Archer, A J
2009-01-07
In recent years, a number of dynamical density functional theories (DDFTs) have been developed for describing the dynamics of the one-body density of both colloidal and atomic fluids. In the colloidal case, the particles are assumed to have stochastic equations of motion and theories exist for both the case when the particle motion is overdamped and also in the regime where inertial effects are relevant. In this paper, we extend the theory and explore the connections between the microscopic DDFT and the equations of motion from continuum fluid mechanics. In particular, starting from the Kramers equation, which governs the dynamics of the phase space probability distribution function for the system, we show that one may obtain an approximate DDFT that is a generalization of the Euler equation. This DDFT is capable of describing the dynamics of the fluid density profile down to the scale of the individual particles. As with previous DDFTs, the dynamical equations require as input the Helmholtz free energy functional from equilibrium density functional theory (DFT). For an equilibrium system, the theory predicts the same fluid one-body density profile as one would obtain from DFT. Making further approximations, we show that the theory may be used to obtain the mode coupling theory that is widely used for describing the transition from a liquid to a glassy state.
Sundararaman, Ravishankar
2014-01-01
Classical density-functional theory provides an efficient alternative to molecular dynamics simulations for understanding the equilibrium properties of inhomogeneous fluids. However, application of density-functional theory to multi-site molecular fluids has so far been limited by complications due to the implicit molecular geometry constraints on the site densities, whose resolution typically requires expensive Monte Carlo methods. Here, we present a general scheme of circumventing this so-called inversion problem: compressed representations of the orientation density. This approach allows us to combine the superior iterative convergence properties of multipole representations of the fluid configuration with the improved accuracy of site-density functionals. Next, from a computational perspective, we show how to extend the DFT++ algebraic formulation of electronic density-functional theory to the classical fluid case and present a basis-independent discretization of our formulation for molecular classical de...
Radousky, H. B.; Nellis, W. J.; Ross, M.; Hamilton, D. C.; Mitchell, A. C.
1986-01-01
Radiative temperatures and electrical conductivities were measured for fluid nitrogen compressed dynamically to pressures of 18-90 GPa, temperatures of 4000-14,000 K, and densities of 2-3 g/cu cm. The data show a continuous phase transition above 30 GPa shock pressure and confirm that (delta-P/delta-T)v is less than 0, as indicated previously by Hugoniot equation-of-state experiments. The first observation of shock-induced cooling is also reported. The data are interpreted in terms of molecular dissociation, and the concentration of dissociated molecules is calculated as a function of density and temperature.
Rognlien, Thomas; Rensink, Marvin
2016-10-01
Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.
Indian Academy of Sciences (India)
G A Adebayo; B C Anusionwu; A N Njah; O J Adeniran; B Mathew; R S Sunmonu
2010-09-01
Detailed classical molecular dynamics simulation of transport coefficients and collision frequencies at high densities in rare gases are presented in this paper with a view to investigate the likely cause of discrepancy between theory and experiments. The results, when compared with experiments, showed an underestimation of the viscosity calculated through the Green–Kubo formalism, but the results are in agreement with some other calculations performed by other groups. The origin of the underestimation was considered in the present work. Analyses of the transport coefficients showed a very high collision frequency which suggested that an atom might spend much less time in the neighbourhood of the fields of force of another atom. The distribution of atoms in the systems adjusts itself to a nearly Maxwellian type that resulted in a locally and temporarily slowly varying temperature. We showed that during collision, the time spent by an atom in the fields of force of other atoms is so small compared with its relaxation time, leading to a possible reduction in local velocity autocorrelation between atoms.
Cattes, Stefanie M.; Gubbins, Keith E.; Schoen, Martin
2016-05-01
In this work, we employ classical density functional theory (DFT) to investigate for the first time equilibrium properties of a Heisenberg fluid confined to nanoscopic slit pores of variable width. Within DFT pair correlations are treated at modified mean-field level. We consider three types of walls: hard ones, where the fluid-wall potential becomes infinite upon molecular contact but vanishes otherwise, and hard walls with superimposed short-range attraction with and without explicit orientation dependence. To model the distance dependence of the attractions, we employ a Yukawa potential. The orientation dependence is realized through anchoring of molecules at the substrates, i.e., an energetic discrimination of specific molecular orientations. If the walls are hard or attractive without specific anchoring, the results are "quasi-bulk"-like in that they can be linked to a confinement-induced reduction of the bulk mean field. In these cases, the precise nature of the walls is completely irrelevant at coexistence. Only for specific anchoring nontrivial features arise, because then the fluid-wall interaction potential affects the orientation distribution function in a nontrivial way and thus appears explicitly in the Euler-Lagrange equations to be solved for minima of the grand potential of coexisting phases.
Cattes, Stefanie M; Gubbins, Keith E; Schoen, Martin
2016-05-21
In this work, we employ classical density functional theory (DFT) to investigate for the first time equilibrium properties of a Heisenberg fluid confined to nanoscopic slit pores of variable width. Within DFT pair correlations are treated at modified mean-field level. We consider three types of walls: hard ones, where the fluid-wall potential becomes infinite upon molecular contact but vanishes otherwise, and hard walls with superimposed short-range attraction with and without explicit orientation dependence. To model the distance dependence of the attractions, we employ a Yukawa potential. The orientation dependence is realized through anchoring of molecules at the substrates, i.e., an energetic discrimination of specific molecular orientations. If the walls are hard or attractive without specific anchoring, the results are "quasi-bulk"-like in that they can be linked to a confinement-induced reduction of the bulk mean field. In these cases, the precise nature of the walls is completely irrelevant at coexistence. Only for specific anchoring nontrivial features arise, because then the fluid-wall interaction potential affects the orientation distribution function in a nontrivial way and thus appears explicitly in the Euler-Lagrange equations to be solved for minima of the grand potential of coexisting phases.
Molecular thermodynamics of nonideal fluids
Lee, Lloyd L
2013-01-01
Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept
Why are Fluid Densities So Low in Carbon Nanotubes?
Wang, Gerald J
2014-01-01
The equilibrium density of fluids under nanoconfinement can differ substantially from their bulk density. Using a mean-field approach to describe the energetic landscape near the carbon nanotube (CNT) wall, we obtain analytical results describing the lengthscales associated with the layering observed at the fluid-CNT interface. When combined with molecular simulation results for the fluid density in the layered region, this approach allows us to derive a closed-form prediction for the overall equilibrium fluid density as a function of the CNT radius that is in excellent agreement with molecular dynamics simulations. We also show how aspects of this theory can be extended to describe water confined within CNTs and find good agreement with results from the literature.
Molecular mechanics and structure of the fluid-solid interface in simple fluids
Wang, Gerald J.; Hadjiconstantinou, Nicolas G.
2017-09-01
Near a fluid-solid interface, the fluid spatial density profile is highly nonuniform at the molecular scale. This nonuniformity can have profound effects on the dynamical behavior of the fluid and has been shown to play an especially important role when modeling a wide variety of nanoscale heat and momentum transfer phenomena. We use molecular-mechanics arguments and molecular-dynamics (MD) simulations to develop a better understanding of the structure of the first fluid layer directly adjacent to the solid in the layering regime, as delineated by a nondimensional number that compares the effects of wall-fluid interaction to thermal energy. Using asymptotic analysis of the Nernst-Planck equation, we show that features of the fluid density profile close to the wall, such as the areal density of the first layer ΣFL (defined as the number of atoms in this layer per unit of fluid-solid interfacial area), can be expressed as polynomial functions of the fluid average density ρave. This is found to be in agreement with MD simulations, which also show that the width of the first layer hFL is a linear function of the average density and only a weak function of the temperature T . These results can be combined to show that, for system average densities corresponding to a dense fluid (ρave≥0.7 ), the ratio C ≡ΣFLρavehFL, representing a density enhancement with respect to the bulk fluid, depends only weakly on temperature and is essentially independent of density. Further MD simulations suggest that the above results, nominally valid for large systems (solid in contact with semi-infinite fluid), also describe fluid-solid interfaces under considerable nanoconfinement, provided ρave is appropriately defined.
Quartz resonator fluid density and viscosity monitor
Martin, Stephen J.; Wiczer, James J.; Cernosek, Richard W.; Frye, Gregory C.; Gebert, Charles T.; Casaus, Leonard; Mitchell, Mary A.
1998-01-01
A pair of thickness-shear mode resonators, one smooth and one with a textured surface, allows fluid density and viscosity to be independently resolved. A textured surface, either randomly rough or regularly patterned, leads to trapping of liquid at the device surface. The synchronous motion of this trapped liquid with the oscillating device surface allows the device to weigh the liquid; this leads to an additional response that depends on liquid density. This additional response enables a pair of devices, one smooth and one textured, to independently resolve liquid density and viscosity; the difference in responses determines the density while the smooth device determines the density-viscosity product, and thus, the pair determines both density and viscosity.
On Shearing Fluids with Homogeneous Densities
Srivastava, D C; Kumar, Rajesh
2016-01-01
In this paper, we study shearing spherically symmetric homogeneous density fluids in comoving coordinates. It is found that the expansion of the four-velocity of a perfect fluid is homogeneous, whereas its shear is generated by an arbitrary function of time M(t), related to the mass function of the distribution. This function is found to bear a functional relationship with density. The field equations are reduced to two coupled first order ordinary differential equations for the metric coefficients, g 11 and g 22. We have explored a class of solutions assuming that M is a linear function of the density. This class embodies, as a subcase, the complete class of shear-free solutions. We have discussed the off quoted work of Kustaanheimo (1947) and have noted that it deals with shear-free fluids having anisotropic pressure. It is shown that the anisotropy of the fluid is characterized by an arbitrary function of time. We have discussed some issues of historical priorities and credentials related to shear-free sol...
Molecular Rheology of Complex Fluids
DEFF Research Database (Denmark)
Huang, Qian; Rasmussen, Henrik Koblitz
The processing of polymer materials is highly governed by its rheology, and influences the properties of the final product. For example, a recurring problem is instability in extrusion that leads to imperfect plastic parts. The ability to predict and control the rheological behavior of polymer......–state viscosity between melts and solutions is still an open question. Branched polymer melts have more complex molecular structures. A stress maximum during the start–up of uniaxial extensional flow was reported in 1979 for a low–density polyethylene (LDPE) melt. Subsequently observations of a steady stress......) linear polystyrene melts and solutions; 2) the bidisperse and polydisperse linear polystyrene melts; 3) the NMMD branched polystyrene melts; and 4) the polydisperse branched polyethylene melts. The experimental results are also compared with some developing theoretical models. Finally, to ensure...
Density fluctuations and correlations of confined fluids
Varea, C.; Robledo, A.
The density fluctuations about the equilibrium structure of fluids confined by parallel planar walls are analyzed for the cases of identical and symmetrically opposed fields at the walls. We determine the stability matrix (of the second derivatives of the free energy functional with respect to the density) for conditions both above and below the wetting transition temperature Tw of the semi-infinite system and corroborate in all cases that the equilibrium configurations are stable. We identify the fluctuations close to the walls and in the middle of the slab and discuss their effect when the wall separation L diverges. For competing walls above Tw the localized fluctuation with lowest eigenvalue describes the displacements of the incipient wetting films that become unimpeded interfacial translations for L→∞. Below Tw the fluctuations with lowest eigenvalue correspond to stiffer deformations extended across the slab. For identical walls above Tw coexisting states display incipient prewetting films and the lowest eigenvalue describes the nature of their growth as L increases. We also calculate the pair correlation function for the inhomogeneous states and, for symmetrically opposed walls, we obtain standard Ornstein-Zernike (OZ) behavior at the walls, but find significant deviations from this law at the interface-like region in the middle of the slab. To model fluids with short-ranged forces we use a ferromagnetic Ising-type Hamiltonian in mean-field approximation.
Jain, Shekhar; Dominik, Aleksandra; Chapman, Walter G
2007-12-28
A density functional theory based on Wertheim's first order perturbation theory is developed for inhomogeneous complex fluids. The theory is derived along similar lines as interfacial statistical associating fluid theory [S. Tripathi and W. G. Chapman, J. Chem. Phys. 122, 094506 (2005)]. However, the derivation is more general and applies broadly to a range of systems, retaining the simplicity of a segment density based theory. Furthermore, the theory gives the exact density profile for ideal chains in an external field. The general avail of the theory has been demonstrated by applying the theory to lipids near surfaces, lipid bilayers, and copolymer thin films. The theoretical results show excellent agreement with the results from molecular simulations.
Physical Properties of Low-Molecular Weight Polydimethylsiloxane Fluids
Energy Technology Data Exchange (ETDEWEB)
Roberts, Christine Cardinal [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Graham, Alan [Univ. of Colorado, Denver, CO (United States); Nemer, Martin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Phinney, Leslie M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Garcia, Robert M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Soehnel, Melissa Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Stirrup, Emily Kate [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-02-01
Physical property measurements including viscosity, density, thermal conductivity, and heat capacity of low-molecular weight polydimethylsiloxane (PDMS) fluids were measured over a wide temperature range (-50°C to 150°C when possible). Properties of blends of 1 cSt and 20 cSt PDMS fluids were also investigated. Uncertainties in the measurements are cited. These measurements will provide greater fidelity predictions of environmental sensing device behavior in hot and cold environments.
Molecular Graphics of Convex Body Fluids.
Gabriel, Adrian T; Meyer, Timm; Germano, Guido
2008-03-01
Coarse-grained modeling of molecular fluids is often based on nonspherical convex rigid bodies like ellipsoids or spherocylinders representing rodlike or platelike molecules or groups of atoms, with site-site interaction potentials depending both on the distance among the particles and the relative orientation. In this category of potentials, the Gay-Berne family has been studied most extensively. However, conventional molecular graphics programs are not designed to visualize such objects. Usually the basic units are atoms displayed as spheres or as vertices in a graph. Atomic aggregates can be highlighted through an increasing amount of stylized representations, e.g., Richardson ribbon diagrams for the secondary structure of proteins, Connolly molecular surfaces, density maps, etc., but ellipsoids and spherocylinders are generally missing, especially as elementary simulation units. We fill this gap providing and discussing a customized OpenGL-based program for the interactive, rendered representation of large ensembles of convex bodies, useful especially in liquid crystal research. We pay particular attention to the performance issues for typical system sizes in this field. The code is distributed as open source.
Density and Phase State of a Confined Nonpolar Fluid
Kienle, Daniel F.; Kuhl, Tonya L.
2016-07-01
Measurements of the mean refractive index of a spherelike nonpolar fluid, octamethytetracylclosiloxane (OMCTS), confined between mica sheets, demonstrate direct and conclusive experimental evidence of the absence of a first-order liquid-to-solid phase transition in the fluid when confined, which has been suggested to occur from previous experimental and simulation results. The results also show that the density remains constant throughout confinement, and that the fluid is incompressible. This, along with the observation of very large increases (many orders of magnitude) in viscosity during confinement from the literature, demonstrate that the molecular motion is limited by the confining wall and not the molecular packing. In addition, the recently developed refractive index profile correction method, which enables the structural perturbation inherent at a solid-liquid interface and that of a liquid in confinement to be determined independently, was used to show that there was no measurable excess or depleted mass of OMCTS near the mica surface in bulk films or confined films of only two molecular layers.
Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields
DEFF Research Database (Denmark)
Karlsen, Jonas Tobias; Augustsson, Per; Bruus, Henrik
2016-01-01
We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems...
Optical density measurements in a multiphase cryogenic fluid flow system
Korman, Valentin; Wiley, John; Gregory, Don A.
2006-05-01
An accurate determination of fluid flow in a cryogenic propulsion environment is difficult under the best of circumstances. The extreme thermal environment increases the mechanical constraints, and variable density conditions create havoc with traditional flow measurement schemes. Presented here are secondary results of cryogenic testing of an all-optical sensor capable of a mass flow measurement by directly interrogating the fluid's density state and a determination of the fluid's velocity. The sensor's measurement basis does not rely on any inherent assumptions as to the state of the fluid flow (density or otherwise). The fluid sensing interaction model will be discussed. Current test and evaluation data and future development work will be presented.
Molecular simulation of the surface tension of real fluids
Werth, Stephan; Hasse, Hans
2016-01-01
Molecular models of real fluids are validated by comparing the vapor-liquid surface tension from molecular dynamics (MD) simulation to correlations of experimental data. The considered molecular models consist of up to 28 interaction sites, including Lennard-Jones sites, point charges, dipoles and quadrupoles. They represent 38 real fluids, such as ethylene oxide, sulfur dioxide, phosgene, benzene, ammonia, formaldehyde, methanol and water, and were adjusted to reproduce the saturated liquid density, vapor pressure and enthalpy of vaporization. The models were not adjusted to interfacial properties, however, so that the present MD simulations are a test of model predictions. It is found that all of the considered models overestimate the surface tension. In most cases, however, the relative deviation between the simulation results and correlations to experimental data is smaller than 20 %. This observation corroborates the outcome of our previous studies on the surface tension of 2CLJQ and 2CLJD fluids where a...
Viscosity kernel of molecular fluids
DEFF Research Database (Denmark)
Puscasu, Ruslan; Todd, Billy; Daivis, Peter
2010-01-01
, temperature, and chain length dependencies of the reciprocal and real-space viscosity kernels are presented. We find that the density has a major effect on the shape of the kernel. The temperature range and chain lengths considered here have by contrast less impact on the overall normalized shape. Functional...... forms that fit the wave-vector-dependent kernel data over a large density and wave-vector range have also been tested. Finally, a structural normalization of the kernels in physical space is considered. Overall, the real-space viscosity kernel has a width of roughly 3–6 atomic diameters, which means...
Molecular Modeling of Solid Fluid Phase Behavior
Energy Technology Data Exchange (ETDEWEB)
Peter A. Monson
2007-12-20
This report gives a summary of the achievements under DOE contract No. DOE/ER/14150 during the period September 1, 1990 to December 31, 2007. This project was concerned with the molecular modeling of solid-fluid equilibrium. The focus was on understanding how solid-fluid and solid-solid phase behavior are related to molecular structure, and the research program made a seminal contribution in this area. The project led to 34 journal articles, including a comprehensive review article published in Advances in Chemical Physics. The DOE funding supported the work of 5 Ph.D. students, 2 M.S. students and 5 postdoctoral researchers.
Molecular Thermodynamics of Charged Hard-Dumbbell Fluids
Institute of Scientific and Technical Information of China (English)
秦原; 刘洪来; 胡英
2001-01-01
Chemical potentials of charged hard-dumbbell fluids are obtained by Monte Carlo simulations using Widom's test-particle method, corresponding compressibility factors are achieved by integration of chemical potentials at different densities. A molecular thermodynamic model is also developed for these charged hard-dumbbell fluids where the residual Helmholtz function is composed of two terms: a reference term responsible for the charged hard spheres and a bonding contribution measuring the sticky interactions between positive and negative hard ions.Model predictions are in good agreement with simulation results.
The force distribution probability function for simple fluids by density functional theory.
Rickayzen, G; Heyes, D M
2013-02-28
Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.
Density Fluctuations of Hard-Sphere Fluids in Narrow Confinement
Nygârd, Kim; Sarman, Sten; Hyltegren, Kristin; Chodankar, Shirish; Perret, Edith; Buitenhuis, Johan; van der Veen, J. Friso; Kjellander, Roland
2016-01-01
Spatial confinement induces microscopic ordering of fluids, which in turn alters many of their dynamic and thermodynamic properties. However, the isothermal compressibility has hitherto been largely overlooked in the literature, despite its obvious connection to the underlying microscopic structure and density fluctuations in confined geometries. Here, we address this issue by probing density profiles and structure factors of hard-sphere fluids in various narrow slits, using x-ray scattering from colloid-filled nanofluidic containers and integral-equation-based statistical mechanics at the level of pair distributions for inhomogeneous fluids. Most importantly, we demonstrate that density fluctuations and isothermal compressibilities in confined fluids can be obtained experimentally from the long-wavelength limit of the structure factor, providing a formally exact and experimentally accessible connection between microscopic structure and macroscopic, thermodynamic properties. Our approach will thus, for example, allow direct experimental verification of theoretically predicted enhanced density fluctuations in liquids near solvophobic interfaces.
Dependence of Reaction Rate Constants on Density in Supercritical Fluids
Institute of Scientific and Technical Information of China (English)
WANGTao; SHENZhongyao
2002-01-01
A new method,which correlates rate constants of chemical reactions and density or pressure in supercritical fluids,was developed.Based on the transition state theory and thermodynamic principles, the rate constant can be reasonably correlated with the density of the supercritical fluid,and a correlation equation was obtained. Coupled with the equation of state (EOS) of a supercritical solvent,the effect of pressure on reaction rate constant could be represented.Two typical systems were used to test this method.The result indicates that this method is suitable for dilute supercritical fluid solutions.
Dependence of quartz wettability on fluid density
Al-Yaseri, Ahmed Zarzor; Roshan, Hamid; Lebedev, Maxim; Barifcani, Ahmed; Iglauer, Stefan
2016-04-01
Wettability is one of the most important parameters in multiphase flow through porous rocks. However, experimental measurements or theoretical predictions are difficult and open to large uncertainty. In this work we demonstrate that gas densities (which are much simpler to determine than wettability and typically well known) correlate remarkably well with wettability. This insight can significantly improve wettability predictions, thus derisking subsurface operations (e.g., CO2 geostorage or hydrocarbon recovery), and significantly enhance fundamental understanding of natural geological processes.
Institute of Scientific and Technical Information of China (English)
李卫华; 诸蔚朝; 马红孺
2003-01-01
One component hard-sphere fluid confined in two planar hard walls is studied by means of density functional theory with Rosenfeld functional and molecular dynamics simulation. The validity of the Rosenfeld functional is examined. Chemical potential, grand potential and free energy as functions of the wall separation are obtained.
Molecular Density Functional Theory of Water
Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel; 10.1021/jz301956b
2013-01-01
Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short range. The approach is shown to provide the correct three-dimensional microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two-three orders of magnitude lower tha...
Solvation of complex surfaces via molecular density functional theory
Levesque, Maximilien; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel
2012-01-01
We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular CLAYFF force field. Solvent energetics and structure are found to depend weakly upon ...
Kinetic theory of correlated fluids: from dynamic density functional to Lattice Boltzmann methods.
Marconi, Umberto Marini Bettolo; Melchionna, Simone
2009-07-07
Using methods of kinetic theory and liquid state theory we propose a description of the nonequilibrium behavior of molecular fluids, which takes into account their microscopic structure and thermodynamic properties. The present work represents an alternative to the recent dynamic density functional theory, which can only deal with colloidal fluids and is not apt to describe the hydrodynamic behavior of a molecular fluid. The method is based on a suitable modification of the Boltzmann transport equation for the phase space distribution and provides a detailed description of the local structure of the fluid and its transport coefficients. Finally, we propose a practical scheme to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the Lattice Boltzmann method.
Effects of nanoscale density inhomogeneities on shearing fluids
DEFF Research Database (Denmark)
Ben, Dalton,; Peter, Daivis,; Hansen, Jesper Schmidt
2013-01-01
It is well known that density inhomogeneities at the solid-liquid interface can have a strong effect on the velocity profile of a nanoconfined fluid in planar Poiseuille flow. However, it is difficult to control the density inhomogeneities induced by solid walls, making this type of system...... systems. Using the sinusoidal transverse force method to produce shearing velocity profiles and the sinusoidal longitudinal force method to produce inhomogeneous density profiles, we are able to observe the interactions between the two property inhomogeneities at the level of individual Fourier components....... This gives us a method for direct measurement of the coupling between the density and velocity fields and allows us to introduce various feedback control mechanisms which customize fluid behavior in individual Fourier components. We briefly discuss the role of temperature inhomogeneity and consider whether...
Non-invasive fluid density and viscosity measurement
Sinha, Dipen N.
2012-05-01
The noninvasively measurement of the density and viscosity of static or flowing fluids in a section of pipe such that the pipe performs as the sensing apparatus, is described. Measurement of a suitable structural vibration resonance frequency of the pipe and the width of this resonance permits the density and viscosity to be determined, respectively. The viscosity may also be measured by monitoring the decay in time of a vibration resonance in the pipe.
Transport Properties of Fluids in Micropores by Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
LIU, Ying-Chun(刘迎春); WANG, Qi(王琦); Lü, Ling-Hong(吕玲红)
2004-01-01
The transport properties of fluid argon in micropores, i.e. diffusivity and viscosity, were studied by molecular dynamics simulations. The effects of pore width, temperature and density on diffusivity and viscosity were analyzed in micropores with pore widths from 0.8 to 4.0 nm. The results show that the diffusivity in micropores is much lower than the bulk diffusivity, and it decreases as the pore width decreases; but the viscosity in micropores is significantly larger than the bulk one, and it increases sharply in narrow micropores. The diffusivity in channel parallel direction is obviously larger than that in channel perpendicular direction. The temperature and density are important factors that obviously affect diffusivity and viscosity in micropores.
Molecular dynamics of fluid flow at solid surfaces
Koplik, Joel; Banavar, Jayanth R.; Willemsen, Jorge F.
1989-05-01
Molecular dynamics techniques are used to study the microscopic aspects of several slow viscous flows past a solid wall, where both fluid and wall have a molecular structure. Systems of several thousand molecules are found to exhibit reasonable continuum behavior, albeit with significant thermal fluctuations. In Couette and Poiseuille flow of liquids it is found that the no-slip boundary condition arises naturally as a consequence of molecular roughness, and that the velocity and stress fields agree with the solutions of the Stokes equations. At lower densities slip appears, which can be incorporated into a flow-independent slip-length boundary condition. The trajectories of individual molecules in Poiseuille flow are examined, and it is also found that their average behavior is given by Taylor-Aris hydrodynamic dispersion. An immiscible two-fluid system is simulated by a species-dependent intermolecular interaction. A static meniscus is observed whose contact angle agrees with simple estimates and, when motion occurs, velocity-dependent advancing and receding angles are observed. The local velocity field near a moving contact line shows a breakdown of the no-slip condition and, up to substantial statistical fluctuations, is consistent with earlier predictions of Dussan [AIChE J. 23, 131 (1977)].
A gravitational test of wave reinforcement versus fluid density models
Johnson, Jacqueline Umstead
1990-10-01
Spermatozoa, protozoa, and algae form macroscopic patterns somewhat analogous to thermally driven convection cells. These bioconvective patterns have attracted interest in the fluid dynamics community, but whether in all cases these waves were gravity driven was unknown. There are two conflicting theories, one gravity dependent (fluid density model), the other gravity independent (wave reinforcement theory). The primary objectives of the summer faculty fellows were to: (1) assist in sample collection (spermatozoa) and preparation for the KC-135 research airplane experiment; and (2) to collaborate on ground testing of bioconvective variables such as motility, concentration, morphology, etc., in relation to their macroscopic patterns. Results are very briefly given.
High Density Thermal Energy Storage with Supercritical Fluids
Ganapathi, Gani B.; Wirz, Richard
2012-01-01
A novel approach to storing thermal energy with supercritical fluids is being investigated, which if successful, promises to transform the way thermal energy is captured and utilized. The use of supercritical fluids allows cost-affordable high-density storage with a combination of latent heat and sensible heat in the two-phase as well as the supercritical state. This technology will enhance penetration of several thermal power generation applications and high temperature water for commercial use if the overall cost of the technology can be demonstrated to be lower than the current state-of-the-art molten salt using sodium nitrate and potassium nitrate eutectic mixtures.
Annihilation Radiation Gauge for Relative Density and Multiphase Fluid Monitoring
Directory of Open Access Journals (Sweden)
Vidal A.
2014-03-01
Full Text Available The knowledge of the multi-phase flow parameters are important for the petroleum industry, specifically during the transport in pipelines and network related to exploitation’s wells. Crude oil flow is studied by Monte Carlo simulation and experimentally to determine transient liquid phase in a laboratory system. Relative density and fluid phase time variation is monitored employing a fast nuclear data acquisition setup that includes two large volume BaF2 scintillator detectors coupled to an electronic chain and data display in a LabView® environment. Fluid parameters are determined by the difference in count rate of coincidence pulses. The operational characteristics of the equipment indicate that 2 % deviation in the CCR corresponds to a variation, on average, of 20 % in the fraction of liquid of the multiphase fluid.
Nucleation for Lennard-Jones Fluid by Density Functional Theory
Institute of Scientific and Technical Information of China (English)
FU Dong
2005-01-01
@@ A non-mean field density functional theory is employed to investigate the vapour-liquid nucleation. The excess Helmholtz free energy functional is formulated in terms of a local density approximation for short ranged repulsion and a density-gradient expansion for long-ranged attractions. An analytical expression for the direct correlation function of a Lennard-Jones fluid is utilized to take into account the effect of long-ranged attractions on intermolecular correlations. With the predicted bulk properties and surface tension as input, the nucleation properties including density profile, work of formation and number of particles at the reduced temperatures T* = 0.694 and 0.741 are inuestigated. The obtained number of particles in the critical nucleus agrees well with the simulation data.
A glimpse of fluid turbulence from the molecular scale
Komatsu, Teruhisa S.
2014-08-01
Large-scale molecular dynamics (MD) simulations of freely decaying turbulence in three-dimensional space are reported. Fluid components are defined from the microscopic states by eliminating thermal components from the coarse-grained fields. The energy spectrum of the fluid components is observed to scale reasonably well according to Kolmogorov scaling determined from the energy dissipation rate and the viscosity of the fluid, even though the Kolmogorov length is of the order of the molecular scale. © 2014 The Authors.
Low-Density Fluid Phase of Dipolar Hard Spheres
Sear, Richard P.
1996-03-01
Unexpectedly, recent computer simulation studies [Weis and Levesque, Phys. Rev. Lett. 71, 2729 (1993); Leeuwen and Smit, ibid. 71, 3991 (1993)] failed to find a liquid phase for dipolar hard spheres. We argue that the liquid was not observed because the dipolar spheres form long chains which interact only weakly. To support this argument we derive a simple theory for noninteracting chains of dipolar spheres and show that it provides a reasonable description of the low-density fluid phase.
Energy Technology Data Exchange (ETDEWEB)
Zaghloul, Mofreh R. [Department of Physics, College of Science, United Arab Emirates University, P.O. Box 15551, Al-Ain (United Arab Emirates)
2015-06-15
We investigate the dissociation and ionization equilibria of deuterium fluid over a wide range of temperatures and densities. The partition functions for molecular and atomic species are evaluated, in a statistical-mechanically consistent way, implementing recent developments in the literature and taking high-density effects into account. A new chemical model (free energy function) is introduced in which the fluid is considered as a mixture of diatomic molecules, atoms, ions, and free electrons. Intensive short range hard core repulsion is taken into account together with partial degeneracy of free electrons and Coulomb interactions among charged particles. Samples of computational results are presented as a set of isotherms for the degree of ionization, dissociated fraction of molecules, pressure, and specific internal energy for a wide range of densities and temperatures. Predictions from the present model calculations show an improved and sensible physical behavior compared to other results in the literature.
Transport of molecular fluids through three-dimensional porous media
Adler, Pierre; Pazdniakou, Aliaksei
2014-05-01
The main purpose of this study is to extend the analysis which has been made for the double layer theory (summarized by [1]) to situations where the distance between the solid walls is of the order of several molecular diameters. This is of a large interest from a scientific viewpoint and for various engineering applications. The intermolecular forces and their influence on fluid structure and dynamics can be taken into account by using the mesoscopic scale models based on the Boltzmann equation [2]. The numerical methods derived from these models are less demanding in computational resources than conventional molecular dynamics methods and therefore long time evolution of large samples can be considered. Three types of fluid particles are considered, namely the anions, the cations and the solvent. They possess a finite diameter which should be at least a few lattice units. The collision frequency between particles is increased by the pair correlation function for hard spheres. The lattice Boltzmann model is built in three dimensions with 19 velocities; it involves two relaxation times. The particle distribution functions are discretized over a basis of Hermite polynomial tensors. Electric forces are included and a Poisson equation is simultaneously solved by a successive over-relaxation method. The numerical algorithm is detailed; it is devised in order to be able to address any three-dimensional porous media. It involves the determination of the densities of each particle species, of the overall density and of the equilibrium distribution function. Then, the electric forces are determined. Collision operators are applied as well as the boundary conditions. Finally, the propagation step is performed and the algorithm starts a new loop. The influence of parameters can be illustrated by systematic calculations in a plane Poiseuille configuration. The drastic influence of the ratio between the channel width and the particle sizes on the local densities and the
Background Oriented Schlieren in a Density Stratified Fluid
Verso, Lilly
2015-01-01
Non-intrusive quantitative fluid density measurements methods are essential in stratified flow experiments. Digital imaging leads to synthetic Schlieren methods in which the variations of the index of refraction are reconstructed computationally. In this study, an important extension to one of these methods, called Background Oriented Schlieren (BOS), is proposed. The extension enables an accurate reconstruction of the density field in stratified liquid experiments. Typically, the experiments are performed by the light source, background pattern, and the camera positioned on the opposite sides of a transparent vessel. The multi-media imaging through air-glass-water-glass-air leads to an additional aberration that destroys the reconstruction. A two-step calibration and image remapping transform are the key components that correct the images through the stratified media and provide non-intrusive full-field density measurements of transparent liquids.
Background oriented schlieren in a density stratified fluid
Verso, Lilly; Liberzon, Alex
2015-10-01
Non-intrusive quantitative fluid density measurement methods are essential in the stratified flow experiments. Digital imaging leads to synthetic schlieren methods in which the variations of the index of refraction are reconstructed computationally. In this study, an extension to one of these methods, called background oriented schlieren, is proposed. The extension enables an accurate reconstruction of the density field in stratified liquid experiments. Typically, the experiments are performed by the light source, background pattern, and the camera positioned on the opposite sides of a transparent vessel. The multimedia imaging through air-glass-water-glass-air leads to an additional aberration that destroys the reconstruction. A two-step calibration and image remapping transform are the key components that correct the images through the stratified media and provide a non-intrusive full-field density measurements of transparent liquids.
Nonequilibrium molecular dynamics simulations of nanoconfined fluids at solid-liquid interfaces
Morciano, M.; Fasano, M.; Nold, A.; Braga, C.; Yatsyshin, P.; Sibley, D. N.; Goddard, B. D.; Chiavazzo, E.; Asinari, P.; Kalliadasis, S.
2017-06-01
We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory.
Selection and Evaluation of a new Pu Density Measurement Fluid
Energy Technology Data Exchange (ETDEWEB)
Dziewinska, Krystyna [Los Alamos National Laboratory; Peters, Michael A [Los Alamos National Laboratory; Martinez, Patrick P [Los Alamos National Laboratory; Dziewinski, Jacek J [Los Alamos National Laboratory; Pugmire, David L [Los Alamos National Laboratory; Trujillo, Stephen M [Los Alamos National Laboratory; La Verne, Jake A [UNIV OF NOTRE DAME; Rajesh, P [UNIV OF NOTRE DAME
2009-01-01
This paper summarizes efforts leading to selection of a new fluid for the determination of the density of large Pu parts. Based on an extended literature search, perfluorotributylamine (FC-43) was chosen for an experimental study. Plutonium coupon corrosion studies were performed by exposing Pu to deaerated and aerated solutions and measuring corrosion gravimetrically. Corrosion rates were determined. Samples of deaerated and aerated perfuluorotributylamine (FC-43) were also irradiated with {sup 60}Co gamma rays (96 Gy/min) to various doses. The samples were extracted with NaOH and analyzed by IC and showed the presence of F and Cl{sup -}. The G-values were established. In surface study experiments Pu coupons were exposed to deaerated and aerated solutions of FC-43 and analyzed by X-ray photoelectron spectroscopy (XPS). The XPS data indicate that there is no detectable surface effect caused by the new fluid. In conclusion the FC-43 was determined to be a very effective and practical fluid for Pu density measurements.
Molecular tumor-diagnostics in body fluids
Kok, Jacques Benno de
2000-01-01
Tumor-derived nucleic acids are frequently present in body fluids (e.g. urine, blood, sputum, stool, bile, and cerebrospinal fluid) that had contact with malignant or premalignant tissues. Detection of this mutant DNA or quantification of aberrant gene expression may offer new noninvasive methods fo
Solvation of complex surfaces via molecular density functional theory.
Levesque, Maximilien; Marry, Virginie; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel
2012-12-14
We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.
Institute of Scientific and Technical Information of China (English)
Zhou Shi-Qi
2007-01-01
A universal theoretical approach is proposed which enables all hard sphere density functional approximations(DFAs) applicable to van der Waals fluids. The resultant DFA obtained by combining the universal theoretical approach with any hard sphere DFAs only needs as input a second-order direct correlation function (DCF) of a coexistence bulk fluid, and is applicable in both supercritical and subcritical temperature regions. The associated effective hard sphere density can be specified by a hard wall sum rule. It is indicated that the value of the effective hard sphere density so determined can be universal, i.e. can be applied to any external potentials different from the single hard wall. As an illustrating example, the universal theoretical approach is combined with a hard sphere bridge DFA to predict the density profile of a hard core attractive Yukawa model fluid influenced by diverse external fields; agreement between the present formalism's predictions and the corresponding simulation data is good or at least comparable to several previous DFT approaches. The primary advantage of the present theoretical approach combined with other hard sphere DFAs is discussed.
Investigation of Vapor-Liquid Nucleation for Associating Fluids by Density Gradient Theory
Institute of Scientific and Technical Information of China (English)
FU Dong; LIU Jianmin
2009-01-01
An equation of state (EOS) applicable to both the uniform and non-uniform associating fluids was established by using the density-gradient expansion, in which the influence parameter κis formulated as a function of tempera-ture. The molecular parameters were regressed by fitting to the experimental data of vapor pressures and liquid den-sities. Within the framework of density gradient theory (DGT), the nucleation rates for water, heavy water, metha-nol, ethanol, 1-propanoi, 1-butanol, 1-pentanol and 1-hexanol were calculated. The results were satisfactory com-pared with the experimental data. Our study shows that DGT preserves all the advantages of density functional the-ory (DFT) in capturing the structure and properties of nucleus but gives much more accurate nucleation rates by adjusting the influence parameter.
Malijevský, Alexandr; Jackson, George; Varga, Szabolcs
2008-10-14
The extension of Onsager's second-virial theory [L. Onsager, Ann. N.Y. Acad. Sci. 51, 627 (1949)] for the orientational ordering of hard rods to mixtures of nonspherical hard bodies with finite length-to-breadth ratios is examined using the decoupling approximations of Parsons [Phys. Rev. A 19, 1225 (1979)] and Lee [J. Chem. Phys. 86, 6567 (1987); 89, 7036 (1988)]. Invariably the extension of the Parsons-Lee (PL) theory to mixtures has in the past involved a van der Waals one-fluid treatment in which the properties of the mixture are approximated by those of a reference one-component hard-sphere fluid with an effective diameter which depends on the composition of the mixture and the molecular parameters of the various components; commonly this is achieved by equating the molecular volumes of the effective hard sphere and of the components in the mixture and is referred to as the PL theory of mixtures. It is well known that a one-fluid treatment is not the most appropriate for the description of the thermodynamic properties of isotropic fluids, and inadequacies are often rectified with a many-fluid (MF) theory. Here, we examine MF theories which are developed from the virial theorem and the virial expansion of the Helmholtz free energy of anisotropic fluid mixtures. The use of the decoupling approximation of the pair distribution function at the level of a multicomponent hard-sphere reference system leads to our MF Parsons (MFP) theory of anisotropic mixtures. Alternatively the mapping of the virial coefficients of the hard-body mixtures onto those of equivalent hard-sphere systems leads to our MF Lee (MFL) theory. The description of the isotropic-nematic phase behavior of binary mixtures of hard Gaussian overlap particles is used to assess the adequacy of the four different theories, namely, the original second-virial theory of Onsager, the usual PL one-fluid theory, and the MF theories based on the Lee (MFL) and Parsons (MFP) approaches. A comparison with the
van Westen, Thijs; Vlugt, Thijs J H; Gross, Joachim
2015-06-14
We study the isotropic (vapor and liquid) phase behavior of attractive chain fluids. Special emphasis is placed on the role of molecular flexibility, which is studied by means of a rod-coil model. Two new equations of state (EoSs) are developed for square-well- (SW) and Lennard-Jones (LJ) chain fluids. The EoSs are developed by applying the perturbation theory of Barker and Henderson (BH) to a reference fluid of hard chain molecules. The novelty of the approach is based on (1) the use of a recently developed hard-chain reference EoS that explicitly incorporates the effects of molecular flexibility, (2) the use of recent molecular simulation data for the radial distribution function of hard-chain fluids, and (3) a newly developed effective segment size, which effectively accounts for the soft repulsion between segments of LJ chains. It is shown that the effective segment size needs to be temperature-, density-, and chain-length dependent. To obtain a simplified analytical EoS, the perturbation terms are fitted by polynomials in density (SW and LJ), chain length (SW and LJ), and temperature (only for LJ). It is shown that the equations of state result in an accurate description of molecular simulation data for vapor-liquid equilibria (VLE) and isotherms of fully flexible SW- and LJ chain fluids and their mixtures. To evaluate the performance of the equations of state in describing the effects of molecular flexibility on VLE, we present new Monte Carlo simulation results for the VLE of rigid linear- and partially flexible SW- and LJ chain fluids. For SW chains, the developed EoS is in a good agreement with simulation results. For increased rigidity of the chains, both theory and simulations predict an increase of the VL density difference and a slight increase of the VL critical temperature. For LJ chains, the EoS proves incapable of reproducing part of these trends.
MOLECULAR DESIGN OF COLLOIDS IN SUPERCRITICAL FLUIDS
Energy Technology Data Exchange (ETDEWEB)
Keith P. Johnston
2009-04-06
The environmentally benign, non-toxic, non-flammable fluids water and carbon dioxide (CO2) are the two most abundant and inexpensive solvents on earth. Emulsions of these fluids are of interest in many industrial processes, as well as CO2 sequestration and enhanced oil recovery. Until recently, formation of these emulsions required stabilization with fluorinated surfactants, which are expensive and often not environmentally friendly. In this work we overcame this severe limitation by developing a fundamental understanding of the properties of surfactants the CO2-water interface and using this knowledge to design and characterize emulsions stabilized with either hydrocarbon-based surfactants or nanoparticle stabilizers. We also discovered a new concept of electrostatic stabilization for CO2-based emulsions and colloids. Finally, we were able to translate our earlier work on the synthesis of silicon and germanium nanocrystals and nanowires from high temperatures and pressures to lower temperatures and ambient pressure to make the chemistry much more accessible.
Institute of Scientific and Technical Information of China (English)
SUN Zong-Li; KANG Yan-Shuang
2011-01-01
Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii. The interfacial properties including contact density and fluid-solid interfacial tension are investigated. The influences of associating energy, curvature of hard wall and the bulk density of Huids on these properties are analyzed in detail. The results may provide helpful clues to understand the interfacial properties of other complex fluids.%@@ Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii.The interfacial properties including contact density and fluid-solid intcrfacial tension are investigated.The influences of associating energy, curvature of hard wall and the hulk density of fluids on these properties are analyzed in detail.The results may provide helpful clues to understand the interfacial properties of other complex fluids.
Thermodynamic of fluids from a general equation of state: The molecular discrete perturbation theory
Energy Technology Data Exchange (ETDEWEB)
Gámez, Francisco, E-mail: fgammar@upo.es [C/ Clavel 101, Mairena del Aljarafe, 41927 Seville (Spain)
2014-06-21
An extensive generalisation of the discrete perturbation theory for molecular multipolar non-spherical fluids is presented. An analytical expression for the Helmholtz free energy for an equivalent discrete potential is given as a function of density, temperature, and intermolecular parameters with implicit shape and multipolar dependence. By varying the intermolecular parameters through their geometrical and multipolar dependence, a set of molecular fluids are considered and their vapor–liquid phase diagrams are tested against available simulation data. Concretely, multipolar and non-polar Kihara and chainlike fluids are tested and it is found that this theoretical approach is able to reproduce qualitatively and quantitatively well the Monte Carlo data for the selected molecular potentials, except near the critical region.
Molecular rattling in two-dimensional fluids: Simulations and theory
Variyar, Jayasankar E.; Kivelson, Daniel; Tarjus, Gilles; Talbot, Julian
1992-01-01
We have carried out molecular dynamic simulations over a range of densities for two-dimensional fluids consisting of hard, soft, and Lennard-Jones disks. For comparison we have also carried out simulations for the corresponding systems in which all but one particle are frozen in position. We have studied the velocity autocorrelation functions and the closely related velocity-sign autocorrelation functions, and have examined the probabilities per unit time that a particle will undergo a first velocity sign reversal after an elapsed time t measured alternately from the last velocity reversal or from a given arbitrary time. At all densities studied, the first of these probabilities per unit time is zero at t=0 and rises to a maximum at a later time, but as the hardness of the disks is increased, the maximum moves in toward t→0. This maximum can be correlated with the ``negative'' dip observed in the velocity correlation functions when plotted versus time. Our conclusion is that all these phenomena can be explained qualitatively on the basis of a model where memory does not extend back beyond the last velocity reversal. However, at high density, the velocity-sign-autocorrelation function not only shows a negative dip (which is explained by the model) but also a second ``oscillation'' which is not described, even qualitatively, by the model. We conclude that the first dip in the velocity and velocity-sign correlation functions can occur even if there are no correlated or coherent librations, but the existence of a ``second'' oscillation is a better indication of such correlations.
Kalani, Mahshid; Yunus, Robiah
2012-01-01
The reported work demonstrates and discusses the effect of supercritical fluid density (pressure and temperature of supercritical fluid carbon dioxide) on particle size and distribution using the supercritical antisolvent (SAS) method in the purpose of drug encapsulation. In this study, paracetamol was encapsulated inside L-polylactic acid, a semicrystalline polymer, with different process parameters, including pressure and temperature, using the SAS process. The morphology and particle size of the prepared nanoparticles were determined by scanning electron microscopy and transmission electron microscopy. The results revealed that increasing temperature enhanced mean particle size due to the plasticizing effect. Furthermore, increasing pressure enhanced molecular interaction and solubility; thus, particle size was reduced. Transmission electron microscopy images defined the internal structure of nanoparticles. Thermal characteristics of nanoparticles were also investigated via differential scanning calorimetry. Furthermore, X-ray diffraction pattern revealed the changes in crystallinity structure during the SAS process. In vitro drug release analysis determined the sustained release of paracetamol in over 4 weeks.
Vibrational spectra of molecular fluids in nanopores
Arakcheev, V. G.; Morozov, V. B.
2012-12-01
Coherent anti-Stokes Raman spectroscopy (CARS) is applied for quantitative analysis of carbon dioxide phase composition in pores of nanoporous glass samples at nearcritical temperatures. Measurements of the 1388 1/cm Q-branch were made in a wide pressure range corresponding to coexistence of gas (gas-like), adsorbed and condensed phases within pores. At temperatures several degrees below the critical value, CARS spectra behavior is easy to interpret in terms of thermodynamic model of surface adsorption and capillary condensation. It allows estimating mass fractions of different phase components. Moreover, spectra measured at near critical temperatures 30.5 and 33°C have pronounced inhomogeneous shapes and indicate the presence of condensed phase in the volume of pores. The effect obviously reflects the fluid behaviour near the critical point in nanopores. Pores with smaller radii are filled with condensed phase at lower pressures. The analysis of the CARS spectra is informative for quantitative evaluation of phase composition in nanopores.
Haghmoradi, Amin; Wang, Le; Chapman, Walter G.
2017-02-01
In this manuscript we extend Wertheim’s two-density formalism beyond its first order to model a system of fluid molecules with a single association site close to a planar hard wall with association sites on its surface in a density functional theory framework. The association sites of the fluid molecules are small enough that they can form only one bond, while the wall association sites are large enough to bond with more than one fluid molecule. The effects of temperature and of bulk fluid and wall site densities on the fluid density profile, extent of association, and competition between single and double bonding of fluid segments at the wall sites versus distance from the wall are presented. The theory predictions are compared with new Monte Carlo simulation results and they are in good agreement. The theory captures the surface coverage over wide ranges of temperature and bulk density by introducing the effect of steric hindrance in fluid association at a wall site.
Molecular correlations and solvation in simple fluids.
Barbosa, Marco A A; Widom, B
2010-06-01
We study the molecular correlations in a lattice model of a solution of a low-solubility solute, with emphasis on how the thermodynamics is reflected in the correlation functions. The model is treated in the Bethe-Guggenheim approximation, which is exact on a Bethe lattice (Cayley tree). The solution properties are obtained in the limit of infinite dilution of the solute. With h(11)(r), h(12)(r), and h(22)(r) the three pair correlation functions as functions of the separation r (subscripts 1 and 2 referring to solvent and solute, respectively), we find for r > or = 2 lattice steps that h(22)(r)/h(12)(r) is identical with h(12)(r)/h(11)(r). This illustrates a general theorem that holds in the asymptotic limit of infinite r. The three correlation functions share a common exponential decay length (correlation length), but when the solubility of the solute is low the amplitude of the decay of h(22)(r) is much greater than that of h(12)(r), which in turn is much greater than that of h(11)(r). As a consequence the amplitude of the decay of h(22)(r) is enormously greater than that of h(11)(r). The effective solute-solute attraction then remains discernible at distances at which the solvent molecules are essentially no longer correlated, as found in similar circumstances in an earlier model. The second osmotic virial coefficient is large and negative, as expected. We find that the solvent-mediated part W(r) of the potential of mean force between solutes, evaluated at contact, r = 1, is related in this model to the Gibbs free energy of solvation at fixed pressure, DeltaG(p)(*), by (Z/2)W(1) + DeltaG(p)(*) is identical with pv(0), where Z is the coordination number of the lattice, p is the pressure, and v(0) is the volume of the cell associated with each lattice site. A large, positive DeltaG(p)(*) associated with the low solubility is thus reflected in a strong attraction (large negative W at contact), which is the major contributor to the second osmotic virial coefficient
Molecular dynamics, density functional theory of the metal--electrolyte interface
Energy Technology Data Exchange (ETDEWEB)
Price, D.L. [Department of Physics, University of Memphis, Memphis Tennessee 38152 (United States); Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
1995-04-22
Quantitative, predictive theories for metal--electrolyte interfaces require an atomic-scale representation of the interface, which must include an accurate statistical description of a polar fluid in contact with a solid surface; and also a description of the electronic density and structure of a metal surface in contact with a fluid. Such a complex system presents a difficult computational problem, and has been dealt with in the past essentially by parts; either by molecular dynamics calculations of the fluid structure, or density functional calculations of the metal--surface electronic structure. A complete and self-consistent determination of the surface structure would, however, involve a simultaneous calculation of both the atomic and electronic structure of the interface. This suggests a combination of these two calculational techniques, and it is just this sort of molecular dynamics and density functional combination which comprises the Car--Parrinello, and related, methods. We have developed a Car--Parrinello type combination of molecular dynamics and density functional methods, suitable for application to the metal--electrolyte interface. We briefly describe this calculation and discuss our initial results for a fairly simple metal--water interface.
Ginzburg-Landau free energy for molecular fluids: Determination and coarse-graining
Desgranges, Caroline; Delhommelle, Jerome
2017-02-01
Using molecular simulation, we determine Ginzburg-Landau free energy functions for molecular fluids. To this aim, we extend the Expanded Wang-Landau method to calculate the partition functions, number distributions and Landau free energies for Ar,CO2 and H2O . We then parametrize a coarse-grained free energy function of the density order parameter and assess the performance of this free energy function on its ability to model the onset of criticality in these systems. The resulting parameters can be readily used in hybrid atomistic/continuum simulations that connect the microscopic and mesoscopic length scales.
Huang, Kuo-Ying; Yoo, Hee Young; Jho, YongSeok; Han, Songi; Hwang, Dong Soo
2016-05-24
An exceptionally low interfacial tension of a dense fluid of concentrated polyelectrolyte complexes, phase-separated from a biphasic fluid known as complex coacervates, represents a unique and highly sought-after materials property that inspires novel applications from superior coating to wet adhesion. Despite extensive studies and broad interest, the molecular and structural bases for the unique properties of complex coacervates are unclear. Here, a microphase-separated complex coacervate fluid generated by mixing a recombinant mussel foot protein-1 (mfp-1) as the polycation and hyaluronic acid (HA) as the polyanion at stoichiometric ratios was macroscopically phase-separated into a dense complex coacervate and a dilute supernatant phase to enable separate characterization of the two fluid phases. Surprisingly, despite up to 4 orders of magnitude differing density of the polyelectrolytes, the diffusivity of water in these two phases was found to be indistinguishable. The presence of unbound, bulk-like, water in the dense fluid can be reconciled with a water population that is only weakly perturbed by the polyelectrolyte interface and network. This hypothesis was experimentally validated by cryo-TEM of the macroscopically phase-separated dense complex coacervate phase that was found to be a bicontinuous and biphasic nanostructured network, in which one of the phases was confirmed by staining techniques to be water and the other polyelectrolyte complexes. We conclude that a weak cohesive energy between water-water and water-polyelectrolytes manifests itself in a bicontinuous network, and is responsible for the exceptionally low interfacial energy of this complex fluid phase with respect to virtually any surface within an aqueous medium.
