7,642 research outputs found
Equivalence of domains for hyperbolic Hubbard-Stratonovich transformations
We settle a long standing issue concerning the traditional derivation of
non-compact non-linear sigma models in the theory of disordered electron
systems: the hyperbolic Hubbard-Stratonovich (HS) transformation of
Pruisken-Schaefer type. Only recently the validity of such transformations was
proved in the case of U(p,q) (non-compact unitary) and O(p,q) (non-compact
orthogonal) symmetry. In this article we give a proof for general non-compact
symmetry groups. Moreover we show that the Pruisken-Schaefer type
transformations are related to other variants of the HS transformation by
deformation of the domain of integration. In particular we clarify the origin
of surprising sign factors which were recently discovered in the case of
orthogonal symmetry.Comment: 30 pages, 3 figure
Diffusion limited reactions in confined environments
We study the effect of confinement on diffusion limited bimolecular reactions
within a lattice model where a small number of reactants diffuse amongst a much
larger number of inert particles. When the number of inert particles is held
constant the rate of the reaction is slow for small reaction volumes due to
limited mobility from crowding, and for large reaction volumes due to the
reduced concentration of the reactants. The reaction rate proceeds fastest at
an intermediate confinement corresponding to volume fraction near 1/2 and 1/3
in two and three dimensions, respectively. We generalize the model to
off-lattice systems with hydrodynamic coupling and predict that the optimal
reaction rate for monodisperse colloidal systems occurs when the volume
fraction is ~0.18. Finally, we discuss the application of our model to
bimolecular reactions inside cells as well as the dynamics of confined
polymers.Comment: 4 pages, 3 figure
Building block libraries and structural considerations in the self-assembly of polyoxometalate and polyoxothiometalate systems
Inorganic metal-oxide clusters form a class of compounds that are unique in their topological and electronic versatility and are becoming increasingly more important in a variety of applications. Namely, Polyoxometalates (POMs) have shown an unmatched range of physical properties and the ability to form structures that can bridge several length scales. The formation of these molecular clusters is often ambiguous and is governed by self-assembly processes that limit our ability to rationally design such molecules. However, recent years have shown that by considering new building block principles the design and discovery of novel complex clusters is aiding our understanding of this process. Now with current progress in thiometalate chemistry, specifically polyoxothiometalates (POTM), the field of inorganic molecular clusters has further diversified allowing for the targeted development of molecules with specific functionality. This chapter discusses the main differences between POM and POTM systems and how this affects synthetic methodologies and reactivities. We will illustrate how careful structural considerations can lead to the generation of novel building blocks and further deepen our understanding of complex systems
Genetic noise control via protein oligomerization
Gene expression in a cell entails random reaction events occurring over
disparate time scales. Thus, molecular noise that often results in phenotypic
and population-dynamic consequences sets a fundamental limit to biochemical
signaling. While there have been numerous studies correlating the architecture
of cellular reaction networks with noise tolerance, only a limited effort has
been made to understand the dynamic role of protein-protein interactions. Here
we have developed a fully stochastic model for the positive feedback control of
a single gene, as well as a pair of genes (toggle switch), integrating
quantitative results from previous in vivo and in vitro studies. We find that
the overall noise-level is reduced and the frequency content of the noise is
dramatically shifted to the physiologically irrelevant high-frequency regime in
the presence of protein dimerization. This is independent of the choice of
monomer or dimer as transcription factor and persists throughout the multiple
model topologies considered. For the toggle switch, we additionally find that
the presence of a protein dimer, either homodimer or heterodimer, may
significantly reduce its random switching rate. Hence, the dimer promotes the
robust function of bistable switches by preventing the uninduced (induced)
state from randomly being induced (uninduced). The specific binding between
regulatory proteins provides a buffer that may prevent the propagation of
fluctuations in genetic activity. The capacity of the buffer is a non-monotonic
function of association-dissociation rates. Since the protein oligomerization
per se does not require extra protein components to be expressed, it provides a
basis for the rapid control of intrinsic or extrinsic noise
Crossover between Thermally Assisted and Pure Quantum Tunneling in Molecular Magnet Mn12-Acetate
The crossover between thermally assisted and pure quantum tunneling has been
studied in single crystals of high spin (S=10) uniaxial molecular magnet Mn12
using micro-Hall-effect magnetometry. Magnetic hysteresis and relaxation
experiments have been used to investigate the energy levels that determine the
magnetization reversal as a function of magnetic field and temperature. These
