92 research outputs found
Scattering of a proton with the Li4 cluster: non-adiabatic molecular dynamics description based on time-dependent density-functional theory
We have employed non-adiabatic molecular dynamics based on time-dependent
density-functional theory to characterize the scattering behaviour of a proton
with the Li cluster. This technique assumes a classical approximation for
the nuclei, effectively coupled to the quantum electronic system. This
time-dependent theoretical framework accounts, by construction, for possible
charge transfer and ionization processes, as well as electronic excitations,
which may play a role in the non-adiabatic regime. We have varied the incidence
angles in order to analyze the possible reaction patterns. The initial proton
kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects.
For all the incidence angles considered the proton is scattered away, except in
one interesting case in which one of the Lithium atoms captures it, forming a
LiH molecule. This theoretical formalism proves to be a powerful, effective and
predictive tool for the analysis of non-adiabatic processes at the nanoscale.Comment: 18 pages, 4 figure
Plasma Dynamics
Contains reports on two research projects.U. S. Energy Research and Development Administration (Contract E(l1-1)-3070)National Science Foundation (Grant ENG75-06242
The Genopolis Microarray Database
<p>Abstract</p> <p>Background</p> <p>Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood.</p> <p>Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions.</p> <p>Results</p> <p>The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip<sup>® </sup>platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users.</p> <p>Conclusion</p> <p>The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local database and a public repository, where the development of a common coherent annotation is important. In its current implementation, it provides a uniform coherently annotated dataset on dendritic cells and macrophage differentiation.</p
Plasma Dynamics
Contains research objectives and summary of research on eighteen research projects split into seven sections and reports on four research projects.U.S. Atomic Energy Commission (Contract AT(l1-1)-3070)National Science Foundation (Grant GK-37979X1
A modified Ehrenfest formalism for efficient large-scale ab initio molecular dynamics
We present in detail the recently derived ab-initio molecular dynamics (AIMD)
formalism [Phys. Rev. Lett. 101 096403 (2008)], which due to its numerical
properties, is ideal for simulating the dynamics of systems containing
thousands of atoms. A major drawback of traditional AIMD methods is the
necessity to enforce the orthogonalization of the wave-functions, which can
become the bottleneck for very large systems. Alternatively, one can handle the
electron-ion dynamics within the Ehrenfest scheme where no explicit
orthogonalization is necessary, however the time step is too small for
practical applications. Here we preserve the desirable properties of Ehrenfest
in a new scheme that allows for a considerable increase of the time step while
keeping the system close to the Born-Oppenheimer surface. We show that the
automatically enforced orthogonalization is of fundamental importance for large
systems because not only it improves the scaling of the approach with the
system size but it also allows for an additional very efficient parallelization
level. In this work we provide the formal details of the new method, describe
its implementation and present some applications to some test systems.
Comparisons with the widely used Car-Parrinello molecular dynamics method are
made, showing that the new approach is advantageous above a certain number of
atoms in the system. The method is not tied to a particular wave-function
representation, making it suitable for inclusion in any AIMD software package.Comment: 28 pages, 5 figures, published in a special issue of J. Chem. Theory
Comp. in honour of John Perde
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