Evidence for compact cooperatively rearranging regions in a supercooled liquid

We examine structural relaxation in a supercooled glass-forming liquid simulated by NVE molecular dynamics. Time correlations of the total kinetic energy fluctuations are used as a comprehensive measure of the system's approach to the ergodic equilibrium. We find that, under cooling, the total structural relaxation becomes delayed as compared with the decay of the component of the intermediate scattering function corresponding to the main peak of the structure factor. This observation can be explained by collective movements of particles preserving many-body structural correlations within compact 3D cooperatively rearranging regions.Comment: 8 pages, 4 figure

Synergistic Activation of RD29A Via Integration of Salinity Stress and Abscisic Acid in Arabidopsis thaliana.

Plants perceive information from the surroundings and elicit appropriate molecular responses. How plants dynamically respond to combinations of external inputs is yet to be revealed, despite the detailed current knowledge of intracellular signaling pathways. We measured dynamics of Response-to-Dehydration 29A (RD29A) expression induced by single or combined NaCl and ABA treatments in Arabidopsis thaliana. RD29A expression in response to a combination of NaCl and ABA leads to unique dynamic behavior that cannot be explained by the sum of responses to individual NaCl and ABA. To explore the potential mechanisms responsible for the observed synergistic response, we developed a mathematical model of the DREB2 and AREB pathways based on existing knowledge, where NaCl and ABA act as the cognate inputs, respectively, and examined various system structures with cross-input modulation, where non-cognate input affects expression of the genes involved in adjacent signaling pathways. The results from the analysis of system structures, combined with the insights from microarray expression profiles and model-guided experiments, predicted that synergistic activation of RD29A originates from enhancement of DREB2 activity by ABA. Our analysis of RD29A expression profiles demonstrates that a simple mathematical model can be used to extract information from temporal dynamics induced by combinatorial stimuli and produce experimentally testable hypotheses

Simulation of the deep-sea biosphere by a continuous high-pressure bioreactor

In ocean system Anaerobic Oxidation of Methane (AOM) followed by carbonate precipitation has a significant effect on the climate regulation, since this process avoids large methane emissions to the atmosphere and fixes carbon dioxide into carbonate structures. However the main difficulty to study AOM is that the consortia involved have extremely long doubling time (2-7 months) at ambient or low pressures. To simulate the in situ condition better and obtain a faster growth, we designed and constructed a unique continuous high-pressure bioreactor. The reactor can reach pressure up to 100 bars, representing a depth of 1000m below sea level; it can be operated in continuous or non-continuous style, simulating the different types of methane resource. By the help of this high pressure bioreactor system, we are also able to study the effect of environmental factors on AOM activity and on microbial community. Captain Arutyunov Mud Volcano (Gulf of Cadiz) sediment has been used as biomass resource and different molecular techniques (DGGE, cloning library, FISH) have been applied to examine the microbial community structure. By increasing methane partial pressure, an immediate increase of AOM activity has been observed before significant enrichment of biomass. A continuous methane flux is necessary to obtain optimal AOMactivity. Bacterial community is more sensitive to the change of pressure compared with archaeal community

Magnetic Field Confinement in the Corona: The Role of Magnetic Helicity Accumulation

A loss of magnetic field confinement is believed to be the cause of coronal mass ejections (CMEs), a major form of solar activity in the corona. The mechanisms for magnetic energy storage are crucial in understanding how a field may possess enough free energy to overcome the Aly limit and open up. Previously, we have pointed out that the accumulation of magnetic helicity in the corona plays a significant role in storing magnetic energy. In this paper, we investigate another hydromagnetic consequence of magnetic-helicity accumulation. We propose a conjecture that there is an upper bound on the total magnetic helicity that a force-free field can contain. This is directly related to the hydromagnetic property that force-free fields in unbounded space have to be self-confining. Although a mathematical proof of this conjecture for any field configuration is formidable, its plausibility can be demonstrated with the properties of several families of power-law, axisymmetric force-free fields. We put forth mathematical evidence, as well as numerical, indicating that an upper bound on the magnetic helicity may exist for such fields. Thus, the accumulation of magnetic helicity in excess of this upper bound would initiate a non-equilibrium situation, resulting in a CME expulsion as a natural product of coronal evolution.Comment: 6 figures, ApJ in pres

Structural and dynamical properties of liquid Si. An orbital-free molecular dynamics study

