News and Events

Francis Crick first called for a coordinated worldwide scientific effort to determine a “complete solution” of the bacterium Escherichia coli. We have been working for some years now to complete a model of E. coli that takes into account all of the known functions of every well-annotated gene, in order to better understand and predict the behavior of this scientifically-relevant and industrially-significant model organism. I will discuss our ongoing efforts to improve this model, most recently with new modeling added to better describe growth rate control, transcription unit architecture and tRNA metabolism. I will then highlight our newest “whole-colony” models, a multi-scale modeling effort in which every individual within a simulated colony is running the latest version of the whole-cell model, to calculate population-level emergent behaviors based on molecular interactions and events as the colony responds to the sudden introduction of antibiotics.


Temp: | 76 °F | N2 Boiling: | 76.0 K |
Humidity: | 42% | H2O Boiling: | 368.6 K |
Pressure: | 86 kPa | Sunrise: | 6:51 AM |
Wind: | 2 m/s | Sunset: | 8:05 PM |
Precip: | 0 mm | Sunlight: | 246 W/m² |

Selected Publications

Vehicles in the upper atmosphere travel through increasingly rarefied media. As acoustic radiation is dependent upon its media, acoustic radiation losses of vibrating structures in lower density air are investigated. An aluminum Euler beam is placed in a vacuum chamber, supported by thin nylon wires at known nodal positions, according to the excited mode. These strings are laced across a large cavity in a small steel table, effectively minimizing losses due to boundary supports. An impulse hammer excites the beam into its flexural state, while a laser vibrometer measures the velocity response. Extraction of mechanical loss factors occurs as the vacuum pressure increases (atmospheric pressure decreases) in experimental increments, thus determining the dependence of acoustic radiation losses on the rarefied media. Analysis of experimental results is presented as a topic of discussion for vibrations of launch vehicles and satellites. Other inferences and inductions are also considered.

The very low-frequency noise from merchant ships provides a good broadband sound source to study the deep layers of the seabed. The nested striations that characterize ship time-frequency spectrograms contain unique acoustic features corresponding to where the waveguide invariant beta becomes infinite. In this dataset, these features occur at frequencies between 20 and 80 Hz, where pairs of modal group velocities become equal. The goal of this study is to identify these beta = infinity frequencies in ship noise spectrograms and use them to perform statistical inference for the deep layer sound speeds and thicknesses in the New England Mudpatch for a larger number of ships and acoustic arrays over a larger geographical region than previously studied. Marginal probability distributions of the data indicate that using singular points for a feature-based inversion yields an estimate of the sound speed and a limiting value for the thickness of the first deep layer. Heterogeneity is examined by correlating spatial variability of the deep layer sound speeds with ship tracks.

We present time-series near-infrared spectra for the classical Cepheid, CP Cephei, from the Astrophysical Research Consortium 3.5-m telescope and near-infrared spectrograph, TripleSpec, at Apache Point Observatory, NM, USA. Spectral observations were made at nine points through the minimum and partway up the ascending portion of the optical light curve for the star. Carbon monoxide (CO) was detected in absorption in the 2.3-$\mu$m region for each observation. We measured the strength of CO absorption using the 2-0 band head in the feature for each observation and confirm that the CO varies with pulsation. We show that these measurements follow the $(J-K)$ colour curve, confirming that temperature drives the destruction of CO. By obtaining convolved filter magnitudes from the spectral data we found that the effect of the CO feature on K magnitudes is small, unlike the CO feature in the mid-infrared at 4.5 $\mu$m. The dissociation of CO in the near-infrared spectra tracks with the effect seen in the mid-infrared photometric measurements of a similar Galactic Cepheid. Confirmation of the varying CO feature illustrates the need for further investigations into the related mid-infrared period-colour-metallicity relation in order to address the impact of Cepheid metallicities on the Hubble tension.

