317 research outputs found
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.
Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.Acknowledgements go to Mike Payne for careful reading of the paper; Peter Freddolino, Chris Baker, David Payne, and Bracken King for helpful discussions; Stuart Rankin for technical help; and the NVIDIA CUDA Centre of Excellence at the Cambridge HPCS for use of the CUDA-accelerated GPUs. Thanks also go to the reviewers for their helpful comments. All calculations were performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/) provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and were funded by the Engineering and Physical Sciences Research Consul (United Kingdom) (EPSRC) under Grant No. EP/F032773/1. Thanks for financial support go to the MRC, Wellcome Trust, and EPSRC.This is the author accepted manuscript. The final version is available from AIP Publishing via http://dx.doi.org/10.1063/1.368344
Full optimization of Jastrow-Slater wave functions with application to the first-row atoms and homonuclear diatomic molecules
We pursue the development and application of the recently-introduced linear
optimization method for determining the optimal linear and nonlinear parameters
of Jastrow-Slater wave functions in a variational Monte Carlo framework. In
this approach, the optimal parameters are found iteratively by diagonalizing
the Hamiltonian matrix in the space spanned by the wave function and its
first-order derivatives, making use of a strong zero-variance principle. We
extend the method to optimize the exponents of the basis functions,
simultaneously with all the other parameters, namely the Jastrow, configuration
state function and orbital parameters. We show that the linear optimization
method can be thought of as a so-called augmented Hessian approach, which helps
explain the robustness of the method and permits us to extend it to minimize a
linear combination of the energy and the energy variance. We apply the linear
optimization method to obtain the complete ground-state potential energy curve
of the C_2 molecule up to the dissociation limit, and discuss size consistency
and broken spin-symmetry issues in quantum Monte Carlo calculations. We perform
calculations of the first-row atoms and homonuclear diatomic molecules with
fully optimized Jastrow-Slater wave functions, and we demonstrate that
molecular well depths can be obtained with near chemical accuracy quite
systematically at the diffusion Monte Carlo level for these systems.Comment: 15 pages, 3 figures, to appear in Journal of Chemical Physic
A discrete model of water with two distinct glassy phases
We investigate a minimal model for non-crystalline water, defined on a Husimi
lattice. The peculiar random-regular nature of the lattice is meant to account
for the formation of a random 4-coordinated hydrogen-bond network. The model
turns out to be consistent with most thermodynamic anomalies observed in liquid
and supercooled-liquid water. Furthermore, the model exhibits two glassy phases
with different densities, which can coexist at a first-order transition. The
onset of a complex free-energy landscape, characterized by an exponentially
large number of metastable minima, is pointed out by the cavity method, at the
level of 1-step replica symmetry breaking.Comment: expanded version: 6 pages, 7 figure
Predicting vapor liquid equilibria using density functional theory: a case study of argon
Predicting vapor liquid equilibria (VLE) of molecules governed by weak van der Waals (vdW) interactions using the first principles approach is a significant challenge. Due to the poor scaling of the post Hartree-Fock wave function theory with system size/basis functions, the Kohn-Sham density functional theory (DFT) is preferred for systems with a large number of molecules. However, traditional DFT cannot adequately account for medium to long range correlations which are necessary for modeling vdW interactions. Recent developments in DFT such as dispersion corrected models and nonlocal van der Waals functionals have attempted to address this weakness with a varying degree of success. In this work, we predict the VLE of argon and assess the performance of several density functionals and the second order Møller-Plesset perturbation theory (MP2) by determining critical and structural properties via first principles Monte Carlo simulations. PBE-D3, BLYP-D3, and rVV10 functionals were used to compute vapor liquid coexistence curves, while PBE0-D3, M06-2X-D3, and MP2 were used for computing liquid density at a single state point. The performance of the PBE-D3 functional for VLE is superior to other functionals (BLYP-D3 and rVV10). At T = 85 K and P = 1 bar, MP2 performs well for the density and structural features of the first solvation shell in the liquid phase
Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials.
