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At least 559 records · Page 31Linked to original sources
PubMed2001

Equilibrating metal-oxide cluster ensembles for oxidation reactions using oxygen in water.

Although many enzymes can readily and selectively use oxygen in water-the most familiar and attractive of all oxidants and solvents, respectively-the design of synthetic catalysts for selective water-based oxidation processes utilizing molecular oxygen remains a daunting task. Particularly problematic is the fact that oxidation of substrates by O2 involves radical chemistry, which is intrinsically non-selective and difficult to control. In addition, metallo-organic catalysts are inherently susceptible to degradation by oxygen-based radicals, while their transition-metal-ion active sites often react with water to give insoluble, and thus inactive, oxides or hydroxides. Furthermore, pH control is often required to avoid acid or base degradation of organic substrates or products. Unlike metallo-organic catalysts, polyoxometalate anions are oxidatively stable and are reversible oxidants for use with O2 (refs 8,9,10). Here we show how thermodynamically controlled self-assembly of an equilibrated ensemble of polyoxometalates, with the heteropolytungstate anion [AIVVW11O40]6- as its main component, imparts both stability in water and internal pH-management. Designed to operate at near-neutral pH, this system facilitates a two-step O2-based process for the selective delignification of wood (lignocellulose) fibres. By directly monitoring the central Al atom, we show that equilibration reactions typical of polyoxometalate anions keep the pH of the system near 7 during both process steps.

Journal Article↗
PubMed2001

Long-distance quantum communication with atomic ensembles and linear optics.

Quantum communication holds promise for absolutely secure transmission of secret messages and the faithful transfer of unknown quantum states. Photonic channels appear to be very attractive for the physical implementation of quantum communication. However, owing to losses and decoherence in the channel, the communication fidelity decreases exponentially with the channel length. Here we describe a scheme that allows the implementation of robust quantum communication over long lossy channels. The scheme involves laser manipulation of atomic ensembles, beam splitters, and single-photon detectors with moderate efficiencies, and is therefore compatible with current experimental technology. We show that the communication efficiency scales polynomially with the channel length, and hence the scheme should be operable over very long distances.

Journal Article↗
PubMed2002

Constraints on radiative forcing and future climate change from observations and climate model ensembles.

The assessment of uncertainties in global warming projections is often based on expert judgement, because a number of key variables in climate change are poorly quantified. In particular, the sensitivity of climate to changing greenhouse-gas concentrations in the atmosphere and the radiative forcing effects by aerosols are not well constrained, leading to large uncertainties in global warming simulations. Here we present a Monte Carlo approach to produce probabilistic climate projections, using a climate model of reduced complexity. The uncertainties in the input parameters and in the model itself are taken into account, and past observations of oceanic and atmospheric warming are used to constrain the range of realistic model responses. We obtain a probability density function for the present-day total radiative forcing, giving 1.4 to 2.4 W m-2 for the 5-95 per cent confidence range, narrowing the global-mean indirect aerosol effect to the range of 0 to -1.2 W m-2. Ensemble simulations for two illustrative emission scenarios suggest a 40 per cent probability that global-mean surface temperature increase will exceed the range predicted by the Intergovernmental Panel on Climate Change (IPCC), but only a 5 per cent probability that warming will fall below that range.

Journal Article↗
PubMed2003

Generation of nonclassical photon pairs for scalable quantum communication with atomic ensembles.

Quantum information science attempts to exploit capabilities from the quantum realm to accomplish tasks that are otherwise impossible in the classical domain. Although sufficient conditions have been formulated for the physical resources required to achieve quantum computation and communication, there is a growing understanding of the power of quantum measurement combined with the conditional evolution of quantum states for accomplishing diverse tasks in quantum information science. For example, a protocol has recently been developed for the realization of scalable long-distance quantum communication and the distribution of entanglement over quantum networks. Here we report the first enabling step in the realization of this protocol, namely the observation of quantum correlations for photon pairs generated in the collective emission from an atomic ensemble. The nonclassical character of the fields is demonstrated by the violation of an inequality involving their normalized correlation functions. Compared to previous investigations of non-classical correlations for photon pairs produced in atomic cascades and in parametric down-conversion, our experiment is distinct in that the correlated photons are separated by a programmable time interval (of about 400 nanoseconds in our initial experiments).

