liquid media employed, with little contributions from the nanoparticles. Seawater was shown to have reduced the ORP value, which was attributed to an increase in the concentration of reducing agents such as sulphites or the reduction of dissolved oxygen concentration. The lack of redox potential value contribution from the particles themselves is thought to be due to insufficient interaction of the particles at the Pt electrode of the ORP probe.

Measurement of Redox Potential in Nanoecotoxicological Investigations

PubMed Central

Tantra, Ratna; Cackett, Alex; Peck, Roger; Gohil, Dipak; Snowden, Jacqueline

2012-01-01

Redox potential has been identified by the Organisation for Economic Co-operation and Development (OECD) as one of the parameters that should be investigated for the testing of manufactured nanomaterials. There is still some ambiguity concerning this parameter, i.e., as to what and how to measure, particularly when in a nanoecotoxicological context. In this study the redox potentials of six nanomaterials (either zinc oxide (ZnO) or cerium oxide (CeO2)) dispersions were measured using an oxidation-reduction potential (ORP) electrode probe. The particles under testing differed in terms of their particle size and dispersion stability in deionised water and in various ecotox media. The ORP values of the various dispersions and how they fluctuate relative to each other are discussed. Results show that the ORP values are mainly governed by the type of liquid media employed, with little contributions from the nanoparticles. Seawater was shown to have reduced the ORP value, which was attributed to an increase in the concentration of reducing agents such as sulphites or the reduction of dissolved oxygen concentration. The lack of redox potential value contribution from the particles themselves is thought to be due to insufficient interaction of the particles at the Pt electrode of the ORP probe. PMID:22131988

Mixed micelles of 7,12-dioxolithocholic acid and selected hydrophobic bile acids: interaction parameter, partition coefficient of nitrazepam and mixed micelles haemolytic potential.

PubMed

Poša, Mihalj; Tepavčević, Vesna

2011-09-01

The formation of mixed micelles built of 7,12-dioxolithocholic and the following hydrophobic bile acids was examined by conductometric method: cholic (C), deoxycholic (D), chenodeoxycholic (CD), 12-oxolithocholic (12-oxoL), 7-oxolithocholic (7-oxoL), ursodeoxycholic (UD) and hiodeoxycholic (HD). Interaction parameter (β) in the studied binary mixed micelles had negative value, suggesting synergism between micelle building units. Based on β value, the hydrophobic bile acids formed two groups: group I (C, D and CD) and group II (12-oxoL, 7-oxoL, UD and HD). Bile acids from group II had more negative β values than bile acids from group I. Also, bile acids from group II formed intermolecular hydrogen bonds in aggregates with both smaller (2) and higher (4) aggregation numbers, according to the analysis of their stereochemical (conformational) structures and possible structures of mixed micelles built of these bile acids and 7,12-dioxolithocholic acid. Haemolytic potential and partition coefficient of nitrazepam were higher in mixed micelles built of the more hydrophobic bile acids (C, D, CD) and 7,12-dioxolithocholic acid than in micelles built only of 7,12-dioxolithocholic acid. On the other hand, these mixed micelles still had lower values of haemolytic potential than micelles built of C, D or CD. The mixed micelles that included bile acids: 12-oxoL, 7-oxoL, UD or HD did not significantly differ from the micelles of 7,12-dioxolithocholic acid, observing the values of their haemolytic potential. Copyright © 2011 Elsevier B.V. All rights reserved.

Enantioselective inhibition of carprofen towards UDP-glucuronosyltransferase (UGT) 2B7.

PubMed

Fang, Zhong-Ze; Wang, Haina; Cao, Yun-Feng; Sun, Dong-Xue; Wang, Li-Xuan; Hong, Mo; Huang, Ting; Chen, Jian-Xing; Zeng, Jia

2015-03-01

UDP-glucuronosyltransferases (UGTs)-catalyzed glucuronidation conjugation reaction plays an important role in the elimination of many important clinical drugs and endogenous substances. The present study aims to investigate the enantioselective inhibition of carprofen towards UGT isoforms. In vitro a recombinant UGT isoforms-catalyzed 4-methylumbelliferone (4-MU) glucuronidation incubation mixture was used to screen the inhibition potential of (R)-carprofen and (S)-carprofen towards multiple UGT isoforms. The results showed that (S)-carprofen exhibited stronger inhibition potential than (R)-carprofen towards UGT2B7. However, no significant difference was observed for the inhibition of (R)-carprofen and (S)-carprofen towards other UGT isoforms. Furthermore, the inhibition kinetic behavior was compared for the inhibition of (S)-carprofen and (R)-carprofen towards UGT2B7. A Lineweaver-Burk plot showed that both (S)-carprofen and (R)-carprofen exhibited competitive inhibition towards UGT2B7-catalyzed 4-MU glucuronidation. The inhibition kinetic parameter (Ki ) was calculated to be 7.0 μM and 31.1 μM for (S)-carprofen and (R)-carprofen, respectively. Based on the standard for drug-drug interaction, the threshold for (S)-carprofen and (R)-carprofen to induce a drug-drug interaction is 0.7 μM and 3.1 μM, respectively. In conclusion, enantioselective inhibition of carprofen towards UDP-glucuronosyltransferase (UGT) 2B7 was demonstrated in the present study. Using the in vitro inhibition kinetic parameter, the concentration threshold of (S)-carprofen and (R)-carprofen to possibly induce the drug-drug interaction was obtained. Therefore, clinical monitoring of the plasma concentration of (S)-carprofen is more important than (R)-carprofen to avoid a possible drug-drug interaction between carprofen and the drugs mainly undergoing UGT2B7-catalyzed metabolism. © 2014 Wiley Periodicals, Inc.

Studies of $$\\Lambda n$$ interaction through polarization observables for final-state interactions in exclusive $$\\Lambda$$ photoproduction off the deuteron

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

Ilieva, Yordanka; Cao, Tongtong; Zachariou, Nicholas

2016-06-01

Theoretical studies suggest that experimental observables for hyperon production reactions can place stringent constraints on the free parameters of hyperon-nucleon potentials, which are critical for the understanding of hypernuclear matter and neutron stars. Here we present preliminary experimental results for the polarization observables S, Py, Ox, Oz, Cx, and Cz for final-state interactions (FSI) in exclusive L photoproduction off the deuteron. The observables were obtained from data collected during the E06-103 (g13) experiment with the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B at Jefferson Lab. The g13 experiment ran with unpolarized deuteron target and circularly- and linearly-polarized photon beamsmore » with energies between 0.5 GeV and 2.5 GeV and collected about 51010 events with multiple charged particles in the final state. To select the reaction of interest, the K+ and the L decay products, a proton and a negative pion, were detected in the CLAS. The missing-mass technique was used to identify exclusive hyperon photoproduction events. Final-state interaction events were selected by requesting that the reconstructed neutron has a momentum larger than 200 MeV/c. The large statistics of E06-103 provided statistically meaningful FSI event samples, which allow for the extraction of one- and two-fold differential single- and double-polarization observables. Here we present preliminary results for a set of six observables for photon energies between 0.9 GeV and 2.3 GeV and for several kinematic variables in the Ln center-of-mass frame. Our results are the very first estimates of polarization observables for FSI in hyperon photoproduction and will be used to constrain the free parameters of hyperon-nucleon potentials.« less

Interaction of real and virtual p p bar pairs in J / ψ → p p bar γ (ρ , ω) decays

NASA Astrophysics Data System (ADS)

Milstein, A. I.; Salnikov, S. G.

2017-10-01

The p p bar invariant mass spectra of the processes J / ψ → p p bar ω, J / ψ → p p bar ρ, and J / ψ → p p bar γ close to the p p bar threshold are calculated by means of the N N bar optical potential. The potential model for N N bar interaction in the S10 state is proposed. The parameters of the model are obtained by fitting the cross section of N N bar scattering together with the p p bar invariant mass spectra of the J / ψ decays. Good agreement with the available experimental data is achieved. Using our potential and the Green's function approach we also describe the peak in the η‧π+π- invariant mass spectrum in the decay J / ψ → γη‧π+π- in the energy region near the N N bar threshold.

Ab initio study on the ground and low-lying states of BAlk (Alk = Li, Na, K) molecules.

PubMed

Xiao, Ke-La; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang

2014-10-02

The potential energy curves (PECs) and dipole moment functions of (1)Π, (3)Π, (1)Σ(+), and (3)Σ(+) states of BAlk (Alk = Li, Na, K) are calculated using multireference configuration interaction method and large all-electron basis sets. The effects of inner-shell correlation electron for BAlk are considered. The ro-vibrational energy levels are obtained by solving the Schrödinger equation of nuclear motion based on the ab initio PECs. The spectroscopic parameters are determined from the ro-vibrational levels with Dunham expansion. The PECs are fitted into analytical potential energy functions using the Morse long-range potential function. The dipole moment functions for the states of BAlk are presented. The transition dipole moments for (1)Σ(+) → (1)Π and (3)Σ(+) → (3)Π states of BAlk are obtained. The interactions between the outermost electron of Alk and B 2p electrons for (1)Π, (3)Π, (1)Σ(+), and (3)Σ(+) states are also analyzed, respectively.

Effect of fortification with parsley (Petroselinum crispum Mill.) leaves on the nutraceutical and nutritional quality of wheat pasta.

PubMed

Sęczyk, Łukasz; Świeca, Michał; Gawlik-Dziki, Urszula; Luty, Marcin; Czyż, Jarosław

2016-01-01

This study examines the nutraceutical (phenolics content, antioxidant activity, biological activity) and nutritional potential (starch and protein digestibility) of wheat pasta supplemented with 1-4% of powdered parsley leaves. Compared to the control, the potentially bioaccessible fraction of pasta fortified with 4% parsley leaves was characterized by 67% increased phenolics content, a 146% higher antiradical ability and 220% additional reducing power. Elevation of these parameters in fortified pasta was accompanied by an augmentation of its antiproliferative effect on carcinoma cells, which confirms their biological relevance. Supplementation of pasta had no significant effect on starch digestibility, while negatively affecting protein digestibility (a reduction by about 20% for pasta with a 4% supplement). Electrophoretic and chromatographic analyses indicated the presence of phenolic interactions with proteins and/or digestive enzymes. Fortification improved the nutraceutical and nutritional potential of the studied pasta; however, the final effect is made by many factors, including phenolics-food matrix interactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of Fortification with Fish (Pseudophycis bachus) Powder on Nutritional Quality of Durum Wheat Pasta.

PubMed

Desai, Ajay S; Brennan, Margaret A; Brennan, Charles S

2018-04-17

This paper investigates the nutraceutical (phenolic content and antioxidant activity) and nutritional potential (protein and starch digestibility) of supplementation of durum wheat semolina with 5–20% fish powder ( Pseudophycis bachus ). In general, all enriched pasta with fish powder showed a significant decrease ( p < 0.05) in reducing sugar released during an in vitro digestion, and reductions in standardized area under the curve (AUC) values, compared to control pasta. The potentially bioaccessible fraction of pasta enriched with 20% fish powder (FP) was characterized as having a 177–191% increase in phenolic content and a 145–556% higher antiradical activity. Elevation of these parameters in fortified pasta was accompanied by interaction of wheat starch, protein, and fish powder protein. Supplementation of fish powder also influenced protein digestibility (a reduction from 84.60% for control pasta to 80.80% for pasta with 20% fish powder). Fortification improved the nutraceutical and nutritional potential of the studied pasta with the effects depending on factors including protein-starch-phenolic interactions.

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

PubMed Central

Zhao, Linjie; Sun, Tanlin; Pei, Jianfeng; Ouyang, Qi

2015-01-01

It has been a consensus in cancer research that cancer is a disease caused primarily by genomic alterations, especially somatic mutations. However, the mechanism of mutation-induced oncogenesis is not fully understood. Here, we used the mitochondrial apoptotic pathway as a case study and performed a systematic analysis of integrating pathway dynamics with protein interaction kinetics to quantitatively investigate the causal molecular mechanism of mutation-induced oncogenesis. A mathematical model of the regulatory network was constructed to establish the functional role of dynamic bifurcation in the apoptotic process. The oncogenic mutation enrichment of each of the protein functional domains involved was found strongly correlated with the parameter sensitivity of the bifurcation point. We further dissected the causal mechanism underlying this correlation by evaluating the mutational influence on protein interaction kinetics using molecular dynamics simulation. We analyzed 29 matched mutant–wild-type and 16 matched SNP—wild-type protein systems. We found that the binding kinetics changes reflected by the changes of free energy changes induced by protein interaction mutations, which induce variations in the sensitive parameters of the bifurcation point, were a major cause of apoptosis pathway dysfunction, and mutations involved in sensitive interaction domains show high oncogenic potential. Our analysis provided a molecular basis for connecting protein mutations, protein interaction kinetics, network dynamics properties, and physiological function of a regulatory network. These insights provide a framework for coupling mutation genotype to tumorigenesis phenotype and help elucidate the logic of cancer initiation. PMID:26170328

Potential for the dynamics of pedestrians in a socially interacting group

NASA Astrophysics Data System (ADS)

Zanlungo, Francesco; Ikeda, Tetsushi; Kanda, Takayuki

2014-01-01

We introduce a simple potential to describe the dynamics of the relative motion of two pedestrians socially interacting in a walking group. We show that the proposed potential, based on basic empirical observations and theoretical considerations, can qualitatively describe the statistical properties of pedestrian behavior. In detail, we show that the two-dimensional probability distribution of the relative distance is determined by the proposed potential through a Boltzmann distribution. After calibrating the parameters of the model on the two-pedestrian group data, we apply the model to three-pedestrian groups, showing that it describes qualitatively and quantitatively well their behavior. In particular, the model predicts that three-pedestrian groups walk in a V-shaped formation and provides accurate values for the position of the three pedestrians. Furthermore, the model correctly predicts the average walking velocity of three-person groups based on the velocity of two-person ones. Possible extensions to larger groups, along with alternative explanations of the social dynamics that may be implied by our model, are discussed at the end of the paper.

Density Scaling of Glassy Dynamics and Dynamic Heterogeneities in Glass-forming Liquids.

NASA Astrophysics Data System (ADS)

Hu, Yuan-Chao; Yang, Yong; Wang, Wei-Hua

The discovery of density scaling in strongly correlating systems is an important progress for understanding the dynamic behaviors of supercooled liquids. Here we found for a ternary metallic glass-forming liquid, it is not strongly correlating thermodynamically, but its average dynamics, dynamic heterogeneities and static structure are still well described by density scaling with the same scaling exponent γ. As an intrinsic material constant stemming from the fundamental interatomic interactions, γ is theoretically predicted from the thermodynamic fluctuations of potential energy and the virial. Although γ is conventionally understood merely from the repulsive part of the inter-particle potentials, the strong correlation between γ and the Grüneisen parameter up to the accuracy of the Dulong-Petit approximation demonstrates the important roles of anharmonicity and attractive force of the interatomic potential in governing glass transition of metallic glass-formers. The supercooled dynamics and density scaling behaviors will also be discussed in model glass-forming liquids with tunable attractive potentials to further quantify the nonperturbative roles of attractive interactions. We acknowledge the support from ''Peter Ho Conference Scholarships'' of City University of Hong Kong.

Transitions of interaction outcomes in a uni-directional consumer-resource system

USGS Publications Warehouse

Wang, Y.; DeAngelis, D.L.

2011-01-01

A uni-directional consumer-resource system of two species is analyzed. Our aim is to understand the mechanisms that determine how the interaction outcomes depend on the context of the interaction; that is, on the model parameters. The dynamic behavior of the model is described and, in particular, it is demonstrated that no periodic orbits exist. Then the parameter (factor) space is shown to be divided into four regions, which correspond to the four forms of interaction outcomes; i.e. mutualism, commensalism, parasitism and amensalism. It is shown that the interaction outcomes of the system transition smoothly among these four forms when the parameters of the system are varied continuously. Varying each parameter individually or varying pairs of parameters can also lead to smooth transitions between the interaction outcomes. The analysis leads to both conditions for which each species achieves its maximal density, and situations in which periodic oscillations of the interaction outcomes emerge. ?? 2011 Elsevier Ltd.

Theoretical Probing of Weak Anion-Cation Interactions in Certain Pyridinium-Based Ionic Liquid Ion Pairs and the Application of Molecular Electrostatic Potential in Their Ionic Crystal Density Determination: A Comparative Study Using Density Functional Approach.

PubMed

Joseph, Aswathy; Thomas, Vibin Ipe; Żyła, Gaweł; Padmanabhan, A S; Mathew, Suresh

2018-01-11

A comprehensive study on the structure, nature of interaction, and properties of six ionic pairs of 1-butylpyridinium and 1-butyl-4-methylpyridinium cations in combination with tetrafluoroborate (BF 4 - ), chloride (Cl - ), and bromide (Br - ) anions have been carried out using density functional theory (DFT). The anion-cation interaction energy (ΔE int ), thermochemistry values, theoretical band gap, molecular orbital energy order, DFT-based chemical activity descriptors [chemical potential (μ), chemical hardness (η), and electrophilicity index (ω)], and distribution of density of states (DOS) of these ion pairs were investigated. The ascendancy of the -CH 3 substituent at the fourth position of the 1-butylpyridinium cation ring on the values of ΔE int , theoretical band gap and chemical activity descriptors was evaluated. The ΔE int values were negative for all six ion pairs and were highest for Cl - containing ion pairs. The theoretical band gap value after -CH 3 substitution increased from 3.78 to 3.96 eV (for Cl - ) and from 2.74 to 2.88 eV (for Br - ) and decreased from 4.9 to 4.89 eV (for BF 4 - ). Ion pairs of BF 4 - were more susceptible to charge transfer processes as inferred from their significantly high η values and comparatively small difference in ω value after -CH 3 substitution. The change in η and μ values due to the -CH 3 substituent is negligibly small in all cases except for the ion pairs of Cl - . Critical-point (CP) analyses were carried out to investigate the AIM topological parameters at the interionic bond critical points (BCPs). The RDG isosurface analysis indicated that the anion-cation interaction was dominated by strong H cat ···X ani and C cat ···X ani interactions in ion pairs of Cl - and Br - whereas a weak van der Waal's effect dominated in ion pairs of BF 4 - . The molecular electrostatic potential (MESP)-based parameter ΔΔV min measuring the anion-cation interaction strength showed a good linear correlation with ΔE int for all 1-butylpyridinium ion pairs (R 2 = 0.9918). The ionic crystal density values calculated by using DFT-based MESP showed only slight variations from experimentally reported values.

Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

PubMed

Slepoy, A; Peters, M D; Thompson, A P

2007-11-30

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

PubMed

Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

2011-09-26

The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

PubMed

Berry, David; Widder, Stefanie

2014-01-01

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

Study of the Spin Dependent 3HE-NUCLEUS Interaction at 450 Mev

NASA Astrophysics Data System (ADS)

Kamiya, J.; Hatanaka, K.; Sakemi, Y.; Wakasa, T.; Yoshida, H. P.; Obayashi, E.; Hara, K.; Kitamura, K.; Shimizu, Y.; Fujita, K.; Sakamoto, N.; Shimbara, Y.; Adachi, T.; Sakaguchi, H.; Yosoi, M.; Uchida, M.; Yasuda, Y.; Kawabata, T.; Noro, T.

2003-04-01

Differential cross sections and induced polarizations of 3He+12C, 58Ni, and 90Zr elastic scattering were measured at E3He = 450 MeV. This is the first measurement of the polarization for 3He scattering at intermediate energies. The optical potential parameters including the spin-orbit potential were determined with small uncertainties. The volume integrals per nucleon of the potentials were investigated for 3He and their energy dependence showed the similar behavior to that for protons at intermediate energies. The single folding calculations were compared with the data. The real central and spin-orbit parts of the folded potentials had to be reduced by a few tens of percent in order to reproduce the experimental results.

Gaussian process model for extrapolation of scattering observables for complex molecules: From benzene to benzonitrile

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

Cui, Jie; Krems, Roman V.; Li, Zhiying

2015-10-21

We consider a problem of extrapolating the collision properties of a large polyatomic molecule A–H to make predictions of the dynamical properties for another molecule related to A–H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A–X. We assume that the effect of the −H →−X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can bemore » used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C{sub 6}H{sub 5}CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He — C{sub 6}H{sub 6} collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C{sub 6}H{sub 5}CN with He.« less

Pre-linguistic infants employ complex communicative loops to engage mothers in social exchanges and repair interaction ruptures

PubMed Central

Singer, Magi; Saint Georges, Catherine; Bodeau, Nicolas; Chetouani, Mohamed; Cohen, David; Feldman, Ruth

2018-01-01

Language has long been identified as a powerful communicative tool among humans. Yet, pre-linguistic communication, which is common in many species, is also used by human infants prior to the acquisition of language. The potential communicational value of pre-linguistic vocal interactions between human infants and mothers has been studied in the past decades. With 120 dyads (mothers and three- or six-month-old infants), we used the classical Still Face Paradigm (SFP) in which mothers interact freely with their infants, then refrain from communication (Still Face, SF), and finally resume play. We employed innovative automated techniques to measure infant and maternal vocalization and pause, and dyadic parameters (infant response to mother, joint silence and overlap) and the emotional component of Infant Directed Speech (e-IDS) throughout the interaction. We showed that: (i) during the initial free play mothers use longer vocalizations and more e-IDS when they interact with older infants and (ii) infant boys exhibit longer vocalizations and shorter pauses than girls. (iii) During the SF and reunion phases, infants show marked and sustained changes in vocalizations but their mothers do not and (iv) mother–infant dyadic parameters increase in the reunion phase. Our quantitative results show that infants, from the age of three months, actively participate to restore the interactive loop after communicative ruptures long before vocalizations show clear linguistic meaning. Thus, auditory signals provide from early in life a channel by which infants co-create interactions, enhancing the mother–infant bond. PMID:29410790

Thermodynamic properties of diamond and wurtzite model fluids from computer simulation and thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Zhou, S.; Solana, J. R.

2018-03-01

Monte Carlo NVT simulations have been performed to obtain the thermodynamic and structural properties and perturbation coefficients up to third order in the inverse temperature expansion of the Helmholtz free energy of fluids with potential models proposed in the literature for diamond and wurtzite lattices. These data are used to analyze performance of a coupling parameter series expansion (CPSE). The main findings are summarized as follows, (1) The CPSE provides accurate predictions of the first three coefficient in the inverse temperature expansion of Helmholtz free energy for the potential models considered and the thermodynamic properties of these fluids are predicted more accurately when the CPSE is truncated at second or third order. (2) The Barker-Henderson (BH) recipe is appropriate for determining the effective hard sphere diameter for strongly repulsive potential cores, but its performance worsens with increasing the softness of the potential core. (3) For some thermodynamic properties the first-order CPSE works better for the diamond potential, whose tail is dominated by repulsive interactions, than for the potential, whose tail is dominated by attractive interactions. However, the first-order CPSE provides unsatisfactory results for the excess internal energy and constant-volume excess heat capacity for the two potential models.

Rotationally mediated selective adsorption as a probe of isotropic and anisotropic molecule. Surface interaction potentials: HD(J)/Ag(111)

NASA Astrophysics Data System (ADS)

Uy, C. F.; Hogg, C. S.; Cowin, J. P.; Whaley, K. B.; Light, J. C.; Sibener, S. J.

1982-08-01

Rotationally mediated selective adsorption scattering resonances are used to make an experimental and theoretical study of the laterally averaged interaction potential between HD and a weakly corrugated system, Ag(111). The experimentally observed resonances determine the vibrational levels of the HD/Ag(111) physisorption potential as a function of bound rotational state. These vibrational levels show J-dependent shifts due to the orientational anisotropy of the potential. Exact quantum scattering calculations using a full laterally averaged potential of the form V sub o(z,0) = v sub o (z) (1 + beta P sub 2 (cos theta)) have been carried out to obtain rotationally inelastic transition probabilities. Experimental and theoretical resonance energies are compared for two forms of v sub o(z), a Morse and a variable exponent potential, as a function of Beta, and are found to be very close to the first order perturbed energies of a free rotor in bound states of v sub o(z). Both potential forms give equally good fits to the data, yielding an optimum value of the asymmetry parameter, Beta approx. -0.05. The determination of Beta is relatively insensitive to small changes in the v sub o(z) well depth.

Instant preheating in quintessential inflation with α -attractors

NASA Astrophysics Data System (ADS)

Dimopoulos, Konstantinos; Wood, Leonora Donaldson; Owen, Charlotte

2018-03-01

We investigate a compelling model of quintessential inflation in the context of α -attractors, which naturally result in a scalar potential featuring two flat regions; the inflationary plateau and the quintessential tail. The "asymptotic freedom" of α -attractors, near the kinetic poles, suppresses radiative corrections and interactions, which would otherwise threaten to lift the flatness of the quintessential tail and cause a 5th-force problem respectively. Since this is a nonoscillatory inflation model, we reheat the Universe through instant preheating. The parameter space is constrained by both inflation and dark energy requirements. We find an excellent correlation between the inflationary observables and model predictions, in agreement with the α -attractors setup. We also obtain successful quintessence for natural values of the parameters. Our model predicts potentially sizeable tensor perturbations (at the level of 1%) and a slightly varying equation of state for dark energy, to be probed in the near future.

Physical scales in the Wigner–Boltzmann equation

PubMed Central

Nedjalkov, M.; Selberherr, S.; Ferry, D.K.; Vasileska, D.; Dollfus, P.; Querlioz, D.; Dimov, I.; Schwaha, P.

2013-01-01

The Wigner–Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner–Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. It is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner–Boltzmann evolution is demonstrated. PMID:23504194

A Gibbs point field model for the spatial pattern of coronary capillaries

NASA Astrophysics Data System (ADS)

Karch, R.; Neumann, M.; Neumann, F.; Ullrich, R.; Neumüller, J.; Schreiner, W.

2006-09-01

We propose a Gibbs point field model for the pattern of coronary capillaries in transverse histologic sections from human hearts, based on the physiology of oxygen supply from capillaries to tissue. To specify the potential energy function of the Gibbs point field, we draw on an analogy between the equation of steady-state oxygen diffusion from an array of parallel capillaries to the surrounding tissue and Poisson's equation for the electrostatic potential of a two-dimensional distribution of identical point charges. The influence of factors other than diffusion is treated as a thermal disturbance. On this basis, we arrive at the well-known two-dimensional one-component plasma, a system of identical point charges exhibiting a weak (logarithmic) repulsive interaction that is completely characterized by a single dimensionless parameter. By variation of this parameter, the model is able to reproduce many characteristics of real capillary patterns.

