A photoconversion model for full spectral programming and multiplexing of optogeneticﾠsystems

Optogenetics combines externally applied light signals and genetically engineered photoreceptors to control cellular processes with unmatched precision. Here, we develop a mathematical model of wavelength‐ and intensity‐dependent photoconversion, signaling, and output gene expression for our two previously engineered light‐sensing Escherichia coli two‐component systems. To parameterize the model, we develop a simple set of spectral and dynamical calibration experiments using our recent open‐source “Light Plate Apparatus” device. In principle, the parameterized model should predict the gene expression response to any time‐varying signal from any mixture of light sources with known spectra. We validate this capability experimentally using a suite of challenging light sources and signals very different from those used during the parameterization process. Furthermore, we use the model to compensate for significant spectral cross‐reactivity inherent to the two sensors in order to develop a new method for programming two simultaneous and independent gene expression signals within the same cell. Our optogenetic multiplexing method will enable powerful new interrogations of how metabolic, signaling, and decision‐making pathways integrate multiple input signals

A new capacitive sensor for displacement measurement in a surface force apparatus

We present a new capacitive sensor for displacement measurement in a Surface Forces Apparatus (SFA) which allows dynamical measurements in the range of 0-100 Hz. This sensor measures the relative displacement between two macroscopic opaque surfaces over periods of time ranging from milliseconds to in principle an indefinite period, at a very low price and down to atomic resolution. It consists of a plane capacitor, a high frequency oscillator, and a high sensitivity frequency to voltage conversion. We use this sensor to study the nanorheological properties of dodecane confined between glass surfaces.Comment: 7 pages, 8 figure

Star Formation, Radio Sources, Cooling X-ray Gas, and Galaxy Interactions in the Brightest Cluster Galaxy in 2A0335+096

We present deep emission-line imaging taken with the SOAR Optical Imaging Camera of the brightest cluster galaxy (BCG) in the nearby (z=0.035) X-ray cluster 2A0335+096. We analyze long-slit optical spectroscopy, archival VLA, Chandra X-ray, and XMM UV data. 2A0335+096 is a bright, cool-core X-ray cluster, once known as a cooling flow. Within the highly disturbed core revealed by Chandra X-ray observations, 2A0335+096 hosts a highly structured optical emission-line system. The redshift of the companion is within 100 km/s of the BCG and has certainly interacted with the BCG, and is likely bound to it. The comparison of optical and radio images shows curved filaments in H-alpha emission surrounding the resolved radio source. The velocity structure of the emission-line bar between the BCG nucleus and the companion galaxy provides strong evidence for an interaction between the two in the last ~50 Myrs. The age of the radio source is similar to the interaction time, so this interaction may have provoked an episode of radio activity. We estimate a star formation rate of >7 solar mass/yr based on the Halpha and archival UV data, a rate similar to, but somewhat lower than, the revised X-ray cooling rate of 10-30 solar masses/year estimated from XMM spectra by Peterson & workers. The Halpha nebula is limited to a region of high X-ray surface brightness and cool X-ray temperature. The detailed structures of H-alpha and X-ray gas differ. The peak of the X-ray emission is not the peak of H-alpha emission, nor does it lie in the BCG. The estimated age of the radio lobes and their interaction with the optical emission-line gas, the estimated timescale for depletion and accumulation of cold gas, and the dynamical time in the system are all similar, suggesting a common trigger mechanism.Comment: Accepted AJ, July 2007 publication. Vol 134, p. 14-2

Cosmological Effects of Powerful AGN Outbursts in Galaxy Clusters: Insights from an XMM-Newton Observation of MS0735+7421

We report on the results of an analysis of XMM-Newton observations of MS0735+7421, the galaxy cluster which hosts the most energetic AGN outburst currently known. The previous Chandra image shows twin giant X-ray cavities (~200 kpc diameter) filled with radio emission and surrounded by a weak shock front. XMM data are consistent with these findings. The total energy in cavities and shock (~6 \times 10^{61} erg) is enough to quench the cooling flow and, since most of the energy is deposited outside the cooling region (~100 kpc), to heat the gas within 1 Mpc by ~1/4 keV per particle. The cluster exhibits an upward departure (factor ~2) from the mean L-T relation. The boost in emissivity produced by the ICM compression in the bright shells due to the cavity expansion may contribute to explain the high luminosity and high central gas mass fraction that we measure. The scaled temperature and metallicity profiles are in general agreement with those observed in relaxed clusters. Also, the quantities we measure are consistent with the observed M-T relation. We conclude that violent outbursts such as the one in MS0735+7421 do not cause dramatic instantaneous departures from cluster scaling relations (other than the L-T relation). However, if they are relatively common they may play a role in creating the global cluster properties.Comment: 69 pages, 30 figures, accepted for publication in ApJ Main Journa

Accuracy of Trace Formulas

Using quantum maps we study the accuracy of semiclassical trace formulas. The role of chaos in improving the semiclassical accuracy, in some systems, is demonstrated quantitatively. However, our study of the standard map cautions that this may not be most general. While studying a sawtooth map we demonstrate the rather remarkable fact that at the level of the time one trace even in the presence of fixed points on singularities the trace formula may be exact, and in any case has no logarithmic divergences observed for the quantum bakers map. As a byproduct we introduce fantastic periodic curves akin to curlicues.Comment: 20 pages, uuencoded and gzipped, 1 LaTex text file and 9 PS files for figure

Matter-field theory of the Casimir force

A matter-field theory of the Casimir force is formulated in which the electromagnetic field and collective modes of dielectric media are treated on an equal footing. In our theory, the Casimir force is attributed to zero-point energies of the combined matter-field modes. We analyze why some of the existing theories favor the interpretation of the Casimir force as originating from zero-point energies of the electromagnetic field and others from those of the matter.Comment: 12pages, 1 Postscript figur

Integrability and chaos: the classical uncertainty

In recent years there has been a considerable increase in the publishing of textbooks and monographs covering what was formerly known as random or irregular deterministic motion, now named by the more fashionable term of deterministic chaos. There is still substantial interest in a matter that is included in many graduate and even undergraduate courses on classical mechanics. Based on the Hamiltonian formalism, the main objective of this article is to provide, from the physicist's point of view, an overall and intuitive review of this broad subject (with some emphasis on the KAM theorem and the stability of planetary motions) which may be useful to both students and instructors.Comment: 24 pages, 10 figure

Half-life and spin of 60Mn^g

A value of 0.28 +/- 0.02 s has been deduced for the half-life of the ground state of 60Mn, in sharp contrast to the previously adopted value of 51 +/- 6 s. Access to the low-spin 60Mn ground state was accomplished via beta decay of the 0+ 60Cr parent nuclide. New, low-energy states in 60Mn have been identified from beta-delayed gamma-ray spectroscopy. The new, shorter half-life of 60Mn^g is not suggestive of isospin forbidden beta decay, and new spin and parity assignments of 1+ and 4+ have been adopted for the ground and isomeric beta-decaying states, respectively, of 60Mn.Comment: 13 pages, 5 figures, Accepted for publication in Phys. Rev.

Functional Approach to Quantum Decoherence and the Classical Final Limit

For a wide set of quantum systems it is demonstrated that the quantum regime can be considered as the transient phase while the final classical statistical regime is a permanent state. A basis where exact matrix decoherence appears for these final states is found. The relation with the decoherence of histories formalism is studied. A set of final intrinsically consistent histories is found.Comment: 20 pages. Phys. Rev A in press 200