Journal Article↗
PubMed2006

Malaria early warnings based on seasonal climate forecasts from multi-model ensembles.

The control of epidemic malaria is a priority for the international health community and specific targets for the early detection and effective control of epidemics have been agreed. Interannual climate variability is an important determinant of epidemics in parts of Africa where climate drives both mosquito vector dynamics and parasite development rates. Hence, skilful seasonal climate forecasts may provide early warning of changes of risk in epidemic-prone regions. Here we discuss the development of a system to forecast probabilities of anomalously high and low malaria incidence with dynamically based, seasonal-timescale, multi-model ensemble predictions of climate, using leading global coupled ocean-atmosphere climate models developed in Europe. This forecast system is successfully applied to the prediction of malaria risk in Botswana, where links between malaria and climate variability are well established, adding up to four months lead time over malaria warnings issued with observed precipitation and having a comparably high level of probabilistic prediction skill. In years in which the forecast probability distribution is different from that of climatology, malaria decision-makers can use this information for improved resource allocation.

Animals↗
PubMed2004

First spikes in ensembles of human tactile afferents code complex spatial fingertip events.

It is generally assumed that primary sensory neurons transmit information by their firing rates. However, during natural object manipulations, tactile information from the fingertips is used faster than can be readily explained by rate codes. Here we show that the relative timing of the first impulses elicited in individual units of ensembles of afferents reliably conveys information about the direction of fingertip force and the shape of the surface contacting the fingertip. The sequence in which different afferents initially discharge in response to mechanical fingertip events provides information about these events faster than the fastest possible rate code and fast enough to account for the use of tactile signals in natural manipulation.

Action Potentials↗
PubMed2025

Oncogenic DEAD-box ATPase DDX41 establishes transcript ensembles via CLK3-dependent and -independent mechanisms.

Post-transcriptional diversification of RNA transcripts mediated by complex processing machinery, including DEAD-box ATPases, establishes and maintains cellular phenotypes. For example, DDX41 controls RNA splicing, innate immune signaling, and genome stability. Although heterozygous DDX41 germline genetic variation occurs in familial myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), the DDX41 contributions to splicing globally, biological processes, and pathogenic mechanisms are incompletely defined. Using a genetic rescue system with Ddx41+/- myeloid progenitors, we established global wildtype DDX41 and pathogenic variant mechanisms. Differing from pathogenic variants of other RNA splicing regulators, DDX41 deficiency compromised multiple splicing steps. DDX41-regulated transcripts encoded factors controlling RNA splicing, including Cdc2-like kinase 3 (CLK3). DDX41 regulated Clk3 transcripts, and elevated CLK3 during myeloid differentiation. Loss-of-function analysis revealed DDX41-regulated splicing commonly, but not always, required CLK3. Thus, through a mechanism utilizing a splicing factor kinase that itself is DDX41-regulated, DDX41 establishes transcript ensembles in myeloid progenitors.

DEAD-box RNA Helicases↗
PubMed2003

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase.

The enzyme hydroxymethylbilane synthase (HMBS, EC 4.3.1.8), 313 amino acid residues and MW 34 kDa, also known as porphobilinogen deaminase (PBGD), catalyses the stepwise polymerization of four molecules of porphobilinogen (PBG) to the linear tetrapyrrole 1-hydroxymethylbilane. Several crystallographic structures of HMBS have been previously determined, most recently including by time-resolved Laue protein crystallography of the Lys59Gln mutant form with reaction initiation undertaken by use of a flow cell carrying the substrate PBG. In this paper we review these structures and add new molecular graphics representations and analyses. Moreover we present a new structure refined at 1.66 A resolution using diffraction data recorded at cryo-temperature (100 K) in an attempt at trapping the polypeptide loop (residues 47 to 58) in the vicinity of the enzyme active site, missing in all previous structure determinations. This loop still has not appeared in the electron density maps, in spite of the advantage of cryo-temperature, but nevertheless the 1.66 A cryo-structure extends the ensemble of known HMBS structures. The cryomodel of protein, cofactor and 320 bound water molecules has been refined to a final R-factor and R-free of 0.198 and 0.247 respectively; the PDB deposition codes, coordinates and structure factors are 1GTK and R1GTKSF respectively. Finally a protein comparison study is presented of the Mycobacterium tuberculosis (MTb) HMBS, with the E. coli HMBS. This has been done as preparation for future structural studies on the MTb HMBS from this important disease bearing organism. The overall amino acid sequence identity is 41%. Most interestingly there is a two-residue reduction in length of the loop referred to above (Asp 50 and Gly 58 being missing in the MTb form). This gives the hope that this loop will be less flexible and thus might become visible to crystallographic analysis.

