34,052 research outputs found
Generating functional analysis of complex formation and dissociation in large protein interaction networks
We analyze large systems of interacting proteins, using techniques from the
non-equilibrium statistical mechanics of disordered many-particle systems.
Apart from protein production and removal, the most relevant microscopic
processes in the proteome are complex formation and dissociation, and the
microscopic degrees of freedom are the evolving concentrations of unbound
proteins (in multiple post-translational states) and of protein complexes. Here
we only include dimer-complexes, for mathematical simplicity, and we draw the
network that describes which proteins are reaction partners from an ensemble of
random graphs with an arbitrary degree distribution. We show how generating
functional analysis methods can be used successfully to derive closed equations
for dynamical order parameters, representing an exact macroscopic description
of the complex formation and dissociation dynamics in the infinite system
limit. We end this paper with a discussion of the possible routes towards
solving the nontrivial order parameter equations, either exactly (in specific
limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of
Phys Conference Series
Antiferromagnetic order in (Ga,Mn)N nanocrystals: A density functional theory study
We investigate the electronic and magnetic properties of (Ga,Mn)N
nanocrystals using the density functional theory. We study both wurtzite and
zinc-blende structures doped with one or two substitutional Mn impurities. For
a single Mn dopant placed close to surface, the behavior of the empty
Mn-induced state, hereafter referred to as "Mn hole", is different from bulk
(Ga,Mn)N. The energy level corresponding to this off-center Mn hole lies within
the nanocrystal gap near the conduction edge. For two Mn dopants, the most
stable magnetic configuration is antiferromagnetic, and this was unexpected
since (Ga,Mn)N bulk shows ferromagnetism in the ground state. The surprising
antiferromagnetic alignment of two Mn spins is ascribed also to the holes
linked to the Mn impurities located close to surface. Unlike Mn holes in
(Ga,Mn)N bulk, these Mn holes in confined (Ga,Mn)N nanostructures do not
contribute to the ferromagnetic alignment of the two Mn spins
Optical spin control in nanocrystalline magnetic nanoswitches
We investigate the optical properties of (Cd,Mn)Te quantum dots (QDs) by
looking at the excitons as a function of the Mn impurities positions and their
magnetic alignments. When doped with two Mn impurities, the Mn spins, aligned
initially antiparallel in the ground state, have lower energy in the parallel
configuration for the optically active spin-up exciton. Hence, the
photoexcitation of the QD ground state with antiparallel Mn spins induces one
of them to flip and they align parallel. This suggests that (Cd,Mn)Te QDs are
suitable for spin-based operations handled by light
First-principles calculations of the magnetic properties of (Cd,Mn)Te nanocrystals
We investigate the electronic and magnetic properties of Mn-doped CdTe
nanocrystals (NCs) with 2 nm in diameter which can be experimentally
synthesized with Mn atoms inside. Using the density-functional theory, we
consider two doping cases: NCs containing one or two Mn impurities. Although
the Mn d peaks carry five up electrons in the dot, the local magnetic moment on
the Mn site is 4.65 mu_B. It is smaller than 5 mu_B because of the sp-d
hybridization between the localized 3d electrons of the Mn atoms and the s- and
p-type valence states of the host compound. The sp-d hybridization induces
small magnetic moments on the Mnnearest- neighbor Te sites, antiparallel to the
Mn moment affecting the p-type valence states of the undoped dot, as usual for
a kinetic-mediated exchange magnetic coupling. Furthermore, we calculate the
parameters standing for the sp-d exchange interactions. Conduction N0\alpha and
valence N0\beta are close to the experimental bulk values when the Mn
impurities occupy bulklike NCs' central positions, and they tend to zero close
to the surface. This behavior is further explained by an analysis of
valence-band-edge states showing that symmetry breaking splits the states and
in consequence reduces the exchange. For two Mn atoms in several positions, the
valence edge states show a further departure from an interpretation based in a
perturbative treatment. We also calculate the d-d exchange interactions |Jdd|
between Mn spins. The largest |Jdd| value is also for Mn atoms on bulklike
central sites; in comparison with the experimental d-d exchange constant in
bulk Cd0.95Mn0.05Te, it is four times smaller
A standardised method for measuring in situ denitrification in shallow aquifers: numerical validation and measurements in riparian wetlands
A tracer test to examine in situ denitrification in shallow groundwater by a piezometer with a packer system used bromide as a tracer of dilution and acetylene (10%) to block the denitrification process at the nitrous oxide stage. During the test, dissolved oxygen, nitrate (NO3-), bromide (Br-), nitrous oxide (N2O) and dissolved organic carbon (DOC) were measured. To calibrate the experimental method, comparison with numerical simulations of the groundwater transfer were carried out, taking into account the environmental characteristics. The method was tested by measurements undertaken in different environmental conditions (geology, land use and hydrology) in two riparian wetlands. Denitrification rates measured by this method ranged from 5.7 10-6 g N-NO3-L-1 h-1 to 1.97 10-3 g N-NO3-L-1 h-1 The method is applicable in shallow aquifers with a permeability from 10-2 to 10-4m s-1
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