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

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

Multiple-mouse Neuroanatomical Magnetic Resonance Imaging

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and evaluating mouse models of human disease. MRI is an excellent modality for investigating genetically altered animals. It is capable of whole brain coverage, can be used in vivo, and provides multiple contrast mechanisms for investigating different aspects of neuranatomy and physiology. The advent of high-field scanners along with the ability to scan multiple mice simultaneously allows for rapid phenotyping of novel mutations

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$_\gamma$ 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

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

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

DFT Study of Planar Boron Sheets: A New Template for Hydrogen Storage

We study the hydrogen storage properties of planar boron sheets and compare them to those of graphene. The binding of molecular hydrogen to the boron sheet (0.05 eV) is stronger than that to graphene. We find that dispersion of alkali metal (AM = Li, Na, and K) atoms onto the boron sheet markedly increases hydrogen binding energies and storage capacities. The unique structure of the boron sheet presents a template for creating a stable lattice of strongly bonded metal atoms with a large nearest neighbor distance. In contrast, AM atoms dispersed on graphene tend to cluster to form a bulk metal. In particular the boron-Li system is found to be a good candidate for hydrogen storage purposes. In the fully loaded case this compound can contain up to 10.7 wt. % molecular hydrogen with an average binding energy of 0.15 eV/H2.Comment: 19 pages, 7 figures, and 3 table

Assessment of interatomic potentials for atomistic analysis of static and dynamic properties of screw dislocations in W

Screw dislocations in bcc metals display non-planar cores at zero temperature which result in high lattice friction and thermally activated strain rate behavior. In bcc W, electronic structure molecular statics calculations reveal a compact, non-degenerate core with an associated Peierls stress between 1.7 and 2.8 GPa. However, a full picture of the dynamic behavior of dislocations can only be gained by using more efficient atomistic simulations based on semiempirical interatomic potentials. In this paper we assess the suitability of five different potentials in terms of static properties relevant to screw dislocations in pure W. As well, we perform molecular dynamics simulations of stress-assisted glide using all five potentials to study the dynamic behavior of screw dislocations under shear stress. Dislocations are seen to display thermally-activated motion in most of the applied stress range, with a gradual transition to a viscous damping regime at high stresses. We find that one potential predicts a core transformation from compact to dissociated at finite temperature that affects the energetics of kink-pair production and impacts the mechanism of motion. We conclude that a modified embedded-atom potential achieves the best compromise in terms of static and dynamic screw dislocation properties, although at an expense of about ten-fold compared to central potentials

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