Crystallography, X-Ray↗
PubMed2002

Reversible zinc phthalocyanine fullerene ensembles.

Novel zinc phthalocyanine (ZnPc)/fullerene ligand (L) ensembles are assembled following simple biomimetic principles, which upon photoexcitation give rise to intra complex electron transfer quenching of the 1*ZnPc fluorescence.

Journal Article↗
PubMed2003

Meso-tetrakis[o-(N-methyl)pyridinium]porphyrin ensembles with axially coordinated cyclodextrin-penetrating phenethylimidazole: reversible dioxygen-binding in aqueous DMF solution.

alpha-Cyclodextrin (alpha CD)-penetrating 2-methyl-1-phenethylimidazole coordinates to the zinc(II) and iron(II) complexes of meso-tetrakis[o-(N-methyl)pyridinium] porphyrinate, giving non-covalently linked alpha CD-porphyrin ensembles; the iron(II) complex can reversibly bind and release dioxygen in aqueous DMF solution.

Journal Article↗
PubMed1998

Reactivation of neuronal ensembles in hippocampal dentate gyrus during sleep after spatial experience.

Patterns of neuronal activity recorded in CA1 of the hippocampus and in neocortex during waking-behavior, are reactivated during subsequent slow-wave sleep (SWS). It has been suggested that this reactivation may originate in the hippocampal CA3 region, where modifiable excitatory recurrent connections are abundant and where sharp-waves in which the reactivation is most robust, appear to arise. The present experiment investigated whether ensemble firing patterns of granule cells in the fascia dentata (FD), an area 'upstream' from CA3, are also reactivated during sleep. Populations of FD granule cells were recorded from during spatial behavior and during prior and subsequent SWS. firing rate correlations between cell-pairs with overlapping place fields were significantly enhanced during post behavioral sleep compared to pre behavioral sleep. Correlations between cells with non-overlapping place fields or which were silent during maze behavior, were not changed. Thus reactivation of experience-specific correlation states also occurs in granule cells during sleep. Because these cells do not have excitatory interconnections, but form a major input to CA3 pyramidal cells, current models predicted that sleep reactivation would appear first in CA3. There are, however, both extensive polysynaptic excitatory interactions among granule cells and feedback from CA3 pyramidal cells. Granule cells also receive indirect input from neocortical regions known to undergo trace reactivation. Although a simple model for a CA3 origin of the reactivation phenomenon cannot be confirmed, the present results extend our understanding of the generality of this phenomenon.

Animals↗
PubMed2003

Dopamine gating of forebrain neural ensembles.

Dopamine may exert different actions depending on a number of factors. A common view is that D1 receptors may be responsible for excitatory actions whereas D2 receptors are involved in inhibitory actions. However, this position cannot be reconciled with several findings indicating otherwise. The role of dopamine on forebrain neural ensembles may be better understood in the light of functional states of the system. Pyramidal cortical neurons and striatal medium spiny neurons alternate between two membrane potential states ('up' and 'down') that could shape dopamine actions. It is proposed that D1 receptors can act as state-stabilizers by sustaining up states and thereby facilitating plasticity mechanisms by providing postsynaptic depolarization and increasing NMDA function. In this way, dopamine can sustain activity in depolarized units. This action is accompanied by a decrease in cell firing (perhaps mediated by D2 receptors), which renders the cells responsive only to strong stimuli. The result would be a net increase in signal-to-noise ratio in a selected assembly of neurons.

Animals↗
PubMed2003

Glutamate motivational ensembles in nucleus accumbens: rostrocaudal shell gradients of fear and feeding.