Measurements and calculations of H2-broadening and shift parameters of water vapour transitions of the ν1 + ν2 + ν3 band

NASA Astrophysics Data System (ADS)

Petrova, T. M.; Solodov, A. M.; Solodov, A. A.; Deichuli, V. M.; Starikov, V. I.

2018-05-01

The water vapour line broadening and shifting for 97 lines in the ν1 + ν2 + ν3 band induced by hydrogen pressure are measured with Bruker IFS 125 HR FTIR spectrometer. The measurements were performed at room temperature, at the spectral resolution of 0.01 cm-1 and in a wide pressure range of H2. The calculations of the broadening γ and shift δ coefficients were performed in the semi-classical method framework with use of an effective vibrationally depended interaction potential. Two potential parameters were optimised to improve the quality of calculations. Good agreements with measured broadening coefficients were achieved. The comparison of calculated broadening coefficients γ with the previous measurements is discussed. The analytical expressions that reproduce these coefficients for rotational, ν2, ν1, and ν3 vibrational bands are presented.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

PubMed

Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

Symmetry breaking in (gravitating) scalar field models describing interacting boson stars and Q-balls

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

Brihaye, Yves; Caebergs, Thierry; Hartmann, Betti

2009-09-15

We investigate the properties of interacting Q-balls and boson stars that sit on top of each other in great detail. The model that describes these solutions is essentially a (gravitating) two-scalar field model where both scalar fields are complex. We construct interacting Q-balls or boson stars with arbitrarily small charges but finite mass. We observe that in the interacting case--where the interaction can be either due to the potential or due to gravity--two types of solutions exist for equal frequencies: one for which the two-scalar fields are equal, but also one for which the two-scalar fields differ. This constitutes amore » symmetry breaking in the model. While for Q-balls asymmetric solutions have always corresponding symmetric solutions and are thus likely unstable to decay to symmetric solutions with lower energy, there exists a parameter regime for interacting boson stars, where only asymmetric solutions exist. We present the domain of existence for two interacting nonrotating solutions as well as for solutions describing the interaction between rotating and nonrotating Q-balls and boson stars, respectively.« less

Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay.

PubMed

Hudry, Bruno; Viala, Séverine; Graba, Yacine; Merabet, Samir

2011-01-28

Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels. Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners. Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development.

Gas-liquid phase coexistence and crossover behavior of binary ionic fluids with screened Coulomb interactions.

PubMed

Patsahan, O

2014-06-01

We study the effects of an interaction range on the gas-liquid phase diagram and the crossover behavior of a simple model of ionic fluids: an equimolar binary mixture of equisized hard spheres interacting through screened Coulomb potentials which are repulsive between particles of the same species and attractive between particles of different species. Using the collective variables theory, we find explicit expressions for the relevant coefficients of the effective φ{4} Ginzburg-Landau Hamiltonian in a one-loop approximation. Within the framework of this approximation, we calculate the critical parameters and gas-liquid phase diagrams for varying inverse screening length z. Both the critical temperature scaled by the Yukawa potential contact value and the critical density rapidly decrease with an increase of the interaction range (a decrease of z) and then for z<0.05 they slowly approach the values found for a restricted primitive model (RPM). We find that gas-liquid coexistence region reduces with an increase of z and completely vanishes at z≃2.78. Our results clearly show that an increase in the interaction range leads to a decrease of the crossover temperature. For z≃0.01, the crossover temperature is the same as for the RPM.

Establishing the importance of oil-membrane interactions on the transmembrane diffusion of physicochemically diverse compounds.

PubMed

Najib, Omaima N; Martin, Gary P; Kirton, Stewart B; Sallam, Al-Sayed; Murnane, Darragh

2016-06-15

The diffusion process through a non-porous barrier membrane depends on the properties of the drug, vehicle and membrane. The aim of the current study was to investigate whether a series of oily vehicles might have the potential to interact to varying degrees with synthetic membranes and to determine whether any such interaction might affect the permeation of co-formulated permeants: methylparaben (MP); butylparaben (BP) or caffeine (CF). The oils (isopropyl myristate (IPM), isohexadecane (IHD), hexadecane (HD), oleic acid (OA) and liquid paraffin (LP)) and membranes (silicone, high density polyethylene and polyurethane) employed in the study were selected such that they displayed a range of different structural, and physicochemical properties. Diffusion studies showed that many of the vehicles were not inert and did interact with the membranes resulting in a modification of the permeants' flux when corrected for membrane thickness (e.g. normalized flux of MP increased from 1.25±0.13μgcm(-1)h(-1) in LP to 17.94±0.25μgcm(-1)h(-1)in IPM). The oils were sorbed differently to membranes (range of weight gain: 2.2±0.2% for polyurethane with LP to 105.6±1.1% for silicone with IHD). Membrane interaction was apparently dependent upon the physicochemical properties including; size, shape, flexibility and the Hansen solubility parameter values of both the membranes and oils. Sorbed oils resulted in modified permeant diffusion through the membranes. No simple correlation was found to exist between the Hansen solubility parameters of the oils or swelling of the membrane and the normalized fluxes of the three compounds investigated. More sophisticated modelling would appear to be required to delineate and quantify the key molecular parameters of membrane, permeant and vehicle compatibility and their interactions of relevance to membrane permeation. Copyright © 2016 Elsevier B.V. All rights reserved.

Simplified TiO2 force fields for studies of its interaction with biomolecules

NASA Astrophysics Data System (ADS)

Luan, Binquan; Huynh, Tien; Zhou, Ruhong

2015-06-01

Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

Long-range Self-interacting Dark Matter in the Sun

NASA Astrophysics Data System (ADS)

Chen, Jing; Liang, Zheng-Liang; Wu, Yue-Liang; Zhou, Yu-Feng

2015-12-01

We investigate the implications of the long-rang self-interaction on both the self-capture and the annihilation of the self-interacting dark matter (SIDM) trapped in the Sun. Our discussion is based on a specific SIDM model in which DM particles self-interact via a light scalar mediator, or Yukawa potential, in the context of quantum mechanics. Within this framework, we calculate the self-capture rate across a broad region of parameter space. While the self-capture rate can be obtained separately in the Born regime with perturbative method, and in the classical limits with the Rutherford formula, our calculation covers the gap between in a non-perturbative fashion. Besides, the phenomenology of both the Sommerfeld-enhanced s- and p-wave annihilation of the solar SIDM is also involved in our discussion. Moreover, by combining the analysis of the Super-Kamiokande (SK) data and the observed DM relic density, we constrain the nuclear capture rate of the DM particles in the presence of the dark Yukawa potential. The consequence of the long-range dark force on probing the solar SIDM turns out to be significant if the force-carrier is much lighter than the DM particle, and a quantitative analysis is provided.

Accurate calculation and modeling of the adiabatic connection in density functional theory

NASA Astrophysics Data System (ADS)

Teale, A. M.; Coriani, S.; Helgaker, T.

2010-04-01

Using a recently implemented technique for the calculation of the adiabatic connection (AC) of density functional theory (DFT) based on Lieb maximization with respect to the external potential, the AC is studied for atoms and molecules containing up to ten electrons: the helium isoelectronic series, the hydrogen molecule, the beryllium isoelectronic series, the neon atom, and the water molecule. The calculation of AC curves by Lieb maximization at various levels of electronic-structure theory is discussed. For each system, the AC curve is calculated using Hartree-Fock (HF) theory, second-order Møller-Plesset (MP2) theory, coupled-cluster singles-and-doubles (CCSD) theory, and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, expanding the molecular orbitals and the effective external potential in large Gaussian basis sets. The HF AC curve includes a small correlation-energy contribution in the context of DFT, arising from orbital relaxation as the electron-electron interaction is switched on under the constraint that the wave function is always a single determinant. The MP2 and CCSD AC curves recover the bulk of the dynamical correlation energy and their shapes can be understood in terms of a simple energy model constructed from a consideration of the doubles-energy expression at different interaction strengths. Differentiation of this energy expression with respect to the interaction strength leads to a simple two-parameter doubles model (AC-D) for the AC integrand (and hence the correlation energy of DFT) as a function of the interaction strength. The structure of the triples-energy contribution is considered in a similar fashion, leading to a quadratic model for the triples correction to the AC curve (AC-T). From a consideration of the structure of a two-level configuration-interaction (CI) energy expression of the hydrogen molecule, a simple two-parameter CI model (AC-CI) is proposed to account for the effects of static correlation on the AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.

Association of pharmacokinetic and metabolic parameters derived using simultaneous PET/MRI: Initial findings and impact on response evaluation in breast cancer.

PubMed

Jena, Amarnath; Taneja, Sangeeta; Singh, Aru; Negi, Pradeep; Mehta, Shashi Bhushan; Ahuja, Aashim; Singhal, Manish; Sarin, Ramesh

2017-07-01

To study relationships among pharmacokinetic and 18 F-fluorodeoxyglucose ( 18 F-FDG) PET parameters obtained through simultaneous PET/MRI in breast cancer patients and evaluate their combined potential for response evaluation. The study included 41 breast cancer patients for correlation study and 9 patients (pre and post therapy) for response evaluation. All patients underwent simultaneous PET/MRI with dedicated breast imaging. Pharmacokinetic parameters and PET parameters for tumor were derived using an in- house developed and vendor provided softwares respectively. Relationships between SUV and pharmacokinetic parameters and clinical as well as histopathologic parameters were evaluated using Spearman correlation analysis. Response to chemotherapy was derived as percentage reduction in size and in parameters post therapy. Significant correlations were observed between SUVmean, max, peak, TLG with K trans (ρ=0.446, 0.417, 0.491, 0.430; p≤0.01); with Kep(ρ=0.303, ρ=0.315, ρ=0.319; p≤0.05); and with iAUC(ρ=0.401, ρ=0.410, ρ=0.379; p≤0.05, p≤0.01). The ratio of ve/iAUC showed significant negative correlation to SUVmean, max, peak and TLG (ρ=0.420, 0.446, 0.443, 0.426; p≤0.01). Ability of SUV as well as pharmacokinetic parameters to predict response to therapy matched the RECIST criteria in 9 out of 11 lesions in 9 patients. Maximum post therapy quantitative reduction was observed in SUVpeak, TLG and K trans . Simultaneous PET/MRI enables illustration of close interactions between glucose metabolism and pharmacokinetic parameters in breast cancer patients and potential of their simultaneity in response assessment to therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Qian, Ping

2006-08-14

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Identification of New Potential Scientific and Technology Areas for DoD Application. Summary of Activities

DTIC Science & Technology

1986-07-31

designer will be able to more rapid- ly assemble a total software package from perfected modules that can be easily de - bugged or replaced with more...antinuclear interactions e. gravitational effects of antimatter 2. possible machine parameters and lattice design 3. electron and stochastic cooling needs 4...implementation, reliability requirements; development of design environments and of experimental methodology; technology transfer methods from

Interlayer interaction and mechanical properties in multi-layer graphene, Boron-Nitride, Aluminum-Nitride and Gallium-Nitride graphene-like structure: A quantum-mechanical DFT study

NASA Astrophysics Data System (ADS)

Ghorbanzadeh Ahangari, Morteza; Fereidoon, A.; Hamed Mashhadzadeh, Amin

2017-12-01

In present study, we investigated mechanical, electronic and interlayer properties of mono, bi and 3layer of Boron-Nitride (B-N), Aluminum-Nitride (Al-N) and Gallium-Nitride (Ga-N) graphene sheets and compared these results with results obtained from carbonic graphenes (C-graphenes). For reaching this purpose, first we optimized the geometrical parameters of these graphenes by using density functional theory (DFT) method. Then we calculated Young's modulus of graphene sheet by compressing and then elongating these sheets in small increment. Our results indicates that Young's modulus of graphenes didn't changed obviously by increasing the number of layer sheet. We also found that carbonic graphene has greatest Young's modulus among another mentioned sheets because of smallest equilibrium distance between its elements. Next we modeled the van der Waals interfacial interaction exist between two sheets with classical spring model by using general form of Lennard-Jones (L-J) potential for all of mentioned graphenes. For calculating L-J parameters (ε and σ), the potential energy between layers of mentioned graphene as a function of the separation distance was plotted. Moreover, the density of states (DOS) are calculated to understand the electronic properties of these systems better.

Disorder effects in the evolution from BCS to BEC superfluidity

NASA Astrophysics Data System (ADS)

Han, Li; de Melo, Carlos A. R. Sa

2009-03-01

We discuss the effects of disorder on the critical temperature of superfluids during the evolution from BCS to BEC. For s-wave superfluids we find that the critical temperature is weakly affected by disorder in the BCS regime as described in Anderson’s theorem, even less affected by disorder at zero chemical potential (near unitarity), but strongly affected by disorder in the BEC regime, where Anderson's theorem does not apply. This suggests that the superfluid is more robust to the effects of disorder at the interaction parameter where the chemical potential vanishes (close to unitarity). We construct a three dimensional phase diagram of critical temperature, disorder and interaction parameter [1], and show that there are regions of localized superfluidity, as well as insulating regions due to Anderson localization of fermions (BCS regime) and molecular bosons (BEC regime). The phase diagram for higher angular momentum (e.g. p-wave and d-wave) is also analyzed, where the effects of disorder are much more dramatic in the BCS regime in comparison to the s-wave case because pair breaking is strong, while the disorder effects in BEC regime are similar to what occurs in the s-wave case. [1] Li Han, C. A. R. Sa de Melo, arXiv:0812.xxxx

A four-layer model for the heat budget of homogeneous land surfaces

NASA Technical Reports Server (NTRS)

Choudhury, B. J.; Monteith, J. L.

1988-01-01

The present model envisions the heat balance of a homogeneous land surface in terms of available energy, a set of driving potentials, and parameters for the physical state of the soil and vegetation. Two unique features of the model are: (1) the expression of the interaction of evaporation from the soil and from foliage by changes in the value of the saturation vapor pressure deficit of air in the canopy (the conclusions of this interaction being consistent with field observations); and (2) the treatment of sensible and latent heat exchange between the atmosphere and a soil consisting of two discrete layers.

Electron trajectory evaluation in laser-plasma interaction for effective output beam

NASA Astrophysics Data System (ADS)

Zobdeh, P.; Sadighi-Bonabi, R.; Afarideh, H.

2010-06-01

Using the ellipsoidal cavity model, the quasi-monoenergetic electron output beam in laser-plasma interaction is described. By the cavity regime the quality of electron beam is improved in comparison with those generated from other methods such as periodic plasma wave field, spheroidal cavity regime and plasma channel guided acceleration. Trajectory of electron motion is described as hyperbolic, parabolic or elliptic paths. We find that the self-generated electron bunch has a smaller energy width and more effective gain in energy spectrum. Initial condition for the ellipsoidal cavity is determined by laser-plasma parameters. The electron trajectory is influenced by its position, energy and cavity electrostatic potential.

Helium Atom Scattering from C2H6, F2HCCH3, F3CCH2F and C2F6 in Crossed Molecular Beams

NASA Astrophysics Data System (ADS)

Hammer, Markus; Seidel, Wolfhart

1997-10-01

Rotationally unresolved differential cross sections were measured in crossed molecular beam experiments by scattering Helium atoms from Ethane, 1,1-Difluoroethane, 1,1,1,2-Tetrafluoroethane and Hexafluoroethane. The damping of observed diffraction oscillations was used to extract anisotropic interaction potentials for these scattering systems applying the infinite order sudden approximation (IOSA). Binary macroscopic parameters such as second heterogeneous virial coefficients and the coefficients of diffusion and viscosity were computed from these potentials and compared to results from macroscopic experiments.

Electrical resistivity of Al-Cu liquid binary alloy

NASA Astrophysics Data System (ADS)

Thakor, P. P.; Patel, J. J.; Sonvane, Y. A.; Jani, A. R.

2013-06-01

Present paper deals with the electrical resistivity (ρ) of liquid Al-Cu binary alloy. To describe electron-ion interaction we have used our parameter free model potential along with Faber-Ziman formulation combined with Ashcroft-Langreth (AL) partial structure factor. To see the influence of exchange and correlation effect, Hartree, Taylor and Sarkar et al local field correlation functions are used. From present results, it is seen that good agreements between present results and experimental data have been achieved. Lastly we conclude that our model potential successfully produces the data of electrical resistivity (ρ) of liquid Al-Cu binary alloy.

Parameter optimization of a hydrologic model in a snow-dominated basin using a modular Python framework

NASA Astrophysics Data System (ADS)

Volk, J. M.; Turner, M. A.; Huntington, J. L.; Gardner, M.; Tyler, S.; Sheneman, L.

2016-12-01

Many distributed models that simulate watershed hydrologic processes require a collection of multi-dimensional parameters as input, some of which need to be calibrated before the model can be applied. The Precipitation Runoff Modeling System (PRMS) is a physically-based and spatially distributed hydrologic model that contains a considerable number of parameters that often need to be calibrated. Modelers can also benefit from uncertainty analysis of these parameters. To meet these needs, we developed a modular framework in Python to conduct PRMS parameter optimization, uncertainty analysis, interactive visual inspection of parameters and outputs, and other common modeling tasks. Here we present results for multi-step calibration of sensitive parameters controlling solar radiation, potential evapo-transpiration, and streamflow in a PRMS model that we applied to the snow-dominated Dry Creek watershed in Idaho. We also demonstrate how our modular approach enables the user to use a variety of parameter optimization and uncertainty methods or easily define their own, such as Monte Carlo random sampling, uniform sampling, or even optimization methods such as the downhill simplex method or its commonly used, more robust counterpart, shuffled complex evolution.

Deriving percentage study weights in multi-parameter meta-analysis models: with application to meta-regression, network meta-analysis and one-stage individual participant data models.

PubMed

Riley, Richard D; Ensor, Joie; Jackson, Dan; Burke, Danielle L

2017-01-01

Many meta-analysis models contain multiple parameters, for example due to multiple outcomes, multiple treatments or multiple regression coefficients. In particular, meta-regression models may contain multiple study-level covariates, and one-stage individual participant data meta-analysis models may contain multiple patient-level covariates and interactions. Here, we propose how to derive percentage study weights for such situations, in order to reveal the (otherwise hidden) contribution of each study toward the parameter estimates of interest. We assume that studies are independent, and utilise a decomposition of Fisher's information matrix to decompose the total variance matrix of parameter estimates into study-specific contributions, from which percentage weights are derived. This approach generalises how percentage weights are calculated in a traditional, single parameter meta-analysis model. Application is made to one- and two-stage individual participant data meta-analyses, meta-regression and network (multivariate) meta-analysis of multiple treatments. These reveal percentage study weights toward clinically important estimates, such as summary treatment effects and treatment-covariate interactions, and are especially useful when some studies are potential outliers or at high risk of bias. We also derive percentage study weights toward methodologically interesting measures, such as the magnitude of ecological bias (difference between within-study and across-study associations) and the amount of inconsistency (difference between direct and indirect evidence in a network meta-analysis).

Two-Drug Antimicrobial Chemotherapy: A Mathematical Model and Experiments with Mycobacterium marinum

PubMed Central

Ankomah, Peter; Levin, Bruce R.

2012-01-01

Multi-drug therapy is the standard-of-care treatment for tuberculosis. Despite this, virtually all studies of the pharmacodynamics (PD) of mycobacterial drugs employed for the design of treatment protocols are restricted to single agents. In this report, mathematical models and in vitro experiments with Mycobacterium marinum and five antimycobacterial drugs are used to quantitatively evaluate the pharmaco-, population and evolutionary dynamics of two-drug antimicrobial chemotherapy regimes. Time kill experiments with single and pairs of antibiotics are used to estimate the parameters and evaluate the fit of Hill-function-based PD models. While Hill functions provide excellent fits for the PD of each single antibiotic studied, rifampin, amikacin, clarithromycin, streptomycin and moxifloxacin, two-drug Hill functions with a unique interaction parameter cannot account for the PD of any of the 10 pairs of these drugs. If we assume two antibiotic-concentration dependent functions for the interaction parameter, one for sub-MIC and one for supra-MIC drug concentrations, the modified biphasic Hill function provides a reasonably good fit for the PD of all 10 pairs of antibiotics studied. Monte Carlo simulations of antibiotic treatment based on the experimentally-determined PD functions are used to evaluate the potential microbiological efficacy (rate of clearance) and evolutionary consequences (likelihood of generating multi-drug resistance) of these different drug combinations as well as their sensitivity to different forms of non-adherence to therapy. These two-drug treatment simulations predict varying outcomes for the different pairs of antibiotics with respect to the aforementioned measures of efficacy. In summary, Hill functions with biphasic drug-drug interaction terms provide accurate analogs for the PD of pairs of antibiotics and M. marinum. The models, experimental protocols and computer simulations used in this study can be applied to evaluate the potential microbiological and evolutionary efficacy of two-drug therapy for any bactericidal antibiotics and bacteria that can be cultured in vitro. PMID:22253599

Search for Screened Interactions Associated with Dark Energy below the 100 μm Length Scale.

PubMed

Rider, Alexander D; Moore, David C; Blakemore, Charles P; Louis, Maxime; Lu, Marie; Gratta, Giorgio

2016-09-02

We present the results of a search for unknown interactions that couple to mass between an optically levitated microsphere and a gold-coated silicon cantilever. The scale and geometry of the apparatus enable a search for new forces that appear at distances below 100  μm and which would have evaded previous searches due to screening mechanisms. The data are consistent with electrostatic backgrounds and place upper limits on the strength of new interactions at <0.1  fN in the geometry tested. For the specific example of a chameleon interaction with an inverse power law potential, these results exclude matter couplings β>5.6×10^{4} in the region of parameter space where the self-coupling Λ≳5  meV and the microspheres are not fully screened.

Evidence of a slight nuclear transparency in the alpha-nucleus systems

DOE PAGES

Chamon, L. C.; Gasques, L. R.; Nobre, G. P. A.; ...

2015-02-19

In earlier works, we proposed a model for the nuclear potential of the α + α and α + ¹²C systems. In addition, this theoretical model successfully described data related to the elastic and inelastic scattering processes as well as resonances that correspond to the capture reaction channel. In the present work, we extend the same model to obtain bare nuclear potentials for several α-nucleus systems. We adopt this parameter-free interaction to analyze fusion, elastic, and inelastic scattering data within the context of the coupled-channel formalism. Our results indicate that, for these systems, the absorption of flux of the elasticmore » channel at internal distances of interaction is not complete. In addition, we present new experimental angular distributions for the 2⁺ inelastic target excitation of α on ¹²⁰ ,¹³⁰Te.« less

A possible four-phase coexistence in a single-component system

NASA Astrophysics Data System (ADS)

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-08-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger-Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids.

Solitonlike pulses along a modified Noguchi nonlinear electrical network with second-neighbor interactions: Analytical studies

NASA Astrophysics Data System (ADS)

Kengne, E.; Liu, W. M.

2018-05-01

A modified lossless nonlinear Noguchi transmission network with second-neighbor interactions is considered. In the semidiscrete limit, we apply the reductive perturbation method and show that the dynamics of modulated waves propagating through the network are governed by an NLS equation with linear external potential. Classes of exact solitonic solutions of this network equation are derived, proving possible transmission of both bright and dark solitonlike pulses through the network. The effects of both the coupling second-neighbor parameter L3 and the strength λ of the linear potential on the dynamics of modulated waves through the network are investigated. One of the main results of our work is that with the introduction of the second neighbors in the network, two solitary signals, either two bright solitary signals or one bright and one dark solitary signal, may simultaneously propagate at the same frequency through the network.

Binary nanoparticle superlattices of soft-particle systems

DOE PAGES

Travesset, Alex

2015-08-04

The solid-phase diagram of binary systems consisting of particles of diameter σ A=σ and σ B=γσ (γ≤1) interacting with an inverse p = 12 power law is investigated as a paradigm of a soft potential. In addition to the diameter ratio γ that characterizes hard-sphere models, the phase diagram is a function of an additional parameter that controls the relative interaction strength between the different particle types. Phase diagrams are determined from extremes of thermodynamic functions by considering 15 candidate lattices. In general, it is shown that the phase diagram of a soft repulsive potential leads to the morphological diversitymore » observed in experiments with binary nanoparticles, thus providing a general framework to understand their phase diagrams. In addition, particular emphasis is shown to the two most successful crystallization strategies so far: evaporation of solvent from nanoparticles with grafted hydrocarbon ligands and DNA programmable self-assembly.« less

A possible four-phase coexistence in a single-component system

PubMed Central

Akahane, Kenji; Russo, John; Tanaka, Hajime

2016-01-01

For different phases to coexist in equilibrium at constant temperature T and pressure P, the condition of equal chemical potential μ must be satisfied. This condition dictates that, for a single-component system, the maximum number of phases that can coexist is three. Historically this is known as the Gibbs phase rule, and is one of the oldest and venerable rules of thermodynamics. Here we make use of the fact that, by varying model parameters, the Gibbs phase rule can be generalized so that four phases can coexist even in single-component systems. To systematically search for the quadruple point, we use a monoatomic system interacting with a Stillinger–Weber potential with variable tetrahedrality. Our study indicates that the quadruple point provides flexibility in controlling multiple equilibrium phases and may be realized in systems with tunable interactions, which are nowadays feasible in several soft matter systems such as patchy colloids. PMID:27558452

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

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de; Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de

In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial chargesmore » within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.« less

Coagulation-flocculation mechanisms in wastewater treatment plants through zeta potential measurements.

PubMed

López-Maldonado, E A; Oropeza-Guzman, M T; Jurado-Baizaval, J L; Ochoa-Terán, A

2014-08-30

Based on the polyelectrolyte-contaminant physical and chemical interactions at the molecular level, this article analyzed and discussed the coagulation-flocculation and chemical precipitation processes in order to improve their efficiency. Bench experiments indicate that water pH, polyelectrolyte (PE) dosing strategy and cationic polyelectrolyte addition are key parameters for the stability of metal-PE complexes. The coagulation-flocculation mechanism is proposed based on zeta potential (ζ) measurement as the criteria to define the electrostatic interaction between pollutants and coagulant-flocculant agents. Polyelectrolyte and wastewater dispersions are exposed to an electrophoretic effect to determine ζ. Finally, zeta potential values are compared at pH 9, suggesting the optimum coagulant dose at 162mg/L polydadmac and 67mg/L of flocculant, since a complete removal of TSS and turbidity is achieved. Based on the concentration of heavy metals (0.931mg/L Sn, 0.7mg/L Fe and 0.63mg/L Pb), treated water met the Mexican maximum permissible limits. In addition, the treated water has 45mg O2/L chemical oxygen demand (COD) and 45mg C/L total organic carbon (TOC). The coagulation-flocculation mechanism is proposed taking into account both: zeta potential (ζ)-pH measurement and chemical affinity, as the criteria to define the electrostatic and chemical interaction between pollutants and polyelectrolytes. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding.

