2,503 research outputs found
Renormalization of myoglobin-ligand binding energetics by quantum many-body effects
We carry out a first-principles atomistic study of the electronic mechanisms
of ligand binding and discrimination in the myoglobin protein. Electronic
correlation effects are taken into account using one of the most advanced
methods currently available, namely a linear-scaling density functional theory
(DFT) approach wherein the treatment of localized iron 3d electrons is further
refined using dynamical mean-field theory (DMFT). This combination of methods
explicitly accounts for dynamical and multi-reference quantum physics, such as
valence and spin fluctuations, of the 3d electrons, whilst treating a
significant proportion of the protein (more than 1000 atoms) with density
functional theory. The computed electronic structure of the myoglobin complexes
and the nature of the Fe-O2 bonding are validated against experimental
spectroscopic observables. We elucidate and solve a long standing problem
related to the quantum-mechanical description of the respiration process,
namely that DFT calculations predict a strong imbalance between O2 and CO
binding, favoring the latter to an unphysically large extent. We show that the
explicit inclusion of many body-effects induced by the Hund's coupling
mechanism results in the correct prediction of similar binding energies for
oxy- and carbonmonoxymyoglobin.Comment: 7 pages, 5 figures. Accepted for publication in the Proceedings of
the National Academy of Sciences of the United States of America (2014). For
the published article see
http://www.pnas.org/content/early/2014/04/09/1322966111.abstrac
A Variational Approach to the Structure and Thermodynamics of Linear Polyelectrolytes with Coulomb and Screened Coulomb Interactions
A variational approach, based on a discrete representation of the chain, is
used to calculate free energy and conformational properties in
polyelectrolytes. The true bond and Coulomb potentials are approximated by a
trial isotropic harmonic energy containing force constants between {\em
all}monomer-pairs as variational parameters. By a judicious choice of
representation and the use of incremental matrix inversion, an efficient and
fast-convergent iterative algorithm is constructed, that optimizes the free
energy. The computational demand scales as rather than as expected
in a more naive approach. The method has the additional advantage that in
contrast to Monte Carlo calculations the entropy is easily computed. An
analysis of the high and low temperature limits is given. Also, the variational
formulation is shown to respect the appropriate virial identities.The accuracy
of the approximations introduced are tested against Monte Carlo simulations for
problem sizes ranging from to 1024. Very good accuracy is obtained for
chains with unscreened Coulomb interactions. The addition of salt is described
through a screened Coulomb interaction, for which the accuracy in a certain
parameter range turns out to be inferior to the unscreened case. The reason is
that the harmonic variational Ansatz becomes less efficient with shorter range
interactions.
As a by-product a very efficient Monte Carlo algorithm was developed for
comparisons, providing high statistics data for very large sizes -- 2048
monomers. The Monte Carlo results are also used to examine scaling properties,
based on low- approximations to end-end and monomer-monomer separations. It
is argued that the former increases faster than linearly with the number of
bonds.Comment: 40 pages LaTeX, 13 postscript figure
Large scale ab-initio simulations of dislocations
We present a novel methodology to compute relaxed dislocations core configurations, and their energies in crystalline metallic materials using large-scale ab-intio simulations. The approach is based on MacroDFT, a coarse-grained density functional theory method that accurately computes the electronic structure with sub-linear scaling resulting in a tremendous reduction in cost. Due to its implementation in real-space, MacroDFT has the ability to harness petascale resources to study materials and alloys through accurate ab-initio calculations. Thus, the proposed methodology can be used to investigate dislocation cores and other defects where long range elastic effects play an important role, such as in dislocation cores, grain boundaries and near precipitates in crystalline materials. We demonstrate the method by computing the relaxed dislocation cores in prismatic dislocation loops and dislocation segments in magnesium (Mg). We also study the interaction energy with a line of Aluminum (Al) solutes. Our simulations elucidate the essential coupling between the quantum mechanical aspects of the dislocation core and the long range elastic fields that they generate. In particular, our quantum mechanical simulations are able to describe the logarithmic divergence of the energy in the far field as is known from classical elastic theory. In order to reach such scaling, the number of atoms in the simulation cell has to be exceedingly large, and cannot be achieved with the state-of-the-art density functional theory implementations
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