Energy Technology Data Exchange (ETDEWEB)
Singh, Ram Chandra [Department of Physics, Hindustan Institute of Technology, 32, 34 Knowledge Park-III, Greater Noida-201306, UP (India)
2007-09-19
We have used the density-functional theory to study the effect of varying temperature on the isotropic-nematic transition of a fluid of molecules interacting via the Gay-Berne intermolecular potential. The nematic phase is found to be stable with respect to isotropic phase in the temperature range 0.80{<=}T*{<=}1.25. Pair correlation functions needed as input information in density-functional theory is calculated using the Percus-Yevick integral equation theory. We find that the density-functional theory is good for studying the isotropic-nematic transition in molecular fluids if the values of the pair-correlation functions in the isotropic phase are known accurately. We have also compared our results with computer simulation results wherever they are available.
Rahmatipour, Hamed; Azimian, Ahmad-Reza; Atlaschian, Omid
2017-01-01
The method of molecular dynamics simulation is applied in order to study the behavior of liquid Argon flow within oscillatory Couette flows, in both smooth and rough nanochannels. To accomplish this study, the fluid velocity and the fluid slip in oscillatory Couette flows were used to assess the effects of: oscillatory velocity amplitude, speed frequency rate, channel height, wall density, and the amount of interaction between fluid and wall particles. Both smooth and rough walls were modelled in order to investigate the effect on the fluid patterns as well. Rectangular and triangular wall roughnesses in different dimensions were used to study this effect. The results indicate that an increase in the velocity amplitude increases the fluid slip, and decreases the fluid velocity fluctuations near the walls. Similar to the steady-state Couette flow, in oscillatory flow we observe a decrease in fluid slip by reducing the wall density. Moreover, by reducing the energy parameter between the fluid and wall, the fluid slip increases, and by reducing the length parameter the fluid slip decreases. Implementing the rectangular and triangular roughness to the bottom wall in the oscillatory flow results in a decrease in fluid slip, which is also similar to the usual non-oscillating flows.
Shear viscosity of hard chain fluids through molecular dynamics simulation techniques
Directory of Open Access Journals (Sweden)
Ratanapisit, J.
2005-07-01
Full Text Available In this paper, we represent the viscosity of hard chain fluids. This study was initiated with an investigation of the equilibrium molecular dynamic simulations of pure hard-sphere molecules. The natural extension of that work was to hard chain fluids. The hard chain model is one in which each molecule is represented as a chain of freely jointed hard spheres that interact on a site-site basis. The major use of the results from this study lie in the future development of a transport perturbation theory in which the hard chain serves as the reference. Our results show agreement to within the combined uncertainties with the previous studies. Comparisons have also been made to a modified Enskog theory. Results show the failure of the Enskog theory to predict the high density viscosity and that the theory fails more rapidly with density as the chain length increases. We attribute this to a failure of the molecular chaos assumption used in the Enskog theory. Further comparisons are made to real fluids using the SAFT-MET and TRAPP approaches. As expected, the hard sphere model is not appropriate to estimate properties of real fluids. However, the hard sphere model provides the good starting point to serve as the reference basis to study chain molecule systems.
Molecularly Imprinted Polymers for 5-Fluorouracil Release in Biological Fluids
Francesco Puoci; Francesca Iemma; Giuseppe Cirillo; Nevio Picci; Pietro Matricardi; Franco Alhaique
2007-01-01
The aim of this work was to investigate the possibility of employing Molecularly Imprinted Polymers (MIPs) as a controlled release device for 5-fluorouracil (5-FU) in biological fluids, especially gastrointestinal ones, compared to Non Imprinted Polymers (NIPs). MIPs were synthesized using methacrylic acid (MAA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as crosslinking agent. The capacity of the polymer to recognize and to bind the template selectively in both organic a...
Molecular dynamics of a dense fluid of polydisperse hard spheres
Sear, Richard P.
2000-01-01
Slow dynamics in a fluid are studied in one of the most basic systems possible: polydisperse hard spheres. Monodisperse hard spheres cannot be studied as the slow down in dynamics as the density is increased is preempted by crystallisation. As the dynamics slow they become more heterogeneous, the spread in the distances traveled by different particles in the same time increases. However, the dynamics appears to be less heterogeneous than in hard-sphere-like colloids at the same volume fractio...
Molecular partitioning based on the kinetic energy density
Noorizadeh, Siamak
2016-05-01
Molecular partitioning based on the kinetic energy density is performed to a number of chemical species, which show non-nuclear attractors (NNA) in their gradient maps of the electron density. It is found that NNAs are removed using this molecular partitioning and although the virial theorem is not valid for all of the basins obtained in the being used AIM, all of the atoms obtained using the new approach obey this theorem. A comparison is also made between some atomic topological parameters which are obtained from the new partitioning approach and those calculated based on the electron density partitioning.
Specification of Density Functional Approximation by Radial Distribution Function of Bulk Fluid
Institute of Scientific and Technical Information of China (English)
ZHOUShi－Qi
2002-01-01
A systematic methodology is proposed to deal with the weighted density approximation version of classical density functional theory by employing the knowledge of radial distribution function of bulk fluid.The present methodology results from the concept of universality of the free energy density functional combined with the test particle method.It is shown that the new method is very accurate for the predictions of density distribution of a hard sphere fluid at different confining geometries.The physical foundation of the present methodology is also applied to the quantum density functional theory.
Combining Molecular Dynamics and Density Functional Theory
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Molecular modelling and simulation of the surface tension of real quadrupolar fluids
Werth, Stephan; Klein, Peter; Küfer, Karl-Heinz; Horsch, Martin; Hasse, Hans
2014-01-01
Molecular modelling and simulation of the surface tension of fluids with force fields is discussed. 29 real fluids are studied, including nitrogen, oxygen, carbon dioxide, carbon monoxide, fluorine, chlorine, bromine, iodine, ethane, ethylene, acetylene, propyne, propylene, propadiene, carbon disulfide, sulfur hexafluoride, and many refrigerants. The fluids are represented by two-centre Lennard-Jones plus point quadrupole models from the literature. These models were adjusted only to experimental data of the vapour pressure and saturated liquid density so that the results for the surface tension are predictions. The deviations between the predictions and experimental data for the surface tension are of the order of 20 percent. The surface tension is usually overestimated by the models. For further improvements, data on the surface tension can be included in the model development. A suitable strategy for this is multi-criteria optimization based on Pareto sets. This is demonstrated using the model for carbon d...
Thermodynamic Behavior of a Perfect Fluid with Negative Energy Density
Christensen, W
2005-01-01
Starting from a perfect cosmolgical fluid, one class of frequency metrics that satisfies both Einstein's General Relativitic equation and the perfect fluid condition is: g_uv = e^iwt N_uv. Such a metric indicates spacetime behaves locally like a simple harmonic oscillator. During spacetime compressions and rarefactions particles are exuded with a mass equal to the compressive work that produced them. They comprise the cosmic dark matter that makes up this perfect fluid. By treating spacetime as a classical thermodynamic problem, the mass of these particles is determined to be in the range of an axion particle sought by the Lawrence Livermore National Laboratory. When axion particles collide they give off a photon having a microwave frequency inversely equal to that of the frequency of the spacetime compression that produced them. These microwave photons make up the 2.7K cosmic background radiation.
Scaling of Langevin and molecular dynamics persistence times of nonhomogeneous fluids.
Olivares-Rivas, Wilmer; Colmenares, Pedro J
2012-01-01
The existing solution for the Langevin equation of an anisotropic fluid allowed the evaluation of the position-dependent perpendicular and parallel diffusion coefficients, using molecular dynamics data. However, the time scale of the Langevin dynamics and molecular dynamics are different and an ansatz for the persistence probability relaxation time was needed. Here we show how the solution for the average persistence probability obtained from the backward Smoluchowski-Fokker-Planck equation (SE), associated to the Langevin dynamics, scales with the corresponding molecular dynamics quantity. Our SE perpendicular persistence time is evaluated in terms of simple integrals over the equilibrium local density. When properly scaled by the perpendicular diffusion coefficient, it gives a good match with that obtained from molecular dynamics.
A modified SPH approach for fluids with large density differences
Ott, F; Ott, Frank; Schnetter, Erik
2003-01-01
We introduce a modified SPH approach that is based on discretising the particle density instead of the mass density. This approach makes it possible to use SPH particles with very different masses to simulate multi-phase flows with large differences in mass density between the phases. We test our formulation with a simple advection problem, with sound waves encountering a density discontinuity, and with shock tubes containing an interface between air and Diesel oil. For all examined problems where particles have different masses, the new formulation yields better results than standard SPH, even in the case of a single-phase flow.
Study on Surface Properties for Non-polar Fluids with Density Functional Theory
Institute of Scientific and Technical Information of China (English)
吴畏; 陆九芳; 付东; 刘金晨; 李以圭
2004-01-01
The density functional theory, simplified by the local density approximation and mean-field approximation, is applied to study the surface properties of pure non-polar fluids. A reasonable long rang correction is adopted to avoid the truncation of the potential. The perturbation theory is applied to establish the equation for the phase equilibrium, in which the hard-core chain fluid is as the reference fluid and the Yukawa potential is used as the perturbation term. Three parameters, elk, d and ms, are regressed from the vapor-liquid equilibria, and the surface properties, including density profile, surface tension and local surface tension profile are predicted with these parameters.
Olivares-Rivas, Wilmer; Colmenares, Pedro J; López, Floralba
2013-08-21
We derive expressions for the transverse diffusion coefficient D(z) and the average persistence time τ(z; L) within a layer of width L, for particles of a non-homogeneous fluid enclosed in a planar nanopore. The method allows the direct evaluation of these position-dependent dynamical quantities from the equilibrium local particle density profile. We use results for the density and persistence time profiles from the virtual layer molecular dynamics method to numerically assess the significance of the Smoluchowski approximation.
Molecular density functional theory of water including density-polarization coupling.
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2016-06-22
We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
Molecular density functional theory of water including density-polarization coupling
Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2016-01-01
We present a three-dimensional molecular density functional theory (MDFT) of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: ($i$) a scalar density and a vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and ($ii$) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
Molecular Density Functional Theory for water with liquid-gas coexistence and correct pressure
Jeanmairet, Guillaume; Sergiievskyi, Volodymyr; Borgis, Daniel
2015-01-01
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. With this correction, molecular density functional theory gives, at a modest computational cost, quantita...
Herrera, L
2011-01-01
We identify the factors responsible for the appearance of energy-density inhomogeneities in a self-gravitating fluid, and describe the evolution of those factors from an initially homogeneous distribution. It is shown that a specific combination of the Weyl tensor and/or local anisotropy of pressure and/or dissipative fluxes entails the formation of energy-density inhomogeneities. Different cases are analyzed in detail and in the particular case of dissipative fluids, the role of relaxational processes as well as non-local effects are brought out.
Bridge density functional approximation for non-uniform hard core repulsive Yukawa fluid
Institute of Scientific and Technical Information of China (English)
Zhou Shi-Qi
2008-01-01
In this work,a bridge density functional approximation(BDFA)(J.Chem.Phys.112,8079(2000))for a non-uniform hard-sphere fluid is extended to a non-uniform hard-core repulsive Yukawa(HCRY)fluid.It is found that the choice of a bulk bridge functional approximation is crucial for both a uniform HCRY fluid and a non-uniform HCRY fluid.A new bridge functional approximation is proposed,which can accurately predict the radial distribution function of the bulk HCRY fluid.With the new bridge functional approximation and its associated bulk second order direct correlation function as input,the BDFA can be used to well calculate the density profile of the HCRY fluid subjected to the influence of varying external fields,and the theoretical predictions are in good agreement with the corresponding simulation data.The calculated results indicate that the present BDFA captures quantitatively the phenomena such as the coexistence of solid-like high density phase and low density gas phase,and the adsorption properties of the HCRY fluid,which qualitatively differ from those of the fluids combining both hard-core repulsion and an attractive tail.
Direct experimental determination of spectral densities of molecular complexes
Energy Technology Data Exchange (ETDEWEB)
Pachón, Leonardo A. [Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6 (Canada); Brumer, Paul [Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)
2014-11-07
Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need to be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.
Direct Experimental Determination of Spectral Densities of Molecular Complexes
Pachon, Leonardo A
2014-01-01
Determining the spectral density of a molecular system immersed in a proteomic scaffold and in contact to a solvent is a fundamental challenge in the coarse-grained description of, e.g., electron and energy transfer dynamics. Once the spectral density is characterized, all the time scales are captured and no artificial separation between fast and slow processes need be invoked. Based on the fluorescence Stokes shift function, we utilize a simple and robust strategy to extract the spectral density of a number of molecular complexes from available experimental data. Specifically, we show that experimental data for dye molecules in several solvents, amino acid proteins in water, and some photochemical systems (e.g., rhodopsin and green fluorescence proteins), are well described by a three-parameter family of sub-Ohmic spectral densities that are characterized by a fast initial Gaussian-like decay followed by a slow algebraic-like decay rate at long times.
Coupling lattice Boltzmann and molecular dynamics models for dense fluids
Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.
2007-04-01
We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.
Molecular dynamics simulation of nanochannel flows with effects of wall lattice-fluid interactions.
Soong, C Y; Yen, T H; Tzeng, P Y
2007-09-01
In the present paper, molecular dynamics simulations are performed to explore the effects of wall lattice-fluid interactions on the hydrodynamic characteristics in nanochannels. Couette and Poiseuille flows of liquid argon with channel walls of face-centered cubic (fcc) lattice structure are employed as the model configurations. Truncated and shifted Lennard-Jones (LJ) 12-6 potentials for evaluations of fluid-fluid and wall-fluid interactions, and a nonlinear spring potential for wall-wall interaction, are used as interatomistic or molecular models. The hydrodynamics at various flow orientation angles with respect to channel walls of lattice planes (111), (100), and (110) are explored. The present work discloses that the effects of key parameters, such as wall density, lattice plane, flow orientation, and LJ interaction energy, have a very significant impact on the nanochannel flow characteristics. The related interfacial phenomena and the underlying physical mechanisms are explored and interpreted. These results are significant in the understanding of nanoscale hydrodynamics, as well as in various applications where an accurate nanoscale flow rate control is necessary.
Fluid-like elasticity induced by anisotropic effective mass density
DEFF Research Database (Denmark)
Ma, Guancong; Fu, Caixing; Wang, Guanghao
We present a three-dimensional anisotropic elastic metamaterial, which can generate dipolar resonances. Repeating these subwavelength units can lead to one-dimensional arrays, which are essentially elastic rods that can withstand both longitudinal, and flexural vibrations. Band structure analysis...... scenarios such as civil engineering and seismic wave control....... shows the systems can have distinctive responses to waves with each polarization. In particular, we demonstrate that only longitudinal wave can propagate within a finite frequency regime, whereas transverse (flexural) waves meet a bandgap — a property conventionally found only in fluids. Effective...
Relationship between molecular cloud structure and density PDFs
Stanchev, Orlin; Veltchev, Todor V; Shetty, Rahul
2013-01-01
Volume and column density PDFs in molecular clouds are important diagnostics for understanding their general structure. We developed a novel approach to trace the cloud structure by varying the lower PDF cut-off and exploring a suggested mass-density relationship with a power-law index $x^\\prime$. The correspondence of x' as a function of spatial scale to the slope of the high-density PDF tail is studied. To validate the proposed model, we use results from hydrodynamical simulations of a turbulent self-gravitating cloud and recent data on dust continuum emission from the Planck mission.
DIFFUSE MOLECULAR CLOUD DENSITIES FROM UV MEASUREMENTS OF CO ABSORPTION
Energy Technology Data Exchange (ETDEWEB)
Goldsmith, Paul F. [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States)
2013-09-10
We use UV measurements of interstellar CO toward nearby stars to calculate the density in the diffuse molecular clouds containing the molecules responsible for the observed absorption. Chemical models and recent calculations of the excitation rate coefficients indicate that the regions in which CO is found have hydrogen predominantly in molecular form and that collisional excitation is by collisions with H{sub 2} molecules. We carry out statistical equilibrium calculations using CO-H{sub 2} collision rates to solve for the H{sub 2} density in the observed sources without including effects of radiative trapping. We have assumed kinetic temperatures of 50 K and 100 K, finding this choice to make relatively little difference to the lowest transition. For the sources having T{sup ex}{sub 10} only for which we could determine upper and lower density limits, we find (n(H{sub 2})) = 49 cm{sup -3}. While we can find a consistent density range for a good fraction of the sources having either two or three values of the excitation temperature, there is a suggestion that the higher-J transitions are sampling clouds or regions within diffuse molecular cloud material that have higher densities than the material sampled by the J = 1-0 transition. The assumed kinetic temperature and derived H{sub 2} density are anticorrelated when the J = 2-1 transition data, the J = 3-2 transition data, or both are included. For sources with either two or three values of the excitation temperature, we find average values of the midpoint of the density range that is consistent with all of the observations equal to 68 cm{sup -3} for T{sup k} = 100 K and 92 cm{sup -3} for T{sup k} = 50 K. The data for this set of sources imply that diffuse molecular clouds are characterized by an average thermal pressure between 4600 and 6800 K cm{sup -3}.
Observational Diagnostics for Two-Fluid Turbulence in Molecular Clouds As Suggested by Simulations
Meyer, Chad D; Burkhart, Blakesely; Lazarian, Alex
2013-01-01
We present high resolution simulations of two-fluid (ion-neutral) MHD turbulence with resolutions as large as 512^3. The simulations are supersonic and mildly sub-Alfvenic, in keeping with the conditions present in molecular clouds. Such turbulence is thought to influence star formation processes in molecular clouds because typical cores form on length scales that are comparable to the dissipation scales of this turbulence in the ions. The simulations are motivated by the fact that recent studies of isophotologue lines in molecular clouds have found significant differences in the linewidth-size relationship for neutral and ion species. The goals of this paper are to explain those observations using simulations and analytic theory, present a new set of density-based diagnostics by drawing on similar diagnostics that have been obtained by studying single-fluid turbulence, and show that our two-fluid simulations play a vital role in reconciling alternative models of star formation. The velocity-dependent diagnos...
Ju, Feng; Ling, Shih-Fu
2013-05-01
This paper presents a new technique for fluid viscosity and density sensing through measuring the mechanical impedance of the fluid load applied on a sphere. A piezoelectric whisker transducer (WT) is proposed which acts simultaneously as both the actuator to excite the sphere tip to oscillate in the fluid and the sensor to measure the force, velocity and mechanical impedance. The relationship between mechanical impedance of the fluid load and electrical impedance of the WT is derived based on a transduction matrix model which characterizes the electro-mechanical transduction process of the WT in both directions. The mechanical impedance is further related to the fluid viscosity and density using a theoretical model. The establishment of this fluid-mechanical-electrical relationship allows the WT to extract the fluid viscosity and density conveniently and accurately just from its electrical impedance. Experimental studies are carried out to calibrate the WT and test its performance using glycerol-water mixtures. It is concluded that the WT is capable of providing results comparable to those of standard viscometers within a wide measurement range due to its low working frequency and large vibration amplitude. Its unique self-actuation-and-sensing feature makes it a suitable solution for online fluid sensing.
Fluid epitaxialization effect on velocity dependence of dynamic contact angle in molecular scale.
Ito, Takahiro; Hirata, Yosuke; Kukita, Yutaka
2010-02-07
Molecular dynamics simulations were used to investigate the effect of epitaxial ordering of the fluid molecules on the microscopic dynamic contact angle. The simulations were performed in a Couette-flow-like geometry where two immiscible fluids were confined between two parallel walls moving in opposite directions. The extent of ordering was varied by changing the number density of the wall particles. As the ordering becomes more evident, the change in the dynamic contact angle tends to be more sensitive to the increase in the relative velocity of the contact line to the wall. Stress components around the contact line is evaluated in order to examine the stress balance among the hydrodynamic stresses (viscous stress and pressure), the deviation of Young's stress from the static equilibrium condition, and the fluid-wall shear stress induced by the relative motion between them. It is shown that the magnitude of the shear stress on the fluid-wall surface is the primary contribution to the sensitivity of the dynamic contact angle and that the sensitivity is intensified by the fluid ordering near the wall surface.
Molecular Design of Low-Density Multifunctional Hybrid Materials
2016-01-01
Structure -Property Relationships of Hybrid Mixed Oxide Organic - Inorganic Films for Multilayer Adhesive Bonding”, MRS 2012 Spring Meeting, San Francisco...AVAILABILITY STATEMENT No distribution limitation. 13. SUPPLEMENTARY NOTES 14. ABSTRACT Low-density hybrid materials, which contain organic and... hybrid materials, which contain organic and inorganic molecular components, can be engineered over a wide range of length scales to exhibit unique
Molecular hydrogen emission as a density and temperature indicator
Wang, Xiang; Ferland, Gary J.; Baldwin, Jack A.; Loh, Edwin D.; Fabian, Andy C.; Williams, Robin
2016-01-01
Infrared observations have discovered a variety of objects, including filaments in the Crab Nebula and cool-core clusters of galaxies, where the 1-0 S(1) line is stronger than the infrared H I lines. A variety of processes could be responsible for this emission. Although many complete shock or PDR calculations of emission have been published, we know of no previous simple calculation that shows the emission spectrum and level populations of thermally excited low-density . We present a range of purely thermal collisional simulations, corresponding to constant gas kinetic temperature at different densities. We consider the cases where the collisions affecting H2 are predominantly with atomic or molecular hydrogen. The resulting level population (often called "excitation") diagrams show that excitation temperatures are sometimes lower than the gas kinetic temperature when the density is too low for the level populations to go to LTE. The atomic case goes to LTE at much lower densities than the molecular case due to larger collision rates. At low densities for the v=1 and 2 vibrational manifolds level populations are quasi-thermal, which could be misinterpreted as showing the gas is in LTE at high density. At low densities for the molecular case the level population diagrams are discontinuous between v=0 and 1 vibrational manifolds and between v=2, J=0, 1 and other higher J levels within the same vibrational manifold. These jumps could be used as density diagnostics. We show how much the H2 mass would be underestimated using the 1-0 S(1) line strength if the density is below that required for LTE. We give diagnostic diagrams showing level populations over a range of density and temperature. The density where the level populations are given by a Boltzmann distribution relative to the total molecular abundance (required to get the correct H2 mass), is shown for various cases. We discuss the implications of these results for the interpretation of H2 observations of the
ADSORPTION OF ASSOCIATING FLUIDS AT ACTIVE SURFACES: A DENSITY FUNCTIONAL THEORY
Directory of Open Access Journals (Sweden)
S.Tripathi
2003-01-01
Full Text Available We present a density functional theory (DFT to describe adsorption in systems where molecules of associating fluids can bond (or associate with discrete, localized functional groups attached to the surfaces, in addition to other fluid molecules. For such systems as water adsorbing on activated carbon, silica, clay minerals etc. this is a realistic model to account for surface heterogeneity rather than using a continuous smeared surface-fluid potential employed in most of the theoretical works on adsorption on heterogeneous surfaces. Association is modelled within the framework of first order thermodynamic perturbation theory (TPT1. The new theory accurately predicts the distribution of bonded and non-bonded species and adsorption behavior under various conditions of bulk pressure, surface-fluid and fluid-fluid association strengths. Competition between the surface-fluid and fluid-fluid association is analyzed for fluids with multiple association sites and its impact on adsorption is discussed. The theory, supported by simulations demonstrates that the extent and the nature of adsorption (e.g. monolayer vary with the number of association sites on the fluid molecules.
Molecularly Imprinted Polymers for 5-Fluorouracil Release in Biological Fluids
Directory of Open Access Journals (Sweden)
Franco Alhaique
2007-04-01
Full Text Available The aim of this work was to investigate the possibility of employing Molecularly Imprinted Polymers (MIPs as a controlled release device for 5-fluorouracil (5-FU in biological fluids, especially gastrointestinal ones, compared to Non Imprinted Polymers (NIPs. MIPs were synthesized using methacrylic acid (MAA as functional monomer and ethylene glycol dimethacrylate (EGDMA as crosslinking agent. The capacity of the polymer to recognize and to bind the template selectively in both organic and aqueous media was evaluated. An in vitro release study was performed both in gastrointestinal and in plasma simulating fluids. The imprinted polymers bound much more 5-Fu than the corresponding non-imprinted ones and showed a controlled/sustained drug release, with MIPs release rate being indeed much more sustained than that obtained from NIPs. These polymers represent a potential valid system for drug delivery and this study indicates that the selective binding characteristic of molecularly imprinted polymers is promising for the preparation of novel controlled release drug dosage form.
Molecularly imprinted polymers for 5-fluorouracil release in biological fluids.
Puoci, Francesco; Iemma, Francesca; Cirillo, Giuseppe; Picci, Nevio; Matricardi, Pietro; Alhaiqu, Franco
2007-04-18
The aim of this work was to investigate the possibility of employing Molecularly Imprinted Polymers (MIPs) as a controlled release device for 5-fluorouracil (5-FU) in biological fluids, especially gastrointestinal ones, compared to Non Imprinted Polymers (NIPs). MIPs were synthesized using methacrylic acid (MAA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as crosslinking agent. The capacity of the polymer to recognize and to bind the template selectively in both organic and aqueous media was evaluated. An in vitro release study was performed both in gastrointestinal and in plasma simulating fluids. The imprinted polymers bound much more 5-Fu than the corresponding non-imprinted ones and showed a controlled/sustained drug release, with MIPs release rate being indeed much more sustained than that obtained from NIPs. These polymers represent a potential valid system for drug delivery and this study indicates that the selective binding characteristic of molecularly imprinted polymers is promising for the preparation of novel controlled release drug dosage form.
Góźdź, W T
2017-08-30
We have calculated the values of the critical packing fractions for the mixtures of symmetric nonadditive hard spheres at high densities for small values of the nonadditivity parameter. Calculations have been performed for solid-solid and fluid-fluid demixing transitions. A cluster algorithm for Monte Carlo simulations in a semigrand ensemble was used, and the waste recycling method was applied to improve the accuracy of the calculations. The finite size scaling analysis was employed to compute the critical packing fractions for infinite systems with high accuracy.
Density Functional Theory Approach for Charged Hard Sphere Fluids Confined in Spherical Micro-Cavity
Institute of Scientific and Technical Information of China (English)
KANG Yan-Shuang; WANG Hai-Jun
2009-01-01
Within the framework of the density functional theory for classical fluids,the equilibrium density profiles of charged hard sphere fluid confined in micro-cavity are studied by means of the modified fundamental measure theory.The dimension of micro-cavity,the charge of hard sphere and the applied electric field are found to have significant effects on the density profiles.In particular,it is shown that Coulomb interaction,excluded volume interaction and applied electric Geld play the central role in controlling the aggregated structure of the system.
The acoustic force density acting on inhomogeneous fluids in acoustic fields
Karlsen, Jonas T; Bruus, Henrik
2016-01-01
We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems, the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip.
Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun
2014-07-31
By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.
Density functional theory for inhomogeneous associating chain fluids.
Bryk, P; Sokołowski, S; Pizio, O
2006-07-14
We propose a nonlocal density functional theory for associating chain molecules. The chains are modeled as tangent spheres, which interact via Lennard-Jones (12,6) attractive interactions. A selected segment contains additional, short-ranged, highly directional interaction sites. The theory incorporates an accurate treatment of the chain molecules via the intramolecular potential formalism and should accurately describe systems with strongly varying external fields, e.g., attractive walls. Within our approach we investigate the structure of the liquid-vapor interface and capillary condensation of a simple model of associating chains with only one associating site placed on the first segment. In general, the properties of inhomogeneous associating chains depend on the association energy. Similar to the bulk systems we find the behavior of associating chains of a given length to be in between that for the nonassociating chains of the same length and that for the nonassociating chains twice as large.
Molecular group dynamics study on slip flow of thin fluid film based on the Hamaker hypotheses
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
The thin fluid film was assumed to consist of a number of spherical fluid molecular groups and the attractive forces of molecular group pairs were calculated by the derived equation according to the three Hamaker homogeneous material hypotheses. Regarding each molecular group as a dynamics individual, the simulation method for the shearing motion of multilayer fluid molecular groups, which was initiated by two moving walls, was proposed based on the Verlet velocity iterative algorithm. The simulations reveal that the velocities of fluid molecular groups change about their respective mean velocities within a narrow range in steady state. It is also found that the velocity slips occur at the wall boundary and in a certain number of fluid film layers close to the wall. Because the dimension of molecular group and the number of group layers are not restricted, the hypothetical thickness of fluid film model can be enlarged from nanometer to micron by using the proposed simulation method.
Mielke, Amy F.; Seasholtz, Richard G.; Elam, Kristie A.; Panda, Jayanta
2005-01-01
Nonintrusive optical point-wise measurement techniques utilizing the principles of molecular Rayleigh scattering have been developed at the NASA Glenn Research Center to obtain time-averaged information about gas velocity, density, temperature, and turbulence, or dynamic information about gas velocity and density in unseeded flows. These techniques enable measurements that are necessary for validating computational fluid dynamics (CFD) and computational aeroacoustic (CAA) codes. Dynamic measurements allow the calculation of power spectra for the various flow properties. This type of information is currently being used in jet noise studies, correlating sound pressure fluctuations with velocity and density fluctuations to determine noise sources in jets. These nonintrusive techniques are particularly useful in supersonic flows, where seeding the flow with particles is not an option, and where the environment is too harsh for hot-wire measurements.
Bond Orientational Order, Molecular Motion and Free Energy of High Density DNA Mesophases
Podgornik, R; Gawrisch, K; Rau, D C; Rupprecht, A; Parsegian, V A
1995-01-01
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change between two distinct regions on the liquid crystalline phase digram: a higher-density hexagonally packed region with long-range bond orientational order in the plane perpendicular to the average molecular direction; and a lower-density cholesteric region with fluid-like positional order. X-rays scattering on highly ordered DNA arrays at high density and with the helical axis oriented parallel to the incoming beam showed a six-fold azimuthal modulation of the first order diffraction peak that reflects the macroscopic bond-orientational order. Transition to the less-dense cholesteric phase through osmotically controlled swelling shows the loss of this bond orientational order that had been expected from the change in optical birefringence patterns and that is consistent with a rap...
Puckett, Elbridge Gerry; Almgren, Ann S.; Bell, John B.; Marcus, Daniel L.; Rider, William J.
1997-01-01
We present a numerical method for computing solutions of the incompressible Euler or Navier-Stokes equations when a principal feature of the flow is the presence of an interface between two fluids with different fluid properties. The method is based on a second-order projection method for variable density flows using an "approximate projection" formulation. The boundary between the fluids is tracked with a second-order, volume-of-fluid interface tracking algorithm. We present results for viscious Rayleigh-Taylor problems at early time with equal and unequal viscosities to demonstrate the convergence of the algorithm. We also present computational results for the Rayleigh-Taylor instability in air-helium and for bubbles and drops in an air-water system without surface tension to demonstrate the behavior of the algorithm on problems with large density and viscosity contrasts.
Baggaley, A W
2013-01-01
Superfluid helium is an intimate mixture of a viscous normal fluid, with continuous vorticity, and an inviscid superfluid, where vorticity is constrained to thin, stable topological defects. One mechanism to generate turbulence in this system is through the application of a heat flux, so called thermal counterflow. Of particular interest is how turbulence in the superfluid responds to both a laminar and turbulent normal fluid in the presence of walls. We model superfluid vortex lines as reconnecting space curves with fixed circulation, and consider both laminar (Poiseuille) and turbulent normal fluid flows in a channel configuration. Using high resolution numerical simulations we show that turbulence in the normal fluid sustains a notably higher vortex line density than a laminar flow with the same mean flow rate. We exam Vinen's relation, $\\sqrt{L}=\\gamma v_{ns}$, between the steady state vortex line density $L$ and the counterflow velocity $v_{ns}$. Our results support the hypothesis that transition to turb...
Molecular modeling the microstructure and phase behavior of bulk and inhomogeneous complex fluids
Bymaster, Adam
Accurate prediction of the thermodynamics and microstructure of complex fluids is contingent upon a model's ability to capture the molecular architecture and the specific intermolecular and intramolecular interactions that govern fluid behavior. This dissertation makes key contributions to improving the understanding and molecular modeling of complex bulk and inhomogeneous fluids, with an emphasis on associating and macromolecular molecules (water, hydrocarbons, polymers, surfactants, and colloids). Such developments apply broadly to fields ranging from biology and medicine, to high performance soft materials and energy. In the bulk, the perturbed-chain statistical associating fluid theory (PC-SAFT), an equation of state based on Wertheim's thermodynamic perturbation theory (TPT1), is extended to include a crossover correction that significantly improves the predicted phase behavior in the critical region. In addition, PC-SAFT is used to investigate the vapor-liquid equilibrium of sour gas mixtures, to improve the understanding of mercaptan/sulfide removal via gas treating. For inhomogeneous fluids, a density functional theory (DFT) based on TPT1 is extended to problems that exhibit radially symmetric inhomogeneities. First, the influence of model solutes on the structure and interfacial properties of water are investigated. The DFT successfully describes the hydrophobic phenomena on microscopic and macroscopic length scales, capturing structural changes as a function of solute size and temperature. The DFT is used to investigate the structure and effective forces in nonadsorbing polymer-colloid mixtures. A comprehensive study is conducted characterizing the role of polymer concentration and particle/polymer size ratio on the structure, polymer induced depletion forces, and tendency towards colloidal aggregation. The inhomogeneous form of the association functional is used, for the first time, to extend the DFT to associating polymer systems, applicable to any
MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS
Energy Technology Data Exchange (ETDEWEB)
Athanassios Z. Panagiotopoulos
2009-09-09
The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.
Anisotropic pressure molecular dynamics for atomic fluid systems
Energy Technology Data Exchange (ETDEWEB)
Romero-Bastida, M [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209 (Mexico); Lopez-Rendon, R [Departamento de QuImica, Universidad Autonoma Metropolitana-Iztapalapa, Av San Rafael Atlixco 186, 09340 Mexico DF (Mexico)
2007-07-20
The MTK equations (Martyna G J, Tobias D J and Klein M L 1994 J. Chem. Phys. 101 4177-89), which simulate the constant-pressure, constant-temperature NPT ensemble, have been modified to simulate an anisotropic pressure along a single coordinate axis, thus rendering the NP{sub zz}T ensemble. The necessary theory of non-Hamiltonian systems is briefly reviewed in order to analytically prove that the proposed equations indeed sample the desired ensemble. A previously derived geometric integrator for the MTK equations is modified to take into account the anisotropic pressure and volume fluctuations. We choose a Lennard-Jones fluid as an illustrative example. The density distribution function, as well as various thermodynamic and interfacial properties of the model system in a liquid-vapour coexistence state, was computed to test the robustness of the proposed equations of motion to simulate the NP{sub zz}T ensemble.
A molecular density functional theory to study solvation in water
Jeanmairet, Guillaume
2014-01-01
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...
Molecular simulation of fluid adsorption in buckytubes and MCM-41
Energy Technology Data Exchange (ETDEWEB)
Maddox, M.W.; Gubbins, K.E. [Cornell Univ., Ithaca, NY (United States)
1994-11-01
We report canonical Monte Carlo (GCMC) molecular-simulation studies of argon and nitrogen in models of two novels adsorbents, buckytubes and MCM-41. Buckytubes are monodisperse carbon tubes with internal diameters of 1-5 nm and a regular pore structure. MCM-41 is one member of a new family of highly uniform mesoporous aluminosilicates produced by Mobil. The pore size of MM-41 can be accurately controlled within the range 1.5-1.0 nm. The adsorption of argon in a buckytube and the adsorption of nitrogen in two different MCM-41 pores are studied at 77 K. Both fluids are modeled as Lennard-Jones spheres, and an averaged fluid-wall potential, dependent only on the distance of the adsorbed molecule from the center of the tube or pore is used. Isotherms and isosteric heats are calculated. Layering transitions and a hysteresis loop are observed for the buckytube and good agreement is found between simulated and experimental isotherms for the MCM-41 systems.
Charge, density and electron temperature in a molecular ultracold plasma
Rennick, C J; Ortega-Arroyo, J; Godin, P J; Grant, E R
2009-01-01
A Rydberg gas of NO entrained in a supersonic molecular beam releases electrons as it evolves to form an ultracold plasma. The size of this signal, compared with that extracted by the subsequent application of a pulsed electric field, determines the absolute magnitude of the plasma charge. This information, combined with the number density of ions, supports a simple thermochemical model that explains the evolution of the plasma to an ultracold electron temperature.
Density functional theory study on the molecular structure of loganin
Pandey, Anoop Kumar; Siddiqui, Shamoon Ahmad; Dwivedi, Apoorva; Raj, Kanwal; Misra, Neeraj
2011-01-01
The computational Quantum Chemistry (QC) has been used for different types of problems, for example: structural biology, surface phenomena and liquid phase. In this paper we have employed the density functional method for the study of molecular structure of loganin. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by B3LYP/6-311G (d, p) method and basis set combinations. It was found that the optimized parameters obtained by the DFT/B3LYP met...
Comparison of apoprotein B of low density lipoproteins of human interstitial fluid and plasma.
Hong, J L; Pflug, J; Reichl, D
1984-08-15
Virtually all apoprotein B (apoB)-containing lipoproteins of the peripheral interstitial fluid of subjects with primary lymphoedema float in the ultracentrifugal field in the density interval 1.019-1.063 g/ml; in this respect they are similar to plasma low-density lipoproteins (LDL). 2. Virtually all apo-B-containing lipoproteins of interstitial fluid migrate in the electrophoretic field with pre-beta mobility; in this respect they are similar to plasma very-low-density lipoproteins. 3. The apoB of lipoproteins of interstitial fluid does not differ in terms of Mr from apoB-100 of human plasma [Kane, Hardman & Paulus (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 2465-2469] as determined by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. 4. Both apoB of interstitial fluid and plasma are heterogenous in terms of their charge as determined by isoelectric focusing of their complexes with the nonionic detergent Nonidet P40. ApoB of plasma LDL focuses between pH5.9 and 6.65, and that of interstitial fluid LDL between pH 5.9 and 6.1. Thus the overall charge of apoB of interstitial fluid is more negative than that of its plasma LDL counterpart.
Sowers, Susanne Lynn
1997-11-01
Microporous sorbents such as carbons, silicas and aluminas are used commercially in a variety of separation, purification and selective reaction applications. A detailed study of the effects of the porous material characteristics on the adsorption equilibrium properties such as selectivity and phase equilibria of fluid mixtures can enhance our understanding of adsorption on a molecular level. Such knowledge will improve our utilization of such adsorbents and provide a tool for directing the future of tailoring sorbents for particular separation processes. The effect of pore size, shape and pressure on the selective adsorption of trace pollutants from an inert gas was studied using prototype mixtures of Lennard-Tones (LJ) N2/CCl4, CF4, and SO2. Both nonlocal density functional theory (DFT) and grand canonical Monte Carlo (GCMC) molecular simulations were used in order to investigate the validity of the theory, which is much quicker and easier to use. Our results indicate that there is an optimal pore size and shape for which the pollutant selectivity is greatly enhanced. In many industrial adsorption processes relative humidity can greatly affect the life of an adsorbent bed, as seen in breakthrough curves. Therefore, the influence of water vapor on the selective adsorption of CCl4 from a mixture of N2/CCl4/H20 in activated carbon was studied using GCMC simulations. The equilibrium adsorption properties are found to be dependent upon both the density of active sites on the pore walls and the relative humidity. Liquid-liquid transitions in porous materials are of interest in connection with oil recovery, lubrication, coating technology and pollution control. The results of a study on the effect of confinement on the liquid-liquid equilibrium of binary LJ mixtures using DFT are compared with those of molecular simulation and experiments. Our findings show that the phase coexistence for the confined mixture is in general decreased and shifted toward the component which
Specification of Density Functional Approximation by Radial Distribution Function of Bulk Fluid
Institute of Scientific and Technical Information of China (English)
ZHOU Shi-Qi
2002-01-01
A systematic methodology is proposed to deal with the weighted density approximation version of clas-sical density functional theory by employing the knowledge of radial distribution function of bulk fluid. The presentmethodology results from the concept of universality of the free energy density functional combined with the test particlemethod. It is shown that the new method is very accurate for the predictions of density distribution ofa hard sphere fluidat different confining geometries. The physical foundation of the present methodology is also applied to the quantumdensity functional theory.
Obstructive renal injury: from fluid mechanics to molecular cell biology
Directory of Open Access Journals (Sweden)
Alvaro C Ucero
2010-04-01
Full Text Available Alvaro C Ucero1,*, Sara Gonçalves2,*, Alberto Benito-Martin1, Beatriz Santamaría1, Adrian M Ramos1, Sergio Berzal1, Marta Ruiz-Ortega1, Jesus Egido1, Alberto Ortiz11Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Fundación Renal Iñigo Alvarez de Toledo, Madrid, Spain; 2Nefrologia e Transplantação Renal, Hospital de Santa Maria EPE, Lisbon, Portugal *Both authors contributed equally to the manuscriptAbstract: Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1 and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.Keywords: urinary tract obstruction, renal injury, fluid mechanics, molecular cell biology
A New Calculation Method of Dynamic Kill Fluid Density Variation during Deep Water Drilling
Directory of Open Access Journals (Sweden)
Honghai Fan
2017-01-01
Full Text Available There are plenty of uncertainties and enormous challenges in deep water drilling due to complicated shallow flow and deep strata of high temperature and pressure. This paper investigates density of dynamic kill fluid and optimum density during the kill operation process in which dynamic kill process can be divided into two stages, that is, dynamic stable stage and static stable stage. The dynamic kill fluid consists of a single liquid phase and different solid phases. In addition, liquid phase is a mixture of water and oil. Therefore, a new method in calculating the temperature and pressure field of deep water wellbore is proposed. The paper calculates the changing trend of kill fluid density under different temperature and pressure by means of superposition method, nonlinear regression, and segment processing technique. By employing the improved model of kill fluid density, deep water kill operation in a well is investigated. By comparison, the calculated density results are in line with the field data. The model proposed in this paper proves to be satisfactory in optimizing dynamic kill operations to ensure the safety in deep water.
Maximizing performance in supercritical fluid chromatography using low-density mobile phases.
Gritti, Fabrice; Fogwill, Michael; Gilar, Martin; Jarrell, Joseph A
2016-10-14
The performance of a 3.0mm×150mm column packed with 1.8μm fully porous HSS-SB-C18 particles was investigated in supercritical fluid chromatography (SFC) with low-density, highly expansible carbon dioxide. These conditions are selected for the analysis of semi-volatile compounds. Elevated temperatures (>100°C) were then combined with low column back pressures (temperature of pure carbon dioxide was set at 107°C, the active back pressure regulator (ABPR) pressure was fixed at 100bar, and the flow rate was set at 2.1mL/min at 12°C (liquefied carbon dioxide) and at an inlet column pressure close to 300bar. Nine n-alkylbenzenes (from benzene to octadecylbenzene) were injected under linear (no sample overload) conditions. The severe steepness of the temperature gradients across the column diameter were predicted from a simplified heat transfer model. Such conditions dramatically lower the column performance by affecting the symmetry of the peak shape. In order to cope with this problem, three different approaches were experimentally tested. They include (1) the decoupling and the proper selection of the inlet eluent temperature with respect to the oven temperature, (2) the partial thermal insulation of the column using polyethylene aerogel, and (3) the application of a high vacuum (10(-5)Torr provided by a turbo-molecular pump) in a housing chamber surrounding the whole column body. The results reveal that (1) the column efficiency can be maximized by properly selecting the difference between the eluent and the oven temperatures, (2) the mere wrapping of the column with an excellent insulating material is insufficient to fully eliminate heat exchanges by conduction and the undesirable radial density gradients across the column i.d., and (3) the complete thermal insulation of the SFC column under high vacuum allows to maximize the column efficiency by maintaining the integrity of the peak shape.
Dib, R F A; Ould-Kaddour, F; Levesque, D
2006-07-01
Numerous theoretical and numerical works have been devoted to the study of the algebraic decrease at large times of the velocity autocorrelation function of particles in a fluid. The derivation of this behavior, the so-called long-time tail, generally based on linearized hydrodynamics, makes no reference to any specific characteristic of the particle interactions. However, in the literature doubts have been expressed about the possibility that by numerical simulations the long-time tail can be observed in the whole fluid phase domain of systems in which the particles interact by soft-core and attractive pair potentials. In this work, extensive and accurate molecular-dynamics simulations establish that the predicted long-time tail of the velocity autocorrelation function exists in a low-density fluid of particles interacting by a soft-repulsive potential and near the liquid-gas critical point of a Lennard-Jones system. These results contribute to the confirmation that the algebraic decay of the velocity autocorrelation function is universal in these fluid systems.
Directory of Open Access Journals (Sweden)
S. Dastgeer
2005-01-01
Full Text Available Interstellar scintillation and angular radio wave broadening measurements show that interstellar and solar wind (electron density fluctuations exhibit a Kolmogorov-like k-5/3 power spectrum extending over many decades in wavenumber space. The ubiquity of the Kolmogorov-like interstellar medium (ISM density spectrum led to an explanation based on coupling incompressible magnetohydrodynamic (MHD fluctuations to density fluctuations through a 'pseudosound' relation within the context of 'nearly incompressible' (NI hydrodynamics (HD and MHD models. The NI theory provides a fundamentally different explanation for the observed ISM density spectrum in that the density fluctuations can be a consequence of passive scalar convection due to background incompressible fluctuations. The theory further predicts generation of long-scale structures and various correlations between the density, temperature and the (magneto acoustic as well as convective pressure fluctuations in the compressible ISM fluids in different thermal regimes that are determined purely by the thermal fluctuation level. In this paper, we present the results of our two dimensional nonlinear fluid simulations, exploring various nonlinear aspects that lead to inertial range ISM turbulence within the context of a NI hydrodymanics model. In qualitative agreement with the NI predictions and the in-situ observations, we find that i the density fluctuations exhibit a Kolmogorov-like spectrum via a passive convection in the field of the background incompressible fluctuations, ii the compressible ISM fluctuations form long scale flows and structures, and iii the density and the temperature fluctuations are anti-correlated.
[Ultrasonographic density of amniotic fluid and its correlation with fetal pulmonary maturity].
Romero-Gutiérrez, G; Avelar-Jaime, R
1996-07-01
In order to determine if the amniotic fluid density is correlated with fetal lung maturity, we carried out a prospective study in the Hospital de Gineco-Obstetricia del Centro Médico León del Instituto Mexicano del Seguro Social. One hundred and forty one patients with pregnancies between 13 and 41 gestation weeks were included. The amniotic fluid density was calculated by counting the level of echoes (free-floating particles) in the amniotic fluid. We found a significant correlation (P < 0.05) between the level of echoes and the gestation age, nevertheless, the correlation coefficient was very low (R = 0.28), therefore we concluded that this procedure is not a reliable predictor of fetal lung maturity.
Measurement of average density and relative volumes in a dispersed two-phase fluid
Sreepada, Sastry R.; Rippel, Robert R.
1992-01-01
An apparatus and a method are disclosed for measuring the average density and relative volumes in an essentially transparent, dispersed two-phase fluid. A laser beam with a diameter no greater than 1% of the diameter of the bubbles, droplets, or particles of the dispersed phase is directed onto a diffraction grating. A single-order component of the diffracted beam is directed through the two-phase fluid and its refraction is measured. Preferably, the refracted beam exiting the fluid is incident upon a optical filter with linearly varing optical density and the intensity of the filtered beam is measured. The invention can be combined with other laser-based measurement systems, e.g., laser doppler anemometry.
Molecular simulation of fluid mixtures in bulk and at solid-liquid interfaces
Kern, Jesse L.
The properties of a diverse range of mixture systems at interfaces are investigated using a variety of computational techniques. Molecular simulation is used to examine the thermodynamic, structural, and transport properties of heterogeneous systems of theoretical and practical importance. The study of binary hard-sphere mixtures at a hard wall demonstrates the high accuracy of recently developed classical-density functionals. The study of aluminum--gallium solid--liquid heterogeneous interfaces predicts a significant amount of prefreezing of the liquid by adopting the structure of the solid surface. The study of ethylene-expanded methanol within model silica mesopores shows the effect of confinement and surface functionalzation on the mixture composition and transport inside of the pores. From our molecular-dynamics study of binary hard-sphere fluid mixtures at a hard wall, we obtained high-precision calculations of the wall-fluid interfacial free energies, gamma. We have considered mixtures of varying diameter ratio, alpha = 0.7,0.8,0.9; mole fraction, x 1 = 0.25,0.50,0.75; and packing fraction, eta compressive stress on the Ga atoms. Bulk methanol--ethylene mixtures under vapor-liquid equilibrium conditions have been characterized using Monte Carlo and molecular dynamics. The simulated vapor-liquid coexistence curves for the pure-component and binary mixtures agree well with experiment, as do the mixture volumetric expansion results. Using chemical potentials obtained from the bulk simulations, the filling of a number of model silica mesopores with ethylene and methanol is simulated. We report the compositions of the confined fluid mixtures over a range of pressures and for three degrees of nominal pore hydrophobicity.
Ultracold molecular Rydberg physics in a high density environment
Eiles, Matthew T; Robicheaux, F; Greene, Chris H
2016-01-01
Sufficiently high densities in Bose-Einstein condensates provide favorable conditions for the production of ultralong-range polyatomic molecules consisting of one Rydberg atom and a number of neutral ground state atoms. The chemical binding properties and electronic wave functions of these exotic molecules are investigated analytically via hybridized diatomic states. The effects of the molecular geometry on the system's properties are studied through comparisons of the adiabatic potential curves and electronic structures for both symmetric and randomly configured molecular geometries. General properties of these molecules with increasing numbers of constituent atoms and in different geometries are presented. These polyatomic states have spectral signatures that lead to non-Lorentzian line-profiles.
Institute of Scientific and Technical Information of China (English)
周世琦
2003-01-01
Based on the functional integral procedure, a recently proposed bridge density function [J. Chem. Phys. 112 (2000) 8079] is developed to calculate global thermodynamic properties of non-uniform fluids. The resulting surface tension of a hard wall-hard sphere interface as a function of the bulk hard sphere fluid density is in good agreement with the available simulation data. The proposed numerical procedure from the approximation of non-uniform first=order direct correlation function to a non=uniform system with excess Helmholtz free energy is of fundamental importance for phase behaviour under the confined condition due to the fact that many available simple approximations in classical density functional theory are for non=uniform first=order direct correlation function.
Supercritical fluid molecular spray thin films and fine powders
Smith, Richard D.
1988-01-01
Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. The solvent is vaporized and pumped away. Solution pressure is varied to determine, together with flow rate, the rate of deposition and to control in part whether a film or powder is produced and the granularity of each. Solution temperature is varied in relation to formation of a two-phase system during expansion to control porosity of the film or powder. A wide variety of film textures and powder shapes are produced of both organic and inorganic compounds. Films are produced with regular textural feature dimensions of 1.0-2.0 .mu.m down to a range of 0.01 to 0.1 .mu.m. Powders are formed in very narrow size distributions, with average sizes in the range of 0.02 to 5 .mu.m.
Supercritical fluid molecular spray film deposition and powder formation
Smith, Richard D.
1986-01-01
Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. Upon expansion and supersonic interaction with background gases in the low pressure region, any clusters of solvent are broken up and the solvent is vaporized and pumped away. Solute concentration in the solution is varied primarily by varying solution pressure to determine, together with flow rate, the rate of deposition and to control in part whether a film or powder is produced and the granularity of each. Solvent clustering and solute nucleation are controlled by manipulating the rate of expansion of the solution and the pressure of the lower pressure region. Solution and low pressure region temperatures are also controlled.
Monte Carlo Simulations of Density Profiles for Hard-Sphere Chain Fluids Confined Between Surfaces
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Covering a wide range of bulk densities, density profiles for hard-sphere chain fluids (HSCFs) with chain length of 3,4,8,20,32 and 64 confined between two surfaces were obtained by Monte Carlo simulations using extended continuum configurational-bias (ECCB) method. It is shown that the enrichment of beads near surfaces is happened at high densities due to the bulk packing effect, on the contrary, the depletion is revealed at low densities owing to the configurational entropic contribution. Comparisons with those calculated by density functional theory presented by Cai et al. indicate that the agreement between simulations and predictions is good. Compressibility factors of bulk HSCFs calculated using volume fractions at surfaces were also used to test the reliability of various equations of state of HSCFs by different authors.