PubMed

Cole, Daniel J; Payne, Mike C; Csányi, Gábor; Spearing, S Mark; Colombi Ciacchi, Lucio

2007-11-28

We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.

Implementing quantum gates through scattering between a static and a flying qubit

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

Cordourier-Maruri, G.; Coss, R. de; Ciccarello, F.

2010-11-15

We investigate whether a two-qubit quantum gate can be implemented in a scattering process involving a flying and a static qubit. To this end, we focus on a paradigmatic setup made out of a mobile particle and a quantum impurity, whose respective spin degrees of freedom couple to each other during a one-dimensional scattering process. Once a condition for the occurrence of quantum gates is derived in terms of spin-dependent transmission coefficients, we show that this can be actually fulfilled through the insertion of an additional narrow potential barrier. An interesting observation is that under resonance conditions this procedure enablesmore » a gate only for isotropic Heisenberg (exchange) interactions and fails for an XY interaction. We show the existence of parameter regimes for which gates able to establish a maximum amount of entanglement can be implemented. The gates are found to be robust to variations of the optimal parameters.« less

Governing Influence of Thermodynamic and Chemical Equilibria on the Interfacial Properties in Complex Fluids.

PubMed

Harikrishnan, A R; Dhar, Purbarun; Gedupudi, Sateesh; Das, Sarit K

2018-04-12

We propose a comprehensive analysis and a quasi-analytical mathematical formalism to predict the surface tension and contact angles of complex surfactant-infused nanocolloids. The model rests on the foundations of the interaction potentials for the interfacial adsorption-desorption dynamics in complex multicomponent colloids. Surfactant-infused nanoparticle-laden interface problems are difficult to deal with because of the many-body interactions and interfaces involved at the meso-nanoscales. The model is based on the governing role of thermodynamic and chemical equilibrium parameters in modulating the interfacial energies. The influence of parameters such as the presence of surfactants, nanoparticles, and surfactant-capped nanoparticles on interfacial dynamics is revealed by the analysis. Solely based on the knowledge of interfacial properties of independent surfactant solutions and nanocolloids, the same can be deduced for complex surfactant-based nanocolloids through the proposed approach. The model accurately predicts the equilibrium surface tension and contact angle of complex nanocolloids available in the existing literature and present experimental findings.

Magnetosonic waves interactions in a spin-1/2 degenerate quantum plasma

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

Li, Sheng-Chang, E-mail: lsc1128lsc@126.com; Han, Jiu-Ning

2014-03-15

We investigate the magnetosonic waves and their interactions in a spin-1/2 degenerate quantum plasma. With the help of the extended Poincaré-Lighthill-Kuo perturbation method, we derive two Korteweg-de Vries-Burgers equations to describe the magnetosonic waves. The parameter region where exists magnetosonic waves and the phase diagram of the compressive and rarefactive solitary waves with different plasma parameters are shown. We further explore the effects of quantum diffraction, quantum statistics, and electron spin magnetization on the head-on collisions of magnetosonic solitary waves. We obtain the collision-induced phase shifts (trajectory changes) analytically. Both for the compressive and rarefactive solitary waves, it is foundmore » that the collisions only lead to negative phase shifts. Our present study should be useful to understand the collective phenomena related to the magnetosonic wave collisions in degenerate plasmas like those in the outer shell of massive white dwarfs as well as to the potential applications of plasmas.« less

The Rock Engineering System (RES) applied to landslide susceptibility zonation of the northeastern flank of Etna: methodological approach and results

NASA Astrophysics Data System (ADS)

Apuani, Tiziana; Corazzato, Claudia

2015-04-01

Ground deformations in the northeastern flank of Etna are well known. Despite only a few landslide events have been documented, these have significantly involved and damaged lifelines and buildings. These events are mainly related to the activity of the volcano-tectonic structures and associated seismicity, as in the case of the 2002 reactivation of the Presa landslide during an increased activity of the Pernicana fault system. In order to highlight the areal distribution of potentially unstable slopes based on a detailed, site-specific study of the factors responsible for landslide, and to ultimately contribute to risk management, a landslide susceptibility analysis of the northeastern flank of Etna in the Pernicana area was carried out, and a susceptibility map at 1:10.000 scale was produced, extending over an area of 168 km2. Different methods are proposed in the literature to obtain the regional distribution of potentially unstable slopes, depending on the problem scale, the slope dynamic evolution in the geological context, and the availability of data. Among semi-quantitative approaches, the present research combines the Rock Engineering System (RES) methodology with parameter zonation mapping in a GIS environment. The RES method represents a structured approach to manage a high number of interacting factors involved in the instability problem. A numerically coded, site-specific interaction matrix (IM) analyzes the cause-effect relationship in these factors, and calculates the degree of interactivity of each parameter, normalized by the overall interactivity of the system (weight factor). In the specific Etna case, the considered parameters are: slope attitude, lithotechnical properties (lithology, structural complexity, soil and rock mass quality), land use, tectonic structures, seismic activity (horizontal acceleration) and hydrogeological conditions (groundwater and drainage). Thematic maps are prepared at 1:10.000 scale for each of these parameters, and instability-related numerical ratings are assigned to classes. An instability index map is then produced by assigning, to each areal elementary cell (in our case a 10 m pixel), the sum of the products of each weight factor to the normalized parameter rating coming from each input zonation map. This map is then opportunely classified in landslide susceptibility classes (expressed as a percentage), enabling to discriminate areas prone to instability. Overall, the study area is characterized by a low propensity to slope instability. Few areas have an instability index of more than 45% of the theoretical maximum imposed by the matrix. These are located in the few steep slopes associated with active faults, and strongly depending on the seismic activity. Some other areas correspond to limited outcrops characterized by significantly reduced lithotechnical properties (low shear strength). The produced susceptibility map combines the application of the RES with the parameter zonation, following methodology which had never been applied up to now in in active volcanic environments. The comparison of the results with the ground deformation evidence coming from monitoring networks suggests the validity of the approach.

Interaction-induced effects on Bose-Hubbard parameters

NASA Astrophysics Data System (ADS)

Kremer, Mark; Sachdeva, Rashi; Benseny, Albert; Busch, Thomas

2017-12-01

We study the effects of repulsive on-site interactions on the broadening of the localized Wannier functions used for calculating the parameters to describe ultracold atoms in optical lattices. For this, we replace the common single-particle Wannier functions, which do not contain any information about the interactions, by two-particle Wannier functions obtained from an exact solution which takes the interactions into account. We then use these interaction-dependent basis functions to calculate the Bose-Hubbard model parameters, showing that they are substantially different both at low and high lattice depths from the ones calculated using single-particle Wannier functions. Our results suggest that density effects are not negligible for many parameter ranges and need to be taken into account in metrology experiments.

Observations on the interaction of nanomaterials with bacteria

NASA Astrophysics Data System (ADS)

Raja, P. M.; Ajayan, P. M.; Nalamasu, O.; Sharma, A.

2006-05-01

Large scale commercial manufacturing of nanomaterials raises the important issue of their environmental fate. With increased production (estimated to be in million gallon range) the nanomaterial interactions with environmental microbial ecology would be significant. However, there are scant studies that have addressed this concern. It is therefore essential to experimentally determine some fundamental parameters to ascertain any environmental stresses related to microbiological interactions of nanomaterials. There are concerns that such an interaction may be similar to the biogeochemical interactions of asbestos fibers, which continues to be an alarming environmental issue. Carbon nanotubes (CNTs) are newly emerging nanomaterials, with a wide range of potential electronic and medical applications. Though CNTs are dimensionally similar to the mineral fibers, they differ morphologically, and can possess different surface chemistries, capable of complex and varied biological interactions within the environment. In this study, we present experimental data that show discernible effects on microbial morphology, biofilm formation, substrate consumption rates and growth of Escherichia coli in the presence of carbon nanotubes with the aim of developing a fundamental understanding of the environmental implications of CNT-microbial interactions.

Bioinformatic prediction and in vivo validation of residue-residue interactions in human proteins

NASA Astrophysics Data System (ADS)

Jordan, Daniel; Davis, Erica; Katsanis, Nicholas; Sunyaev, Shamil

2014-03-01

Identifying residue-residue interactions in protein molecules is important for understanding both protein structure and function in the context of evolutionary dynamics and medical genetics. Such interactions can be difficult to predict using existing empirical or physical potentials, especially when residues are far from each other in sequence space. Using a multiple sequence alignment of 46 diverse vertebrate species we explore the space of allowed sequences for orthologous protein families. Amino acid changes that are known to damage protein function allow us to identify specific changes that are likely to have interacting partners. We fit the parameters of the continuous-time Markov process used in the alignment to conclude that these interactions are primarily pairwise, rather than higher order. Candidates for sites under pairwise epistasis are predicted, which can then be tested by experiment. We report the results of an initial round of in vivo experiments in a zebrafish model that verify the presence of multiple pairwise interactions predicted by our model. These experimentally validated interactions are novel, distant in sequence, and are not readily explained by known biochemical or biophysical features.

Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions.

PubMed

Takemoto, Kazuhiro; Aie, Kazuki

2017-05-25

Host-pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. We re-evaluated the importance of the reverse ecology method for evaluating host-pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host-pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host-pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host-pathogen interactions.

Tuning the phase diagram of colloid-polymer mixtures via Yukawa interactions

NASA Astrophysics Data System (ADS)

González García, Álvaro; Tuinier, Remco

2016-12-01

Theory that predicts the phase behavior of interacting Yukawa spheres in a solution containing nonadsorbing polymer is presented. Our approach accounts for multiple overlap of depletion zones. It is found that additional Yukawa interactions beyond hard core interactions strongly affect the location and presence of coexistence regions and phase states. The theoretical phase diagrams are compared with Monte Carlo simulations. The agreement between the two approaches supports the validity of the theoretical approximations made and confirms that, by choosing the parameters of the interaction potentials, tuning of the binodals is possible. The critical end point characterizes the phase diagram topology. It is demonstrated how an additional Yukawa interaction shifts this point with respect to the hard sphere case. Provided a certain depletant-to-colloid size ratio for which a stable colloidal gas-liquid phase coexistence takes place for hard spheres, added direct interactions turn this into a metastable gas-liquid equilibrium. The opposite case, the induction of a stable gas-liquid coexistence where only fluid-solid was present for hard spheres, is also reported.

Development and modulation of intrinsic membrane properties control the temporal precision of auditory brain stem neurons.

PubMed

Franzen, Delwen L; Gleiss, Sarah A; Berger, Christina; Kümpfbeck, Franziska S; Ammer, Julian J; Felmy, Felix

2015-01-15

Passive and active membrane properties determine the voltage responses of neurons. Within the auditory brain stem, refinements in these intrinsic properties during late postnatal development usually generate short integration times and precise action-potential generation. This developmentally acquired temporal precision is crucial for auditory signal processing. How the interactions of these intrinsic properties develop in concert to enable auditory neurons to transfer information with high temporal precision has not yet been elucidated in detail. Here, we show how the developmental interaction of intrinsic membrane parameters generates high firing precision. We performed in vitro recordings from neurons of postnatal days 9-28 in the ventral nucleus of the lateral lemniscus of Mongolian gerbils, an auditory brain stem structure that converts excitatory to inhibitory information with high temporal precision. During this developmental period, the input resistance and capacitance decrease, and action potentials acquire faster kinetics and enhanced precision. Depending on the stimulation time course, the input resistance and capacitance contribute differentially to action-potential thresholds. The decrease in input resistance, however, is sufficient to explain the enhanced action-potential precision. Alterations in passive membrane properties also interact with a developmental change in potassium currents to generate the emergence of the mature firing pattern, characteristic of coincidence-detector neurons. Cholinergic receptor-mediated depolarizations further modulate this intrinsic excitability profile by eliciting changes in the threshold and firing pattern, irrespective of the developmental stage. Thus our findings reveal how intrinsic membrane properties interact developmentally to promote temporally precise information processing. Copyright © 2015 the American Physiological Society.

Do mobile phones pose a potential risk to autonomic modulation of the heart?

PubMed

Barutcu, Irfan; Esen, Ali Metin; Kaya, Dayimi; Turkmen, Muhsin; Karakaya, Osman; Saglam, Mustafa; Melek, Mehmet; Çelik, Ataç; Kilit, Celal; Onrat, Ersel; Kirma, Cevat

2011-11-01

It has long been speculated that mobile phones may interact with the cardiac devices and thereby cardiovascular system may be a potential target for the electromagnetic fields emitted by the mobile phones. Therefore, the present study was designed to test possible effects of radiofrequency waves emitted by digital mobile phones on cardiac autonomic modulation by short-time heart rate variability (HRV) analysis. A total of 20 healthy young subjects were included to the study. All participants were rested in supine position at least for 15 minutes on a comfortable bed, and then time and frequency domain HRV parameters were recorded at baseline in supine position for 5 minutes. After completion of baseline records, by using a mobile GSM (Global System for Mobile Communication) phone, HRV parameters were recorded at turned off mode, at turned on mode, and at calling mode over 5 minutes periods for each stage. Neither time nor frequency domain HRV parameters altered significantly during off mode compare to their baseline values. Also, neither time nor frequency domain HRV parameters altered significantly during turned on and calling mode compared to their baseline values. Short-time exposure to electromagnetic fields emitted by mobile phone does not affect cardiac autonomic modulation in healthy subjects.

Experimental Proof for the Role of Nonlinear Photoionization in Plasmonic Phototherapy.

PubMed

Minai, Limor; Zeidan, Adel; Yeheskely-Hayon, Daniella; Yudovich, Shimon; Kviatkovsky, Inna; Yelin, Dvir

2016-07-13

Targeting individual cells within a heterogeneous tissue is a key challenge in cancer therapy, encouraging new approaches for cancer treatment that complement the shortcomings of conventional therapies. The highly localized interactions triggered by focused laser beams promise great potential for targeting single cells or small cell clusters; however, most laser-tissue interactions often involve macroscopic processes that may harm healthy nearby tissue and reduce specificity. Specific targeting of living cells using femtosecond pulses and nanoparticles has been demonstrated promising for various potential therapeutic applications including drug delivery via optoporation, drug release, and selective cell death. Here, using an intense resonant femtosecond pulse and cell-specific gold nanorods, we show that at certain irradiation parameters cell death is triggered by nonlinear plasmonic photoionization and not by thermally driven processes. The experimental results are supported by a physical model for the pulse-particle-medium interactions. A good correlation is found between the calculated total number and energy of the generated free electrons and the observed cell death, suggesting that femtosecond photoionization plays the dominant role in cell death.

Vibration-rotation interactions and ring-puckering in 3,3-dimethyl oxetane by microwave spectroscopy

NASA Astrophysics Data System (ADS)

López, Juan C.; Lesarri, Alberto G.; Villamañán, Rosa M.; Alonso, Josél.

1990-06-01

Ring puckering in 3,3-dimethyl oxetane has been investigated using microwave spectroscopy. Microwave spectra of the ground state, the first six ring-puckering excited states, and nine excited states of the methyl groups' deformation vibrations have been observed. The μa electric dipole moment component has been determined as 2.03(3) D from Stark-effect measurements. The vibrational dependence of the rotational constants is consistent with the ring-puckering potential function derived by Duckett et al. ( J. Mol. Spectrosc.69, 159-165 (1978)). Coriolis coupling interactions have been observed and are satisfactorily accounted for with a quartic centrifugal distortion Hamiltonian. The vibrational dependence of the centrifugal distortion constants has been analyzed using the theory developed by Creswell and Mills. In order to reproduce the experimental value of the vibration-rotation interaction parameter, {δμ ab}/{δQ}, a dynamical model allowing the rocking of the CH 3CCH 3 group should be used. The equilibrium ring puckering angle calculated with this model and the ring-puckering potential function is 17.5°.

LSST Survey Data: Models for EPO Interaction

NASA Astrophysics Data System (ADS)

Olsen, J. K.; Borne, K. D.

2007-12-01

The potential for education and public outreach with the Large Synoptic Survey Telescope is as far reaching as the telescope itself. LSST data will be available to the public, giving anyone with a web browser a movie-like window on the Universe. The LSST project is unique in designing its data management and data access systems with the public and community users in mind. The enormous volume of data to be generated by LSST is staggering: 30 Terabytes per night, 10 Petabytes per year. The final database of extracted science parameters from the images will also be enormous -- 50-100 Petabytes -- a rich gold mine for data mining and scientific discovery potential. LSST will also generate 100,000 astronomical alerts per night, for 10 years. The LSST EPO team is examining models for EPO interaction with the survey data, particularly in how the community (amateurs, teachers, students, and general public) can participate in the discovery process. We will outline some of our models of community interaction for inquiry-based science using the LSST survey data, and we invite discussion on these topics.

Water-vapor foreign-continuum absorption in the 8-12 and 3-5 μm atmospheric windows

NASA Astrophysics Data System (ADS)

Klimeshina, T. E.; Rodimova, O. B.

2015-08-01

The frequency and temperature dependence of the water vapor-nitrogen continuum in the 8-12 and 3-5 μm spectral regions obtained experimentally by CAVIAR and NIST is described with the use of the line contour constructed on the basis of asymptotic line shape theory. The parameters of the theory found from fitting the calculated values of the absorption coefficient to the pertinent experimental data enter into the expression for the classical potential describing the center-of-mass motion of interacting molecules and into the expression for the quantum potential of two interacting molecules. The frequency behavior of the line wing contours appears to depend on the band the lines of which make a major contribution to the absorption in a given spectral interval. The absorption coefficients in the wings of the band in question calculated with the line contours obtained for other bands are outside of experimental errors. The distinction in the line wing behavior may be explained by the difference in the quantum energies of molecules interacting in different vibrational states.

Understanding the Phase Behavior of Tetrahydrofuran + Carbon Dioxide, + Methane, and + Water Binary Mixtures from the SAFT-VR Approach.

PubMed

Míguez, J M; Piñeiro, M M; Algaba, J; Mendiboure, B; Torré, J P; Blas, F J

2015-11-05

The high-pressure phase diagrams of the tetrahydrofuran(1) + carbon dioxide(2), + methane(2), and + water(2) mixtures are examined using the SAFT-VR approach. Carbon dioxide molecule is modeled as two spherical segments tangentially bonded, water is modeled as a spherical segment with four associating sites to represent the hydrogen bonding, methane is represented as an isolated sphere, and tetrahydrofuran is represented as a chain of m tangentially bonded spherical segments. Dispersive interactions are modeled using the square-well intermolecular potential. In addition, two different molecular model mixtures are developed to take into account the subtle balance between water-tetrahydrofuran hydrogen-bonding interactions. The polar and quadrupolar interactions present in water, tetrahydrofuran, and carbon dioxide are treated in an effective way via square-well potentials of variable range. The optimized intermolecular parameters are taken from the works of Giner et al. (Fluid Phase Equil. 2007, 255, 200), Galindo and Blas (J. Phys. Chem. B 2002, 106, 4503), Patel et al. (Ind. Eng. Chem. Res. 2003, 42, 3809), and Clark et al. (Mol. Phys. 2006, 104, 3561) for tetrahydrofuran, carbon dioxide, methane, and water, respectively. The phase diagrams of the binary mixtures exhibit different types of phase behavior according to the classification of van Konynenburg and Scott, ranging from types I, III, and VI phase behavior for the tetrahydrofuran(1) + carbon dioxide(2), + methane(2), and + water(2) binary mixtures, respectively. This last type is characterized by the presence of a Bancroft point, positive azeotropy, and the so-called closed-loop curves that represent regions of liquid-liquid immiscibility in the phase diagram. The system exhibits lower critical solution temperatures (LCSTs), which denote the lower limit of immiscibility together with upper critical solution temperatures (UCSTs). This behavior is explained in terms of competition between the incompatibility with the alkyl parts of the tetrahydrofuran ring chain and the hydrogen bonding between water and the ether group. A minimum number of unlike interaction parameters are fitted to give the optimal representation of the most representative features of the binary phase diagrams. In the particular case of tetrahydrofuran(1) + water(2), two sets of intermolecular potential model parameters are proposed to describe accurately either the hypercritical point associated with the closed-loop liquid-liquid immiscibility region or the location of the mixture lower- and upper-critical end-points. The theory is not only able to predict the type of phase behavior of each mixture, but also provides a reasonably good description of the global phase behavior whenever experimental data are available.

Characteristics of Turbulent Airflow Deduced from Rapid Surface Thermal Fluctuations: An Infrared Surface Anemometer

NASA Astrophysics Data System (ADS)

Aminzadeh, Milad; Breitenstein, Daniel; Or, Dani

2017-12-01

The intermittent nature of turbulent airflow interacting with the surface is readily observable in fluctuations of the surface temperature resulting from the thermal imprints of eddies sweeping the surface. Rapid infrared thermography has recently been used to quantify characteristics of the near-surface turbulent airflow interacting with the evaporating surfaces. We aim to extend this technique by using single-point rapid infrared measurements to quantify properties of a turbulent flow, including surface exchange processes, with a view towards the development of an infrared surface anemometer. The parameters for the surface-eddy renewal (α and β ) are inferred from infrared measurements of a single-point on the surface of a heat plate placed in a wind tunnel with prescribed wind speeds and constant mean temperatures of the surface. Thermally-deduced parameters are in agreement with values obtained from standard three-dimensional ultrasonic anemometer measurements close to the plate surface (e.g., α = 3 and β = 1/26 (ms)^{-1} for the infrared, and α = 3 and β = 1/19 (ms)^{-1} for the sonic-anemometer measurements). The infrared-based turbulence parameters provide new insights into the role of surface temperature and buoyancy on the inherent characteristics of interacting eddies. The link between the eddy-spectrum shape parameter α and the infrared window size representing the infrared field of view is investigated. The results resemble the effect of the sampling height above the ground in sonic anemometer measurements, which enables the detection of larger eddies with higher values of α . The physical basis and tests of the proposed method support the potential for remote quantification of the near-surface momentum field, as well as scalar-flux measurements in the immediate vicinity of the surface.

Variation in cassava germplasm for tolerance to post-harvest physiological deterioration.

PubMed

Venturini, M T; Santos, L R; Vildoso, C I A; Santos, V S; Oliveira, E J

2016-05-06

Tolerant varieties can effectively control post-harvest physiological deterioration (PPD) of cassava, although knowledge on the genetic variability and inheritance of this trait is needed. The objective of this study was to estimate genetic parameters and identify sources of tolerance to PPD and their stability in cassava accessions. Roots from 418 cassava accessions, grown in four independent experiments, were evaluated for PPD tolerance 0, 2, 5, and 10 days post-harvest. Data were transformed into area under the PPD-progress curve (AUP-PPD) to quantify tolerance. Genetic parameters, stability (Si), adaptability (Ai), and the joint analysis of stability and adaptability (Zi) were obtained via residual maximum likelihood (REML) and best linear unbiased prediction (BLUP) methods. Variance in the genotype (G) x environment (E) interaction and genotypic variance were important for PPD tolerance. Individual broad-sense heritability (hg(2)= 0.38 ± 0.04) and average heritability in accessions (hmg(2)= 0.52) showed high genetic control of PPD tolerance. Genotypic correlation of AUP-PPD in different experiments was of medium magnitude (ȓgA = 0.42), indicating significant G x E interaction. The predicted genotypic values o f G x E free of interaction (û + ĝi) showed high variation. Of the 30 accessions with high Zi, 19 were common to û + ĝi, Si, and Ai parameters. The genetic gain with selection of these 19 cassava accessions was -55.94, -466.86, -397.72, and -444.03% for û + ĝi, Si, Ai, and Zi, respectively, compared with the overall mean for each parameter. These results demonstrate the variability and potential of cassava germplasm to introduce PPD tolerance in commercial varieties.

Analytic functions for potential energy curves, dipole moments, and transition dipole moments of LiRb molecule.

PubMed

You, Yang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Liu, Wen-Wang; Wang, Li-Zhi

2016-01-15

The analytic potential energy functions (APEFs) of the X(1)Σ(+), 2(1)Σ(+), a(3)Σ(+), and 2(3)Σ(+) states of the LiRb molecule are obtained using Morse long-range potential energy function with damping function and nonlinear least-squares method. These calculations were based on the potential energy curves (PECs) calculated using the multi-reference configuration interaction (MRCI) method. The reliability of the APEFs is confirmed using the curves of their first and second derivatives. By using the obtained APEFs, the rotational and vibrational energy levels of the states are determined by solving the Schrödinger equation of nuclear movement. The spectroscopic parameters, which are deduced using Dunham expansion, and the obtained rotational and vibrational levels are compared with the reported theoretical and experimental values. The correlation effect of the electrons of the inner shell remarkably improves the results compared with the experimental spectroscopic parameters. For the first time, the APEFs for the dipole moments and transition dipole moments of the states have been determined based on the curves obtained from the MRCI calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamic Light Scattering and Zeta Potential of Colloidal Mixtures of Amelogenin and Hydroxyapatite in Calcium and Phosphate Rich Ionic Milieus

PubMed Central

Uskoković, Vuk; Odsinada, Roselyn; Djordjevic, Sonia; Habelitz, Stefan

2011-01-01

The concept of zeta-potential has been used for more than a century as a basic parameter in controlling the stability of colloidal suspensions, irrespective of the nature of their particulate ingredients – organic or inorganic. There are prospects that self-assembly of peptide species and the protein-mineral interactions related to biomineralization may be controlled using this fundamental physicochemical parameter. In this study, we have analyzed the particle size and zeta-potential of the full-length recombinant human amelogenin (rH174), the main protein of the developing enamel matrix, in the presence of calcium and phosphate ions and hydroxyapatite (HAP) particles. As calcium and phosphate salts are introduced to rH174 sols in increments, zeta-potential of the rH174 nanospheres is more affected by negatively charged ions, suggesting their tendency to locate within the double charge layer. Phosphate ions have a more pronounced effect on both the zeta-potential and aggregation propensity of rH174 nanospheres compared to calcium ions. The isoelectric point of amelogenin was independent on the ionic strength of the solution and the concentration of calcium and/or phosphate ions. Whereas rH174 shows a higher affinity for phosphate than for calcium, HAP attracts both of these ions to the shear plane of the double layer. The parallel size and zeta-potential analysis of HAP and rH174 colloidal mixtures indicated that at pH 7.4, despite both HAP and rH174 particles being negatively charged, rH174 adsorbs well onto HAP particles. The process is slower at pH 7.4 than at pH 4.5 when the HAP surface is negatively charged and the rH174 nanosphere carries an overall positive charge. The results presented hereby demonstrate that electrostatic interactions can affect the kinetics of the adsorption of rH174 onto HAP. PMID:21146151

Genetic potential of common bean progenies obtained by different breeding methods evaluated in various environments.

