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