Theory and simulations of quantum glass forming liquids

A comprehensive microscopic dynamical theory is presented for the description of quantum fluids as they transform into glasses. The theory is based on a quantum extension of mode-coupling theory. Novel effects are predicted, such as reentrant behavior of dynamical relaxation times. These predictions are supported by path integral ring polymer molecular dynamics simulations. The simulations provide detailed insight into the factors that govern slow dynamics in glassy quantum fluids. Connection to other recent work on both quantum glasses as well as quantum optimization problems is presented.Comment: 11 pages, 5 figures, 1 Tabl

Quantum fluctuations can promote or inhibit glass formation

The very nature of glass is somewhat mysterious: while relaxation times in glasses are of sufficient magnitude that large-scale motion on the atomic level is essentially as slow as it is in the crystalline state, the structure of glass appears barely different than that of the liquid that produced it. Quantum mechanical systems ranging from electron liquids to superfluid helium appear to form glasses, but as yet no unifying framework exists connecting classical and quantum regimes of vitrification. Here we develop new insights from theory and simulation into the quantum glass transition that surprisingly reveal distinct regions where quantum fluctuations can either promote or inhibit glass formation.Comment: Accepted for publication in Nature Physics. 22 pages, 3 figures, 1 Tabl

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

<p>Abstract</p> <p>Background</p> <p>Fission yeast <it>Schizosaccharomyces pombe </it>and budding yeast <it>Saccharomyces cerevisiae </it>are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast.</p> <p>Results</p> <p>By integrating genome-wide data from multiple time course cell cycle microarray experiments we reconstructed a gene regulatory network. Based on the network, we discovered in addition to previously known regulatory hubs in M phase, a new putative regulatory hub in the form of the HMG box transcription factor <it>SPBC19G7.04</it>. Further, we inferred periodic activities of several less known transcription factors over the course of the cell cycle, identified over 500 putative regulatory targets and detected many new phase-specific and conserved <it>cis</it>-regulatory motifs. In particular, we show that <it>SPBC19G7.04 </it>has highly significant periodic activity that peaks in early M phase, which is coordinated with the late G2 activity of the forkhead transcription factor <it>fkh2</it>. Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1) which constitute regulatory modules from different phases of the cell cycle, 2) whose phase order is coherent across the 10 time course experiments, and 3) which lead to identification of phase-specific control elements at both the transcriptional and post-transcriptional levels in <it>S. pombe</it>. In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs.</p> <p>Conclusion</p> <p>Using a systems-level analysis of the phase-specific nature of the <it>S. pombe </it>cell cycle gene regulation, we have provided new testable evidence for post-transcriptional regulation in the G2 phase of the fission yeast cell cycle. Based on this comprehensive gene regulatory network, we demonstrated how one can generate and investigate plausible hypotheses on fission yeast cell cycle regulation which can potentially be explored experimentally.</p

Chemistry of a polluted cloudy boundary layer

A one-dimensional photochemical model for cloud-topped boundary layers is developed which includes detailed descriptions of gas-phase and aqueous-phase chemistry, and of the radiation field in and below cloud. The model is used to interpret the accumulation of pollutants observed over Bakersfield, California, during a wintertime stagnation episode with low stratus. The main features of the observations are well simulated; in particular, sulfate accumulates progressively over the course of the episode due to sustained aqueous-phase oxidation of SO2 in the stratus cloud. The major source of sulfate is the reaction S(IV) + Fe(III), provided that this reaction proceeds by a non radical mechanism in which Fe(III) is not reduced. A radical mechanism with SO3 − and Fe(II) as immediate products would quench sulfate production because of depletion of Fe(III). The model results suggest that the non radical mechanism is more consistent with observations, although this result follows from the absence of a rapid Fe(II) oxidation pathway in the model. Even with the non-radical mechanism, most of the soluble iron is present as Fe(II) because Fe(III) is rapidly reduced by O2 −. The S(IV) + Fe(III) reaction provides the principal source of H2O2 in the model; photochemical production of H2O2 from HO2 or O2(−I) is slow because HO2 is depleted by high levels of NOx. The aqueous-phase reaction S(IV) + OH initiates a radical-assisted S(IV) oxidation chain but we find that the chain is not propagated due to efficient termination by SO4 − + Cl− followed by Cl + H2O. A major uncertainty attached to that result is that the reactivities of S(IV)-carbonyl adducts with radical oxidants are unknown. The chain could be efficiently propagated, with high sulfate yields, if the S(IV)-carbonyl adducts were involved in chain propagation. A remarkable feature of the observations, which is well reproduced by the model, is the close balance between total atmospheric concentrations of acids and bases. We argue that this balance reflects the control of sulfate production by NH3, which follows from the pH dependence of the S(IV) + Fe(III) reaction. Such a balance should be a general characteristic of polluted environments where aqueous-phase oxidation of SO2 is the main source of acidity. At night, the acidity of the cloud approaches a steady state between NH3 emissions and H2SO4 production by the S(IV) + Fe(III) reaction. A steady state analysis suggests that [H+] at night should be proportional to (ESO 2/ENH 3)1/2 where ESO 2 and ENH 3 are emission rates of SO2 and NH3, respectively. From this analysis it appears that cloud water pH values below 3 are unlikely to occur in the Bakersfield atmosphere during the nighttime hours. Very high acidities could, however, be achieved in the daytime because of photochemical acid production by the gas-phase reactions NO2 + OH and SO2 + OH