Fluid and gyrokinetic modelling of particle transport in plasmas with hollow density profiles
Tegnered, D.; Oberparleiter, M.; Nordman, H.; Strand, P.
2016-11-01
Hollow density profiles occur in connection with pellet fuelling and L to H transitions. A positive density gradient could potentially stabilize the turbulence or change the relation between convective and diffusive fluxes, thereby reducing the turbulent transport of particles towards the center, making the fuelling scheme inefficient. In the present work, the particle transport driven by ITG/TE mode turbulence in regions of hollow density profiles is studied by fluid as well as gyrokinetic simulations. The fluid model used, an extended version of the Weiland transport model, Extended Drift Wave Model (EDWM), incorporates an arbitrary number of ion species in a multi-fluid description, and an extended wavelength spectrum. The fluid model, which is fast and hence suitable for use in predictive simulations, is compared to gyrokinetic simulations using the code GENE. Typical tokamak parameters are used based on the Cyclone Base Case. Parameter scans in key plasma parameters like plasma β, R/LT , and magnetic shear are investigated. It is found that β in particular has a stabilizing effect in the negative R/Ln region, both nonlinear GENE and EDWM show a decrease in inward flux for negative R/Ln and a change of direction from inward to outward for positive R/Ln . This might have serious consequences for pellet fuelling of high β plasmas.
Dissipative particle dynamics simulation for the density currents of polymer fluids
Li, Yanggui; Geng, Xingguo; Liu, Zhijun; Liu, Qingsheng; Ouyang, Jie
2016-11-01
In this work, the two-dimensional lock-exchange density currents of polymer fluids are numerically investigated using dissipative particle dynamics (DPD) at the mesoscale particle level. A modified finitely extensible nonlinear elastic (FENE) chain model is chosen to describe the polymer system, which perfectly depicts not only the elastic tension but also the elastic repulsion between the adjacent beads with bond length as the equilibrium length of one segment. Through the model and numerical simulation, we analyze the dynamics behavior of the density currents of polymer fluids. A comparison with its Newtonian counterpart suggests that the interface between two polymer fluids is more smoothed, and the front structure is different from the Newtonian case because the Kelvin-Helmholtz instability and cleft instability are suppressed by the polymer. Besides, we also probe the influences of polymer volume concentration, chain length and extensibility on the density currents. These simulation results show that increasing any of the parameters, concentration, chain length, and extensibility, the inhibiting effect of polymer on the density currents becomes more significant.
Incommensurate Chirality Density Wave Transition in a Hybrid Molecular Framework
Hill, Joshua A.; Christensen, Kirsten E.; Goodwin, Andrew L.
2017-09-01
Using single-crystal x-ray diffraction we characterize the 235 K incommensurate phase transition in the hybrid molecular framework tetraethylammonium silver(I) dicyanoargentate, [NEt4]Ag3(CN )4 . We demonstrate the transition to involve spontaneous resolution of chiral [NEt4]+ conformations, giving rise to a state in which molecular chirality is incommensurately modulated throughout the crystal lattice. We refer to this state as an incommensurate chirality density wave (XDW) phase, which represents a fundamentally new type of chiral symmetry breaking in the solid state. Drawing on parallels to the incommensurate ferroelectric transition of NaNO2 , we suggest the XDW state arises through coupling between acoustic (shear) and molecular rotoinversion modes. Such coupling is symmetry forbidden at the Brillouin zone center but symmetry allowed for small but finite modulation vectors q =[0 ,0 ,qz]* . The importance of long-wavelength chirality modulations in the physics of this hybrid framework may have implications for the generation of mesoscale chiral textures, as required for advanced photonic materials.
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Jover, Julio; Galindo, Amparo; Jackson, George; Müller, Erich A.; Haslam, Andrew J.
2015-09-01
Using both theory and continuum simulation, we examine a system comprising a mixture of polymer chains formed from 100 hard-sphere (HS) segments and HS colloids with a diameter which is 20 times that of the polymer segments. According to Wertheim's first-order thermodynamic perturbation theory (TPT1) this athermal system is expected to phase separate into a colloid-rich and a polymer-rich phase. Using a previously developed continuous pseudo-HS potential [J. F. Jover, A. J. Haslam, A. Galindo, G. Jackson, and E. A. Muller, J. Chem. Phys. 137, 144505 (2012)], we simulate the system at a phase point indicated by the theory to be well within the two-phase binodal region. Molecular-dynamics simulations are performed from starting configurations corresponding to completely phase-separated and completely pre-mixed colloids and polymers. Clear evidence is seen of the stabilisation of two coexisting fluid phases in both cases. An analysis of the interfacial tension of the phase-separated regions is made; ultra-low tensions are observed in line with previous values determined with square-gradient theory and experiment for colloid-polymer systems. Further simulations are carried out to examine the nature of these coexisting phases, taking as input the densities and compositions calculated using TPT1 (and corresponding to the peaks in the probability distribution of the density profiles obtained in the simulations). The polymer chains are seen to be fully penetrable by other polymers. By contrast, from the point of view of the colloids, the polymers behave (on average) as almost-impenetrable spheres. It is demonstrated that, while the average interaction between the polymer molecules in the polymer-rich phase is (as expected) soft-repulsive in nature, the corresponding interaction in the colloid-rich phase is of an entirely different form, characterised by a region of effective intermolecular attraction.
Yu, Yang-Xin
2009-07-14
A novel weighted density functional theory (WDFT) for an inhomogeneous 12-6 Lennard-Jones fluid is proposed based on the modified fundamental measure theory for repulsive contribution, the mean-field approximation for attractive contribution, and the first-order mean-spherical approximation with a weighted density for correlation contribution. Extensive comparisons of the theoretical results with molecular simulation and experimental data indicate that the new WDFT yields accurate density profiles, adsorption isotherms, fluid-solid interfacial tensions, as well as disjoining potentials and pressures of simple gases such as argon, nitrogen, methane, ethane, and neon confined in slitlike pores or near graphitic solid surfaces. The present WDFT performs better than the nonlocal density functional theory, which is frequently used in the study of adsorption on porous materials. Since the proposed theory possesses a good dimensional crossover and is able to correctly reduce to two-dimensional case, it performs very well even in very narrow pores. In addition, the present WDFT reproduces very well the supercritical fluid-solid interfacial tensions, whereas the theory of Sweatman underestimates them at high bulk densities. The present WDFT predicts that the increase in the fluid-wall attraction may change the sign of the interfacial tension and hence may make the wall from "phobic" to "philic" with respect to the fluid. The new WDFT is computationally as simple and efficient as the mean-field theory and avoids the second-order direct correlation function as an input. It provides a universal way to construct the excess Helmholtz free-energy functional for inhomogeneous fluids such as Yukawa, square-well, and Sutherland fluids.
He 2++ molecular ion in a strong time-dependent magnetic field: a current-density functional study.
Vikas
2011-08-01
The He 2++ molecular ion exposed to a strong ultrashort time-dependent (TD) magnetic field of the order of 10(9) G is investigated through a quantum fluid dynamics (QFD) and current-density functional theory (CDFT) based approach using vector exchange-correlation (XC) potential and energy density functional that depend not only on the electronic charge-density but also on the current density. The TD-QFD-CDFT computations are performed in a parallel internuclear-axis and magnetic field-axis configuration at the field-free equilibrium internuclear separation R = 1.3 au with the field-strength varying between 0 and 10(11) G. The TD behavior of the exchange- and correlation energy of the He 2++ is analyzed and compared with that obtained using a [B-TD-QFD-density functional theory (DFT)] approach based on the conventional TD-DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge-density alone. The CDFT based approach yields TD exchange- and correlation energy and TD electronic charge-density significantly different from that obtained using the conventional TD-DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT-based approach is traced to the TD current-density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He 2++ molecular ion is elucidated by treating electronic charge density as an electron-"fluid" in the terminology of QFD.
Indian Academy of Sciences (India)
Amita Wadehra; B M Deb
2007-09-01
A time-dependent generalized non-linear Schrödinger equation (GNLSE) of motion was earlier derived in our laboratory by combining density functional theory and quantum fluid dynamics in threedimensional space. In continuation of the work reported previously, the GNLSE is applied to provide additional knowledge on the femtosecond dynamics of the electron density in the hydrogen molecule interacting with high-intensity laser fields. For this purpose, the GNLSE is solved numerically for many time-steps over a total interaction time of 100 fs, by employing a finite-difference scheme. Various time-dependent (TD) quantities, namely, electron density, ground-state survival probability and dipole moment have been obtained for two laser wavelengths and four different intensities. The high-order harmonics generation (HHG) is also examined. The present approach goes beyond the linear response formalism and, in principle, calculates the TD electron density to all orders of change.
Spinodal decomposition in multicomponent fluid mixtures: A molecular dynamics study
DEFF Research Database (Denmark)
Laradji, Mohamed; Mouritsen, Ole G.; Toxvaerd, Søren
1996-01-01
We have investigated the effect of the number p of components on the dynamics of phase separation in two-dimensional symmetric multicomponent fluids. In contrast to concentrated two-dimensional binary fluids, where the growth dynamics is controlled by the coupling of the velocity held to the orde...
Compressibility and Density Fluctuations in Molecular-Cloud Turbulence
Pan, Liubin; Haugbolle, Troels; Nordlund, Aake
2015-01-01
The compressibility of molecular cloud (MC) turbulence plays a crucial role in star formation models, because it controls the amplitude and distribution of density fluctuations. The relation between the compressive ratio (the ratio of powers in compressive and solenoidal motions) and the statistics of turbulence has been studied systematically only in idealized simulations with random external forces. In this work, we analyze a simulation of large-scale turbulence(250 pc) driven by supernova (SN) explosions that has been shown to yield realistic MC properties. We demonstrate that SN driving results in MC turbulence that is only mildly compressive, with the turbulent ratio of compressive to solenoidal modes ~0.3 on average, lower than the equilibrium value of 0.5 found in the inertial range of isothermal simulations with random solenoidal driving. We also find that the compressibility of the turbulence is not noticeably affected by gravity, nor is the mean cloud expansion or contraction velocity (MCs do not co...
Deformation Mechanisms and Safe Drilling Fluids Density in Extremely Thick Salt Formations
Institute of Scientific and Technical Information of China (English)
Yang Henglin; Chen Mian; Zhang Guangqing
2007-01-01
Hydrocarbons are very often associated with salt structures. The oil and gas industry is often required to drill along and through long salt sections to reach and recover hydrocarbons. The unique physical properties of salt require special techniques to ensure borehole stability and adequate casing design. This paper assumed that the mechanical behavior of salt is regulated by the magnitude of mean stress and octahedral shear stress and under the influence of different stress conditions,the deformation of rock salt can be represented by three domains, i.e. compression domain, volume unchanged domain, and dilatancy domain, which are separated by a stress dependent boundary. In the compression domain, the volume of salt decreases until all microcracks are closed, with only elastic deformation and pure creep; in the volume unchanged domain the deformation is considered steady incompressible flow controlled by pure creep; and in the dilatancy domain the volume of salt increases during deformation due to micro-cracking, causing damage and accelerating "creep" until failure. This paper presents a hypothesis that the borehole is stable only when the magnitude of octahedral shear stress is below the dilatancy boundary. It gives the design method for determining drilling fluids density, and calculates the closure rate of borehole with the recommended drilling fluids density. If the closure rate of the borehole is less than 0.1%, the drilling fluids density window can be used during drilling through extremely thick salt formations.
Energy Technology Data Exchange (ETDEWEB)
R. James Kirkpatrick; Andrey G. Kalinichev
2008-11-25
Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for
Hu, Ya-Peng; Wu, Xiao-Ning
2014-01-01
Using the gravity/fluid correspondence in our paper, we investigate the holographic fluid at finite cutoff surface in the Einstein gravity. After constructing the first order perturbative solution of the Schwarzschild-AdS black brane solution in the Einstein gravity, we focus on the stress-energy tensor of the dual fluid with transport coefficients at the finite cutoff surface. Besides the pressure and energy density of dual fluid are obtained, the shear viscosity is also obtained. The most important results are that we find that if we adopt different conditions to fix the undetermined parameters contained in the stress-energy tensor of the dual fluid, the pressure and energy density of the dual fluid can be perturbed. Particularly, the bulk viscosity of the dual fluid can also be given in this case.
Analysis of renal cyst of high density containing proteinaceous fluid: report of 6 cases
Institute of Scientific and Technical Information of China (English)
Jin Wen; Han zhong Li; He Xiao
2008-01-01
Objective:To investigate clinical features and imageology of renal cysts of high density, containing proteinaceous fluid and increase the diagnosis and treatment level of this special type renal cyst. Methods:Six cases were proven to be renal cysts of high density(pathologically) from 2002 to 2007 were reviewed. Among 6 cases, 1 was in the upper pole of kidney, 4 were medial and 1 was located in the anus perineum. All were 2-5 cm in size. Ultrasonography(US) excretory unognaphy, multiphase CT and renal angiography DSA imaging was performed for preoperative diagnosis. The preoperative diagnosis found renal neoplasms in 4 and renal cysts in 2. All of them were operated by partial nephrectomy. Results:All of the 6 renal high density renal masses were reseoted surgically, which were proved pathologically to be renal cysts; high density present. All of them contained proteinaceous fluid with benign cyst walls on histologic examination. No recurrence was seen in any of these cases during a long follow-up. Conclusion:CT and B-US have a higher diagnostic value, which can show the internal shape and character better. B-US or CT guided puncturing biopsy can be better applied to atypical renal cysts. Once the correct diagnosis is acquired, laparoscopic surgical treatment should be carried out.
Impact of a hollow density profile on turbulent particle fluxes: Gyrokinetic and fluid simulations
Tegnered, D.; Oberparleiter, M.; Strand, P.; Nordman, H.
2017-07-01
Hollow density profiles may occur in connection with pellet fuelling and L to H transitions. A positive density gradient could potentially stabilize the turbulence or change the relation between convective and diffusive fluxes, thereby reducing the turbulent transport of particles towards the center, making the pellet fuelling scheme inefficient. In the present work, the particle transport driven by Ion Temperature Gradient/Trapped Electron (ITG/TE) mode turbulence in hollow density profiles is studied by fluid as well as gyrokinetic simulations. The fluid model used, an extended version of the Weiland transport model, Extended Drift Wave Model (EDWM), incorporates an arbitrary number of ion species in a multi-fluid description and an extended wavelength spectrum. The fluid model, which is fast and hence suitable for use in predictive simulations, is compared to gyrokinetic simulations using the code GENE. Typical tokamak parameters are used based on the Cyclone Base Case. Parameter scans in key plasma parameters like plasma β, R/LT, and magnetic shear are investigated. In addition, the effects of a fast species are studied and global ITG simulations in a simplified physics description are performed in order to investigate nonlocal effects. It is found that β in particular, has a stabilizing effect in the negative R/Ln region. Both nonlinear GENE and EDWM simulations show a decrease in inward flux for negative R/Ln and a change in the direction from inward to outward for positive R/Ln. Moreover, the addition of fast particles was shown to decrease the inward main ion particle flux in the positive gradient region further. This might have serious consequences for pellet fuelling of high β plasmas. Additionally, the heat flux in global ITG turbulence simulations indicates that nonlocal effects can play a different role from usual in connection with pellet fuelling.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure
Energy Technology Data Exchange (ETDEWEB)
Jeanmairet, Guillaume, E-mail: g.jeanmairet@fkf.mpg.de; Levesque, Maximilien, E-mail: maximilien.levesque@ens.fr [École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris (France); Sergiievskyi, Volodymyr [SIS2M, LIONS, CEA, Saclay (France); Borgis, Daniel [École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris (France); Maison de la Simulation, USR 3441, CEA - CNRS - INRIA - Univ. Paris-Sud - Univ. de Versailles, 91191 Gif-sur-Yvette Cedex (France)
2015-04-21
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.
Development and application of ZM-2 drilling fluid density adjustment mixing device
Directory of Open Access Journals (Sweden)
Zongming Lei
2015-01-01
Full Text Available High-pressure shallow (gas/water flow is often hidden in the deepwater seabed, so penetrating shallow flow in drilling without BOP will be highly risky. In this case, the conventional well killing method to balance the formation pressure with back pressure generated by well head equipment is no longer suitable. Based on the analysis of structural characteristics of domestic and foreign multi-phase mixing systems, a ZM-2 drilling fluid density adjustment mixing device with independent intellectual property right was developed according to the principles of dynamic well killing. The device is mainly composed of a throttle valve, a high-precision electromagnetic flowmeter, a mixer, dumbbell-shaped nozzles, connecting pipes and other components. Fixed on the mixer are three inlets to fill heavy mud, seawater and additives. Opposed jetting is adopted to realize rapid and uniform mixing of fluids with different densities. A laboratory test was conducted to work out the relationship between throttle opening and injection flow rate and establish a linear relationship between killing fluid density and heavy mud flow. The results of field test conducted in the Nanhai No.8 drill ship showed that the mixing device was stable in operation and excellent in mixing performance. The density difference of ingredient mixture could be controlled within 0.05 g/cm3 after the mixture flowed out of the mixing chamber of the mixer of about 0.3 m long, so such high precision can meet the requirement of dynamic well killing.
Molecular Momentum Transport at Fluid-Solid Interfaces in MEMS/NEMS: A Review
Directory of Open Access Journals (Sweden)
Zeng-Yuan Guo
2009-10-01
Full Text Available This review is focused on molecular momentum transport at fluid-solid interfaces mainly related to microfluidics and nanofluidics in micro-/nano-electro-mechanical systems (MEMS/NEMS. This broad subject covers molecular dynamics behaviors, boundary conditions, molecular momentum accommodations, theoretical and phenomenological models in terms of gas-solid and liquid-solid interfaces affected by various physical factors, such as fluid and solid species, surface roughness, surface patterns, wettability, temperature, pressure, fluid viscosity and polarity. This review offers an overview of the major achievements, including experiments, theories and molecular dynamics simulations, in the field with particular emphasis on the effects on microfluidics and nanofluidics in nanoscience and nanotechnology. In Section 1 we present a brief introduction on the backgrounds, history and concepts. Sections 2 and 3 are focused on molecular momentum transport at gas-solid and liquid-solid interfaces, respectively. Summary and conclusions are finally presented in Section 4.
Molecular momentum transport at fluid-solid interfaces in MEMS/NEMS: a review.
Cao, Bing-Yang; Sun, Jun; Chen, Min; Guo, Zeng-Yuan
2009-10-29
This review is focused on molecular momentum transport at fluid-solid interfaces mainly related to microfluidics and nanofluidics in micro-/nano-electro-mechanical systems (MEMS/NEMS). This broad subject covers molecular dynamics behaviors, boundary conditions, molecular momentum accommodations, theoretical and phenomenological models in terms of gas-solid and liquid-solid interfaces affected by various physical factors, such as fluid and solid species, surface roughness, surface patterns, wettability, temperature, pressure, fluid viscosity and polarity. This review offers an overview of the major achievements, including experiments, theories and molecular dynamics simulations, in the field with particular emphasis on the effects on microfluidics and nanofluidics in nanoscience and nanotechnology. In Section 1 we present a brief introduction on the backgrounds, history and concepts. Sections 2 and 3 are focused on molecular momentum transport at gas-solid and liquid-solid interfaces, respectively. Summary and conclusions are finally presented in Section 4.
Parlak, Z.; Biet, C.; Zauscher, S.
2013-08-01
We describe the physical understanding of a method which differentiates between the frequency shift caused by fluid viscosity and density from that caused by mass adsorption in the resonance of a quartz crystal resonator. This method uses the normalized conductance of the crystal to determine a critical frequency at which the fluid mass and fluid loss compensate each other. Tracking the shift in this critical frequency allows us to determine purely mass adsorption on the crystal. We extended this method to Maxwellian fluids for understanding the mass adsorption in non-Newtonian fluids. We validate our approach by real-time mass adsorption measurements using glycerol and albumin solutions.
Morrison, Benjamin C.; Borrero-Echeverry, Daniel
2015-11-01
Index-matching fluids play an important role in many fluid dynamics experiments, particularly those involving particle tracking, as they can be used to minimize errors due to distortion from the refraction of light across interfaces of the apparatus. Common index-matching fluids, such as sodium iodide solutions or mineral oils, often have densities or viscosities very different from those of water. This can make them undesirable for use as a working fluid when using commercially available tracer particles or at high Reynolds numbers. A solution of ammonium thiocyanate (NH4SCN) can be used for index-matching common materials such as borosilicate glass and acrylic, and has material properties similar to those of water (ν ~ 1 . 6 cSt and ρ ~ 1 . 1 g/cc). We present an empirical model for predicting the refractive index of aqueous NH4SCN solutions as a function of temperature and NH4SCN concentration that allows experimenters to develop refractive index matching solutions for various common materials. This work was supported by the National Science Foundation (CBET-0853691) and by the James Borders Physics Student Fellowship at Reed College.
Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory.
Frink, Laura J Douglas; Frischknecht, Amalie L; Heroux, Michael A; Parks, Michael L; Salinger, Andrew G
2012-04-10
We describe methods to determine optimal coarse-grained models of lipid bilayers for use in fluids density functional theory (fluids-DFT) calculations. Both coarse-grained lipid architecture and optimal parametrizations of the models based on experimental measures are discussed in the context of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in water. The calculations are based on a combination of the modified-iSAFT theory for bonded systems and an accurate fundamental measures theory (FMT) for hard sphere reference fluids. We furthermore discuss a novel approach for pressure control in the fluids-DFT calculations that facilitates both partitioning studies and zero tension control for the bilayer studies. A detailed discussion of the numerical implementations for both solvers and pressure control capabilities are provided. We show that it is possible to develop a coarse-grained lipid bilayer model that is consistent with experimental properties (thickness and area per lipid) of DPPC provided that the coarse-graining is not too extreme. As a final test of the model, we find that the predicted area compressibility moduli and lateral pressure profiles of the optimized models are in reasonable agreement with prior results.
Sega, Marcello; Sbragaglia, Mauro; Kantorovich, Sofia Sergeevna; Ivanov, Alexey Olegovich
2013-01-01
Complex fluid-fluid interfaces featuring mesoscale structures with adsorbed particles are key components of newly designed materials which are continuously enriching the field of soft matter. Simulation tools which are able to cope with the different scales characterizing these systems are fundamental requirements for efficient theoretical investigations. In this paper we present a novel simulation method, based on the approach of Ahlrichs and D\\"unweg [Ahlrichs and D\\"unweg, Int. J. Mod. Phy...
Kwon, Deuk-Chul; Song, Mi-Young; Yoon, Jung-Sik
2014-10-01
It is well known that the dielectric relaxation scheme (DRS) can efficiently overcome the limitation on the simulation time step for fluid transport simulations of high density plasma discharges. By imitating a realistic and physical shielding process of electric field perturbation, the DRS overcomes the dielectric limitation on time step. However, the electric field was obtained with assuming the drift-diffusion approximation. Although the drift-diffusion expressions are good approximations for both the electrons and ions at high pressure, the inertial term cannot be neglected in the ion momentum equation for low pressure. Therefore, in this work, we developed the extended DRS by introducing an effective electric field. To compare the extended DRS with the previous method, two-dimensional fluid simulations for inductively coupled plasma discharges were performed. This work was supported by the Industrial Strategic Technology Development Program (10041637, Development of Dry Etch System for 10 nm class SADP Process) funded by the Ministry of Knowledge Economy (MKE, Korea).
Institute of Scientific and Technical Information of China (English)
YU Yang-Xin; WU Jian-Zhong; YOU Feng-Qi; GAO Guang-Hua
2005-01-01
@@ An extended test-particle method is used to predict the inter- and intramolecular correlation functions of freely jointed hard-sphere-Yukawa-chain fluids by calculating the segmental density distributions around a fixed seg ment. The underlying density functional theory for chain fluids is based on a modified fundamental measure theory for the hard-sphere repulsive and a mean-field approximation for attraction between different segments.The calculated intra- and inter-molecular distribution functions agree well with the results from Monte Carlo simulations, better than those from alternative approaches.
Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory
Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.
2017-07-01
We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.
Characterization of Phase Transition in Heisenberg Fluids from Density Functional Theory
Li, Liang-Sheng; Li, Li; Chen, Xiao-Song
2009-02-01
The phase transition of Heisenberg fluid has been investigated with the density functional theory in mean-field approximation (MF). The matrix of the second derivatives of the grand canonical potential Ω with respect to the particle density fluctuations and the magnetization fluctuations has been investigated and diagonalized. The smallest eigenvalue being 0 signalizes the phase instability and the related eigenvector characterizes this phase transition. We find a Curie line where the order parameter is pure magnetization and a spinodal where the order parameter is a mixture of particle density and magnetization. Along the spinodal, the character of phase instability changes continuously from predominant condensation to predominant ferromagnetic phase transition with the decrease of total density. The spinodal meets the Curie line at the critical endpoint with the reduced density ρ* = ρσ3 = 0.224 and the reduced temperature T* = kT/in = 1.87 (σ is the diameter of Heisenberg hard sphere and in is the coupling constant).
Characterization of Phase Transition in Heisenberg Fluids from Density Functional Theory
Institute of Scientific and Technical Information of China (English)
LI Liang-Sheng; LI Li; CHEN Xiao-Song
2009-01-01
The phase transition of Heisenberg fluid has been investigated with the density functional theory in mean-field approximation (MF).The matrix of the second derivatives of the grand canonical potential Ω with respect to the particle density fluctuations and the magnetization fluctuations has been investigated and diagonalized.The smallest eigenvalue being 0 signalizes the phase instability and the related eigenvector characterizes this phase transition.We find a Curie line where the order parameter is pure magnetization and a spinodM where the order parameter is a mixture of particle density and magnetization.Along the spinodal, the character of phase instability changes continuously from predominant condensation to predominant ferromagnetic phase transition with the decrease of total density.The spinodal meets the Curie line at the critical endpoint with the reduced density ρ*= ρσ3=0.224 and the reduced temperature T* = kT/ε = 1.87 (σ is the diameter of Heisenberg hard sphere and e is the coupling constant).
Institute of Scientific and Technical Information of China (English)
Tianwei TAN; Peiyong QIN
2010-01-01
@@ This special issue of Frontiers of Chemical Engineering in China is dedicated to the topic of Computational Fluid Dynamics (CFD) and Molecular Simulation. It features a selection of some of the best papers presented at the Symposium on CFD and Molecular Simulation, which was held in Beijing, China, on 22-23 May 2009.
Low-grade meningioma showing nearly equal density with spinal fluid on radiographic images.
Tamura, Ryota; Tomita, Hideyuki; Shimizu, Kazuhiko; Sugiyama, Kazutoshi
2013-06-21
A 61-year-old woman had an intracranial tumour that was located on the falx. Meningioma was suspected and the tumour rapidly grew over 1 year. It showed nearly equal density with spinal fluid showing almost no enhancement on radiographic images, like microcystic meningioma. Successful removal of the tumour was achieved. Histopathologically, the tumour was diagnosed as low-grade meningioma. The meningioma had variable sized microcysts and the appearance of solid area was meningothelial meningioma. This is a rare radiographic image for meningothelial meningioma.
Application of a density functional approach to nonuniform ionic fluids: the effect of association
Directory of Open Access Journals (Sweden)
J.Reszko-Zygmunt
2004-01-01
Full Text Available In the present paper we discuss a density functional approach for nonuniform ionic fluids, which takes into account the existence of ion pairs. The theory is based on a fundamental measure theory of hard-spheres, the theory of Gillespie et al., which leads to a more accurate description of the electrostatic part of the grand potential as well as on Wertheim's association theory. The results of model calculations indicate that the inclusion of the associative term in the grand potential leads to the structure of the double layer, which differs from the structure evaluated by neglecting the association. These differences are important at low temperatures only.
Yong, Xin
Nano fluidics has shown promising potential for applications that could significantly impact our daily life, such as energy harvest, lab on a chip, desalination, etc. Current techniques to realize nano fluidic ideas are still very limited due to manufacturing technology. Although sub-micron fabrication techniques are undergoing rapid development recently, scientists and engineers are still not able to access actual nanometric systems. This reason prompts the development of computational tools to reveal physical principles underlying nano fluidic phenomena. Among various numerical approaches ranging from macroscopic to microscopic, molecular dynamics stands out because of its ability to faithfully model both equilibrium and non-equilibrium nanosystems by involving an appropriate amount of molecular details. The results from molecular dynamics simulations could elucidate essential physics and benefit designs of practical nano fluidic systems. This thesis attempts to provide the theoretical foundation for modeling nano fluidic systems, by investigating nanoscale fluid behaviors and nanoscale fluid-solid interfacial physics and transport for simple fluids via molecular dynamics simulations. Boundary-driven-shear, homogeneous-shear and reverse non-equilibrium molecular dynamics methods are implemented to generate non-equilibrium systems. The fundamental fluid behaviors such as velocity profile, temperature distribution and rheological material functions under steady planar shear are explored comprehensively by each method corresponding to different perspectives. The influences of nanoscale confinement are analyzed from the comparison among these methods. The advantages and disadvantages of each method are clarified, which provide guidance to conduct appropriate molecular dynamics simulations for nano fluidics. Further studies on the intrinsic slip of smooth solid surfaces is realized by the boundary-driven-shear method. Inspired by previous hypothesis of momentum
Enhancing Understanding of High Energy Density Plasmas Using Fluid Modeling with Kinetic Closures
Hansen, David; Held, Eric; Srinivasan, Bhuvana; Masti, Robert; King, Jake
2016-10-01
This work seeks to understand possible stabilization mechanisms of the early-time electrothermal instability in the evolution of the Rayleigh-Taylor instability in MagLIF (Magnetized Liner Inertial Fusion) experiments. Such mechanisms may include electron thermal conduction, viscosity, and large magnetic fields. Experiments have shown that the high-energy density plasmas from wire-array implosions require physics modelling that goes well beyond simple models such as ideal MHD. The plan is to develop a multi-fluid extended-MHD model that includes kinetic closures for thermal conductivity, resistivity, and viscosity using codes that are easily available to the wider research community. Such an effort would provide the community with a well-benchmarked tool capable of advanced modeling of high-energy-density plasmas.
Energy Technology Data Exchange (ETDEWEB)
Ji Peijun [College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029 (China); Feng Wei [College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029 (China)]. E-mail: fengwei@mail.buct.edu.cn; Tan Tianwei [College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029 (China)
2007-07-15
The density of aqueous solutions of amino acids has been modeled with the statistical associating fluid theory (SAFT) equation of state. The modeling is accomplished by extending the previously developed new method to determine the SAFT parameters for amino acids. The modeled systems include {alpha}-alanine/H{sub 2}O, {beta}-alanine/H{sub 2}O, proline/H{sub 2}O, L-asparagine/H{sub 2}O, L-glutamine/H{sub 2}O, L-histidine/H{sub 2}O, serine/H{sub 2}O, glycine/H{sub 2}O, alanine/H{sub 2}O/sucrose, DL-valine/H{sub 2}O/sucrose, arginine/H{sub 2}O/sucrose, serine/H{sub 2}O/ethylene glycol, and glycine/H{sub 2}O/ethylene glycol. The density of binary solutions of amino acids has been correlated or predicted with a high precision. And then the density of multicomponent aqueous solutions of amino acids has been modeled based on the modeling results of binary systems, and a high accuracy of density calculations has been obtained. Finally, the water activities of DL-valine/H{sub 2}O, glycine/H{sub 2}O, and proline/H{sub 2}O have been predicted without using binary interaction parameters, and good results have been obtained.
A fundamental measure density functional for fluid and crystal phases of the Asakura-Oosawa model
Mortazavifar, Mostafa; Oettel, Martin
2016-06-01
We investigate a density functional for the Asakura-Oosawa model of colloid-polymer mixtures, describing both fluid and crystal phases. It is derived by linearizing the two-component fundamental-measure hard sphere tensor functional in the second (polymer) component. We discuss the formulation of an effective density functional for colloids only. For small polymer-colloid size ratios the effective, polymer-induced potential between colloids is short-range attractive and of two-body form but we show that the effective density functional is not equivalent to standard mean-field approaches where attractions are taken into account by terms second order in the colloid density. We calculate numerically free energies and phase diagrams in good agreement with available simulations, furthermore we discuss the colloid and polymer distributions in the crystal and determine equilibrium vacancy concentrations. Numerical results reveal a fairly strong sensitivity to the specific type of underlying fundamental measure hard sphere functional which could aid further development of fundamental measure theory.
An SV-GMR Needle Sensor-Based Estimation of Volume Density of Magnetic Fluid inside Human Body
Directory of Open Access Journals (Sweden)
C. P. Gooneratne
2008-01-01
Full Text Available A spin-valve giant magneto-resistive (SV-GMR sensor of needle-type configuration is reported to estimate the volume density of magnetic fluid inside human body. The magnetic fluid is usually injected into human body to kill cancerous cell using hyperthermia-based treatment. To control the heat treatment, a good knowledge of temperature is very much essential. The SV-GMR-based needle-type sensor is used to measure the magnetic flux density of the magnetic fluid inside the human body from which the temperature is estimated. The needle-type sensor provides a semi-invasive approach of temperature determination.
Hlushak, Stepan P; McCabe, Clare; Cummings, Peter T
2012-09-14
We present a Fourier space density functional approach for hard particles with attractive interactions, which is based on a previously developed two-dimensional approach [S. Hlushak, W. Rżysko, and S. Sokołowski, J. Chem. Phys. 131, 094904 (2009)] for hard-sphere chains. The interactions are incorporated by means of a three-dimensional Fourier image of the direct correlation function that is obtained from the first-order mean-spherical approximation. In order to improve the computational efficiency, we make extensive use of fast Fourier transforms for calculating density convolution integrals. A two-dimensional implementation of the new density functional approach, based on the expansion of the functional around the bulk fluid density, is used to study structure and adsorption of two model fluids in narrow cylindrical pores. We also investigate two methods that improve the accuracy of the theory as compared to the conventional DFT approach, which expands the free energy functional around the bulk fluid density: One a variant of the reference fluid density functional theory used by Gillespie et al. [Phys. Rev. E 68, 031503 (2003)], and the second a weighted density approach with energy route thermodynamics. Results from these two methods are compared to the conventional approach and also to the results of Monte Carlo simulations. We find that the method of Gillespie et al. and the weighted density approach with energy route thermodynamics yield significant improvement over the conventional approach.
Molecular density functional theory of water including density–polarization coupling
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2016-01-01
International audience; We present a three-dimensional molecular density functional theory of water derived fromfirst-principles that relies on the particle’s density and multipolar polarization density andincludes the density–polarization coupling. This brings two main benefits: (i) scalar densityand vectorial multipolar polarization density fields are much more tractable and give morephysical insight than the full position and orientation densities, and (ii) it includes the fulldensity–pola...
The viscosity and density of sour gas fluids at high temperatures and high pressures
Energy Technology Data Exchange (ETDEWEB)
Giri, B.R.; Marriott, R.A.; Blais, P.; Clark, P.D. [Alberta Sulphur Research Ltd., Calgary, AB (Canada); Calgary Univ., AB (Canada). Dept. of Chemistry
2010-01-15
This poster session discussed an experiment designed to measure the viscosity and density of sour gas fluids at high temperatures and pressures. An option for disposing acid gases while enhancing the production of oil and gas fields is the re-injection of gases rich in hydrogen sulphide/carbon dioxide (H{sub 2}S/CO{sub 2}) into reservoirs up to very high pressures, but issues with respect to corrosion, compression, pumping, and transport need addressing, and the reliable high-density/high-pressure data needed to arrive at an optimum process concept and the design of pumps, compressors, and transport lines had up to this point been lacking. The experimental set up involved the use of a Vibrating Tube Densimeter and a Cambridge Viscometer. Working with toxic gases at very high pressures and obtaining highly accurate data in a wide range of conditions were two of the challenges faced during the experiment. The experiment resulted in physical property measurement systems being recalibrated and a new daily calibration routine being adopted for accuracy. The densities and viscosities of pure CO{sub 2} and sulphur dioxide (SO{sub 2}) in a wide pressure and temperature range were determined. 1 tab., 9 figs.
Biosensor Arrays for Estimating Molecular Concentration in Fluid Flows
Abolfath-Beygi, Maryam
2011-01-01
This paper constructs dynamical models and estimation algorithms for the concentration of target molecules in a fluid flow using an array of novel biosensors. Each biosensor is constructed out of protein molecules embedded in a synthetic cell membrane. The concentration evolves according to an advection-diffusion partial differential equation which is coupled with chemical reaction equations on the biosensor surface. By using averaging theory methods and the divergence theorem, an approximate model is constructed that describes the asymptotic behaviour of the concentration as a system of ordinary differential equations. The estimate of target molecules is then obtained by solving a nonlinear least squares problem. It is shown that the estimator is strongly consistent and asymptotically normal. An explicit expression is obtained for the asymptotic variance of the estimation error. As an example, the results are illustrated for a novel biosensor built out of protein molecules.
Asiaee, Alireza; Benjamin, Kenneth M.
2016-08-01
For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (no SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0-1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.
Birdsell, D.; Rajaram, H.; Dempsey, D.; Viswanathan, H.
2014-12-01
Understanding the transport of hydraulic fracturing (HF) fluid that is injected into the deep subsurface for shale gas extraction is important to ensure that shallow drinking water aquifers are not contaminated from an environmental and public health perspective and to understand formation damage from an oil and gas production perspective. Upward pressure gradients, permeable pathways such as faults or improperly abandoned wellbores, and the density contrast of the HF fluid to the surrounding brine encourages upward HF fluid migration. In contrast, the very low shale permeability and the imbibition of water into partially-saturated shale may sequester much of the HF fluid. Using the Finite Element Heat and Mass Transfer Code (FEHM), single-phase flow and transport simulations are performed to quantify how much HF fluid is removed via the wellbore as flowback and produced water and how much reaches overlying aquifers; imbibition is calculated with a semi-analytical one-dimensional solution and treated as a sink term. The travel time for HF fluid to reach the shallow aquifers is highly dependent on the amount of water imbibed and the suction applied to the well. If imbibition rates and suction are small, the pressure transient due to injection and the density contrast allows rapid upward plume migration at early times. The density contrast diminishes considerably within tens to hundreds of years as mixing occurs. We present estimates of HF fluid migration to shallow aquifers during the first 1,000 years after hydraulic fracturing begins for ranges of subsurface properties.
Yadav, Hari O. S.; Chakravarty, Charusita
2017-05-01
We employ molecular dynamics simulations to study the structure and solvation thermodynamics of thiolated gold nanoparticles of size 1.2 and 1.6 nm with ligand of chain length 8-16 carbons in ethane and propane over a wide range of densities close to the critical isotherm. The Helmholtz free energy is estimated by explicitly calculating the change in entropy and internal energy of solvation, and the effect of density and temperature on fluctuation-driven inherent anisotropy in the ligand corona is characterized. Since the topological variation further accentuates this instantaneous asymmetry in the ligand cloud, the anisotropy with varying surface coverage and chain length is also studied including the solvent contributions to the entropic and energetic metrics. Our results are consistent with the experiment, suggesting a route of obtaining structural insights into solvation thermodynamics that could be useful for understanding the stability of nanoparticle dispersions.
Density-functional theory for fluid-solid and solid-solid phase transitions
Bharadwaj, Atul S.; Singh, Yashwant
2017-03-01
We develop a theory to describe solid-solid phase transitions. The density functional formalism of classical statistical mechanics is used to find an exact expression for the difference in the grand thermodynamic potentials of the two coexisting phases. The expression involves both the symmetry conserving and the symmetry broken parts of the direct pair correlation function. The theory is used to calculate phase diagram of systems of soft spheres interacting via inverse power potentials u (r ) =ɛ "close="1 /n )">σ /r n , where parameter n measures softness of the potential. We find that for 1 /n ≥0.154 the body-centred-cubic (bcc) structure is preferred. The bcc structure transforms into the fcc structure upon increasing the density. The calculated phase diagram is in good agreement with the one found from molecular simulations.
Danel, J-F; Kazandjian, L; Piron, R
2016-04-01
Of the two approaches of density-functional theory molecular dynamics, quantum molecular dynamics is limited at high temperature by computational cost whereas orbital-free molecular dynamics, based on an approximation of the kinetic electronic free energy, can be implemented in this domain. In the case of deuterium, it is shown how orbital-free molecular dynamics can be regarded as the limit of quantum molecular dynamics at high temperature for the calculation of the equation of state. To this end, accurate quantum molecular dynamics calculations are performed up to 20 eV at mass densities as low as 0.5g/cm^{3} and up to 10 eV at mass densities as low as 0.2g/cm^{3}. As a result, the limitation in temperature so far attributed to quantum molecular dynamics is overcome and an approach combining quantum and orbital-free molecular dynamics is used to construct an equation of state of deuterium. The thermodynamic domain addressed is that of the fluid phase above 1 eV and 0.2g/cm^{3}. Both pressure and internal energy are calculated as functions of temperature and mass density, and various exchange-correlation contributions are compared. The generalized gradient approximation of the exchange-correlation functional, corrected to approximately include the influence of temperature, is retained and the results obtained are compared to other approaches and to experimental shock data; in parts of the thermodynamic domain addressed, these results significantly differ from those obtained in other first-principles investigations which themselves disagree. The equations of state of hydrogen and tritium above 1 eV and above, respectively, 0.1g/cm^{3} and 0.3g/cm^{3}, can be simply obtained by mass density scaling from the results found for deuterium. This ab initio approach allows one to consistently cover a very large domain of temperature on the domain of mass density outlined above.
Muon radiolysis affected by density inhomogeneity in near-critical fluids.
Cormier, P J; Alcorn, C; Legate, G; Ghandi, K
2014-04-01
In this article we show the significant tunability of radiation chemistry in supercritical ethane and to a lesser extent in near critical CO2. The information was obtained by studies of muonium (Mu = μ(+)e(-)), which is formed by the thermalization of positive muons in different materials. The studies of the proportions of three fractions of muon polarization, PMu, diamagnetic PD and lost fraction, PL provided the information on radiolysis processes involved in muon thermalization. Our studies include three different supercritical fluids, water, ethane and carbon dioxide. A combination of mobile electrons and other radiolysis products such as (•)C2H5 contribute to interesting behavior at densities ∼40% above the critical point in ethane. In carbon dioxide, an increase in electron mobility contributes to the lost fraction. The hydrated electron in water is responsible for the lost fraction and decreases the muonium fraction.
Sun, Hongbing; Feistel, Rainer; Koch, Manfred; Markoe, Andrew
2008-10-01
A set of fitted polynomial equations for calculating the physical variables density, entropy, heat capacity and potential temperature of a thermal saline fluid for a temperature range of 0-374 °C, pressure range of 0.1-100 MPa and absolute salinity range of 0-40 g/kg is established. The freshwater components of the equations are extracted from the recently released tabulated data of freshwater properties of Wagner and Pruß [2002. The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. Journal of Physical and Chemical Reference Data 31, 387-535]. The salt water component of the equation is based on the near-linear relationship between density, salinity and specific heat capacity and is extracted from the data sets of Feistel [2003. A new extended Gibbs thermodynamic potential of seawater. Progress in Oceanography 58, 43-114], Bromley et al. [1970. Heat capacities and enthalpies of sea salt solutions to 200 °C. Journal of Chemical and Engineering Data 15, 246-253] and Grunberg [1970. Properties of sea water concentrates. In: Third International Symposium on Fresh Water from the Sea, vol. 1, pp. 31-39] in a temperature range 0-200 °C, practical salinity range 0-40, and varying pressure and is also calibrated by the data set of Millero et al. [1981. Summary of data treatment for the international high pressure equation of state for seawater. UNESCO Technical Papers in Marine Science 38, 99-192]. The freshwater and salt water components are combined to establish a workable multi-polynomial equation, whose coefficients were computed through standard linear regression analysis. The results obtained in this way for density, entropy and potential temperature are comparable with those of existing models, except that our new equations cover a wider temperature—(0-374 °C) than the traditional (0-40 °C) temperature range. One can apply these newly established equations to the calculation of in-situ or
Energy Technology Data Exchange (ETDEWEB)
Morgen, Michael Mark [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
1997-05-01
We develop a polarization-sensitive femtosecond pump probe technique, Raman induced polarization spectroscopy (RIPS), to study coherent rotation in molecular fluids. By observing the collisional dephasing of the coherently prepared rotational states, we are able to extract information concerning the effects of molecular interactions on the rotational motion. The technique is quite sensitive because of the zero background detection method, and is also versatile due to its nonresonant nature.
Ma, Haibo; Ma, Jing
2011-08-07
Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.
Chemical equilibrium in high pressure molecular fluid mixtures
Energy Technology Data Exchange (ETDEWEB)
Shaw, M.S.
1993-09-01
The N{sub atoms}PT Monte Carlo simulation method has been reformulated to incorporate multiple species and chemical reactions with changes in total number of molecules. While maintaining a constant number of each type of atom, the number of molecules is changed by turning on and off the interactions of any particular position with other molecules. Chemical reactions are allowed as a correlated move of atoms to differnt molecular locations. Equilibrium chemical composition is determined as an average over the simulation along with equation of state quantities. A large set of simulations has been made with the system N{sub 2} + O{sub 2} {rightleftharpoons} NO covering a wide range in P and T. Both Hugoniot states and the CJ point have been determined and are shown to be sensitive to the potentials between unlike species.
Obstructive renal injury: from fluid mechanics to molecular cell biology
Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto
2010-01-01
Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making. PMID:24198613
Obstructive renal injury: from fluid mechanics to molecular cell biology.
Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto
2010-04-22
Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.
Evolving Molecular Cloud Structure and the Column Density Probability Distribution Function
Ward, Rachel L; Sills, Alison
2014-01-01
The structure of molecular clouds can be characterized with the probability distribution function (PDF) of the mass surface density. In particular, the properties of the distribution can reveal the nature of the turbulence and star formation present inside the molecular cloud. In this paper, we explore how these structural characteristics evolve with time and also how they relate to various cloud properties as measured from a sample of synthetic column density maps of molecular clouds. We find that, as a cloud evolves, the peak of its column density PDF will shift to surface densities below the observational threshold for detection, resulting in an underlying lognormal distribution which has been effectively lost at late times. Our results explain why certain observations of actively star-forming, dynamically older clouds, such as the Orion molecular cloud, do not appear to have any evidence of a lognormal distribution in their column density PDFs. We also study the evolution of the slope and deviation point ...
Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry.
Domingo, Luis R
2016-09-30
A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT), is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT), the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.
Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry
Directory of Open Access Journals (Sweden)
Luis R. Domingo
2016-09-01
Full Text Available A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT, is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT, the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.
Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza
2016-11-01
By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.
Molecular simulation studies on thermophysical properties with application to working fluids
Raabe, Gabriele
2017-01-01
This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.
Multi-fluid modeling of density segregation in a dense binary fluidized bed
Institute of Scientific and Technical Information of China (English)
Zhongxi Chao; Yuefa Wang; Jana P.Jakobsen; Maria Fernandino; Hugo A.Jakobsen
2012-01-01
This paper presents simulation results of the density segregation in a dense binary gas fluidized bed using a multi-fluid model from Chao et al.(2011).The segregation behavior of two types of particles with approximately same particle diameters and different particle densities was studied and validated using the experimental data from Formisani et al.(2008),Some detailed information regarding the gas,particle velocity profiles,the distributions of the particle volume fractions and the flotsam-to-total particle volume fraction ratios is presented.The simulation results show that the simulated axial average flotsam-to-total particle volume fraction ratio distribution agrees reasonably with the experimental data of Formisani et al.(2008).The binary particle velocities are closely coupled though the segregation exists.The segregation behavior and the particle velocity profiles are superficial gas velocity dependent.The number and distribution of particle velocity vortices change dramatically with superficial gas velocity:at a comparatively low superficial gas velocity,the particles mainly segregate axially,and at a comparatively high superficial gas velocity,the particles segregate both axially and radially.
带电硬哑铃流体的分子热力学%Molecular Thermodynamics of Charged Hard-Dumbbell Fluids
Institute of Scientific and Technical Information of China (English)
秦原; 刘洪来; 胡英
2001-01-01
Chemical potentials of charged hard-dumbbell fluids are obtained by Monte Carlo simulations using Widom's test-particle method, corresponding compressibility factors are achieved by integration of chemical potentials at different densities. A molecular thermodynamic model is also developed for these charged hard-dumbbell fluids where the residual Helmholtz function is composed of two terms: a reference term responsible for the charged hard spheres and a bonding contribution measuring the sticky interactions between positive and negative hard ions.Model predictions are in good agreement with simulation results.``
Generalized extended Navier-Stokes theory: Multiscale spin relaxation in molecular fluids
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt
2013-01-01
This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia...... per unit mass. In the regime of large moment of inertia the fast relaxation is wave-vector independent and dominated by the coupling between spin and the fluid streaming velocity, whereas for small inertia the relaxation is slow and spin diffusion plays a significant role. The fast wave...
Orbital-Free Density Functional Theory for Molecular Structure Calculations
Institute of Scientific and Technical Information of China (English)
Huajie Chen; Aihui Zhou
2008-01-01
We give here an overview of the orbital-free density functional theory that is used for modeling atoms and molecules. We review typical approximations to the kinetic energy, exchange-correlation corrections to the kinetic and Hartree energies, and constructions of the pseudopotentials. We discuss numerical discretizations for the orbital-free methods and include several numerical results for illustrations.
Zhang, Yongbin
2015-06-01
Quantitative comparisons were made between the flow factor approach model and the molecular dynamics simulation (MDS) results both of which describe the flow of a molecularly thin fluid film confined between two solid walls. Although these two approaches, respectively, calculate the flow of a confined molecularly thin fluid film by different ways, very good agreements were found between them when the Couette and Poiseuille flows, respectively, calculated from them were compared. It strongly indicates the validity of the flow factor approach model in modeling the flow of a confined molecularly thin fluid film.
Kuskov, Oleg L.; Belashchenko, David K.
2016-09-01
Density and sound velocity of Fe-S liquids for the P-T parameters of the lunar core have not been constrained well. From the analysis of seismic wave travel time, Weber et al. (2011) proposed that the lunar core is composed of iron alloyed with ⩽6 wt% of light elements, such as S. A controversial issue in models of planetary core composition concerns whether Fe-S liquids under high pressure - temperature conditions provide sound velocity and density data, which match the seismic model. Here we report the results of molecular dynamics (MD) simulations of iron-sulfur alloys based on Embedded Atom Model (EAM). The results of calculations include caloric, thermal and elastic properties of Fe-S alloys at concentrations of sulfur 0-18 at.%, temperatures up to 2500 K and pressures up to 14 GPa. The effect of sulfur on the elastic properties of Fe-rich melts is most evident in the notably decreased density with added S content. In the MD simulation, the density and bulk modulus KT of liquid Fe-S decrease with increasing sulfur content, while the bulk modulus KS decreases as a whole but has some fluctuations with increasing sulfur content. The sound velocity increases with increasing pressure, but depends weakly on temperature and the concentration of sulfur. For a fluid Fe-S core of the Moon (∼5 GPa/2000 K) with 6-16 at.% S (3.5-10 wt%), the sound velocity and density may be estimated at the level of 4000 m s-1 and 6.25-7.0 g cm-3. Comparison of thermodynamic calculations with the results of interpretation of seismic observations shows good agreement of P-wave velocities in the liquid outer core, while the core density does not match the seismic models. At such concentrations of sulfur and a density by 20-35% higher than the model seismic density, a radius for the fluid outer core should be less than about 330 km found by Weber et al. because at the specified mass and moment of inertia values of the Moon an increase of the core density leads to a decrease of the core
Universal iso-density polarizable continuum model for molecular solvents
Gunceler, Deniz
2014-01-01
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from first-principles quantum mechanics. However, despite much recent interest in such models, to date the applicability of such models to non-aqueous solvents has been limited because the determination of the model parameters requires fitting to a large database of experimental solvation energies for each new solvent considered. This work presents an alternate approach which allows development of new solvation models for a large class of protic and aprotic solvents from only simple, single-molecule ab initio calculations and readily available bulk thermodynamic data. We find that this model is accurate to nearly 1.7 kcal/mol even for solvents outside our development set.