In this paper, we explore the strengths and weaknesses of a cavity-based method to calculate the excess chemical potential of a large molecular solute in a dense liquid solvent. Use of the cavity alleviates some technical problems associated with the appearance of (integrable) divergences in the integrand during alchemical particle growth. The excess chemical potential calculated using the cavity-based method should be independent of the cavity attributes. However, the performance of the method (equilibration time and the robustness) does depend on the cavity attributes. To illustrate the importance of a suitable choice of the cavity attributes, we calculate the partition coefficient of pyrene in toluene and heptane using a coarse-grained model. We find that a poor choice for the functional form of the cavity may lead to hysteresis between growth and shrinkage of the cavity. Somewhat unexpectedly, we find that, by allowing the cavity to move as a pseudo-particle within the simulation box, the decay time of fluctuations in the integrand of the thermodynamic integration can be reduced by an order of magnitude, thereby increasing the statistical accuracy of the calculation.BP ICA
Infrared spectra of protonated polycyclic aromatic hydrocarbon molecules: Azulene
The infrared (IR) spectrum of protonated azulene (AzuH(+), C10H9+) has been measured in the fingerprint range (600-1800 cm(-1)) by means of IR multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance mass spectrometer equipped with an electrospray ionization source using a free electron laser. The potential energy surface of AzuH(+) has been characterized at the B3LYP/6-311G** level in order to determine the global and local minima and the corresponding transition states for interconversion. The energies of the local and global minima, the dissociation energies for the lowest-energy fragmentation pathways, and the proton affinity have been evaluated at the CBS-QB3 level. Comparison with calculated linear IR absorption spectra supports the assignment of the IRMPD spectrum to C4-protonated AzuH(+), the most stable of the six distinguishable C-protonated AzuH(+) isomers. Comparison between Azu and C4-AzuH(+) reveals the effects of protonation on the geometry, vibrational properties, and the charge distribution of these fundamental aromatic molecules. Calculations at the MP2 level indicate that this technique is not suitable to predict reliable IR spectra for this type of carbocations even for relatively large basis sets. The IRMPD spectrum of protonated azulene is compared to that of isomeric protonated naphthalene and to an astronomical spectrum of the unidentified IR emission bands
Improving the efficiency of calculations with approximate spectral decompositions of dielectric matrices
Recently it was shown that the calculation of quasiparticle energies using
the approximation can be performed without computing explicitly any
virtual electronic states, by expanding the Green function and screened Coulomb
interaction in terms of the eigenstates of the static dielectric matrix.
Avoiding the evaluation of virtual electronic states leads to improved
efficiency and ease of convergence of calculations. Here we propose a
further improvement of the efficiency of these calculations, based on an
approximation of density-density response functions of molecules and solids.
The approximation relies on the calculation of a subset of eigenvectors of the
dielectric matrix using the kinetic operator instead of the full Hamiltonian,
and it does not lead to any substantial loss of accuracy for the quasiparticle
energies. The computational savings introduced by this approximation depend on
the system, and they become more substantial as the number of electrons
increases
Amine-Gold Linked Single-Molecule Junctions: Experiment and Theory
The measured conductance distribution for single molecule benzenediamine-gold
junctions, based on 59,000 individual conductance traces recorded while
breaking a gold point contact in solution, has a clear peak at 0.0064 G
with a width of 40%. Conductance calculations based on density functional
theory (DFT) for 15 distinct junction geometries show a similar spread.
Differences in local structure have a limited influence on conductance because
the amine-Au bonding motif is well-defined and flexible. The average calculated
conductance (0.046 G) is seven times larger than experiment, suggesting
the importance of many-electron corrections beyond DFT
Predictions of Heat Transfer and Flow Circulations in Differentially Heated Liquid Columns With Applications to Low-Pressure Evaporators
Numerical computations are presented for the temperature and velocity distributions of two differentially heated liquid columns with liquor depths of 0.1 m and 2.215 m, respectively. The temperatures in the liquid columns vary considerably with respect to position for pure conduction, free convection, and nucleate boiling cases using one-dimensional (1D) thermal resistance networks. In the thermal resistance networks the solutions are not sensitive to the type of condensing and boiling heat transfer coefficients used. However, these networks are limited and give no indication of velocity distributions occurring within the liquor. To alleviate this issue, two-dimensional (2D) axisymmetric and three-dimensional (3D) computational fluid dynamics (CFD) simulations of the test rigs have been performed. The axisymmetric conditions of the 2D simulations produce unphysical solutions; however, the full 3D simulations do not exhibit these behaviors. There is reasonable agreement for the predicted temperatures, heat fluxes, and heat transfer coefficients when comparing the boiling case of the 1D thermal resistance networks and the CFD simulations
Strongly Correlated Quantum Fluids: Ultracold Quantum Gases, Quantum Chromodynamic Plasmas, and Holographic Duality
Strongly correlated quantum fluids are phases of matter that are
intrinsically quantum mechanical, and that do not have a simple description in
terms of weakly interacting quasi-particles. Two systems that have recently
attracted a great deal of interest are the quark-gluon plasma, a plasma of
strongly interacting quarks and gluons produced in relativistic heavy ion
collisions, and ultracold atomic Fermi gases, very dilute clouds of atomic
gases confined in optical or magnetic traps. These systems differ by more than
20 orders of magnitude in temperature, but they were shown to exhibit very
similar hydrodynamic flow. In particular, both fluids exhibit a robustly low
shear viscosity to entropy density ratio which is characteristic of quantum
fluids described by holographic duality, a mapping from strongly correlated
quantum field theories to weakly curved higher dimensional classical gravity.
This review explores the connection between these fields, and it also serves as
an introduction to the Focus Issue of New Journal of Physics on Strongly
Correlated Quantum Fluids: from Ultracold Quantum Gases to QCD Plasmas. The
presentation is made accessible to the general physics reader and includes
discussions of the latest research developments in all three areas.Comment: 138 pages, 25 figures, review associated with New Journal of Physics
special issue "Focus on Strongly Correlated Quantum Fluids: from Ultracold
Quantum Gases to QCD Plasmas"
(http://iopscience.iop.org/1367-2630/focus/Focus%20on%20Strongly%20Correlated%20Quantum%20Fluids%20-%20from%20Ultracold%20Quantum%20Gases%20to%20QCD%20Plasmas
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