PubMed

Pontes Júnior, V A; Melo, P G S; Pereira, H S; Melo, L C

2016-09-02

Grain yield is strongly influenced by the environment, has polygenic and complex inheritance, and is a key trait in the selection and recommendation of cultivars. Breeding programs should efficiently explore the genetic variability resulting from crosses by selecting the most appropriate method for breeding in segregating populations. The goal of this study was to evaluate and compare the genetic potential of common bean progenies of carioca grain for grain yield, obtained by different breeding methods and evaluated in different environments. Progenies originating from crosses between lines and CNFC 7812 and CNFC 7829 were replanted up to the F 7 generation using three breeding methods in segregating populations: population (bulk), bulk within F 2 progenies, and single-seed descent (SSD). Fifteen F 8 progenies per method, two controls (BRS Estilo and Perola), and the parents were evaluated in a 7 x 7 simple lattice design, with plots of two 4-m rows. The tests were conducted in 10 environments in four States of Brazil and in three growing seasons in 2009 and 2010. Genetic parameters including genetic variance, heritability, variance of interaction, and expected selection gain were estimated. Genetic variability among progenies and the effect of progeny-environment interactions were determined for the three methods. The breeding methods differed significantly due to the effects of sampling procedures on the progenies and due to natural selection, which mainly affected the bulk method. The SSD and bulk methods provided populations with better estimates of genetic parameters and more stable progenies that were less affected by interaction with the environment.

Collaborative GIS for flood susceptibility mapping: An example from Mekong river basin of Viet Nam

NASA Astrophysics Data System (ADS)

Thanh, B.

2016-12-01

Flooding is one of the most dangerous natural disasters in Vietnam. Floods have caused serious damages to people and made adverse impact on social economic development across the country, especially in lower river basin where there is high risk of flooding as consequences of the climate change and social activities. This paper presents a collaborative platform of a combination of an interactive web-GIS framework and a multi-criteria evaluation (MCE) tool. MCE is carried out in server side through web interface, in which parameters used for evaluation are groups into three major categories, including (1) climatic factor: precipitation, typhoon frequency, temperature, humidity (2) physiographic data: DEM, topographic wetness index, NDVI, stream power index, soil texture, distance to river (3) social factor: NDBI, land use pattern. Web-based GIS is based on open-source technology that includes an information page, a page for MCE tool that users can interactively alter parameters in flood susceptible mapping, and a discussion page. The system is designed for local participation in prediction of the flood risk magnitude under impacts of natural processes and human intervention. The proposed flood susceptibility assessment prototype was implemented in the Mekong river basin, Viet Nam. Index images were calculated using Landsat data, and other were collected from authorized agencies. This study shows the potential to combine web-GIS and spatial analysis tool to flood hazard risk assessment. The combination can be a supportive solution that potentially assists the interaction between stakeholders in information exchange and in disaster management, thus provides for better analysis, control and decision-making.

Benefit-Risk Monitoring of Vaccines Using an Interactive Dashboard: A Methodological Proposal from the ADVANCE Project.

PubMed

Bollaerts, Kaatje; De Smedt, Tom; Donegan, Katherine; Titievsky, Lina; Bauchau, Vincent

2018-03-26

New vaccines are launched based on their benefit-risk (B/R) profile anticipated from clinical development. Proactive post-marketing surveillance is necessary to assess whether the vaccination uptake and the B/R profile are as expected and, ultimately, whether further public health or regulatory actions are needed. There are several, typically not integrated, facets of post-marketing vaccine surveillance: the surveillance of vaccination coverage, vaccine safety, effectiveness and impact. With this work, we aim to assess the feasibility and added value of using an interactive dashboard as a potential methodology for near real-time monitoring of vaccine coverage and pre-specified health benefits and risks of vaccines. We developed a web application with an interactive dashboard for B/R monitoring. The dashboard is demonstrated using simulated electronic healthcare record data mimicking the introduction of rotavirus vaccination in the UK. The interactive dashboard allows end users to select certain parameters, including expected vaccine effectiveness, age groups, and time periods and allows calculation of the incremental net health benefit (INHB) as well as the incremental benefit-risk ratio (IBRR) for different sets of preference weights. We assessed the potential added value of the dashboard by user testing amongst a range of stakeholders experienced in the post-marketing monitoring of vaccines. The dashboard was successfully implemented and demonstrated. The feedback from the potential end users was generally positive, although reluctance to using composite B/R measures was expressed. The use of interactive dashboards for B/R monitoring is promising and received support from various stakeholders. In future research, the use of such an interactive dashboard will be further tested with real-life data as opposed to simulated data.

Radical-Driven Silicon Surface Passivation for Organic-Inorganic Hybrid Photovoltaics

NASA Astrophysics Data System (ADS)

Chandra, Nitish

The advent of metamaterials has increased the complexity of possible light-matter interactions, creating gaps in knowledge and violating various commonly used approximations and rendering some common mathematical frameworks incomplete. Our forward scattering experiments on metallic shells and cavities have created a need for a rigorous geometry-based analysis of scattering problems and more rigorous current distribution descriptions in the volume of the scattering object. In order to build an accurate understanding of these interactions, we have revisited the fundamentals of Maxwell's equations, electromagnetic potentials and boundary conditions to build a bottom-up geometry-based analysis of scattering. Individual structures or meta-atoms can be designed to localize the incident electromagnetic radiation in order to create a change in local constitutive parameters and possible nonlinear responses. Hence, in next generation engineered materials, an accurate determination of current distribution on the surface and in the structure's volume play an important role in describing and designing desired properties. Multipole expansions of the exact current distribution determined using principles of differential geometry provides an elegant way to study these local interactions of meta-atoms. The dynamics of the interactions can be studied using the behavior of the polarization and magnetization densities generated by localized current densities interacting with the electromagnetic potentials associated with the incident waves. The multipole method combined with propagation of electromagnetic potentials can be used to predict a large variety of linear and nonlinear physical phenomena. This has been demonstrated in experiments that enable the analog detection of sources placed at subwavelength separation by using time reversal of observed signals. Time reversal is accomplished by reversing the direction of the magnetic dipole in bianisotropic metasurfaces while simultaneously providing a method to reduce the losses often observed when light interacts with meta-structures.

r.avaflow v1, an advanced open-source computational framework for the propagation and interaction of two-phase mass flows

NASA Astrophysics Data System (ADS)

Mergili, Martin; Fischer, Jan-Thomas; Krenn, Julia; Pudasaini, Shiva P.

2017-02-01

r.avaflow represents an innovative open-source computational tool for routing rapid mass flows, avalanches, or process chains from a defined release area down an arbitrary topography to a deposition area. In contrast to most existing computational tools, r.avaflow (i) employs a two-phase, interacting solid and fluid mixture model (Pudasaini, 2012); (ii) is suitable for modelling more or less complex process chains and interactions; (iii) explicitly considers both entrainment and stopping with deposition, i.e. the change of the basal topography; (iv) allows for the definition of multiple release masses, and/or hydrographs; and (v) serves with built-in functionalities for validation, parameter optimization, and sensitivity analysis. r.avaflow is freely available as a raster module of the GRASS GIS software, employing the programming languages Python and C along with the statistical software R. We exemplify the functionalities of r.avaflow by means of two sets of computational experiments: (1) generic process chains consisting in bulk mass and hydrograph release into a reservoir with entrainment of the dam and impact downstream; (2) the prehistoric Acheron rock avalanche, New Zealand. The simulation results are generally plausible for (1) and, after the optimization of two key parameters, reasonably in line with the corresponding observations for (2). However, we identify some potential to enhance the analytic and numerical concepts. Further, thorough parameter studies will be necessary in order to make r.avaflow fit for reliable forward simulations of possible future mass flow events.

Computational Modeling of Hydroxypropyl-Methylcellulose Acetate Succinate (HPMCAS) and Phenytoin Interactions: A Systematic Coarse-Graining Approach.

PubMed

Huang, Wenjun; Mandal, Taraknath; Larson, Ronald G

2017-03-06

We present coarse-grained (CG) force fields for hydroxypropyl-methylcellulose acetate succinate (HPMCAS) polymers and the drug molecule phenytoin using a bead/stiff spring model, with each bead representing a HPMCAS monomer or monomer side group (hydroxypropyl acetyl, acetyl, or succinyl) or a single phenytoin ring. We obtain the bonded and nonbonded interaction parameters in our CG model using the RDFs from atomistic simulations of short HPMCAS model oligomers (20-mer) and atomistic simulations of phenytoin molecules. The nonbonded interactions are modeled using a LJ 12-6 potential, with separate parameters for each monomer substitution type, which allows heterogeneous polymer chains to be modeled. The cross interaction terms between the polymer and phenytoin CG beads are obtained explicitly from atomistic level polymer-phenytoin simulations, rather than from mixing rules. We study the solvation behavior of 50-mer and 100-mer polymer chains and find chain-length-dependent aggregation. We also compare the phenytoin CG force field developed in this work with that in Mandal et al. (Soft Matter, 2016, 12, 8246-8255) and conclude both are suitable for studying the interaction between polymer and drug in solvated solid dispersion formulation, in the absence of drug crystallization. Finally, we present simulations of heterogeneous HPMCAS model polymer chains and phenytoin molecules. Polymer and drug form a complex in a short period of simulation time due to strong intermolecular interactions. Moreover, the protonated polymer chains are more effective than deprotonated ones in inhibiting the drug aggregation in the polymer-drug complex.

Interactions of molecules and the properties of crystals

NASA Astrophysics Data System (ADS)

McConnell, Thomas Daniel Leigh

In this thesis the basic theory of the lattice dynamics of molecular crystals is considered, with particular reference to the specific case of linear molecules. The objective is to carry out a critical investigation of a number of empirical potentials as models for real systems. Suitable coordinates are introduced, in particular vibrational coordinates which are used to describe the translational and rotational modes of the free molecule. The Taylor expansion of the intermolecular potential is introduced and its terms considered, in particular the (first-order) equilibrium conditions for such a system and the (second-order) lattice vibrations. The elastic properties are also considered, in particular with reference to the specific case of rhombohedral crystals. The compressibility and a number of conditions for elastic stability are introduced. The total intermolecular interaction potential is divided into three components using perturbation methods, the electrostatic energy, the repulsion energy and the dispersion energy. A number of models are introduced for these various components. The induction energy is neglected. The electrostatic interaction is represented by atomic multipole and molecular multipole models. The repulsion and dispersion energies are modelled together in a central interaction potential, either the Lennard-Jones atom-atom potential or the anisotropic Berne-Pechukas molecule-molecule potential. In each case, the Taylor expansion coefficients, used to calculate the various molecular properties, are determined. An algorithm is described which provides a relatively simple method for calculating cartesian tensors, which are found in the Taylor expansion coefficients of the multipolar potentials. This proves to be particularly useful from a computational viewpoint, both in terms of programming and calculating efficiency. The model system carbonyl sulphide is introduced and its lattice properties are described. Suitable parameters for potentials used to model the system are discussed and the simplifications to the Taylor expansion coefficients due to crystal symmetry are detailed. Four potential parameters are chosen to be fitted to four lattice properties, representing zero, first and second order Taylor expansion coefficients. The supplementary tests of a given fitted potential are detailed. A number of forms for the electrostatic interaction of carbonyl sulphide are considered, each combined with a standard atom-atom potential. The success of the molecular octupole model is considered and the inability of more complex electrostatic potentials to improve on this simple model is noted. The anisotropic Berne-Pechukas potential, which provides an increased estimate of the compressibility is considered as being an improvement on the various atom-atom potentials. The effect of varying the exponents in the atom-atom (or molecule-molecule) potential, representing a systematic variation of the repulsion and dispersion energy models, is examined and a potential which is able to reproduce all of the given lattice properties for carbonyl sulphide is obtained. The molecular crystal of cyanogen iodide is investigated. Superficially it is similar to the crystal of carbonyl sulphide and the potentials used with success for the latter are applied to cyanogen iodide to determine whether they are equally as effective models for this molecule. These potentials are found to be far less successful, in all cases yielding a number of unrealistic results. Reasons for the failure of the model are considered, in particular the 3 differences between the electrostatic properties of the two molecules are discussed. It is concluded that some of the simplifications which proved satisfactory for carbonyl sulphide are invalid for simple extension to the case of cyanogen iodide. A first estimate of the differences in the electrostatic properties is attempted, calculating the induction energies of the two molecules. The assumption that the induction energy may be neglected is justified for the case of carbonyl sulphide but found to be far less satisfactory for cyanogen iodide. Finally details of ab initio calculations are outlined. The amount of experimental data available for the electrostatic properties of the two molecules under consideration is relatively small and the experimental data which is available is supplemented by values obtained from these calculations.

Calculating broad neutron resonances in a cut-off Woods-Saxon potential

NASA Astrophysics Data System (ADS)

Baran, Á.; Noszály, Cs.; Salamon, P.; Vertse, T.

2015-07-01

In a cut-off Woods-Saxon (CWS) potential with realistic depth S -matrix poles being far from the imaginary wave number axis form a sequence where the distances of the consecutive resonances are inversely proportional with the cut-off radius value, which is an unphysical parameter. Other poles lying closer to the imaginary wave number axis might have trajectories with irregular shapes as the depth of the potential increases. Poles being close repel each other, and their repulsion is responsible for the changes of the directions of the corresponding trajectories. The repulsion might cause that certain resonances become antibound and later resonances again when they collide on the imaginary axis. The interaction is extremely sensitive to the cut-off radius value, which is an apparent handicap of the CWS potential.

Quantum temporal probabilities in tunneling systems

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

Anastopoulos, Charis, E-mail: anastop@physics.upatras.gr; Savvidou, Ntina, E-mail: ksavvidou@physics.upatras.gr

We study the temporal aspects of quantum tunneling as manifested in time-of-arrival experiments in which the detected particle tunnels through a potential barrier. In particular, we present a general method for constructing temporal probabilities in tunneling systems that (i) defines ‘classical’ time observables for quantum systems and (ii) applies to relativistic particles interacting through quantum fields. We show that the relevant probabilities are defined in terms of specific correlation functions of the quantum field associated with tunneling particles. We construct a probability distribution with respect to the time of particle detection that contains all information about the temporal aspects ofmore » the tunneling process. In specific cases, this probability distribution leads to the definition of a delay time that, for parity-symmetric potentials, reduces to the phase time of Bohm and Wigner. We apply our results to piecewise constant potentials, by deriving the appropriate junction conditions on the points of discontinuity. For the double square potential, in particular, we demonstrate the existence of (at least) two physically relevant time parameters, the delay time and a decay rate that describes the escape of particles trapped in the inter-barrier region. Finally, we propose a resolution to the paradox of apparent superluminal velocities for tunneling particles. We demonstrate that the idea of faster-than-light speeds in tunneling follows from an inadmissible use of classical reasoning in the description of quantum systems. -- Highlights: •Present a general methodology for deriving temporal probabilities in tunneling systems. •Treatment applies to relativistic particles interacting through quantum fields. •Derive a new expression for tunneling time. •Identify new time parameters relevant to tunneling. •Propose a resolution of the superluminality paradox in tunneling.« less

Influence of dense plasma on the energy levels and transition properties in highly charged ions

NASA Astrophysics Data System (ADS)

Chen, Zhan-Bin; Hu, Hong-Wei; Ma, Kun; Liu, Xiao-Bin; Guo, Xue-Ling; Li, Shuang; Zhu, Bo-Hong; Huang, Lian; Wang, Kai

2018-03-01

The studies of the influence of plasma environments on the level structures and transition properties for highly charged ions are presented. For the relativistic treatment, we implemented the multiconfiguration Dirac-Fock method incorporating the ion sphere (IS) model potential, in which the plasma screening is taken into account as a modified interaction potential between the electron and the nucleus. For the nonrelativistic treatment, analytical solutions of the Schrödinger equation with two types of the IS screened potential are proposed. The Ritz variation method is used with hydrogenic wave function as a trial wave function that contains two unknown variational parameters. Bound energies are derived from an energy equation, and the variational parameters are obtained from the minimisation condition of the expectation value of the energy. Numerical results for hydrogen-like ions in dense plasmas are presented as examples. A detailed analysis of the influence of relativistic effects on the energy levels and transition properties is also reported. Our results are compared with available results in the literature showing a good quantitative agreement.

Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

PubMed

Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

2013-05-01

Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

Critical point of gas-liquid type phase transition and phase equilibrium functions in developed two-component plasma model.

PubMed

Butlitsky, M A; Zelener, B B; Zelener, B V

2014-07-14

A two-component plasma model, which we called a "shelf Coulomb" model has been developed in this work. A Monte Carlo study has been undertaken to calculate equations of state, pair distribution functions, internal energies, and other thermodynamics properties. A canonical NVT ensemble with periodic boundary conditions was used. The motivation behind the model is also discussed in this work. The "shelf Coulomb" model can be compared to classical two-component (electron-proton) model where charges with zero size interact via a classical Coulomb law. With important difference for interaction of opposite charges: electrons and protons interact via the Coulomb law for large distances between particles, while interaction potential is cut off on small distances. The cut off distance is defined by an arbitrary ɛ parameter, which depends on system temperature. All the thermodynamics properties of the model depend on dimensionless parameters ɛ and γ = βe(2)n(1/3) (where β = 1/kBT, n is the particle's density, kB is the Boltzmann constant, and T is the temperature) only. In addition, it has been shown that the virial theorem works in this model. All the calculations were carried over a wide range of dimensionless ɛ and γ parameters in order to find the phase transition region, critical point, spinodal, and binodal lines of a model system. The system is observed to undergo a first order gas-liquid type phase transition with the critical point being in the vicinity of ɛ(crit) ≈ 13(T(*)(crit) ≈ 0.076), γ(crit) ≈ 1.8(v(*)(crit) ≈ 0.17), P(*)(crit) ≈ 0.39, where specific volume v* = 1/γ(3) and reduced temperature T(*) = ɛ(-1).

Bioinformatic prediction of leader genes in human periodontitis.

PubMed

Covani, Ugo; Marconcini, Simone; Giacomelli, Luca; Sivozhelevov, Victor; Barone, Antonio; Nicolini, Claudio

2008-10-01

Genes involved in different biologic processes form complex interaction networks. However, only a few have a high number of interactions with the other genes in the network. In previous bioinformatics and experimental studies concerning the T lymphocyte cell cycle, these genes were identified and termed "leader genes." In this work, genes involved in human periodontitis were tentatively identified and ranked according to their number of interactions to obtain a preliminary, broader view of molecular mechanisms of periodontitis and plan targeted experimentation. Genes were identified with interrelated queries of several databases. The interactions among these genes were mapped and given a significance score. The weighted number of links (weighted sum of scores for every interaction in which the given gene is involved) was calculated for each gene. Genes were clustered according to this parameter. The genes in the highest cluster were termed leader genes. Sixty-one genes involved or potentially involved in periodontitis were identified. Only five were identified as leader genes, whereas 12 others were ranked in an immediately lower cluster. For 10 of 17 genes there is evidence of involvement in periodontitis; seven new genes that are potentially involved in this disease were identified. The involvement in periodontitis has been completely established for only two leader genes. We applied a validated bioinformatics algorithm to increase our knowledge of molecular mechanisms of periodontitis. Even with the limitations of this ab initio analysis, this theoretical study can suggest ad hoc experimentation targeted on significant genes and, therefore, simpler than mass-scale molecular genomics. Moreover, the identification of leader genes might suggest new potential risk factors and therapeutic targets.

Corresponding-states laws for protein solutions.

PubMed

Katsonis, Panagiotis; Brandon, Simon; Vekilov, Peter G

2006-09-07

The solvent around protein molecules in solutions is structured and this structuring introduces a repulsion in the intermolecular interaction potential at intermediate separations. We use Monte Carlo simulations with isotropic, pair-additive systems interacting with such potentials. We test if the liquid-liquid and liquid-solid phase lines in model protein solutions can be predicted from universal curves and a pair of experimentally determined parameters, as done for atomic and colloid materials using several laws of corresponding states. As predictors, we test three properties at the critical point for liquid-liquid separation: temperature, as in the original van der Waals law, the second virial coefficient, and a modified second virial coefficient, all paired with the critical volume fraction. We find that the van der Waals law is best obeyed and appears more general than its original formulation: A single universal curve describes all tested nonconformal isotropic pair-additive systems. Published experimental data for the liquid-liquid equilibrium for several proteins at various conditions follow a single van der Waals curve. For the solid-liquid equilibrium, we find that no single system property serves as its predictor. We go beyond corresponding-states correlations and put forth semiempirical laws, which allow prediction of the critical temperature and volume fraction solely based on the range of attraction of the intermolecular interaction potential.

Robust Nonlinear Causality Analysis of Nonstationary Multivariate Physiological Time Series.

PubMed

Schack, Tim; Muma, Michael; Feng, Mengling; Guan, Cuntai; Zoubir, Abdelhak M

2018-06-01

An important research area in biomedical signal processing is that of quantifying the relationship between simultaneously observed time series and to reveal interactions between the signals. Since biomedical signals are potentially nonstationary and the measurements may contain outliers and artifacts, we introduce a robust time-varying generalized partial directed coherence (rTV-gPDC) function. The proposed method, which is based on a robust estimator of the time-varying autoregressive (TVAR) parameters, is capable of revealing directed interactions between signals. By definition, the rTV-gPDC only displays the linear relationships between the signals. We therefore suggest to approximate the residuals of the TVAR process, which potentially carry information about the nonlinear causality by a piece-wise linear time-varying moving-average model. The performance of the proposed method is assessed via extensive simulations. To illustrate the method's applicability to real-world problems, it is applied to a neurophysiological study that involves intracranial pressure, arterial blood pressure, and brain tissue oxygenation level (PtiO2) measurements. The rTV-gPDC reveals causal patterns that are in accordance with expected cardiosudoral meachanisms and potentially provides new insights regarding traumatic brain injuries. The rTV-gPDC is not restricted to the above problem but can be useful in revealing interactions in a broad range of applications.

Time-Domain Modeling of RF Antennas and Plasma-Surface Interactions

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.

2017-10-01

Recent advances in finite-difference time-domain (FDTD) modeling techniques allow plasma-surface interactions such as sheath formation and sputtering to be modeled concurrently with the physics of antenna near- and far-field behavior and ICRF power flow. Although typical sheath length scales (micrometers) are much smaller than the wavelengths of fast (tens of cm) and slow (millimeter) waves excited by the antenna, sheath behavior near plasma-facing antenna components can be represented by a sub-grid kinetic sheath boundary condition, from which RF-rectified sheath potential variation over the surface is computed as a function of current flow and local plasma parameters near the wall. These local time-varying sheath potentials can then be used, in tandem with particle-in-cell (PIC) models of the edge plasma, to study sputtering effects. Particle strike energies at the wall can be computed more accurately, consistent with their passage through the known potential of the sheath, such that correspondingly increased accuracy of sputtering yields and heat/particle fluxes to antenna surfaces is obtained. The new simulation capabilities enable time-domain modeling of plasma-surface interactions and ICRF physics in realistic experimental configurations at unprecedented spatial resolution. We will present results/animations from high-performance (10k-100k core) FDTD/PIC simulations of Alcator C-Mod antenna operation.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

NASA Astrophysics Data System (ADS)

Gimenez, M. Cecilia; Reinaudi, Luis; Leiva, Ezequiel P. M.

2015-12-01

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations were made for the case of silver-gold alloys when the medium interacted selectively with Ag.

The superconducting state parameters of glassy superconductors

NASA Astrophysics Data System (ADS)

Vora, Aditya M.

2011-11-01

We present theoretical investigations of the superconducting state parameters (SSPs), i.e. the electron-phonon coupling strength, λ, Coulomb pseudopotential, μ*, transition temperature, Tc, isotope effect exponent, α, and effective interaction strength, N0V, of glassy superconductors by employing Ashcroft's well know empty core model potential for the first time using five screening functions proposed by Hartree (H), Taylor, Ichimaru-Utsumi (IU), Farid et al and Sarkar et al. The Tc obtained from the H and IU screening functions is found to be in excellent agreement with available experimental data. Also, the present results confirm the superconducting phase in bulk metallic glass superconductors. A strong dependency of the SSPs of the glassy superconductors on the 'Z' valence is found.

Temporal characterization of plasma cw high-power CO2 laser-matter interaction: contribution to the welding process control

NASA Astrophysics Data System (ADS)

Engel, Thierry; Kane, M.; Fontaine, Joel

1997-08-01

During high-power laser welding, gas ionization occurs above the sample. The resulting plasma ignition threshold is related to ionization potential of metallic vapors from the sample, and shielding gases used in the process. In this work, we have characterized the temporal behavior of the radiation emitted by the plasma during laser welding in order to relate the observed signals to the process parameters.

Investigation of Laser Based Thomson Scattering

DTIC Science & Technology

2015-06-04

laser liquid interaction has the potential to provide sources of energetic ions and fission products such as neutrons . The development of strong...by the production of heavy water d-d fusion and the production of neutrons . Finally, in section VII the tight focusing of light by a 2π mirror is...laser system is estimated to be 10 -15 , using cross- polarization modulation and two plasma mirrors. These parameters allow prepulse expansion to be

Interaction Between Low-Dose Methotrexate and Nonsteroidal Anti-inflammatory Drugs, Penicillins, and Proton Pump Inhibitors.

PubMed

Hall, Jill J; Bolina, Monika; Chatterley, Trish; Jamali, Fakhreddin

2017-02-01

To review the potential drug interactions between low-dose methotrexate (LD-MTX) and nonsteroidal anti-inflammatory drugs (NSAIDs), penicillins, and proton-pump inhibitors (PPIs) given the disparity between interactions reported for high-dose and low-dose MTX to help guide clinicians. A literature search was performed in MEDLINE (1946 to September 2016), EMBASE (1974 to September 2016), and International Pharmaceutical Abstracts (1970 to January 2015) to identify reports describing potential drug interactions between LD-MTX and NSAIDS, penicillins, or PPIs. Reference lists of included articles were reviewed to find additional eligible articles. All English-language observational, randomized, and pharmacokinetic (PK) studies assessing LD-MTX interactions in humans were analyzed to determine clinical relevance in making recommendations to clinicians. Clinical case reports were assigned a Drug Interaction Probability Scale score. A total of 32 articles were included (28 with NSAIDs, 3 with penicillins, and 2 with PPIs [1 including both PPI and NSAID]). Although there are some PK data to describe increased LD-MTX concentrations when NSAIDs are used concomitantly, the clinical relevance remains unclear. Based on the limited data on LD-MTX with penicillins and PPIs, no clinically meaningful interaction was identified. Given the available evidence, the clinical importance of the interaction between LD-MTX and NSAIDs, penicillins, and PPIs cannot be substantiated. Health care providers should assess the benefit and risk of LD-MTX regardless of concomitant drug use, including factors known to predispose patients to MTX toxicity, and continue to monitor clinical and laboratory parameters per guideline recommendations.

Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.

PubMed

Bourgeas, Raphaël; Basse, Marie-Jeanne; Morelli, Xavier; Roche, Philippe

2010-03-09

In the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains challenging. Here we describe this particular PPI chemical space through the presentation of 2P2I(DB), a hand-curated database dedicated to the structure of PPIs with known inhibitors. We have analyzed protein/protein and protein/inhibitor interfaces in terms of geometrical parameters, atom and residue properties, buried accessible surface area and other biophysical parameters. The interfaces found in 2P2I(DB) were then compared to those of representative datasets of heterodimeric complexes. We propose a new classification of PPIs with known inhibitors into two classes depending on the number of segments present at the interface and corresponding to either a single secondary structure element or to a more globular interacting domain. 2P2I(DB) complexes share global shape properties with standard transient heterodimer complexes, but their accessible surface areas are significantly smaller. No major conformational changes are seen between the different states of the proteins. The interfaces are more hydrophobic than general PPI's interfaces, with less charged residues and more non-polar atoms. Finally, fifty percent of the complexes in the 2P2I(DB) dataset possess more hydrogen bonds than typical protein-protein complexes. Potential areas of study for the future are proposed, which include a new classification system consisting of specific families and the identification of PPI targets with high druggability potential based on key descriptors of the interaction. 2P2I database stores structural information about PPIs with known inhibitors and provides a useful tool for biologists to assess the potential druggability of their interfaces. The database can be accessed at http://2p2idb.cnrs-mrs.fr.

Gas-surface interactions using accommodation coefficients for a dilute and a dense gas in a micro- or nanochannel: heat flux predictions using combined molecular dynamics and Monte Carlo techniques.

PubMed

Nedea, S V; van Steenhoven, A A; Markvoort, A J; Spijker, P; Giordano, D

2014-05-01

The influence of gas-surface interactions of a dilute gas confined between two parallel walls on the heat flux predictions is investigated using a combined Monte Carlo (MC) and molecular dynamics (MD) approach. The accommodation coefficients are computed from the temperature of incident and reflected molecules in molecular dynamics and used as effective coefficients in Maxwell-like boundary conditions in Monte Carlo simulations. Hydrophobic and hydrophilic wall interactions are studied, and the effect of the gas-surface interaction potential on the heat flux and other characteristic parameters like density and temperature is shown. The heat flux dependence on the accommodation coefficient is shown for different fluid-wall mass ratios. We find that the accommodation coefficient is increasing considerably when the mass ratio is decreased. An effective map of the heat flux depending on the accommodation coefficient is given and we show that MC heat flux predictions using Maxwell boundary conditions based on the accommodation coefficient give good results when compared to pure molecular dynamics heat predictions. The accommodation coefficients computed for a dilute gas for different gas-wall interaction parameters and mass ratios are transferred to compute the heat flux predictions for a dense gas. Comparison of the heat fluxes derived using explicit MD, MC with Maxwell-like boundary conditions based on the accommodation coefficients, and pure Maxwell boundary conditions are discussed. A map of the heat flux dependence on the accommodation coefficients for a dense gas, and the effective accommodation coefficients for different gas-wall interactions are given. In the end, this approach is applied to study the gas-surface interactions of argon and xenon molecules on a platinum surface. The derived accommodation coefficients are compared with values of experimental results.

Heat conduction in diatomic chains with correlated disorder

NASA Astrophysics Data System (ADS)

Savin, Alexander V.; Zolotarevskiy, Vadim; Gendelman, Oleg V.

2017-01-01

The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter - the probability for two neighboring particles to have the same mass. As this parameter grows from zero to unity, the structure of the chain varies from regular staggering chain to completely random configuration, and then - to very long clusters of particles with equal masses. Therefore, this correlation parameter allows a control of typical cluster size in the chain. In order to explore different regimes of the heat transport, two interatomic potentials are considered. The first one is an infinite potential wall, corresponding to instantaneous elastic collisions between the neighboring particles. In homogeneous chains such interaction leads to an anomalous heat transport. The other one is classical Lennard-Jones interatomic potential, which leads to a normal heat transport. The simulations demonstrate that the correlated disorder of the particle arrangement does not change the convergence properties of the heat conduction coefficient, but essentially modifies its value. For the collision potential, one observes essential growth of the coefficient for fixed chain length as the limit of large homogeneous clusters is approached. The thermal transport in these models remains superdiffusive. In the Lennard-Jones chain the effect of correlation appears to be not monotonous in the limit of low temperatures. This behavior stems from the competition between formation of long clusters mentioned above, and Anderson localization close to the staggering ordered state.

Estimating Colloidal Contact Model Parameters Using Quasi-Static Compression Simulations.

PubMed

Bürger, Vincent; Briesen, Heiko

2016-10-05

For colloidal particles interacting in suspensions, clusters, or gels, contact models should attempt to include all physical phenomena experimentally observed. One critical point when formulating a contact model is to ensure that the interaction parameters can be easily obtained from experiments. Experimental determinations of contact parameters for particles either are based on bulk measurements for simulations on the macroscopic scale or require elaborate setups for obtaining tangential parameters such as using atomic force microscopy. However, on the colloidal scale, a simple method is required to obtain all interaction parameters simultaneously. This work demonstrates that quasi-static compression of a fractal-like particle network provides all the necessary information to obtain particle interaction parameters using a simple spring-based contact model. These springs provide resistances against all degrees of freedom associated with two-particle interactions, and include critical forces or moments where such springs break, indicating a bond-breakage event. A position-based cost function is introduced to show the identifiability of the two-particle contact parameters, and a discrete, nonlinear, and non-gradient-based global optimization method (simplex with simulated annealing, SIMPSA) is used to minimize the cost function calculated from deviations of particle positions. Results show that, in principle, all necessary contact parameters for an arbitrary particle network can be identified, although numerical efficiency as well as experimental noise must be addressed when applying this method. Such an approach lays the groundwork for identifying particle-contact parameters from a position-based particle analysis for a colloidal system using just one experiment. Spring constants also directly influence the time step of the discrete-element method, and a detailed knowledge of all necessary interaction parameters will help to improve the efficiency of colloidal particle simulations.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

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

Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

Maximum Mass of Hybrid Stars in the Quark Bag Model

NASA Astrophysics Data System (ADS)

Alaverdyan, G. B.; Vartanyan, Yu. L.

2017-12-01

The effect of model parameters in the equation of state for quark matter on the magnitude of the maximum mass of hybrid stars is examined. Quark matter is described in terms of the extended MIT bag model including corrections for one-gluon exchange. For nucleon matter in the range of densities corresponding to the phase transition, a relativistic equation of state is used that is calculated with two-particle correlations taken into account based on using the Bonn meson-exchange potential. The Maxwell construction is used to calculate the characteristics of the first order phase transition and it is shown that for a fixed value of the strong interaction constant αs, the baryon concentrations of the coexisting phases grow monotonically as the bag constant B increases. It is shown that for a fixed value of the strong interaction constant αs, the maximum mass of a hybrid star increases as the bag constant B decreases. For a given value of the bag parameter B, the maximum mass rises as the strong interaction constant αs increases. It is shown that the configurations of hybrid stars with maximum masses equal to or exceeding the mass of the currently known most massive pulsar are possible for values of the strong interaction constant αs > 0.6 and sufficiently low values of the bag constant.

Motion in a modified Chermnykh's restricted three-body problem with oblateness

NASA Astrophysics Data System (ADS)

Singh, Jagadish; Leke, Oni

2014-03-01

In this paper, the restricted problem of three bodies is generalized to include a case when the passively gravitating test particle is an oblate spheroid under effect of small perturbations in the Coriolis and centrifugal forces when the first primary is a source of radiation and the second one an oblate spheroid, coupled with the influence of the gravitational potential from the belt. The equilibrium points are found and it is seen that, in addition to the usual three collinear equilibrium points, there appear two new ones due to the potential from the belt and the mass ratio. Two triangular equilibrium points exist. These equilibria are affected by radiation of the first primary, small perturbation in the centrifugal force, oblateness of both the test particle and second primary and the effect arising from the mass of the belt. The linear stability of the equilibrium points is explored and the stability outcome of the collinear equilibrium points remains unstable. In the case of the triangular points, motion is stable with respect to some conditions which depend on the critical mass parameter; influenced by the small perturbations, radiating effect of the first primary, oblateness of the test body and second primary and the gravitational potential from the belt. The effects of each of the imposed free parameters are analyzed. The potential from the belt and small perturbation in the Coriolis force are stabilizing parameters while radiation, small perturbation in the centrifugal force and oblateness reduce the stable regions. The overall effect is that the region of stable motion increases under the combine action of these parameters. We have also found the frequencies of the long and short periodic motion around stable triangular points. Illustrative numerical exploration is rendered in the Sun-Jupiter and Sun-Earth systems where we show that in reality, for some values of the system parameters, the additional equilibrium points do not in general exist even when there is a belt to interact with.

Calcium-Induced Mitochondrial Permeability Transitions: Parameters of Ca2+ Ion Interactions with Mitochondria and Effects of Oxidative Agents.

PubMed

Golovach, Nina G; Cheshchevik, Vitali T; Lapshina, Elena A; Ilyich, Tatsiana V; Zavodnik, Ilya B

2017-04-01

We evaluated the parameters of Ca 2+ -induced mitochondrial permeability transition (MPT) pore formations, Ca 2+ binding constants, stoichiometry, energy of activation, and the effect of oxidative agents, tert-butyl hydroperoxide (tBHP), and hypochlorous acid (HOCl), on Ca 2+ -mediated process in rat liver mitochondria. From the Hill plot of the dependence of MPT rate on Ca 2+ concentration, we determined the order of interaction of Ca 2+ ions with the mitochondrial sites, n = 3, and the apparent K d = 60 ± 12 µM. We also found the apparent Michaelis-Menten constant, K m , for Ca 2+ interactions with mitochondria to be equal to 75 ± 20 µM, whereas that in the presence of 300 µM tBHP was 120 ± 20 µM. Using the Arrhenius plots of the temperature dependences of apparent mitochondrial swelling rate at various Ca 2+ concentrations, we calculated the activation energy of the MPT process. ΔE a was 130 ± 20 kJ/mol at temperatures below the break point of the Arrhenius plot (30-34 °C) and 50 ± 9 kJ/mol at higher temperatures. Ca 2+ ions induced rapid mitochondrial NADH depletion and membrane depolarization. Prevention of the pore formation by cyclosporin A inhibited Ca 2+ -dependent mitochondrial depolarization and Mg 2+ ions attenuated the potential dissipation. tBHP (10-150 µM) dose-dependently enhanced the rate of MPT opening, whereas the effect of HOCl on MPT depended on the ratio of HOCl/Ca 2+ . The apparent K m of tBHP interaction with mitochondria in the swelling reaction was found to be K m = 11 ± 3 µM. The present study provides evidence that three calcium ions interact with mitochondrial site with high affinity during MPT. Ca 2+ -induced MPT pore formations due to mitochondrial membrane protein denaturation resulted in membrane potential dissipation. Oxidants with different mechanisms, tBHP and HOCl, reduced mitochondrial membrane potential and oxidized mitochondrial NADH in EDTA-free medium and had an effect on Ca 2+ -induced MPT onset.

Power Law and Logarithmic Ricci Dark Energy Models in Hořava-Lifshitz Cosmology

NASA Astrophysics Data System (ADS)

Pasqua, Antonio; Chattopadhyay, Surajit; Khurshudyan, Martiros; Myrzakulov, Ratbay; Hakobyan, Margarit; Movsisyan, Artashes

2015-03-01

In this work, we studied the Power Law and the Logarithmic Entropy Corrected versions of the Ricci Dark Energy (RDE) model in a spatially non-flat universe and in the framework of Hořava-Lifshitz cosmology. For the two cases containing non-interacting and interacting RDE and Dark Matter (DM), we obtained the exact differential equation that determines the evolutionary form of the RDE energy density. Moreover, we obtained the expressions of the deceleration parameter q and, using a parametrization of the equation of state (EoS) parameter ω D given by the relation ω D ( z) = ω 0+ ω 1 z, we derived the expressions of both ω 0 and ω 1. We interestingly found that the expression of ω 0 is the same for both non-interacting and interacting case. The expression of ω 1 for the interacting case has strong dependence from the interacting parameter b 2. The parameters derived in this work are done in small redshift approximation and for low redshift expansion of the EoS parameter.

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

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

Reeve, Samuel Temple; Strachan, Alejandro, E-mail: strachan@purdue.edu

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated undermore » three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.« less

Computer modeling of high-voltage solar array experiment using the NASCAP/LEO (NASA Charging Analyzer Program/Low Earth Orbit) computer code

NASA Astrophysics Data System (ADS)

Reichl, Karl O., Jr.

1987-06-01

The relationship between the Interactions Measurement Payload for Shuttle (IMPS) flight experiment and the low Earth orbit plasma environment is discussed. Two interactions (parasitic current loss and electrostatic discharge on the array) may be detrimental to mission effectiveness. They result from the spacecraft's electrical potentials floating relative to plasma ground to achieve a charge flow equilibrium into the spacecraft. The floating potentials were driven by external biases applied to a solar array module of the Photovoltaic Array Space Power (PASP) experiment aboard the IMPS test pallet. The modeling was performed using the NASA Charging Analyzer Program/Low Earth Orbit (NASCAP/LEO) computer code which calculates the potentials and current collection of high-voltage objects in low Earth orbit. Models are developed by specifying the spacecraft, environment, and orbital parameters. Eight IMPS models were developed by varying the array's bias voltage and altering its orientation relative to its motion. The code modeled a typical low Earth equatorial orbit. NASCAP/LEO calculated a wide variety of possible floating potential and current collection scenarios. These varied directly with both the array bias voltage and with the vehicle's orbital orientation.

Anomalous transport of charged dust grains in a magnetized collisional plasma: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Bezbaruah, Pratikshya; Das, Nilakshi

2018-05-01

Anomalous diffusion of charged dust grains immersed in a plasma in the presence of strong ion-neutral collision, flowing ions, and a magnetic field has been observed. Molecular Dynamics simulation confirms the deviation from normal diffusion in an ensemble of dust grains probed in laboratory plasma chambers. Collisional effects are significant in governing the nature of diffusion. In order to have a clear idea on the transport of particles in a real experimental situation, the contribution of streaming ions and the magnetic field along with collision is considered through the relevant interaction potential. The nonlinear evolution of Mean Square Displacement is an indication of the modification in particle trajectories due to several effects as mentioned above. It is found that strong collision and ion flow significantly affect the interparticle interaction potential in the presence of the magnetic field and lead to the appearance of the asymmetric type of Debye Hückel (D H) potential. Due to the combined effect of the magnetic field, ion flow, and collision, dusty plasma exhibits a completely novel behavior. The coupling parameter Γ enhances the asymmetric D H type potential arising due to ion flow, and this may drive the system to a disordered state.

A new multimedia contaminant fate model for China: how important are environmental parameters in influencing chemical persistence and long-range transport potential?

PubMed

Zhu, Ying; Price, Oliver R; Tao, Shu; Jones, Kevin C; Sweetman, Andy J

2014-08-01

We present a new multimedia chemical fate model (SESAMe) which was developed to assess chemical fate and behaviour across China. We apply the model to quantify the influence of environmental parameters on chemical overall persistence (POV) and long-range transport potential (LRTP) in China, which has extreme diversity in environmental conditions. Sobol sensitivity analysis was used to identify the relative importance of input parameters. Physicochemical properties were identified as more influential than environmental parameters on model output. Interactive effects of environmental parameters on POV and LRTP occur mainly in combination with chemical properties. Hypothetical chemicals and emission data were used to model POV and LRTP for neutral and acidic chemicals with different KOW/DOW, vapour pressure and pKa under different precipitation, wind speed, temperature and soil organic carbon contents (fOC). Generally for POV, precipitation was more influential than the other environmental parameters, whilst temperature and wind speed did not contribute significantly to POV variation; for LRTP, wind speed was more influential than the other environmental parameters, whilst the effects of other environmental parameters relied on specific chemical properties. fOC had a slight effect on POV and LRTP, and higher fOC always increased POV and decreased LRTP. Example case studies were performed on real test chemicals using SESAMe to explore the spatial variability of model output and how environmental properties affect POV and LRTP. Dibenzofuran released to multiple media had higher POV in northwest of Xinjiang, part of Gansu, northeast of Inner Mongolia, Heilongjiang and Jilin. Benzo[a]pyrene released to the air had higher LRTP in south Xinjiang and west Inner Mongolia, whilst acenaphthene had higher LRTP in Tibet and west Inner Mongolia. TCS released into water had higher LRTP in Yellow River and Yangtze River catchments. The initial case studies demonstrated that SESAMe performed well on comparing POV and LRTP of chemicals in different regions across China in order to potentially identify the most sensitive regions. This model should not only be used to estimate POV and LRTP for screening and risk assessments of chemicals, but could potentially be used to help design chemical monitoring programmes across China in the future. Copyright © 2014 Elsevier Ltd. All rights reserved.

The electrical transport properties of liquid Rb using pseudopotential theory

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

Patel, A. B., E-mail: amit07patel@gmail.com; Bhatt, N. K., E-mail: amit07patel@gmail.com; Thakore, B. Y., E-mail: amit07patel@gmail.com

2014-04-24

Certain electric transport properties of liquid Rb are reported. The electrical resistivity is calculated by using the self-consistent approximation as suggested by Ferraz and March. The pseudopotential due to Hasegawa et al for full electron-ion interaction, which is valid for all electrons and contains the repulsive delta function due to achieve the necessary s-pseudisation was used for the calculation. Temperature dependence of structure factor is considered through temperature dependent potential parameter in the pair potential. Finally, thermo-electric power and thermal conductivity are obtained. The outcome of the present study is discussed in light of other such results, and confirms themore » applicability of pseudopotential at very high temperature via temperature dependent pair potential.« less

Dynamics and Melting of Finite Plasma Crystals

NASA Astrophysics Data System (ADS)

Ludwig, Patrick; K"Ahlert, Hanno; Baumgartner, Henning; Thomsen, Hauke; Bonitz, Michael

2009-11-01

Interacting few-particle systems in external trapping potentials are of strong current interest since they allow to realize and control strong correlation and quantum effects [1]. Here, we present our recent results on the structural and thermodynamic properties of the crystal-like Wigner phase of complex plasma confined in a 3D harmonic potential. We discuss the linear response of the strongly correlated system to external excitations, which can be described in terms of normal modes [2]. By means of first-principle simulations the details of the melting phase transitions of these mesoscopic systems are systematically analysed with the melting temperatures being determined by a modified Lindemann parameter for the pair distance fluctuations [3]. The critical temperatures turn out to be utmost sensitive to finite size effects (i.e., the exact particle number), and form of the (screened) interaction potential.[4pt] [1] PhD Thesis, P. Ludwig, U Rostock (2008)[0pt] [2] C. Henning et al., J. Phys. A 42, 214023 (2009)[0pt] [3] B"oning et al., Phys. Rev. Lett. 100, 113401 (2008)

Effect of Fortification with Fish (Pseudophycis bachus) Powder on Nutritional Quality of Durum Wheat Pasta

PubMed Central

Desai, Ajay S.; Brennan, Margaret A.

2018-01-01

This paper investigates the nutraceutical (phenolic content and antioxidant activity) and nutritional potential (protein and starch digestibility) of supplementation of durum wheat semolina with 5–20% fish powder (Pseudophycis bachus). In general, all enriched pasta with fish powder showed a significant decrease (p < 0.05) in reducing sugar released during an in vitro digestion, and reductions in standardized area under the curve (AUC) values, compared to control pasta. The potentially bioaccessible fraction of pasta enriched with 20% fish powder (FP) was characterized as having a 177–191% increase in phenolic content and a 145–556% higher antiradical activity. Elevation of these parameters in fortified pasta was accompanied by interaction of wheat starch, protein, and fish powder protein. Supplementation of fish powder also influenced protein digestibility (a reduction from 84.60% for control pasta to 80.80% for pasta with 20% fish powder). Fortification improved the nutraceutical and nutritional potential of the studied pasta with the effects depending on factors including protein-starch-phenolic interactions. PMID:29673139

Photosynthesis and leaf water relations in four American sycamore clones

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

Tang, Z.; Land, S.B. Jr.

1995-11-01

Photosynthesis, transpiration, stomatal conductance, and xylem pressure potential were studied to examine clonal variation and clone-by-season interactions in rooted cuttings of four sycamore clones (Platanus occidentalis L.). These physiological parameters were measured during June through November of the second and third growing seasons in the field. Stomatal conductance, xylem pressure potential, and photosynthesis were higher in June-July than in August-November. The four clones did not differ significantly in yearly average photosynthetic rates, but clone 11 tended to have higher rates early in each growing season (June-July) than did the other three clones. Dry periods during August-September of the second seasonmore » and during October of the third season apparently caused clone 11 to close its stomata more than clone 17, as indicated by significant clone-by-season interactions for reductions in stomatal conductance and transpiration late in the morning. Clone 17 was generally able to maintain high xylem pressure potential, stomatal conductance, and transpiration throughout the growing season, probably because of its large root system. 36 refs., 2 figs., 5 tabs.« less

Electrical circuit modeling and analysis of microwave acoustic interaction with biological tissues.

PubMed

Gao, Fei; Zheng, Qian; Zheng, Yuanjin

2014-05-01

Numerical study of microwave imaging and microwave-induced thermoacoustic imaging utilizes finite difference time domain (FDTD) analysis for simulation of microwave and acoustic interaction with biological tissues, which is time consuming due to complex grid-segmentation and numerous calculations, not straightforward due to no analytical solution and physical explanation, and incompatible with hardware development requiring circuit simulator such as SPICE. In this paper, instead of conventional FDTD numerical simulation, an equivalent electrical circuit model is proposed to model the microwave acoustic interaction with biological tissues for fast simulation and quantitative analysis in both one and two dimensions (2D). The equivalent circuit of ideal point-like tissue for microwave-acoustic interaction is proposed including transmission line, voltage-controlled current source, envelop detector, and resistor-inductor-capacitor (RLC) network, to model the microwave scattering, thermal expansion, and acoustic generation. Based on which, two-port network of the point-like tissue is built and characterized using pseudo S-parameters and transducer gain. Two dimensional circuit network including acoustic scatterer and acoustic channel is also constructed to model the 2D spatial information and acoustic scattering effect in heterogeneous medium. Both FDTD simulation, circuit simulation, and experimental measurement are performed to compare the results in terms of time domain, frequency domain, and pseudo S-parameters characterization. 2D circuit network simulation is also performed under different scenarios including different sizes of tumors and the effect of acoustic scatterer. The proposed circuit model of microwave acoustic interaction with biological tissue could give good agreement with FDTD simulated and experimental measured results. The pseudo S-parameters and characteristic gain could globally evaluate the performance of tumor detection. The 2D circuit network enables the potential to combine the quasi-numerical simulation and circuit simulation in a uniform simulator for codesign and simulation of a microwave acoustic imaging system, bridging bioeffect study and hardware development seamlessly.

Exploring the DNA damaging potential of chitosan and citrate-reduced gold nanoparticles: Physicochemical approach.

PubMed

Sonia; Komal; Kukreti, Shrikant; Kaushik, Mahima

2018-04-24

Nanomaterials offer a wide range of biomedical applications including gene/drug delivery, biosensing and bioimaging. The cytotoxic and genotoxic potential of nanoparticles need to be thoroughly investigated before their biomedical usage. This study aims to investigate and compare the nanotoxicology of chitosan (CH-Au-Np) and citrate (CI-Au-Np) reduced gold nanoparticles via exploring their interaction with Calf thymus DNA (Ct-DNA) utilizing various physicochemical techniques. Structural characterization of these Nps was done using UV-Visible Spectroscopy and Transmission Electron Microscopy (TEM). Analysis of UV-Visible absorbance spectra indicates that interaction of CH-Au-Np with Ct-DNA causes destabilization of DNA by inducing significant structural and conformational changes in Ct-DNA in a concentration dependent manner, whereas there was negligible interaction between CI-Au-Np and Ct-DNA. These observations were further supported by the results of agarose gel mobility, UV-thermal melting, Circular Dichroism (CD), Dynamic Light Scattering (DLS) and TEM studies. Fluorescence spectral studies using acridine orange (AO) as a fluorescence probe and analysis of thermodynamic parameters reveal that the interactions between Ct-DNA and CH-Au-Np were mainly governed by Van der Waal interactions and Hydrogen bonding. An insightful understanding of genotoxicity induced by CH-Au-Np can be advantageous, as it may provide valuable anticancer approach for cytotoxic drug designing. Copyright © 2018 Elsevier B.V. All rights reserved.

Systematical investigation of in vitro interaction of InP/ZnS quantum dots with human serum albumin by multispectroscopic approach.

PubMed

Huang, Shan; Qiu, Hangna; Liu, Yi; Huang, Chusheng; Sheng, Jiarong; Cui, Jianguo; Su, Wei; Xiao, Qi

2016-12-01

Cadmium-free quantum dots (QDs) have attracted great attention in biological and biomedical applications due to their less content of toxic metals, but their potential toxicity investigations on molecular biology level are rarely involved. Since few studies have addressed whether InP/ZnS QDs could bind and alter the structure and function of human serum albumin (HSA), in vitro interaction between InP/ZnS QDs and HSA was systematically characterized by multispectroscopic approaches. InP/ZnS QDs could quench the intrinsic fluorescence of HSA via static mode. The binding site of InP/ZnS QDs was mainly located at subdomain IIA of HSA. Some thermodynamic parameters suggested that InP/ZnS QDs interacted with HSA mainly through electrostatic interactions. As further revealed by three-dimensional spectrometry, FT-IR spectrometry and circular dichroism technique, InP/ZnS QDs caused more global and local conformational change of HSA than CdSe/ZnS QDs, which illustrated the stronger binding interaction and higher potential toxicity of InP/ZnS QDs on biological function of HSA. Our results offer insights into the in vitro binding mechanism of InP/ZnS QDs with HSA and provide important information for possible toxicity risk of these cadmium-free QDs to human health. Copyright © 2016 Elsevier B.V. All rights reserved.

system

NASA Astrophysics Data System (ADS)

Garcilazo, H.; Valcarce, A.; Vijande, J.