Choosing a density functional for static molecular polarizabilities
Wu, Taozhe; Thakkar, Ajit J
2015-01-01
Coupled-cluster calculations of static electronic dipole polarizabilities for 145 organic molecules are performed to create a reference data set. The molecules are composed from carbon, hydrogen, nitrogen, oxygen, fluorine, sulfur, chlorine, and bromine atoms. They range in size from triatomics to 14 atoms. The Hartree-Fock and 2nd-order M{\\o}ller-Plesset methods and 34 density functionals, including local functionals, global hybrid functionals, and range-separated functionals of the long-range-corrected and screened-exchange varieties, are tested against this data set. On the basis of the test results, detailed recommendations are made for selecting density functionals for polarizability computations on relatively small organic molecules.
Liu, Song; Zhu, Lizhe; Sheong, Fu Kit; Wang, Wei; Huang, Xuhui
2017-01-30
We present an efficient density-based adaptive-resolution clustering method APLoD for analyzing large-scale molecular dynamics (MD) trajectories. APLoD performs the k-nearest-neighbors search to estimate the density of MD conformations in a local fashion, which can group MD conformations in the same high-density region into a cluster. APLoD greatly improves the popular density peaks algorithm by reducing the running time and the memory usage by 2-3 orders of magnitude for systems ranging from alanine dipeptide to a 370-residue Maltose-binding protein. In addition, we demonstrate that APLoD can produce clusters with various sizes that are adaptive to the underlying density (i.e., larger clusters at low-density regions, while smaller clusters at high-density regions), which is a clear advantage over other popular clustering algorithms including k-centers and k-medoids. We anticipate that APLoD can be widely applied to split ultra-large MD datasets containing millions of conformations for subsequent construction of Markov State Models. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Calcara, Massimo; Borgia, Andrea
2013-04-01
Current global warming theories have produced some benefits: among them, detailed studies on CO2 and its properties, possible applications and perspectives. Starting from its use as a "green solvent" (for instance in decaffeination process), to enhance system in oil recovery, to capture and storage enough amount of CO2 in geological horizon. So, a great debate is centred around this molecule. One More useful research in natural horizon studies is its theorised use in Enhanced Geothermal Systems with CO2 as the only working fluid. In any case, the CO2 characteristics should be deeply understood, before injecting a molecule prone to change easily its aggregation state at relatively shallow depth. CO2 Rock interaction becomes therefore a focal point in approaching research sectors linked in some manner to natural or induced presence of carbon dioxide in geological horizons. Possible chemical interactions between fluids and solids have always been a central topic in defining evolution of the system as a whole in terms of dissolutions, reactions, secondary mineral formation and, in case of whichever plant, scaling. Questions arise in case of presence of CO2 with host rocks. Chemical and molecular properties are strategic. CO2 Rock interactions are based on eventual solubility capability of pure liquid and supercritical CO2 seeking and eventually quantifying its polar and/or ionic solvent capabilities. Single molecule at STP condition is linear, with central carbon atom and oxygen atoms at opposite site on a straight line with a planar angle. It has a quadrupolar moment due to the electronegativity difference between carbon and oxygen. As soon as CO2 forms bond with water, it deforms even at atmospheric pressure, assuming an induced dipole moment with a value around 0.02 Debye. Hydrated CO2 forms a hydrophilic bond; it deforms with an angle of 178 degrees. Pure CO2 forms self aggregates. In the simplest case a dimer, with two molecules of CO2 exerting mutual attraction
Energy Technology Data Exchange (ETDEWEB)
Tabacchi, G; Hutter, J; Mundy, C
2005-04-07
A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density functional calculations.
Fattah, K. A.; Lashin, A.
2016-05-01
Drilling fluid density/type is an important factor in drilling and production operations. Most of encountered problems during rotary drilling are related to drilling mud types and weights. This paper aims to investigate the effect of mud weight on filter cake properties and formation damage through two experimental approaches. In the first approach, seven water-based drilling fluid samples with same composition are prepared with different densities (9.0-12.0 lb/gal) and examined to select the optimum mud weight that has less damage. The second approach deals with investigating the possible effect of the different weighting materials (BaSO4 and CaCO3) on filter cake properties. High pressure/high temperature loss tests and Scanning Electron Microscopy (SEM) analyses were carried out on the filter cake (two selected samples). Data analysis has revealed that mud weigh of 9.5 lb/gal has the less reduction in permeability of ceramic disk, among the seven used mud densities. Above 10.5 ppg the effect of the mud weight density on formation damage is stabilized at constant value. Fluids of CaCO3-based weighting material, has less reduction in the porosity (9.14%) and permeability (25%) of the filter disk properties than the BaSO4-based fluid. The produced filter cake porosity increases (from 0.735 to 0.859) with decreasing of fluid density in case of drilling samples of different densities. The filtration loss tests indicated that CaCO3 filter cake porosity (0.52) is less than that of the BaSO4 weighted material (0.814). The thickness of the filter cake of the BaSO4-based fluid is large and can cause some problems. The SEM analysis shows that some major elements do occur on the tested samples (Ca, Al, Si, and Ba), with dominance of Ca on the expense of Ba for the CaCO3 fluid sample and vice versa. The less effect of 9.5 lb/gal mud sample is reflected in the well-produced inter-particle pore structure and relatively crystal size. A general recommendation is given to
Molecular gas temperature and density in spiral galaxies
Wall, W. F.; Jaffe, D. T.; Bash, F. N.; Israel, F. P.; Maloney, P. R.; Baas, F.
1993-01-01
We combine beam-matched CO-13, CO-12 J = 3 yields 2 and J = 2 yields 1 line data to infer the molecular gas excitation conditions in the central 500 to 1600 pc diameters of a small sample of infrared-bright external galaxies: NGC253, IC342, M 83, Maffei 2, and NGC6946. Additional observations of the J = 1 yields 0 lines of C-18O and CO-13 set limits on the opacity of the CO-13 J = 1 yields 0 line averaged over the central kiloparsec of these spiral galaxies.
Institute of Scientific and Technical Information of China (English)
Chen Xiao-Gang; Guo Zhi-Ping; Song Jin-Bao
2008-01-01
In the present paper,the random interfacial waves in N-layer density-stratified fluids moving at different steady uniform speeds are researched by using an expansion technique,and the second-order asymptotic solutions of the random displacements of the density interfaces and the associated velocity potentials in N-layer fluid are presented based on the small amplitude wave theory.The obtained results indicate that the wave-wave second-order nonlinear interactions of the wave components and the second-order nonlinear interactions between the waves and currents are described.As expected,the solutions include those derived by Chen(2006)as a special case where the steady uniform currents of the N-layer fluids are taken as zero,and the solutions also reduce to those obtained by Song(2005)for second-order solutions for random interracial waves with steady uniform currents if N=2.
Measurement of the Density of Base Fluids at Pressures 0.422 to 2.20 Gpa
Hamrock, B. J.; Jacobson, B. O.; Bergstroem, S. I.
1985-01-01
The influence of pressure on the density of six base fluids is experimentally studied for a range of pressures from 0.422 to 2.20 GPa. An important parameter used to describe the results is the change in relative volume with change in pressure dv sub r/dp. For pressures less than the solidification pressure (p ps) a small change in pressure results in a large change in dv sub r/ps. For pressures greater than the solidification pressure (p ps) there is no change in dv sub r/dp with changing pressure. The solidification pressures of the base fluids varies considerably, as do the slopes that the experimental data assumes for p ps. A new formula is developed that describes the effect of pressure on density in terms of four constants. These constants vary for the different base fluids tested.
Statistics of initial density perturbations in heavy ion collisions and their fluid dynamic response
Floerchinger, Stefan; Wiedemann, Urs Achim
2014-08-01
An interesting opportunity to determine thermodynamic and transport properties in more detail is to identify generic statistical properties of initial density perturbations. Here we study event-by-event fluctuations in terms of correlation functions for two models that can be solved analytically. The first assumes Gaussian fluctuations around a distribution that is fixed by the collision geometry but leads to non-Gaussian features after averaging over the reaction plane orientation at non-zero impact parameter. In this context, we derive a three-parameter extension of the commonly used Bessel-Gaussian event-by-event distribution of harmonic flow coefficients. Secondly, we study a model of N independent point sources for which connected n-point correlation functions of initial perturbations scale like 1 /N n-1. This scaling is violated for non-central collisions in a way that can be characterized by its impact parameter dependence. We discuss to what extent these are generic properties that can be expected to hold for any model of initial conditions, and how this can improve the fluid dynamical analysis of heavy ion collisions.
Duran-Olivencia, Miguel A.; Goddard, Ben; Kalliadasis, Serafim
2015-11-01
Over the last few decades the classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become a remarkably powerful tool in the study of colloidal fluids. Recently there has been extensive research to generalise all previous DDFTs finally yielding a general DDFT equation (for spherical particles) which takes into account both inertia and hydrodynamic interactions (HI) which strongly influence non-equilibrium properties. The present work will be devoted to a further generalisation of such a framework to systems of anisotropic particles. To this end, the kinetic equation for the Brownian particle distribution function is derived starting from the Liouville equation and making use of Zwanzig's projection-operator techniques. By averaging over all but one particle, a DDFT equation is finally obtained with some similarities to that for spherical colloids. However, there is now an inevitable translational-rotational coupling which affects the diffusivity of asymmetric particles. Lastly, in the overdamped (high friction) limit the theory is notably simplified leading to a DDFT equation which agrees with previous derivations. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.
Radial distribution function of penetrable sphere fluids to the second order in density.
Santos, Andrés; Malijevský, Alexandr
2007-02-01
The simplest bounded potential is that of penetrable spheres, which takes a positive finite value epsilon if the two spheres are overlapped, being zero otherwise. In this paper we derive the cavity function to second order in density and the fourth virial coefficient as functions of T* identical with k(B)T/epsilon (where k(B is the Boltzmann constant and T is the temperature) for penetrable sphere fluids. The expressions are exact, except for the function represented by an elementary diagram inside the core, which is approximated by a polynomial form in excellent agreement with accurate results obtained by Monte Carlo integration. Comparison with the hypernetted-chain (HNC) and Percus-Yevick (PY) theories shows that the latter is better than the former for T* hard sphere limit), the PY solution is not accurate inside the overlapping region, where no practical cancellation of the neglected diagrams takes place. The exact fourth virial coefficient is positive for T* compressibility route is the best one for T* or similar to 0.7.
Institute of Scientific and Technical Information of China (English)
Zhi-jie Zhang; Zhong-yuan Lu; Ze-sheng Li
2009-01-01
The phase behavior of bimodal molecular weight high density polyethylene (BHDPE) in solid state was investigated. Hildebrand solubility parameters (δ) were calculated for the models of blends of higher molecular weight branch polyethylene (HBPE) with different branch contents and lower molecular weight linear polyethylene (LLPE), by using molecular dynamics (MD) simulations. These δ values were then used to calculate the corresponding Flory-Huggins interaction parameter (χ) between HBPE and LLPE models. In order to better understand the compatibility between LLPE and various HBPE, Mesodyn simulations were used to show the density profiles of the blends of LLPE with various HBPE at different compositions. The results indicated that the phase behavior of BHDPE was influenced by both the global branch content of the system and the local branch content, I.e., the branch content of HBPE.
Łazarski, Roman; Burow, Asbjörn Manfred; Grajciar, Lukáš; Sierka, Marek
2016-10-30
A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn-Sham density functional theory using Gaussian-type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange-correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn-Sham matrix formation. © 2016 Wiley Periodicals, Inc.
Chen, Carl P C; Hsu, Chih Chin; Pei, Yu-Cheng; Chen, Ruo Li; Zhou, Shaobo; Shen, Hsuan-Chen; Lin, Shih-Cherng; Tsai, Wen Chung
2014-04-01
Knee pain is commonly seen in orthopedic and rehabilitation outpatient clinical settings, and in the aging population. Bursitis of the knee joint, especially when the volume of the synovial fluid is large enough, can compress and distend the nearby soft tissues, causing pain in the knee joint. Out of all the bursae surrounding the knee joint, supra-patellar bursitis is most often associated with knee pain. Treatment strategies in managing supra-patellar bursitis include the aspiration of joint synovial fluid and then followed by steroid injection into the bursa. When supra-patellar bursitis is caused by degenerative disorders, the concept of viscosupplementation treatment may be effective by injecting hyaluronic acid into the bursa. However, the rheology or the changes in the concentrations of proteins (biomarkers) that are related to the development of bursitis in the synovial fluid is virtually unexplored. Therefore, this study aimed to identify the concentration changes in the synovial fluid total protein amount and individual proteins associated with supra-patellar bursitis using the Bradford protein assay and western immunoglobulin methods. A total of 20 patients were divided into two groups with 10 patients in each group. One group received the high molecular weight hyaluronic acid product of Synvisc Hylan G-F 20 and the other group received the low molecular weight hyaluronic acid product of Hya-Joint Synovial Fluid Supplement once per week injection into the bursa for a total of 3 weeks. Significant decreases in the synovial fluid total protein concentrations were observed after the second dosage of high molecular weight hyaluronic acid injections. Apolipoprotein A-I, interleukin 1 beta, alpha 1 antitrypsin, and matrix metalloproteinase 1 proteins revealed a trend of decreasing western immunoblotting band densities after hyaluronic acid injections. The decreases in apolipoprotein A-I and interleukin 1 beta protein band densities were significant in the high
Yu, Zhaosheng; Lin, Zhaowu; Shao, Xueming; Wang, Lian-Ping
2017-09-01
A parallel direct-forcing fictitious domain method is employed to perform fully resolved numerical simulations of turbulent channel flow laden with finite-size particles. The effects of the particle-fluid density ratio on the turbulence modulation in the channel flow are investigated at the friction Reynolds number of 180, the particle volume fraction of 0.84 % , and the particle-fluid density ratio ranging from 1 to 104.2. The results show that the variation of the flow drag with the particle-fluid density ratio is not monotonic, with a larger flow drag for the density ratio of 10.42, compared to those of unity and 104.2. A significant drag reduction by the particles is observed for large particle-fluid density ratios during the transient stage, but not at the statistically stationary stage. The intensity of particle velocity fluctuations generally decreases with increasing particle inertia, except that the particle streamwise root-mean-square velocity and streamwise-transverse velocity correlation in the near-wall region are largest at the density ratio of the order of 10. The averaged momentum equations are derived with the spatial averaging theorem and are used to analyze the mechanisms for the effects of the particles on the flow drag. The results indicate that the drag-reduction effect due to the decrease in the fluid Reynolds shear stress is counteracted by the drag-enhancement effect due to the increase in the total particle stress or the interphase drag force for the large particle-inertia case. The sum of the total Reynolds stress and particle inner stress contributions to the flow drag is largest at the density ratio of the order of 10, which is the reason for the largest flow drag at this density ratio. The interphase drag force obtained from the averaged momentum equation (the balance theory) is significantly smaller than (but agrees qualitatively with) that from the empirical drag formula based on the phase-averaged slip velocity for large density
Molecular dynamics simulation for the baryon-quark phase transition at finite baryon density
Energy Technology Data Exchange (ETDEWEB)
Akimura, Y. [Saitama University, Department of physics, Sakura-Ku, Saitama City (Japan); Japan Atomic Energy Research Institute, Advanced Science Research Center, Tokai (Japan); Maruyama, T.; Chiba, S. [Japan Atomic Energy Research Institute, Advanced Science Research Center, Tokai (Japan); Yoshinaga, N. [Saitama University, Department of physics, Sakura-Ku, Saitama City (Japan)
2005-09-01
We study the baryon-quark phase transition in the molecular dynamics (MD) of the quark degrees of freedom at finite baryon density. The baryon state at low baryon density, and the deconfined quark state at high baryon density are reproduced. We investigate the equations of state of matters with different u-d-s compositions. It is found that the baryon-quark transition is sensitive to the quark width. (orig.)
Molecular Weight and Charge Density Asymmetry in Polyelectrolyte Complexation
Audus, Debra; Fredrickson, Glenn; Duechs, Dominik
2009-03-01
We investigate the phase diagram of oppositely charged polymers in a good solvent using a field-theoretic model. Mean-field solutions fail to predict the experimentally observed macroscopic phase separation into a solvent-rich phase and a dense liquid aggregate of polymers - a ``complex coacervate.'' We therefore study the model within a one-loop approximation, which accounts for Gaussian fluctuations in electrostatic and chemical potentials. Our particular focus is the effect of molecular weight, ionic strength, and charge asymmetry on the phase envelope. A set of dimensionless parameters is identified that dictate the size and shape of the two-phase region. Our results should be helpful in guiding experimental studies of coacervation.
Avoiding self-repulsion in density functional description of biased molecular junctions
Energy Technology Data Exchange (ETDEWEB)
Baer, Roi [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: roi.baer@huji.ac.il; Livshits, Ester [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Neuhauser, Daniel [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: dxn@chem.ucla.edu
2006-10-26
We examine the effects of self-repulsion on the predictions of charge distribution in biased molecular junctions by the local density functional theory methods. This is done using a functional with explicit long-range exchange term effects [R. Baer, D. Neuhauser, Phys. Rev. Lett. 94 (2005) 043002]. We discuss in detail the new density functional, pointing out some of the remaining difficulties in the theory. We find that in weakly coupled junctions (the typical molecular electronics case) local-density functionals fail to describe correctly the charge distribution in the intermediate bias regime.
DEFF Research Database (Denmark)
Khan, Faheem; Schmid, Silvan; Larsen, Peter Emil
2013-01-01
Physical characterization of viscous samples is crucial in chemical, pharma and petroleum industry. For example, in the refining industry of petroleum, water percentage is verified by measuring the density of a sample. In this article we present a suspended microchannel resonator (SMR) which uses 5...... pL of a fluid sample and measures its density with a resolution of 0.01 kg/m 3 and a sensitivity of 16 Hz/kg/m3. The resonator can also simultaneously measure viscosity of the solutions with an accuracy of 0.025 mPa s. The SMR is part of a system which contains packaging and tubing to deliver...... samples to the resonator. The system can easily handle multiple viscous fluids to measure their densities and viscosities. The SMR is transparent, facilitating visual inspection of the microchannel content. © 2013 Elsevier B.V....
Simon, Sílvia; Duran, Miquel
1997-08-01
Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.
Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D
2017-08-14
Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.
Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.
2017-08-01
Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.
Rebolledo, David; Green, Anne; Braiding, Catherine; Molinari, Sergio; Wong, Graeme; Blackwell, Rebecca; Elia, Davide; Schisano, Eugenio
2015-01-01
We report high resolution observations of the $^{12}$CO$(1\\rightarrow0)$ and $^{13}$CO$(1\\rightarrow0)$ molecular lines in the Carina Nebula and the Gum 31 region obtained with the 22-m Mopra telescope as part of the The Mopra Southern Galactic Plane CO Survey. We cover 8 deg$^2$ from $l = 285^{\\circ}$ to 290$^{\\circ}$, and from $b = -1.5^{\\circ}$ to +0.5$^{\\circ}$. The molecular gas column density distributions from both tracers have a similar range of values. By fitting a grey-body function to the observed infrared spectral energy distribution from Herschel maps, we derive gas column densities and dust temperatures. The gas column density has values in the range from $6.3\\times\\ 10^{20}$ to $1.4\\times 10^{23}$ cm$^{-2}$, while the dust temperature has values in the range from 17 to 43 K. The gas column density derived from the dust emission is approximately described by a log-normal function for a limited range of column densities. A high-column density tail is clearly evident for the gas column density dis...
Alkindi, A.; Bijeljic, B.; Muggeridge, A.
2008-12-01
Diffusion and advective dispersion may have a significant influence on the mixing between miscible fluids during displacement processes in porous media. This is particularly important when intimate mixing may result in important changes to the fluid behaviour. For example in oil recovery, mixing between injected and connate water will tend to reduce the efficiency of low salinity water injection. On the other hand recovery may be increased if injected gas mixes with high viscosity oil increasing its mobility. Most experimental data for longitudinal and transverse dispersion have been obtained using fluid pairs with very similar viscosities and densities. The traditional description (Perkins and Johnston, 1963) suggests that longitudinal dispersion decreases as mobility ratio increases. It also suggests that gravity will tend to reduce transverse dispersion. We provide experimental measurements of longitudinal (KL) and transverse (KT) dispersion at low Reynolds number as a function of Peclet number for the first contact miscible ethanol- glycerol fluid system flowing in a porous media formed from glass beads. These fluids have a high viscosity ratio of over 1000 and a significant density difference of 470 kg m-3. We show that both KL and KT are similar to values measured for a water-brine system but that KT is reduced when the less dense ethanol is flowing above the denser glycerol.
Ultra-high Density SNParray in Neuroblastoma Molecular Diagnostics
Directory of Open Access Journals (Sweden)
Inge M. Ambros
2014-08-01
Full Text Available Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e. amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses: so called segmental chromosomal aberrations, i.e. gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as chromothripsis are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism (SNP arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.
Sun, Shuyu
2013-06-01
This paper introduces an efficient technique to generate new molecular simulation Markov chains for different temperature and density conditions, which allow for rapid extrapolation of canonical ensemble averages at a range of temperatures and densities different from the original conditions where a single simulation is conducted. Obtained information from the original simulation are reweighted and even reconstructed in order to extrapolate our knowledge to the new conditions. Our technique allows not only the extrapolation to a new temperature or density, but also the double extrapolation to both new temperature and density. The method was implemented for Lennard-Jones fluid with structureless particles in single-gas phase region. Extrapolation behaviors as functions of extrapolation ranges were studied. Limits of extrapolation ranges showed a remarkable capability especially along isochors where only reweighting is required. Various factors that could affect the limits of extrapolation ranges were investigated and compared. In particular, these limits were shown to be sensitive to the number of particles used and starting point where the simulation was originally conducted.
Krishna, Hemanth; Kumar, Hemantha; Gangadharan, Kalluvalappil
2016-06-01
A magneto rheological (MR) fluid damper offers cost effective solution for semiactive vibration control in an automobile suspension. The performance of MR damper is significantly depends on the electromagnetic circuit incorporated into it. The force developed by MR fluid damper is highly influenced by the magnetic flux density induced in the fluid flow gap. In the present work, optimization of electromagnetic circuit of an MR damper is discussed in order to maximize the magnetic flux density. The optimization procedure was proposed by genetic algorithm and design of experiments techniques. The result shows that the fluid flow gap size less than 1.12 mm cause significant increase of magnetic flux density.
Krishna, Hemanth; Kumar, Hemantha; Gangadharan, Kalluvalappil
2017-08-01
A magneto rheological (MR) fluid damper offers cost effective solution for semiactive vibration control in an automobile suspension. The performance of MR damper is significantly depends on the electromagnetic circuit incorporated into it. The force developed by MR fluid damper is highly influenced by the magnetic flux density induced in the fluid flow gap. In the present work, optimization of electromagnetic circuit of an MR damper is discussed in order to maximize the magnetic flux density. The optimization procedure was proposed by genetic algorithm and design of experiments techniques. The result shows that the fluid flow gap size less than 1.12 mm cause significant increase of magnetic flux density.
Molecular dynamics simulation for baryon-quark phase transition at finite temperature and density
Akimura, Y; Yoshinaga, N; Chiba, S; Akimura, Yuka; Maruyama, Toshiki; Yoshinaga, Naotaka; Chiba, Satoshi
2005-01-01
We study the baryon-quark phase transition in a molecular dynamics (MD) of quark degrees of freedom at finite temperature and density. The baryon state at low density and temperature, and the deconfined quark state at high density and temperature are reproduced. We investigate the equations of state of matters with different $u$-$d$-$s$ compositions. Then we draw phase diagrams in the temperature-density plane by this simulation. It is found that the baryon-quark transition is sensitive to the quark width.
Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.
2017-03-01
Context. Recent submillimeter and far-infrared wavelength observations of absorption in the rotational ground-state lines of various simple molecules against distant Galactic continuum sources have opened the possibility of studying the chemistry of diffuse molecular clouds throughout the Milky Way. In order to calculate abundances, the column densities of molecular and atomic hydrogen, H i, must be known. Aims: We aim at determining the atomic hydrogen column densities for diffuse clouds located on the sight lines toward a sample of prominent high-mass star-forming regions that were intensely studied with the HIFI instrument onboard Herschel. Methods: Based on Jansky Very Large Array data, we employ the 21 cm H i absorption-line technique to construct profiles of the H i opacity versus radial velocity toward our target sources. These profiles are combined with lower resolution archival data of extended H i emission to calculate the H i column densities of the individual clouds along the sight lines. We employ Bayesian inference to estimate the uncertainties of the derived quantities. Results: Our study delivers reliable estimates of the atomic hydrogen column density for a large number of diffuse molecular clouds at various Galactocentric distances. Together with column densities of molecular hydrogen derived from its surrogates observed with HIFI, the measurements can be used to characterize the clouds and investigate the dependence of their chemistry on the molecular fraction, for example. The data sets are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/600/A2
Displacement of one Newtonian fluid by another: density effects in axial annular flow
DEFF Research Database (Denmark)
Szabo, Peter; Hassager, Ole
1997-01-01
. Comparison with a simple theory for drainage of thin films is performed. It is found that recirculations deform the fluid-fluidinterface significantly in situations dominated by buoyancy forces. Also, a deviation from the concentric annular geometry is shown to induce azimuthal transport of fluid. Finally...
Energy Technology Data Exchange (ETDEWEB)
Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)
2014-12-09
The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.
Xu, Yu-lei; Gong, Xing-long; Peng, Chao; Sun, Ying-qiang; Jiang, Wan-quan; Zhang, Zhong
2010-06-01
Shear thickening fluids (STFs) based on additives with different concentrations and molecular chain lengths were investigated. STF samples were prepared with silica and additive dispersed in polyethylene glycol (PEG) 400, where three types of additives with different molecular chain lengths of PEG4000, PEG6000, and PEG10000 were used. For PEG10000, different concentrations, including 0, 1%, 3%, and 5%, were selected to study the influences of additive concentrations. Rheological properties of the samples were measured with a rheometer. The results show that the shear thickening effect was significantly enhanced with the increase of the concentration and the molecular chain length of additives. The mechanism of enhancement was quantitatively explained with the formation of large particles clusters.
Energy Technology Data Exchange (ETDEWEB)
Crawley, M.E.
1988-05-01
The primary objectives of the Pressure - Density Survey were to obtain the middle-of-formation pressures, determine well-bore fluid densities, define well-bore fluid density stratification, and to provide, where possible, formation water density values for wells where little or no information on densities exists. The survey collected ground-water pressure and density data during three field testing periods during the years 1986 and 1987. Data were collected from 33 individual wells located in the vicinity of the WIPP Site. 18 refs., 10 figs., 10 tabs.
Institute of Scientific and Technical Information of China (English)
Fu Dong; Liao Tao
2007-01-01
The excess Helmholtz free energy functional for nonpolar chain-like molecules is formulated in terms of a weighted density approximation (WDA) for short-range interactions and a Weaks-Chandler-Andersen (WCA) approximation and a Barker-Henderson (BH) theory for long-range attraction. Within the framework of density functional theory (DFT), vapour-liquid interfacial properties including density profile and surface tension, and vapour-liquid nucleation properties including density profile, work of formation and number of particles are investigated for spherical and chainlike molecules. The obtained vapour-liquid surface tension and the number of particles in critical nucleus for LennardJones (L J) fluids are consistent with the simulation results. The influences of supersaturation, temperature and chain length on vapour-liquid nucleation properties are discussed.
Zhu, W.; Knapp, Y.; Deplano, V.
2016-05-01
A novel refractive index and density-matched liquid-solid suspension system taking into account chemical hazard and health concerns was developed and characterized. The solid phase is made of PMMA spheres, the refractive index of which being adapted with a mixture of 2,2'-thiodiethanol and phosphate-buffered saline (PBS), while the density is adapted with a mixture of PBS and glycerol. The proposed chemicals present low hazard characteristics in comparison with former solutions. Data collected from density and refractive index measurements of the solid phase and of the different fluid constituents are used to define a specific ternary mixture adapted to commercial grade micron-size particles. The defined mixture is validated in a micron-sized granular flow experiment. The described method can be applied to other low-density solids.
Salacuse, J. J.; Denton, A. R.; Egelstaff, P. A.; Tau, M.; Reatto, L.
1996-03-01
The method described in the preceding paper [J. J. Salacuse, A. R. Denton, and P. A. Egelstaff, preceding paper, Phys. Rev. E 53, 2382 (1996)] for computing the static structure factor S(Q) of a bulk fluid is used to analyze molecular dynamics computer simulation data for a model krypton fluid whose atoms interact via a truncated Aziz pair potential. Simulations have been carried out for two system sizes of N=706 and 2048 particles and two thermodynamic states, described by a common reduced temperature T*=1.51 and reduced densities ρ*=0.25 and 0.4. Results presented include the N-particle radial distribution function gN(r) and the bulk static structure factor S(Q). In addition we calculate the direct correlation function c(r) from the full S(Q). In comparison with corresponding predictions of the modified hypernetted chain theory, the results are generally in excellent agreement at all r and Q, to within random statistical errors in the simulation data.
Energy Technology Data Exchange (ETDEWEB)
Welty, C. (Drexel Univ., Philadelphia, PA (United States)); Gelhar, L.W. (Massachusetts Inst. of Tech., Cambridge (United States))
1991-08-01
Both porous medium heterogeneities and fluid density and viscosity contrasts affect solute transport in miscible fluid displacement. The effect of interaction of these processes on large-scale mixing are evaluated using spectral-based perturbation theory. A three-dimensional, statistically isotropic, exponential log permeability autocovariance is used to represent the spatial variability of the porous medium. State equations linearly relating log density and log viscosity perturbations to concentration perturbations represent the density and viscosity variability and strongly couple the flow and solute transport perturbation equations. Analytical expressions for longitudinal macrodispersivity, derived for one-dimensional mean solute transport, are functionally dependent on mean displacement distance, mean concentration and concentration gradient, density and viscosity differences, mean velocity, gravity, and correlation scale and variance of the log permeability process. Transient analysis shows that longitudinal macrodispersivity grows exponentially in time (or mean displacement distance) without bound for the case where instabilities due to viscous or gravity fingering arise (the unstable or fingering case) and that it grows at early time then decreases exponentially to an asymptotic value close to that of local dispersivity for the case where density or viscosity contrasts produce a stabilizing effect (the stable case).
Jeanmairet, Guillaume; Borgis, Daniel
2013-01-01
We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619, 2013] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields, the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional ...
Indian Academy of Sciences (India)
Amita Wadehra; Swapan K Ghosh
2005-09-01
The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole polarizability within the framework of density functional theory based linear response theory. The resulting polarizability is expressed in terms of the contributions from individual atoms in the molecule. A few illustrative numerical calculations are shown to predict the molecular polarizabilities in good agreement with available results. The usefulness of the approach to the calculation of intermolecular interaction needed for computer simulation is highlighted.
Schneider, N; Csengeri, T; Klessen, R; Federrath, C; Tremblin, P; Girichidis, P; Bontemps, S; Andre, Ph
2014-01-01
Column density maps of molecular clouds are one of the most important observables in the context of molecular cloud- and star-formation (SF) studies. With Herschel it is now possible to reveal rather precisely the column density of dust, which is the best tracer of the bulk of material in molecular clouds. However, line-of-sight (LOS) contamination from fore- or background clouds can lead to an overestimation of the dust emission of molecular clouds, in particular for distant clouds. This implies too high values for column density and mass, and a misleading interpretation of probability distribution functions (PDFs) of the column density. In this paper, we demonstrate by using observations and simulations how LOS contamination affects the PDF. We apply a first-order approximation (removing a constant level) to the molecular clouds of Auriga and Maddalena (low-mass star-forming), and Carina and NGC3603(both high-mass SF regions). In perfect agreement with the simulations, we find that the PDFs become broader, ...
Chemical descriptors, convexity and structure of density matrices in molecular systems
Bochicchio, Roberto C
2015-01-01
The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and consequently higher order derivatives are undefined. The introduction of the interaction between the physical domain with an environment induces a coherent structure for the density matrix in the grand-canonical formulation suppressing the discontinuities leading to the proper definitions of the descriptors.
Institute of Scientific and Technical Information of China (English)
LU Dong-qiang; SUN Cui-zhi
2013-01-01
Generation of the transient flexural-and capillary-gravity waves by impulsive disturbances in a two-layer fluid is investigated analytically.The upper fluid is covered by a thin elastic plate or by an inertial surface with the capillary effect.The density of each of the two immiscible layers is constant.The fluids are assumed to be inviscid and incompressible and the motion be irrotational.A point force on the surface and simple mass sources in the upper and lower fluid layers are considered.A linear system is established within the framework of potential theory.The integral solutions for the surface and interfacial waves are obtained by means of the Laplace-Fourier transform.A new representation for the dispersion relation of flexural-and capillary-gravity waves in a two-layer fluid is derived.The asymptotic representations of the wave motions are derived for large time with a fixed distance-to-time ratio with the Stokes and Scorer methods of stationary phase.It is shown that there are two different modes,namely the surface and interfacial wave modes.The wave systems observed depend on the relation between the observer's moving speed and the intrinsic minimal and maximal group velocities.
Browne, Richard W; Bloom, Michael S; Shelly, Wendy B; Ocque, Andrew J; Huddleston, Heather G; Fujimoto, Victor Y
2009-01-01
To investigate whether follicular fluid lipid-soluble micronutrients are associated with embryo morphology parameters during IVF. Follicle fluid and oocytes were obtained prospectively from 81 women. Embryo morphology parameters were used as surrogate markers of oocyte health. HDL lipids and lipid-soluble micronutrients were analyzed by high-pressure liquid chromatography. Non-parametric bi-variate analysis and multivariable ordinal logistic regression models were employed to examine associations between biochemical and embryo morphology parameters. Follicular fluid HDL cholesterol (r = -0.47, p fragmentation. Ordinal logistic regression models indicate that a 0.1 mumol/L increase in beta-cryptoxanthine, adjusted for gamma-tocopherol, is associated with a 75% decrease in the cumulative odds of higher embryo fragmentation (p = 0.010). Follicular fluid HDL micronutrients may play an important role in the development of the human oocyte as evident by embryo fragmentation during IVF.
Fitting density models to observational data - The local Schmidt law in molecular clouds
Lombardi, Marco; Alves, João
2013-01-01
We consider the general problem of fitting a parametric density model to discrete observations, taken to follow a non-homogeneous Poisson point process. This class of models is very common, and can be used to describe many astrophysical processes, including the distribution of protostars in molecular clouds. We give the expression for the likelihood of a given spatial density distribution of protostars and apply it to infer the most probable dependence of the protostellar surface density on the gas surface density. Finally, we apply this general technique to model the distribution of protostars in the Orion molecular cloud and robustly derive the local star formation scaling (Schmidt) law for a molecular cloud. We find that in this cloud the protostellar surface density, \\Sigma_YSO, is directly proportional to the square gas column density, here expressed as infrared extinction in the K-band, A_K: more precisely, \\Sigma_YSO = (1.65 +/- 0.19) A_K^(2.03 +/- 0.15) stars pc^-2.
Molecular Mechanisms of the Lubrucating Function of the Synovial Fluid Control
Directory of Open Access Journals (Sweden)
Dmitry A. Antonov
2013-12-01
Full Text Available The author in his review presents up-to-date information, concerning the composition and properties of human synovial fluid with an emphasis on detailed description of the molecular mechanisms of the lubricating function control. Three main groups of molecules: (surface-active phospholipids (1, hyaluronic acid (2, and proteins group SZP/lubricine (3, were described in synovial fluid being able to support lubrication; the latter group was considered as the main biopolymers, ensuring the boundary lubrication. On author’s opinion, the modern practice of viscosupplementation is not fully functional, since it did not restore the function of the boundary lubrication, lost in the osteoarthritis progression. Besides the need to correct the composition of current drugs for viscosupplementary therapy, the ensuring of lubricating properties of tissue engineering constructs and media to grow cartilage tissue was in vitro attributed to the practical tasks of joints regenerative biomedicine.
Tellgren, E I; Teale, A M; Furness, J W; Lange, K K; Ekström, U; Helgaker, T
2014-01-21
We present a novel implementation of Kohn-Sham density-functional theory utilizing London atomic orbitals as basis functions. External magnetic fields are treated non-perturbatively, which enable the study of both magnetic response properties and the effects of strong fields, using either standard density functionals or current-density functionals-the implementation is the first fully self-consistent implementation of the latter for molecules. Pilot applications are presented for the finite-field calculation of molecular magnetizabilities, hypermagnetizabilities, and nuclear magnetic resonance shielding constants, focusing on the impact of current-density functionals on the accuracy of the results. Existing current-density functionals based on the gauge-invariant vorticity are tested and found to be sensitive to numerical details of their implementation. Furthermore, when appropriately regularized, the resulting magnetic properties show no improvement over standard density-functional results. An advantage of the present implementation is the ability to apply density-functional theory to molecules in very strong magnetic fields, where the perturbative approach breaks down. Comparison with high accuracy full-configuration-interaction results show that the inadequacies of current-density approximations are exacerbated with increasing magnetic field strength. Standard density-functionals remain well behaved but fail to deliver high accuracy. The need for improved current-dependent density-functionals, and how they may be tested using the presented implementation, is discussed in light of our findings.
Energy Technology Data Exchange (ETDEWEB)
Tellgren, E. I., E-mail: erik.tellgren@kjemi.uio.no; Lange, K. K.; Ekström, U.; Helgaker, T. [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo (Norway); Teale, A. M., E-mail: andrew.teale@nottingham.ac.uk [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo (Norway); School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom); Furness, J. W. [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)
2014-01-21
We present a novel implementation of Kohn–Sham density-functional theory utilizing London atomic orbitals as basis functions. External magnetic fields are treated non-perturbatively, which enable the study of both magnetic response properties and the effects of strong fields, using either standard density functionals or current-density functionals—the implementation is the first fully self-consistent implementation of the latter for molecules. Pilot applications are presented for the finite-field calculation of molecular magnetizabilities, hypermagnetizabilities, and nuclear magnetic resonance shielding constants, focusing on the impact of current-density functionals on the accuracy of the results. Existing current-density functionals based on the gauge-invariant vorticity are tested and found to be sensitive to numerical details of their implementation. Furthermore, when appropriately regularized, the resulting magnetic properties show no improvement over standard density-functional results. An advantage of the present implementation is the ability to apply density-functional theory to molecules in very strong magnetic fields, where the perturbative approach breaks down. Comparison with high accuracy full-configuration-interaction results show that the inadequacies of current-density approximations are exacerbated with increasing magnetic field strength. Standard density-functionals remain well behaved but fail to deliver high accuracy. The need for improved current-dependent density-functionals, and how they may be tested using the presented implementation, is discussed in light of our findings.
Uddayasankar, Uvaraj; Krull, Ulrich J
2013-11-25
The high quenching efficiency of metal nanoparticles has facilitated its use as quenchers in molecular beacons. To optimize this system, a good understanding of the many factors that influence molecular beacon performance is required. In this study, molecular beacon performance was evaluated as a function of gold nanoparticle size and its immobilization characteristics. Gold nanoparticles of 4 nm, 15 nm and 87 nm diameter, were immobilized onto glass slides. Each size regime offered distinctive optical properties for fluorescence quenching of molecular dyes that were conjugated to oligonucleotides that were immobilized to the gold nanoparticles. Rigid double stranded DNA was used as a model to place fluorophores at different distances from the gold nanoparticles. The effect of particle size and also the immobilization density of nanoparticles was evaluated. The 4 nm and 87 nm gold nanoparticles offered the highest sensitivity in terms of the change in fluorescence intensity as a function of distance (3-fold improvement for Cy5). The optical properties of the molecular fluorophore was of significance, with Cy5 offering higher contrast ratios than Cy3 due to the red-shifted emission spectrum relative to the plasmon peak. A high density of gold nanoparticles reduced contrast ratios, indicating preference for a monolayer of immobilized nanoparticles when considering analytical performance. Molecular beacon probes were then used in place of the double stranded oligonucleotides. There was a strong dependence of molecular beacon performance on the length of a linker used for attachment to the nanoparticle surface. The optimal optical performance was obtained with 4 nm gold nanoparticles that were immobilized as monolayers of low density (5.7×10(11)particles cm(-2)) on glass surfaces. These nanoparticle surfaces offered a 2-fold improvement in analytical performance of the molecular beacons when compared to other nanoparticle sizes investigated. The principles developed
Institute of Scientific and Technical Information of China (English)
Ahmed Asad; Wu Jiang-Tao
2011-01-01
We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient,D,of a Lennard Jones fluid over a wide density and temperature range.The change in self-diffusion coefficient with temperature decreases by increasing density.For density p* =pσ3 =0.84 we observe a peak at the value of the self-diffusion coefficient and the critical temperature T* =kT/ε =1.25.The value of the self-diffusion coefficient strongly depends on system size.The data of the self-diffusion coefficient are fitted to a simple analytic relation based on hydrodynamic arguments.This correction scales as N-α,where α is an adjustable parameter and N is the number of particles.It is observed that the values of α ＜ 1 provide quite a good correction to the simulation data.The system size dependence is very strong for lower densities,but it is not as strong for higher densities.The self-diffusion coefficient calculated with non-equilibrium molecular dynamic simulations at different temperatures and densities is in good agreement with other calculations from the literature.
Swann, D A; Silver, F H; Slayter, H S; Stafford, W; Shore, E
1985-01-01
Lubricin was isolated from bovine ankle, metacarpophalangeal and knee and human knee synovial fluids. The lubricins isolated from the bovine joint fluids had the same amino acid and carbohydrate compositions, but differences were observed in the relative molecular masses. The Mr values of bovine metacarpophalangeal and ankle lubricin determined by light-scattering measurements were about 200 000, whereas values of 132 000 and 143 000 were obtained for the bovine knee lubricin. The human knee lubricin had a similar carbohydrate composition to bovine knee lubricin except for the higher glucosamine content, and the amino acid composition differed slightly. The human sample had a lower glutamic acid content and a leucine/isoleucine ratio of 2:1 compared with 1:1 in the bovine. The Mr value of the human knee lubricin (166 000) was also lower than that of the bovine metacarpophalangeal and ankle samples. The Mr value of the bovine knee lubricin determined by sedimentation-equilibrium measurements was 171 000. The length measurements determined by electron microscopy and also the sedimentation measurements showed considerable polydispersity and indicate that the degree of extension of lubricin molecules can vary. Friction measurements showed that the human knee synovial-fluid lubricin had equivalent lubricating ability in a test system in vitro to that observed for lubricin isolated from normal bovine synovial fluids. The lubricating ability of lubricin was concentration-dependent, and each lubricin sample was able to act as a lubricant in vitro in an equivalent manner to whole synovial fluid at concentrations that are thought to occur in vivo. PMID:3977823
Opazo, A; Bustamante, G; Labbé, R
2015-01-01
We report experimental results for fluctuations of injected power in confined von K\\'arm\\'an swirling flows with constant external torque applied to the stirrers. Two experiments were performed at nearly equal Reynolds numbers in geometrically similar experimental setups, using air in one of them and water in the other. We found that the probability density function of power fluctuations is strongly asymmetric in air, while in water it is closer to a Gaussian, showing that the effect that a big change on the fluid density has on the flow-stirrer interaction is not reflected merely by a change in the amplitude of stirrers' response. In the case of water, with a density roughly 830 times greater than air density, the forcing exerted by the flow on the stirrers is stronger, so that they follow more closely the locally averaged rotation of the flow. When the fluid is air, the forcing is much weaker, resulting not only in a smaller stirrer response to the torque exerted by the flow, but also in power fluctuations ...
Indian Academy of Sciences (India)
Y Pathania; P K Ahluwalla
2005-09-01
We have carried out a molecular dynamics simulation of two- and three- dimensional double Yukawa fluids near the triple point. We have compared some of the static and dynamic correlation functions with those of Lennard{Jones, when parameters occurring in double Yukawa potential are chosen to fit Lennard-Jones potential. The results are in good agreement. However, when repulsive and attractive parameters occurring in double Yukawa potential are varied, we found distinct differences in static and dynamic correlation functions. We have also compared the two-dimensional correlation functions with those of three-dimensional to study the effect of dimensionality, near the triple point region.
Departure of microscopic friction from macroscopic drag in molecular fluid dynamics
Hanasaki, Itsuo; Fujiwara, Daiki; Kawano, Satoyuki
2016-03-01
Friction coefficient of the Langevin equation and drag of spherical macroscopic objects in steady flow at low Reynolds numbers are usually regarded as equivalent. We show that the microscopic friction can be different from the macroscopic drag when the mass is taken into account for particles with comparable scale to the surrounding fluid molecules. We illustrate it numerically by molecular dynamics simulation of chloride ion in water. Friction variation by the atomistic mass effect beyond the Langevin regime can be of use in the drag reduction technology as well as the electro or thermophoresis.
Desgranges, Caroline; Delhommelle, Jerome
2009-06-28
In recent years, powerful and accurate methods, based on a Wang-Landau sampling, have been developed to determine phase equilibria. However, while these methods have been extensively applied to study the phase behavior of model fluids, they have yet to be applied to molecular systems. In this work, we show how, by combining hybrid Monte Carlo simulations in the isothermal-isobaric ensemble with the Wang-Landau sampling method, we determine the vapor-liquid equilibria of various molecular fluids. More specifically, we present results obtained on rigid molecules, such as benzene, as well as on flexible chains of n-alkanes. The reliability of the method introduced in this work is assessed by demonstrating that our results are in excellent agreement with the results obtained in previous work on simple fluids, using either transition matrix or conventional Monte Carlo simulations with a Wang-Landau sampling, and on molecular fluids, using histogram reweighting or Gibbs ensemble Monte Carlo simulations.
Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2013-10-21
We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619 (2013)] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields: the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast, the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density, and making the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.
Molecular communication in fluid media: The additive inverse Gaussian noise channel
Srinivas, K V; Eckford, Andrew W
2010-01-01
We consider molecular communication, with information conveyed in the time of release of molecules. The main contribution of this paper is the development of a theoretical foundation for such a communication system. Specifically, we develop the additive inverse Gaussian (IG) noise channel model: a channel in which the information is corrupted by noise with an inverse Gaussian distribution. We show that such a channel model is appropriate for molecular communication in fluid media - when propagation between transmitter and receiver is governed by Brownian motion and when there is positive drift from transmitter to receiver. Taking advantage of the available literature on the IG distribution, upper and lower bounds on channel capacity are developed, and a maximum likelihood receiver is derived. Theory and simulation results are presented which show that such a channel does not have a single quality measure analogous to signal-to-noise ratio in the AWGN channel. It is also shown that the use of multiple molecule...
Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann
Melenev, Petr
2017-06-01
Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces.
Alekseeva, L A; Shatik, S V; Sorokina, M N; Karasev, V V
2002-05-01
Low molecular-weight (oligopeptide) fraction of the cerebrospinal fluid was analyzed by high-performance reversed phase liquid chromatography in 30 children with bacterial and viral neuroinfections. The incidence and height of chromathoraphic peaks in bacterial meningitis depended on the disease etiology, stage, and severity. Qualitative and quantitative composition of low molecular-weight fraction of the liquor varied in patients with viral neuroinfections, depending on the severity of the cerebral parenchyma involvement. Differences in chromatographic profiles in complicated and uneventful course of neuroinfections indicate a possible damaging, protective, or regulatory effect of the liquor peptides. These data focus the attention on the role of oligopeptides in the genesis of neuroinfectious process, significance of search for peptide markers, their further isolation, identification, and development of test systems available for clinical application.
Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics
Directory of Open Access Journals (Sweden)
COELHO L. A. F.
1999-01-01
Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.
Directory of Open Access Journals (Sweden)
Dr. Shankar H S Ram
2010-01-01
Full Text Available This study was aimed to correlate echogenic amniotic fluid particle size (AFPS in late third trimester to fetal lung maturity and amniotic fluid optical density (AFOD at labor. AFPS were measured with specified criteria by real time transabdominal USG (3.5MHz while Amniotic Fluid Index (AFI was measured during routine antenatal visits. The criteria for AFPS score which are taken into account are the amniotic fluid particle size, number and distribution. Serial AFPS measurements were done till onset of labor. AFPS was correlated to AFOD value at spontaneous labor in 123 women. Uncentrifuged fresh amniotic fluid samples were obtained during ARM/amniotomy and used for AFOD estimation at 650 nm. The mean AFPS and AFOD at onset of labor was found to be 5.14 ± 0.69 mm (3.67 – 6.7 CI 95% and 1.03 ± 0.31 (0.35 -1.69 CI 95% respectively in 116 women who delivered normal babies devoid of respiratory distress syndrome (RDS. Serial AFPS measurements showed a definite AFOD surge after a value in the region of 3.8 mm which is obtained culminating in onset of Labor. 28 women (24.1% had dense clusters of free floating particles across the vertical pool in amniotic fluid with mean AFPS and AFOD of 5.6 ± 0.68 mm and 1.12 ± 0.21 respectively. In 123 women, AFPS < 3.8 mm had sensitivity of 85.74% and positive predictive value of 66.67% in predicting RDS. AFPS serves as a sonological marker for fetal lung maturity and labor. The range of AFOD values can be measured in terms of AFPS (r =0.6, F = 69.8, β= + 0.23, p < 0.001. Serial AFPS estimation predicts fetal maturity and onset of labor.
Measuring the Density of a Molecular Cluster Injector via Visible Emission from an Electron Beam
Energy Technology Data Exchange (ETDEWEB)
Lundberg, D. P.; Kaita, R.; Majeski, R. M.; Stotler, D. P.
2010-06-28
A method to measure the density distribution of a dense hydrogen gas jet is pre- sented. A Mach 5.5 nozzle is cooled to 80K to form a flow capable of molecular cluster formation. A 250V, 10mA electron beam collides with the jet and produces Hα emission that is viewed by a fast camera. The high density of the jet, several 10^{16}cm^{-3}, results in substantial electron depletion, which attenuates the H_{α} emission. The attenuated emission measurement, combined with a simplified electron-molecule collision model, allows us to determine the molecular density profile via a simple iterative calculation.
Li, Guang-Xing; Burkert, Andreas
2016-09-01
Gravity is believed to be important on multiple physical scales in molecular clouds. However, quantitative constraints on gravity are still lacking. We derive an analytical formula which provides estimates on multiscale gravitational energy distribution using the observed surface density probability distribution function (PDF). Our analytical formalism also enables one to convert the observed column density PDF into an estimated volume density PDF, and to obtain average radial density profile ρ(r). For a region with N_col ˜ N^{-γ _N}, the gravitational energy spectra is E_p(k)˜ k^{-4(1 - 1/γ _N)}. We apply the formula to observations of molecular clouds, and find that a scaling index of -2 of the surface density PDF implies that ρ ˜ r-2 and Ep(k) ˜ k-2. The results are valid from the cloud scale (a few parsec) to around ˜ 0.1 pc. Because of the resemblance the scaling index of the gravitational energy spectrum and the that of the kinetic energy power spectrum of the Burgers turbulence (where E ˜ k-2), our result indicates that gravity can act effectively against turbulence over a multitude of physical scales. This is the critical scaling index which divides molecular clouds into two categories: clouds like Orion and Ophiuchus have shallower power laws, and the amount of gravitational energy is too large for turbulence to be effective inside the cloud. Because gravity dominates, we call this type of cloud g-type clouds. On the other hand, clouds like the California molecular cloud and the Pipe nebula have steeper power laws, and turbulence can overcome gravity if it can cascade effectively from the large scale. We call this type of cloud t-type clouds. The analytical formula can be used to determine if gravity is dominating cloud evolution when the column density PDF can be reliably determined.
Charge Density Analysis and Transport Properties of TTF Based Molecular Nanowires: A DFT Approach
Directory of Open Access Journals (Sweden)
Karuppannan Selvaraju
2015-01-01
Full Text Available The present study has been performed to understand the charge density distribution and the electrical characteristics of Au and thiol substituted tetrathiafulvalene (TTF based molecular nanowire. A quantum chemical calculation has been carried out using DFT method (B3LYP with the LANL2DZ basis set under various applied electric fields (EFs. The bond topological analysis characterizes the terminal Au–S and S–C bonds as well as all the bonds of central TTF unit of the molecule. The variation of electron density and Laplacian of electron density at the bond critical point of bonds for zero and different applied fields reveal the electron density distribution of the molecule. The molecular conformation, the variation of atomic charges and energy density distribution of the molecule have been analyzed for the various levels of applied EFs. The HOMO-LUMO gap calculated from quantum chemical calculations has been compared with the value calculated from the density of states. The variation of dipole moment due to the polarization effect and the I-V characteristics of the molecule for the various applied EFs have been well discussed.
