1,708 research outputs found
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
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
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
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
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
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
Energetics and atomic mechanisms of dislocation nucleation in strained epitaxial layers
We study numerically the energetics and atomic mechanisms of misfit
dislocation nucleation and stress relaxation in a two-dimensional atomistic
model of strained epitaxial layers on a substrate with lattice misfit.
Relaxation processes from coherent to incoherent states for different
transition paths are studied using interatomic potentials of Lennard-Jones type
and a systematic saddle point and transition path search method. The method is
based on a combination of repulsive potential minimization and the Nudged
Elastic Band method. For a final state with a single misfit dislocation, the
minimum energy path and the corresponding activation barrier are obtained for
different misfits and interatomic potentials. We find that the energy barrier
decreases strongly with misfit. In contrast to continuous elastic theory, a
strong tensile-compressive asymmetry is observed. This asymmetry can be
understood as manifestation of asymmetry between repulsive and attractive
branches of pair potential and it is found to depend sensitively on the form of
the potential.Comment: 11 pages, 9 figures, to appear in Phys. Rev.
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
Nunalleq, Stories from the Village of Our Ancestors:Co-designing a multivocal educational resource based on an archaeological excavation
This work was funded by the UK-based Arts and Humanities Research Council through grants (AH/K006029/1) and (AH/R014523/1), a University of Aberdeen IKEC Award with additional support for travel and subsistence from the University of Dundee, DJCAD Research Committee RS2 project funding. Thank you to the many people who contributed their support, knowledge, feedback, voices and faces throughout the project, this list includes members of the local community, colleagues, specialists, students, and volunteers. If we have missed out any names we apologize but know that your help was appreciated. Jimmy Anaver, John Anderson, Alice Bailey, Kieran Baxter, Pauline Beebe, Ellinor Berggren, Dawn Biddison, Joshua Branstetter, Brendan Body, Lise Bos, Michael Broderick, Sarah Brown, Crystal Carter, Joseph Carter, Lucy Carter, Sally Carter, Ben Charles, Mary Church, Willard Church, Daniele Clementi, Annie Cleveland, Emily Cleveland, Joshua Cleveland, Aron Crowell, Neil Curtis, Angie Demma, Annie Don, Julia Farley, Veronique Forbes, Patti Fredericks, Tricia Gillam, Sean Gleason, Sven Haakanson, Cheryl Heitman, Grace Hill, Diana Hunter, Joel Isaak, Warren Jones, Stephan Jones, Ana Jorge, Solveig Junglas, Melia Knecht, Rick Knecht, Erika Larsen, Paul Ledger, Jonathan Lim Soon, Amber Lincoln, Steve Luke, Francis Lukezic, Eva Malvich, Pauline Matthews, Roy Mark, Edouard Masson-MacLean, Julie Masson-MacLean, Mhairi Maxwell, Chuna Mcintyre, Drew Michael, Amanda Mina, Anna Mossolova, Carl Nicolai Jr, Chris Niskanen, Molly Odell, Tom Paxton, Lauren Phillips, Lucy Qin, Charlie Roberts, Chris Rowe, Rufus Rowe,Chris Rowland, John Rundall, Melissa Shaginoff, Monica Shah, Anna Sloan, Darryl Small Jr, John Smith, Mike Smith, Joey Sparaga, Hannah Strehlau, Dora Strunk, Larissa Strunk, Lonny Strunk, Larry Strunk, Robbie Strunk, Sandra Toloczko, Richard Vanderhoek, the Qanirtuuq Incorporated Board, the Quinhagak Dance Group and the staff at Kuinerrarmiut Elitnaurviat. We also extend our thanks to three anonymous reviewers for their valuable comments on our paper.Peer reviewedPublisher PD
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