787 research outputs found
Assessment of two hybrid van der Waals density functionals for covalent and non-covalent binding of molecules
Two hybrid van der Waals density functionals (vdW-DFs) are constructed using
25%, Fock exchange with i) the consistent-exchange vdW-DF-cx functional and ii)
with the vdW-DF2 functional. The ability to describe covalent and non-covalent
binding properties of molecules are assessed. For properties related to
covalent binding, atomization energies (G2-1 set), molecular reaction energies
(G2RC set), as well as ionization energies (G21IP set) are benchmarked against
experimental reference values. We find that hybrid-vdW-DF-cx yields results
that are rather similar to those of the standard non-empirical hybrid PBE0 [JCP
110, 6158 (1996)]. Hybrid vdW-DF2 follows somewhat different trends, showing on
average significantly larger deviations from the reference energies, with a MAD
of 14.5 kcal/mol for the G2-1 set. Non-covalent binding properties of molecules
are assessed using the S22 benchmark set of non-covalently bonded dimers and
the X40 set of dimers of small halogenated molecules, using wavefunction-based
quantum chemistry results for references. For the S22 set, hybrid-vdW-DF-cx
performs better than standard vdW-DF-cx for the mostly hydrogen-bonded systems.
Hybrid-vdW-DF2 offers a slight improvement over standard vdW-DF2. Similar
trends are found for the X40 set, with hybrid-vdW-DF-cx performing particularly
well for binding involving the strongly polar hydrogen halides, but poorly for
systems with tiny binding energies. Our study of the X40 set reveals both the
potential of mixing Fock exchange with vdW-DF, but also highlights shortcomings
of the hybrids constructed here. The solid performance of hybrid-vdW-DF-cx for
covalent-bonded systems, as well as the strengths and issues uncovered for
non-covalently bonded systems, makes this study a good starting point for
developing even more precise hybrid vdW-DFs
Protein Inhibitors of Calcium Salt Crystal Growth in Saliva, Bile and Pancreatic Juice
The control of the formation of crystals in biological fluids is one of the most exciting field of research involving both organic and biochemical areas. Many organisms have evolved mechanisms which minimize or avoid the effects of nucleation and crystal growth formation. One of the most important mechanism is the interaction of specific proteins, called inhibitors, with crystals which alters their habits and leads to their elimination. This article, focused on saliva, pancreatic juice and bile, reviews our present knowledge on the structure-function relationships existing between these proteins and their ability to inhibit the growth of different calcium salt crystals
van der Waals density functionals built upon the electron-gas tradition: Facing the challenge of competing interactions
The theoretical description of sparse matter attracts much interest, in
particular for those ground-state properties that can be described by density
functional theory (DFT). One proposed approach, the van der Waals density
functional (vdW-DF) method, rests on strong physical foundations and offers
simple yet accurate and robust functionals. A very recent functional within
this method called vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89,
035412] stands out in its attempt to use an exchange energy derived from the
same plasmon-based theory from which the nonlocal correlation energy was
derived. Encouraged by its good performance for solids, layered materials, and
aromatic molecules, we apply it to several systems that are characterized by
competing interactions. These include the ferroelectric response in PbTiO,
the adsorption of small molecules within metal-organic frameworks (MOFs), the
graphite/diamond phase transition, and the adsorption of an aromatic-molecule
on the Ag(111) surface. Our results indicate that vdW-DF-cx is overall well
suited to tackle these challenging systems. In addition to being a competitive
density functional for sparse matter, the vdW-DF-cx construction presents a
more robust general purpose functional that could be applied to a range of
materials problems with a variety of competing interactions
Understanding adhesion at as-deposited interfaces from ab initio thermodynamics of deposition growth: thin-film alumina on titanium carbide
We investigate the chemical composition and adhesion of chemical vapour
deposited thin-film alumina on TiC using and extending a recently proposed