Kim, Hwan-Choong; Han, Chulhee; Kim, Pyunghwa; Choi, Seung-Bok
2015-08-01
This work proposes a new approach with which to measure the magnetic flux density using the characteristics of magnetorheological fluid (MRF) that is integrated with a variable resistor. For convenience, it is called a magnetorheological fluid variable resistor (MRF-VR) system in this study. The mechanism of the MRF-VR is based on the interaction between ferromagnetic iron particles of the MRF due to an external magnetic field, which causes its electrical resistance to be field dependent. Using this salient principle, the proposed MRF-VR system is constructed with electrodes and MRF, and its performance is demonstrated by evaluating its electrical resistive characteristics such as dimensional influence, response time, hysteresis and frequency response. After evaluating the performance characteristics, a feedback control system with a proportional-integral-derivative (PID) controller is established, and resistance-trajectory control experiments are carried out. Based on this MRF-VR system, a magnetic field-sensing system is constructed using a Wheatstone bridge circuit, and a polynomial model for calculating the magnetic flux density is formulated from the measured voltage. Finally, the accuracy and effectiveness of the proposed sensing system associated with the empirical polynomial model is successfully verified by comparing the calculated values of magnetic flux density with those measured by a commercial tesla meter.
Unfolding the laws of star formation: the density distribution of molecular clouds.
Kainulainen, Jouni; Federrath, Christoph; Henning, Thomas
2014-04-11
The formation of stars shapes the structure and evolution of entire galaxies. The rate and efficiency of this process are affected substantially by the density structure of the individual molecular clouds in which stars form. The most fundamental measure of this structure is the probability density function of volume densities (ρ-PDF), which determines the star formation rates predicted with analytical models. This function has remained unconstrained by observations. We have developed an approach to quantify ρ-PDFs and establish their relation to star formation. The ρ-PDFs instigate a density threshold of star formation and allow us to quantify the star formation efficiency above it. The ρ-PDFs provide new constraints for star formation theories and correctly predict several key properties of the star-forming interstellar medium.
Dissecting molecular descriptors into atomic contributions in density functional reactivity theory.
Rong, Chunying; Lu, Tian; Liu, Shubin
2014-01-14
Density functional reactivity theory (DFRT) employs the electron density of a molecule and its related quantities such as gradient and Laplacian to describe its structure and reactivity properties. Proper descriptions at both molecular (global) and atomic (local) levels are equally important and illuminating. In this work, we make use of Bader's zero-flux partition scheme and consider atomic contributions for a few global reactivity descriptors in DFRT, including the density-based quantification of steric effect and related indices. Earlier, we proved that these quantities are intrinsically correlated for atomic and molecular systems [S. B. Liu, J. Chem. Phys. 126, 191107 (2007); ibid. 126, 244103 (2007)]. In this work, a new basin-based integration algorithm has been implemented, whose reliability and effectiveness have been extensively examined. We also investigated a list of simple hydrocarbon systems and different scenarios of bonding processes, including stretching, bending, and rotating. Interesting changing patterns for the atomic and molecular values of these quantities have been revealed for different systems. This work not only confirms the strong correlation between these global reactivity descriptors for molecular systems, as theoretically proven earlier by us, it also provides new and unexpected changing patterns for their atomic values, which can be employed to understand the origin and nature of chemical phenomena.
Effect of initial densities in the lattice Boltzmann model for non-ideal fluid with curved interface
Gong, Jiaming; Oshima, Nobuyuki
2017-06-01
The effect of initial densities in a free energy based two-phase-flow lattice Boltzmann method for non-ideal fluids with a curved interface was investigated in the present work. To investigate this effect, the initial densities in the liquid and gas phases coming from the saturation points and the equilibrium state were adopted in the simulation of a static droplet in an open and a closed system. For the purpose of simplicity and easier comparison, the closed system is fabricated by the implementation of the periodic boundary condition at the inlet and outlet of a gas channel, and the open system is fabricated by the implementation of a constant flux boundary condition at the inlet and a free-out boundary condition at the outlet of the same gas channel. By comparing the simulation results from the two types of initial densities in the open and closed systems, it is proven that the commonly used saturation initial densities setting is the reason for droplet mass and volume variation which occurred in the simulation, particularly in the open system with a constant flux boundary condition. Such problems are believed to come from the curvature effect of the surface tension and can be greatly reduced by adopting the initial densities in the two phases from equilibrium state.
Fluid-solid transition in simple systems using density functional theory
Energy Technology Data Exchange (ETDEWEB)
Bharadwaj, Atul S.; Singh, Yashwant [Department of Physics, Banaras Hindu University, Varanasi-221 005 (India)
2015-09-28
A free energy functional for a crystal which contains both the symmetry-conserved and symmetry-broken parts of the direct pair correlation function has been used to investigate the fluid-solid transition in systems interacting via purely repulsive Weeks-Chandler-Anderson Lennard–Jones potential and the full Lennard–Jones potential. The results found for freezing parameters for the fluid-face centred cubic crystal transition are in very good agreement with simulation results. It is shown that although the contribution made by the symmetry broken part to the grand thermodynamic potential at the freezing point is small compared to that of the symmetry conserving part, its role is crucial in stabilizing the crystalline structure and on values of the freezing parameters.
Krčo, Marko
2016-01-01
We present a geometry-independent method for determining the shapes of radial volume density profiles of astronomical objects whose geometries are unknown, based on a single column density map. Such profiles are often critical to understand the physics and chemistry of molecular cloud cores, in which star formation takes place. The method presented here does not assume any geometry for the object being studied, thus removing a significant source of bias. Instead it exploits contour self-similarity in column density maps which appears to be common in data for astronomical objects. Our method may be applied to many types of astronomical objects and observable quantities so long as they satisfy a limited set of conditions which we describe in detail. We derive the method analytically, test it numerically, and illustrate its utility using 2MASS-derived dust extinction in molecular cloud cores. While not having made an extensive comparison of different density profiles, we find that the overall radial density dist...
Statistical link between the structure of molecular clouds and their density distribution
Donkov, Sava; Klessen, Ralf S
2016-01-01
We introduce the concept of a class of equivalence of molecular clouds represented by an abstract spherically symmetric, isotropic object. This object is described by use of abstract scales in respect to a given mass density distribution. Mass and average density are ascribed to each scale and thus are linked to the density distribution: a power-law type and an arbitrary continuous one. In the latter case, we derive a differential relationship between the mean density at a given scale and the structure parameter which defines the mass-density relationship. The two-dimensional (2D) projection of the cloud along the line of sight is also investigated. Scaling relations of mass and mean density are derived in the considered cases of power-law and arbitrary continuous distributions. We obtain relations between scaling exponents in the 2D and 3D cases. The proposed classes of equivalence are representative for the general structure of real clouds with various types of column-density distributions: power law, logno...
2017-05-05
frequencies within the IR and UV - visible ranges. The absorption spectrum corresponding to excitation states of SixOy-nH2O molecular clusters consisting of...Energies and IR Spectra……………………….......................….4 DFT Calculation of UV -Vis Spectra………………………………………………………….……5 Conclusion...calculation of approximate UV -Vis absorption spectra for SixOy molecular clusters, which uses time-dependent density functional theory (TD-DFT) as
Molecular Dynamical Simulation of Ice Phase Transition: Ice Ih to High-Density Amorphous
Institute of Scientific and Technical Information of China (English)
DONG Shun-Le; WANG Yan
2005-01-01
@@ We put 5kbar and 12kbar on perfect ice Ih lattice at 77K and 180K. After 30000 simulation steps (in units of 10-15 s), high-density amorphous ice is formed. Four-site simple-pair potential TIP4P is used for molecular interactions and the rigid molecular model is employed. Phase transition processes are fitted by an exponential function, and different phase transition times τ are obtained from O-O radial distribution functions (366 and 359fs for 77K and 180K) and O-O-O angle distribution functions (126 and 116fs for 77K and 180K).
Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory
Runge, Keith; Karasiev, Valentin; Deymier, Pierre
2014-03-01
The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.
Directory of Open Access Journals (Sweden)
I. A. Zhidkova
2016-01-01
Full Text Available Antiepileptic drugs (AEDs may have a negative effect on bone tissue, by increasing the risk of fractures in epileptic patients compared to the general population. Many investigations have shown lower bone mineral density and a higher risk for osteopenia and osteoporosis in patients taking traditional and novel AEDs. Multidrug therapy and the duration of AED intake are associated with the most significant risk for lower bone mineral density. Nevertheless, the molecular mechanisms of action of different AEDs on bone tissue remain little studied.
Bellissima, S.; Neumann, M.; Guarini, E.; Bafile, U.; Barocchi, F.
2017-01-01
Extending a preceding study of the velocity autocorrelation function (VAF) in a simulated Lennard-Jones fluid [Phys. Rev. E 92, 042166 (2015), 10.1103/PhysRevE.92.042166] to cover higher-density and lower-temperature states, we show that the recently demonstrated multiexponential expansion method allows for a full account and understanding of the basic dynamical processes encompassed by a fundamental quantity as the VAF. In particular, besides obtaining evidence of a persisting long-time tail, we assign specific and unambiguous physical meanings to groups of exponential modes related to the longitudinal and transverse collective dynamics, respectively. We have made this possible by consistently introducing the interpretation of the VAF frequency spectrum as a global density of states in fluids, generalizing a solid-state concept, and by giving to specific spectral components, obtained through the VAF exponential expansion, the corresponding meaning of partial densities of states relative to specific dynamical processes. The clear identification of a high-frequency oscillation of the VAF with the near-top excitation frequency in the dispersion curve of acoustic waves is a neat example of the power of the method. As for the transverse mode contribution, its analysis turns out to be particularly important, because the multiexponential expansion reveals a transition marking the onset of propagating excitations when the density is increased beyond a threshold value. While this finding agrees with the recent literature debating the issue of dynamical crossover boundaries, such as the one identified with the Frenkel line, we can add detailed information on the modes involved in this specific process in the domains of both time and frequency. This will help obtain a still missing full account of transverse dynamics, in both its nonpropagating and propagating aspects which are linked through dynamical transitions depending on both the thermodynamic states and the excitation
Investigation of the silicon ion density during molecular beam epitaxy growth
Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.
2002-05-01
Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.
Frutiger, Jerome; Abildskov, Jens; Sin, Gürkan
2015-01-01
Computer Aided Molecular Design (CAMD) is an important tool to generate, test and evaluate promising chemical products. CAMD can be used in thermodynamic cycle for the design of pure component or mixture working fluids in order to improve the heat transfer capacity of the system. The safety assessment of novel working fluids relies on accurate property data. Flammability data like the lower and upper flammability limit (LFL and UFL) play an important role in quantifying the risk of fire and e...
Optical Absorption in Molecular Crystals from Time-Dependent Density Functional Theory
2017-04-23
quantitatively and non-empirically within the framework of time-dependent density functional theory (TDDFT), using the recently-developed optimally-tuned...showing that fundamental gaps and optical spectra of molecular solids can be predicted quantitatively and non-empirically within the framework of...II. THEORETICAL AND COMPUTATIONAL APPROACH A. Optimally-tuned range-separated hybrid functionals In the range-separated hybrid (RSH) method, the
Coe, Joshua D; Sewell, Thomas D; Shaw, M Sam
2009-08-21
An optimized variant of the nested Markov chain Monte Carlo [n(MC)(2)] method [J. Chem. Phys. 130, 164104 (2009)] is applied to fluid N(2). In this implementation of n(MC)(2), isothermal-isobaric (NPT) ensemble sampling on the basis of a pair potential (the "reference" system) is used to enhance the efficiency of sampling based on Perdew-Burke-Ernzerhof density functional theory with a 6-31G(*) basis set (PBE6-31G(*), the "full" system). A long sequence of Monte Carlo steps taken in the reference system is converted into a trial step taken in the full system; for a good choice of reference potential, these trial steps have a high probability of acceptance. Using decorrelated samples drawn from the reference distribution, the pressure and temperature of the full system are varied such that its distribution overlaps maximally with that of the reference system. Optimized pressures and temperatures then serve as input parameters for n(MC)(2) sampling of dense fluid N(2) over a wide range of thermodynamic conditions. The simulation results are combined to construct the Hugoniot of nitrogen fluid, yielding predictions in excellent agreement with experiment.
Chaplin, Vernon H.; Bellan, Paul M.
2015-12-01
A time-dependent two-fluid model has been developed to understand axial variations in the plasma parameters in a very high density (peak ne≳ 5 ×1019 m-3 ) argon inductively coupled discharge in a long 1.1 cm radius tube. The model equations are written in 1D with radial losses to the tube walls accounted for by the inclusion of effective particle and energy sink terms. The ambipolar diffusion equation and electron energy equation are solved to find the electron density ne(z ,t ) and temperature Te(z ,t ) , and the populations of the neutral argon 4s metastable, 4s resonant, and 4p excited state manifolds are calculated to determine the stepwise ionization rate and calculate radiative energy losses. The model has been validated through comparisons with Langmuir probe ion saturation current measurements; close agreement between the simulated and measured axial plasma density profiles and the initial density rise rate at each location was obtained at pA r=30 -60 mTorr . We present detailed results from calculations at 60 mTorr, including the time-dependent electron temperature, excited state populations, and energy budget within and downstream of the radiofrequency antenna.
Institute of Scientific and Technical Information of China (English)
Li Chen; Yu-fang Xiang; Ke Wang; Qin Zhang; Rong-ni Du; Qiang Fu
2011-01-01
Three types of high-density polyethylene (HDPE) with different molecular weights (high, medium and Iow) were adopted to evaluate the influence of matrix molecular weight on the structure-property relation of injection-molded HDPE/mica composites through a combination of SEM, 2d-WAXS, DSC, DMA and tensile testing. Various structural factors including orientation, filler dispersion, interfacial interaction between HDPE and mica, etc., which can impact the macroscopic mechanics, were compared in detail among the three HDPE/mica composites. The transcrystallization of HDPE on the mica surface was observed and it exhibited strong matrix molecular weight dependence. Obvious transcrystalline structure was found in the composite with Iow molecular weight HDPE, whereas it was hard to be detected in the composites with increased HDPE molecular weight. The best reinforcement effect in the composite with low molecular weight HDPE can be understood as mainly due to substantially improved interracial adhesion between matrix and mica filler, which arises from the transerystallization mechanism.
Cooling of Water in a Flask: Convection Currents in a Fluid with a Density Maximum
Velasco, S.; White, J. A.; Roman, F. L.
2010-01-01
The effect of density inversion on the convective flow of water in a spherical glass flask cooled with the help of an ice-water bath is shown. The experiment was carried out by temperature measurements (cooling curves) taken at three different heights along the vertical diameter of the flask. Flows inside the flask are visualized by seeding the…
Cooling of Water in a Flask: Convection Currents in a Fluid with a Density Maximum
Velasco, S.; White, J. A.; Roman, F. L.
2010-01-01
The effect of density inversion on the convective flow of water in a spherical glass flask cooled with the help of an ice-water bath is shown. The experiment was carried out by temperature measurements (cooling curves) taken at three different heights along the vertical diameter of the flask. Flows inside the flask are visualized by seeding the…
The gas density measurement of one long distance supersonic molecular beam
Liu, D.; Han, J. F.; Chen, Z. Y.; Bai, L. X.; Zhou, J. X.
2016-12-01
The gas density of the supersonic molecular beam (SMB) is a crucial parameter for the fueling or diagnostic process in the tokamak experiments. Using the microphone, one improved method of gas density measurement is proposed, which can greatly improve the measurement capacity by about 3 orders of magnitude by studying the pulsed signal characteristic of the microphone when it is pushed by the SMB. The gas density of the SMB is measured within the axial range of 20-2000 mm, and the axial central density at 2000 mm is about 100 times less than that at 20 mm. It is also found that the radial density distribution follows the Gaussian function in both free expansion (where the SMB can expand freely without any influence from the vacuum chamber) and restricted expansion (where the expansion of the SMB is restricted inside the flight tube of the vacuum system). And the axial central density decreases with the axial distance, which follows the inverse square law in the free expansion, but it deviates from this law in the restricted expansion.
Towards the design of new and improved drilling fluid additives using molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Richard L. Anderson
2010-03-01
Full Text Available During exploration for oil and gas, a technical drilling fluid is used to lubricate the drill bit, maintain hydrostatic pressure, transmit sensor readings, remove rock cuttings and inhibit swelling of unstable clay based reactive shale formations. Increasing environmental awareness and resulting legislation has led to the search for new, improved biodegradable drilling fluid components. In the case of additives for clay swelling inhibition, an understanding of how existing effective additives interact with clays must be gained to allow the design of improved molecules. Owing to the disordered nature and nanoscopic dimension of the interlayer pores of clay minerals, computer simulations have become an increasingly useful tool for studying clay-swelling inhibitor interactions. In this work we briefly review the history of the development of technical drilling fluids, the environmental impact of drilling fluids and the use of computer simulations to study the interactions between clay minerals and swelling inhibitors. We report on results from some recent large-scale molecular dynamics simulation studies on low molecular weight water-soluble macromolecular inhibitor molecules. The structure and interactions of poly(propylene oxide-diamine, poly(ethylene glycol and poly(ethylene oxide-diacrylate inhibitor molecules with montmorillonite clay are studied.Durante a exploração de óleo e gás um fluido de perfuração é usado para lubrificar 'bit' da perfuradora, manter a pressão hidrostática, transmitir sensores de leitura, remover resíduos da rocha e inibir o inchamento da argila instável baseada nas formações dos folhelhos. O aumento das preocupações ambientais bem como a legislação resultante levou à procura de novos fluidos de perfuração com componentes biodegradáveis. No caso dos aditivos para inibir o inchamento das argilas o entendimento das interações entre os aditivos e as argilas tem que ser adquirido para permitir o
Molecular dynamics study of phase separation in fluids with chemical reactions.
Krishnan, Raishma; Puri, Sanjay
2015-11-01
We present results from the first d=3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A⇌B). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓ(eq)) in the steady state suggests a power-law dependence on the reaction rate ε:ℓ(eq)∼ε(-θ) with θ≃1.0.
DEFF Research Database (Denmark)
Koivuniemi, A.; Vattulainen, I.
2012-01-01
The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further......, because of the complex composition of HDL, understanding the impact of its structure and dynamics on the function of HDL in reverse cholesterol transport has also been a major issue. Recent progress in molecular simulation methodology and computing power has made a difference, as it has enabled...... essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...
Equipartition and Cosmic Ray Energy Densities in Central Molecular Zones of Starbursts
Yoast-Hull, Tova M; Zweibel, Ellen G
2015-01-01
The energy densities in magnetic fields and cosmic rays (CRs) in galaxies are often assumed to be in equipartition, allowing for an indirect estimate of the magnetic field strength from the observed radio synchrotron spectrum. However, both primary and secondary CRs contribute to the synchrotron spectrum, and the CR electrons also loose energy via bremsstrahlung and inverse Compton. While classical equipartition formulae avoid these intricacies, there have been recent revisions that account for the extreme conditions in starbursts. Yet, the application of the equipartition formula to starburst environments also presupposes that timescales are long enough to reach equilibrium. Here, we test equipartition in the central molecular zones (CMZs) of nearby starburst galaxies by modeling the observed gamma-ray spectra, which provide a direct measure of the CR energy density, and the radio spectra, which provide a probe of the magnetic field strength. We find that in starbursts, the magnetic field energy density is s...
Critical CuI buffer layer surface density for organic molecular crystal orientation change
Ahn, Kwangseok; Kim, Jong Beom; Kim, Hyo Jung; Lee, Hyun Hwi; Lee, Dong Ryeol
2015-01-01
We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 -2) by a CuI buffer layer with a very low surface density, so low that a large proportion of the substrate surface is bare.
Ma, Haibo
2012-06-07
We perform molecular dynamics simulations of supercritical water (SCW) with a wide range of densities along a near critical isotherm using the simple point charge extended (SPC/E) pair potential in order to study the entropy and the solvation shell structure around a central water molecule. It is shown that both the translational and orientational two-particle correlation entropy terms can serve as the metrics of the translational-orientational structural orders in water and it is revealed that the translational structural order is very sensitive to the density variation in the gas-like and liquid-like region, while the orientational structural order is much more dependent upon compression in the medium-density SCW region. The comparison of the magnitudes of the full thermodynamic excess entropy and two-particle correlation entropy confirms the recent findings that the many-body terms other than two-body ones also present significant and non-neglectable contributions to the full excess entropy for the highly anomalous fluids like water. The analysis of entropy terms as a function of intermolecular distance and the orientational distribution functions as well as the three-dimensional spatial distribution functions indicate that the structural order occurs only in a much more diffused first solvation shell due to the elongated hydrogen bonds under supercritical conditions. It is revealed that no obvious second or higher neighbor shells occur in SCW, in contrast with the feature of normal liquid water that the anomalous decrease of translational order upon compression occurs mainly in the second shell.
Apparatus for accurate density measurements of fluids based on a magnetic suspension balance
Gong, Maoqiong; Li, Huiya; Guo, Hao; Dong, Xueqiang; Wu, J. F.
2012-06-01
A new apparatus for accurate pressure, density and temperature (p, ρ, T) measurements over wide ranges of (p, ρ, T) (90 K to 290 K; 0 MPa to 3 MPa; 0 kg/m3 to 2000 kg/m3) is described. This apparatus is based on a magnetic suspension balance which applies the Archimedes' buoyancy principle. In order to verify the new apparatus, comprehensive (p, ρ, T) measurements on pure nitrogen were carried out. The maximum relative standard uncertainty is 0.09% in density. The maximum standard uncertainty in temperature is 5 mK, and that in pressure is 250 Pa for 1.5 MPa and 390 Pa for 3MPa full scale range respectively. The experimental data were compared with selected literature data and good agreements were found.
Turbo-alternator-compressor design for supercritical high density working fluids
Wright, Steven A.; Fuller, Robert L.
2013-03-19
Techniques for generating power are provided. Such techniques involve a thermodynamic system including a housing, a turbine positioned in a turbine cavity of the housing, a compressor positioned in a compressor cavity of the housing, and an alternator positioned in a rotor cavity between the turbine and compressor cavities. The compressor has a high-pressure face facing an inlet of the compressor cavity and a low-pressure face on an opposite side thereof. The alternator has a rotor shaft operatively connected to the turbine and compressor, and is supported in the housing by bearings. Ridges extending from the low-pressure face of the compressor may be provided for balancing thrust across the compressor. Seals may be positioned about the alternator for selectively leaking fluid into the rotor cavity to reduce the temperature therein.
Combined temperature and density series for fluid-phase properties. I. Square-well spheres
Energy Technology Data Exchange (ETDEWEB)
Elliott, J. Richard [Chemical and Biomolecular Engineering Department, The University of Akron, Akron, Ohio 44325-3906 (United States); Schultz, Andrew J.; Kofke, David A. [Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200 (United States)
2015-09-21
Cluster integrals are evaluated for the coefficients of the combined temperature- and density-expansion of pressure: Z = 1 + B{sub 2}(β) η + B{sub 3}(β) η{sup 2} + B{sub 4}(β) η{sup 3} + ⋯, where Z is the compressibility factor, η is the packing fraction, and the B{sub i}(β) coefficients are expanded as a power series in reciprocal temperature, β, about β = 0. The methodology is demonstrated for square-well spheres with λ = [1.2-2.0], where λ is the well diameter relative to the hard core. For this model, the B{sub i} coefficients can be expressed in closed form as a function of β, and we develop appropriate expressions for i = 2-6; these expressions facilitate derivation of the coefficients of the β series. Expanding the B{sub i} coefficients in β provides a correspondence between the power series in density (typically called the virial series) and the power series in β (typically called thermodynamic perturbation theory, TPT). The coefficients of the β series result in expressions for the Helmholtz energy that can be compared to recent computations of TPT coefficients to fourth order in β. These comparisons show good agreement at first order in β, suggesting that the virial series converges for this term. Discrepancies for higher-order terms suggest that convergence of the density series depends on the order in β. With selection of an appropriate approximant, the treatment of Helmholtz energy that is second order in β appears to be stable and convergent at least to the critical density, but higher-order coefficients are needed to determine how far this behavior extends into the liquid.
Combined temperature and density series for fluid-phase properties. I. Square-well spheres
Elliott, J. Richard; Schultz, Andrew J.; Kofke, David A.
2015-09-01
Cluster integrals are evaluated for the coefficients of the combined temperature- and density-expansion of pressure: Z = 1 + B2(β) η + B3(β) η2 + B4(β) η3 + ⋯, where Z is the compressibility factor, η is the packing fraction, and the Bi(β) coefficients are expanded as a power series in reciprocal temperature, β, about β = 0. The methodology is demonstrated for square-well spheres with λ = [1.2-2.0], where λ is the well diameter relative to the hard core. For this model, the Bi coefficients can be expressed in closed form as a function of β, and we develop appropriate expressions for i = 2-6; these expressions facilitate derivation of the coefficients of the β series. Expanding the Bi coefficients in β provides a correspondence between the power series in density (typically called the virial series) and the power series in β (typically called thermodynamic perturbation theory, TPT). The coefficients of the β series result in expressions for the Helmholtz energy that can be compared to recent computations of TPT coefficients to fourth order in β. These comparisons show good agreement at first order in β, suggesting that the virial series converges for this term. Discrepancies for higher-order terms suggest that convergence of the density series depends on the order in β. With selection of an appropriate approximant, the treatment of Helmholtz energy that is second order in β appears to be stable and convergent at least to the critical density, but higher-order coefficients are needed to determine how far this behavior extends into the liquid.
Hybrid Kinetic-Fluid Electromagnetic Simulations of Imploding High Energy Density Plasmas for IFE
Welch, Dale; Rose, Dave; Thoma, Carsten; Genoni, Thomas; Bruner, Nichelle; Clark, Robert; Stygar, William; Leeper, Ramon
2011-10-01
A new simulation technique is being developed to study high current and moderate density-radius product (ρR) z-pinch plasmas relevant to Inertial Fusion Energy (IFE). Fully kinetic, collisional, and electromagnetic simulations of the time evolution of up to 40-MA current (deuterium and DT) z-pinches, but with relatively low ρR, have yielded new insights into the mechanisms of neutron production. At fusion relevant conditions (ρR > 0.01 gm/cm2) , however, this technique requires a prohibitively large number of cells and particles. A new hybrid implicit technique has been developed that accurately describes high-density and magnetized imploding plasmas. The technique adapts a recently published algorithm, that enables accurate descriptions of highly magnetized particle orbits, to high density plasmas and also makes use of an improved kinetic particle remap technique. We will discuss the new technique, stable range of operation, and application to an IFE relevant z-pinch design at 60 MA. Work supported by Sandia National Laboratories.
Wang, X.; Chou, I.-Ming; Hu, W.; Burruss, R.C.; Sun, Q.; Song, Y.
2011-01-01
Raman spectroscopy is a powerful method for the determination of CO2 densities in fluid inclusions, especially for those with small size and/or low fluid density. The relationship between CO2 Fermi diad split (??, cm-1) and CO2 density (??, g/cm3) has been documented by several previous studies. However, significant discrepancies exist among these studies mainly because of inconsistent calibration procedures and lack of measurements for CO2 fluids having densities between 0.21 and 0.75g/cm3, where liquid and vapor phases coexist near room temperature.In this study, a high-pressure optical cell and fused silica capillary capsules were used to prepare pure CO2 samples with densities between 0.0472 and 1.0060g/cm3. The measured CO2 Fermi diad splits were calibrated with two well established Raman bands of benzonitrile at 1192.6 and 1598.9cm-1. The relationship between the CO2 Fermi diad split and density can be represented by: ??=47513.64243-1374.824414????+13.25586152????2-0.04258891551????3 (r2=0.99835, ??=0.0253g/cm3), and this relationship was tested by synthetic fluid inclusions and natural CO2-rich fluid inclusions. The effects of temperature and the presence of H2O and CH4 on this relationship were also examined. ?? 2011 Elsevier Ltd.
Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R
2015-02-25
A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.
Avendaño, Carlos; Lafitte, Thomas; Adjiman, Claire S; Galindo, Amparo; Müller, Erich A; Jackson, George
2013-03-07
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement
Alia, Joseph D
2007-03-29
The valency interaction formula (VIF) method is given a broader and more general interpretation in which these simple molecular structural formulas implicitly include all overlaps between valence atomic orbitals even for interactions not drawn in the VIF picture. This applies for VIF pictures as one-electron Hamiltonian operators as well as VIF pictures as one-electron density operators that constitute a new implementation of the VIF method simpler in its application and more accurate in its results than previous approaches. A procedure for estimating elements of the effective charge density-bond order matrix, Pmunu, from electron configurations in atoms is presented, and it is shown how these lead to loop and line constants in the VIF picture. From these structural formulas, one finds the number of singly, doubly, and unoccupied molecular orbitals, as well as the number of molecular orbitals with energy lower, equal, and higher than -1/2Eh, the negative of the hydrogen atom's ionization energy. The VIF results for water are in qualitative agreement with MP2/6311++G3df3pd, MO energy levels where the simple VIF for water presented in the earlier literature does not agree with computed energy levels. The method presented here gives the simplest accurate VIF pictures for hydrocarbons. It is shown how VIF can be used to predict thermal barriers to chemical reactions. Insertion of singlet carbene into H2 is given as an example. VIF pictures as one-electron density operators describe the ground-state multiplicities of B2, N2, and O2 molecules and as one-electron Hamiltonian operators give the correct electronegativity trend across period two. Previous implementations of VIF do not indicate singly occupied molecular orbitals directly from the pictorial VIF rules for these examples. The direct comparison between structural formulas that represent electron density and those that represent energy is supported by comparison of a simple electronegativity scale, chiD=N/n2, with
Jacob, Christoph R; Neugebauer, Johannes; Jensen, Lasse; Visscher, Lucas
2006-05-28
We investigate the performance of two discrete solvent models in connection with density functional theory (DFT) for the calculation of molecular properties. In our comparison we include the discrete reaction field (DRF) model, a combined quantum mechanics and molecular mechanics (QM/MM) model using a polarizable force field, and the frozen-density embedding (FDE) scheme. We employ these solvent models for ground state properties (dipole and quadrupole moments) and response properties (electronic excitation energies and frequency-dependent polarizabilities) of a water molecule in the liquid phase. It is found that both solvent models agree for ground state properties, while there are significant differences in the description of response properties. The origin of these differences is analyzed in detail and it is found that they are mainly caused by a different description of the ground state molecular orbitals of the solute. In addition, for the calculation of the polarizabilities, the inclusion of the response of the solvent to the polarization of the solute becomes important. This effect is included in the DRF model, but is missing in the FDE scheme. A way of including it in FDE calculations of the polarizabilities using finite field calculations is demonstrated.
Rinkevicius, Zilvinas; Murugan, N Arul; Kongsted, Jacob; Aidas, Kestutis; Steindal, Arnfinn Hykkerud; Agren, Hans
2011-04-21
A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.
Investigation of the silicon ion density during molecular beam epitaxy growth
Eifler, G; Ashurov, K; Morozov, S
2002-01-01
Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...
Directory of Open Access Journals (Sweden)
Xin Zhao
2017-06-01
Full Text Available In deepwater oil and gas drilling, the high-molecular-weight encapsulator aggravates the thickening of the drilling fluid at low temperatures. Therefore, it is hard to manage the downhole pressure, and drilling fluid loss occurs. In this paper, a zwitterionic polymer P(AM-DMC-AMPS which was the terpolymer of acrylamide, methacrylatoethyl trimethyl ammonium chloride, and 2-acrylamido-2-methylpropane sulfonic acid, was developed as a low-molecular-weight encapsulator. It was characterized by Fourier transform infrared spectrum analysis, nuclear magnetic resonance, and gel permeation chromatography. Moreover, the low-temperature rheology, shale inhibition and filtration properties of water-based drilling fluids (WBDFs containing different encapsulators were experimentally investigated and compared. The results showed that the molecular weight of P(AM-DMC-AMPS was about 260,000, much lower than that of the conventional encapsulators. In the deepwater drilling temperature range 4–75 °C, WBDF containing P(AM-DMC-AMPS had lower and more stable rheological property because of its short molecular chains. The high shale recovery rate and low swelling rate indicated its strong shale inhibition performance, owing to its adsorption on the clay surface and the wrapping effect through both hydrogen bonding and electrostatic interaction. It also improved the filtration property of WBDF, and was compatible with other WBDF components. This product is expected to simultaneously realize the good encapsulation performance and low-temperature rheological property for deepwater drilling fluid.
Lattice Boltzmann Simulations for High Density Ratio Flows of Multiphase Fluids
Wei, Yikun; Qian, Yuehong
2010-11-01
In the present communication, we will show that the compression effect of the Redlich-Kwong equation of state(EOS) is lower than that of the van der Waals (vdW) EOS. The Redlich-Kwong equation of state has a better agreement with experimental data for the coexistence curve than the van derWaals (vdW) EOS. We implement the Redlich-Kwong EOS in the lattice Boltzmann simulations via a pseudo-potential. As a result, multi-phase flows with large density ratios may be simulated, thus many real applications in engineering problems can be applied. Acknowledgement: This research is supported in part by Ministry of Education in China via project IRT0844 and NSFC project 10625210 and Shanghai Sci and Tech. Com. Project 08ZZ43
Directory of Open Access Journals (Sweden)
Juan F. Saldarriaga
2014-06-01
Full Text Available Determination of the particle density is required to address the hydrodynamic study of a moving bed contactor. The measurement of this parameter is complicated when particles are irregularly shaped. In this study, two different techniques were use: compaction by mechanical compression and an alternative proposal, which contemplates the potential of mercury porosimetry for determining the surface and structural properties. It was observed that the results obtained by compacting in all cases are higher than expected. However, the values obtained by mercury porosimetry are more consistent with expected values. For example in the sawdust valued at 500kg/m3, very similar to the value of the original wood (502kg/m3. Values obtained by this procedure adequately represent the relationship between mass and volume of the particle and therefore are valid for hydrodynamic characterization of the biomass.
Directory of Open Access Journals (Sweden)
América eVera
2015-05-01
Full Text Available During early stages of development, encephalic vesicles are composed by a layer of neuroepithelial cells surrounding a central cavity filled with embryonic cerebrospinal fluid (eCSF. This fluid contains several morphogens that regulate proliferation and differentiation of neuroepithelial cells. One of these neurogenic factors is SCO-spondin, a giant protein secreted to the eCSF from early stages of development. Inhibition of this protein in vivo or in vitro drastically decreases the neurodifferentiation process. Other important neurogenic factors of the eCSF are low density lipoproteins (LDL, the depletion of which generates a 60% decrease in mesencephalic explant neurodifferentiation. The presence of several LDL receptor class A (LDLrA domains (responsible for LDL binding in other proteins in the SCO-spondin sequence suggests a possible interaction between both molecules. This possibility was analyzed using three different experimental approaches: 1 Bioinformatics analyses of the SCO-spondin region, that contains eight LDLrA domains in tandem, and of comparisons with the LDL receptor consensus sequence; 2 Analysis of the physical interactions of both molecules through immunohistochemical colocalization in embryonic chick brains and through the immunoprecipitation of LDL with anti-SCO-spondin antibodies; and 3 Analysis of functional interactions during the neurodifferentiation process when these molecules were added to a culture medium of mesencephalic explants. The results revealed that LDL and SCO-spondin interact to form a complex that diminishes the neurogenic capacities that both molecules have separately. Our work suggests that the embryonic cerebrospinal fluid is an active signaling center with a complex regulation system that allows for correct brain development.
DEFF Research Database (Denmark)
Frutiger, Jerome; Abildskov, Jens; Sin, Gürkan
allows the ranking ofsignificance of properties and also the identification of a set of properties which are relevant for the design of a workingfluids.In this study the CAMD problem for the development of novel working fluids for organic Rankine cycles (ORC) isformulated as a mathematical optimization...... technical tool to convert this waste heat into usable energy. So far the low-temperature heat cannot be utilized efficiently for electricity generation.In order to optimize the heat transfer process and the power generation, the influence of the working fluid, the cycledesigns and the operating conditions...... is vital. Multi-criteria database search and Computer Aided Molecular Design(CAMD) can be applied to generate, test and evaluate promising pure component/mixture candidate as process fluids to help optimize cycle design and performance. The problem formulation for the development of novel working fluids...
Tretyakov, Nikita; Papadopoulos, Periklis; Vollmer, Doris; Butt, Hans-Jürgen; Dünweg, Burkhard; Daoulas, Kostas Ch.
2016-10-01
Classical density functional theory is applied to investigate the validity of a phenomenological force-balance description of the stability of the Cassie state of liquids on substrates with nanoscale corrugation. A bulk free-energy functional of third order in local density is combined with a square-gradient term, describing the liquid-vapor interface. The bulk free energy is parameterized to reproduce the liquid density and the compressibility of water. The square-gradient term is adjusted to model the width of the water-vapor interface. The substrate is modeled by an external potential, based upon the Lennard-Jones interactions. The three-dimensional calculation focuses on substrates patterned with nanostripes and square-shaped nanopillars. Using both the force-balance relation and density-functional theory, we locate the Cassie-to-Wenzel transition as a function of the corrugation parameters. We demonstrate that the force-balance relation gives a qualitatively reasonable description of the transition even on the nanoscale. The force balance utilizes an effective contact angle between the fluid and the vertical wall of the corrugation to parameterize the impalement pressure. This effective angle is found to have values smaller than the Young contact angle. This observation corresponds to an impalement pressure that is smaller than the value predicted by macroscopic theory. Therefore, this effective angle embodies effects specific to nanoscopically corrugated surfaces, including the finite range of the liquid-solid potential (which has both repulsive and attractive parts), line tension, and the finite interface thickness. Consistently with this picture, both patterns (stripes and pillars) yield the same effective contact angles for large periods of corrugation.
Fluid mechanics in fluids at rest.
Brenner, Howard
2012-07-01
Using readily available experimental thermophoretic particle-velocity data it is shown, contrary to current teachings, that for the case of compressible flows independent dye- and particle-tracer velocity measurements of the local fluid velocity at a point in a flowing fluid do not generally result in the same fluid velocity measure. Rather, tracer-velocity equality holds only for incompressible flows. For compressible fluids, each type of tracer is shown to monitor a fundamentally different fluid velocity, with (i) a dye (or any other such molecular-tagging scheme) measuring the fluid's mass velocity v appearing in the continuity equation and (ii) a small, physicochemically and thermally inert, macroscopic (i.e., non-Brownian), solid particle measuring the fluid's volume velocity v(v). The term "compressibility" as used here includes not only pressure effects on density, but also temperature effects thereon. (For example, owing to a liquid's generally nonzero isobaric coefficient of thermal expansion, nonisothermal liquid flows are to be regarded as compressible despite the general perception of liquids as being incompressible.) Recognition of the fact that two independent fluid velocities, mass- and volume-based, are formally required to model continuum fluid behavior impacts on the foundations of contemporary (monovelocity) fluid mechanics. Included therein are the Navier-Stokes-Fourier equations, which are now seen to apply only to incompressible fluids (a fact well-known, empirically, to experimental gas kineticists). The findings of a difference in tracer velocities heralds the introduction into fluid mechanics of a general bipartite theory of fluid mechanics, bivelocity hydrodynamics [Brenner, Int. J. Eng. Sci. 54, 67 (2012)], differing from conventional hydrodynamics in situations entailing compressible flows and reducing to conventional hydrodynamics when the flow is incompressible, while being applicable to both liquids and gases.
Wang, Xiang; Yang, Li; Liu, Yao; Gao, Wei; Peng, Weiyan; Sung, K-L Paul; Sung, Lanping Amy
2009-10-16
The oxidized low-density lipoprotein (Ox-LDL) plays an important role in atherosclerosis, yet it remains unclear if it damages circulating erythrocytes. In this study, erythrocyte deformability and its membrane proteins after Ox-LDL incubations are investigated by micropipette aspiration, thiol radical measurement, and sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Results show that Ox-LDL incubation reduces the erythrocyte deformability, decreases free thiol radical contents in erythrocytes, and induces the cross-linking among membrane proteins. SDS-PAGE analysis reveals a high molecular weight (HMW) complex as well as new bands between spectrins and band 3 and reduced ratios between band 3 and other major membrane skeletal proteins. Analyses indicate that Ox-LDL makes erythrocytes harder to deform through a molecular mechanism by which the oxidation of free thiol radicals forms disulfide bonds among membrane skeletal proteins.
Jeanmairet, Guillaume; Levesque, Maximilien; Rotenberg, Benjamin; Borgis, Daniel
2014-01-01
We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the most recent advances, we show that the strength of this implicit method is that (i) it is in quantitative or semi-quantitative agreement with reference all-atoms simulations (molecular dynamics here) for both the solvation structure and energetics, and that (ii) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect, in that it locally overestimates the polarization of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry a systematic study of the electrostatic and van der Waals components of the surface-solvant interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend u...
Arun Sasi, B. S.; Twinkle, A. R.; James, C.
2017-08-01
The density functional theoretical (DFT) calculations have been carried out at the B3LYP/6-311G(d,p) level of theory for nitroxoline monomer and dimer molecule. The dimer molecule formed between two nitroxoline subunits has the largest stability, and is held together by two Osbnd H⋯N hydrogen bonds. Stability of the molecule arising from hyperconjugative interaction and intra/inter molecular charge transfer has been analyzed using natural bond orbital (NBO) analysis. The topological analysis of electron localization function (ELF) provides effect of delocalization. Quantum theory of atoms in molecule (QTAIM) has been applied to gain deep understanding to the existence of intra- and inter-molecular interaction.
Molecular Kohn-Sham exchange-correlation potential from the correlated ab initio electron density
Gritsenko, Oleg V.; van Leeuwen, Robert; Baerends, Evert Jan
1995-09-01
The molecular Kohn-Sham (KS) exchange-correlation potential vxc has been constructed for LiH from the correlated ab initio density ρ by means of the simple iterative procedure developed by van Leeuwen and Baerends [Phys. Rev. A 49, 2421 (1994)]. The corresponding KS energy characteristics, such as the kinetic energy of noninteracting particles Ts, kinetic part of the exchange-correlation energy Tc, and energy of the highest occupied molecular orbital ɛN, have been obtained with reasonable accuracy. A relation between the form of vxc and the electronic structure of LiH has been discussed. Test calculations for the two-electron H2 molecule have shown the efficiency of the procedure.
Density functional theory for molecular multiphoton ionization in the perturbative regime.
Toffoli, Daniele; Decleva, Piero
2012-10-07
A general implementation of the lowest nonvanishing order perturbation theory for the calculation of molecular multiphoton ionization cross sections is proposed in the framework of density functional theory. Bound and scattering wave functions are expanded in a multicentric basis set and advantage is taken of the full molecular point group symmetry, thus enabling the application of the formalism to medium-size molecules. Multiphoton ionization cross sections and angular asymmetry parameters have been calculated for the two- and four-photon ionization of the H(2) (+) molecule, for linear and circular light polarizations. Both fixed and random orientations of the target molecule have been considered. To demonstrate the efficiency of the proposed methodology, the two-photon cross section and angular asymmetry parameters for the HOMO and HOMO-1 orbital ionization of benzene are also presented.
Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors
Vanfleteren, Diederik; Bultinck, Patrick; Ayers, Paul W; Waroquier, Michel; 10.1063/1.3521493
2011-01-01
A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.
Carney, Randy P.
2011-06-07
Nanoparticles are finding many research and industrial applications, yet their characterization remains a challenge. Their cores are often polydisperse and coated by a stabilizing shell that varies in size and composition. No single technique can characterize both the size distribution and the nature of the shell. Advances in analytical ultracentrifugation allow for the extraction of the sedimentation (s) and diffusion coefficients (D). Here we report an approach to transform the s and D distributions of nanoparticles in solution into precise molecular weight (M), density (?P) and particle diameter (dp) distributions. M for mixtures of discrete nanocrystals is found within 4% of the known quantities. The accuracy and the density information we achieve on nanoparticles are unparalleled. A single experimental run is sufficient for full nanoparticle characterization, without the need for standards or other auxiliary measurements. We believe that our method is of general applicability and we discuss its limitations. 2011 Macmillan Publishers Limited. All rights reserved.
Structure of solvent-free grafted nanoparticles: Molecular dynamics and density-functional theory
Chremos, Alexandros
2011-01-01
The structure of solvent-free oligomer-grafted nanoparticles has been investigated using molecular dynamics simulations and density-functional theory. At low temperatures and moderate to high oligomer lengths, the qualitative features of the core particle pair probability, structure factor, and the oligomer brush configuration obtained from the simulations can be explained by a density-functional theory that incorporates the configurational entropy of the space-filling oligomers. In particular, the structure factor at small wave numbers attains a value much smaller than the corresponding hard-sphere suspension, the first peak of the pair distribution function is enhanced due to entropic attractions among the particles, and the oligomer brush expands with decreasing particle volume fraction to fill the interstitial space. At higher temperatures, the simulations reveal effects that differ from the theory and are likely caused by steric repulsions of the expanded corona chains. © 2011 American Institute of Physics.
Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Warm Dense Matter
Militzer, Burkhard; Driver, Kevin
2011-10-01
We analyze the applicability of two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), to study the regime of warm dense matter. We discuss the advantages as well as the limitations of each method and propose directions for future development. Results for dense, liquid helium, where both methods have been applied, demonstrate the range of each method's applicability. Comparison of the equations of state from simulations with analytical theories and free energy models show that DFT is useful for temperatures below 100000 K and then PIMC provides accurate results for all higher temperatures. We characterize the structure of the liquid in terms of pair correlation functions and study the closure of the band gap with increasing density and temperature. Finally, we discuss simulations of heavier elements and demonstrate the reliability are both methods in such cases with preliminary results.
Titantah, John Tatini; Karttunen, Mikko
2013-10-21
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.
A Molecular Electron Density Theory Study of the Chemical Reactivity of Cis- and Trans-Resveratrol.
Frau, Juan; Muñoz, Francisco; Glossman-Mitnik, Daniel
2016-12-01
The chemical reactivity of resveratrol isomers with the potential to play a role as inhibitors of the nonenzymatic glycation of amino acids and proteins, both acting as antioxidants and as chelating agents for metallic ions such as Cu, Al and Fe, have been studied by resorting to the latest family of Minnesota density functionals. The chemical reactivity descriptors have been calculated through Molecular Electron Density Theory encompassing Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the dual descriptor f ( 2 ) ( r ) and the electrophilic and nucleophilic Parr functions. The validity of "Koopmans' theorem in DFT" has been assessed by means of a comparison between the descriptors calculated through vertical energy values and those arising from the HOMO and LUMO values.
Marinescu, Maria; Tudorache, Diana Gabriela; Marton, George Iuliu; Zalaru, Christina-Marie; Popa, Marcela; Chifiriuc, Mariana-Carmen; Stavarache, Cristina-Elena; Constantinescu, Catalin
2017-02-01
Eco-friendly, one-pot, solvent-free synthesis of biologically active 2-substituted benzimidazoles is presented and discussed herein. Novel N-Mannich bases are synthesized from benzimidazoles, secondary amines and formaldehyde, and their structures are confirmed by 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and elemental analysis. All benzimidazole derivatives are evaluated by qualitative and quantitative methods against 9 bacterial strains. The largest microbicide and anti-biofilm effect is observed for the 2-(1-hydroxyethyl)-compounds. Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software. Antimicrobial activity is correlated with the electronic parameters (chemical hardness, electronic chemical potential, global electrophilicity index), Mullikan atomic charges and geometric parameters of the benzimidazole compounds. The planarity of the compound, symmetry of the molecule, and the presence of a nucleophilic group, are advantages for a high antimicrobial activity. Finally, we briefly show that further accurate processing of such compounds into thin films and hybrid structures, e.g. by laser ablation matrix-assisted pulsed laser evaporation and/or laser-induced forward transfer, may indeed provide simple and environmental friendly, state-of-the-art solutions for antimicrobial coatings.
Communication: Reduced density matrices in molecular systems: Grand-canonical electron states
Energy Technology Data Exchange (ETDEWEB)
Bochicchio, Roberto C., E-mail: rboc@df.uba.ar [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Ciudad Universitaria, 1428 Buenos Aires (Argentina); Miranda-Quintana, Ramón A. [Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Zapata e G y Mazón, 10400 Havana (Cuba); Rial, Diego [Departamento de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IMAS, CONICET, Ciudad Universitaria, 1428 Buenos Aires (Argentina)
2013-11-21
Grand-canonical like descriptions of many electron atomic and molecular open systems which are characterized by a non-integer number of electrons are presented. Their associated reduced density matrices (RDMs) are obtained by introducing the contracting mapping for this type of distributions. It is shown that there is loss of information when connecting RDMs of different order by partial contractions. The energy convexity property of these systems simplifies the description. Consequently, this formulation opens the possibility to a new look for chemical descriptors such as chemical potential and reactivity among others. Examples are presented to discuss the theoretical aspects of this work.
The impact of treatment density and molecular weight for fractional laser-assisted drug delivery
DEFF Research Database (Denmark)
Haak, Christina S; Bhayana, Brijesh; Farinelli, William A
2012-01-01
Ablative fractional lasers (AFXL) facilitate uptake of topically applied drugs by creating narrow open micro-channels into the skin, but there is limited information on optimal laser settings for delivery of specific molecules. The objective of this study was to investigate the impact of laser tr...... treatment density (% of skin occupied by channels) and molecular weight (MW) for fractional CO(2) laser-assisted drug delivery. AFXL substantially increased intra- and transcutaneous delivery of polyethylene glycols (PEGs) in a MW range from 240 to 4300 Da (Nuclear Magnetic Resonance, p...
Abrahams, Ryan D; Paglione, Timothy A D
2016-01-01
Diffuse gamma-ray emission from interstellar clouds results largely from cosmic ray (CR) proton collisions with ambient gas, regardless of the gas state, temperature, or dust properties of the cloud. The interstellar medium is predominantly transparent to both CRs and gamma-rays, so GeV emission is a unique probe of the total gas column density. The gamma-ray emissivity of a cloud of known column density is then a measure of the impinging CR population and may be used to map the kpc-scale CR distribution in the Galaxy. To this end, we test a number of commonly used column density tracers to evaluate their effectiveness in modeling the GeV emission from the relatively quiescent, nearby $\\rho$ Ophiuchi molecular cloud. We confirm that both \\hi\\ and an appropriate H$_2$ tracer are required to reproduce the total gas column densities probed by diffuse gamma-ray emisison. We find that the optical depth at 353 GHz $\\tau_{353}$ from Planck reproduces the gamma-ray data best overall based on the test statistic across...
Calibrating Column Density Tracers with Gamma-Ray Observations of the ρ Ophiuchi Molecular Cloud
Abrahams, Ryan D.; Teachey, Alex; Paglione, Timothy A. D.
2017-01-01
Diffuse gamma-ray emission from interstellar clouds results largely from cosmic ray (CR) proton collisions with ambient gas, regardless of the gas state, temperature, or dust properties of the cloud. The interstellar medium is predominantly transparent to both CRs and gamma-rays, so GeV emission is a unique probe of the total gas column density. The gamma-ray emissivity of a cloud of known column density is then a measure of the impinging CR population and may be used to map the k-scale CR distribution in the Galaxy. To this end, we test a number of commonly used column density tracers to evaluate their effectiveness in modeling the GeV emission from the relatively quiescent, nearby ρ Ophiuchi molecular cloud. We confirm that both H i and an appropriate {{{H}}}2 tracer are required to reproduce the total gas column densities probed by diffuse gamma-ray emisison. We find that the optical depth at 353 GHz ({τ }353) from Planck best reproduces the gamma-ray data overall, based on the test statistic across the entire region of interest, but near-infrared stellar extinction also performs very well, with smaller spatial residuals in the densest parts of the cloud.
Statistics of initial density perturbations in heavy ion collisions and their fluid dynamic response
Floerchinger, Stefan
2014-01-01
An interesting opportunity to determine thermodynamic and transport properties in more detail is to identify generic statistical properties of initial density perturbations. Here we study event-by-event fluctuations in terms of correlation functions for two models that can be solved analytically. The first assumes Gaussian fluctuations around a distribution that is fixed by the collision geometry but leads to non-Gaussian features after averaging over the reaction plane orientation at non-zero impact parameter. In this context, we derive a three-parameter extension of the commonly used Bessel-Gaussian event-by-event distribution of harmonic flow coefficients. Secondly, we study a model of N independent point sources for which connected n-point correlation functions of initial perturbations scale like 1/N^(n-1). This scaling is violated for non-central collisions in a way that can be characterized by its impact parameter dependence. We discuss to what extent these are generic properties that can be expected to...
