51 research outputs found
Time-dependent density functional theory calculation of van der Waals coefficient of sodium clusters
In this paper we employ all-electron \textit{ab-initio} time-dependent
density functional theory based method to calculate the long range
dipole-dipole dispersion coefficient (van der Waals coefficient) of
sodium atom clusters containing even number of atoms ranging from 2 to 20
atoms. The dispersion coefficients are obtained via Casimir-Polder relation.
The calculations are carried out with two different exchange-correlation
potentials: (i) the asymptotically correct statistical average of orbital
potential (SAOP) and (ii) Vosko-Wilk-Nusair representation of
exchange-correlation potential within local density approximation. A comparison
with the other theoretical results has been performed. We also present the
results for the static polarizabilities of sodium clusters and also compare
them with other theoretical and experimental results. These comparisons reveal
that the SAOP results for C_{6} and static polarizability are quite accurate
and very close to the experimental results. We examine the relationship between
volume of the cluster and van der Waals coefficient and find that to a very
high degree of correlation C_{6} scales as square of the volume. We also
present the results for van der Waals coefficient corresponding to cluster-Ar
atom and cluster-N_{2} molecule interactions.Comment: 22 pages including 6 figures. To be published in Journal of Chemical
Physic
SCN1A variants from bench to bedside-improved clinical prediction from functional characterization
Variants in the SCN1A gene are associated with a wide range of disorders including genetic epilepsy with febrile seizures plus (GEFS+), familial hemiplegic migraine (FHM), and the severe childhood epilepsy Dravet syndrome (DS). Predicting disease outcomes based on variant type remains challenging. Despite thousands of SCN1A variants being reported, only a minority has been functionally assessed.
We review the functional SCN1A work performed to date, critically appraise electrophysiological measurements, compare this to in silico predictions, and relate our findings to the clinical phenotype.
Our results show, regardless of the underlying phenotype, that conventional in silico software correctly predicted benign from pathogenic variants in nearly 90%, however was unable to differentiate within the disease spectrum (DS vs. GEFS+ vs. FHM). In contrast, patch‐clamp data from mammalian expression systems revealed functional differences among missense variants allowing discrimination between disease severities. Those presenting with milder phenotypes retained a degree of channel function measured as residual whole‐cell current, whereas those without any whole‐cell current were often associated with DS (p = .024).
These findings demonstrate that electrophysiological data from mammalian expression systems can serve as useful disease biomarker when evaluating SCN1A variants, particularly in view of new and emerging treatment options in DS
Calculation of valence electron momentum densities using the projector augmented-wave method
We present valence electron Compton profiles calculated within the
density-functional theory using the all-electron full-potential projector
augmented-wave method (PAW). Our results for covalent (Si), metallic (Li, Al)
and hydrogen-bonded ((H_2O)_2) systems agree well with experiments and
computational results obtained with other band-structure and basis set schemes.
The PAW basis set describes the high-momentum Fourier components of the valence
wave functions accurately when compared with other basis set schemes and
previous all-electron calculations.Comment: Submitted to Journal of Physics and Chemistry of Solids on September
17 2004. Revised version submitted on December 13 200
Work functions, ionization potentials, and in-between: Scaling relations based on the image charge model
We revisit a model in which the ionization energy of a metal particle is
associated with the work done by the image charge force in moving the electron
from infinity to a small cut-off distance just outside the surface. We show
that this model can be compactly, and productively, employed to study the size
dependence of electron removal energies over the range encompassing bulk
surfaces, finite clusters, and individual atoms. It accounts in a
straightforward manner for the empirically known correlation between the atomic
ionization potential (IP) and the metal work function (WF), IP/WF2. We
formulate simple expressions for the model parameters, requiring only a single
property (the atomic polarizability or the nearest neighbor distance) as input.
Without any additional adjustable parameters, the model yields both the IP and
the WF within 10% for all metallic elements, as well as matches the size
evolution of the ionization potentials of finite metal clusters for a large
fraction of the experimental data. The parametrization takes advantage of a
remarkably constant numerical correlation between the nearest-neighbor distance
in a crystal, the cube root of the atomic polarizability, and the image force
cutoff length. The paper also includes an analytical derivation of the relation
of the outer radius of a cluster of close-packed spheres to its geometric
structure.Comment: Original submission: 8 pages with 7 figures incorporated in the text.
Revised submission (added one more paragraph about alloy work functions): 18
double spaced pages + 8 separate figures. Accepted for publication in PR
Ab initio studies of structures and properties of small potassium clusters
We have studied the structure and properties of potassium clusters containing
even number of atoms ranging from 2 to 20 at the ab initio level. The geometry
optimization calculations are performed using all-electron density functional
theory with gradient corrected exchange-correlation functional. Using these
optimized geometries we investigate the evolution of binding energy, ionization
potential, and static polarizability with the increasing size of the clusters.
The polarizabilities are calculated by employing Moller-Plesset perturbation
theory and time dependent density functional theory. The polarizabilities of
dimer and tetramer are also calculated by employing large basis set coupled
cluster theory with single and double excitations and perturbative triple
excitations. The time dependent density functional theory calculations of
polarizabilities are carried out with two different exchange-correlation
potentials: (i) an asymptotically correct model potential and (ii) within the
local density approximation. A systematic comparison with the other available
theoretical and experimental data for various properties of small potassium
clusters mentioned above has been performed. These comparisons reveal that both
the binding energy and the ionization potential obtained with gradient
corrected potential match quite well with the already published data.
Similarly, the polarizabilities obtained with Moller-Plesset perturbation
theory and with model potential are quite close to each other and also close to
experimental data.Comment: 33 pages including 10 figure
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition
A Density Functional Approach to Hardness, Polarizability, and Valency of Molecules in Chemical Reactions
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