nonequilibrium method of ab initio thermodynamics of deposition growth (AIT-DG)
[Rohrer J and Hyldgaard P 2010 Phys. Rev. B 82 045415]. A previous study of
this system [Rohrer J, Ruberto C and Hyldgaard P 2010 J. Phys.: Condens. Matter
22 015004] found that use of equilibrium thermodynamics leads to predictions of
a non-binding TiC/alumina interface, despite the industrial use as a
wear-resistant coating. This discrepancy between equilibrium theory and
experiment is resolved by the AIT-DG method which predicts interfaces with
strong adhesion. The AIT-DG method combines density functional theory
calculations, rate-equation modelling of the pressure evolution of the
deposition environment and thermochemical data. The AIT-DG method was
previously used to predict prevalent terminations of growing or as-deposited
surfaces of binary materials. Here we extent the method to predict surface and
interface compositions of growing or as-deposited thin films on a substrate and
find that inclusion of the nonequilibrium deposition environment has important
implications for the nature of buried interfaces.Comment: 8 pages, 6 figures, submitted to J. Phys.: Condens. Matte
Insights from the shell proteome : Biomineralization to adaptation
Acknowledgments This work was supported by funding from the CACHE (Calcium in a Changing Environment) initial training network (ITN) under the European Union Seventh Framework Programme, reference grant agreement number 605051. We acknowledge E. Dufour (UMR 7209, MNHN) for shell sample preparation. We thank G. Bolbach and L. Matheron (IBPS-FR3631, Paris) for proteomic analysis and discussionsPeer reviewedPublisher PD
Assessing the reproductive biology of the Greenland shark (Somniosus microcephalus)
The Greenland shark (Somniosus microcephalus, Squaliformes: Somniosidae) is a long-lived Arctic top predator, which in combination with the high historical and modern fishing pressures, has made it subject to increased scientific focus in recent years. Key aspects of reproduction are not well known as exemplified by sparse and contradictory information e.g. on birth size and number of pups per pregnancy. This study represents the first comprehensive work on Greenland shark reproductive biology based on data from 312 specimens collected over the past 60 years. We provide guidelines quantifying reproductive parameters to assess specific maturation stages, as well as calculate body length-at-maturity (TL50) which was 2.84±0.06 m for males and 4.19±0.04 m for females. From the available information on the ovarian fecundity of Greenland sharks as well as a meta-analysis of Squaliform reproductive parameters, we estimate up to 200–324 pups per pregnancy (depending on maternal size) with a body length-at-birth of 35–45 cm. These estimates remain to be verified by future observations from gravid Greenland sharks
On post-Lie algebras, Lie--Butcher series and moving frames
Pre-Lie (or Vinberg) algebras arise from flat and torsion-free connections on
differential manifolds. They have been studied extensively in recent years,
both from algebraic operadic points of view and through numerous applications
in numerical analysis, control theory, stochastic differential equations and
renormalization. Butcher series are formal power series founded on pre-Lie
algebras, used in numerical analysis to study geometric properties of flows on
euclidean spaces. Motivated by the analysis of flows on manifolds and
homogeneous spaces, we investigate algebras arising from flat connections with
constant torsion, leading to the definition of post-Lie algebras, a
generalization of pre-Lie algebras. Whereas pre-Lie algebras are intimately
associated with euclidean geometry, post-Lie algebras occur naturally in the
differential geometry of homogeneous spaces, and are also closely related to
Cartan's method of moving frames. Lie--Butcher series combine Butcher series
with Lie series and are used to analyze flows on manifolds. In this paper we
show that Lie--Butcher series are founded on post-Lie algebras. The functorial
relations between post-Lie algebras and their enveloping algebras, called
D-algebras, are explored. Furthermore, we develop new formulas for computations
in free post-Lie algebras and D-algebras, based on recursions in a magma, and
we show that Lie--Butcher series are related to invariants of curves described
by moving frames.Comment: added discussion of post-Lie algebroid
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