Three-dimensional modeling of radiative disks in binaries

Circumstellar disks in binaries are perturbed by the companion gravity causing significant alterations of the disk morphology. Spiral waves due to the companion tidal force also develop in the vertical direction and affect the disk temperature profile. These effects may significantly influence the process of planet formation. We perform 3D numerical simulations of disks in binaries with different initial dynamical configurations and physical parameters. Our goal is to investigate their evolution and their propensity to grow planets. We use an improved version of the SPH code VINE modified to better account for momentum and energy conservation. The energy equation includes a flux--limited radiative transfer algorithm and the disk cooling is obtained via "boundary particles". We model a system made of star/disk + star/disk where the secondary star (and relative disk) is less massive than the primary. The numerical simulations performed for different values of binary separation and disk density show that the disk morphology is substantially affected by the companion perturbations. Trailing spiral shock waves develop when the stars approach their pericenter. Strong hydraulic jumps occur at the shock front creating breaking waves and a consistent mass stream between the two disks, significantly heating them. The high gas temperature may prevent the ice condensation by moving outward the "snow line". The hydraulic jumps may slow down or even halt the dust coagulation process. At apocenter these perturbations are reduced and the disks are cooled down and less eccentric. The strength of the hydraulic jumps, disk heating, and mass exchange depends on the binary separation, and for larger semi-major axes, the tidal spiral pattern is substantially reduced.Comment: 15 pages, 17 figures, accepted for publication in A&

Three Dimensional Modeling of Hot Jupiter Atmospheric Flows

We present a three dimensional hot Jupiter model, extending from 200 bar to 1 mbar, using the Intermediate General Circulation Model from the University of Reading. Our horizontal spectral resolution is T31 (equivalent to a grid of 48x96), with 33 logarithmically spaced vertical levels. A simplified (Newtonian) scheme is employed for the radiative forcing. We adopt a physical set up nearly identical to the model of HD 209458b by Cooper & Showman (2005,2006) to facilitate a direct model inter-comparison. Our results are broadly consistent with theirs but significant differences also emerge. The atmospheric flow is characterized by a super-rotating equatorial jet, transonic wind speeds, and eastward advection of heat away from the dayside. We identify a dynamically-induced temperature inversion ("stratosphere") on the planetary dayside and find that temperatures at the planetary limb differ systematically from local radiative equilibrium values, a potential source of bias for transit spectroscopic interpretations. While our model atmosphere is quasi-identical to that of Cooper & Showman (2005,2006) and we solve the same meteorological equations, we use different algorithmic methods, spectral-implicit vs. grid-explicit, which are known to yield fully consistent results in the Earth modeling context. The model discrepancies identified here indicate that one or both numerical methods do not faithfully capture all of the atmospheric dynamics at work in the hot Jupiter context. We highlight the emergence of a shock-like feature in our model, much like that reported recently by Showman et al. (2009), and suggest that improved representations of energy conservation may be needed in hot Jupiter atmospheric models, as emphasized by Goodman (2009).Comment: 25 pages, 6 figures, minor revisions, ApJ accepted, version with hi-res figures: http://www.astro.columbia.edu/~kristen/Hires/hotjup.3d.deep.ps.g

Analysis and three-dimensional modeling of vanadium flow batteries

This study presents 1.) a multi-dimensional model of vanadium Redox Flow Batteries (RFB); 2.) rigorous explanation of porelevel transport resistance, dilute solution assumption, and pumping power; and 3.) analysis of time constants of heat and mass transfer and dimensionless parameter. The model, describing the dynamic system of a RFB, consists of a set of partial differential equations of mass, momentum, species, charges, and energy conservation, in conjunctionwith the electrode's electrochemical reaction kinetics. The governing equations are successfully implemented into three-dimensional numerical simulation of charging, idling, and discharging operations. The model, validated against experimental data, predicts fluid flow, concentration increase/decrease, temperature contours and local reaction rate. The prediction indicates a large variation in local reaction rate across electrodes and the time constants for reactant variation and temperature evolution, which are consistent with theoretical analysis. © 2014 The Electrochemical Society. All rights reserved

Three-dimensional modeling of the HI kinematics of NGC 2915

The nearby blue compact dwarf, NGC 2915, has its stellar disc embedded in a large, extended (~ 22 B-band scale-lengths) HI disc. New high-resolution HI synthesis observations of NGC 2915 have been obtained with the Australia Telescope Compact Array. These observations provide evidence of extremely complex HI kinematics within the immediate vicinity of the galaxy's star-forming core. We identify and quantify double-peaked HI line profiles near the centre of the galaxy and show that the HI energetics can be accounted for by the mechanical energy output of the central high-mass stellar population within time-scales of 10^6-10^7 yr. Full three-dimensional models of the HI data cube are generated and compared to the observations to test various physical scenarios associated with the high-mass star-forming core of NGC 2915. Purely circular HI kinematics are ruled out together with the possibility of a high-velocity-dispersion inter-stellar medium at inner radii. Radial velocities of ~ 30 km/s are required to describe the central-most HI kinematics of the system. Our results lend themselves to the simple physical scenario in which the young stellar core of the galaxy expels the gas outwards from the centre of the disc, thereby creating a central HI under-density. These kinematics should be thought of as being linked to a central HI outflow rather than a large-scale galactic blow-out or wind.Comment: 11 pages, 6 figures, accepted for publication in MNRA

Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors.

Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors