838 research outputs found
(FNMR)-F-19 and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis
Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use 19F NMR chemical shifts in the MgF3− transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3− oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3− group based on the structure of a RhoA/GAP-GDP-MgF3− TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85′ side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln-63 carboxamide by Arg85′ to preclude direct hydrogen bonding from water to the target γ-PO3− group
How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
Procedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to "best practice" in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly
Computation of protein geometry and its applications: Packing and function prediction
This chapter discusses geometric models of biomolecules and geometric
constructs, including the union of ball model, the weigthed Voronoi diagram,
the weighted Delaunay triangulation, and the alpha shapes. These geometric
constructs enable fast and analytical computaton of shapes of biomoleculres
(including features such as voids and pockets) and metric properties (such as
area and volume). The algorithms of Delaunay triangulation, computation of
voids and pockets, as well volume/area computation are also described. In
addition, applications in packing analysis of protein structures and protein
function prediction are also discussed.Comment: 32 pages, 9 figure
A characteristic particle method for traffic flow simulations on highway networks
A characteristic particle method for the simulation of first order
macroscopic traffic models on road networks is presented. The approach is based
on the method "particleclaw", which solves scalar one dimensional hyperbolic
conservations laws exactly, except for a small error right around shocks. The
method is generalized to nonlinear network flows, where particle approximations
on the edges are suitably coupled together at the network nodes. It is
demonstrated in numerical examples that the resulting particle method can
approximate traffic jams accurately, while only devoting a few degrees of
freedom to each edge of the network.Comment: 15 pages, 5 figures. Accepted to the proceedings of the Sixth
International Workshop Meshfree Methods for PDE 201
Absence of First-order Transition and Tri-critical Point in the Dynamic Phase Diagram of a Spatially Extended Bistable System in an Oscillating Field
It has been well established that spatially extended, bistable systems that
are driven by an oscillating field exhibit a nonequilibrium dynamic phase
transition (DPT). The DPT occurs when the field frequency is on the order of
the inverse of an intrinsic lifetime associated with the transitions between
the two stable states in a static field of the same magnitude as the amplitude
of the oscillating field. The DPT is continuous and belongs to the same
universality class as the equilibrium phase transition of the Ising model in
zero field [G. Korniss et al., Phys. Rev. E 63, 016120 (2001); H. Fujisaka et
al., Phys. Rev. E 63, 036109 (2001)]. However, it has previously been claimed
that the DPT becomes discontinuous at temperatures below a tricritical point
[M. Acharyya, Phys. Rev. E 59, 218 (1999)]. This claim was based on
observations in dynamic Monte Carlo simulations of a multipeaked probability
density for the dynamic order parameter and negative values of the fourth-order
cumulant ratio. Both phenomena can be characteristic of discontinuous phase
transitions. Here we use classical nucleation theory for the decay of
metastable phases, together with data from large-scale dynamic Monte Carlo
simulations of a two-dimensional kinetic Ising ferromagnet, to show that these
observations in this case are merely finite-size effects. For sufficiently
small systems and low temperatures, the continuous DPT is replaced, not by a
discontinuous phase transition, but by a crossover to stochastic resonance. In
the infinite-system limit the stochastic-resonance regime vanishes, and the
continuous DPT should persist for all nonzero temperatures
Displaced but not replaced: the impact of e-learning on academic identities in higher education.
Challenges facing universities are leading many to implement institutional strategies to incorporate e-learning rather than leaving its adoption up to enthusiastic individuals. Although there is growing understanding about the impact of e-learning on the student experience, there is less understanding of academics’ perceptions of e-learning and its impact on their identities. This paper explores the changing nature of academic identities revealed through case study research into the implementation of e-learning at one UK university. By providing insight into the lived experiences of academics in a university in which technology is not only transforming access to knowledge but also influencing the balance of power between academic and student in knowledge production and use, it is suggested that academics may experience a jolt to their ‘trajectory of self’ when engaging with e-learning. The potential for e-learning to prompt loss of teacher presence and displacement as knowledge expert may appear to undermine the ontological security of their academic identity
Current Fluctuations of the One Dimensional Symmetric Simple Exclusion Process with Step Initial Condition
For the symmetric simple exclusion process on an infinite line, we calculate
exactly the fluctuations of the integrated current during time
through the origin when, in the initial condition, the sites are occupied with
density on the negative axis and with density on the positive
axis. All the cumulants of grow like . In the range where , the decay of the distribution of is
non-Gaussian. Our results are obtained using the Bethe ansatz and several
identities recently derived by Tracy and Widom for exclusion processes on the
infinite line.Comment: 2 figure
Using GIS-linked Bayesian Belief Networks as a tool for modelling urban biodiversity
The ability to predict spatial variation in biodiversity is a long-standing but elusive objective of landscape ecology. It depends on a detailed understanding of relationships between landscape and patch structure and taxonomic richness, and accurate spatial modelling. Complex heterogeneous environments such as cities pose particular challenges, as well as heightened relevance, given the increasing rate of urbanisation globally. Here we use a GIS-linked Bayesian Belief Network approach to test whether landscape and patch structural characteristics (including vegetation height, green-space patch size and their connectivity) drive measured taxonomic richness of numerous invertebrate, plant, and avian groups. We find that modelled richness is typically higher in larger and better-connected green-spaces with taller vegetation, indicative of more complex vegetation structure and consistent with the principle of ‘bigger, better, and more joined up’. Assessing the relative importance of these variables indicates that vegetation height is the most influential in determining richness for a majority of taxa. There is variation, however, between taxonomic groups in the relationships between richness and landscape structural characteristics, and the sensitivity of these relationships to particular predictors. Consequently, despite some broad commonalities, there will be trade-offs between different taxonomic groups when designing urban landscapes to maximise biodiversity. This research demonstrates the feasibility of using a GIS-coupled Bayesian Belief Network approach to model biodiversity at fine spatial scales in complex landscapes where current data and appropriate modelling approaches are lacking, and our findings have important implications for ecologists, conservationists and planners
Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV
A search for a Higgs boson decaying into two photons is described. The
analysis is performed using a dataset recorded by the CMS experiment at the LHC
from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an
integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross
section of the standard model Higgs boson decaying to two photons. The expected
exclusion limit at 95% confidence level is between 1.4 and 2.4 times the
standard model cross section in the mass range between 110 and 150 GeV. The
analysis of the data excludes, at 95% confidence level, the standard model
Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The
largest excess of events above the expected standard model background is
observed for a Higgs boson mass hypothesis of 124 GeV with a local significance
of 3.1 sigma. The global significance of observing an excess with a local
significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is
estimated to be 1.8 sigma. More data are required to ascertain the origin of
this excess.Comment: Submitted to Physics Letters
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS
We present the results of a search for new, heavy particles that decay at a
significant distance from their production point into a final state containing
charged hadrons in association with a high-momentum muon. The search is
conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV
and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS
detector operating at the Large Hadron Collider. Production of such particles
is expected in various scenarios of physics beyond the standard model. We
observe no signal and place limits on the production cross-section of
supersymmetric particles in an R-parity-violating scenario as a function of the
neutralino lifetime. Limits are presented for different squark and neutralino
masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final
version to appear in Physics Letters
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