Equation of state of fluid helium at high temperatures and densities
Institute of Scientific and Technical Information of China (English)
CAI; Lingcang; CHEN; Qifeng; GU; Yunjun; ZHANG; Ying; ZHOU
2005-01-01
Hugoniot curves and shock temperatures of gas helium with initial temperature 293 K and three initial pressures 0.6, 1.2, and 5.0 Mpa were measured up to 15000 K using a two-stage light-gas gun and transient radiation pyrometer. It was found that the calculated Hugoniot EOS of gas helium at the same initial pressure using Saha equation with Debye-Hückel correction was in good agreement with the experimental data. The curve of the calculated shock wave velocity with the particle velocity of gas helium which is shocked from the initial pressure 5 Mpa and temperature 293 K, I.e., the D～u relation, D = C0+λu (u < 10 km/s, λ = 1.32) in a low pressure region, is approximately parallel with the fitted D～u (λ = 1.36) of liquid helium from the experimental data of Nellis et al. Our calculations show that the Hugoniot parameterλis independent of the initial density ρ0. The D～u curves of gas helium will transfer to another one and approach a limiting value of compression when their temperature elevates to about 18000 K and the ionization degree of the shocked gas helium reaches 10-3.
Energy Technology Data Exchange (ETDEWEB)
Kadoura, Ahmad; Sun, Shuyu, E-mail: shuyu.sun@kaust.edu.sa; Salama, Amgad
2014-08-01
Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system's potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide.
Kadoura, Ahmad Salim
2014-08-01
Accurate determination of thermodynamic properties of petroleum reservoir fluids is of great interest to many applications, especially in petroleum engineering and chemical engineering. Molecular simulation has many appealing features, especially its requirement of fewer tuned parameters but yet better predicting capability; however it is well known that molecular simulation is very CPU expensive, as compared to equation of state approaches. We have recently introduced an efficient thermodynamically consistent technique to regenerate rapidly Monte Carlo Markov Chains (MCMCs) at different thermodynamic conditions from the existing data points that have been pre-computed with expensive classical simulation. This technique can speed up the simulation more than a million times, making the regenerated molecular simulation almost as fast as equation of state approaches. In this paper, this technique is first briefly reviewed and then numerically investigated in its capability of predicting ensemble averages of primary quantities at different neighboring thermodynamic conditions to the original simulated MCMCs. Moreover, this extrapolation technique is extended to predict second derivative properties (e.g. heat capacity and fluid compressibility). The method works by reweighting and reconstructing generated MCMCs in canonical ensemble for Lennard-Jones particles. In this paper, system\\'s potential energy, pressure, isochoric heat capacity and isothermal compressibility along isochors, isotherms and paths of changing temperature and density from the original simulated points were extrapolated. Finally, an optimized set of Lennard-Jones parameters (ε, σ) for single site models were proposed for methane, nitrogen and carbon monoxide. © 2014 Elsevier Inc.
Lācis, Uǧis; Bagheri, Shervin
2015-01-01
Dispersion of low-density rigid particles with complex geometries is ubiquitous in both natural and industrial environments. We show that while explicit methods for coupling the incompressible Navier-Stokes equations and Newton's equations of motion are often sufficient to solve for the motion of cylindrical particles with low density ratios, for more complex particles - such as a body with a protrusion - they become unstable. We present an implicit formulation of the coupling between rigid body dynamics and fluid dynamics within the framework of the immersed boundary projection method. Similar to previous work on this method, the resulting matrix equation in the present approach is solved using a block-LU decomposition. Each step of the block-LU decomposition is modified to incorporate the rigid body dynamics. We show that our method achieves second-order accuracy in space and first-order in time (third-order for practical settings), only with a small additional computational cost to the original method. Our...
Method of making supercritical fluid molecular spray films, powder and fibers
Smith, Richard D.
1988-01-01
Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a heated nozzle having a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. In another embodiment, the temperature of the solution and nozzle is elevated above the melting point of the solute, which is preferably a polymer, and the solution is maintained at a pressure such that, during expansion, the solute precipitates out of solution within the nozzle in a liquid state. Alternatively, a secondary solvent mutually soluble with the solute and primary solvent and having a higher critical temperature than that of primary solvent is used in a low concentration (<20%) to maintain the solute in a transient liquid state. The solute is discharged in the form of long, thin fibers. The fibers are collected at sufficient distance from the orifice to allow them to solidify in the low pressure/temperature region.
Chen, Kaihui; Wang, Yu; Xuan, Shouhu; Gong, Xinglong
2017-07-01
To investigate the microstructural evolution dependency on the apparent viscosity in shear-thickening fluids (STFs), a hybrid mesoscale model combined with stochastic rotation dynamics (SRD) and molecular dynamics (MD) is used. Muller-Plathe reverse perturbation method is adopted to analyze the viscosities of STFs in a two-dimensional model. The characteristic of microstructural evolution of the colloidal suspensions under different shear rate is studied. The effect of diameter of colloidal particles and the phase volume fraction on the shear thickening behavior is investigated. Under low shear rate, the two-atom structure is formed, because of the strong particle attractions in adjacent layers. At higher shear rate, the synergetic pair structure extends to layered structure along flow direction because of the increasing hydrodynamics action. As the shear rate rises continuously, the layered structure rotates and collides with other particles, then turned to be individual particles under extension or curve string structure under compression. Finally, at the highest shear rate, the strings curve more severely and get into two-dimensional cluster. The apparent viscosity of the system changes from shear-thinning behavior to the shear-thickening behavior. This work presents valuable information for further understanding the shear thickening mechanism.
Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald
2013-06-28
Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.
Lopez-Encarnacion, Juan M.
2016-06-01
In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21
A reduced density-matrix theory of absorption line shape of molecular aggregate.
Yang, Mino
2005-09-22
A theory for the absorption line shape of molecular aggregates in condensed phase is formulated based on a reduced density-matrix approach. Intermolecular couplings in the aggregates are assumed to be weak (Förster type of energy transfer mechanism). The spin-Boson model is employed to include the effect of electron-phonon coupling. Using the projection operator technique, we derive kinetic equations for the reduced electronic density matrix associated with the absorption spectrum. General expressions of time-dependent rate constants in the kinetic equations are derived by using the cumulant expansion technique. The resulting time-dependent kinetic equations are solved numerically. We illustrate the applicability of the present theory by calculating the line shape of a dimer (a pair of donor and acceptor of energy transfer). For a J-aggregate type of molecular pair (with excitonic redshift), a tail appears on the blue side of the absorption spectrum due to the existence of inhomogeneity in electronic state mixing which is originated from the electron-phonon coupling.
Reimers, Jeffrey R; Cai, Zheng-Li; Bilić, Ante; Hush, Noel S
2003-12-01
As molecular electronics advances, efficient and reliable computation procedures are required for the simulation of the atomic structures of actual devices, as well as for the prediction of their electronic properties. Density-functional theory (DFT) has had widespread success throughout chemistry and solid-state physics, and it offers the possibility of fulfilling these roles. In its modern form it is an empirically parameterized approach that cannot be extended toward exact solutions in a prescribed way, ab initio. Thus, it is essential that the weaknesses of the method be identified and likely shortcomings anticipated in advance. We consider four known systematic failures of modern DFT: dispersion, charge transfer, extended pi conjugation, and bond cleavage. Their ramifications for molecular electronics applications are outlined and we suggest that great care is required when using modern DFT to partition charge flow across electrode-molecule junctions, screen applied electric fields, position molecular orbitals with respect to electrode Fermi energies, and in evaluating the distance dependence of through-molecule conductivity. The causes of these difficulties are traced to errors inherent in the types of density functionals in common use, associated with their inability to treat very long-range electron correlation effects. Heuristic enhancements of modern DFT designed to eliminate individual problems are outlined, as are three new schemes that each represent significant departures from modern DFT implementations designed to provide a priori improvements in at least one and possible all problem areas. Finally, fully semiempirical schemes based on both Hartree-Fock and Kohn-Sham theory are described that, in the short term, offer the means to avoid the inherent problems of modern DFT and, in the long term, offer competitive accuracy at dramatically reduced computational costs.
Rahman, Adhip; Ali, Mohammad Tuhin; Shawan, Mohammad Mahfuz Ali Khan; Sarwar, Mohammed Golam; Khan, Mohammad A K; Halim, Mohammad A
2016-01-01
A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.
Directory of Open Access Journals (Sweden)
Tonatiuh Rangel
2015-06-01
Full Text Available Using benzenediamine and benzenedithiol molecular junctions as benchmarks, we investigate the widespread analysis of the quantum transport conductance in terms of the projected density of states (PDOS onto molecular orbitals (MOs. We first consider two different methods for identifying the relevant MOs: (1 diagonalization of the Hamiltonian of the isolated molecule and (2 diagonalization of a submatrix of the junction Hamiltonian constructed by considering only basis elements localized on the molecule. We find that these two methods can lead to substantially different MOs and hence PDOS. Furthermore, within Method 1, the PDOS can differ depending on the isolated molecule chosen to represent the molecular junction (e.g., with or without dangling bonds; within Method 2, the PDOS depends on the chosen basis set. We show that these differences can be critical when the PDOS is used to provide a physical interpretation of the conductance (especially when its value is small, as it happens typically at zero bias. In this work, we propose a new approach in an attempt to reconcile the two traditional methods. Although some improvements were achieved, the main problems remain unsolved. Our results raise more general questions and doubts on a PDOS-based analysis of the conductance.
Path integral Monte Carlo and density functional molecular dynamics simulations of hot, dense helium
Militzer, B.
2009-04-01
Two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), are applied to study hot, dense helium in the density-temperature range of 0.387-5.35gcm-3 and 500K-1.28×108K . One coherent equation of state is derived by combining DFT-MD data at lower temperatures with PIMC results at higher temperatures. Good agreement between both techniques is found in an intermediate-temperature range. For the highest temperatures, the PIMC results converge to the Debye-Hückel limiting law. In order to derive the entropy, a thermodynamically consistent free-energy fit is used that reproduces the internal energies and pressure derived from the first-principles simulations. The equation of state is presented in the form of a table as well as a fit and is compared with different free-energy models. Pair-correlation functions and the electronic density of states are discussed. Shock Hugoniot curves are compared with recent laser shock-wave experiments.
Ruggiero, Michael T; Gooch, Jonathan; Zubieta, Jon; Korter, Timothy M
2016-02-18
The problem of nonlocal interactions in density functional theory calculations has in part been mitigated by the introduction of range-corrected functional methods. While promising solutions, the continued evaluation of range corrections in the structural simulations of complex molecular crystals is required to judge their efficacy in challenging chemical environments. Here, three pyridinium-based crystals, exhibiting a wide range of intramolecular and intermolecular interactions, are used as benchmark systems for gauging the accuracy of several range-corrected density functional techniques. The computational results are compared to low-temperature experimental single-crystal X-ray diffraction and terahertz spectroscopic measurements, enabling the direct assessment of range correction in the accurate simulation of the potential energy surface minima and curvatures. Ultimately, the simultaneous treatment of both short- and long-range effects by the ωB97-X functional was found to be central to its rank as the top performer in reproducing the complex array of forces that occur in the studied pyridinium solids. These results demonstrate that while long-range corrections are the most commonly implemented range-dependent improvements to density functionals, short-range corrections are vital for the accurate reproduction of forces that rapidly diminish with distance, such as quadrupole-quadrupole interactions.
Molecular Rayleigh Scattering Diagnostic for Dynamic Temperature, Velocity, and Density Measurements
Mielke, Amy R.; Elam, Kristie A.; Sung, Chi-Jen
2006-01-01
A molecular Rayleigh scattering technique is developed to measure dynamic gas temperature, velocity, and density in unseeded turbulent flows at sampling rates up to 16 kHz. A high power CW laser beam is focused at a point in an air jet plume and Rayleigh scattered light is collected and spectrally resolved. The spectrum of the light, which contains information about the temperature and velocity of the flow, is analyzed using a Fabry-Perot interferometer. The circular interference fringe pattern is divided into four concentric regions and sampled at 1 and 16 kHz using photon counting electronics. Monitoring the relative change in intensity within each region allows for measurement of gas temperature and velocity. Independently monitoring the total scattered light intensity provides a measure of gas density. A low speed heated jet is used to validate the measurement of temperature fluctuations and an acoustically excited nozzle flow is studied to validate velocity fluctuation measurements. Power spectral density calculations of the property fluctuations, as well as mean and fluctuating quantities are presented. Temperature fluctuation results are compared with constant current anemometry measurements and velocity fluctuation results are compared with constant temperature anemometry measurements at the same locations.
Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S
2014-11-18
CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium
Energy Technology Data Exchange (ETDEWEB)
Tang, Qian [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Department of Science and Environmental Studies, The Hong Kong Institute of Education (Hong Kong); Li, Zai-yong; Wei, Yu-bo; Yang, Xia; Liu, Lan-tao [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Gong, Cheng-bin, E-mail: gongcbtq@swu.edu.cn [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Ma, Xue-bing [The Key Laboratory of Applied Chemistry of Chongqing Municipality, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Lam, Michael Hon-wah [Department of Biology and Chemistry, City University of Hong Kong (Hong Kong); Chow, Cheuk-fai, E-mail: cfchow@ied.edu.hk [Department of Science and Environmental Studies, The Hong Kong Institute of Education (Hong Kong)
2016-09-01
A photoresponsive surface molecularly imprinted polymer for uric acid in physiological fluids was fabricated through a facile and effective method using bio-safe and biocompatible ZnO nanorods as a support. The strategy was carried out by introducing double bonds on the surface of the ZnO nanorods with 3-methacryloxypropyltrimethoxysilane. The surface molecularly imprinted polymer on ZnO nanorods was then prepared by surface polymerization using uric acid as template, water-soluble 5-[(4-(methacryloyloxy)phenyl)diazenyl]isophthalic acid as functional monomer, and triethanolamine trimethacryl ester as cross-linker. The surface molecularly imprinted polymer on ZnO nanorods showed good photoresponsive properties, high recognition ability, and fast binding kinetics toward uric acid, with a dissociation constant of 3.22 × 10{sup −5} M in aqueous NaH{sub 2}PO{sub 4} buffer at pH = 7.0 and a maximal adsorption capacity of 1.45 μmol g{sup −1}. Upon alternate irradiation at 365 and 440 nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. - Highlights: • Novel surface molecularly imprinted polymer on ZnO nanorods was synthesized. • ZnO-SMIP showed good selectivity toward uric acid in physiological fluids. • ZnO-SMIP displayed good photoresponsive properties.
Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin
2016-12-01
Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.
The effect of ambipolar diffusion on low-density molecular ISM filaments
Ntormousi, Evangelia; André, Philippe; Masson, Jacques
2016-01-01
The filamentary structure of the molecular interstellar medium and the potential link of this morphology to star formation have been brought into focus recently by high resolution observational surveys. An especially puzzling matter is that local interstellar filaments appear to have the same thickness, independent of their column density. This requires a theoretical understanding of their formation process and the physics that governs their evolution. In this work we explore a scenario in which filaments are dissipative structures of the large-scale interstellar turbulence cascade and ion-neutral friction (also called ambipolar diffusion) is affecting their sizes by preventing small-scale compressions. We employ high-resolution, 3D MHD simulations, performed with the grid code RAMSES, to investigate non-ideal MHD turbulence as a filament formation mechanism. We focus the analysis on the mass and thickness distributions of the resulting filamentary structures. Simulations of both driven and decaying MHD turbu...
Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO
Institute of Scientific and Technical Information of China (English)
HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)
2002-01-01
The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.
Quasi-classical theory of electronic flux density in electronically adiabatic molecular processes.
Diestler, D J
2012-11-26
The standard Born-Oppenheimer (BO) description of electronically adiabatic molecular processes predicts a vanishing electronic flux density (EFD). A previously proposed "coupled-channels" theory permits the extraction of the EFD from the BO wave function for one-electron diatomic systems, but attempts at generalization to many-electron polyatomic systems are frustrated by technical barriers. An alternative "quasi-classical" approach, which eliminates the explicit quantum dynamics of the electrons within a classical framework, yet retains the quantum character of the nuclear motion, appears capable of yielding EFDs for arbitrarily complex systems. Quasi-classical formulas for the EFD in simple systems agree with corresponding coupled-channels formulas. Results of the application of the new quasi-classical formula for the EFD to a model triatomic system indicate the potential of the quasi-classical scheme to elucidate the dynamical role of electrons in electronically adiabatic processes in more complex multiparticle systems.
Tanikawa, Kousei; Ohno, Kaoru; Noda, Yusuke; Ono, Shota; Kuwahara, Riichi; Takashima, Akito; Nakaya, Masato; Onoe, Jun
2017-10-01
We have performed first-principles density functional calculations of a molecular heterojunction of a zinc phthalocyanine (ZnPc) molecule and a peanut-shaped fullerene polymer (PSFP) made from several coalesced cross-linked C60 molecules. The PSFP has many isomers and all have both spatially localized (near ZnPc) and metallic conducting levels. Here we consider four typical isomers. From the resulting electronic structure, we discuss the applicability of these isomers to organic photovoltaics (OPV), electrodes, and light harvesting materials. If one of the isomers called T3, which has the largest energy gap, is used together with ZnPc for OPV, this system shows more than 20% energy conversion efficiency.
Molecular adsorbates on HOPG: Toward modulation of graphene density of states
Groce, Michelle; Einstein, Theodore; Cullen, William
2013-03-01
Ordered molecular superlattices, particularly those made of planar aromatics with their attendant pi orbitals, have the potential to break the graphene sublattice degeneracy and create a band gap. Trimesic acid (TMA) is a promising candidate due to its self-assembly into symmetry-breaking superlattices nearly commensurate with that of graphene. We have used the graphite (0001) surface as a model system to explore the impact of TMA thin films on band structure. By examining correlations between STM topography and STS maps of corresponding regions, we are able to investigate the effects of TMA on the local density of states. Work supported by the University of Maryland NSF-MRSEC, DMR 0520471 and Shared Experimental Facilities.
Takaba, Hiromitsu; Kimura, Shou; Alam, Md. Khorshed
2017-03-01
Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.
High density gas state at water/graphite interface studied by molecular dynamics simulation
Institute of Scientific and Technical Information of China (English)
Wang Chun-Lei; Li Zhao-Xia; Li Jing-Yuan; Xiu Peng; Hu Jun; Fang Hai-Ping
2008-01-01
In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results: gas films (pancake-like) for a larger ratio and nanobubbles for a Smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film (pancake-like) and nanobubbles.
Energy Technology Data Exchange (ETDEWEB)
Cummins, S.E.; Green, S.; Thaddeus, P.; Linke, R.A.
1983-03-01
From observations with the Bell Laboratories 7 m telescope of the K components of the CH/sub 3/CH J = 4..-->..3 rotational transition at 73.6 GHz, 6..-->..5 transition at 110.4 GHz, and 7..-->..6 transition at 128.7 GHz, a mean kinetic temperature of 85 +- 10 K and a mean H/sub 2/ density of (1.1 +- 0.5) x 10/sup 5/ cm/sup -3/ are deduced for the central 2' of the Sgr B2 molecular cloud. Within the K = 0--4 ladders of CH/sub 3/CN in Sgr B2 the populations of the radiatively coupled J levels are relaxed, with a rotational temperature of approximately 16 K: similar to that of several linear molecules.
A molecular dynamics study of structure and dynamics in high-density liquids
Variyar, Jayasankar E.; Noro, Massimo; Kivelson, Daniel
By means of molecular dynamics simulations we have investigated increasing configurational ordering and decreasing particle mobility with increasing density ρ of a three-dimensional equilibrated liquid composed of soft discs. The equal-time correlation function h(n)3 (0) which includes two-, three- and four-body correlations is introduced as a measure of structural order; this function is related to the dipole-induced-dipole equal-time correlation function and its sensitivity to structural order in the liquid is associated with the cancellation effect, i.e. the cancellation of the positive contributions of the two- and four- body correlations by the negative contribution of the three-body correlations. The analogous time-dependent correlation function h(4)3 (t) is also studied. The possible implications of these results to the study of supercooled liquids and glasses is discussed.
Mohammadi, M; Chen, P
2015-09-01
Solid tumors with different microvascular densities (MVD) have been shown to have different outcomes in clinical studies. Other studies have demonstrated the significant correlation between high MVD, elevated interstitial fluid pressure (IFP) and metastasis in cancers. Elevated IFP in solid tumors prevents drug macromolecules reaching most cancerous cells. To overcome this barrier, antiangiogenesis drugs can reduce MVD within the tumor and lower IFP. A quantitative approach is essential to compute how much reduction in MVD is required for a specific tumor to reach a desired amount of IFP for drug delivery purposes. Here we provide a computational framework to investigate how IFP is affected by the tumor size, the MVD, and location of vessels within the tumor. A general physiologically relevant tumor type with a heterogenous vascular structure surrounded by normal tissue is utilized. Then the continuity equation, Darcy's law, and Starling's equation are applied in the continuum mechanics model, which can calculate IFP for different cases of solid tumors. High MVD causes IFP elevation in solid tumors, and IFP distribution correlates with microvascular distribution within tumor tissue. However, for tumors with constant MVD but different microvascular structures, the average values of IFP were found to be the same. Moreover, for a constant MVD and vascular distribution, an increase in tumor size leads to increased IFP.
Indian Academy of Sciences (India)
Shubin Liu
2005-09-01
Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes. Exemplary molecular systems like CH$^{+}_{5}$ , Cl- (H2O)30 and Ca2+ (H2O)15 are studied at 300 K in the gas phase, demonstrating that HOMO is more dynamic than LUMO, chemical potential and hardness often fluctuate concurrently. It is argued that DFT concepts and indices may serve as a good framework to understand molecular conformation changes as well as other dynamic phenomena.
CHANGES OF DUST OPACITY WITH DENSITY IN THE ORION A MOLECULAR CLOUD
Energy Technology Data Exchange (ETDEWEB)
Roy, Arabindo; Martin, Peter G.; Nguyen-Luong, Quang [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Polychroni, Danae [INAF-IFSI, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Bontemps, Sylvain; Schneider, Nicola [Universite de Bordeaux, LAB, UMR5804, F-33270 Floirac (France); Abergel, Alain; Konyves, Vera [IAS, CNRS (UMR 8617), Universite Paris-Sud 11, Batiment 121, F-91400 Orsay (France); Andre, Philippe; Arzoumanian, Doris; Hill, Tracey [Laboratoire AIM, C.E.A. Saclay, F-90091 Gif-sur-Yvette (France); Di Francesco, James [National Research Council of Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Pezzuto, Stefano [Istituto di Astrofisica e Planetologia Spaziali IAPS, Istituto Nazionale di Astrofisica INAF, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Testi, Leonardo [European Southern Observatory, Karl Schwarzschild Strasse 2, D-85748 Garching (Germany); White, Glenn [Department of Physics and Astronomy, The Open University, Walton Hall, Milton Keynes, MK7 6AA (United Kingdom)
2013-01-20
We have studied the opacity of dust grains at submillimeter wavelengths by estimating the optical depth from imaging at 160, 250, 350, and 500 {mu}m from the Herschel Gould Belt Survey and comparing this to a column density obtained from the Two Micron All Sky Survey derived color excess E(J - K {sub s}). Our main goal was to investigate the spatial variations of the opacity due to 'big' grains over a variety of environmental conditions and thereby quantify how emission properties of the dust change with column (and volume) density. The central and southern areas of the Orion A molecular cloud examined here, with N {sub H} ranging from 1.5 Multiplication-Sign 10{sup 21} cm{sup -2} to 50 Multiplication-Sign 10{sup 21} cm{sup -2}, are well suited to this approach. We fit the multi-frequency Herschel spectral energy distributions (SEDs) of each pixel with a modified blackbody to obtain the temperature, T, and optical depth, {tau}{sub 1200}, at a fiducial frequency of 1200 GHz (250 {mu}m). Using a calibration of N {sub H}/E(J - K{sub s} ) for the interstellar medium (ISM) we obtained the opacity (dust emission cross-section per H nucleon), {sigma}{sub e}(1200), for every pixel. From a value {approx}1 Multiplication-Sign 10{sup -25} cm{sup 2} H{sup -1} at the lowest column densities that is typical of the high-latitude diffuse ISM, {sigma}{sub e}(1200) increases as N {sup 0.28} {sub H} over the range studied. This is suggestive of grain evolution. Integrating the SEDs over frequency, we also calculated the specific power P (emission power per H) for the big grains. In low column density regions where dust clouds are optically thin to the interstellar radiation field (ISRF), P is typically 3.7 Multiplication-Sign 10{sup -31} W H{sup -1}, again close to that in the high-latitude diffuse ISM. However, we find evidence for a decrease of P in high column density regions, which would be a natural outcome of attenuation of the ISRF that heats the grains, and for
Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.
2017-04-01
Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.
PSD-95 is required to sustain the molecular organization of the postsynaptic density.
Chen, Xiaobing; Nelson, Christopher D; Li, Xiang; Winters, Christine A; Azzam, Rita; Sousa, Alioscka A; Leapman, Richard D; Gainer, Harold; Sheng, Morgan; Reese, Thomas S
2011-04-27
PSD-95, a membrane-associated guanylate kinase, is the major scaffolding protein in the excitatory postsynaptic density (PSD) and a potent regulator of synaptic strength. Here we show that PSD-95 is in an extended configuration and positioned into regular arrays of vertical filaments that contact both glutamate receptors and orthogonal horizontal elements layered deep inside the PSD in rat hippocampal spine synapses. RNA interference knockdown of PSD-95 leads to loss of entire patches of PSD material, and electron microscopy tomography shows that the patchy loss correlates with loss of PSD-95-containing vertical filaments, horizontal elements associated with the vertical filaments, and putative AMPA receptor-type, but not NMDA receptor-type, structures. These observations show that the orthogonal molecular scaffold constructed from PSD-95-containing vertical filaments and their associated horizontal elements is essential for sustaining the three-dimensional molecular organization of the PSD. Our findings provide a structural basis for understanding the functional role of PSD-95 at the PSD.
A Census of the High-Density Molecular Gas in M82
Naylor, B J; Aguirre, J E; Bock, J J; Earle, L; Glenn, J; Inami, H; Kamenetzky, J; Maloney, P R; Matsuhara, H; Nguyen, H T; Zmuidzinas, J
2010-01-01
We present a three-pointing study of the molecular gas in the starburst nucleus of M82 based on 190 - 307 GHz spectra obtained with Z-Spec at the Caltech Submillimeter Observatory. We measure intensities or upper-limits for 20 transitions, including several new detections of CS, HNC, C2H, H2CO and CH3CCH lines. We combine our measurements with previously-published measurements at other frequencies for HCN, HNC, CS, C34S, and HCO+ in a multi-species likelihood analysis constraining gas mass, density and temperature, and the species' relative abundances. We find some 1.7 - 2.7 x 10^8 M_sun of gas with n_H2 between 1 - 6 x 10^4 cm^-3 and T > 50 K. While the mass and temperature are comparable to values inferred from mid-J CO transitions, the thermal pressure is a factor of 10 - 20 greater. The molecular ISM is largely fragmented and is subject to UV irradiation from the star clusters. It is also likely subject to cosmic rays and mechanical energy input from the supernovae, and is warmer on average than the molec...
Changes Of Dust Opacity With Density in the Orion A Molecular Cloud
Roy, Arabindo; Polychroni, Danae; Bontemps, Sylvain; Abergel, Alain; Andre, Philippe; Arzoumanian, Doris; Di Francesco, James; Hill, Tracey; Konyves, Vera; Nguyen-Luong, Quang; Pezzuto, Stefano; Schneider, Nicola; Testi, Leonardo; White, Glenn
2012-01-01
We have studied the opacity of dust grains at submillimeter wavelengths by estimating the optical depth from imaging at 160, 250, 350, and 500 um from the Herschel Gould Belt Survey and comparing this to a column density obtained from the 2MASS-derived color excess E(J-Ks). Our main goal was to investigate the spatial variations of the opacity due to "big" grains over a variety of environmental conditions and thereby quantify how emission properties of the dust change with column (and volume) density. The central and southern areas of the Orion A molecular cloud examined here, with NH ranging from 1.5X10^21 cm^-2 to 50X10^21 cm^-2, are well suited to this approach. We fit the multi-frequency Herschel spectral energy distributions (SEDs) of each pixel with a modified blackbody to obtain the temperature, T, and optical depth, \\tau(1200), at a fiducial frequency of 1200 GHz (250 um). Using a calibration of NH/E(J-Ks)for the interstellar medium (ISM) we obtained the opacity (dust emission cross-section per H nucl...
Applicability of Density Functional Theory to Model Molecular Solvation in Superfluid 4He
Isojärvi, Teemu; Lehtovaara, Lauri; Eloranta, Jussi
2006-09-01
Density functional theory (DFT) has been extensively applied to model solvation of atomic and molecular species ("impurities") in superfluid helium. The interaction between the impurity and the surrounding liquid may range from purely repulsive (e.g. alkali metal atoms and most diatomic excimers) to deeply bound potentials (e:g. aromatic compounds). In order to apply DFT to model processes relevant to low temperature chemistry in superfluid 4He, it is essential to obtain the limits of applicability of the theory. For purely repulsive potentials, the spatial gradient of the liquid density remains small and DFT is expected to produce accurate results. This has been verified previously by comparing DFT results to quantum Monte Carlo calculations. For strong binding potentials, however, DFT fails since the individual He atoms tend to localize about the potential minimum. The present work tests the accuracy of DFT between the weakly and strongly bound regimes. This is done by comparing DFT and quantum Monte Carlo (diffusion Monte Carlo) results for various realistic model potentials with varying degree of binding.
温度和压力对井内流体密度的影响%The Impact of Temperature & Pressure on Borehole Fluids Density
Institute of Scientific and Technical Information of China (English)
罗宇维; 朱江林; 李东; 方国伟; 凌伟汉
2012-01-01
The safety pressure window is narrow in deep well with HPHT conditions,the differential pressure and differential temperature at different depth of wellbore are very huge; at the same time, the density of the fluid in the well would change when expanding due to formation heat and pressure of fluid column; therefore the improper selection of initial density of in-well fluid would lead to pressure instability. With independently developed HTHP fluid density measuring apparatus, the experiment was conducted to test the influence of temperature and pressure on fresh water,spacer fluid, water mud and mineral oil density and relevant curves were obtained; the proper density model for temperature and pressure change in well cementation was selected—Dodson-Standing Model; With Drillbench software, the water-based and oil-based drilling fluid with initial in-well density of 1. 2 kg/L and 2. 0 kg/L was calculated,four corresponding curves, including static equivalent density variation curve were acquired under different geo-thermal gradient. These curves could serve as reference to the density design of drilling fluid and cement slurry for deep wells under HTHP conditions. The experiment results indicated that,in the wells deeper than 5000 m with BHST higher than 270 ℃, the density of water-based fluid could be decreased by 5. 58% and that of oil-based fluid decreased by 6. 41%,compared with the in-well density of 1. 2 g/L.%高温高压深井的安全压力窗口窄,井筒内不同深度之间的流体温差和压差大,且井内流体受到地层加热膨胀和液柱压力压缩造成密度变化,因而容易因入井流体初始密度选择不当造成压力失稳.利用自主研制的高温高压流体密度变化测量仪,进行了温度和压力对淡水、隔离液、水泥浆和矿物白油密度的影响试验,得到了相应的关系曲线；筛选出了适合固井水泥浆温度、压力变化的密度模型—Dodson-Standing模型；通过Drillbench软件,
Marshall, Bennett D; Chapman, Walter G
2013-08-07
We develop a new theory for associating fluids with multiple association sites. The theory accounts for small bond angle effects such as steric hindrance, ring formation, and double bonding. The theory is validated against Monte Carlo simulations for the case of a fluid of patchy colloid particles with three patches and is found to be very accurate. Once validated, the theory is applied to study the phase diagram of a fluid composed of three patch colloids. It is found that bond angle has a significant effect on the phase diagram and the very existence of a liquid-vapor transition.
Energy Technology Data Exchange (ETDEWEB)
Wyrick, Jonathan; Bartels, Ludwig, E-mail: ludwig.bartels@ucr.edu [Pierce Hall, University of California-Riverside, Riverside, California 92521 (United States); Einstein, T. L. [Department of Physics and Condensed Matter Theory Center, University of Maryland, College Park, Maryland 20742-4111 (United States)
2015-03-14
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig
2015-03-01
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
Energy Technology Data Exchange (ETDEWEB)
Kawasumi, Yusuke, E-mail: ssu@rad.med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Clinical Imaging, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Kawabata, Tomoyoshi; Sugai, Yusuke [Tohoku University Graduate School of Medicine, Department of Clinical Imaging, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Usui, Akihito, E-mail: t7402r0506@med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Diagnostic Image Analysis, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Hosokai, Yoshiyuki, E-mail: hosokai@med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Diagnostic Image Analysis, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Sato, Miho, E-mail: meifan58@m.tains.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Clinical Imaging, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Saito, Haruo, E-mail: hsaito@med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Diagnostic Image Analysis, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Ishibashi, Tadashi, E-mail: tisibasi@med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Clinical Imaging, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Hayashizaki, Yoshie, E-mail: yoshie@forensic.med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Forensic Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan); Funayama, Masato, E-mail: funayama@forensic.med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Department of Forensic Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 (Japan)
2013-10-01
Recent studies have reported that drowning victims frequently have fluid accumulation in the paranasal sinuses, most notably the maxillary and sphenoid sinuses. However, in our previous study, many non-drowning victims also had fluid accumulation in the sinuses. Therefore, we evaluated the qualitative difference in fluid accumulation between drowning and non-drowning cases in the present study. Thirty-eight drowning and 73 non-drowning cases were investigated retrospectively. The fluid volume and density of each case were calculated using a DICOM workstation. The drowning cases were compared with the non-drowning cases using the Mann–Whitney U-test because the data showed non-normal distribution. The median fluid volume was 1.82 (range 0.02–11.7) ml in the drowning cases and 0.49 (0.03–8.7) ml in the non-drowning cases, and the median fluid density was 22 (−14 to 66) and 39 (−65 to 77) HU, respectively. Both volume and density differed significantly between the drowning and non-drowning cases (p = 0.001, p = 0.0007). Regarding cut-off levels in the ROC analysis, the points on the ROC curve closest (0, 1) were 1.03 ml (sensitivity 68%, specificity 68%, PPV 53%, NPV 81%) and 27.5 HU (61%, 70%, 51%, 77%). The Youden indices were 1.03 ml and 37.8 HU (84%, 51%, 47%, 86%). When the cut-off level was set at 1.03 ml and 27.5 HU, the sensitivity was 42%, specificity 45%, PPV 29% and NPV 60%. When the cut-off level was set at 1.03 ml and 37.8 HU, sensitivity was 58%, specificity 32%, PPV 31% and NPV 59%.
DEFF Research Database (Denmark)
Frutiger, Jerome; Abildskov, Jens; Sin, Gürkan
identify the target properties of the CAMD problem for working fluids. In this study the CAMD problem for the development of novel working fluids for organic Rankine cycles (ORC) is formulated mathematically. It integrates both a system model for the ORC and property models including the Peng...... will be applied in a case study of an Organic Rankine Cycle (ORC) with a low-temperature heat source. The heat source is a hot water stream from waste heat of a chemical site. Giving this pre-exquisite the method allows to identify the most favorable working fluid along with the corresponding optimal process...... conditions in order to get the highest possible power output. The study presents a new approach for the identification of target properties of CAMD problems based on sensitivity analysis and shows its application for the development of novel working fluids of organic Rankine cycles for low temperature heat...
Hecker, Michael; Fitzner, Brit; Wendt, Matthias; Lorenz, Peter; Flechtner, Kristin; Steinbeck, Felix; Schröder, Ina; Thiesen, Hans-Jürgen; Zettl, Uwe Klaus
2016-04-01
Intrathecal immunoglobulin G (IgG) synthesis and oligoclonal IgG bands in cerebrospinal fluid (CSF) are hallmarks of multiple sclerosis (MS), but the antigen specificities remain enigmatic. Our study is the first investigating the autoantibody repertoire in paired serum and CSF samples from patients with relapsing-remitting MS (RRMS), primary progressive MS (PPMS), and other neurological diseases by the use of high-density peptide microarrays. Protein sequences of 45 presumed MS autoantigens (e.g.MOG, MBP, and MAG) were represented on the microarrays by overlapping 15mer peptides. IgG reactivities were screened against a total of 3991 peptides, including also selected viral epitopes. The measured antibody reactivities were highly individual but correlated for matched serum and CSF samples. We found 54 peptides to be recognized significantly more often by serum or CSF antibodies from MS patients compared with controls (pvalues <0.05). The results for RRMS and PPMS clearly overlapped. However, PPMS patients presented a broader peptide-antibody signature. The highest signals were detected for a peptide mapping to a region of the Epstein-Barr virus protein EBNA1 (amino acids 392-411), which is homologous to the N-terminal part of human crystallin alpha-B. Our data confirmed several known MS-associated antigens and epitopes, and they delivered additional potential linear epitopes, which await further validation. The peripheral and intrathecal humoral immune response in MS is polyspecific and includes antibodies that are also found in serum of patients with other diseases. Further studies are required to assess the pathogenic relevance of autoreactive and anti-EBNA1 antibodies as well as their combinatorial value as biomarkers for MS. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Salacuse, J. J.; Egelstaff, P. A.
2001-11-01
We describe a method for obtaining the intermediate scattering function I(Q,t) from a computer simulation: it is an extension of our earlier calculation [Salacuse, Denton, and Egelstaff, Phys. Rev. E 53, 2382 (1996)] for the t-->0 limit. We use this approach to obtain I(Q,t) for low Q and t from molecular dynamics (MD) simulations of a model krypton fluid whose atoms interact via a truncated Aziz pair potential, and the results are compared over their range of validity to I(Q,t) determined by the standard MD method and also by a time expansion approach. In its range of validity our approach is much more efficient than the standard MD method; however, it covers a restricted range of t due to the movement of density fluctuations (sound waves) through the simulated fluid which produces an anomaly in the time behavior of I(Q,t). By analyzing I(Q=0,t) the velocity of sound in the simulation is determined, and the results compare favorably with published experimental results for the sound velocity of liquid krypton.
2017-05-04
College, City University of New York, New York, NY 10065 ONR Absorption spectra Density Functional Theory Molecular clusters Contents Introduction ...Clusters using Density Functional Theory May 4, 2017 Approved for public release; distribution is unlimited. L. Huang S.g. LambrakoS Center for...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching
Damas, Aurélie; Chamoreau, Lise-Marie; Cooksy, Andrew L; Jutand, Anny; Amouri, Hani
2013-02-04
The synthesis and X-ray molecular structure of the first metal-stabilized o-dithiobenzoquinone [Cp*Ir-o-(η(4)-C(6)H(4)S(2))] (2) are described. The presence of the metal stabilizes this elusive intermediate by π coordination and increases the nucleophilic character of the sulfur atoms. Indeed, the π-bonded dithiolene complex 2 was found to react with the organometallic solvated species [Cp*M(acetone)(3)][OTf](2) (M = Rh, Ir) to give a unique class of binuclear dithiolene compounds [Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) [M = Rh (3), Ir (4)] in which the elusive dithiolene η-C(6)H(4)S(2) acts as a bridging ligand toward the two Cp*M moieties. The electrochemical behavior of all complexes was investigated and provided us with valuable information about their redox properties. Density functional theory (DFT) calculations on the π-bonded dithiobenzoquinone ligand and related bimetallic systems show that the presence of Cp*M at the arene system of the dithiolene ligand increases the stability compared to the known monomeric species [Cp*Ir-o-(C(6)H(4)S(2)-κ(2)-S,S)] and enables these complexes Cp*Ir(C(6)H(4)S(2))MCp*][OTf](2) (3 and 4) to act as electron reservoirs. Time-dependent DFT calculations also predict the qualitative trends in the experimental UV-vis spectra and indicate that the strongest transitions arise from ligand-metal charge transfer involving primarily the HOMO-1 and LUMO. All of these compounds were fully characterized and identified by single-crystal X-ray crystallography. These results illustrate the first examples describing the coordination chemistry of the elusive o-dithiobenzoquinone to yield bimetallic complexes with an o-benzodithiolene ligand. These compounds might have important applications in the area of molecular materials.
Härtel, Andreas; Samin, Sela; van Roij, René
2016-06-01
The ongoing scientific interest in the properties and structure of electric double layers (EDLs) stems from their pivotal role in (super)capacitive energy storage, energy harvesting, and water treatment technologies. Classical density functional theory (DFT) is a promising framework for the study of the in- and out-of-plane structural properties of double layers. Supported by molecular dynamics simulations, we demonstrate the adequate performance of DFT for analyzing charge layering in the EDL perpendicular to the electrodes. We discuss charge storage and capacitance of the EDL and the impact of screening due to dielectric solvents. We further calculate, for the first time, the in-plane structure of the EDL within the framework of DFT. While our out-of-plane results already hint at structural in-plane transitions inside the EDL, which have been observed recently in simulations and experiments, our DFT approach performs poorly in predicting in-plane structure in comparison to simulations. However, our findings isolate fundamental issues in the theoretical description of the EDL within the primitive model and point towards limitations in the performance of DFT in describing the out-of-plane structure of the EDL at high concentrations and potentials.
Starko-Bowes, Ryan; Pramanik, Sandipan
2013-06-18
In recent years π-conjugated organic semiconductors have emerged as the active material in a number of diverse applications including large-area, low-cost displays, photovoltaics, printable and flexible electronics and organic spin valves. Organics allow (a) low-cost, low-temperature processing and (b) molecular-level design of electronic, optical and spin transport characteristics. Such features are not readily available for mainstream inorganic semiconductors, which have enabled organics to carve a niche in the silicon-dominated electronics market. The first generation of organic-based devices has focused on thin film geometries, grown by physical vapor deposition or solution processing. However, it has been realized that organic nanostructures can be used to enhance performance of above-mentioned applications and significant effort has been invested in exploring methods for organic nanostructure fabrication. A particularly interesting class of organic nanostructures is the one in which vertically oriented organic nanowires, nanorods or nanotubes are organized in a well-regimented, high-density array. Such structures are highly versatile and are ideal morphological architectures for various applications such as chemical sensors, split-dipole nanoantennas, photovoltaic devices with radially heterostructured "core-shell" nanowires, and memory devices with a cross-point geometry. Such architecture is generally realized by a template-directed approach. In the past this method has been used to grow metal and inorganic semiconductor nanowire arrays. More recently π-conjugated polymer nanowires have been grown within nanoporous templates. However, these approaches have had limited success in growing nanowires of technologically important π-conjugated small molecular weight organics, such as tris-8-hydroxyquinoline aluminum (Alq3), rubrene and methanofullerenes, which are commonly used in diverse areas including organic displays, photovoltaics, thin film transistors
Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume
2017-09-01
The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.
Energy Technology Data Exchange (ETDEWEB)
Ko, Soon Heum [Linkoeping University, Linkoeping (Sweden); Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel [Louisiana State University, Baton Rouge (United States); Jha, Shantenu [Rutgers University, Piscataway (United States)
2014-01-15
Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.
Far-Infrared Dust Temperatures and Column Densities of the MALT90 Molecular Clump Sample
Guzmán, Andrés E; Contreras, Yanett; Smith, Howard A; Jackson, James M; Hoq, Sadia; Rathborne, Jill M
2015-01-01
We present dust column densities and dust temperatures for $\\sim3000$ young high-mass molecular clumps from the Millimetre Astronomy Legacy Team 90 GHz (MALT90) survey, derived from adjusting single temperature dust emission models to the far-infrared intensity maps measured between 160 and 870 \\micron\\ from the Herschel/Hi-Gal and APEX/ATLASGAL surveys. We discuss the methodology employed in analyzing the data, calculating physical parameters, and estimating their uncertainties. The population average dust temperature of the clumps are: $16.8\\pm0.2$ K for the clumps that do not exhibit mid-infrared signatures of star formation (Quiescent clumps), $18.6\\pm0.2$ K for the clumps that display mid-infrared signatures of ongoing star formation but have not yet developed an HII region (Protostellar clumps), and $23.7\\pm0.2$ and $28.1\\pm0.3$ K for clumps associated with HII and photo-dissociation regions, respectively. These four groups exhibit large overlaps in their temperature distributions, with dispersions rang...
Tan, Osbert; Clark, S J; Szablewski, M; Cross, G H
2010-12-28
We present results of first principles density functional theory calculations of the electronic and atomic structural properties of model Z-type Langmuir-Blodgett (LB) layers comprising amphiphilic quinolinium tricyanoquinodimethanide (Q3CNQ) chromophores. We find that the chromophore electronic ground state is not as clearly "zwitterionic" as required by models to explain electrical rectification purportedly seen in such systems. The computed visible region transitions are not what have been assumed to be the intervalence charge transfer bands seen in the visible region of molecules in Z-type LB films. Our own LB deposition and spectroscopic studies suggest that almost all visible region features previously seen may be ascribed to aggregates. The calculated lowest energy electronic excitation between HOMO and LUMO levels, which is located in the near infrared region, has a transition moment aligned approximately 9° off the molecular long axis, and has a normalized oscillator strength of 1 order of magnitude higher than those of the visible region transitions. This most dominant feature has been neglected from discussions of Langmuir-Blodgett layer rectification but our own deposition studies show no sign of this feature, indicating that the structure of the modeled system differs from that of typical experimental structures. The model indicates that such idealized LB layer structures cannot confidently be invoked to explain their experimental optical or electrical properties.
Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics
Falk von Rudorff, Guido; Jakobsen, Rasmus; Rosso, Kevin M.; Blumberger, Jochen
2016-10-01
The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O-) and doubly protonated oxygens (-OH2+ ) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.
Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.
2017-10-01
Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.
Cho, Eugene N; Zhitomirsky, David; Han, Grace G D; Liu, Yun; Grossman, Jeffrey C
2017-03-15
Solar thermal fuels (STFs) harvest and store solar energy in a closed cycle system through conformational change of molecules and can release the energy in the form of heat on demand. With the aim of developing tunable and optimized STFs for solid-state applications, we designed three azobenzene derivatives functionalized with bulky aromatic groups (phenyl, biphenyl, and tert-butyl phenyl groups). In contrast to pristine azobenzene, which crystallizes and makes nonuniform films, the bulky azobenzene derivatives formed uniform amorphous films that can be charged and discharged with light and heat for many cycles. Thermal stability of the films, a critical metric for thermally triggerable STFs, was greatly increased by the bulky functionalization (up to 180 °C), and we were able to achieve record high energy density of 135 J/g for solid-state STFs, over a 30% improvement compared to previous solid-state reports. Furthermore, the chargeability in the solid state was improved, up to 80% charged from 40% charged in previous solid-state reports. Our results point toward molecular engineering as an effective method to increase energy storage in STFs, improve chargeability, and improve the thermal stability of the thin film.
Chen, Mohan; Xia, Junchao; Huang, Chen; Dieterich, Johannes M.; Hung, Linda; Shin, Ilgyou; Carter, Emily A.
2015-05-01
Orbital-free density functional theory (OFDFT) is a linear-scaling first-principles quantum mechanics method used to calculate the ground-state energy of a given system. Here we present a new version of PRinceton Orbital-Free Electronic Structure Software (PROFESS) with new features. First, PROFESS 3.0 provides a set of new kinetic energy density functionals (KEDFs) which are designed to model semiconductors or transition metals. Specifically, PROFESS 3.0 includes the Huang-Carter (HC) KEDF [1], a density decomposition method with fixed localized electronic density [2], the Wang-Govind-Carter (WGC) decomposition KEDF [3], and the Enhanced von Weizsäcker (EvW)-WGC KEDF [4]. Other major new functions are included, such as molecular dynamics with different statistical mechanical ensembles and spin-polarized density optimizers.
Bulk and interfacial properties of chain fluids: a molecular modelling approach
2003-01-01
En este trabajo se han desarrollado técnicas de modelado molecular, concretamente la teoría estadística de los fluidos asociantes (en inglés, SAFT) y la simulación molecular (Monte Carlo y dinámica molecular), y se han aplicado en el área de la termodinámica molecular moderna. Las técnicas mencionadas se han utilizado en el estudio del comportamiento de propiedades de sistemas fluidos en equilibrio termodinámico, principalmente equilibrios líquido-vapor, pero también coexistencia líquido-líqu...
Simple bond length dependence: A correspondence between reactive fluid theories
Dyer, Kippi M.; Perkyns, John S.; Pettitt, B. M.
2005-06-01
Two elementary models of reactive fluids are examined, the first being a standard construction assuming molecular dissociation at infinite separation; the second is an open mixture of nondissociative molecules and free atoms in which the densities of free atoms and molecules are coupled. An approximation to the density of molecules, to low order in site density, is derived in terms of the classical associating fluid theory variously described by Wertheim [J. Chem. Phys. 87, 7323 (1987)] and Stell [Physica A 231, 1 (1996)]. The results are derived for a fluid of dimerizing hard spheres, and predict dependence of the molecular density on the total site density, the hard sphere diameter, and the bond length of the dimer. The results for the two reactive models are shown to be qualitatively similar, and lead to equivalent predictions of the molecular density for the infinitely short and infinitely long bond lengths.
DEFF Research Database (Denmark)
Frutiger, Jerome; Abildskov, Jens; Sin, Gürkan
2016-01-01
study involving the design of a working fluid for an Organic Ranking Cycle (ORC) design for power generation. Morris Screening is found to be favorable over Monte Carlo based standard regression. Monte Carlo based standard regression cannot be applied, because the current model cannot be sufficiently......This study compares two methods for global sensitivity analysis as a new approach for the identification and ranking of target properties in molecular design problems: A modified Morris Screening technique and Monte Carlo based standard regression. The two methodologies are highlighted in a case...
Directory of Open Access Journals (Sweden)
Redzic Zoran
2011-01-01
Full Text Available Abstract Efficient processing of information by the central nervous system (CNS represents an important evolutionary advantage. Thus, homeostatic mechanisms have developed that provide appropriate circumstances for neuronal signaling, including a highly controlled and stable microenvironment. To provide such a milieu for neurons, extracellular fluids of the CNS are separated from the changeable environment of blood at three major interfaces: at the brain capillaries by the blood-brain barrier (BBB, which is localized at the level of the endothelial cells and separates brain interstitial fluid (ISF from blood; at the epithelial layer of four choroid plexuses, the blood-cerebrospinal fluid (CSF barrier (BCSFB, which separates CSF from the CP ISF, and at the arachnoid barrier. The two barriers that represent the largest interface between blood and brain extracellular fluids, the BBB and the BCSFB, prevent the free paracellular diffusion of polar molecules by complex morphological features, including tight junctions (TJs that interconnect the endothelial and epithelial cells, respectively. The first part of this review focuses on the molecular biology of TJs and adherens junctions in the brain capillary endothelial cells and in the CP epithelial cells. However, normal function of the CNS depends on a constant supply of essential molecules, like glucose and amino acids from the blood, exchange of electrolytes between brain extracellular fluids and blood, as well as on efficient removal of metabolic waste products and excess neurotransmitters from the brain ISF. Therefore, a number of specific transport proteins are expressed in brain capillary endothelial cells and CP epithelial cells that provide transport of nutrients and ions into the CNS and removal of waste products and ions from the CSF. The second part of this review concentrates on the molecular biology of various solute carrier (SLC transport proteins at those two barriers and underlines
Niklasson, Anders; Coe, Joshua; Cawkwell, Marc
2011-06-01
Linear response calculations based on density matrix perturbation theory [A. M. N. Niklasson and M. Challacombe, Phys. Rev. Lett. 92, 193001 (2004)] have been developed within a self-consistent tight-binding method for extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008)]. Besides the nuclear coordinates, extended auxiliary electronic degrees of freedom are added to the regular Born-Oppenheimer Lagrangian, both for the electronic ground state and response densities. This formalism enables highly efficient, on-the-fly, analytic computations of the polarizability autocorrelation functions and the Raman spectra during energy conserving Born-Oppenheimer molecular dynamics trajectories. We will illustrate these capabilities via time-resolved Raman spectra computed during explicit, reactive molecular dynamics simulations of the shock compression of methane, benzene, tert-butylacetylene. Comparisons will be made with experimental results where possible.
