208,360 research outputs found
Euclidean distance geometry and applications
Euclidean distance geometry is the study of Euclidean geometry based on the
concept of distance. This is useful in several applications where the input
data consists of an incomplete set of distances, and the output is a set of
points in Euclidean space that realizes the given distances. We survey some of
the theory of Euclidean distance geometry and some of the most important
applications: molecular conformation, localization of sensor networks and
statics.Comment: 64 pages, 21 figure
Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields
We apply Density Functional Theory (DFT) and the DFT+U technique to study the
adsorption of transition metal porphine molecules on atomistically flat Au(111)
surfaces. DFT calculations using the Perdew-Burke-Ernzerhof (PBE) exchange
correlation functional correctly predict the palladium porphine (PdP) low-spin
ground state. PdP is found to adsorb preferentially on gold in a flat geometry,
not in an edgewise geometry, in qualitative agreement with experiments on
substituted porphyrins. It exhibits no covalent bonding to Au(111), and the
binding energy is a small fraction of an eV. The DFT+U technique, parameterized
to B3LYP predicted spin state ordering of the Mn d-electrons, is found to be
crucial for reproducing the correct magnetic moment and geometry of the
isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111)
substantially alters the Mn ion spin state. Its interaction with the gold
substrate is stronger and more site-specific than PdP. The binding can be
partially reversed by applying an electric potential, which leads to
significant changes in the electronic and magnetic properties of adsorbed MnP,
and ~ 0.1 Angstrom, changes in the Mn-nitrogen distances within the porphine
macrocycle. We conjecture that this DFT+U approach may be a useful general
method for modeling first row transition metal ion complexes in a
condensed-matter setting.Comment: 14 pages, 6 figure
GreMuTRRR: A Novel Genetic Algorithm to Solve Distance Geometry Problem for Protein Structures
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to
predict the native structure of proteins. However, NMR machines are only able
to report approximate and partial distances between pair of atoms. To build the
protein structure one has to solve the Euclidean distance geometry problem
given the incomplete interval distance data produced by NMR machines. In this
paper, we propose a new genetic algorithm for solving the Euclidean distance
geometry problem for protein structure prediction given sparse NMR data. Our
genetic algorithm uses a greedy mutation operator to intensify the search, a
twin removal technique for diversification in the population and a random
restart method to recover stagnation. On a standard set of benchmark dataset,
our algorithm significantly outperforms standard genetic algorithms.Comment: Accepted for publication in the 8th International Conference on
Electrical and Computer Engineering (ICECE 2014
Effects of bonding type and interface geometry on coherent transport through the single-molecule magnet Mn12
We examine theoretically coherent electron transport through the
single-molecule magnet Mn, bridged between Au(111) electrodes, using the
non-equilibrium Green's function method and the density-functional theory. We
analyze the effects of bonding type, molecular orientation, and geometry
relaxation on the electronic properties and charge and spin transport across
the single-molecule junction. We consider nine interface geometries leading to
five bonding mechanisms and two molecular orientations: (i) Au-C bonding, (ii)
Au-Au bonding, (iii) Au-S bonding, (iv) Au-H bonding, and (v) physisorption via
van der Waals forces. The two molecular orientations of Mn correspond to
the magnetic easy axis of the molecule aligned perpendicular [hereafter denoted
as orientation (1)] or parallel [orientation (2)] to the direction of electron
transport. We find that the electron transport is carried by the lowest
unoccupied molecular orbital (LUMO) level in all the cases that we have
simulated. Relaxation of the junction geometries mainly shifts the relevant
occupied molecular levels toward the Fermi energy as well as slightly reduces
the broadening of the LUMO level. As a result, the current slightly decreases
at low bias voltage. Our calculations also show that placing the molecule in
the orientation (1) broadens the LUMO level much more than in the orientation
(2), due to the internal structure of the Mn. Consequently, junctions
with the former orientation yield a higher current than those with the latter.
Among all of the bonding types considered, the Au-C bonding gives rise to the
highest current (about one order of magnitude higher than the Au-S bonding),
for a given distance between the electrodes. The current through the junction
with other bonding types decreases in the order of Au-Au, Au-S, and Au-H.
Importantly, the spin-filtering effect in all the nine geometries stays robust
and their ratios of the majority-spin to the minority-spin transmission
coefficients are in the range of 10 to 10. The general trend in
transport among the different bonding types and molecular orientations obtained
from this study may be applied to other single-molecular magnets.Comment: Accepted for publication in Phys. Rev. B
A Computational Methodology to Screen Activities of Enzyme Variants
We present a fast computational method to efficiently screen enzyme activity.
In the presented method, the effect of mutations on the barrier height of an
enzyme-catalysed reaction can be computed within 24 hours on roughly 10
processors. The methodology is based on the PM6 and MOZYME methods as
implemented in MOPAC2009, and is tested on the first step of the amide
hydrolysis reaction catalyzed by Candida Antarctica lipase B (CalB) enzyme. The
barrier heights are estimated using adiabatic mapping and are shown to give
barrier heights to within 3kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a
small model system. Relatively strict convergence criteria
(0.5kcal/(mol{\AA})), long NDDO cutoff distances within the MOZYME method
(15{\AA}) and single point evaluations using conventional PM6 are needed for
reliable results. The generation of mutant structure and subsequent setup of
the semiempirical calculations are automated so that the effect on barrier
heights can be estimated for hundreds of mutants in a matter of weeks using
high performance computing
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