We present 0.'' 22 resolution CO(2-1) observations of the circumnuclear gas disk in the local compact galaxy NGC 384 with the Atacama Large Millimeter/submillimeter Array (ALMA). While the majority of the disk displays regular rotation with projected velocities rising to 370 km s-1, the inner similar to 0.'' 5 exhibits a kinematic twist. We develop warped disk gas-dynamical models to account for this twist, fit those models to the ALMA data cube, and find a stellar mass-to-light ratio in the H band of M/L H = 1.34 +/- 0.01 [1 sigma statistical] +/- 0.02 [systematic] M circle dot/L circle dot and a supermassive black hole (BH) mass (M BH) of M BH =(7.26-0.48+0.43[1 sigma statistical]-1.00+0.55[systematic])x108M circle dot . In contrast to most previous dynamical M BH measurements in local compact galaxies, which typically found over-massive BHs compared to the local BH mass-bulge luminosity and BH mass-bulge mass relations, NGC 384 lies within the scatter of those scaling relations. NGC 384 and other local compact galaxies are likely relics of z similar to 2 red nuggets, and over-massive BHs in these relics indicate BH growth may conclude before the host galaxy stars have finished assembly. Our NGC 384 results may challenge this evolutionary picture, suggesting there may be increased scatter in the scaling relations than previously thought. However, this scatter could be inflated by systematic differences between stellar- and gas-dynamical measurement methods, motivating direct comparisons between the methods for NGC 384 and the other compact galaxies in the sample.

We present new JWST observations of the nearby, prototypical edge-on, spiral galaxy NGC 891. The northern half of the disk was observed with NIRCam in its F150W and F277W filters. Absorption is clearly visible in the mid-plane of the F150W image, along with vertical dusty plumes that closely resemble the ones seen in the optical. A similar to 10 x 3 kpc(2) area of the lower circumgalactic medium (CGM) was mapped with MIRI F770W at 12 pc scales. Thanks to the sensitivity and resolution of JWST, we detect dust emission out to similar to 4 kpc from the disk, in the form of filaments, arcs, and super-bubbles. Some of these filaments can be traced back to regions with recent star formation activity, suggesting that feedback-driven galactic winds play an important role in regulating baryonic cycling. The presence of dust at these altitudes raises questions about the transport mechanisms at play and suggests that small dust grains are able to survive for several tens of million years after having been ejected by galactic winds in the disk-halo interface. We lay out several scenarios that could explain this emission: dust grains may be shielded in the outer layers of cool dense clouds expelled from the galaxy disk, and/or the emission comes from the mixing layers around these cool clumps where material from the hot gas is able to cool down and mix with these cool cloudlets. This first set of data and upcoming spectroscopy will be very helpful to understand the survival of dust grains in energetic environments, and their contribution to recycling baryonic material in the mid-plane of galaxies.

We here investigate how the synthesis method affects the crystallite size and atomic structure of cobalt iron oxide nanoparticles. By using a simple solvothermal method, we first synthesized cobalt ferrite nanoparticles of ca. 2 and 7 nm, characterized by Transmission Electron Microscopy (TEM), Small Angle X-ray scattering (SAXS), X-ray and neutron total scattering. The smallest particle size corresponds to only a few spinel unit cells. Nevertheless, Pair Distribution Function (PDF) analysis of X-ray and neutron total scattering data shows that the atomic structure, even in the smallest nanoparticles, is well described by the spinel structure, although with significant disorder and a contraction of the unit cell parameter. These effects can be explained by the surface oxidation of the small nanoparticles, which is confirmed by X-ray near edge absorption spectroscopy (XANES). Neutron total scattering data and PDF analysis reveal a higher degree of inversion in the spinel structure of the smallest nanoparticles. Neutron total scattering data also allow magnetic PDF (mPDF) analysis, which shows that the ferrimagnetic domains correspond to ca. 80% of the crystallite size in the larger particles. A similar but less well-defined magnetic ordering was observed for the smallest nanoparticles. Finally, we used a co-precipitation synthesis method at room temperature to synthesize ferrite nanoparticles similar in size to the smallest crystallites synthesized by the solvothermal method. Structural analysis with PDF demonstrates that the ferrite nanoparticles synthesized via this method exhibit a significantly more defective structure compared to those synthesized via a solvothermal method.