This study demonstrates that microinjection of an AMPA/kainate glutamate antagonist elicits motivated fear and feeding behaviour mapped along rostrocaudal gradients of positive-to-negative valence in nucleus accumbens shell (similar to rostrocaudal shell gradients recently reported for GABA agonist microinjections). Rats received rostral or caudal microinjections of the glutamate AMPA/kainate receptor antagonist DNQX (0, 50, 450 or 850 ng in 0.5 micro L) or the NMDA receptor antagonist MK-801 (0, 0.5, 1 or 2 micro g in 0.5 micro L), into medial accumbens shell prior to behavioural tests for fear, feeding or conditioning of place preference or avoidance. Another group received rostral or caudal microinjections of DNQX in nucleus accumbens core. Rostral shell DNQX microinjections potently increased appetitive food intake and established only weak conditioned place avoidance. Caudal shell DNQX microinjections elicited defensive treading behaviour, caused rats to defensively bite the experimenter and emit fearful distress vocalizations when handled, and established strong conditioned place avoidance. By contrast, no rostrocaudal gradients of motivational bivalence were produced by microinjections of the glutamate AMPA/kainate receptor antagonist DNQX into the core, or by microinjections of the NMDA antagonist MK-801 into the shell. Our results indicate that appetitive and aversive motivation is carried in anatomically differentiated channels by mesocorticolimbic glutamate signals to microcircuits in the medial shell. Hyperpolarization of local shell ensembles by AMPA/kainate glutamate receptor blockade elicits fear and feeding behaviours mapped along distinct positive-to-negative rostrocaudal gradients.

Animals↗
PubMed2004

Water in nanopores. I. Coexistence curves from Gibbs ensemble Monte Carlo simulations.

Coexistence curves of water in cylindrical and slitlike nanopores of different size and water-substrate interaction strength were simulated in the Gibbs ensemble. The two-phase coexistence regions cover a wide range of pore filling level and temperature, including ambient temperature. Five different kinds of two-phase coexistence are observed. A single liquid-vapor coexistence is observed in hydrophobic and moderately hydrophilic pores. Surface transitions split from the main liquid-vapor coexistence region, when the water-substrate interaction becomes comparable or stronger than the water-water pair interaction. In this case prewetting, one and two layering transitions were observed. The critical temperature of the first layering transition decreases with strengthening water-substrate interaction towards the critical temperature expected for two-dimensional systems and is not sensitive to the variation of pore size and shape. Liquid-vapor phase transition in a pore with a wall which is already covered with two water layers is most typical for hydrophilic pores. The critical temperature of this transition is very sensitive to the pore size, in contrast to the liquid-vapor critical temperature in hydrophobic pores. The observed rich phase behavior of water in pores evidences that the knowledge of coexistence curves is of crucial importance for the analysis of experimental results and a prerequiste of meaningful simulations.

Journal Article↗
PubMed2004

Phase separation in mixtures of Yukawa and charged Yukawa particles from Gibbs ensemble Monte Carlo simulations and the mean spherical approximation.

The phase equilibrium of mixtures of Yukawa and charged Yukawa particles is studied by means of Gibbs ensemble Monte Carlo (GEMC) simulation method and the mean spherical approximation (MSA). The strength of the Coulomb energy compared to that of the Yukawa attraction is characterized by a coupling constant. For low coupling constants a classical vapor--liquid phase separation appears with a good agreement between GEMC and the MSA. For high coupling constant, a phase separation between a salt poor and a salt rich phase occurs that resembles the phase equilibrium behavior of the solvent primitive model.

Journal Article↗
PubMed2004

Polymorphism in simple liquids: a Gibbs ensemble Monte Carlo study.

We perform Gibbs ensemble Monte Carlo (GEMC) simulations of a one-component system of hard spheres with a repulsive shoulder and an attractive well. We show the existence of two distinct liquid-gas and liquid-liquid phase equilibria. The GEMC estimate of the critical parameters, as following from an interpolation of the binodal points, is only slightly influenced by finite size effects. The liquid-gas critical temperature and pressure are lower than those of the liquid-liquid phase separation. A discussion of our findings in comparison with those of previous numerical studies is also presented.

Journal Article↗