Several static and dynamic properties of liquid silicon near melting have been determined from an orbital free {\em ab-initio} molecular dynamics simulation. The calculated static structure is in good agreement with the available X-ray and neutron diffraction data. The dynamical structure shows collective density excitations with an associated dispersion relation which closely follows recent experimental data. It is found that liquid silicon can not sustain the propagation of shear waves which can be related to the power spectrum of the velocity autocorrelation function. Accurate estimates have also been obtained for several transport coefficients. The overall picture is that the dynamic properties have many characteristics of the simple liquid metals although some conspicuous differences have been found.Comment: 12 pages, 11 figure

Comment on ``Lyapunov Exponent of a Many Body System and Its Transport Coefficients''

In a recent Letter, Barnett, Tajima, Nishihara, Ueshima and Furukawa obtained a theoretical expression for the maximum Lyapunov exponent $\lambda_1$ of a dilute gas. They conclude that $\lambda_1$ is proportional to the cube root of the self-diffusion coefficient $D$, independent of the range of the interaction potential. They validate their conjecture with numerical data for a dense one-component plasma, a system with long-range forces. We claim that their result is highly non-generic. We show in the following that it does not apply to a gas of hard spheres, neither in the dilute nor in the dense phase.Comment: 1 page, Revtex - 1 PS Figs - Submitted to Physical Review Letter

Three Dimensional Hydrodynamic Modeling Study, Craney Island eastward expansion, lower James River and Elizabeth River, Virginia

The Craney Island Eastward Expansion Hydrodynamic Model Study was conducted in three phases: 1) model calibration and verification for the Elizabeth River, 2) model testing of four Craney Island expansion options using single variable runs (using a single variable, tidal range, for model input), 3) model testing of two expansion options using historical runs (using multiple variables in real time for model input). The expansion option designs were evaluated for both global and local hydrodynamic change through simulation comparisons with the Base Case condition

Acoustic and relaxation processes in supercooled o-ter-phenyl by optical-heterodyne transient grating experiment

The dynamics of the fragile glass-forming o-ter-phenyl is investigated by time-resolved transient grating experiment with an heterodyne detection technique in a wide temperature range. We investigated the dynamics processes of this glass-former over more then 6 decades in time with an excellent signal/noise. Acoustic, structural and thermal relaxations have been clearly identify and measured in a time-frequency window not covered by previous spectroscopic investigations. A detailed comparison with the density response function, calculated on the basis of generalized hydrodynamics model, has been worked out

Subretinal fluid morphology in chronic central serous chorioretinopathy and its relationship to treatment: a retrospective analysis on PLACE trial data

Purpose To explore subretinal fluid (SRF) morphology in chronic central serous chorioretinopathy (cCSC) after one session of either high-density subthreshold micropulse laser (HSML) treatment or half-dose photodynamic therapy (PDT).Methods We retrospectively obtained optical coherence tomography (OCT) scans from a subset of patients from a randomized controlled trial on treatment-naive eyes with cCSC allocated to either HSML treatment or half-dose PDT. OCT scans were evaluated prior to treatment and 6-8 weeks post-treatment, where we measured maximum SRF height and width, calculated the maximum height-to-maximum width-ratio (maxHWR) and calculated the total SRF volume.Results Forty-one eyes of 39 cCSC patients were included. SRF morphology ranged from flat to dome-shaped, quantified as maxHWR ranging between 0.02 and 0.12. SRF volume was median 0.373 mu l (range: 0.010-4.425 mu l) and did not correlate to maxHWR (rho = -0.004, p = 0.982). Half-dose PDT was superior to HSML treatment in complete SRF resolution (RR = 3.28, p = 0.003) and in morphological changes of SRF (Delta(maximum height), p = 0.001; Delta(maximum width), p < 0.001; Delta(volume), p = 0.025). SRF resolved completely in 19/22 PDT-treated eyes (86%) and 5/19 HSML-treated eyes (26%). SRF volume increased in five eyes (26%) after HSML treatment, and in none of the eyes after half-dose PDT. SRF morphology at baseline did not predict treatment outcomes.Conclusion SRF morphology changed after both HSML treatment and half-dose PDT in cCSC, with SRF disappearing in most PDT-treated patients, whereas SRF volume increased in a sizeable proportion of HSML-treated patients. Baseline SRF characteristics measured in this study were unable to predict outcomes after either HSML treatment or half-dose PDT

Pressure induced structural and dynamical changes in liquid Si. An ab-initio study

The static and dynamic properties of liquid Si at high-pressure have been studied using the orbital free ab-initio molecular dynamics method. Four thermodynamic states at pressures 4, 8, 14 and 23 GPa are considered. The calculated static structure shows qualitative agreement with the available experimental data. We analize the remarkable structural changes occurring between 8 and 14 GPa along with its effect on several dynamic properties.Comment: 10 pages, 11 figures. Accepted for publication in Journal of Physics: Condensed Matte