2017-07-01

Using local central Yukawa-type Malfliet-Tjon interactions reproducing the low-energy parameters and phase shifts of the nn system, and the latest updates of the nΛ and ΛΛ Nijmegen ESC08c potentials, we study the possible existence of a bound state. Our results indicate that the is unbound, being just above threshold. We discuss the role played by the 1 S 0 nn repulsive term of the Yukawa-type Malfliet-Tjon interaction. Supported by COFAA-IPN (México), Ministerio de Economía, Industria y Competitividad and EU FEDER (FPA2013-47443, FPA2015-69714-REDT, FPA2016-77177), Junta de Castilla y León (SA041U16) and Generalitat Valenciana PrometeoII/2014/066

Stochastic resonance and noise delayed extinction in a model of two competing species

NASA Astrophysics Data System (ADS)

Valenti, D.; Fiasconaro, A.; Spagnolo, B.

2004-01-01

We study the role of the noise in the dynamics of two competing species. We consider generalized Lotka-Volterra equations in the presence of a multiplicative noise, which models the interaction between the species and the environment. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence of a periodic driving term, which accounts for the environment temperature variation. We find noise-induced periodic oscillations of the species concentrations and stochastic resonance phenomenon. We find also a nonmonotonic behavior of the mean extinction time of one of the two competing species as a function of the additive noise intensity.

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

PubMed Central

Berry, David; Widder, Stefanie

2014-01-01

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets. PMID:24904535

Ab initio study of the Coulomb interaction in NbxCo clusters: Strong on-site versus weak nonlocal screening

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Mertig, I.; Katsnelson, M. I.

2018-01-01

By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the full-potential linearized augmented plane wave method, we study the screening of the Coulomb interaction in NbxCo (1 ≤x ≤9 ) clusters. In addition, these results are compared with pure bcc Nb bulk. We find that for all clusters the on-site Coulomb interaction in RPA is strongly screened, whereas the intersite nonlocal Coulomb interaction is weakly screened and for some clusters it is unscreened or even antiscreened. This is in strong contrast with pure Nb bulk, where the intersite Coulomb interaction is almost completely screened. Furthermore, constrained RPA calculations reveal that the contribution of the Co 3 d → 3 d channel to the total screening of the Co 3 d electrons is small. Moreover, we find that both the on-site and intersite Coulomb interaction parameters decrease in a reasonable approximation linearly with the cluster size and for clusters having more than 20 Nb atoms a transition from 0D to 3D screening is expected to take place.

Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay

PubMed Central

2011-01-01

Background Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC) technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels. Results Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners. Conclusion Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development. PMID:21276241

Computation of energy interaction parameters as well as electric dipole intensity parameters for the absorption spectral study of the interaction of Pr(III) with L-phenylalanine, L-glycine, L-alanine and L-aspartic acid in the presence and absence of Ca 2+ in organic solvents

NASA Astrophysics Data System (ADS)

Moaienla, T.; Singh, Th. David; Singh, N. Rajmuhon; Devi, M. Indira

2009-10-01

Studying the absorption difference and comparative absorption spectra of the interaction of Pr(III) and Nd(III) with L-phenylalanine, L-glycine, L-alanine and L-aspartic acid in the presence and absence of Ca 2+ in organic solvents, various energy interaction parameters like Slater-Condon ( FK), Racah ( Ek), Lande factor ( ξ4f), nephelauxetic ratio ( β), bonding ( b1/2), percentage-covalency ( δ) have been evaluated applying partial and multiple regression analysis. The values of oscillator strength ( P) and Judd-Ofelt electric dipole intensity parameter Tλ ( λ = 2, 4, 6) for different 4f-4f transitions have been computed. On analysis of the variation of the various energy interaction parameters as well as the changes in the oscillator strength ( P) and Tλ values reveal the mode of binding with different ligands.

Seabed roughness parameters from joint backscatter and reflection inversion at the Malta Plateau.

PubMed

Steininger, Gavin; Holland, Charles W; Dosso, Stan E; Dettmer, Jan

2013-09-01

This paper presents estimates of seabed roughness and geoacoustic parameters and uncertainties on the Malta Plateau, Mediterranean Sea, by joint Bayesian inversion of mono-static backscatter and spherical wave reflection-coefficient data. The data are modeled using homogeneous fluid sediment layers overlying an elastic basement. The scattering model assumes a randomly rough water-sediment interface with a von Karman roughness power spectrum. Scattering and reflection data are inverted simultaneously using a population of interacting Markov chains to sample roughness and geoacoustic parameters as well as residual error parameters. Trans-dimensional sampling is applied to treat the number of sediment layers and the order (zeroth or first) of an autoregressive error model (to represent potential residual correlation) as unknowns. Results are considered in terms of marginal posterior probability profiles and distributions, which quantify the effective data information content to resolve scattering/geoacoustic structure. Results indicate well-defined scattering (roughness) parameters in good agreement with existing measurements, and a multi-layer sediment profile over a high-speed (elastic) basement, consistent with independent knowledge of sand layers over limestone.

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

Mamedov, Bahtiyar A.; Somuncu, Elif; Askerov, Iskender M.

In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physicalmore » properties.« less

Tower Illuminance Model

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

Ho, Clifford K.; Sims, Cianan

TIM is a real-time interactive concentrating solar field simulation. TIM models a concentrating tower (receiver), heliostat field, and potential reflected glare based on user-specified parameters such as field capacity, tower height and location. TIM provides a navigable 3D interface, allowing the user to “fly” around the field to determine the potential glare hazard from off-target heliostats. Various heliostat aiming strategies are available for specifying how heliostats behave when in standby mode. Strategies include annulus, point-per-group, up-aiming and single-point-focus. Additionally, TIM includes an avian path feature for approximating the irradiance and feather temperature of a bird flying through the field airspace.

Separating the effects of repulsive and attractive forces on the phase diagram, interfacial, and critical properties of simple fluids

NASA Astrophysics Data System (ADS)

Fuentes-Herrera, M.; Moreno-Razo, J. A.; Guzmán, O.; López-Lemus, J.; Ibarra-Tandi, B.

2016-06-01

Molecular simulations in the canonical and isothermal-isobaric ensembles were performed to study the effect of varying the shape of the intermolecular potential on the phase diagram, critical, and interfacial properties of model fluids. The molecular interactions were modeled by the Approximate Non-Conformal (ANC) theory potentials. Unlike the Lennard-Jones or Morse potentials, the ANC interactions incorporate parameters (called softnesses) that modulate the steepness of the potential in their repulsive and attractive parts independently. This feature allowed us to separate unambiguously the role of each region of the potential on setting the thermophysical properties. In particular, we found positive linear correlation between all critical coordinates and the attractive and repulsive softness, except for the critical density and the attractive softness which are negatively correlated. Moreover, we found that the physical properties related to phase coexistence (such as span of the liquid phase between the critical and triple points, variations in the P-T vaporization curve, interface width, and surface tension) are more sensitive to changes in the attractive softness than to the repulsive one. Understanding the different roles of attractive and repulsive forces on phase coexistence may contribute to developing more accurate models of liquids and their mixtures.

Separating the effects of repulsive and attractive forces on the phase diagram, interfacial, and critical properties of simple fluids.

PubMed

Fuentes-Herrera, M; Moreno-Razo, J A; Guzmán, O; López-Lemus, J; Ibarra-Tandi, B

2016-06-07

Molecular simulations in the canonical and isothermal-isobaric ensembles were performed to study the effect of varying the shape of the intermolecular potential on the phase diagram, critical, and interfacial properties of model fluids. The molecular interactions were modeled by the Approximate Non-Conformal (ANC) theory potentials. Unlike the Lennard-Jones or Morse potentials, the ANC interactions incorporate parameters (called softnesses) that modulate the steepness of the potential in their repulsive and attractive parts independently. This feature allowed us to separate unambiguously the role of each region of the potential on setting the thermophysical properties. In particular, we found positive linear correlation between all critical coordinates and the attractive and repulsive softness, except for the critical density and the attractive softness which are negatively correlated. Moreover, we found that the physical properties related to phase coexistence (such as span of the liquid phase between the critical and triple points, variations in the P-T vaporization curve, interface width, and surface tension) are more sensitive to changes in the attractive softness than to the repulsive one. Understanding the different roles of attractive and repulsive forces on phase coexistence may contribute to developing more accurate models of liquids and their mixtures.

Developing strategies for predicting hyperkalemia in potassium-increasing drug-drug interactions.

PubMed

Eschmann, Emmanuel; Beeler, Patrick Emanuel; Schneemann, Markus; Blaser, Jürg

2017-01-01

To compare different strategies predicting hyperkalemia (serum potassium level ≥5.5 mEq/l) in hospitalized patients for whom medications triggering potassium-increasing drug-drug interactions (DDIs) were ordered. We investigated 5 strategies that combined prediction triggered at onset of DDI versus continuous monitoring and taking into account an increasing number of patient parameters. The considered patient parameters were identified using generalized additive models, and the thresholds of the prediction strategies were calculated by applying Youden's J statistic to receiver operation characteristic curves. Half of the data served as the calibration set, half as the validation set. We identified 132 incidences of hyperkalemia induced by 8413 potentially severe potassium-increasing DDIs among 76 467 patients. The positive predictive value (PPV) of those strategies predicting hyperkalemia at the onset of DDI ranged from 1.79% (undifferentiated anticipation of hyperkalemia due to the DDI) to 3.02% (additionally considering the baseline serum potassium) and 3.10% (including further patient parameters). Continuous monitoring significantly increased the PPV to 8.25% (considering the current serum potassium) and 9.34% (additional patient parameters). Continuous monitoring of the risk for hyperkalemia based on current potassium level shows a better predictive power than predictions triggered at the onset of DDI. This contrasts with efforts to improve DDI alerts by taking into account more patient parameters at the time of ordering. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Surface Diffusion in Systems of Interacting Brownian Particles

NASA Astrophysics Data System (ADS)

Mazroui, M'hammed; Boughaleb, Yahia

The paper reviews recent results on diffusive phenomena in two-dimensional periodic potential. Specifically, static and dynamic properties are investigated by calculating different correlation functions. Diffusion process is first studied for one-dimensional system by using the Fokker-Planck equation which is solved numerically by the matrix continued fraction method in the case of bistable potential. The transition from hopping to liquid-like diffusion induced by variation of some parameters is discussed. This study will therefore serve to demonstrate the influence of this form of potential. Further, an analytical approximation for the dc-conductivity is derived for a wide damping range in the framework of the Linear Response Theory. On the basis of this expression, calculations of the ac conductivity of two-dimensional system with Frenkel-Kontorova pair interaction in the intermediate friction regime is performed by using the continued fraction expansion method. The dc-conductivity expression is used to determine the rest of the development. By varying the density of mobile ions we discuss commensurability effects. To get information about the diffusion mechanism, the full width at half maximum λω(q), of the quasi-elastic line of the dynamical structure factor S(q,ω) is computed. The calculations are extended up to large values of q covering several Brillouin zones. The analysis of λω(q) with different parameters shows that the most probable diffusion process in good two-dimensional superionic conductors consists of a competition between a back correlated hopping in one direction and forward correlated hopping in addition to liquid-like motions in the other direction.

Soil microbial communities buffer physiological responses to drought stress in three hardwood species.

PubMed

Kannenberg, Steven A; Phillips, Richard P

2017-03-01

Trees possess myriad adaptations for coping with drought stress, but the extent to which their drought responses are influenced by interactions with soil microbes is poorly understood. To explore the role of microbes in mediating tree responses to drought stress, we exposed saplings of three species (Acer saccharum, Liriodendron tulipifera, and Quercus alba) to a four week experimental drought in mesocosms. Half of the pots were inoculated with a live soil slurry (i.e., a microbial inoculum derived from soils beneath the canopies of mature A. saccharum, L. tulipifera or Q. alba stands), while the other half of the pots received a sterile soil slurry. Soil microbes ameliorated drought stress in L. tulipifera by minimizing reductions in leaf water potential and by reducing photosynthetic declines. In A. saccharum, soil microbes reduced drought stress by lessening declines in leaf water potential, though these changes did not buffer the trees from declining photosynthetic rates. In Q. alba, soil microbes had no effects on leaf physiological parameters during drought stress. In all species, microbes had no significant effects on dynamic C allocation during drought stress, suggesting that microbial effects on plant physiology were unrelated to source-sink dynamics. Collectively, our results suggest that soil microbes have the potential to alter key parameters that are used to diagnose drought sensitivity (i.e., isohydry or anisohydry). To the extent that our results reflect dynamics occurring in forests, a revised perspective on plant hydraulic strategies that considers root-microbe interactions may lead to improved predictions of forest vulnerability to drought.

Physical scales in the Wigner-Boltzmann equation

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

Nedjalkov, M., E-mail: mixi@iue.tuwien.ac.at; Selberherr, S.; Ferry, D.K.

2013-01-15

The Wigner-Boltzmann equation provides the Wigner single particle theory with interactions with bosonic degrees of freedom associated with harmonic oscillators, such as phonons in solids. Quantum evolution is an interplay of two transport modes, corresponding to the common coherent particle-potential processes, or to the decoherence causing scattering due to the oscillators. Which evolution mode will dominate depends on the scales of the involved physical quantities. A dimensionless formulation of the Wigner-Boltzmann equation is obtained, where these scales appear as dimensionless strength parameters. A notion called scaling theorem is derived, linking the strength parameters to the coupling with the oscillators. Itmore » is shown that an increase of this coupling is equivalent to a reduction of both the strength of the electric potential, and the coherence length. Secondly, the existence of classes of physically different, but mathematically equivalent setups of the Wigner-Boltzmann evolution is demonstrated. - Highlights: Black-Right-Pointing-Pointer Dimensionless parameters determine the ratio of quantum or classical WB evolution. Black-Right-Pointing-Pointer The scaling theorem evaluates the decoherence effect due to scattering. Black-Right-Pointing-Pointer Evolution processes are grouped into classes of equivalence.« less

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

Effective mass in bilayer graphene at low carrier densities: The role of potential disorder and electron-electron interaction

NASA Astrophysics Data System (ADS)

Li, J.; Tan, L. Z.; Zou, K.; Stabile, A. A.; Seiwell, D. J.; Watanabe, K.; Taniguchi, T.; Louie, Steven G.; Zhu, J.

2016-10-01

In a two-dimensional electron gas, the electron-electron interaction generally becomes stronger at lower carrier densities and renormalizes the Fermi-liquid parameters, such as the effective mass of carriers. We combine experiment and theory to study the effective masses of electrons and holes me* and mh* in bilayer graphene in the low carrier density regime on the order of 1 ×1011c m-2 . Measurements use temperature-dependent low-field Shubnikov-de Haas oscillations observed in high-mobility hexagonal boron nitride supported samples. We find that while me* follows a tight-binding description in the whole density range, mh* starts to drop rapidly below the tight-binding description at a carrier density of n =6 ×1011c m-2 and exhibits a strong suppression of 30% when n reaches 2 ×1011c m-2 . Contributions from the electron-electron interaction alone, evaluated using several different approximations, cannot explain the experimental trend. Instead, the effect of the potential fluctuation and the resulting electron-hole puddles play a crucial role. Calculations including both the electron-electron interaction and disorder effects explain the experimental data qualitatively and quantitatively. This Rapid Communication reveals an unusual disorder effect unique to two-dimensional semimetallic systems.

Long-range Self-interacting Dark Matter in the Sun

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

Chen, Jing; State Key Laboratory of Theoretical Physics, Kavli Institute for Theoretical Physics China,Institute of Theoretical Physics, Chinese Academy of Science,Zhong Guan Cun East Street 55#, Beijing, 100190; Liang, Zheng-Liang

2015-12-10

We investigate the implications of the long-rang self-interaction on both the self-capture and the annihilation of the self-interacting dark matter (SIDM) trapped in the Sun. Our discussion is based on a specific SIDM model in which DM particles self-interact via a light scalar mediator, or Yukawa potential, in the context of quantum mechanics. Within this framework, we calculate the self-capture rate across a broad region of parameter space. While the self-capture rate can be obtained separately in the Born regime with perturbative method, and in the classical limits with the Rutherford formula, our calculation covers the gap between in amore » non-perturbative fashion. Besides, the phenomenology of both the Sommerfeld-enhanced s- and p-wave annihilation of the solar SIDM is also involved in our discussion. Moreover, by combining the analysis of the Super-Kamiokande (SK) data and the observed DM relic density, we constrain the nuclear capture rate of the DM particles in the presence of the dark Yukawa potential. The consequence of the long-range dark force on probing the solar SIDM turns out to be significant if the force-carrier is much lighter than the DM particle, and a quantitative analysis is provided.« less

Transmission through a potential barrier in Luttinger liquids with a topological spin gap

NASA Astrophysics Data System (ADS)

Kainaris, Nikolaos; Carr, Sam T.; Mirlin, Alexander D.

2018-03-01

We study theoretically the transport of the one-dimensional single-channel interacting electron gas through a strong potential barrier in the parameter regime where the spin sector of the low-energy theory is gapped by interaction (Luther-Emery liquid). There are two distinct phases of this nature, of which one is of particular interest as it exhibits nontrivial interaction-induced topological properties. Focusing on this phase and using bosonization and an expansion in the tunneling strength we calculate the conductance through the barrier as a function of the temperature as well as the local density of states (LDOS) at the barrier. Our main result concerns the mechanism of bound-state-mediated tunneling. The characteristic feature of the topological phase is the emergence of protected zero-energy bound states with fractional spin located at the impurity position. By flipping this fractional spin, single electrons can tunnel across the impurity even though the bulk spectrum for spin excitations is gapped. This results in a finite LDOS below the bulk gap and in a nonmonotonic behavior of the conductance. The system represents an important physical example of an interacting symmetry-protected topological phase, which combines features of a topological spin insulator and a topological charge metal, in which the topology can be probed by measuring transport properties.

Assessing rear-end crash potential in urban locations based on vehicle-by-vehicle interactions, geometric characteristics and operational conditions.

PubMed

Dimitriou, Loukas; Stylianou, Katerina; Abdel-Aty, Mohamed A

2018-03-01

Rear-end crashes are one of the most frequently occurring crash types, especially in urban networks. An understanding of the contributing factors and their significant association with rear-end crashes is of practical importance and will help in the development of effective countermeasures. The objective of this study is to assess rear-end crash potential at a microscopic level in an urban environment, by investigating vehicle-by-vehicle interactions. To do so, several traffic parameters at the individual vehicle level have been taken into consideration, for capturing car-following characteristics and vehicle interactions, and to investigate their effect on potential rear-end crashes. In this study rear-end crash potential was estimated based on stopping distance between two consecutive vehicles, and four rear-end crash potential cases were developed. The results indicated that 66.4% of the observations were estimated as rear-end crash potentials. It was also shown that rear-end crash potential was presented when traffic flow and speed standard deviation were higher. Also, locational characteristics such as lane of travel and location in the network were found to affect drivers' car following decisions and additionally, it was shown that speeds were lower and headways higher when Heavy Goods Vehicles lead. Finally, a model-based behavioral analysis based on Multinomial Logit regression was conducted to systematically identify the statistically significant variables in explaining rear-end risk potential. The modeling results highlighted the significance of the explanatory variables associated with rear-end crash potential, however it was shown that their effect varied among different model configurations. The outcome of the results can be of significant value for several purposes, such as real-time monitoring of risk potential, allocating enforcement units in urban networks and designing targeted proactive safety policies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Line shape parameters for the H2O-H2 collision system for application to exoplanet and planetary atmospheres

NASA Astrophysics Data System (ADS)

Renaud, Candice L.; Cleghorn, Kara; Hartmann, Léna; Vispoel, Bastien; Gamache, Robert R.

2018-05-01

Water can be detected throughout the universe: in comets, asteroids, dwarf planets, the inner and outer planets in our solar system, cool stars, brown dwarfs, and on many exoplanets. Here the focus is on locations rich in hydrogen gas. To properly study these environments, there is a need for the line shape parameters for H2O transitions in collision with hydrogen. This work presents calculations of the half-width and line shift, made using the Modified Complex Robert-Bonamy (MCRB) formalism, at a number of temperatures. It is shown that this collision system is strongly off-resonance. For such conditions, the atom-atom part of the intermolecular potential dominates the interaction of the radiating and perturbing molecules. The atom-atom parameters were adjusted by fitting the H2O-H2 measurements of Brown and Plymate (1996). Several techniques were used to extract lines for which there is more confidence in the quality of the data. The final potential yields results that agree with the measurements with ∼0.3% difference and a 5.9% standard deviation. Using this potential, MCRB calculations were made for all transitions in the pure rotation, ν2, ν1, and ν3 bands. The structure of the line shape parameters and the temperature dependence of the half-width, as a function of the rotational and vibrational quantum numbers, are discussed. It is shown that the power law model of the T-dependence of the half-width is inadequate over large temperature ranges.

Interaction of anisotropic dark energy fluid with perfect fluid in the presence of cosmological term Λ

NASA Astrophysics Data System (ADS)

Singh, S. Surendra

2018-05-01

Considering the locally rotationally symmetric (LRS) Bianchi type-I metric with cosmological constant Λ, Einstein’s field equations are discussed based on the background of anisotropic fluid. We assumed the condition A = B 1 m for the metric potentials A and B, where m is a positive constant to obtain the viable model of the Universe. It is found that Λ(t) is positive and inversely proportional to time. The values of matter-energy density Ωm, dark energy density ΩΛ and deceleration parameter q are found to be consistent with the values of WMAP observations. State finder parameters and anisotropic deviation parameter are also investigated. It is also observed that the derived model is an accelerating, shearing and non-rotating Universe. Some of the asymptotic and geometrical behaviors of the derived models are investigated with the age of the Universe.

An opinion-driven behavioral dynamics model for addictive behaviors

NASA Astrophysics Data System (ADS)

Moore, Thomas W.; Finley, Patrick D.; Apelberg, Benjamin J.; Ambrose, Bridget K.; Brodsky, Nancy S.; Brown, Theresa J.; Husten, Corinne; Glass, Robert J.

2015-04-01

We present a model of behavioral dynamics that combines a social network-based opinion dynamics model with behavioral mapping. The behavioral component is discrete and history-dependent to represent situations in which an individual's behavior is initially driven by opinion and later constrained by physiological or psychological conditions that serve to maintain the behavior. Individuals are modeled as nodes in a social network connected by directed edges. Parameter sweeps illustrate model behavior and the effects of individual parameters and parameter interactions on model results. Mapping a continuous opinion variable into a discrete behavioral space induces clustering on directed networks. Clusters provide targets of opportunity for influencing the network state; however, the smaller the network the greater the stochasticity and potential variability in outcomes. This has implications both for behaviors that are influenced by close relationships verses those influenced by societal norms and for the effectiveness of strategies for influencing those behaviors.

Accurate monoenergetic electron parameters of laser wakefield in a bubble model

NASA Astrophysics Data System (ADS)

Raheli, A.; Rahmatallahpur, S. H.

2012-11-01

A reliable analytical expression for the potential of plasma waves with phase velocities near the speed of light is derived. The presented spheroid cavity model is more consistent than the previous spherical and ellipsoidal model and it explains the mono-energetic electron trajectory more accurately, especially at the relativistic region. As a result, the quasi-mono-energetic electrons output beam interacting with the laser plasma can be more appropriately described with this model.

In silico simulations of experimental protocols for cardiac modeling.

PubMed

Carro, Jesus; Rodriguez, Jose Felix; Pueyo, Esther

2014-01-01

A mathematical model of the AP involves the sum of different transmembrane ionic currents and the balance of intracellular ionic concentrations. To each ionic current corresponds an equation involving several effects. There are a number of model parameters that must be identified using specific experimental protocols in which the effects are considered as independent. However, when the model complexity grows, the interaction between effects becomes increasingly important. Therefore, model parameters identified considering the different effects as independent might be misleading. In this work, a novel methodology consisting in performing in silico simulations of the experimental protocol and then comparing experimental and simulated outcomes is proposed for parameter model identification and validation. The potential of the methodology is demonstrated by validating voltage-dependent L-type calcium current (ICaL) inactivation in recently proposed human ventricular AP models with different formulations. Our results show large differences between ICaL inactivation as calculated from the model equation and ICaL inactivation from the in silico simulations due to the interaction between effects and/or to the experimental protocol. Our results suggest that, when proposing any new model formulation, consistency between such formulation and the corresponding experimental data that is aimed at being reproduced needs to be first verified considering all involved factors.

Pharmacokinetic interaction between scutellarin and valsartan in rats.

PubMed

Cui, Ming-Yu; Tian, Chong-Chong; Ju, Ai-Xia; Zhang, Chun-Ting; Li, Qiu-Hong

2013-04-01

Scutellarin is the main effective constituent of breviscapine, a flavonoid mixture isolated from the dried whole plant of Erigeron breviscapus (Vant.) Hand-Mazz, and valsartan is used as an antihypertensive drug. These two drugs have already been clinically used together to treat diabetic nephropathy (DN) in China, and the combined medications showed some enhanced protection against DN. The aim of this study is to investigate the potential pharmacokinetic interaction between scutellarin and valsartan in rats. Breviscapine injection (20 mg x kg(-1), i.v.) and valsartan (15 mg x kg-, i.g.), either alone or together were given to 18 male Sprague-Dawley rats. Concentrations of scutellarin and valsartan were quantified by HPLC, and pharmacokinetic parameters were calculated by non-compartmental methods. We found that the pharmacokinetic parameters of scutellarin altered significantly after co-administration of oral valsartan. The plasma clearance (CL(p)) and the bile clearance (CL(b)) of scutellarin were reduced significantly in the presence of valsartan. After oral administration of valsartan with or without intravenous scutellarin, however, the pharmacokinetic parameters of valsartan were comparable. In conclusion, our data suggests that the concurrent use of valsartan reduces the biliary excretion of scutellarin, and this may be due to the inhibitory effect of valsartan on the biliary excretion of scutellarin mediated by Mrp2 (Multidrug resistance-associated protein 2).

Performance evaluation of the zero-multipole summation method in modern molecular dynamics software.

PubMed

Sakuraba, Shun; Fukuda, Ikuo

2018-05-04

The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter-tuned SPME implementation are performed for various-sized water systems and two protein-water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time-consuming electrostatic convolution and because the ZMM gains short neighbor-list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Biodegradation of bispyribac sodium by a novel bacterial consortium BDAM: Optimization of degradation conditions using response surface methodology.

