36 research outputs found
Structure and bonding of dense liquid oxygen from first principles simulations
Using first principles simulations we have investigated the structural and
bonding properties of dense fluid oxygen up to 180 GPa. We have found that band
gap closure occurs in the molecular liquid, with a "slow" transition from a
semi-conducting to a poor metallic state occurring over a wide pressure range.
At approximately 80 GPa, molecular dissociation is observed in the metallic
fluid. Spin fluctuations play a key role in determining the electronic
structure of the low pressure fluid, while they are suppressed at high
pressure.Comment: 4 figure
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
The electrostatic continuum solvent model developed by Fattebert and Gygi is
combined with a first-principles formulation of the cavitation energy based on
a natural quantum-mechanical definition for the surface of a solute. Despite
its simplicity, the cavitation contribution calculated by this approach is
found to be in remarkable agreement with that obtained by more complex
algorithms relying on a large set of parameters. Our model allows for very
efficient Car-Parrinello simulations of finite or extended systems in solution,
and demonstrates a level of accuracy as good as that of established
quantum-chemistry continuum solvent methods. We apply this approach to the
study of tetracyanoethylene dimers in dichloromethane, providing valuable
structural and dynamical insights on the dimerization phenomenon
Ab initio Molecular Dynamics in Adaptive Coordinates
We present a new formulation of ab initio molecular dynamics which exploits
the efficiency of plane waves in adaptive curvilinear coordinates, and thus
provides an accurate treatment of first-row elements. The method is used to
perform a molecular dynamics simulation of the CO_2 molecule, and allows to
reproduce detailed features of its vibrational spectrum such as the splitting
of the Raman sigma+_g mode caused by Fermi resonance. This new approach opens
the way to highly accurate ab initio simulations of organic compounds.Comment: 11 pages, 3 PostScript figure
Reconstruction and thermal stability of the cubic SiC(001) surfaces
The (001) surfaces of cubic SiC were investigated with ab-initio molecular
dynamics simulations. We show that C-terminated surfaces can have different
c(2x2) and p(2x1) reconstructions, depending on preparation conditions and
thermal treatment, and we suggest experimental probes to identify the various
reconstructed geometries. Furthermore we show that Si-terminated surfaces
exhibit a p(2x1) reconstruction at T=0, whereas above room temperature they
oscillate between a dimer row and an ideal geometry below 500 K, and sample
several patterns including a c(4x2) above 500 K.Comment: 12 pages, RevTeX, figures 1 and 2 available in gif form at
http://irrmawww.epfl.ch/fg/sic/fig1.gif and
http://irrmawww.epfl.ch/fg/sic/fig2.gi
Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain
Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain
Roadmap on Electronic Structure Codes in the Exascale Era
Electronic structure calculations have been instrumental in providing many
important insights into a range of physical and chemical properties of various
molecular and solid-state systems. Their importance to various fields,
including materials science, chemical sciences, computational chemistry and
device physics, is underscored by the large fraction of available public
supercomputing resources devoted to these calculations. As we enter the
exascale era, exciting new opportunities to increase simulation numbers, sizes,
and accuracies present themselves. In order to realize these promises, the
community of electronic structure software developers will however first have
to tackle a number of challenges pertaining to the efficient use of new
architectures that will rely heavily on massive parallelism and hardware
accelerators. This roadmap provides a broad overview of the state-of-the-art in
electronic structure calculations and of the various new directions being
pursued by the community. It covers 14 electronic structure codes, presenting
their current status, their development priorities over the next five years,
and their plans towards tackling the challenges and leveraging the
opportunities presented by the advent of exascale computing.Comment: Submitted as a roadmap article to Modelling and Simulation in
Materials Science and Engineering; Address any correspondence to Vikram
Gavini ([email protected]) and Danny Perez ([email protected]
Ab Initio Simulation of Materials under Extreme Conditions Ab initio simulation of materials under extreme conditions
Abstract The study of materials properties under extreme conditions has made considerable progress over the past decade due to both improvements in experimental techniques and advanced modeling methods. The availability of accurate models is crucial in order to analyze experimental results obtained in extreme conditions of pressure and temperature where experimental data can be scarce. Among theoretical models, ab initio simulations are playing an increasingly important role due to their ability to predict materials properties without the need for any experimental input. Ab initio simulations also allow for an exploration of materials properties in conditions that are unachievable using controlled experiments-such as e.g. the conditions prevailing in the core of large planets. In that limit, they constitute the only quantitative model of condensed matter available today. In this article, we review the current status of ab initio simulations and discuss examples of recent applications in which numerical simulations have provided an essential complement to experimental data