514 research outputs found
Warming Up Density Functional Theory
Density functional theory (DFT) has become the most popular approach to
electronic structure across disciplines, especially in material and chemical
sciences. Last year, at least 30,000 papers used DFT to make useful predictions
or give insight into an enormous diversity of scientific problems, ranging from
battery development to solar cell efficiency and far beyond. The success of
this field has been driven by usefully accurate approximations based on known
exact conditions and careful testing and validation. In the last decade,
applications of DFT in a new area, warm dense matter, have exploded. DFT is
revolutionizing simulations of warm dense matter including applications in
controlled fusion, planetary interiors, and other areas of high energy density
physics. Over the past decade or so, molecular dynamics calculations driven by
modern density functional theory have played a crucial role in bringing
chemical realism to these applications, often (but not always) with excellent
agreement with experiment. This chapter summarizes recent work from our group
on density functional theory at non-zero temperatures, which we call thermal
DFT. We explain the relevance of this work in the context of warm dense matter,
and the importance of quantum chemistry to this regime. We illustrate many
basic concepts on a simple model system, the asymmetric Hubbard dimer
Correlation energies of inhomogeneous many-electron systems
We generalize the uniform-gas correlation energy formalism of Singwi, Tosi,
Land and Sjolander to the case of an arbitrary inhomogeneous many-particle
system. For jellium slabs of finite thickness with a self-consistent LDA
groundstate Kohn-Sham potential as input, our numerical results for the
correlation energy agree well with diffusion Monte Carlo results. For a helium
atom we also obtain a good correlation energy.Comment: 4 pages,1 figur
Symmetry breaking and the random-phase approximation in small quantum dots
The random-phase approximation has been used to compute the properties of
parabolic two-dimensional quantum dots beyond the mean-field approximation.
Special emphasis is put on the ground state correlation energy, the symmetry
restoration and the role of the spurious modes within the random-phase
approximation. A systematics with the Coulombic interaction strength is
presented for the 2-electron dot, while for the 6- and 12-electron dots
selected cases are discussed. The validity of the random-phase approximation is
assessed by comparison with available exact results.Comment: 9 pages, 4 embedded + 6 gif Figs. Published versio
Metal Surface Energy: Persistent Cancellation of Short-Range Correlation Effects beyond the Random-Phase Approximation
The role that non-local short-range correlation plays at metal surfaces is
investigated by analyzing the correlation surface energy into contributions
from dynamical density fluctuations of various two-dimensional wave vectors.
Although short-range correlation is known to yield considerable correction to
the ground-state energy of both uniform and non-uniform systems, short-range
correlation effects on intermediate and short-wavelength contributions to the
surface formation energy are found to compensate one another. As a result, our
calculated surface energies, which are based on a non-local
exchange-correlation kernel that provides accurate total energies of a uniform
electron gas, are found to be very close to those obtained in the random-phase
approximation and support the conclusion that the error introduced by the
local-density approximation is small.Comment: 5 pages, 1 figure, to appear in Phys. Rev.
Density functional calculations of nanoscale conductance
Density functional calculations for the electronic conductance of single
molecules are now common. We examine the methodology from a rigorous point of
view, discussing where it can be expected to work, and where it should fail.
When molecules are weakly coupled to leads, local and gradient-corrected
approximations fail, as the Kohn-Sham levels are misaligned. In the weak bias
regime, XC corrections to the current are missed by the standard methodology.
For finite bias, a new methodology for performing calculations can be
rigorously derived using an extension of time-dependent current density
functional theory from the Schroedinger equation to a Master equation.Comment: topical review, 28 pages, updated version with some revision
Four Lessons in Versatility or How Query Languages Adapt to the Web
Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”
Random-phase approximation and its applications in computational chemistry and materials science
The random-phase approximation (RPA) as an approach for computing the
electronic correlation energy is reviewed. After a brief account of its basic
concept and historical development, the paper is devoted to the theoretical
formulations of RPA, and its applications to realistic systems. With several
illustrating applications, we discuss the implications of RPA for computational
chemistry and materials science. The computational cost of RPA is also
addressed which is critical for its widespread use in future applications. In
addition, current correction schemes going beyond RPA and directions of further
development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012
Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials
Quantum ESPRESSO is an integrated suite of computer codes for
electronic-structure calculations and materials modeling, based on
density-functional theory, plane waves, and pseudopotentials (norm-conserving,
ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn
Source Package for Research in Electronic Structure, Simulation, and
Optimization". It is freely available to researchers around the world under the
terms of the GNU General Public License. Quantum ESPRESSO builds upon
newly-restructured electronic-structure codes that have been developed and
tested by some of the original authors of novel electronic-structure algorithms
and applied in the last twenty years by some of the leading materials modeling
groups worldwide. Innovation and efficiency are still its main focus, with
special attention paid to massively-parallel architectures, and a great effort
being devoted to user friendliness. Quantum ESPRESSO is evolving towards a
distribution of independent and inter-operable codes in the spirit of an
open-source project, where researchers active in the field of
electronic-structure calculations are encouraged to participate in the project
by contributing their own codes or by implementing their own ideas into
existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte
In-depth exploration of the photophysics of a trinuclear palladium complex
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Density functional theories and self-energy approaches
A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to investigate the changes in gene expression within the liver of rainbow trout during exposure to a prolonged period of confinement. Tissue and blood samples were collected from trout at intervals up to 648 h after transfer to a standardised confinement stressor, together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, glucose and lactate were analysed to confirm that the neuroendocrine response to confinement was consistent with previous findings and to provide a phenotypic context to assist interpretation of gene expression data. Liver samples for suppression subtractive hybridisation (SSH) library construction were selected from within the experimental groups comprising “early” stress (2–48 h) and “late” stress (96–504 h). In order to reduce redundancy within the four SSH libraries and yield a higher number of unique clones an additional subtraction was carried out. After printing of the arrays a series of 55 hybridisations were executed to cover 6 time points. At 2 h, 6 h, 24 h, 168 h and 504 h 5 individual confined fish and 5 individual control fish were used with control fish only at 0 h. A preliminary list of 314 clones considered differentially regulated over the complete time course was generated by a combination of data analysis approaches and the most significant gene expression changes were found to occur during the 24 h to 168 h time period with a general approach to control levels by 504 h. Few changes in expression were apparent over the first 6 h. The list of genes whose expression was significantly altered comprised predominantly genes belonging to the biological process category (response to stimulus) and one cellular component category (extracellular region) and were dominated by so-called acute phase proteins. Analysis of the gene expression profile in liver tissue during confinement revealed a number of significant clusters. The major patterns comprised genes that were up-regulated at 24 h and beyond, the primary examples being haptoglobin, β-fibrinogen and EST10729. Two representative genes from each of the six k-means clusters were validated by qPCR. Correlations between microarray and qPCR expression patterns were significant for most of the genes tested. qPCR analysis revealed that haptoglobin expression was up-regulated approximately 8-fold at 24 h and over 13-fold by 168 h.This project was part funded by the European Commission (Q5RS-2001-02211), Enterprise Ireland and the Natural Environment Research Council of the United Kingdom
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