PubMed

Ahmad, Fiaz; Anwar, Samina; Firdous, Sadiqa; Da-Chuan, Yin; Iqbal, Samina

2018-05-05

Bispyribac sodium (BS), is a selective, systemic and post emergent herbicide used to eradicate grasses and broad leaf weeds. Extensive use of this herbicide has engendered serious environmental concerns. Hence it is important to develop strategies for bioremediation of BS in a cost effective and environment friendly way. In this study a bacterial consortium named BDAM, comprising three novel isolates Achromobacter xylosoxidans (BD1), Achromobacter pulmonis (BA2), and Ochrobactrum intermedium (BM2), was developed by virtue of its potential for degradation of BS. Different culture conditions (temperature, pH and inoculum size) were optimized for degradation of BS by the consortium BDAM and the mutual interactions of these parameters were analysed using a 2 3 full factorial central composite design (CCD) based on Response Surface Methodology (RSM). The optimal values for temperature, pH and inoculum size were found to be 40 °C, 8 and 0.4 g/L respectively to achieve maximum degradation of BS (85.6%). Moreover, the interactive effects of these parameters were investigated using three dimensional surface plots in terms of maximum fitness function. Importantly, it was concluded that the newly developed consortium is a potential candidate for biodegradation of BS in a safe, cost-effective and environmentally friendly manner. Copyright © 2017. Published by Elsevier B.V.

Synthesis and spectroscopic characterization of gold nanoparticles via plasma-liquid interaction technique

NASA Astrophysics Data System (ADS)

Khatoon, N.; Yasin, H. M.; Younus, M.; Ahmed, W.; Rehman, N. U.; Zakaullah, M.; Iqbal, M. Zafar

2018-01-01

Fabrication of non-functionalized gold nanoparticles is interesting owing to their potential applications in sensing and biomedicine. We report on the synthesis of surfactant-free gold nanoparticles (AuNPs) by Plasma-Liquid Interaction (PLI) technique, using micro-atmospheric pressure D.C. plasma. The effects of discharge parameters, such as discharge current, precursor concentration and gas flow rates on the structure and morphology of AuNPs have been investigated. Optical Emission Spectroscopy (OES) was employed to estimate the UV radiation intensity and OH radical density. Scanning electron microscopy (SEM) and ultraviolet-visible (UV-Vis) optical spectroscopy were employed to study the morphology and structure of AuNPs. The normalized intensities of UV radiation and OH radical density found to increase with increase in discharge current. We observed that the particle size can be tuned by controlling any of the following parameters: intensity of the UV radiation, OH radical density, and concentration of the Au precursor. Interestingly, we found that addition of 1% Ar in the feedstock gas results in formation of relatively uniform size distribution of nanoparticles. The surfactant-free AuNPs, due to their bare-surface, exhibit excellent surface-enhanced Raman scattering (SERS) properties. The SERS study of Rhodamine 6G using AuNPs as substrates, shows significant Raman enhancement and fluorescence quenching, which makes our technique a potentially powerful route to detection of trace amounts of dangerous explosives and other materials.

Unjamming in models with analytic pairwise potentials

NASA Astrophysics Data System (ADS)

Kooij, Stefan; Lerner, Edan

2017-06-01

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z , which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

Unjamming in models with analytic pairwise potentials.

PubMed

Kooij, Stefan; Lerner, Edan

2017-06-01

Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z, which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

Theoretical study of interaction of winter flounder antifreeze protein with ice

PubMed Central

Jorov, Alexander; Zhorov, Boris S.; Yang, Daniel S.C.

2004-01-01

Antifreeze proteins (AFPs) are synthesized by various organisms to enable their cells to survive subzero environment. These proteins bind to small ice crystals and inhibit their growth, which if left uncontrolled would be fatal to cells. The crystal structures of a number of AFPs have been determined; however, crystallographic analysis of AFP–ice complex is nearly impossible. Molecular modeling studies of AFPs’ interaction with ice surface is therefore invaluable. Early models of AFP–ice interaction suggested H-bond as the primary driving force behind such interaction. Recent experimental evidence, however, suggested that hydrophobic interactions could be the main contributor to AFP–ice association. All computational studies published to date were carried out to verify the H-bond model, and no works attempting to verify the hydrophobic interaction model have been published. In this work, we Monte Carlo–minimized complexes of several AFPs with ice taking into account nonbonded interactions, H-bonds, and the hydration potential for proteins. Parameters of the hydration potential for ice were developed with the assumption that the free energy of the water–ice association should be close to zero at equilibrium melting temperature. Our calculations demonstrate that desolvation of hydrophobic groups in the AFPs upon their binding to the grooves at the ice surface is indeed the major stabilizing contributor to the free energy of AFP–ice binding. This study is consistent with available structural and mutation data on AFPs. In particular, it explains the paradoxical finding that substitution of Thr residues with Val does not affect the potency of winter flounder AFP whereas substitution with Ser abolished its antifreeze activity. PMID:15152087

Simulation of miniature endplate potentials in neuromuscular junctions by using a cellular automaton

NASA Astrophysics Data System (ADS)

Avella, Oscar Javier; Muñoz, José Daniel; Fayad, Ramón

2008-01-01

Miniature endplate potentials are recorded in the neuromuscular junction when the acetylcholine contents of one or a few synaptic vesicles are spontaneously released into the synaptic cleft. Since their discovery by Fatt and Katz in 1952, they have been among the paradigms in neuroscience. Those potentials are usually simulated by means of numerical approaches, such as Brownian dynamics, finite differences and finite element methods. Hereby we propose that diffusion cellular automata can be a useful alternative for investigating them. To illustrate this point, we simulate a miniature endplate potential by using experimental parameters. Our model reproduces the potential shape, amplitude and time course. Since our automaton is able to track the history and interactions of each single particle, it is very easy to introduce non-linear effects with little computational effort. This makes cellular automata excellent candidates for simulating biological reaction-diffusion processes, where no other external forces are involved.

Investigation on nonautonomous soliton management in generalized external potentials via dispersion and nonlinearity

NASA Astrophysics Data System (ADS)

Vijayalekshmi, S.; Mani Rajan, M. S.; Mahalingam, A.; Uthayakumar, A.

2015-09-01

We investigate the controllable behavior of nonautonomous soliton in external potentials with variable dispersion and nonlinearity management functions, which describes the propagation of optical pulses in an inhomogeneous fiber system. We derive the Lax pair with a variable spectral parameter and the exact multi-soliton solution is generated via Darboux transformation. Based on these solutions, several novel optical solitons are constructed by selecting appropriate functions and the main evolution features of these waves are shown by some interesting figures with computer simulation. As few examples, breathers in periodic potential, soliton compression in an exponentially dispersion decreasing fiber and interaction of boomerang solitons are discussed. The presented results have applications in the study of nonautonomous soliton birefringence-managed switching architecture. These results are potentially useful in the management of nonautonomous soliton with external potentials in the optical soliton communications and long-haul telecommunication networks.

Future potential distribution of the emerging amphibian chytrid fungus under anthropogenic climate change.

PubMed

Rödder, Dennis; Kielgast, Jos; Lötters, Stefan

2010-11-01

Anthropogenic climate change poses a major threat to global biodiversity with a potential to alter biological interactions at all spatial scales. Amphibians are the most threatened vertebrates and have been subject to increasing conservation attention over the past decade. A particular concern is the pandemic emergence of the parasitic chytrid fungus Batrachochytrium dendrobatidis, which has been identified as the cause of extremely rapid large-scale declines and species extinctions. Experimental and observational studies have demonstrated that the host-pathogen system is strongly influenced by climatic parameters and thereby potentially affected by climate change. Herein we project a species distribution model of the pathogen onto future climatic scenarios generated by the IPCC to examine their potential implications on the pandemic. Results suggest that predicted anthropogenic climate change may reduce the geographic range of B. dendrobatidis and its potential influence on amphibian biodiversity.

Characterize Eruptive Processes at Yucca Mountain, Nevada

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

G. Valentine

2001-12-20

This Analysis/Model Report (AMR), ''Characterize Eruptive Processes at Yucca Mountain, Nevada'', presents information about natural volcanic systems and the parameters that can be used to model their behavior. This information is used to develop parameter-value distributions appropriate for analysis of the consequences of volcanic eruptions through a potential repository at Yucca Mountain. Many aspects of this work are aimed at resolution of the Igneous Activity Key Technical Issue (KTI) as identified by the Nuclear Regulatory Commission (NRC 1998, p. 3), Subissues 1 and 2, which address the probability and consequence of igneous activity at the proposed repository site, respectively. Withinmore » the framework of the Disruptive Events Process Model Report (PMR), this AMR provides information for the calculations in two other AMRs ; parameters described herein are directly used in calculations in these reports and will be used in Total System Performance Assessment (TSPA). Compilation of this AMR was conducted as defined in the Development Plan, except as noted. The report begins with considerations of the geometry of volcanic feeder systems, which are of primary importance in predicting how much of a potential repository would be affected by an eruption. This discussion is followed by one of the physical and chemical properties of the magmas, which influences both eruptive styles and mechanisms for interaction with radioactive waste packages. Eruptive processes including the ascent velocity of magma at depth, the onset of bubble nucleation and growth in the rising magmas, magma fragmentation, and velocity of the resulting gas-particle mixture are then discussed. The duration of eruptions, their power output, and mass discharge rates are also described. The next section summarizes geologic constraints regarding the interaction between magma and waste packages. Finally, they discuss bulk grain size produced by relevant explosive eruptions and grain shapes.« less

Thruster Plume Plasma Diagnostics: A Ground Chamber Experiment for a 2-Kilowatt Arcjet

NASA Technical Reports Server (NTRS)

Galofaro, Joel T.; Vayner, Boris V.; Hillard, G. Barry; Chornak, Michael T.

2005-01-01

Although detailed near field (0 to 3 cm) information regarding the exhaust plume of a two kilowatt arc jet is available (refs. 1 to 6), there is virtually little or no information (outside of theoretical extrapolations) available concerning the far field (2.6 to 6.1 m). Furthermore real information about the plasma at distances between (3 to 6 m) is of critical importance to high technology satellite companies in understanding the effect of arc jet plume exhausts on space based power systems. It is therefore of utmost importance that one understands the exact nature of the interaction between the arc jet plume, the spacecraft power system and the surrounding electrical plasma environment. A good first step in understanding the nature of the interactions lies in making the needed plume parameter measurements in the far field. All diagnostic measurements are performed inside a large vacuum system (12 m diameter by 18 m high) with a full scale arc jet and solar array panel in the required flight configuration geometry. Thus, necessary information regarding the plume plasma parameters in the far field is obtained. Measurements of the floating potential, the plasma potential, the electron temperature, number density, density distribution, debye length, and plasma frequency are obtained at various locations about the array (at vertical distances from the arc jet nozzle: 2.6, 2.7, 2.8, 3.2, 3.6, 4.0, 4.9, 5.0, 5.4, 5.75, and 6.14 m). Plasma diagnostic parameters are measured for both the floating and grounded configurations of the arc jet anode and array. Spectroscopic optical measurements are then acquired in close proximity to the nozzle, and contamination measurements are made in the vicinity of the array utilizing a mass spectrometer and two Quartz Crystal Microbalances (QCM's).

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic.

PubMed

Xiao, Enzong; Krumins, Valdis; Xiao, Tangfu; Dong, Yiran; Tang, Song; Ning, Zengping; Huang, Zhengyu; Sun, Weimin

2017-02-01

Investigation of microbial communities of soils contaminated by antimony (Sb) and arsenic (As) is necessary to obtain knowledge for their bioremediation. However, little is known about the depth profiles of microbial community composition and structure in Sb and As contaminated soils. Our previous studies have suggested that historical factors (i.e., soil and sediment) play important roles in governing microbial community structure and composition. Here, we selected two different types of soil (flooded paddy soil versus dry corn field soil) with co-contamination of Sb and As to study interactions between these metalloids, geochemical parameters and the soil microbiota as well as microbial metabolism in response to Sb and As contamination. Comprehensive geochemical analyses and 16S rRNA amplicon sequencing were used to shed light on the interactions of the microbial communities with their environments. A wide diversity of taxonomical groups was present in both soil cores, and many were significantly correlated with geochemical parameters. Canonical correspondence analysis (CCA) and co-occurrence networks further elucidated the impact of geochemical parameters (including Sb and As contamination fractions and sulfate, TOC, Eh, and pH) on vertical distribution of soil microbial communities. Metagenomes predicted from the 16S data using PICRUSt included arsenic metabolism genes such as arsenate reductase (ArsC), arsenite oxidase small subunit (AoxA and AoxB), and arsenite transporter (ArsA and ACR3). In addition, predicted abundances of arsenate reductase (ArsC) and arsenite oxidase (AoxA and AoxB) genes were significantly correlated with Sb contamination fractions, These results suggest potential As biogeochemical cycling in both soil cores and potentially dynamic Sb biogeochemical cycling as well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biological potential of oxo-vanadium salicylediene amino-acid complexes as cytotoxic, antimicrobial, antioxidant and DNA interaction.

PubMed

Adam, Mohamed Shaker S; Elsawy, Hany

2018-05-04

New series of oxo-vanadium N-salicyledieneamino acid Schiff base complexes are synthesized and characterized. They are synthesized from the reaction of sodium salicylaldehyde-5-sulfonate, some amino acids, alanine (VOHL1), leucine (VOHL2) or glycine (VOHL3) in an aqueous media, and leucine (VOHLpy1) or tryptophan (VOHLpy2) in pyridine with vanadyl acetylacetonate. The complexes are characterized by EA, TGA, IR, UV-Visible and mass spectra, conductivity and magnetic measurements. The biological activity of the VO-complexes shows that VOHL1, VOHL2 and VOHL3 exhibit anti-proliferative effect and may be used as anticancer drugs. VO-complexes manifest high toxicity, except VOHL2 is less toxic, and could be applied for the human being. VOHL1, VOHL2 and VOHL3 display remarkable SOD like potential and act as high inhibiting reagents. VOHLpy1 and VOHLpy2 show low inhibiting potentials. VO-complexes have good anti-oxidant effect, in which VOHL3 affords the best antioxidant activity. The interaction between VO-complexes and DNA is studied spectrophotometrically and by gel electrophoresis. Binding constants and spectrophotometric parameters indicate a strong interaction between VO-complexes and DNA. VO-complexes have respectable anti-bacterial and antifungal activities, where VOHL3 shows the maximum potential. DFT calculations of VOHL1 and VOHL3 were discussed in the light of their biological activity, which are convenient with the obtained results. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

2002-05-01

To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high-dielectric medium was solved and charges distributed near the molecular surface were indicated as leading to the apparent linearity.

Generation Mechanism of Alternans in Luo-Rudy Model

NASA Astrophysics Data System (ADS)

Kitajima, Hiroyuki; Ioka, Eri; Yazawa, Toru

Electrical alternans is the alternating amplitude from beat to beat in the action potential of the cardiac cell. It has been associated with ventricular arrhythmias in many clinical studies; however, its dynamical mechanisms remain unknown. The reason is that we do not have realistic network models of the heart system. Recently, Yazawa clarified the network structure of the heart and the central nerve system in the crustacean heart. In this study, we construct a simple model of the heart system based on Yazawa’s experimental data. Using this model, we clarify that two parameters (the conductance of sodium ions and free concentration of potassium ions in the extracellular compartment) play the key roles of generating alternans. In particular, we clarify that the inactivation gate of the time-independent potassium channel is the most important parameter. Moreover, interaction between the membrane potential and potassium ionic currents is significant for generating alternate rhythms. This result indicates that if the muscle cell has problems such as channelopathies, there is great risk of generating alternans.

Multi-dimensional stable fundamental solitons and excitations in PT-symmetric harmonic-Gaussian potentials with unbounded gain-and-loss distributions

NASA Astrophysics Data System (ADS)

Chen, Yong; Yan, Zhenya

2018-04-01

We demonstrate the parity-time- (PT-) symmetric harmonic-Gaussian potential with unbounded gain-and-loss distribution can support entirely-real linear spectra, stable spatial and spatio-temporal solitons in an inhomogeneous nonlinear medium (e.g., cubic nonlinear Schrödinger equation with the self-focusing and defocusing cases). Exact analytical solitons are derived in both one-dimensional (1D) and higher-dimensional (e.g., 2D, 3D) geometries such that they are verified to be stable in the given parameters regions. Particularly, several families of numerical fundamental solitons (especially the 1D double-peaked solitons, 2D vortex solitons, and 3D double bullets) can be found to be stable around the propagation parameters for exact solitons. Other significant properties of solitons are also explored including the interactions of solitons, stable soliton excitations, and transverse power flows. The results may excite the corresponding theoretical analysis and experiment designs.

Renewable fluid dynamic energy derived from aquatic animal locomotion.

PubMed

Dabiri, John O

2007-09-01

Aquatic animals swimming in isolation and in groups are known to extract energy from the vortices in environmental flows, significantly reducing muscle activity required for locomotion. A model for the vortex dynamics associated with this phenomenon is developed, showing that the energy extraction mechanism can be described by simple criteria governing the kinematics of the vortices relative to the body in the flow. In this way, we need not make direct appeal to the fluid dynamics, which can be more difficult to evaluate than the kinematics. Examples of these principles as exhibited in swimming fish and existing energy conversion devices are described. A benefit of the developed framework is that the potentially infinite-dimensional parameter space of the fluid-structure interaction is reduced to a maximum of eight combinations of three parameters. The model may potentially aid in the design and evaluation of unsteady aero- and hydrodynamic energy conversion systems that surpass the Betz efficiency limit of steady fluid dynamic energy conversion systems.

Characteristics of activated carbon and carbon nanotubes as adsorbents to remove annatto (norbixin) in cheese whey.

PubMed

Zhang, Yue; Pan, Kang; Zhong, Qixin

2013-09-25

Removing annatto from cheese whey without bleaching has potential to improve whey protein quality. In this work, the potential of two activated carbon products and multiwalled carbon nanotubes (CNT) was studied for extracting annatto (norbixin) in aqueous solutions. Batch adsorption experiments were studied for the effects of solution pH, adsorbent mass, contact duration, and ionic strength. The equilibrium adsorption data were observed to fit both Langmuir and Freundlich isotherm models. The thermodynamic parameters estimated from adsorption isotherms demonstrated that the adsorption of norbixin on three adsorbents is exothermic, and the entropic contribution differs with adsorbent structure. The adsorption kinetics, with CNT showing a higher rate than activated carbon, followed the pseudo first order and second order rate expressions and demonstrated the significance of intraparticle diffusion. Electrostatic interactions were observed to be significant in the adsorption. The established adsorption parameters may be used in the dairy industry to decolorize cheese whey without applying bleaching agents.

Theoretical study on the molecular structure and vibrational properties, NBO and HOMO-LUMO analysis of the POX3 (X = F, Cl, Br, I) series of molecules

NASA Astrophysics Data System (ADS)

Galván, Jorge E.; Gil, Diego M.; Lanús, Hernán E.; Altabef, Aida Ben

2015-02-01

The fourth member of the series of compounds of the type POX3 with X = I was synthesized and characterized by infrared spectroscopy. The geometrical parameters and vibrational properties of POX3 (X = F, Cl, Br, I) molecules were investigated theoretically by means DFT and ab initio methods. Available geometrical and vibrational data were used together with theoretical calculations in order to obtain a set of scaled force constants. The observed trends in geometrical parameters are analyzed and compared with those obtained in a previous work for the VOX3 (X = F, Cl, Br, I) series of compounds. NBO analysis was performed in order to know the hyper-conjugative interactions that favor one structure over another. The molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, chemical hardness, softness and global electrophilicity index have been deduced from HOMO-LUMO analysis.

Dissociation coefficients of protein adsorption to nanoparticles as quantitative metrics for description of the protein corona: A comparison of experimental techniques and methodological relevance.

PubMed

Hühn, Jonas; Fedeli, Chiara; Zhang, Qian; Masood, Atif; Del Pino, Pablo; Khashab, Niveen M; Papini, Emanuele; Parak, Wolfgang J

2016-06-01

Protein adsorption to nanoparticles is described as a chemical reaction in which proteins attach to binding sites on the nanoparticle surface. This process is defined by a dissociation coefficient, which tells how many proteins are adsorbed per nanoparticle in dependence of the protein concentration. Different techniques to experimentally determine dissociation coefficients of protein adsorption to nanoparticles are reviewed. Results of more than 130 experiments in which dissociation coefficients have been determined are compared. Data show that different methods, nanoparticle systems, and proteins can lead to significantly different dissociation coefficients. However, we observed a clear tendency of smaller dissociation coefficients upon less negative towards more positive zeta potentials of the nanoparticles. The zeta potential thus is a key parameter influencing protein adsorption to the surface of nanoparticles. Our analysis highlights the importance of the characterization of the parameters governing protein-nanoparticle interaction for quantitative evaluation and objective literature comparison. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

PubMed

Sweetapple, Christine; Fu, Guangtao; Butler, David

2013-09-01

This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interactive effects between total SO2 , ethanol and storage temperature against Brettanomyces bruxellensis.

PubMed

Edwards, C G; Oswald, T A

2018-01-01

Although Brettanomyces bruxellensis continues to be a problem during red winemaking due to formation of off-odours and flavours, few interactions between intrinsic and extrinsic conditions that would limit spoilage have been identified. Using a commercially prepared Merlot wine, a 3 × 2 × 2 complete factorial design was implemented with total SO 2 (0, 60 or 100 mg l -1 ), ethanol (13% or 14·5% v v -1 ) and storage temperature (15° or 18°C) as variables. Populations of two strains of B. bruxellensis isolated from Washington wines (I1a and F3) were monitored for 100 days before concentrations of 4-ethylphenol, 4-ethylguaiacol and volatile acidity were measured. In wines with 13% v v -1 ethanol and stored at 15°C, addition of 100 mg l -1 total SO 2 resulted in much longer lag phases (>40 days) compared with wines without sulphites. At 14·5% v v -1 ethanol, culturability did not recover from wines with 100 mg l -1 total SO 2 regardless of the storage temperature (15° or 18°C). A few significant interactions were noted between these parameters which also affected synthesis of metabolites. Thus, SO 2 , ethanol concentration and storage temperature should be together used as means to reduce infections by B. bruxellensis. The potential for utilizing SO 2 along with the ethanol and storage temperature was studied to inhibit the spoilage yeast, Brettanomyces bruxellensis, during cellar ageing of red wines. This report is the first to identify the existence of interactions between these parameters that affect growth and/or metabolism of the yeast (i.e., synthesis of 4-ethylphenol, 4-ethylguaiacol and volatile acidity). Based on current and past findings, recommendations are presented related to the use of potential antimicrobial synergies between SO 2 , ethanol concentration and storage temperatures. © 2017 The Society for Applied Microbiology.

Interactions of 172 plant extracts with human organic anion transporter 1 (SLC22A6) and 3 (SLC22A8): a study on herb-drug interactions

PubMed Central

Lu, Hang; Lu, Zhiqiang; Li, Xue; Li, Gentao; Qiao, Yilin

2017-01-01

Background Herb-drug interactions (HDIs) resulting from concomitant use of herbal products with clinical drugs may cause adverse reactions. Organic anion transporter 1 (OAT1) and 3 (OAT3) are highly expressed in the kidney and play a key role in the renal elimination of substrate drugs. So far, little is known about the herbal extracts that could modulate OAT1 and OAT3 activities. Methods HEK293 cells stably expressing human OAT1 (HEK-OAT1) and OAT3 (HEK-OAT3) were established and characterized. One hundred seventy-two extracts from 37 medicinal and economic plants were prepared. An initial concentration of 5 µg/ml for each extract was used to evaluate their effects on 6-carboxylfluorescein (6-CF) uptake in HEK-OAT1 and HEK-OAT3 cells. Concentration-dependent inhibition studies were conducted for those extracts with more than 50% inhibition to OAT1 and OAT3. The extract of Juncus effusus, a well-known traditional Chinese medicine, was assessed for its effect on the in vivo pharmacokinetic parameters of furosemide, a diuretic drug which is a known substrate of both OAT1 and OAT3. Results More than 30% of the plant extracts at the concentration of 5 µg/ml showed strong inhibitory effect on the 6-CF uptake mediated by OAT1 (61 extracts) and OAT3 (55 extracts). Among them, three extracts for OAT1 and fourteen extracts for OAT3 were identified as strong inhibitors with IC50 values being <5 µg/ml. Juncus effusus showed a strong inhibition to OAT3 in vitro, and markedly altered the in vivo pharmacokinetic parameters of furosemide in rats. Conclusion The present study identified the potential interactions of medicinal and economic plants with human OAT1 and OAT3, which is helpful to predict and to avoid potential OAT1- and OAT3-mediated HDIs. PMID:28560096

Pairing matrix elements and pairing gaps with bare, effective, and induced interactions

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

Barranco, F.; Bortignon, P.F.; Colo, G.

2005-11-01

The dependence on the single-particle states of the pairing matrix elements of the Gogny force and of the bare low-momentum nucleon-nucleon potential v{sub low-k}--designed so as to reproduce the low-energy observables avoiding the use of a repulsive core--is studied for a typical finite, superfluid nucleus ({sup 120}Sn). It is found that the matrix elements of v{sub low-k} follow closely those of v{sub Gogny} on a wide range of energy values around the Fermi energy e{sub F}, those associated with v{sub low-k} being less attractive. This result explains the fact that around e{sub F} the pairing gap {delta}{sub Gogny} associated withmore » the Gogny interaction (and with a density of single-particle levels corresponding to an effective k mass m{sub k}{approx_equal}0.7 m) is a factor of about 2 larger than {delta}{sub low-k}, being in agreement with {delta}{sub exp}=1.4 MeV. The exchange of low-lying collective surface vibrations among pairs of nucleons moving in time-reversal states gives rise to an induced pairing interaction v{sub ind} peaked at e{sub F}. The interaction (v{sub low-k}+v{sub ind}) Z{sub {omega}} arising from the renormalization of the bare nucleon-nucleon potential and of the single-particle motion ({omega}-mass and quasiparticle strength Z{sub {omega}}) associated with the particle-vibration coupling mechanism, leads to a value of the pairing gap at the Fermi energy {delta}{sub ren} that accounts for the experimental value. An important question that remains to be studied quantitatively is to what extent {delta}{sub Gogny}, which depends on average parameters, and {delta}{sub ren}, which explicitly depends on the parameters describing the (low-energy) nuclear structure, display or not a similar isotopic dependence and whether this dependence is borne out by the data.« less

Synthesis, crystallographic, spectral, and spectrophotometric studies of proton transfer complex of 1,2-dimethylimidazole with 3,5-dinitrobenzoic acid in different polar solvents

NASA Astrophysics Data System (ADS)

Miyan, Lal; Zulkarnain; Ahmad, Afaq

2017-04-01

The molecular interaction between 1, 2-dimethylimidazole (DMI) and 3,5-dinitrobenzoic acid (DNBA) has been investigated in methanol at room temperature. The stoichiometry of the synthesized CT complex was found to be 1:1 using the straight line method of Benesi-Hildebrand equation. The structure of the resulting CT complex was isolating and characterized using X-ray crystallography, FTIR and 1H NMR spectroscopic techniques. The thermal composition and stability of the CT complex were analyzed using thermogravimetric and differential thermal analysis (TGA and DTA). UV-visible spectrophotometric technique was used to the determine the various important physical parameters such as formation constant (KCT), molar extinction coefficient (εCT), energy of interaction (ECT), ionization potential (ID), resonance energy (RN), free energy (ΔG°), oscillator strength (ƒ) and transition dipole moment (μN). The effect of polarity of the solvent and concentration of acceptor on these parameters have been investigated. The results indicate that charge transfer complex (CTC) is more stable in less polar solvent due to the high value of the formation constant. A polymeric network through hydrogen bonding interaction between neighboring moieties was observed. This has also been attributed to the formation of 1:1 type CT complex.

