1,961 research outputs found
Hydrogen Absorption Properties of Metal-Ethylene Complexes
Recently, we have predicted [Phys. Rev. Lett. 97, 226102 (2006)] that a
single ethylene molecule can form stable complexes with light transition metals
(TM) such as Ti and the resulting TMn-ethylene complex can absorb up to ~12 and
14 wt % hydrogen for n=1 and 2, respectively. Here we extend this study to
include a large number of other metals and different isomeric structures. We
obtained interesting results for light metals such as Li. The ethylene molecule
is able to complex with two Li atoms with a binding energy of 0.7 eV/Li which
then binds up to two H2 molecules per Li with a binding energy of 0.24 eV/H2
and absorption capacity of 16 wt %, a record high value reported so far. The
stability of the proposed metal-ethylene complexes was tested by extensive
calculations such as normal-mode analysis, finite temperature first-principles
molecular dynamics (MD) simulations, and reaction path calculations. The phonon
and MD simulations indicate that the proposed structures are stable up to 500
K. The reaction path calculations indicate about 1 eV activation barrier for
the TM2-ethylene complex to transform into a possible lower energy
configuration where the ethylene molecule is dissociated. Importantly, no
matter which isometric configuration the TM2-ethylene complex possesses, the TM
atoms are able to bind multiple hydrogen molecules with suitable binding energy
for room temperature storage. These results suggest that co-deposition of
ethylene with a suitable precursor of TM or Li into nanopores of light-weight
host materials may be a very promising route to discovering new materials with
high-capacity hydrogen absorption properties
Self-learning Kinetic Monte-Carlo method: application to Cu(111)
We present a novel way of performing kinetic Monte Carlo simulations which
does not require an {\it a priori} list of diffusion processes and their
associated energetics and reaction rates.
Rather, at any time during the simulation, energetics for all possible
(single or multi-atom) processes, within a specific interaction range, are
either computed accurately using a saddle point search procedure, or retrieved
from a database in which previously encountered processes are stored. This
self-learning procedure enhances the speed of the simulations along with a
substantial gain in reliability because of the inclusion of many-particle
processes.
Accompanying results from the application of the method to the case of
two-dimensional Cu adatom-cluster diffusion and coalescence on Cu(111) with
detailed statistics of involved atomistic processes and contributing diffusion
coefficients attest to the suitability of the method for the purpose.Comment: 18 pages, 9 figure
Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction
Atomic motions and energetics for a phosphate transfer reaction catalyzed by
the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density
functional theory, starting from structures of proteins crystallized in both
the reactant conformation (RC) and the transition-state conformation (TC). In
the TC, we calculate that the reactants and products are nearly isoenergetic
with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV
in the RC, with an even higher barrier. With the protein in the TC, the motions
involved in reaction are small, with only P and the catalytic proton
moving more than 0.5 \AA. Examination of the structures reveals that in the RC
the active site cleft is not completely closed and there is insufficient space
for the phosphorylated serine residue in the product state. Together, these
observations imply that the phosphate transfer reaction occurs rapidly and
reversibly in a particular conformation of the protein, and that the reaction
can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc
Screw dislocation in zirconium: An ab initio study
Plasticity in zirconium is controlled by 1/3 screw dislocations
gliding in the prism planes of the hexagonal close-packed structure. This
prismatic and not basal glide is observed for a given set of transition metals
like zirconium and is known to be related to the number of valence electrons in
the d band. We use ab initio calculations based on the density functional
theory to study the core structure of screw dislocations in zirconium.