Roy, Victor
2015-01-01
We estimate the event-by-event (e-by-e) distribution of the ratio ($\\sigma$) of the magnetic field energy to the fluid energy density in the transverse plane of Au-Au collisions at $\\sqrt{s_{\\rm NN}}$ = 200 GeV. A Monte-Carlo (MC) Glauber model is used to calculate the $\\sigma$ in the transverse plane for impact parameter b=0, 12 fm at time $\\tau_i\\sim$0.5 fm. The fluid energy density is obtained by using Gaussian smoothing with two different smoothing parameter $\\sigma_g$=0.25 , 0.5 fm. For $b=0~\\rm fm$ collisions $\\sigma$ is found to be $\\ll$ 1 in the central region of the fireball and $\\sigma\\gtrsim$ 1 at the periphery. For b=12 fm collisions $\\sigma\\gtrsim$ 1. The e-by-e correlation between $\\sigma$ and the fluid energy density ($\\varepsilon$) is studied. We did not find strong correlation between $\\sigma$ and $\\varepsilon$ at the centre of the fireball, whereas they are mostly anti-correlated at the periphery of the fireball.
Energy Technology Data Exchange (ETDEWEB)
Tussupbayev, Samat; Govind, Niranjan; Lopata, Kenneth A.; Cramer, Christopher J.
2015-03-10
We assess the performance of real-time time-dependent density functional theory (RT-TDDFT) for the calculation of absorption spectra of 12 organic dye molecules relevant to photovoltaics and dye sensitized solar cells with 8 exchange-correlation functionals (3 traditional, 3 global hybrids, and 2 range-separated hybrids). We compare the calculations with traditional linear-response (LR) TDDFT. In addition, we demonstrate the efficacy of the RT-TDDFT approach to calculate wide absorption spectra of two large chromophores relevant to photovoltaics and molecular switches.
Raissi, Heidar; Nowroozi, Alireza; Mohammdi, Reza; Hakimi, Mohammad
2006-11-01
The intramolecular hydrogen bond, molecular structure and vibrational frequencies of tetra-acetylethane have been investigated by means of high-level density functional theory (DFT) methods with most popular basis sets. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were recorded in the regions 400-4000 cm(-1) and 40-4000 cm(-1), respectively. The calculated geometrical parameters of tetra-acetylethane were compared to the experimental results of this compound and its parent molecule (acetylacetone), obtained from X-ray diffraction. The O...O distance in tetra-acetylethane, about 2.424A, suggests that the hydrogen bond in this compound is stronger than acetylacetone. This conclusion is well supported by the NMR proton chemical shifts and O-H stretching mode at 2626 cm(-1). Furthermore, the calculated hydrogen bond energy in the title compound is 17.22 kcal/mol, which is greater than the acetylacetone value. On the other hand, the results of theoretical calculations show that the bulky substitution in alpha-position of acetylacetone results in an increase of the conjugation of pi electrons in the chelate ring. Finally, we applied the atoms in molecules (AIM) theory and natural bond orbital method (NBO) for detail analyzing the hydrogen bond in tetra-acetylethane and acetylacetone. These results are in agreement with the vibrational spectra interpretation and quantum chemical calculation results. Also, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.
Vikas, Hash(0x125f4490)
2011-02-01
Evolution of the helium atom in a strong time-dependent (TD) magnetic field ( B) of strength up to 1011 G is investigated through a quantum fluid dynamics (QFD) based current-density functional theory (CDFT). The TD-QFD-CDFT computations are performed through numerical solution of a single generalized nonlinear Schrödinger equation employing vector exchange-correlation potentials and scalar exchange-correlation density functionals that depend both on the electronic charge-density and the current-density. The results are compared with that obtained from a B-TD-QFD-DFT approach (based on conventional TD-DFT) under similar numerical constraints but employing only scalar exchange-correlation potential dependent on electronic charge-density only. The B-TD-QFD-DFT approach, at a particular TD magnetic field-strength, yields electronic charge- and current-densities as well as exchange-correlation potential resembling with that obtained from the time-independent studies involving static (time-independent) magnetic fields. However, TD-QFD-CDFT electronic charge- and current-densities along with the exchange-correlation potential and energy differ significantly from that obtained using B-TD-QFD-DFT approach, particularly at field-strengths >109 G, representing dynamical effects of a TD field. The work concludes that when a helium atom is subjected to a strong TD magnetic field of order >109 G, the conventional TD-DFT based approach differs "dynamically" from the CDFT based approach under similar computational constraints.
Heidenreich, Sebastian; Ilg, Patrick; Hess, Siegfried
2007-06-01
Boundary effects are investigated for fluids with internal orientational degrees of freedom such as molecular liquids, thermotropic and lyotropic liquid crystals, and polymeric fluids. The orientational degrees of freedom are described by the second rank alignment tensor which is related to the birefringence. We use a standard model to describe the orientational dynamics in the presence of flow, the momentum balance equations, and a constitutive law for the pressure tensor to describe our system. In the spirit of irreversible thermodynamics, boundary conditions are formulated for the mechanical slip velocity and the flux of the alignment. They are set up such that the entropy production at the wall inferred from the entropy flux is positive definite. Even in the absence of a true mechanical slip, the coupling between orientation and flow leads to flow profiles with an apparent slip. This has consequences for the macroscopically measurable effective velocity. In analytical investigations, we consider the simplified case of an isotropic fluid in the Newtonian and stationary flow regime. For special geometries such as plane and cylindrical Couette flow, plane Poiseuille flow, and a flow down an inclined plane, we demonstrate explicitly how the boundary conditions lead to an apparent slip. Furthermore, we discuss the dependence of the effective viscosity and of the effective slip length on the model parameters.
Faidas, H.; Christophorou, L. G.; Datskos, P. G.; McCorkle, D. L.
1989-06-01
The ionization threshold IF of N,N,N',N'-tetramethyl-p-phenylenediamine in ethane, has been measured in the density (ρ) range 0.15-13.30 M/l and over the temperature (T) range 295-413 K, using a multiphoton ionization conductivity technique. The IF was found to be a function of both ρ and T in the ranges studied. At a fixed T (=373 K), IF was found first to decrease with increasing ρ and then to level off at densities of ˜10 M/l. For ρ≥11 M/l and T=295 K, the IF was found to increase with increasing density. At constant density (ρ=5.90 M/l ) IF decreased with increasing T between 323 and 413 K. These results are analyzed and discussed in relation to the effect of ρ and T on the electron conduction band energy V0 and the medium polarization energy P+. The changes in the IF with ρ are attributed to the dependence of V0 and P+ on ρ, while the dependence of IF on T is attributed to the effects of T on V0 rather than on P+.
Soler, J. D.; Ade, P. A. R.; Angilè, F. E.; Ashton, P.; Benton, S. J.; Devlin, M. J.; Dober, B.; Fissel, L. M.; Fukui, Y.; Galitzki, N.; Gandilo, N. N.; Hennebelle, P.; Klein, J.; Li, Z.-Y.; Korotkov, A. L.; Martin, P. G.; Matthews, T. G.; Moncelsi, L.; Netterfield, C. B.; Novak, G.; Pascale, E.; Poidevin, F.; Santos, F. P.; Savini, G.; Scott, D.; Shariff, J. A.; Thomas, N. E.; Tucker, C. E.; Tucker, G. S.; Ward-Thompson, D.
2017-07-01
We statistically evaluated the relative orientation between gas column density structures, inferred from Herschel submillimetre observations, and the magnetic field projected on the plane of sky, inferred from polarized thermal emission of Galactic dust observed by the Balloon-borne Large-Aperture Submillimetre Telescope for Polarimetry (BLASTPol) at 250, 350, and 500 μm, towards the Vela C molecular complex. First, we find very good agreement between the polarization orientations in the three wavelength-bands, suggesting that, at the considered common angular resolution of 3.´0 that corresponds to a physical scale of approximately 0.61 pc, the inferred magnetic field orientation is not significantly affected by temperature or dust grain alignment effects. Second, we find that the relative orientation between gas column density structures and the magnetic field changes progressively with increasing gas column density, from mostly parallel or having no preferred orientation at low column densities to mostly perpendicular at the highest column densities. This observation is in agreement with previous studies by the Planck collaboration towards more nearby molecular clouds. Finally, we find a correspondencebetween (a) the trends in relative orientation between the column density structures and the projected magnetic field; and (b) the shape of the column density probability distribution functions (PDFs). In the sub-regions of Vela C dominated by one clear filamentary structure, or "ridges", where the high-column density tails of the PDFs are flatter, we find a sharp transition from preferentially parallel or having no preferred relative orientation at low column densities to preferentially perpendicular at highest column densities. In the sub-regions of Vela C dominated by several filamentary structures with multiple orientations, or "nests", where the maximum values of the column density are smaller than in the ridge-like sub-regions and the high-column density
Li, Guang-Xing
2016-01-01
Gravity is believed to be important on multiple physical scales in molecular clouds. However, quantitative constraints on gravity are still lacking. We derive an analytical formula which provides estimates on multi-scale gravitational energy distribution using the observed surface density PDF. Our analytical formalism also enables one to convert the observed column density PDF into an estimated volume density PDF, and to obtain average radial profile $\\rho(r)$. For a region with $N_{\\rm col} \\sim N^{-\\gamma_{\\rm N}}$, the gravitational energy spectra is $E_{\\rm p}(k)\\sim k^{-4(1 - 1/\\gamma_{\\rm N})}$. We apply the formula to observations of molecular clouds, and find that a scaling index of $-2$ of the surface density PDF implies that $\\rho \\sim r^{-2}$ and $E_{\\rm p}(k) \\sim k^{-2}$. This indicates that gravity can act effectively against turbulence over a multitude of physical scales. This is the critical scaling index which divides molecular clouds into two categories: clouds like Orion and Ophiuchus have ...
Naughton, D P; Knappitt, J; Fairburn, K; Gaffney, K; Blake, D R; Grootveld, M
1995-03-20
Low-molecular-mass copper(II) species have been detected and quantified in ultrafiltrates (n = 7) of rheumatoid synovial fluid (SF) by a highly-sensitive HPLC-based assay system with the ability to determine Cu(II) concentrations of ultrafiltrates resulted in complexation by histidine > alanine > formate > threonine > lactate > tyrosine > phenylalanine, their effectiveness in this context being in the given order. CD spectra of Cu(II)-treated samples of intact SF exhibited absorption bands typical of copper(II)-albumin complexes, in addition to a band attributable to a low-molecular-mass histidinate complex (lambda min 610 nm). Since both albumin and histidine are potent radical scavengers, these results indicate that any .OH radical generated from bound copper ions will be 'site-specifically' scavenged. Hence, low-molecular-mass copper complexes with the ability to promote the generation of .OH radical which can then escape from the metal ion co-ordination sphere (and in turn, cause damage to critical biomolecules) appear to be absent from inflammatory SF.
Institute of Scientific and Technical Information of China (English)
吴畏; 陆九芳; 付东; 刘金晨; 李以圭
2004-01-01
The density functional theory, simplified by the local density approximation and mean-field approximation, is applied to study the surface properties of pure non-polar fluids. A reasonable long rang correction is adopted to avoid the truncation of the potential. The perturbation theory is applied to establish the equation for the phase equilibrium, in which the hard-core chain fluid is as the reference fluid and the Yukawa potential is used as the perturbation term. Three parameters, ε/k, d and ms, are regressed from the vapor-liquid equilibria, and the surface properties, including density profile, surface tension and local surface tension profile are predicted with these parameters.
Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Ågren, Hans
2014-05-21
We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems--such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.
Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti
2012-07-01
Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.
Gao, Hongwei; Xia, FengYi; Huang, ChangJiang; Lin, Kuangfei
2011-04-01
A comparison of six density functional theory (DFT) methods and six basis sets for predicting the molecular structures and vibration spectra of cisplatin is reported. The theoretical results are discussed and compared with the experimental data. It is remarkable that LSDA/SDD level is clearly superior to all the remaining density functional methods (including mPW1PW) in predicting the structures of cisplatin. Mean deviation between the calculated harmonic and observed fundamental vibration frequencies for each method is also calculated. The results indicate that PBE1PBE/SDD is the best method to predict all frequencies on average for cisplatin molecule in DFT methods.
Gong, Yuezheng; Zhao, Jia; Wang, Qi
2017-10-01
A quasi-incompressible hydrodynamic phase field model for flows of fluid mixtures of two incompressible viscous fluids of distinct densities and viscosities is derived by using the generalized Onsager principle, which warrants the variational structure, the mass conservation and energy dissipation law. We recast the model in an equivalent form and discretize the equivalent system in space firstly to arrive at a time-dependent ordinary differential and algebraic equation (DAE) system, which preserves the mass conservation and energy dissipation law at the semi-discrete level. Then, we develop a temporal discretization scheme for the DAE system, where the mass conservation and the energy dissipation law are once again preserved at the fully discretized level. We prove that the fully discretized algorithm is unconditionally energy stable. Several numerical examples, including drop dynamics of viscous fluid drops immersed in another viscous fluid matrix and mixing dynamics of binary polymeric solutions, are presented to show the convergence property as well as the accuracy and efficiency of the new scheme.
DEFF Research Database (Denmark)
Johansen, Per; Roemer, Daniel Beck; Andersen, Torben O.;
2015-01-01
In the past three decades an increasing amount of research has been performed in the field of tribodynamics of fluid power pumps and motors. The main incentives for this research are optimization of reliability and eciency through the study of loss and wear mechanisms. These mechanisms are very d...... assessment of the applicability, of the force balance condition, if it is used in multibody tribodynamic simulations of radial piston digital fluid power displacement motors....... analysis or optimization. The coupling between multibody dynamics and fluid mechanics depend on the formulation of the solid body motion equations, where two approaches have historically been used. One approach is where the external forces on any lubricated joint are balanced by the fluid forces......, such that solid body inertia is neglected. The other approach includes the inertia terms in the calculation of microdynamics. The inclusion of inertia terms entails a need for smaller time steps in comparison to the force balance approach, wherefore it is of interest to analyze the influence of the inertia term...
Modeling CO Emission: I. CO as a Column Density Tracer and the X-Factor in Molecular Clouds
Shetty, Rahul; Dullemond, Cornelis P; Klessen, Ralf S
2010-01-01
Theoretical and observational investigations have indicated that the abundance of carbon monoxide (CO) is very sensitive to intrinsic properties of the gaseous medium, such as density, metallicity, and the background UV field. In order to accurately interpret CO observations, it is thus important to understand how well CO traces the gas, which in molecular clouds (MCs) is predominantly molecular hydrogen (H2). Recent hydrodynamic simulations by Glover & Mac Low have explicitly followed the formation and destruction of molecules in model MCs under varying conditions, confirming that CO formation strongly depends on the cloud properties. Conversely, the H2 formation is primarily determined by the age of the MC. We apply radiative transfer calculations to these MC models in order to investigate the properties of CO line emission. We focus on integrated CO (J=1-0) intensities emerging from individual clouds, including its relationship to the total, H2, and CO column densities, as well as the "X factor," the r...
Marsalek, Ondrej
2015-01-01
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...
A timer-actuated immunoassay cassette for detecting molecular markers in oral fluids.
Liu, Changchun; Qiu, Xianbo; Ongagna, Serge; Chen, Dafeng; Chen, Zongyuan; Abrams, William R; Malamud, Daniel; Corstjens, Paul L A M; Bau, Haim H
2009-03-21
An inexpensive, hand-held, point-of-care, disposable, self-contained immunoassay cassette comprised of air pouches for pumping, a metering chamber, reagents storage chambers, a mixer, and a lateral flow strip was designed, constructed, and tested. The assay was carried out in a consecutive flow format. The detection was facilitated with up-converting phosphor (UCP) reporter particles. The automated, timely pumping of the various reagents was driven by a spring-loaded timer. The utility of the cassette was demonstrated by detecting antibodies to HIV in saliva samples and further evaluated with a non-contagious, haptenized DNA assay. The cassette has several advantages over dip sticks such as sample preprocessing, integrated storage of reagents, and automated operation that reduces operator errors and training. The cassette and actuator described herein can readily be extended to detect biomarkers of other diseases in body fluids and other fluids at the point of care. The system is particularly suitable for resource-poor countries, where funds and trained personnel are in short supply.
Huerta, Adrian; Pizio, Orest; Bryk, Pawel; Sokolowski, Stefan
A density functional approach is used to study the adsorption of the four-bonding-site model associating Lennard-Jones fluid in slit-like pores with energetically heterogeneous walls. The fluid-wall potential is qualitatively similar to that invoked by Röcken, P., Somoza, A., Tarazona, P., and Findenegg, G. H., 1999, J. chem. Phys., 108, 8089, i.e. it consists of a homogeneous part that varies in the direction perpendicular to the wall and a periodic part, varying also in one direction parallel to the wall. Both parts are modelled by Lennard-Jones 9,3-type functions. The structure of the adsorbed film is characterized by the local densities of all particles and the densities of the monomers. The phase diagrams are evaluated for several systems characterized by different corrugation of the adsorbing potential. The adsorbing field is strong enough to allow for the layering transition. As well as the formation of the so-called bridge phase that fills the pore space over the most energetic parts of the wall and of capillary condensation, the layering transition is observed within the first layer adjacent to the pore walls. If the adsorbing potential due to each pore wall is shifted in phase by pi/2, the bridge phase is not formed.
Zhou, C L; Fang, D Q; Zhang, G Q
2013-01-01
Thermodynamic and transport properties of nuclear fireball created in the central region of heavy-ion collisions below 200 MeV/nucleon are investigated within the isospin-dependent quantum molecular dynamic (IQMD) model. These properties include time evolutions of the density, temperature, chemical potential, entropy density ($s$) and shear viscosity ($\\eta$) as well as density and temperature dependencies of the ratio of shear viscosity over entropy density ($\\eta/s$) etc. Based on the shear viscosity parametrization developed by Danilewicz and entropy density which is obtained by a generalized hot Thomas Fermi formalism, the ratio of shear viscosity over entropy density is calculated in the whole collision process as well as in the freeze-out stage. With the collision goes on, a transient minimal $\\eta/s$ with the value around 5/$4\\pi$ occurs in the largest compression stage. While, the relationship of $\\eta/s$ to tempertaure ($T$) in the freeze-out stage displays a local minimum which is about 9-10 times $...
Diaz, Carlos; Baruah, Tunna; Zope, Rajendra
We investigate the effect of solvent on the electronic structure of a biomimetic molecular triad that shows photoinduced charge transfer in laboratory. The supramolecular triad contains three different units - C60, porphyrin, and beta-carotenoid. We have performed classical molecular dynamics simulation of the triad surrounded by 15000 water molecules using NAMD for 20 nanoseconds. Subsequently, we performed an all-electron density functional calculations (DFT) using large basis sets on the 50 snap-shots taken from the molecular dynamics simulation. The solvent effects in the DFT calculations are treated using both the explicit water molecules as well as using the point charge representation of water. The excitation energies and absorption spectra show that the polar solvent induces significant changes in the electronic structure of the triad.
Directory of Open Access Journals (Sweden)
Prudence O Powell
Full Text Available Phytoglycogen (from certain mutant plants and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired.
Powell, Prudence O.; Sullivan, Mitchell A.; Sheehy, Joshua J.; Schulz, Benjamin L.; Warren, Frederick J.; Gilbert, Robert G.
2015-01-01
Phytoglycogen (from certain mutant plants) and animal glycogen are highly branched glucose polymers with similarities in structural features and molecular size range. Both appear to form composite α particles from smaller β particles. The molecular size distribution of liver glycogen is bimodal, with distinct α and β components, while that of phytoglycogen is monomodal. This study aims to enhance our understanding of the nature of the link between liver-glycogen β particles resulting in the formation of large α particles. It examines the time evolution of the size distribution of these molecules during acid hydrolysis, and the size dependence of the molecular density of both glucans. The monomodal distribution of phytoglycogen decreases uniformly in time with hydrolysis, while with glycogen, the large particles degrade significantly more quickly. The size dependence of the molecular density shows qualitatively different shapes for these two types of molecules. The data, combined with a quantitative model for the evolution of the distribution during degradation, suggest that the bonding between β into α particles is different between phytoglycogen and liver glycogen, with the formation of a glycosidic linkage for phytoglycogen and a covalent or strong non-covalent linkage, most probably involving a protein, for glycogen as most likely. This finding is of importance for diabetes, where α-particle structure is impaired. PMID:25799321
Boss, Alan P
2013-01-01
Magnetic fields are important contributers to the dynamics of collapsing molecular cloud cores, and can have a major effect on whether collapse results in a single protostar or fragmentation into a binary or multiple protostar system. New models are presented of the collapse of magnetic cloud cores using the adaptive mesh refinement (AMR) code Enzo2.0. The code was used to calculate the ideal magnetohydrodynamics (MHD) of initially spherical, uniform density and rotation clouds with density perturbations, i.e., the Boss and Bodenheimer (1979) standard isothermal test case for three dimensional (3D) hydrodynamics (HD) codes. After first verifying that Enzo reproduces the binary fragmentation expected for the non-magnetic test case, a large set of models was computed with varied initial magnetic field strengths and directions with respect to the cloud core axis of rotation (parallel or perpendicular), density perturbation amplitudes, and equations of state. Three significantly different outcomes resulted: (1) c...
Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M
2015-09-15
A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup.
Han, Xuesong; Li, Haiyan; Zhao, Fu
2017-07-01
Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD) method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.
Directory of Open Access Journals (Sweden)
Xuesong Han
2017-07-01
Full Text Available Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.
Rosnik, Andreana M; Curutchet, Carles
2015-12-08
Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.
Galofaro, J.; Vayner, B.; Ferguson, D.; Degroot, W.
2002-01-01
Previous experimental studies have hypothesized that the onset of Solar Array Arc (SAA) initiation in low-density space plasmas is caused by a desorbed gas molecular ionization mechanism. Indeed past investigations performed at the NASA Glenn Plasma Interaction Facility tend to not only support the desorbed gas molecular ionization mechanism, but have gone as far as identifying the crucial molecular species that must be present for molecular ion dominated process to occur. When electrical breakdown occurs at a triple junction site on a solar array panel, a quasi-neutral plasma cloud is ejected. Assuming the main component of the expelled plasma cloud by weight is due to water vapor, the fastest process available is due to HO molecules and OH(+) ions, or more succinctly, dissociative molecular-ion dominated recombination processes: H2O(+) + e(-) yields H* + OH*. Recently published spectroscopic observations of solar array arc spectra in ground tests have revealed the well-known molecular OH band (302 to 309nm), as well as the molecular SiH band (387nm peak), and the molecular CH band (432nm peak). Note that the OH band is observed in emission arcs where water vapor is present. Strong atomic lines were also observed for H(sub beta) at 486nm and H(sub alpha) at 656.3nm in prior ground testing. Independent supporting evidence of desorbed gas molecular ionization mechanisms also come from measurements of arc current pulse widths at different capacitances. We will revisit an earlier first order approximation demonstrating the dependence of arc current pulse widths on the square root of the capacitance. The simple arc current pulse width model will be then be used to estimate the temperature of the arc plasma (currently believed to be somewhere in the range of 3 to 5 eV). The current paper then seeks to extend the outlined work by including numerous vacuum chamber measurements obtained with a quadrupole mass spectrometer. A small solar array was mounted inside the vacuum
Energy Technology Data Exchange (ETDEWEB)
Vikas [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, 160014 Chandigrah (India)
2011-02-15
Evolution of the helium atom in a strong time-dependent (TD) magnetic field (B) of strength up to 10{sup 11} G is investigated through a quantum fluid dynamics (QFD) based current-density functional theory (CDFT). The TD-QFD-CDFT computations are performed through numerical solution of a single generalized nonlinear Schroedinger equation employing vector exchange-correlation potentials and scalar exchange-correlation density functionals that depend both on the electronic charge-density and the current-density. The results are compared with that obtained from a B-TD-QFD-DFT approach (based on conventional TD-DFT) under similar numerical constraints but employing only scalar exchange-correlation potential dependent on electronic charge-density only. The B-TD-QFD-DFT approach, at a particular TD magnetic field-strength, yields electronic charge- and current-densities as well as exchange-correlation potential resembling with that obtained from the time-independent studies involving static (time-independent) magnetic fields. However, TD-QFD-CDFT electronic charge- and current-densities along with the exchange-correlation potential and energy differ significantly from that obtained using B-TD-QFD-DFT approach, particularly at field-strengths >10{sup 9} G, representing dynamical effects of a TD field. The work concludes that when a helium atom is subjected to a strong TD magnetic field of order >10{sup 9} G, the conventional TD-DFT based approach differs 'dynamically' from the CDFT based approach under similar computational constraints. (author)
What Determines the Density Structure of Molecular Clouds? A Case Study of Orion B with Herschel
Schneider, N.; André, Ph.; Könyves, V.; Bontemps, S.; Motte, F.; Federrath, C.; Ward-Thompson, D.; Arzoumanian, D.; Benedettini, M.; Bressert, E.; Didelon, P.; Di Francesco, J.; Griffin, M.; Hennemann, M.; Hill, T.; Palmeirim, P.; Pezzuto, S.; Peretto, N.; Roy, A.; Rygl, K. L. J.; Spinoglio, L.; White, G.
2013-04-01
A key parameter to the description of all star formation processes is the density structure of the gas. In this Letter, we make use of probability distribution functions (PDFs) of Herschel column density maps of Orion B, Aquila, and Polaris, obtained with the Herschel Gould Belt survey (HGBS). We aim to understand which physical processes influence the PDF shape, and with which signatures. The PDFs of Orion B (Aquila) show a lognormal distribution for low column densities until A V ~ 3 (6), and a power-law tail for high column densities, consistent with a ρvpropr -2 profile for the equivalent spherical density distribution. The PDF of Orion B is broadened by external compression due to the nearby OB stellar aggregates. The PDF of a quiescent subregion of the non-star-forming Polaris cloud is nearly lognormal, indicating that supersonic turbulence governs the density distribution. But we also observe a deviation from the lognormal shape at A V > 1 for a subregion in Polaris that includes a prominent filament. We conclude that (1) the point where the PDF deviates from the lognormal form does not trace a universal A V -threshold for star formation, (2) statistical density fluctuations, intermittency, and magnetic fields can cause excess from the lognormal PDF at an early cloud formation stage, (3) core formation and/or global collapse of filaments and a non-isothermal gas distribution lead to a power-law tail, and (4) external compression broadens the column density PDF, consistent with numerical simulations. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.
WHAT DETERMINES THE DENSITY STRUCTURE OF MOLECULAR CLOUDS? A CASE STUDY OF ORION B WITH HERSCHEL
Energy Technology Data Exchange (ETDEWEB)
Schneider, N.; Andre, Ph.; Koenyves, V.; Motte, F.; Arzoumanian, D.; Didelon, P.; Hennemann, M.; Hill, T.; Palmeirim, P.; Peretto, N.; Roy, A. [IRFU/SAp CEA/DSM, Laboratoire AIM CNRS, Universite Paris Diderot, F-91191 Gif-sur-Yvette (France); Bontemps, S. [OASU/LAB-UMR5804, CNRS, Universite Bordeaux 1, F-33270 Floirac (France); Federrath, C. [MoCA, School of Mathematical Sciences, Monash University, VIC 3800 (Australia); Ward-Thompson, D. [Jeremiah Horrocks Institute, UCLAN, Preston, Lancashire PR1 2HE (United Kingdom); Benedettini, M.; Pezzuto, S.; Rygl, K. L. J. [IAPS-INAF, Fosso del Cavaliere 100, I-00133 Roma (Italy); Bressert, E. [CSIRO Astronomy and Space Science, Epping (Australia); Di Francesco, J. [NRCC, Herzberg Institute of Astrophysics, University of Victoria (Canada); Griffin, M. [University School of Physics and Astronomy, Cardiff (United Kingdom); and others
2013-04-01
A key parameter to the description of all star formation processes is the density structure of the gas. In this Letter, we make use of probability distribution functions (PDFs) of Herschel column density maps of Orion B, Aquila, and Polaris, obtained with the Herschel Gould Belt survey (HGBS). We aim to understand which physical processes influence the PDF shape, and with which signatures. The PDFs of Orion B (Aquila) show a lognormal distribution for low column densities until A{sub V} {approx} 3 (6), and a power-law tail for high column densities, consistent with a {rho}{proportional_to}r {sup -2} profile for the equivalent spherical density distribution. The PDF of Orion B is broadened by external compression due to the nearby OB stellar aggregates. The PDF of a quiescent subregion of the non-star-forming Polaris cloud is nearly lognormal, indicating that supersonic turbulence governs the density distribution. But we also observe a deviation from the lognormal shape at A{sub V} > 1 for a subregion in Polaris that includes a prominent filament. We conclude that (1) the point where the PDF deviates from the lognormal form does not trace a universal A{sub V} -threshold for star formation, (2) statistical density fluctuations, intermittency, and magnetic fields can cause excess from the lognormal PDF at an early cloud formation stage, (3) core formation and/or global collapse of filaments and a non-isothermal gas distribution lead to a power-law tail, and (4) external compression broadens the column density PDF, consistent with numerical simulations.
What determines the density structure of molecular clouds ? A case study of Orion B with Herschel
Schneider, N; Konyves, V; Bontemps, S; Motte, F; Federrath, C; Ward-Thompson, D; Arzoumanian, D; Benedettini, M; Bressert, E; Didelon, P; Di Francesco, J; Griffin, M; Hennemann, M; Hill, T; Palmeirim, P; Pezzuto, S; Peretto, N; Roy, A; Rygl, K L J; Spinoglio, L; White, G; 10.1088/2041-8205/766/2/L17
2013-01-01
A key parameter to the description of all star formation processes is the density structure of the gas. In this letter, we make use of probability distribution functions (PDFs) of Herschel column density maps of Orion B, Aquila, and Polaris, obtained with the Herschel Gould Belt survey (HGBS). We aim to understand which physical processes influence the PDF shape, and with which signatures. The PDFs of Orion B (Aquila) show a lognormal distribution for low column densities until Av 3 (6), and a power-law tail for high column densities, consistent with a rho r^-2 profile for the equivalent spherical density distribution. The PDF of Orion B is broadened by external compression due to the nearby OB stellar aggregates. The PDF of a quiescent subregion of the non-star-forming Polaris cloud is nearly lognormal, indicating that supersonic turbulence governs the density distribution. But we also observe a deviation from the lognormal shape at Av>1 for a subregion in Polaris that includes a prominent filament. We concl...
Density Profiles in Molecular Cloud Cores Associated with High-Mass Star-Forming Regions
Pirogov, Lev E
2009-01-01
Radial density profiles for the sample of dense cores associated with high-mass star-forming regions from southern hemisphere have been derived using the data of observations in continuum at 250 GHz. Radial density profiles for the inner regions of 16 cores (at distances $\\la 0.2-0.8$ pc from the center) are close on average to the $\\rho\\propto r^{-\\alpha}$ dependence, where $\\alpha=1.6\\pm 0.3$. In the outer regions density drops steeper. An analysis with various hydrostatic models showed that the modified Bonnor-Ebert model, which describes turbulent sphere confined by external pressure, is preferable compared with the logotrope and polytrope models practically in all cases. With a help of the Bonnor-Ebert model, estimates of central density in a core, non-thermal velocity dispersion and core size are obtained. The comparison of central densities with the densities derived earlier from the CS modeling reveals differences in several cases. The reasons of such differences are probably connected with the presen...
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth
2016-09-07
Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.
Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J.; Lopata, Kenneth
2016-09-01
Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.
Tanner, D. B.
Measurements for a number of cuprate families of optical reflectance over a wide spectral range (far-infrared to ultraviolet) have been analyzed using Kramers-Kronig analysis to obtain the optical conductivity σ (ω) and (by integration of the real part of the conductivity) the spectral weight of low- and mid-energy excitations. For the Kramers-Kronig analysis to give reliable results, accurate high-frequency extrapolations, based on x-ray atomic scattering functions, were used. When the optical conductivities of the normal and superconducting states are compared, a transfer of spectral weight from finite frequencies to the zero-frequency delta-function conductivity of the superconductor is seen. The strength of this delta function gives the superfluid density, ρs. In a clean metallic superconductor the superfluid density is essentially equal to the conduction electron density. The cuprates in contrast have only about 20% of the a b-plane low-energy spectral weight in the superfluid. The rest remains in finite-frequency, midinfrared absorption. In underdoped materials the superfluid fraction is even smaller. There are two ways to measure ρs, using either the partial sum rule for the conductivity or by examination of σ2 (ω) . Comparison of these two estimates of the superfluid density shows that 98% of the a b-plane superfluid density comes from energies below 0.15 eV. Many students, postdocs, and materials preparers have contributed to this work; to all I am very grateful.
Dupuis, A.; Koumoutsakos, P.
We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.
Effects of molecular architecture on fluid ingress behavior of glassy polymer networks
Jaskson, Matthew Blaine
This manuscript demonstrates the synthesis of glassy polymer network isomers to control morphological variations and study solvent ingress behavior independent of chemical affinity. Well-controlled network architectures with varying free volume average hole-sizes have been shown to substantially influence solvent ingress within glassy polymer networks. Bisphenol-A diglycidyl ether (DGEBA), bisphenol-F diglycidyl ether (DGEBF), Triglycidyl p-aminophenol (pAP, MY0510), Triglycidyl maminophenol (mAP, MY0610), and tetraglydicyl-4,4'-diamino-diphenyl methane (TGDDM, MY721) were cured with 3,3'- and 4,4'-diaminodiphenyl sulfone (DDS) at a stoichiometric ratio of 1:1 oxirane to amine active hydrogen to generate a series of network architectures with an average free volume hole-size (Vh) ranging between 54-82 A3. Polymer networks were exposed to water and a broad range of organic solvents ranging in van der Waals (vdW) volumes from 18-88 A3 for up to 10,000h time. A clear relationship between glassy polymer network Vh and fluid penetration has been established. As penetrant vdW volume approached Vh, uptake kinetics significantly decreased, and as penetrant vdW volume exceeded Vh, a blocking mechanism dominated ingress and prevented penetrant transport. These results suggest that reducing the free volume hole-size is a reasonable approach to control solvent properties for glassy polymer networks. New techniques to monitor and predict the diffusion behavior of liquids through glassy networks are also presented. Digital Image Correlation (DIC) was employed to accurately measure the strain developed during case II diffusion. This technique also presented a new theory for a relationship between sample topology and irreversible macroscopic brittle failure induced by solvent absorption. A new modeling technique has been developed which can accurately predict the chemical and physical interactions a solvent may have with a glassy network. This new model can be used as a
Sichani, Mehrdad M.; Spearot, Douglas E.
2016-07-01
The molecular dynamics simulation method is used to investigate the dependence of crystal orientation and shock wave strength on dislocation density evolution in single crystal Cu. Four different shock directions , , , and are selected to study the role of crystal orientation on dislocation generation immediately behind the shock front and plastic relaxation as the system reaches the hydrostatic state. Dislocation density evolution is analyzed for particle velocities between the Hugoniot elastic limit ( up H E L ) for each orientation up to a maximum of 1.5 km/s. Generally, dislocation density increases with increasing particle velocity for all shock orientations. Plastic relaxation for shock in the , , and directions is primarily due to a reduction in the Shockley partial dislocation density. In addition, plastic anisotropy between these orientations is less apparent at particle velocities above 1.1 km/s. In contrast, plastic relaxation is limited for shock in the orientation. This is partially due to the emergence of sessile stair-rod dislocations with Burgers vectors of 1/3 and 1/6. The nucleation of 1/6 dislocations at lower particle velocities is mainly due to the reaction between Shockley partial dislocations and twin boundaries. On the other hand, for the particle velocities above 1.1 km/s, the nucleation of 1/3 dislocations is predominantly due to reaction between Shockley partial dislocations at stacking fault intersections. Both mechanisms promote greater dislocation densities after relaxation for shock pressures above 34 GPa compared to the other three shock orientations.
Gautam, Siddharth S.; Ok, Salim; Cole, David R.
2017-06-01
Geo-fluids consisting of C-O-H volatiles are the main mode of transport of mass and energy throughout the lithosphere and are commonly found confined in pores, grain boundaries and fractures. The confinement of these fluids by porous media at the length scales of a few nanometers gives rise to numerous physical and chemical properties that deviate from the bulk behavior. Studying the structural and dynamical properties of these confined fluids at the length and time scales of nanometers and picoseconds respectively forms an important component of understanding their behavior. To study confined fluids, non-destructive penetrative probes are needed. Nuclear magnetic resonance (NMR) by virtue of its ability to monitor longitudinal and transverse magnetization relaxations of spins, and chemical shifts brought about by the chemical environment of a nucleus, and measuring diffusion coefficient provides a good opportunity to study dynamics and chemical structure at the molecular length and time scales. Another technique that gives insights into the dynamics and structure at these length and time scales is neutron scattering (NS). This is because the wavelength and energies of cold and thermal neutrons used in scattering experiments are in the same range as the spatial features and energies involved in the dynamical processes occurring at the molecular level. Molecular Dynamics (MD) simulations on the other hand help with the interpretation of the NMR and NS data. Simulations can also supplement the experiments by calculating quantities not easily accessible to experiments. Thus using NMR, NS and MD simulations in conjunction, a complete description of the molecular structure and dynamics of confined geo-fluids can be obtained. In the current review, our aim is to show how a synergistic use of these three techniques has helped shed light on the complex behavior of water, CO2, and low molecular weight hydrocarbons. After summarizing the theoretical backgrounds of the
Deyranlou, Amin; Niazmand, Hamid; Sadeghi, Mahmood-Reza
2015-09-18
Low-density lipoprotein (LDL), which is recognized as bad cholesterol, typically has been regarded as a main cause of atherosclerosis. LDL infiltration across arterial wall and subsequent formation of Ox-LDL could lead to atherogenesis. In the present study, combined effects of non-Newtonian fluid behavior and fluid-structure interaction (FSI) on LDL mass transfer inside an artery and through its multilayer arterial wall are examined numerically. Navier-Stokes equations for the blood flow inside the lumen and modified Darcy's model for the power-law fluid through the porous arterial wall are coupled with the equations of mass transfer to describe LDL distributions in various segments of the artery. In addition, the arterial wall is considered as a heterogeneous permeable elastic medium. Thus, elastodynamics equation is invoked to examine effects of different wall elasticity on LDL distribution in the artery. Findings suggest that non-Newtonian behavior of filtrated plasma within the wall enhances LDL accumulation meaningfully. Moreover, results demonstrate that at high blood pressure and due to the wall elasticity, endothelium pores expand, which cause significant variations on endothelium physiological properties in a way that lead to higher LDL accumulation. Additionally, results describe that under hypertension, by increasing angular strain, endothelial junctions especially at leaky sites expand more dramatic for the high elastic model, which in turn causes higher LDL accumulation across the intima layer and elevates atherogenesis risk.
Jumper, E. J.; Hugo, R. J.
1992-07-01
This paper discusses the small-aperture beam technique, a relatively new way of experimentally quantifying optically-active, turbulent-fluid-flow-induced optical degradation. The paper lays out the theoretical basis for the technique, and the relationship of the measured jitter of the beam to optical path difference. A numerical simulation of a two-dimensional heated jet is used to explore the validity of beam jitter to obtain optical path difference in a flow region where eddy production constitutes the major character of the 'turbulent' flow field.
Bittrich, Eva; Burkert, Sina; Müller, Martin; Eichhorn, Klaus-Jochen; Stamm, Manfred; Uhlmann, Petra
2012-02-21
Temperature-sensitive poly(N-isopropylacrylamide) (PNIPAAm) brushes with different molecular weights M(n) and grafting densities σ were prepared by the "grafting-to" method. Changes in their physicochemical properties according to temperature were investigated with the help of in situ spectroscopic ellipsometry and in situ attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Brush criteria indicate a transition between a brush conformation below the lower critical solution temperature (LCST) and an intermediate to mushroom conformation above the LCST. By in situ ellipsometry distinct changes in the brush layer parameters (wet thickness, refractive index, buffer content) were observed. A broadening of the temperature region with maximum deswelling occurred with decreasing grafting density. The brush layer properties were independent of the grafting density below the LCST, but showed a virtually monotonic behavior above the LCST. The midtemperature ϑ(half) of the deswelling process increased with increasing grafting density. Thus grafting density-dependent design parameters for such functional films were presented. For the first time, ATR-FTIR spectroscopy was used to monitor segment density and hydrogen bonding changes of these very thin PNIPAAm brushes as a function of temperature based on significant variations of the methyl stretching, Amide I, as well as Amide II bands with respect to intensity and wavenumber position. No dependence on M(n) and σ in the wavenumber shift of these bands above the LCST was found. The temperature profile of these band intensities and thus segment density was found to be rather step-like, exceeding temperatures around the LCST, while the respective profile of their wavenumber positions suggested continuous structural and hydration processes. Remaining buffer amounts and residual intermolecular segment/water interaction in the collapsed brushes above the LCST could be confirmed by both in situ methods.
A molecular Rayleigh scattering setup to measure density fluctuations in thermal boundary layers
Panda, J.
2016-12-01
A Rayleigh scattering-based density fluctuation measurement system was set up inside a low-speed wind tunnel of NASA Ames Research Center. The immediate goal was to study the thermal boundary layer on a heated flat plate. A large number of obstacles had to be overcome to set up the system, such as the removal of dust particles using air filters, the use of photoelectron counting electronics to measure low intensity light, an optical layout to minimize stray light contamination, the reduction in tunnel vibration, and an expanded calibration process to relate photoelectron arrival rate to air density close to the plate surface. To measure spectra of turbulent density fluctuations, a two-PMT cross-correlation system was used to minimize the shot noise floor. To validate the Rayleigh measurements, temperature fluctuations spectra were calculated from density spectra and then compared with temperature spectra measured with a cold-wire probe operated in constant current mode. The spectra from the downstream half of the plate were found to be in good agreement with cold-wire probe, whereas spectra from the leading edge differed. Various lessons learnt are discussed. It is believed that the present effort is the first measurement of density fluctuations spectra in a boundary layer flow.
Directory of Open Access Journals (Sweden)
Daniel B DiGiulio
Full Text Available BACKGROUND: Preterm delivery causes substantial neonatal mortality and morbidity. Unrecognized intra-amniotic infections caused by cultivation-resistant microbes may play a role. Molecular methods can detect, characterize and quantify microbes independently of traditional culture techniques. However, molecular studies that define the diversity and abundance of microbes invading the amniotic cavity, and evaluate their clinical significance within a causal framework, are lacking. METHODS AND FINDINGS: In parallel with culture, we used broad-range end-point and real-time PCR assays to amplify, identify and quantify ribosomal DNA (rDNA of bacteria, fungi and archaea from amniotic fluid of 166 women in preterm labor with intact membranes. We sequenced up to 24 rRNA clones per positive specimen and assigned taxonomic designations to approximately the species level. Microbial prevalence, diversity and abundance were correlated with host inflammation and with gestational and neonatal outcomes. Study subjects who delivered at term served as controls. The combined use of molecular and culture methods revealed a greater prevalence (15% of subjects and diversity (18 taxa of microbes in amniotic fluid than did culture alone (9.6% of subjects; 11 taxa. The taxa detected only by PCR included a related group of fastidious bacteria, comprised of Sneathia sanguinegens, Leptotrichia amnionii and an unassigned, uncultivated, and previously-uncharacterized bacterium; one or more members of this group were detected in 25% of positive specimens. A positive PCR was associated with histologic chorioamnionitis (adjusted odds ratio [OR] 20; 95% CI, 2.4 to 172, and funisitis (adjusted OR 18; 95% CI, 3.1 to 99. The positive predictive value of PCR for preterm delivery was 100 percent. A temporal association between a positive PCR and delivery was supported by a shortened amniocentesis-to-delivery interval (adjusted hazard ratio 4.6; 95% CI, 2.2 to 9.5. A dose
Dependence of Reaction Rate Constants on Density in Supercritical Fluids%超临界流体中反应速率常数与密度的相互关系
Institute of Scientific and Technical Information of China (English)
王涛; 沈忠耀
2002-01-01
A new method, which correlates rate constants of chemical reactions and density or pressure in supercritical fluids, was developed. Based on the transition state theory and thermodynamic principles, the rate constant can be reasonably correlated with the density of the supercritical fluid, and a correlation equation was obtained.Coupled with the equation of state (EOS) of a supercritical solvent, the effect of pressure on reaction rate constant could be represented. Two typical systems were used to test this method. The result indicates that this method is suitable for dilute supercritical fluid solutions.
Kristensen, Kasper; Høyvik, Ida-Marie; Jansik, Branislav; Jørgensen, Poul; Kjærgaard, Thomas; Reine, Simen; Jakowski, Jacek
2012-12-01
Divide-Expand-Consolidate (DEC) is a local correlation method where the inherent locality of the electron correlation problem is used to express the correlated calculation on a large molecular system in terms of small independent fragment calculations employing small subsets of local HF orbitals. A crucial feature of the DEC scheme is that the sizes of the local orbital spaces are determined in a black box manner during the calculation. In this way it is ensured that the correlation energy has been determined to a predefined precision compared to a conventional calculation. In the present work we apply the DEC scheme to calculate the correlation energy as well as the electron density matrix for the insulin molecule using second order Møller-Plesset (MP2) theory. This is the first DEC calculation on a molecular system which is too large to be treated using a conventional MP2 implementation. The fragmentation errors for the insulin DEC calculation are carefully analyzed using internal consistency checks. It is demonstrated that size-intensive properties are determined to the same precision for small and large molecules. For example, the percentage of correlation energy recovered and the error per electron in the correlated density matrix depend only on the predefined precision and not on the molecular size.
Miura, Shinichi; Okazaki, Susumu
2001-09-01
In this paper, the path integral molecular dynamics (PIMD) method has been extended to employ an efficient approximation of the path action referred to as the pair density matrix approximation. Configurations of the isomorphic classical systems were dynamically sampled by introducing fictitious momenta as in the PIMD based on the standard primitive approximation. The indistinguishability of the particles was handled by a pseudopotential of particle permutation that is an extension of our previous one [J. Chem. Phys. 112, 10 116 (2000)]. As a test of our methodology for Boltzmann statistics, calculations have been performed for liquid helium-4 at 4 K. We found that the PIMD with the pair density matrix approximation dramatically reduced the computational cost to obtain the structural as well as dynamical (using the centroid molecular dynamics approximation) properties at the same level of accuracy as that with the primitive approximation. With respect to the identical particles, we performed the calculation of a bosonic triatomic cluster. Unlike the primitive approximation, the pseudopotential scheme based on the pair density matrix approximation described well the bosonic correlation among the interacting atoms. Convergence with a small number of discretization of the path achieved by this approximation enables us to construct a method of avoiding the problem of the vanishing pseudopotential encountered in the calculations by the primitive approximation.
Sofue, Y.; Koda, J.; Kohno, K.; Okumura, S. K.; Honma, M.; Kawamura, A.; Irwin, Judith A.
2001-02-01
We have performed high-resolution synthesis observations of the 12CO (J=1-0) line emission from the radio lobe edge-on spiral galaxy NGC 3079 using a seven-element millimeter-wave interferometer at the Nobeyama Radio Observatory, which consisted of the 45 m telescope and six-element array. The nuclear molecular disk (NMD) of 750 pc radius is found to be inclined by 20° from the optical disk, and the NMD has spiral arms. An ultra-high-density core (UHC) of molecular gas was found at the nucleus. The gaseous mass of the UHC within 125 pc radius is as large as ~3×108 Msolar, an order of magnitude more massive than that in the same area of the Galactic center, and the mean density is as high as ~3×103H2 cm-3. A position-velocity diagram along the major axis indicates that the rotation curve already starts at a finite velocity exceeding 300 km s-1 from the nucleus. The surface mass density in the central region is estimated to be as high as ~105 Msolar pc-2, producing a very deep gravitational potential. We argue that the very large differential rotation in such a deep potential will keep the UHC gravitationally stable during the current star formation.
Csörgö, T; Csanad, M
2007-01-01
A new class of accelerating, exact, explicit and simple solutions of relativistic hydrodynamics is presented. Since these new solutions yield a finite rapidity distribution, they lead to an advanced estimate of the initial energy density and life-time of high energy heavy ion reactions. Accelerating solutions are also given for spherical expansions in arbitrary number of spatial dimensions.
Tretyakov, Nikita; Vollmer, Doris; Butt, Hans-Jürgen; Dünweg, Burkhard; Daoulas, Kostas Ch
2016-01-01
Classical density functional theory is applied to investigate the validity of a phenomenological force-balance description of the stability of the Cassie state of liquids on substrates with nanoscale corrugation. A bulk free-energy functional of third order in local density is combined with a square-gradient term, describing the liquid-vapor interface. The bulk free energy is parameterized to reproduce the liquid density and the compressibility of water. The square-gradient term is adjusted to model the width of the water-vapor interface. The substrate is modeled by an external potential, based upon Lennard-Jones interactions. The three-dimensional calculation focuses on substrates patterned with nanostripes and square-shaped nanopillars. Using both the force-balance relation and density-functional theory, we locate the Cassie-to-Wenzel transition as a function of the corrugation parameters. We demonstrate that the force-balance relation gives a qualitatively reasonable description of the transition even on t...
Shiddiky, Muhammad J. A.; Vaidyanathan, Ramanathan; Rauf, Sakandar; Tay, Zhikai; Trau, Matt
2014-01-01
Early diagnosis of disease requires highly specific measurement of molecular biomarkers from femto to pico-molar concentrations in complex biological (e.g., serum, blood, etc.) samples to provide clinically useful information. While reaching this detection limit is challenging in itself, these samples contain numerous other non-target molecules, most of which have a tendency to adhere to solid surfaces via nonspecific interactions. Herein, we present an entirely new methodology to physically displace nonspecifically bound molecules from solid surfaces by utilizing a newly discovered ``tuneable force'', induced by an applied alternating electric field, which occurs within few nanometers of an electrode surface. This methodology thus offers a unique ability to shear-off loosely bound molecules from the solid/liquid interface. Via this approach, we achieved a 5-fold reduction in nonspecific adsorption of non-target protein molecules and a 1000-fold enhancement for the specific capture of HER2 protein in human serum.
Chemical association in simple models of molecular and ionic fluids. III. The cavity function
Zhou, Yaoqi; Stell, George
1992-01-01
Exact equations which relate the cavity function to excess solvation free energies and equilibrium association constants are rederived by using a thermodynamic cycle. A zeroth-order approximation, derived previously by us as a simple interpolation scheme, is found to be very accurate if the associative bonding occurs on or near the surface of the repulsive core of the interaction potential. If the bonding radius is substantially less than the core radius, the approximation overestimates the association degree and the association constant. For binary association, the zeroth-order approximation is equivalent to the first-order thermodynamic perturbation theory (TPT) of Wertheim. For n-particle association, the combination of the zeroth-order approximation with a ``linear'' approximation (for n-particle distribution functions in terms of the two-particle function) yields the first-order TPT result. Using our exact equations to go beyond TPT, near-exact analytic results for binary hard-sphere association are obtained. Solvent effects on binary hard-sphere association and ionic association are also investigated. A new rule which generalizes Le Chatelier's principle is used to describe the three distinct forms of behaviors involving solvent effects that we find. The replacement of the dielectric-continuum solvent model by a dipolar hard-sphere model leads to improved agreement with an experimental observation. Finally, equation of state for an n-particle flexible linear-chain fluid is derived on the basis of a one-parameter approximation that interpolates between the generalized Kirkwood superposition approximation and the linear approximation. A value of the parameter that appears to be near optimal in the context of this application is obtained from comparison with computer-simulation data.
Park, Hee Eon; Dealy, John M.
2008-07-01
Since high pressures are involved in most plastics forming processes, reliable high-pressure rheological data are required for the simulation of the processes. The effect of pressure is in some ways the reverse of that of temperature; for example increasing temperature decreases the viscosity, while pressure increases it. Supercritical fluids (SCFs) such as carbon dioxide and nitrogen can act as physical blowing agents in the manufacture of foams and as plasticizers to reduce melt viscosity during processing. The effects of dissolved SCF, pressure, and temperature on the rheological properties of a melt must be known to achieve optimum processing conditions. We used a rotational rheometer and a high-pressure sliding plate rheometer, in which the shear strain, temperature, pressure, and SCF concentration are all uniform. A shear stress transducer senses the stress in the center of the sample to avoid edge effects. It was possible to use shift factors for temperature, pressure and SCF (CO2 or N2) concentration to obtain a master curve. The effect of temperature could be described by the Arrhenius or WLF models, and the effect of pressure was described by the Barus equation. The effect of SCF concentration could be described by the Fujita-Kishimoto equation. The relative effects of pressure and temperature on the viscosity were quantified. To study the effects of short and long chain branching and a phenyl side group, three polymers were used: polyethylene, polypropylene, and polystyrene. We quantified the effects of short- and long-chain branching, pressure, temperature and dissolved SCF on the rheological properties of these three polymers by use of shift factors.
Secretory vesicles are preferentially targeted to areas of low molecular SNARE density.