Distinguishing interacting dark energy from wCDM with CMB, lensing, and baryon acoustic oscillation data

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

Väliviita, Jussi; Palmgren, Elina, E-mail: jussi.valiviita@helsinki.fi, E-mail: elina.palmgren@helsinki.fi

2015-07-01

We employ the Planck 2013 CMB temperature anisotropy and lensing data, and baryon acoustic oscillation (BAO) data to constrain a phenomenological wCDM model, where dark matter and dark energy interact. We assume time-dependent equation of state parameter for dark energy, and treat dark matter and dark energy as fluids whose energy-exchange rate is proportional to the dark-matter density. The CMB data alone leave a strong degeneracy between the interaction rate and the physical CDM density parameter today, ω{sub c}, allowing a large interaction rate |Γ| ∼ H{sub 0}. However, as has been known for a while, the BAO data break this degeneracy.more » Moreover, we exploit the CMB lensing potential likelihood, which probes the matter perturbations at redshift z ∼ 2 and is very sensitive to the growth of structure, and hence one of the tools for discerning between the ΛCDM model and its alternatives. However, we find that in the non-phantom models (w{sub de}>−1), the constraints remain unchanged by the inclusion of the lensing data and consistent with zero interaction, −0.14 < Γ/H{sub 0} < 0.02 at 95% CL. On the contrary, in the phantom models (w{sub de}<−1), energy transfer from dark energy to dark matter is moderately favoured over the non-interacting model; 0−0.57 < Γ/H{sub 0} < −0.1 at 95% CL with CMB+BAO, while addition of the lensing data shifts this to −0.46 < Γ/H{sub 0} < −0.01.« less

Interactions in Undersaturated and Supersaturated Lysozyme Solutions: Static and Dynamic Light Scattering Results

NASA Technical Reports Server (NTRS)

Muschol, Martin; Rosenberger, Franz

1995-01-01

We have performed multiangle static and dynamic light scattering studies of lysozyme solutions at pH=4.7. The Rayleigh ratio R(sub g) and the collective diffusion coefficient D(sub c) were determined as function of both protein concentration c(sub p) and salt concentration c(sub s) with two different salts. At low salt concentrations, the scattering ratio K(sub c)(sub p)/R(sub theta) and diffusivity increased with protein concentration above the values for a monomeric, ideal solution. With increasing salt concentration this trend was eventually reversed. The hydrodynamic interactions of lysozyme in solution, extracted from the combination of static and dynamic scattering data, decreased significantly with increasing salt concentration. These observations reflect changes in protein interactions, in response to increased salt screening, from net repulsion to net attraction. Both salts had the same qualitative effect, but the quantitative behavior did not scale with the ionic strength of the solution. This indicates the presence of salt specific effects. At low protein concentrations, the slopes of K(sub c)(sub p)/R(sub theta) and D(sub c) vs c(sub p) were obtained. The dependence of the slopes on ionic strength was modeled using a DLVO potential for colloidal interactions of two spheres, with the net protein charge Z(sub e) and Hamaker constant A(sub H) as fitting parameters. The model reproduces the observed variations with ionic strength quite well. Independent fits to the static and dynamic data, however, led to different values of the fitting parameters. These and other shortcomings suggest that colloidal interaction models alone are insufficient to explain protein interactions in solutions.

Exploring extended scalar sectors with di-Higgs signals: a Higgs EFT perspective

NASA Astrophysics Data System (ADS)

Corbett, Tyler; Joglekar, Aniket; Li, Hao-Lin; Yu, Jiang-Hao

2018-05-01

We consider extended scalar sectors of the Standard Model as ultraviolet complete motivations for studying the effective Higgs self-interaction operators of the Standard Model effective field theory. We investigate all motivated heavy scalar models which generate the dimension-six effective operator, | H|6, at tree level and proceed to identify the full set of tree-level dimension-six operators by integrating out the heavy scalars. Of seven models which generate | H|6 at tree level only two, quadruplets of hypercharge Y = 3 Y H and Y = Y H , generate only this operator. Next we perform global fits to constrain relevant Wilson coefficients from the LHC single Higgs measurements as well as the electroweak oblique parameters S and T. We find that the T parameter puts very strong constraints on the Wilson coefficient of the | H|6 operator in the triplet and quadruplet models, while the singlet and doublet models could still have Higgs self-couplings which deviate significantly from the standard model prediction. To determine the extent to which the | H|6 operator could be constrained, we study the di-Higgs signatures at the future 100 TeV collider and explore future sensitivity of this operator. Projected onto the Higgs potential parameters of the extended scalar sectors, with 30 ab-1 luminosity data we will be able to explore the Higgs potential parameters in all seven models.

Attitude determination and calibration using a recursive maximum likelihood-based adaptive Kalman filter

NASA Technical Reports Server (NTRS)

Kelly, D. A.; Fermelia, A.; Lee, G. K. F.

1990-01-01

An adaptive Kalman filter design that utilizes recursive maximum likelihood parameter identification is discussed. At the center of this design is the Kalman filter itself, which has the responsibility for attitude determination. At the same time, the identification algorithm is continually identifying the system parameters. The approach is applicable to nonlinear, as well as linear systems. This adaptive Kalman filter design has much potential for real time implementation, especially considering the fast clock speeds, cache memory and internal RAM available today. The recursive maximum likelihood algorithm is discussed in detail, with special attention directed towards its unique matrix formulation. The procedure for using the algorithm is described along with comments on how this algorithm interacts with the Kalman filter.

Control mechanisms for stochastic biochemical systems via computation of reachable sets.

PubMed

Lakatos, Eszter; Stumpf, Michael P H

2017-08-01

Controlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic biology. Molecular processes, however, are notoriously noisy and frequently nonlinear. We present an approach to studying the impact of control measures on motifs of molecular interactions that addresses the problems faced in many biological systems: stochasticity, parameter uncertainty and nonlinearity. We show that our reachability analysis formalism can describe the potential behaviour of biological (naturally evolved as well as engineered) systems, and provides a set of bounds on their dynamics at the level of population statistics: for example, we can obtain the possible ranges of means and variances of mRNA and protein expression levels, even in the presence of uncertainty about model parameters.

Control mechanisms for stochastic biochemical systems via computation of reachable sets

PubMed Central

Lakatos, Eszter

2017-01-01

Controlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic biology. Molecular processes, however, are notoriously noisy and frequently nonlinear. We present an approach to studying the impact of control measures on motifs of molecular interactions that addresses the problems faced in many biological systems: stochasticity, parameter uncertainty and nonlinearity. We show that our reachability analysis formalism can describe the potential behaviour of biological (naturally evolved as well as engineered) systems, and provides a set of bounds on their dynamics at the level of population statistics: for example, we can obtain the possible ranges of means and variances of mRNA and protein expression levels, even in the presence of uncertainty about model parameters. PMID:28878957

Results of heavy ion radiotherapy

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

Castro, J.R.

1994-04-01

The potential of heavy ion therapy for clinical use in cancer therapy stems from the biological parameters of heavy charged particles, and their precise dose localization. Biologically, carbon, neon and other heavy ion beams (up to about silicon) are clinically useful in overcoming the radioresistance of hypoxic tumors, thus increasing biological effectiveness relative to low-LET x-ray or electron beams. Cells irradiated by heavy ions show less variation in cell-cycle related radiosensitivity and decreased repair of radiation injury. The physical parameters of these heavy charged particles allow precise delivery of high radiation doses to tumors while minimizing irradiation of normal tissues.more » Clinical use requires close interaction between radiation oncologists, medical physicists, accelerator physicists, engineers, computer scientists and radiation biologists.« less

Three-Dimensional Simulation of Traveling-Wave Tube Cold-Test Characteristics Using MAFIA

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Wilson, Jeffrey D.

1995-01-01

The three-dimensional simulation code MAFIA was used to compute the cold-test parameters - frequency-phase dispersion, beam on-axis interaction impedance, and attenuation - for two types of traveling-wave tube (TWT) slow-wave circuits. The potential for this electromagnetic computer modeling code to reduce the time and cost of TWT development is demonstrated by the high degree of accuracy achieved in calculating these parameters. Generalized input files were developed for ferruled coupled-cavity and TunneLadder slow-wave circuits. These files make it easy to model circuits of arbitrary dimensions. The utility of these files was tested by applying each to a specific TWT slow-wave circuit and comparing the results with experimental data. Excellent agreement was obtained.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

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

Gimenez, M. Cecilia; Reinaudi, Luis, E-mail: luis.reinaudi@unc.edu.ar; Leiva, Ezequiel P. M.

2015-12-28

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations weremore » made for the case of silver-gold alloys when the medium interacted selectively with Ag.« less

Theoretical study of solvent effects on the coil-globule transition

NASA Astrophysics Data System (ADS)

Polson, James M.; Opps, Sheldon B.; Abou Risk, Nicholas

2009-06-01

The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for two simple polymer/solvent models, each employing hard-sphere chains and hard-sphere solvent particles as well as attractive square-well potentials between some interaction sites. For each model, collapse is driven by variation in a parameter which changes the energy mismatch between monomers and solvent particles. The solvation potentials were calculated using two fundamentally different methodologies, each designed to predict the conformational behavior of polymers in solution: (1) the polymer reference interaction site model (PRISM) theory and (2) a many-body solvation potential (MBSP) based on scaled particle theory introduced by Grayce [J. Chem. Phys. 106, 5171 (1997)]. For the PRISM calculations, two well-studied solvation monomer-monomer pair potentials were employed, each distinguished by the closure relation used in its derivation: (i) a hypernetted-chain (HNC)-type potential and (ii) a Percus-Yevick (PY)-type potential. The theoretical predictions were each compared to results obtained from explicit-solvent discontinuous molecular dynamics simulations on the same polymer/solvent model systems [J. Chem. Phys. 125, 194904 (2006)]. In each case, the variation in the coil-globule transition properties with solvent density is mostly qualitatively correct, though the quantitative agreement between the theory and prediction is typically poor. The HNC-type potential yields results that are more qualitatively consistent with simulation. The conformational behavior of the polymer upon collapse predicted by the MBSP approach is quantitatively correct for low and moderate solvent densities but is increasingly less accurate for higher densities. At high solvent densities, the PRISM-HNC and MBSP approaches tend to overestimate, while the PRISM-PY approach underestimates the tendency of the solvent to drive polymer collapse.

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE PAGES

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; ...

2015-12-03

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

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

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

2011-05-19

A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values

PubMed Central

Lambert, Dominic; Draper, David E.

2012-01-01

To investigate the mechanism by which urea destabilizes RNA structure, urea-induced unfolding of four different RNA secondary and tertiary structures was quantified in terms of an m-value, the rate at which the free energy of unfolding changes with urea molality. From literature data and our osmometric study of a backbone analog, we derived average interaction potentials (per Å2 of solvent accessible surface) between urea and three kinds of RNA surfaces: phosphate, ribose, and base. Estimates of the increases in solvent accessible surface areas upon RNA denaturation were based on a simple model of unfolded RNA as a combination of helical and single strand segments. These estimates, combined with the three interaction potentials and a term to account for urea interactions with released ions, yield calculated m-values in good agreement with experimental values (200 mm monovalent salt). Agreement was obtained only if single-stranded RNAs were modeled in a highly stacked, A form conformation. The primary driving force for urea induced denaturation is the strong interaction of urea with the large surface areas of bases that become exposed upon denaturation of either RNA secondary or tertiary structure, though urea interactions with backbone and released ions may account for up to a third of the m-value. Urea m-values for all four RNA are salt-dependent, which we attribute to an increased extension (or decreased charge density) of unfolded RNAs with increased urea concentration. The sensitivity of the urea m-value to base surface exposure makes it a potentially useful probe of the conformations of RNA unfolded states. PMID:23088364

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams.

PubMed

Milan, M; Carraro, L; Fariselli, P; Martino, M E; Cavalieri, D; Vitali, F; Boffo, L; Patarnello, T; Bargelloni, L; Cardazzo, B

2018-01-01

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota. Copyright © 2017 Elsevier B.V. All rights reserved.

Combining Costs and Benefits of Animal Activities to Assess Net Yield Outcomes in Apple Orchards

PubMed Central

Luck, Gary W.

2016-01-01

Diverse animal communities influence ecosystem function in agroecosystems through positive and negative plant-animal interactions. Yet, past research has largely failed to examine multiple interactions that can have opposing impacts on agricultural production in a given context. We collected data on arthropod communities and yield quality and quantity parameters (fruit set, yield loss and net outcomes) in three major apple-growing regions in south-eastern Australia. We quantified the net yield outcome (accounting for positive and negative interactions) of multiple animal activities (pollination, fruit damage, biological control) across the entire growing season on netted branches, which excluded vertebrate predators of arthropods, and open branches. Net outcome was calculated as the number of undamaged fruit at harvest as a proportion of the number of blossoms (i.e., potential fruit yield). Vertebrate exclusion resulted in lower levels of fruit set and higher levels of arthropod damage to apples, but did not affect net outcomes. Yield quality and quantity parameters (fruit set, yield loss, net outcomes) were not directly associated with arthropod functional groups. Model variance and significant differences between the ratio of pest to beneficial arthropods between regions indicated that complex relationships between environmental factors and multiple animal interactions have a combined effect on yield. Our results show that focusing on a single crop stage, species group or ecosystem function/service can overlook important complexity in ecological processes within the system. Accounting for this complexity and quantifying the net outcome of ecological interactions within the system, is more informative for research and management of biodiversity and ecosystem services in agricultural landscapes. PMID:27391022

Combining Costs and Benefits of Animal Activities to Assess Net Yield Outcomes in Apple Orchards.

PubMed

Saunders, Manu E; Luck, Gary W

2016-01-01

Diverse animal communities influence ecosystem function in agroecosystems through positive and negative plant-animal interactions. Yet, past research has largely failed to examine multiple interactions that can have opposing impacts on agricultural production in a given context. We collected data on arthropod communities and yield quality and quantity parameters (fruit set, yield loss and net outcomes) in three major apple-growing regions in south-eastern Australia. We quantified the net yield outcome (accounting for positive and negative interactions) of multiple animal activities (pollination, fruit damage, biological control) across the entire growing season on netted branches, which excluded vertebrate predators of arthropods, and open branches. Net outcome was calculated as the number of undamaged fruit at harvest as a proportion of the number of blossoms (i.e., potential fruit yield). Vertebrate exclusion resulted in lower levels of fruit set and higher levels of arthropod damage to apples, but did not affect net outcomes. Yield quality and quantity parameters (fruit set, yield loss, net outcomes) were not directly associated with arthropod functional groups. Model variance and significant differences between the ratio of pest to beneficial arthropods between regions indicated that complex relationships between environmental factors and multiple animal interactions have a combined effect on yield. Our results show that focusing on a single crop stage, species group or ecosystem function/service can overlook important complexity in ecological processes within the system. Accounting for this complexity and quantifying the net outcome of ecological interactions within the system, is more informative for research and management of biodiversity and ecosystem services in agricultural landscapes.

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins.

PubMed

Orr, Asuka A; Gonzalez-Rivera, Juan C; Wilson, Mark; Bhikha, P Reena; Wang, Daiqi; Contreras, Lydia M; Tamamis, Phanourios

2018-02-01

There are over 150 currently known, highly diverse chemically modified RNAs, which are dynamic, reversible, and can modulate RNA-protein interactions. Yet, little is known about the wealth of such interactions. This can be attributed to the lack of tools that allow the rapid study of all the potential RNA modifications that might mediate RNA-protein interactions. As a promising step toward this direction, here we present a computational protocol for the characterization of interactions between proteins and RNA containing post-transcriptional modifications. Given an RNA-protein complex structure, potential RNA modified ribonucleoside positions, and molecular mechanics parameters for capturing energetics of RNA modifications, our protocol operates in two stages. In the first stage, a decision-making tool, comprising short simulations and interaction energy calculations, performs a fast and efficient search in a high-throughput fashion, through a list of different types of RNA modifications categorized into trees according to their structural and physicochemical properties, and selects a subset of RNA modifications prone to interact with the target protein. In the second stage, RNA modifications that are selected as recognized by the protein are examined in-detail using all-atom simulations and free energy calculations. We implement and experimentally validate this protocol in a test case involving the study of RNA modifications in complex with Escherichia coli (E. coli) protein Polynucleotide Phosphorylase (PNPase), depicting the favorable interaction between 8-oxo-7,8-dihydroguanosine (8-oxoG) RNA modification and PNPase. Further advancement of the protocol can broaden our understanding of protein interactions with all known RNA modifications in several systems. Copyright © 2018 Elsevier Inc. All rights reserved.

Interspecies interactions are an integral determinant of microbial community dynamics

PubMed Central

Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

2015-01-01

This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

Shallow aquifer storage and recovery (SASR): Initial findings from the Willamette Basin, Oregon

NASA Astrophysics Data System (ADS)

Neumann, P.; Haggerty, R.

2012-12-01

A novel mode of shallow aquifer management could increase the volumetric potential and distribution of groundwater storage. We refer to this mode as shallow aquifer storage and recovery (SASR) and gauge its potential as a freshwater storage tool. By this mode, water is stored in hydraulically connected aquifers with minimal impact to surface water resources. Basin-scale numerical modeling provides a linkage between storage efficiency and hydrogeological parameters, which in turn guides rulemaking for how and where water can be stored. Increased understanding of regional groundwater-surface water interactions is vital to effective SASR implementation. In this study we (1) use a calibrated model of the central Willamette Basin (CWB), Oregon to quantify SASR storage efficiency at 30 locations; (2) estimate SASR volumetric storage potential throughout the CWB based on these results and pertinent hydrogeological parameters; and (3) introduce a methodology for management of SASR by such parameters. Of 3 shallow, sedimentary aquifers in the CWB, we find the moderately conductive, semi-confined, middle sedimentary unit (MSU) to be most efficient for SASR. We estimate that users overlying 80% of the area in this aquifer could store injected water with greater than 80% efficiency, and find efficiencies of up to 95%. As a function of local production well yields, we estimate a maximum annual volumetric storage potential of 30 million m3 using SASR in the MSU. This volume constitutes roughly 9% of the current estimated summer pumpage in the Willamette basin at large. The dimensionless quantity lag #—calculated using modeled specific capacity, distance to nearest in-layer stream boundary, and injection duration—exhibits relatively high correlation to SASR storage efficiency at potential locations in the CWB. This correlation suggests that basic field measurements could guide SASR as an efficient shallow aquifer storage tool.

Electrostatic contribution to the persistence length of a semiflexible dipolar chain.

PubMed

Podgornik, Rudi

2004-09-01

We investigate the electrostatic contribution to the persistence length of a semiflexible polymer chain whose segments interact via a screened Debye-Hückel dipolar interaction potential. We derive the expressions for the renormalized persistence length on the level of a 1/D-expansion method already successfully used in other contexts of polyelectrolye physics. We investigate different limiting forms of the renormalized persistence length of the dipolar chain and show that, in, general, it depends less strongly on the screening length than in the context of a monopolar chain. We show that for a dipolar chain the electrostatic persistence length in the same regime of the parameter phase space as the original Odijk-Skolnick-Fixman (OSF) form for a monopolar chain depends logarithmically on the screening length rather than quadratically. This can be understood solely on the basis of a swifter decay of the dipolar interactions with separation compared to the monopolar electrostatic interactions. We comment also on the general contribution of higher multipoles to the electrostatic renormalization of the bending rigidity.

Host-Microbe Interactions in Microgravity: Assessment and Implications

PubMed Central

Foster, Jamie S.; Wheeler, Raymond M.; Pamphile, Regine

2014-01-01

Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes. PMID:25370197

Host-microbe interactions in microgravity: assessment and implications.

PubMed

Foster, Jamie S; Wheeler, Raymond M; Pamphile, Regine

2014-05-26

Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

Synthesis, Characterization, and Preliminary Investigation of Cell Interaction of Magnetic Nanoparticles with Catechol-Containing Shells

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

Wagner, Kerstin; Seemann, Thomas; Wyrwa, Ralf

2010-12-02

Superparamagnetic iron oxide cores were synthesized by co-precipitation of Fe(II) and Fe(III) salts and subsequently stabilized by coating with different catechols (levodopa, dopamine, hydrocaffeic acid, dopamine-containing carboxymethyl dextran) known to act as high-affinity, bidentate ligands for Fe(III). The prepared stable magnetic fluids were characterized with regard to their chemical composition (content of iron and shell material, Fe(II)/Fe(III) ratio) and their physical properties (size, surface charge, magnetic parameters). The nanoparticles showed no or only slight cytotoxic effects within 1 and 4 days of incubation with 3T3 fibroblast cells. Preliminary experiments were performed to study the interaction of the prepared nanoparticles withmore » human MCF-7 breast cancer cells and leukocytes. An intense interaction of the MCF-7 cells with these particles was found whereas the leukocytes showed a lower tendency of interaction. Based on these finding, the novel magnetic nanoparticles possess the potential for use in depletion of tumor cells from peripheral blood.« less

Electron-phonon interaction in three-barrier nanosystems as active elements of quantum cascade detectors

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

Tkach, N. V., E-mail: ktf@chnu.edu.ua; Seti, Ju. A.; Grynyshyn, Yu. B.

2015-04-15

The theory of electron tunneling through an open nanostructure as an active element of a quantum cascade detector is developed, which takes into account the interaction of electrons with confined and interface phonons. Using the method of finite-temperature Green’s functions and the electron-phonon Hamiltonian in the representation of second quantization over all system variables, the temperature shifts and electron-level widths are calculated and the contributions of different electron-phonon-interaction mechanisms to renormalization of the spectral parameters are analyzed depending on the geometrical configuration of the nanosystem. Due to weak electron-phonon coupling in a GaAs/Al{sub 0.34}Ga{sub 0.66}As-based resonant tunneling nanostructure, the temperaturemore » shift and rf field absorption peak width are not very sensitive to the electron-phonon interaction and result from a decrease in potential barrier heights caused by a difference in the temperature dependences of the well and barrier band gaps.« less

Systematic study of rapidity dispersion parameter in high energy nucleus-nucleus interactions

NASA Astrophysics Data System (ADS)

Bhattacharyya, Swarnapratim; Haiduc, Maria; Neagu, Alina Tania; Firu, Elena

2014-03-01

A systematic study of rapidity dispersion parameter as a quantitative measure of clustering of particles has been carried out in the interactions of 16O, 28Si and 32S projectiles at 4.5 A GeV/c with heavy (AgBr) and light (CNO) groups of targets present in the nuclear emulsion. For all the interactions, the total ensemble of events has been divided into four overlapping multiplicity classes depending on the number of shower particles. For all the interactions and for each multiplicity class, the rapidity dispersion parameter values indicate the occurrence of clusterization during the multiparticle production at Dubna energy. The measured rapidity dispersion parameter values are found to decrease with the increase of average multiplicity for all the interactions. The dependence of rapidity dispersion parameter on the average multiplicity can be successfully described by a relation D(η) = a + b + c2. The experimental results have been compared with the results obtained from the analysis of Monte Carlo simulated (MC-RAND) events. MC-RAND events show weaker clusterization among the pions in comparison to the experimental data.

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game

PubMed Central

de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named “Get Coins,” through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user. PMID:29849549

Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations.

PubMed

Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J

2016-01-01

The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.

Analysis of User Interaction with a Brain-Computer Interface Based on Steady-State Visually Evoked Potentials: Case Study of a Game.

PubMed

Leite, Harlei Miguel de Arruda; de Carvalho, Sarah Negreiros; Costa, Thiago Bulhões da Silva; Attux, Romis; Hornung, Heiko Horst; Arantes, Dalton Soares

2018-01-01

This paper presents a systematic analysis of a game controlled by a Brain-Computer Interface (BCI) based on Steady-State Visually Evoked Potentials (SSVEP). The objective is to understand BCI systems from the Human-Computer Interface (HCI) point of view, by observing how the users interact with the game and evaluating how the interface elements influence the system performance. The interactions of 30 volunteers with our computer game, named "Get Coins," through a BCI based on SSVEP, have generated a database of brain signals and the corresponding responses to a questionnaire about various perceptual parameters, such as visual stimulation, acoustic feedback, background music, visual contrast, and visual fatigue. Each one of the volunteers played one match using the keyboard and four matches using the BCI, for comparison. In all matches using the BCI, the volunteers achieved the goals of the game. Eight of them achieved a perfect score in at least one of the four matches, showing the feasibility of the direct communication between the brain and the computer. Despite this successful experiment, adaptations and improvements should be implemented to make this innovative technology accessible to the end user.

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

Chen, Jing; Liang, Zheng-Liang; Wu, Yue-Liang

We investigate the implications of the long-rang self-interaction on both the self-capture and the annihilation of the self-interacting dark matter (SIDM) trapped in the Sun. Our discussion is based on a specific SIDM model in which DM particles self-interact via a light scalar mediator, or Yukawa potential, in the context of quantum mechanics. Within this framework, we calculate the self-capture rate across a broad region of parameter space. While the self-capture rate can be obtained separately in the Born regime with perturbative method, and in the classical limits with the Rutherford formula, our calculation covers the gap between in amore » non-perturbative fashion. Besides, the phenomenology of both the Sommerfeld-enhanced s- and p-wave annihilation of the solar SIDM is also involved in our discussion. Moreover, by combining the analysis of the Super-Kamiokande (SK) data and the observed DM relic density, we constrain the nuclear capture rate of the DM particles in the presence of the dark Yukawa potential. The consequence of the long-range dark force on probing the solar SIDM turns out to be significant if the force-carrier is much lighter than the DM particle, and a quantitative analysis is provided.« less