Dislocations are found to dissociate in the prism plane in two partial
dislocations, each with a pure screw character. Ab initio calculations also
show that the dissociation in the basal plane is unstable. We calculate then
the Peierls barrier for a screw dislocation gliding in the prism plane and
obtain a small barrier. The Peierls stress deduced from this barrier is lower
than 21 MPa, which is in agreement with experimental data. The ability of an
empirical potential relying on the embedded atom method (EAM) to model
dislocations in zirconium is also tested against these ab initio calculations
Investigating Rare Events by Transition Interface Sampling
We briefly review simulation schemes for the investigation of rare
transitions and we resume the recently introduced Transition Interface
Sampling, a method in which the computation of rate constants is recast into
the computation of fluxes through interfaces dividing the reactant and product
state.Comment: 12 pages, 1 figure, contributed paper to the proceedings of NEXT
2003, Second Sardinian International Conference on News and Expectations in
Thermostatistics, 21-28 Sep 2003, Cagliari (Italy
The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein
The folding pathway and rate coefficients of the folding of a knotted protein
are calculated for a potential energy function with minimal energetic
frustration. A kinetic transition network is constructed using the discrete
path sampling approach, and the resulting potential energy surface is
visualized by constructing disconnectivity graphs. Owing to topological
constraints, the low-lying portion of the landscape consists of three distinct
regions, corresponding to the native knotted state and to configurations where
either the N- or C-terminus is not yet folded into the knot. The fastest
folding pathways from denatured states exhibit early formation of the
N-terminus portion of the knot and a rate-determining step where the C-terminus
is incorporated. The low-lying minima with the N-terminus knotted and the
C-terminus free therefore constitute an off-pathway intermediate for this
model. The insertion of both the N- and C-termini into the knot occur late in
the folding process, creating large energy barriers that are the rate limiting
steps in the folding process. When compared to other protein folding proteins
of a similar length, this system folds over six orders of magnitude more
slowly.Comment: 19 page
A new triclinic modification of the pyrochlore-type KOs2O6 superconductor
A new modification of KOs2O6, the representative of a new structural type
(Pearson symbol aP18, a=5.5668(1)A, b=6.4519(2)A, c=7.2356(2)A, space group
P-1, no.2) was synthesized employing high pressure technique. Its structure was
determined by single-crystal X-ray diffraction. The structure can be described
as two OsO6 octahedral chains relating to each other through inversion and
forming big voids with K atoms inside. Quantum chemical calculations were
performed on the novel compound and structurally related cubic compound.
High-pressure X-ray study showed that cubic KOs2O6 phase was stable up to
32.5(2) GPa at room temperature.Comment: 23 pages, 9 figures,6 tables. Accepted for J. Solid State Che
String Method for the Study of Rare Events
We present a new and efficient method for computing the transition pathways,
free energy barriers, and transition rates in complex systems with relatively
smooth energy landscapes. The method proceeds by evolving strings, i.e. smooth
curves with intrinsic parametrization whose dynamics takes them to the most
probable transition path between two metastable regions in the configuration
space. Free energy barriers and transition rates can then be determined by
standard umbrella sampling technique around the string. Applications to
Lennard-Jones cluster rearrangement and thermally induced switching of a
magnetic film are presented.Comment: 4 pages, 4 figure
Semi-Automatic segmentation of multiple mouse embryos in MR images
<p>Abstract</p> <p>Background</p> <p>The motivation behind this paper is to aid the automatic phenotyping of mouse embryos, wherein multiple embryos embedded within a single tube were scanned using Magnetic Resonance Imaging (MRI).</p> <p>Results</p> <p>Our algorithm, a modified version of the simplex deformable model of Delingette, addresses various issues with deformable models including initialization and inability to adapt to boundary concavities. In addition, it proposes a novel technique for automatic collision detection of multiple objects which are being segmented simultaneously, hence avoiding major leaks into adjacent neighbouring structures. We address the initialization problem by introducing balloon forces which expand the initial spherical models close to the true boundaries of the embryos. This results in models which are less sensitive to initial minimum of two fold after each stage of deformation. To determine collision during segmentation, our unique collision detection algorithm finds the intersection between binary masks created from the deformed models after every few iterations of the deformation and modifies the segmentation parameters accordingly hence avoiding collision.</p> <p>We have segmented six tubes of three dimensional MR images of multiple mouse embryos using our modified deformable model algorithm. We have then validated the results of the our semi-automatic segmentation versus manual segmentation of the same embryos. Our Validation shows that except paws and tails we have been able to segment the mouse embryos with minor error.</p> <p>Conclusions</p> <p>This paper describes our novel multiple object segmentation technique with collision detection using a modified deformable model algorithm. Further, it presents the results of segmenting magnetic resonance images of up to 32 mouse embryos stacked in one gel filled test tube and creating 32 individual masks.</p
Relaxation kinetics in two-dimensional structures
We have studied the approach to equilibrium of islands and pores in two
dimensions. The two-regime scenario observed when islands evolve according to a
set of particular rules, namely relaxation by steps at low temperature and
smooth at high temperature, is generalized to a wide class of kinetic models
and the two kinds of structures. Scaling laws for equilibration times are
analytically derived and confirmed by kinetic Monte Carlo simulations.Comment: 6 pages, 7 figures, 1 tabl
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