Directory of Open Access Journals (Sweden)
Lei Yang
Full Text Available Intercellular communication is commonly mediated by the regulated fusion, or exocytosis, of vesicles with the cell surface. SNARE (soluble N-ethymaleimide sensitive factor attachment protein receptor proteins are the catalytic core of the secretory machinery, driving vesicle and plasma membrane merger. Plasma membrane SNAREs (tSNAREs are proposed to reside in dense clusters containing many molecules, thus providing a concentrated reservoir to promote membrane fusion. However, biophysical experiments suggest that a small number of SNAREs are sufficient to drive a single fusion event. Here we show, using molecular imaging, that the majority of tSNARE molecules are spatially separated from secretory vesicles. Furthermore, the motilities of the individual tSNAREs are constrained in membrane micro-domains, maintaining a non-random molecular distribution and limiting the maximum number of molecules encountered by secretory vesicles. Together our results provide a new model for the molecular mechanism of regulated exocytosis and demonstrate the exquisite organization of the plasma membrane at the level of individual molecular machines.
TREATMENT OF NONADIABATIC TRANSITIONS BY DENSITY-MATRIX EVOLUTION AND MOLECULAR-DYNAMICS SIMULATIONS
MAVRI, J; BERENDSEN, HJC
1994-01-01
A density matrix evolution (DME) method (H.J.C. Berendsen and J. Mavri, J. Phys. Chem., 97 (1993) 13469) to simulate the dynamics of quantum systems embedded in a classical environment is presented. The DME method allows treatment of nonadiabatic transitions. As numerical examples the collinear coll
Crystal and molecular structure of a second, high-density polymorph of silver malonate
Prakasha Reddy, J.; Foxman, Bruce M.
2008-11-01
A new orthorhombic polymorph of silver malonate ( II) has been synthesized and structurally characterized. Compound II crystallizes in space group Pnma, with a = 12.8180(11), b = 9.2479(8), c = 4.0219(3) Å; V = 476.75(7) Å 3; Z = 4; ρcalc = 4.427 g cm -3. Full-matrix least-squares refinement converged to R1 = 0.0099 ( I > 2 σ( I), 765 data) and w R2 = 0.0264 ( F2, 785 data, 51 parameters). The familiar eight-membered Ag 2(RCO 2) 2 ring, characteristic of most silver(I) carboxylate complexes, has a Ag-Ag distance of 2.977(1) Å. Puckered sheets in the crystal ab plane are connected along c to form a three-dimensional coordination polymer. The density of II is >30% higher than that of the monoclinic polymorph ( I), first characterized in 1981. A survey of the density ratios of polymorphs in the Cambridge Structural Database indicates that virtually all of the pairs of entries having a density ratio >1.2 involve at least one form with significant void volume, as estimated using PLATON. However, neither I nor II have significant void volume, which suggests that the silver malonate polymorphs represent one of the largest density differences observed to date for a polymorphic pair. To date, it has not been possible to prepare I in our laboratories.
Applications of electron density studies in molecular and solid state science
DEFF Research Database (Denmark)
Overgaard, Jacob
2015-01-01
The present dissertation contains the distillate of my scientific output in the field of experimental and theoretical electron density studies roughly over the last decade and a little more, since earning my PhD-degree in 2001. There are several reasons that I have chosen to write my dissertation...
Hirano, Toshiyuki; Sato, Fumitoshi
2014-07-28
We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.
Energy Technology Data Exchange (ETDEWEB)
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
Tsuji, Tetsuro; Iseki, Hirotaka; Hanasaki, Itsuo; Kawano, Satoyuki
2016-11-01
Thermophoresis of a nano particle in a fluid is investigated using molecular dynamics simulation. In order to elucidate effective factors on the characteristics of thermophoresis, simple models for both the fluid and the nano particle are considered, namely, the surrounding fluid consists of Lennard-Jones (LJ) particles and the model nano particle is a cluster consisting of several tens of LJ particles. Interaction between the fluid particle and the model nano particle is described by the LJ interaction potential or repulsive interaction potential with the Lorentz-Berthelot mixing rule. As a preliminary result, the effect of mass on thermophoretic force acting on the model nano particle is investigated for both interaction potentials.
Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets
Miceli, Giacomo; Pasquarello, Alfredo
2016-01-01
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.
Ma, Xiaorong; Li, Huanqi; Xin, Shujia; Ma, Yueting; Ouyang, Tianxiang
2014-01-01
Human embryonic stem cells (hESCs) are pluripotent cells which can give rise to almost all adult cell lineages. Culture system of hESCs is complex, requiring exogenous b-FGF and feeder cell layer. Human mesenchymal stem cells (MSCs) not only synthesize soluble cytokines or factors such as b-FGF, but also provide other mechanism which might play positive role on sustaining hESCs propagation and pluripotency. Human amniotic fluid stem (AFS) cells, which share characteristics of both embryonic and adult stem cells, have been regarded as promising cells for regenerative medicine. Taking advantage by AFS cells, we studied the ability of AFS cells in supporting undifferentiated propagation and pluripotency of Chinese population derived X-01 hESCs. Human AF-type amniotic fluid stem cells (hAF-AFSCs) transcribed genes including Activin A, TGF-β1, Noggin and b-FGF, which involved in maintaining pluripotency and self-renewal of hESCs. Compared to mouse embryonic fibroblasts (MEFs), hAF-AFSCs secreted higher concentration of b-FGF which was important in hESCs culture (P FGF supplementation, keeping undifferentiated status. While exogenous b-FGF was obviated, propagation of hESCs with undifferentiated status was dependent on density of hAF-AFSC feeder layer. Lower density of hAF-AFSCs resulted in rapid decline in undifferentiated clone number, while higher ones hindered the growth of colonies. The most appropriate hAF-AFSCs feeder density to maintain the X-01 hESC line without exogenous b-FGF was 15-20×10(4)/well. To the best of our knowledge, this is the first study demonstrating that hAF-AFSCs could support undifferentiated propagation and pluripotency of Chinese population derived hESCs without exogenous b-FGF supplementation.
Yilmazer, Nusret Duygu; Korth, Martin
2013-07-11
Correctly ranking protein-ligand interactions with respect to overall free energy of binding is a grand challenge for virtual drug design. Here we compare the performance of various quantum chemical approaches for tackling this so-called "scoring" problem. Relying on systematically generated benchmark sets of large protein/ligand model complexes based on the PDBbind database, we show that the performance depends first of all on the general level of theory. Comparing classical molecular mechanics (MM), semiempirical quantum mechanical (SQM), and density functional theory (DFT) based methods, we find that enhanced SQM approaches perform very similar to DFT methods and substantially different from MM potentials.
Institute of Scientific and Technical Information of China (English)
Mingshi SONG; Qiang XU; Guixian HU; Sizhu WU
2006-01-01
A general expression for the correlation of the simple shear(tanφ)to the molecular parameters and the shear rate(γ)was deduced. It shows that the simple shear(tanφ)may be resolved into free recoil(recoverable strain)and viscous heating(unrecoverable strain). The magnitudes of the simple shears for recoil(tanφE)and(tanφv)for viscous heating not only depended on the molecular parameters and the operational variables,but also on the exponential fractions of the recoverable(1-(W)γ)and unrecoverable((W)γ)conformations for recoil and viscous heating. Therefore the magnitudes of the simple shears(tanφE)for recoil and(tanφv)for viscous heating are, respectively, expressed as the partition function to the(1-(W)γ)th power and the partition function to the(-(W)γ)th power. Thus correlations of the total recoil and the ultimately recoverable strains to the molecular parameters [n', a, η0, G0NN and(1--(W)γ)] and the operational variables(·γ, (L/D)and tr)were deduced respectively, which show that at very different shear rates(0≤·γ≤∞)the polymeric liquids may exhibit a very different viscoelastic behaviors. After introducing the uniform two-dimensional extension, the definition of swelling ratio and the ratio of L to D [De=(L/D)], two expressions for the ultimate die swelling effect and the ultimate extrudate swelling ratio BEVT5 to the molecular parameters [n', a, η0, G0N and(1--(W)·γ)] and the operational variables(·γ,(L/D)and tr)were obtained. The two correlation expressions were verified by the experimental data of high-density polyethylene (HDPE) which shows that the two correlation expressions can be used to predict the correlations of the ultimate extrudate swelling behaviors of polymeric liquids to the molecular parameters and the operational variables.
Brandenburg, Jan Gerit; Grimme, Stefan
2014-06-05
The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
Arnheim, Efrat; Chicco, Gaya; Phillips, Mici; Lebel, Ehud; Foldes, A Joseph; Itzchaki, Menachem; Elstein, Deborah; Zimran, Ari; Altarescu, Gheona
2008-07-01
Bone-related complications in Gaucher disease are considered to be poorly responsive to specific enzyme replacement therapy. Polymorphisms of candidate genes associated with low bone density were investigated to see whether they are correlated with bone mineral density (BMD) and bone involvement in Gaucher disease. Genotyping for polymorphisms in candidate genes (interleukins 1alpha and 1beta, interleukin-1 receptor antagonist; cytochrome P450; collagen 1A1; low-density Lipoprotein Receptor; bone morphogenic protein 4; vitamin D receptor; and estrogen receptor 2beta) were performed using standard methodologies. BMD was measured by dual energy X-ray absorptiometry (DXA). One hundred and ninety-four patients and 100 controls were genotyped for the above polymorphisms. Thirteen haplotypes were obtained, with several correlations with BMD in patients; also, a haplotype (T889-T3954-C511-240VNTR of IL1) was significantly correlated with T-scores and Z-score for femur neck and lumbar spine (p = 0.01) in patients. Haplotypes of bone-specific candidate genes associated with BMD may predict severity of these features in Gaucher disease.
Molecular column densities in selected model atmospheres. [chemical analysis of carbon stars
Johnson, H. R.; Beebe, R. F.; Sneden, C.
1974-01-01
From an examination of predicted column densities, the following conclusions were drawn: (1) The SiO ought to be visible in carbon stars which were generated from triple alpha burning, but absent from carbon stars generated from the CNO bi-cycle. (2) Variation in the observed relative strengths of TiO and ZrO is indicative of real differences in the ratio Ti/Zr. (3) The TiO/ZrO ratio shows a small variation as C/O and effective temperature is changed. (4) Column density of silicon dicarbide (SiC2) is sensitive to abundance, temperature, and gravity; hence all relationships between the strength of SiC2 and other stellar parameters will show appreciable scatter. There is however, a substantial luminosity effect present in the SiC2 column densities. (5) Unexpectedly, SiC2 is anti-correlated with C2. (6) The presence of SiC2 in a carbon star eliminates the possibility of these stars having temperatures greater than or equal to 3000 K, or being produced through the CNO bi-cycle.
Transport Coefficients of Fluids
Eu, Byung Chan
2006-01-01
Until recently the formal statistical mechanical approach offered no practicable method for computing the transport coefficients of liquids, and so most practitioners had to resort to empirical fitting formulas. This has now changed, as demonstrated in this innovative monograph. The author presents and applies new methods based on statistical mechanics for calculating the transport coefficients of simple and complex liquids over wide ranges of density and temperature. These molecular theories enable the transport coefficients to be calculated in terms of equilibrium thermodynamic properties, and the results are shown to account satisfactorily for experimental observations, including even the non-Newtonian behavior of fluids far from equilibrium.
Directory of Open Access Journals (Sweden)
Narimatsu C.P.
2001-01-01
Full Text Available In this work, the effects of particle size and density on the fluid dynamic behavior of vertical gas-solid transport of Group D particles in a 53.4 mm diameter transport tube were studied. For the conditions tested, the experimental curves of pressure gradient versus air velocity presented a minimum pressure gradient point, which is associated with a change in the flow regime from dense to dilute phase. The increases in particle size from 1.00 to 3.68 mm and in density from 935 to 2500 kg/m³ caused an increase in pressure gradient for the dense-phase transport region, but were not relevant in dilute transport. The transition velocity between dense and dilute flow (Umin also increased with increasing particle density and diameter. An empirical equation was fitted for predicting transition air velocity for the transport of glass spheres. Additional experiments, covering a wider range of conditions and particles properties, are still needed to allow the fitting of a generalized equation for prediction of Umin.
Schellart, W. P.
2011-06-01
Analogue models of lithospheric deformation and fluid dynamic models of mantle flow mostly use some kind of syrup such as honey or glucose syrup to simulate the low-viscosity sub-lithospheric mantle. This paper describes detailed rheological tests and density measurements of three brands of glucose syrup and three brands of honey. Additional tests have been done for one brand of glucose syrup that was diluted with water to various degrees (2%, 5% and 10% by weight). The rheological tests have been done to test the effect of shear strain, shear rate and temperature on the dynamic viscosity of the syrup. The results show that the viscosity of all glucose syrups and honeys is independent of shear strain (i.e. no strain hardening or softening). The viscosity of the glucose syrups is independent of shear rate (γ˙), i.e. linear-viscous or Newtonian, in the range γ˙=10-4-10 s with stress exponents that are almost identical to one ( n = 0.995-1.004). All the honeys show a very weak, but consistent, decrease in viscosity with increasing shear rate of 7-14% from 10 -3 to 10 0 s -1 and have stress exponents more distinct from one ( n = 1.007-1.026). All syrups have a viscosity that is strongly dependent on temperature in the range 0-50 °C, where viscosity decreases with increasing temperature. Such decrease can be fitted with exponential and Arrhenius functions, with the latter giving the best results. Furthermore, the viscosity of glucose syrup decreases approximately exponentially with increasing water content. Oscillation tests indicate that the rheology of all the syrups is entirely dominated by viscous behaviour and not by elastic behaviour at frequencies of 10 -3-10 2 Hz. Finally, the density investigations show that the density of glucose syrup and honey decreases approximately linearly with increasing temperature in the range 10-70 °C, with coefficients of thermal volumetric expansion at 20 °C of 3.89-3.95 × 10 -4 °C -1 and 4.57-4.81 × 10 -4 °C -1 for
Faraji, Fahim; Rajabpour, Ali
2016-09-01
In this paper we investigate the fluid transport inside a single-wall carbon nanotube induced by a temperature gradient along the tube length, focusing on the effect of fluid-wall interaction strength. It is found that the fluid moves from the hot side of the nanotube towards the cold side. By increasing the fluid-wall interaction strength, the fluid volumetric flux assumes a maximum, increases, and then decreases. Fluid transport is pressure-driven in weak interactions; in contrast, in strong interactions, the fluid is broken into two parts in the radial direction. Fluid transport in the central regions of the tube is pressure-driven, while it is surface-driven in the areas close to the wall.
Directory of Open Access Journals (Sweden)
Yvonne Förster
Full Text Available Bone healing involves a variety of different cell types and biological processes. Although certain key molecules have been identified, the molecular interactions of the healing progress are not completely understood. Moreover, a clinical routine for predicting the quality of bone healing after a fracture in an early phase is missing. This is mainly due to a lack of techniques to comprehensively screen for cytokines, growth factors and metabolites at their local site of action. Since all soluble molecules of interest are present in the fracture hematoma, its in-depth assessment could reveal potential markers for the monitoring of bone healing. Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids. By using a control group with an isolated soft tissue wound, we could reveal several bone defect-specific molecular features. In bone defect dialysates the neutrophil chemoattractants CXCL1, CXCL2 and CXCL3 were quantified with either a higher or earlier response compared to dialysate from soft tissue wound. Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified to be specific for the bone defect group, e.g. immune modulators, proteases and their corresponding inhibitors. Additionally, the metabolite screening revealed different profiles between the bone defect group and the control group. In summary, we identified potential biomarkers to indicate imbalanced healing progress on all levels of analysis.
Capitán, José A; Cuesta, José A
2007-07-01
In this article we obtain a fundamental measure functional for the model of aligned hard hexagons in the plane. Our aim is not just to provide a functional for an admittedly academic model, but to investigate the structure of fundamental measure theory. A model of aligned hard hexagons has similarities with the hard disk model. Both share "lost cases," i.e. admit configurations of three particles in which there is pairwise overlap but not triple overlap. These configurations are known to be problematic for fundamental measure functionals, which are not able to capture their contribution correctly. This failure lies in the inability of these functionals to yield a correct low density limit of the third order direct correlation function. Here we derive the functional by projecting aligned hard cubes on the plane x+y+z=0 . The correct dimensional crossover behavior of these functionals permits us to follow this strategy. The functional of aligned hard cubes, however, does not have lost cases, so neither had the resulting functional for aligned hard hexagons. The latter exhibits, in fact, a peculiar structure as compared to the one for hard disks. It depends on a uniparametric family of weighted densities through an additional term not appearing in the functional for hard disks. Apart from studying the freezing of this system, we discuss the implications of the functional structure for further developments of fundamental measure theory.
Sheeja, Manaf, O.; Sujith, A.
2017-06-01
Polymer modification by radiation grafting of monomers onto polymers has received much attention recently. In the current study, γ-irradiation technique was used to achieve graft copolymerization of maleic anhydride (MA) onto low-density polyethylene (LDPE). To optimize, the process was performed at different γ-irradiation doses and MA concentration. The microstructure of grafted polymer film has been characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, field emission-scanning electron microscopy, and atomic force microscopy. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield.
Matoga, M; Péhourcq, F; Lagrange, F; Tramu, G; Bannwarth, B
1999-06-01
The diffusion of seven arylpropionic acid non-steroidal anti-inflammatory drugs (NSAIDs) into the cerebrospinal fluid (CSF) has been investigated in male Wistar rats by means of quantitative structure-activity relationship (QSAR) study. After intraperitoneal administration of each drug (5 mg/kg), blood and CSF samples were collected at different times (0.5, 1, 3, and 6 h). The fraction bound to plasma proteins (fb) was determined using ultracentrifugation. The total (CT) and free (CF) plasma concentrations and the concentrations in CSF (CCSF) were measured by a reversed-phase high performance liquid chromatographic (RP-HPLC) method. The areas under the curve of the free plasma (AUCF) and CSF (AUCCSF) concentrations were calculated according to the trapezoidal rule. The overall drug transit into CSF was estimated by the ratio RAUC (AUCCSF: AUCF). The lipophilicity of the compounds was expressed as their polycratic capacity factors (log k'w) measured in a RP-HPLC system. The RAUC ranged from 0.24 to 6.58 and fb from 91.4 to 99.8%. The compounds with an intermediate lipophilicity value (3 RAUC > 1). A parabolic relationship was found between log k'w and log RAUC, emphasizing the role of molecular lipophilicity in the diffusion into CSF. Considering the fb value of each drug in regard to this non-linear relationship, it can be hypothesized that the diffusion rate of NSAIDs into the CSF depends primarily on the lipophilicity.
Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer
2009-12-01
We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.
Smith, William R.; Jirsák, Jan; Nezbeda, Ivo; Qi, Weikai
2017-07-01
The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. We describe the correct methodology required to perform such calculations and illustrate it in this paper for the case of the internal energy and the enthalpy and their corresponding molar heat capacities. We provide numerical results for cP, one of the most important caloric properties. We also consider approximations to the correct calculation procedure previously used in the literature and illustrate their consequences for the examples of the relatively simple molecule 2-propanol, CH3CH(OH)CH3, and for the more complex molecule monoethanolamine, HO(CH2)2NH2, an important fluid used in carbon capture.
Towards a generalized iso-density continuum model for molecular solvents in plane-wave DFT
Gunceler, Deniz; Arias, T. A.
2017-01-01
Implicit electron-density solvation models offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from first-principles quantum mechanics. However, despite much recent interest in such models, to date the applicability of such models in the plane-wave context to non-aqueous solvents has been limited because the determination of the model parameters requires fitting to a large database of experimental solvation energies for each new solvent considered. This work presents a simple approach to quickly find approximations to the non-electrostatic contributions to the solvation energy, allowing for development of new iso-density models for a large class of protic and aprotic solvents from only simple, single-molecule ab initio calculations and readily available bulk thermodynamic data. Finally, to illustrate the capabilities of the resulting theory, we also calculate the surface solvation energies of crystalline LiF in various different non-aqueous solvents, and discuss the observed trends and their relevance to lithium battery technology.
Senet, P; Aparicio, F
2007-04-14
By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology.
Partovi-Azar, Pouya; Kaghazchi, Payam
2017-04-15
We report on real-time time-dependent density functional theory calculations on direction-dependent electron and hole transfer processes in molecular systems. As a model system, we focus on α-sulfur. It is shown that time scale of the electron transfer process from a negatively charged S8 molecule to a neighboring neutral monomer is comparable to that of a strong infrared-active molecular vibrations of the dimer with one negatively charged monomer. This results in a strong coupling between the electrons and the nuclei motion which eventually leads to S8 ring opening before the electron transfer process is completed. The open-ring structure is found to be stable. The similar infrared-active peak in the case of hole transfer, however, is shown to be very weak and hence no significant scattering by the nuclei is possible. The presented approach to study the charge transfer processes in sulfur has direct applications in the increasingly growing research field of charge transport in molecular systems. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Nandi, Rana
2016-01-01
We study the effect of isospin-dependent nuclear forces on the pasta phase in the inner crust of neutron stars. To this end we model the crust within the framework of quantum molecular dynamics (QMD). For maximizing the numerical performance, the newly developed code has been implemented on GPU processors. As a first application of the crust studies we investigate the dependence of the particular pasta phases on the slope of the symmetry energy slope L. To isolate the effect of different values of L, we adopt an established QMD Hamiltonian and extend it to include non-linear terms in the isospin-dependent interaction. The strengths of the isospin-dependent forces are used to adjust the asymmetry energy and slope of the matter. Our results indicate that in contrast to earlier studies the phase diagram of the pasta phase is not very sensitive to the value of L.
Reduction in the crystal defect density of Zn Se layers grown by molecular beam epitaxy
Energy Technology Data Exchange (ETDEWEB)
Lopez L, M.; Perez C, A.; Luyo A, J.; Melendez L, M.; Tamura, M. [Departamento de Fisica, Centro de Investigacion y de Estudios Avanzados del instituto politecnico Nacional, A.P. 14-740, 07000 Mexico D.F. (Mexico); Mendez G, V.H.; Vidal, M.A. [Instituto de Investigacion en Comunicacion Optica, Universidad Autonoma de San Luis Potosi, Alvaro Obregon 64, 78000 San Luis Potosi (Mexico)
2000-07-01
We present a study of the molecular beam epitaxial (MBE) grown of Zn Se layers on Ga-As and Si substrates. For the growth on GaAs substrates we investigated the effects of introducing buffer layers of Al{sub x}Ga{sub 1-x} As and In{sub x}Ga{sub 1-x} As with x = 0.01. Moreover, an analysis by secondary ion mass spectroscopy revealed that the use of AlGaAs buffer layers effectively suppress the Ga segregation onto the Zn Se layers surface. On the other hand, for the growth of Zn Se on Si substrates, we achieved a significant improvement in the crystal quality of Zn Se by irradiating the Si substrates with plasma of nitrogen prior to the growth. (Author)
Sagdinc, Seda; Kandemirli, Fatma; Bayari, Sevgi Haman
2007-02-01
Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.
Wu, Jun; Gygi, François
2012-06-01
We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Based on the density functional theory and the atom-bond electronegativity equalization model (ABEEM), a method is proposed to construct the softness matrix and to obtain the electron population normal modes (PNMs) for a closed system. Using this method the information about the bond charge polarization in a molecule can be obtained easily. The test calculation shows that the PNM obtained by this method includes all the modes about the bond charge polarization explicitly. And the bond charge polarization mode characterized by the biggest eigenvalue, which is the softest one of all modes related with chemical bonds, can describe the charge polarization process in a molecule as exquisitely as the corresponding ab initio method.
Theoretical modelling of photoactive molecular systems: insights using the Density Functional Theory
Energy Technology Data Exchange (ETDEWEB)
Ciofini, I.; Adamo, C. [Ecole Nationale Superieure de Chimie de Paris, Lab. d' Electrochimie et Chimie Analytique, CNRS UMR 7575, 75 - Paris (France); Laine, Ph.P. [Universite Rene-Descartes, Lab. de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, 75 - Paris (France); Bedioui, F. [Ecole Nationale Superieure de Chimie de Paris, Lab. de Pharmacologie Chimique et Genetique, CNRS FRE 2463 and INSERM U 640, 75 - Paris (France); Daul, C.A. [Fribourg Univ., Dept. de Chimie (Switzerland)
2006-02-15
An account of the performance of a modern and efficient approach to Density Functional Theory (DFT) for the prediction of the photophysical behavior of a series of Ru(II) and Os(II) complexes is given. The time-dependent-DFT method was used to interpret their electronic spectra. Two different types of compounds have been analyzed: (1) a complex undergoing a light induced isomerization of one of its coordination bonds; (2) an inorganic dyads expected to undergo intramolecular photoinduced electron transfer to form a charge separated (CS) sate. Besides the noticeable quantitative agreement between computed and experimental absorption spectra, our results allow to clarify, by first principles, both the nature of the excited states and the photochemical behavior of these complex systems, thus underlying the predictive character of the theoretical approach. (authors)
Hartkorn, Oliver; Saur, Joachim; Strobel, Darrell F.
2017-01-01
We develop a model of the ionospheric electron population of Jupiter's moon Callisto using a prescribed neutral atmosphere composed of O2, CO2 and H2O. A kinetic description of ionospheric suprathermal electrons coupled with a fluid description of ionospheric thermal electrons is well suited to jointly analyze and interpret observations of electron density and atmospheric UV emission. Accordingly, we calculate the electron energy distribution function at each point in the ionosphere by solving a coupled set of equations consisting of the Boltzmann equation for suprathermal electrons and the continuity and energy equation for thermal electrons. We assume a stationary balance between local sources and sinks of electrons and electron energy. Electron transport within the ionosphere is neglected, since collision time scales are shorter than transport time scales in the region of Callisto's ionosphere where the major concentrations of electrons is located and the major part of the atmospheric UV emission is generated. We consider photoionization, which is the dominant ionospheric electron source, and secondary ionization from collisions of photoelectrons with neutrals. Our calculations yield electron densities and electron impact generated UV emissions from Callisto's atmosphere. Comparing our modeled UV emission intensities with the Hubble Space Telescope observation of Cunningham et al. (2015) , we find that Callisto's atmosphere has a mean O2 column density of 2.1-1.1+1.1 ×1019 m-2. A joint comparison with this HST observation and radio occultation observations of Kliore et al. (2002) shows that Callisto's atmosphere possesses a day night asymmetry. We derive terminator O2 column densities of ∼ 0.4 × 1019 m-2 , for which we find subsolar O2 column densities in the range of 2.4 - 9.8 ×1019 m-2. Our calculations also show that the electron density is very sensitive to the relative abundance of H2O due to the thermal electron cooling by rotational state excitation
Roemelt, Michael
2015-07-01
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
A mesoscopic model for binary fluids
Echeverria, C; Alvarez-Llamoza, O; Orozco-Guillén, E E; Morales, M; Cosenza, M G
2016-01-01
We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule to simulate segregation processes that does not require the calculation of the interaction forces between particles, thus allowing the description of binary fluids at a mesoscopic scale. The model is conceptually simple, computationally efficient, maintains Galilean invariance, and conserves the mass and the energy in the system at micro and macro scales; while momentum is conserved globally. For a wide range of temperatures and densities, the model yields results in good agreement with the known properties of binary fluids, such as density profile, width of the interface, phase separation and phase growth. We also apply the model to study binary fluids in crowded environments with consistent results.
Hughes, Adam P.; Thiele, Uwe; Archer, Andrew J.
2017-02-01
For a film of liquid on a solid surface, the binding potential g(h) gives the free energy as a function of the film thickness h and also the closely related (structural) disjoining pressure Π =-∂g /∂h . The wetting behaviour of the liquid is encoded in the binding potential and the equilibrium film thickness corresponds to the value at the minimum of g(h). Here, the method we developed in the work of Hughes et al. [J. Chem. Phys. 142, 074702 (2015)], and applied with a simple discrete lattice-gas model, is used with continuum density functional theory (DFT) to calculate the binding potential for a Lennard-Jones fluid and other simple liquids. The DFT used is based on fundamental measure theory and so incorporates the influence of the layered packing of molecules at the surface and the corresponding oscillatory density profile. The binding potential is frequently input in mesoscale models from which liquid drop shapes and even dynamics can be calculated. Here we show that the equilibrium droplet profiles calculated using the mesoscale theory are in good agreement with the profiles calculated directly from the microscopic DFT. For liquids composed of particles where the range of the attraction is much less than the diameter of the particles, we find that at low temperatures g(h) decays in an oscillatory fashion with increasing h, leading to highly structured terraced liquid droplets.
Nold, Andreas; Sibley, David N.; Goddard, Benjamin D.; Kalliadasis, Serafim
2014-07-01
We examine the nanoscale behavior of an equilibrium three-phase contact line in the presence of long-ranged intermolecular forces by employing a statistical mechanics of fluids approach, namely, density functional theory (DFT) together with fundamental measure theory (FMT). This enables us to evaluate the predictive quality of effective Hamiltonian models in the vicinity of the contact line. In particular, we compare the results for mean field effective Hamiltonians with disjoining pressures defined through (i) the adsorption isotherm for a planar liquid film, and (ii) the normal force balance at the contact line. We find that the height profile obtained using (i) shows good agreement with the adsorption film thickness of the DFT-FMT equilibrium density profile in terms of maximal curvature and the behavior at large film heights. In contrast, we observe that while the height profile obtained by using (ii) satisfies basic sum rules, it shows little agreement with the adsorption film thickness of the DFT results. The results are verified for contact angles of 20°, 40°, and 60°.
High Density Molecular Gas in the IR-bright Galaxy System VV114
Iono, D; Yun, M S; Matsushita, S; Peck, A B; Sakamoto, K
2004-01-01
New high resolution CO(3-2) interferometric map of the IR-bright interacting galaxy system VV114 observed with the Submillimeter Array (SMA) reveal a substantial amount of warm and dense gas in the IR-bright but optically obscured galaxy, VV114E, and the overlap region connecting the two nuclei. A 1.8 x 1.4 kpc concentration of CO(3-2) emitting gas with a total mass of 4 x 10^9 Msun coincides with the peaks of NIR, MIR, and radio continuum emission found previously by others, identifying the dense fuel for the AGN and/or the starburst activity there. Extensive CO(2-1) emission is also detected, revealing detailed distribution and kinematics that are consistent with the earlier CO(1-0) results. The widely distributed molecular gas traced in CO(2-1) and the distributed discrete peaks of CO(3-2) emission suggest that a spatially extended intense starbursts may contribute significantly to its large IR luminosity. These new observations further support the notion that VV114 is approaching its final stage of merger...
Lischner, Johannes; Arias, T A
2010-02-11
We present an accurate free-energy functional for liquid water written in terms of a set of effective potential fields in which fictitious noninteracting water molecules move. The functional contains an exact expression of the entropy of noninteracting molecules and thus provides an ideal starting point for the inclusion of complex intermolecular interactions which depend on the orientation of the interacting molecules. We show how an excess free-energy functional can be constructed to reproduce the following properties of water: the dielectric response; the experimental site-site correlation functions; the surface tension; the bulk modulus of the liquid and the variation of this modulus with pressure; the density of the liquid and the vapor phase; and liquid-vapor coexistence. As a demonstration, we present results for the application of this theory to the behavior of liquid water in a parallel plate capacitor. In particular, we make predictions for the dielectric response of water in the nonlinear regime, finding excellent agreement with known data.
Templated high density lipoprotein nanoparticles as potential therapies and for molecular delivery.
Damiano, Marina G; Mutharasan, R Kannan; Tripathy, Sushant; McMahon, Kaylin M; Thaxton, C Shad
2013-05-01
High density lipoproteins (HDLs) are dynamic natural nanoparticles best known for their role in cholesterol transport and the inverse correlation that exists between blood HDL levels and the risk of developing coronary heart disease. In addition, enhanced HDL-cholesterol uptake has been demonstrated in several human cancers. As such, the use of HDL as a therapeutic and as a vehicle for systemic delivery of drugs and as imaging agents is increasingly important. HDLs exist on a continuum from the secreted HDL-scaffolding protein, apolipoprotein A-1 (Apo A1), to complex, spherical "mature" HDLs. Aspects of HDL particles including their size, shape, and surface chemical composition are being recognized as critical to their diverse biological functions. Here we review HDL biology; strategies for synthesizing HDLs; data supporting the clinical use and benefit of directly administered HDL; a rationale for developing synthetic methods for spherical, mature HDLs; and, the potential to employ HDLs as therapies, imaging agents, and drug delivery vehicles. Importantly, methods that utilize nanoparticle templates to control synthetic HDL size, shape, and surface chemistry are highlighted. Copyright © 2012 Elsevier B.V. All rights reserved.
van de Streek, Jacco; Neumann, Marcus A
2010-10-01
This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.
Corrales, Isabel; Giménez, Estela; Aguilar, Gerardo; Delgado, Carlos; Puig, Jaime; Izquierdo, Ana; Belda, Javier; Navarro, David
2015-02-01
Microbiological documentation of peritoneal candidiasis (PC) is hampered by the low numbers of yeasts observable by direct microscopic examination and recoverable by culture methods. The performance of a polymerase chain reaction (PCR) DNA Low-Density Microarray System (CLART STIs B) was compared to that of BACTEC FX automated culture method for the detection of Candida spp. in 161 peritoneal fluids (PF) from patients with peritonitis. The clinical utility of (1-3)-β-d-glucan (BDG) antigenemia in the diagnosis of PC was evaluated in 42 of these patients. The overall agreement between the PCR assay and the culture method was good (κ = 0.790), and their sensitivities were 93.5% and 74.19%, respectively. Serum BDG levels in patients with Candida spp. in PFs (median, 200.3 pg/mL; Range, 22.0-523.4 pg/mL) was significantly higher (P = 0.002) than those found in patients without the yeast (median, 25.3 pg/mL; Range, 0-523.4 pg/mL). Our study demonstrates the potential clinical utility of molecular methods and the measurement of serum BDG levels for the diagnosis of PC.
Wungu, T. D. K.; Marsha, S. E.; Widayani; Suprijadi
2017-07-01
In order to find an alternative biosensor material which enables to detect the glucose level, therefore in this study, the interaction between Methacrylic Acid (MAA) based Molecularly Imprinted Polymer (MIP) with D-Glucose is investigated using the Density Functional Theory (DFT). The aim of this study is to determine whether a molecule of the MAA can be functioned as a bio-sensing of glucose. In this calculation, the Gaussian 09 with B3LYP and 631+G(d) basis sets is used to calculate all electronic properties. It is found that the interaction between a molecule of MAA and a molecule of D-Glucose was observed through the shortened distance between the two molecules. The binding energy of MAA/D-glucose and the Mulliken population analysis are investigated for checking possible interaction. From analysis, the MAA based MIP can be used as a bio-sensing material.
Density functional and molecular dynamics studies of solid electrolyte Li7La3Zr2O12
Johannes, Michelle; Hoang, Khang; Bernstein, Noam
2012-02-01
Garnet-type structured Li7La3Zr2O12(LLZO) is considered as a promising candidate for Li-ion battery solid electrolytes because of its high ionic conductivity and electrochemical and chemical stability. We use first-principles density-functional theory calculations and molecular dynamics simulations to reveal the underlying mechanism that drives a tetragonal to cubic transition at elevated temperatures, and also to explain why the cubic phase can be stabilized with the incorporation of a certain amount of impurities such as Al. We show that the relationship between the observance of a cubic phase and the measurement of a substantially higher ionic conductivity is a secondary effect not directly attributable to the presence of Al in the crystal structure. Suggestions for enhancing the ionic conductivity in LLZO will also be discussed.
DEFF Research Database (Denmark)
van de Streek, Jacco; Neumann, Marcus A
2014-01-01
is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.......In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published...... minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom...
Cummins, S. E.; Green, S.; Thaddeus, P.; Linke, R. A.
1983-01-01
Observations of the K components of the CH3CN J = 4-to-3 rotational transition at 73.6 GHz, the 6-to-5 transition at 110.4 GHz, and the 7-to-6 transition at 128.7 GHz, yield a mean kinetic temperature value of 85 + or - 10 K and a mean H2 density of 110,000 + or - 50,000/cu cm for the central 2.0 arcmin of the Sgr B2 molecular cloud. Within the K = zero-to-4 ladders of CH3CN in Sgr B2, the populations of the radiatively coupled J levels are relaxed and exhibit a rotational temperature of about 16 K, which is similar to that of several linear molecules.
Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.
2016-10-01
The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.
Thermophysical Properties of Fluids and Fluid Mixtures
Energy Technology Data Exchange (ETDEWEB)
Sengers, Jan V.; Anisimov, Mikhail A.
2004-05-03
The major goal of the project was to study the effect of critical fluctuations on the thermophysical properties and phase behavior of fluids and fluid mixtures. Long-range fluctuations appear because of the presence of critical phase transitions. A global theory of critical fluctuations was developed and applied to represent thermodynamic properties and transport properties of molecular fluids and fluid mixtures. In the second phase of the project, the theory was extended to deal with critical fluctuations in complex fluids such as polymer solutions and electrolyte solutions. The theoretical predictions have been confirmed by computer simulations and by light-scattering experiments. Fluctuations in fluids in nonequilibrium states have also been investigated.
Lv, Bei'er; Zhou, Yitian; Cha, Wenli; Wu, Yuanzi; Hu, Jinxing; Li, Liqiang; Chi, Lifeng; Ma, Hongwei
2014-06-11
In previous studies, we reported the first observation of the Au-S bond breakage induced mechanically by the swelling of the surface-tethered weak polyelectrolyte brushes in phosphate buffered saline (PBS), a phenomenon with broad applications in the fields of biosensors and functional surfaces. In this study, three factors, namely the molecular composition, grafting density and film area of the weak polyelectrolyte, carboxylated poly(oligo(ethylene glycol) methacrylate-random-2-hydroxyethyl methacrylate) (poly(OEGMA-r-HEMA)), were studied systematically on how they affected the swelling-induced Au-S bond breakage (ABB). The results showed that, first, the swelling-induced ABB is applicable to a range of molecular compositions and grafting densities; but the critical thickness (Tcritical,dry) varied with both of the two factors. An analysis on the swelling ratio further revealed that the difference in the Tcritical,dry arose from the difference in the swelling ability. A film needed to swell to ∼250 nm to induce ABB regardless of its composition or structure, thus a higher swelling ratio would lead to a lower Tcritical,dry value. Then, the impact of the film area was studied in micrometer- and sub-micrometer-scale brush patterns, which showed that only partial, rather than complete ABB was induced in these microscopic films, resulting in buckling instead of film detaching. These results demonstrated that the ABB is suitable to be used in the design of biosensors, stimulus-responsive materials and mechanochemical devices. Although the >160 μm(2) required area for uniform ABB hinders the application of ABB in nanolithography, the irreversible buckling provides a facile method of generating rough surfaces.
Bertram, Erik; Clark, Paul C; Ragan, Sarah E; Klessen, Ralf S
2015-01-01
We run numerical simulations of molecular clouds (MCs), adopting properties similar to those found in the Central Molecular Zone (CMZ) of the Milky Way. For this, we employ the moving mesh code Arepo and perform simulations which account for a simplified treatment of time-dependent chemistry and the non-isothermal nature of gas and dust. We perform simulations using an initial density of n_0 = 10^3 cm^{-3} and a mass of 1.3x10^5 M_sun. Furthermore, we vary the virial parameter, defined as the ratio of kinetic and potential energy, alpha = E_{kin} / |E_{pot}|. We set it to alpha = 0.5, 2.0 and 8.0, in order to analyze the impact of the kinetic energy on our results. We account for the extreme conditions in the CMZ and increase both the interstellar radiation field (ISRF) and the cosmic-ray flux (CRF) by a factor of 1000 compared to the values found in the solar neighbourhood. We use the radiative transfer code RADMC-3D to compute synthetic images in various diagnostic lines. These are [CII] at 158 micron, [OI]...
Institute of Scientific and Technical Information of China (English)
刘伟龙; 王志刚; 郑植仁; 蒋礼林; 杨延强; 赵连城; 苏文辉
2012-01-01
The molecular structural and Raman spectroscopic characteristics of fl-carotene and lycopene are investigated by density functional calculations. The effects of molecular structure and solvent environment on the Raman spectra are analyzed by comparing the calculated and measured results. It is found that the B3LYP/6-31G(d) method can predict the reasonable result for β-carotene, but the vl Raman activities of lycopene overflow at all the used theo- retical methods because of the longer conjugation length in β-carotene impedes the delocalization of ~r-electrons The calculated results indicate that the rotation of β-rings shortens the effective conjugation length, and results in higher frequency and lower activity of the vl mode in /q-carotene than lycopene. The measured vl bands of β-carotene and lycopene shift respectively to higher and lower frequencies in solution compared with that in crystals since the crystal packing forces can lead to different conformational variations in the carotenoids molecules. The polarized continuum model theoretical analysis suggests that solvent has slight (significant) effects on the Raman frequencies (intensities) of both carotenoids.
Xu, Jie; Wang, Lei; Liang, Guijie; Bai, Zikui; Wang, Luoxin; Xu, Weilin; Shen, Xiaolin
2011-01-01
The molecular structures and absorption spectra of triphenylamine dyes containing variable thiophene units as the spacers (TPA1-TPA3) were investigated by density functional theory (DFT) and time-dependent DFT. The calculated results indicate that the strong conjugation is formed in the dyes and the length of conjugate bridge increases gradually with the increased thiophene spacers. The interfacial charge transfer between the TiO2 electrode and TPA1-TPA3 are electron injection processes from the excited dyes to the semiconductor conduction band. The simulated absorption bands are assigned to π→π* transitions, which exhibit appreciable red-shift with respect to the experimental bands due to the lack of direct solute-solvent interaction and the inherent approximations in TD-DFT. The effect of thiophene spacers on the molecular structures, absorption spectra and photovoltaic performance were comparatively discussed and points out that the choice of appropriate conjugate bridge is very important for the design of new dyes with improved performance.
Gidofalvi, Gergely; Mazziotti, David A
2007-01-14
Molecular ground-state energies and two-electron reduced density matrices (2-RDMs) have recently been computed without the many-electron wave function by constraining the 2-RDM to satisfy a complete set of three-positivity conditions for N representability [D. A. Mazziotti, Phys. Rev. A 74, 032501 (2006)]. Energies at both equilibrium and nonequilibrium geometries are obtained within 0.3% of the correlation energy. In this paper the authors extend this work to examine the accuracy of molecular properties, including multipole moments and components of the ground-state energy, relative to full configuration interaction (FCI). Comparisons are also made with 2-RDM methods with two-positivity conditions and two-positivity plus the generalized T1T2 conditions as well as several approximate wave function methods. Using the 2-RDM method with three-positivity conditions, the authors obtain dipole, quadrupole, and octupole moments for BeH2, BH, H2O, CO, and NH3 at equilibrium geometries that are within 0.04% of their FCI values. In addition, for the potential energy surface of N2, the 2-RDM method with three-positivity yields not only accurate total ground-state energies but also accurate expectation values of the kinetic energy operator, the electron-nuclei potential, and electron-electron repulsion.
Martínez de la Hoz, Julibeth M; Balbuena, Perla B
2013-07-01
We report calculated vibrational spectra in the range of 0-3,500 cm(-1) of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) molecules adsorbed on a model aluminum surface. A molecular film was modeled using two approaches: (1) density functional theory (DFT) was used to optimize a single RDX molecule interacting with its periodic images, and (2) a group of nine molecules extracted from the crystal structure was deposited on the surface and interacted with its periodic images via molecular dynamics (MD) simulations. In both cases, the molecule was initialized in the AAA conformer geometry having the three nitro groups in axial positions, and kept that conformation in the DFT examination, but some molecules were found to change to the AAE conformer (two nitro groups in axial and one in equatorial position) in the MD analysis. The vibrational spectra obtained from both methods are similar to each other, except in the regions where collective RDX intermolecular interactions (captured by MD simulations) are important, and compare fairly well with experimental findings.
The interface of SrTiO3 and H2O from density functional theory molecular dynamics
Holmström, E.; Spijker, P.; Foster, A. S.
2016-09-01
We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO3/H2O solid-liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO2 termination and 5% on the stepped TiO2-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to H2O bonding and surface corrugation. We find a featureless electronic density of states in and around the band gap energy region at the solid-liquid interface. The vibrational spectrum indicates redshifting of the O-H stretching band due to surface-to-liquid hydrogen bonding and blueshifting due to high-frequency stretching vibrations of OH fragments within the liquid, as well as strong suppression of the OH stretching band on the stepped surface. We find highly varying rates of proton transfer above different SrTiO3 surfaces, owing to differences in hydrogen bond strength and the degree of dissociation of incident water. Trends in proton dynamics and the mode of H2O adsorption among studied surfaces can be explained by the differential ionicity of the Ti-O and Sr-O bonds in the SrTiO3 crystal.
Energy Technology Data Exchange (ETDEWEB)
López-Santiago, J.; Ustamujic, S.; Castro, A. I. Gómez de [S. D. Astronomía y Geodesia, Facultad de Ciencias Matemáticas, Universidad Complutense de Madrid, E-28040 Madrid (Spain); Bonito, R.; Orlando, S. [Dipartimento di Fisica e Chimica, Università di Palermo, Piazza del Parlamento 1, I-90134 Palermo (Italy); Orellana, M. [Sede Andina de la Universidad Nacional de Río Negro (Argentina); Miceli, M. [INAF-Osservatorio Astronomico di Palermo, Piazza del Parlamento 1, I-90134 Palermo (Italy); Albacete-Colombo, J. F. [Sede Atlántica de la Universidad Nacional de Río Negro, Don Bosco y Leloir s/n, 8500 Viedma RN (Argentina); Castro, E. de [Dpto. de Astrofísica y CC. de la Atmósfera, Facultad de Física, Universidad Complutense de Madrid, E-28040 Madrid (Spain)
2015-06-10
We investigate the plausibility of detecting X-ray emission from a stellar jet that impacts a dense molecular cloud, a scenario that may be typical for classical T Tauri stars with jets in dense star-forming complexes. We first model the impact of a jet against a dense cloud using two-dimensional axisymmetric hydrodynamic simulations, exploring different configurations of the ambient environment. Then, we compare our results with XMM-Newton observations of the Herbig–Haro object HH 248, where extended X-ray emission aligned with the optical knots is detected at the edge of the nearby IC 434 cloud. Our simulations show that a jet can produce plasma with temperatures up to 10{sup 7} K, consistent with production of X-ray emission, after impacting a dense cloud. We find that jets denser than the ambient medium but less dense than the cloud produce detectable X-ray emission only at impact with the cloud. From an exploration of the model parameter space, we constrain the physical conditions (jet density and velocity and cloud density) that reproduce the intrinsic luminosity and emission measure of the X-ray source possibly associated with HH 248 well. Thus, we suggest that the extended X-ray source close to HH 248 corresponds to a jet impacting a dense cloud.
Energy Technology Data Exchange (ETDEWEB)
Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083 (Japan); Fedorov, Dmitri G., E-mail: d.g.fedorov@aist.go.jp [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Zahariev, Federico; Schmidt, Michael W.; Gordon, Mark S. [Department of Chemistry and Ames Laboratory, US-DOE, Iowa State University, Ames, Iowa 50011 (United States); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)
2015-03-28
Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
Schammé, Benjamin; Mignot, Mélanie; Couvrat, Nicolas; Tognetti, Vincent; Joubert, Laurent; Dupray, Valérie; Delbreilh, Laurent; Dargent, Eric; Coquerel, Gérard
2016-08-04
In this article, we conduct a comprehensive molecular relaxation study of amorphous Quinidine above and below the glass-transition temperature (Tg) through broadband dielectric relaxation spectroscopy (BDS) experiments and theoretical density functional theory (DFT) calculations, as one major issue with the amorphous state of pharmaceuticals is life expectancy. These techniques enabled us to determine what kind of molecular motions are responsible, or not, for the devitrification of Quinidine. Parameters describing the complex molecular dynamics of amorphous Quinidine, such as Tg, the width of the α relaxation (βKWW), the temperature dependence of α-relaxation times (τα), the fragility index (m), and the apparent activation energy of secondary γ relaxation (Ea-γ), were characterized. Above Tg (> 60 °C), a medium degree of nonexponentiality (βKWW = 0.5) was evidenced. An intermediate value of the fragility index (m = 86) enabled us to consider Quinidine as a glass former of medium fragility. Below Tg (origin coming from the rotation of the CH(OH)C9H14N end group. An excess wing observed in amorphous Quinidine was found to be an unresolved Johari-Goldstein relaxation. These studies were supplemented by sub-Tg experimental evaluations of the life expectancy of amorphous Quinidine by X-ray powder diffraction and differential scanning calorimetry. We show that the difference between Tg and the onset temperature for crystallization, Tc, which is 30 K, is sufficiently large to avoid recrystallization of amorphous Quinidine during 16 months of storage under ambient conditions.
Energy Technology Data Exchange (ETDEWEB)
Santos, Valdemir A. dos, E-mail: valdemir.alexandre@pq.cnpq.b [Universidade Catolica de Pernambuco, Recife, PE (Brazil). Centro de Ciencia e Tecnologia; Dantas, Carlos C., E-mail: ccd@ufpe.b [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Luna-Finkler, Christine L., E-mail: chrislluna@yahoo.com.b [Universidade Federal de Pernambuco (UFPE), Vitoria de Santo Antao, PE (Brazil). Centro Academico de Vitoria; Silva, Jose M.F., E-mail: jmfs5@yahoo.com.b [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Engenharia Quimica
2009-07-01
To measure the axial concentration of the solid component with aid of gamma radiation to compare two fluid dynamic models was the goal of this work. An {sup 241}Am radioactive source of a 9 7.4 centre dot10{sup 9} Bq intensity and the detector were collimated. A support of the arrangement allows dislocating source and detector in order to scan along of riser axial length. The gamma measurements are taken with a 0.05 m x 0.05 m NaI(Tl) detector associated to a mono and to a multichannel analyser which is provided by a Genie 2000, Canberra software for spectrum evaluation. By integrating the 0.060 MeV photopeak of the {sup 241}Am gamma spectrum all the attenuation measurements are taken. The catalyst mass absorption coefficient, mu =331 m{sup 2}/kg, was determined in a previous experiment. For the solid volumetric fraction about 0.02, in the solid entrance in riser, the fluid dynamic model performances were compared by four different search numeric methods (Quasi-Newton, Hook-Jeeves Pattern Mooves, Rosenbrock Pattern Search and Simplex Procedure) from user-specified regression (Custom loss function) from nonlinear estimation of SIMULINK/Matlab{sup R} and Statistica software. In this standard multiple regression type it estimates the regression coefficients by 'finding' those coefficients that minimize the residual variance (sum of squared residuals) around the regression line. Any deviation of an observed score from a predicted score signifies some loss in the accuracy of prediction. The comparison tests between experimental and simulated data showed that the Santana's model was more indicated to simulate the solid axial density profile in a cold flow riser of a FCC pilot unit. (author)
The Method to Calculate Cementing Fluids' Density and Rheological Parameters%注水泥流体密度与流变参数匹配的计算方法
Institute of Scientific and Technical Information of China (English)
邓建民; 王永洪; 贾晓斌; 靳文博
2011-01-01
为提高注水泥时的顶替效率,对注水泥流体(钻井液、前置液和水泥浆)之间的密度匹配、流变性能匹配进行设计很重要,但目前缺乏该方面的理论设计方法.针对直井、注水泥流体均为幂律流体、层流、套管居中等条件下的注水泥顶替过程,在对两流体相互顶替的受力分析的基础上,建立了使顶替流体与被顶替流体在横截面上以同一平均流速进行顶替流动(即同步上返)时的两流体密度和流变参数匹配要求的定量计算方法及公式,所建立的公式可以应用于注水泥设计.分析所建立的公式表明,当顶替流体密度大于被顶替流体密度、顶替流体的流性指数大于被顶替流体的流性指数、顶替流体的稠度系数大于被顶替流体的稠度系数时,可提高顶替效率.%In order to increase the displacement efficiency,it is important to design and match the density and rheological parameters of the cementing fluids (drilling fluid,pad fluid and cement slurry), while the theoretical design method is not available at present. A vertical well fluid displacing is analyzed assuming power-law fluid with laminar flow during the cementing displacement process. On the basis of this analysis,a method and formula was established to calculate the fluid density and rheological parameters by which the displacing and displaced fluids have same velocity in flow of replacement. The formula can be applied in cementing design. The analyses show that when fluid density in displacing fluid is higher then displaced fluid,then the flow index and viscosity index of displacing fluid is higher than displaced fluid,and the displacement efficiency is increased.