152 research outputs found
Accurate and efficient linear scaling DFT calculations with universal applicability
Density Functional Theory calculations traditionally suffer from an inherent
cubic scaling with respect to the size of the system, making big calculations
extremely expensive. This cubic scaling can be avoided by the use of so-called
linear scaling algorithms, which have been developed during the last few
decades. In this way it becomes possible to perform ab-initio calculations for
several tens of thousands of atoms or even more within a reasonable time frame.
However, even though the use of linear scaling algorithms is physically well
justified, their implementation often introduces some small errors.
Consequently most implementations offering such a linear complexity either
yield only a limited accuracy or, if one wants to go beyond this restriction,
require a tedious fine tuning of many parameters. In our linear scaling
approach within the BigDFT package, we were able to overcome this restriction.
Using an ansatz based on localized support functions expressed in an underlying
Daubechies wavelet basis -- which offers ideal properties for accurate linear
scaling calculations -- we obtain an amazingly high accuracy and a universal
applicability while still keeping the possibility of simulating large systems
with only a moderate demand of computing resources
Daubechies Wavelets for Linear Scaling Density Functional Theory
We demonstrate that Daubechies wavelets can be used to construct a minimal
set of optimized localized contracted basis functions in which the Kohn-Sham
orbitals can be represented with an arbitrarily high, controllable precision.
Ground state energies and the forces acting on the ions can be calculated in
this basis with the same accuracy as if they were calculated directly in a
Daubechies wavelets basis, provided that the amplitude of these contracted
basis functions is sufficiently small on the surface of the localization
region, which is guaranteed by the optimization procedure described in this
work. This approach reduces the computational costs of DFT calculations, and
can be combined with sparse matrix algebra to obtain linear scaling with
respect to the number of electrons in the system. Calculations on systems of
10,000 atoms or more thus become feasible in a systematic basis set with
moderate computational resources. Further computational savings can be achieved
by exploiting the similarity of the contracted basis functions for closely
related environments, e.g. in geometry optimizations or combined calculations
of neutral and charged systems
Plant Carbohydrate Scavenging through TonB-Dependent Receptors: A Feature Shared by Phytopathogenic and Aquatic Bacteria
TonB-dependent receptors (TBDRs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in Gram-negative bacteria. Analysis of the genome of the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc), predicts 72 TBDRs. Such an overrepresentation is common in Xanthomonas species but is limited to only a small number of bacteria. Here, we show that one Xcc TBDR transports sucrose with a very high affinity, suggesting that it might be a sucrose scavenger. This TBDR acts with an inner membrane transporter, an amylosucrase and a regulator to utilize sucrose, thus defining a new type of carbohydrate utilization locus, named CUT locus, involving a TBDR for the transport of substrate across the outer membrane. This sucrose CUT locus is required for full pathogenicity on Arabidopsis, showing its importance for the adaptation to host plants. A systematic analysis of Xcc TBDR genes and a genome context survey suggested that several Xcc TBDRs belong to other CUT loci involved in the utilization of various plant carbohydrates. Interestingly, several Xcc TBDRs and CUT loci are conserved in aquatic bacteria such as Caulobacter crescentus, Colwellia psychrerythraea, Saccharophagus degradans, Shewanella spp., Sphingomonas spp. or Pseudoalteromonas spp., which share the ability to degrade a wide variety of complex carbohydrates and display TBDR overrepresentation. We therefore propose that TBDR overrepresentation and the presence of CUT loci designate the ability to scavenge carbohydrates. Thus CUT loci, which seem to participate to the adaptation of phytopathogenic bacteria to their host plants, might also play a very important role in the biogeochemical cycling of plant-derived nutrients in marine environments. Moreover, the TBDRs and CUT loci identified in this study are clearly different from those characterized in the human gut symbiont Bacteroides thetaiotaomicron, which allow glycan foraging, suggesting a convergent evolution of TBDRs in Proteobacteria and Bacteroidetes
MICROSCOPE mission analysis, requirements and expected performance
The MICROSCOPE mission aimed to test the Weak Equivalence Principle (WEP) to
a precision of . The WEP states that two bodies fall at the same rate
on a gravitational field independently of their mass or composition. In
MICROSCOPE, two masses of different compositions (titanium and platinum alloys)
are placed on a quasi-circular trajectory around the Earth. They are the
test-masses of a double accelerometer. The measurement of their accelerations
is used to extract a potential WEP violation that would occur at a frequency
defined by the motion and attitude of the satellite around the Earth. This
paper details the major drivers of the mission leading to the specification of
the major subsystems (satellite, ground segment, instrument, orbit...).
Building upon the measurement equation, we derive the objective of the test in
statistical and systematic error allocation and provide the mission's expected
error budget.Comment: References update
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