894 research outputs found
Embedded-Cluster Calculations in a Numeric Atomic Orbital Density-Functional Theory Framework
We integrate the all-electron electronic structure code FHI-aims into the
general ChemShell package for solid-state embedding (QM/MM) calculations. A
major undertaking in this integration is the implementation of pseudopotential
functionality into FHI-aims to describe cations at the QM/MM boundary through
effective core potentials and therewith prevent spurious overpolarization of
the electronic density. Based on numeric atomic orbital basis sets, FHI-aims
offers particularly efficient access to exact exchange and second order
perturbation theory, rendering the established QM/MM setup an ideal tool for
hybrid and double-hybrid level DFT calculations of solid systems. We illustrate
this capability by calculating the reduction potential of Fe in the
Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for
(photo-)catalytic water oxidation at TiO2(110).Comment: 12 pages, 4 figure
Screening of Hydrodynamic Interactions in Semidilute Polymer Solutions: A Computer Simulation Study
We study single-chain motion in semidilute solutions of polymers of length N
= 1000 with excluded-volume and hydrodynamic interactions by a novel algorithm.
The crossover length of the transition from Zimm (short lengths and times) to
Rouse dynamics (larger scales) is proportional to the static screening length.
The crossover time is the corresponding Zimm time. Our data indicate Zimm
behavior at large lengths but short times. There is no hydrodynamic screening
until the chains feel constraints, after which they resist the flow:
"Incomplete screening" occurs in the time domain.Comment: 3 figure
Alkali and Alkaline Earth Metal Compounds: Core-Valence Basis Sets and Importance of Subvalence Correlation
Core-valence basis sets for the alkali and alkaline earth metals Li, Be, Na,
Mg, K, and Ca are proposed. The basis sets are validated by calculating
spectroscopic constants of a variety of diatomic molecules involving these
elements. Neglect of correlation in K and Ca compounds will lead to
erratic results at best, and chemically nonsensical ones if chalcogens or
halogens are present. The addition of low-exponent functions to the K and
Ca basis sets is essential for smooth convergence of molecular properties.
Inclusion of inner-shell correlation is important for accurate spectroscopic
constants and binding energies of all the compounds. In basis set
extrapolation/convergence calculations, the explicit inclusion of alkali and
alkaline earth metal subvalence correlation at all steps is essential for K and
Ca, strongly recommended for Na, and optional for Li and Mg, while in Be
compounds, an additive treatment in a separate `core correlation' step is
probably sufficient. Consideration of inner-shell correlation energy in
first-row elements requires inclusion of `deep core' correlation
energy in K and Ca for consistency. The latter requires special CCVZ `deep
core correlation' basis sets. For compounds involving Ca bound to
electronegative elements, additional functions in the basis set are
strongly recommended. For optimal basis set convergence in such cases, we
suggest the sequence CV(D+3d)Z, CV(T+2d)Z, CV(Q+)Z, and CV5Z on calcium.Comment: Molecular Physics, in press (W. G. Richards issue); supplementary
material (basis sets in G98 and MOLPRO formats) available at
http://theochem.weizmann.ac.il/web/papers/group12.htm
Dynamics and Scaling of 2D Polymers in a Dilute Solution
The breakdown of dynamical scaling for a dilute polymer solution in 2D has
been suggested by Shannon and Choy [Phys. Rev. Lett. {\bf 79}, 1455 (1997)].
However, we show here both numerically and analytically that dynamical scaling
holds when the finite-size dependence of the relevant dynamical quantities is
properly taken into account. We carry out large-scale simulations in 2D for a
polymer chain in a good solvent with full hydrodynamic interactions to verify
dynamical scaling. This is achieved by novel mesoscopic simulation techniques
Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag
We study the electrophoretic separation of polyelectrolytes of varying
lengths by means of end-labeled free-solution electrophoresis (ELFSE). A
coarse-grained molecular dynamics simulation model, using full electrostatic
interactions and a mesoscopic Lattice Boltzmann fluid to account for
hydrodynamic interactions, is used to characterize the drag coefficients of
different label types: linear and branched polymeric labels, as well as
transiently bound micelles.
It is specifically shown that the label's drag coefficient is determined by
its hydrodynamic size, and that the drag per label monomer is largest for
linear labels. However, the addition of side chains to a linear label offers
the possibility to increase the hydrodynamic size, and therefore the label
efficiency, without having to increase the linear length of the label, thereby
simplifying synthesis. The third class of labels investigated, transiently
bound micelles, seems very promising for the usage in ELFSE, as they provide a
significant higher hydrodynamic drag than the other label types.
The results are compared to theoretical predictions, and we investigate how
the efficiency of the ELFSE method can be improved by using smartly designed
drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule
Visible photodissociation spectroscopy of PAH cations and derivatives in the PIRENEA experiment
The electronic spectra of gas-phase cationic polycyclic aromatic hydrocarbons
(PAHs), trapped in the Fourier Transform Ion Cyclotron Resonance cell of the
PIRENEA experiment, have been measured by multiphoton dissociation spectroscopy
in the 430-480 nm spectral range using the radiation of a mid-band optical
parametric oscillator laser. We present here the spectra recorded for different
species of increasing size, namely the pyrene cation (C16H10+), the
1-methylpyrene cation (CH3-C16H9+), the coronene cation (C24H12+), and its
dehydrogenated derivative C24H10+. The experimental results are interpreted
with the help of time-dependent density functional theory calculations and
analysed using spectral information on the same species obtained from matrix
isolation spectroscopy data. A kinetic Monte Carlo code has also been used, in
the case of pyrene and coronene cations, to estimate the absorption
cross-sections of the measured electronic transitions. Gas-phase spectra of
highly reactive species such as dehydrogenated PAH cations are reported for the
first time
Excited States of Proton-bound DNA/RNA Base Homo-dimers: Pyrimidines
We are presenting the electronic photo fragment spectra of the protonated
pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well
structured vibrational progression, while protonated monomer shows broad
vibrational bands. This shows that proton bonding can block some non radiative
processes present in the monomer.Comment: We acknowledge the use of the computing facility cluster GMPCS of the
LUMAT federation (FR LUMAT 2764
Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids
In this review, we describe and analyze a mesoscale simulation method for
fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now
called multi-particle collision dynamics (MPC) or stochastic rotation dynamics
(SRD). The method consists of alternating streaming and collision steps in an
ensemble of point particles. The multi-particle collisions are performed by
grouping particles in collision cells, and mass, momentum, and energy are
locally conserved. This simulation technique captures both full hydrodynamic
interactions and thermal fluctuations. The first part of the review begins with
a description of several widely used MPC algorithms and then discusses
important features of the original SRD algorithm and frequently used
variations. Two complementary approaches for deriving the hydrodynamic
equations and evaluating the transport coefficients are reviewed. It is then
shown how MPC algorithms can be generalized to model non-ideal fluids, and
binary mixtures with a consolute point. The importance of angular-momentum
conservation for systems like phase-separated liquids with different
viscosities is discussed. The second part of the review describes a number of
recent applications of MPC algorithms to study colloid and polymer dynamics,
the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of
viscoelastic fluids
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