experiments demonstrate that the crossover occurs in a narrow (0.1 K) or broad
(1 K) temperature interval depending on the magnitude of the field transverse
to the anisotropy axis.Comment: 5 pages, 4 figure
Trapping an Iron(VI) Water-Splitting Intermediate in Nonaqueous Media
We report in situ spectroscopic measurements in nonaqueous media designed to trap an exceptionally strong oxidant generated electrochemically from an iron-containing nickel layered double hydroxide ([NiFe]-LDH) material. Anodic polarization of this material in acetonitrile produces metal-oxo vibrational spectroscopic signatures along with an extremely narrow near-infrared luminescence peak that strongly indicate that the reactive intermediate is cis-dioxo-iron(VI). Chemical trapping experiments reveal that addition of H_2O to the polarized electrochemical cell produces hydrogen peroxide; and, most importantly, addition of HO– generates oxygen. Repolarization of the electrode restores the iron(VI) spectroscopic features, confirming that the high-valent oxo complex is active in the electrocatalytic water oxidation cycle
Trapping an Iron(VI) Water-Splitting Intermediate in Nonaqueous Media
We report in situ spectroscopic measurements in nonaqueous media designed to trap an exceptionally strong oxidant generated electrochemically from an iron-containing nickel layered double hydroxide ([NiFe]-LDH) material. Anodic polarization of this material in acetonitrile produces metal-oxo vibrational spectroscopic signatures along with an extremely narrow near-infrared luminescence peak that strongly indicate that the reactive intermediate is cis-dioxo-iron(VI). Chemical trapping experiments reveal that addition of H_2O to the polarized electrochemical cell produces hydrogen peroxide; and, most importantly, addition of HO– generates oxygen. Repolarization of the electrode restores the iron(VI) spectroscopic features, confirming that the high-valent oxo complex is active in the electrocatalytic water oxidation cycle
Infrared to millimetre photometry of ultra-luminous IR galaxies: new evidence favouring a 3-stage dust model
Infrared to millimetre spectral energy distributions have been obtained for
41 bright ultra-luminous infrared galaxies. The observations were carried out
with ISOPHOT between 10 and 200 micron and supplemented for 16 sources with
SCUBA at 450 and 850 micron and with SEST at 1.3 mm. In addition, seven sources
were observed at 1.2 and 2.2 m with the 2.2 m telescope on Calar Alto.
These new SEDs represent the most complete set of infrared photometric
templates obtained so far on ULIRGs in the local universe.Comment: 23 pages, 11 figures, accepted for publication in Astronomy &
Astrophysic
Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis
The bacterial PorB porin, an ATP-binding beta-barrel protein of pathogenic Neisseria gonorrhoeae, triggers host cell apoptosis by an unknown mechanism. PorB is targeted to and imported by host cell mitochondria, causing the breakdown of the mitochondrial membrane potential (delta psi m). Here, we show that PorB induces the condensation of the mitochondrial matrix and the loss of cristae structures, sensitizing cells to the induction of apoptosis via signaling pathways activated by BH3-only proteins. PorB is imported into mitochondria through the general translocase TOM but, unexpectedly, is not recognized by the SAM sorting machinery, usually required for the assembly of beta-barrel proteins in the mitochondrial outer membrane. PorB integrates into the mitochondrial inner membrane, leading to the breakdown of delta psi m. The PorB channel is regulated by nucleotides and an isogenic PorB mutant defective in ATP-binding failed to induce delta psi m loss and apoptosis, demonstrating that dissipation of delta psi m is a requirement for cell death caused by neisserial infection
Spatial and topological organization of DNA chains induced by gene co-localization
Transcriptional activity has been shown to relate to the organization of
chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In
particular, highly transcribed genes, RNA polymerases and transcription factors
gather into discrete spatial foci called transcription factories. However, the
mechanisms underlying the formation of these foci and the resulting topological
order of the chromosome remain to be elucidated. Here we consider a
thermodynamic framework based on a worm-like chain model of chromosomes where
sparse designated sites along the DNA are able to interact whenever they are
spatially close-by. This is motivated by recurrent evidence that there exists
physical interactions between genes that operate together. Three important
results come out of this simple framework. First, the resulting formation of
transcription foci can be viewed as a micro-phase separation of the interacting
sites from the rest of the DNA. In this respect, a thermodynamic analysis
suggests transcription factors to be appropriate candidates for mediating the
physical interactions between genes. Next, numerical simulations of the polymer
reveal a rich variety of phases that are associated with different topological
orderings, each providing a way to increase the local concentrations of the
interacting sites. Finally, the numerical results show that both
one-dimensional clustering and periodic location of the binding sites along the
DNA, which have been observed in several organisms, make the spatial
co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on
http://dx.doi.org/10.1371/journal.pcbi.100067
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