Computation with photochromic memory

Unconventional computing is an area of research in which novel materials and paradigms are utilised to implement computation and data storage. This includes attempts to embed computation into biological systems, which could allow the observation and modification of living processes. This thesis explores the storage and computational capabilities of a biocompatible light-sensitive (photochromic) molecular switch (NitroBIPS) that has the potential to be embedded into both natural and synthetic biological systems. To achieve this, NitroBIPS was embedded in a (PDMS) polymer matrix and an optomechanical setup was built in order to expose the sample to optical stimulation and record fluorescent emission. NitroBIPS has two stable forms - one fluorescent and one non-fluorescent - and can be switched between the two via illumination with ultraviolet or visible light. By exposing NitroBIPS samples to specific stimulus pulse sequences and recording the intensity of fluorescence emission, data could be stored in registers and logic gates and circuits implemented. In addition, by moving the area of illumination, sub-regions of the sample could be addressed. This enabled parallel registers, Turing machine tapes and elementary cellular automata to be implemented. It has been demonstrated, therefore, that photochromic molecular memory can be used to implement conventional universal computation in an unconventional manner. Furthermore, because registers, Turing machine tapes, logic gates, logic circuits and elementary cellular automata all utilise the same samples and same hardware, it has been shown that photochromic computational devices can be dynamically repurposed. NitroBIPS and related molecules have been shown elsewhere to be capable of modifying many biological processes. This includes inhibiting protein binding, perturbing lipid membranes and binding to DNA in a manner that is dependent on the molecule's form. The implementation of universal computation demonstrated in this thesis could, therefore, be used in combination with these biological manipulations as key components within synthetic biology systems or in order to monitor and control natural biological processes

Computation with photochromic memory

Unconventional computing is an area of research in which novel materials and paradigms are utilised to implement computation and data storage. This includes attempts to embed computation into biological systems, which could allow the observation and modification of living processes. This thesis explores the storage and computational capabilities of a biocompatible light-sensitive (photochromic) molecular switch (NitroBIPS) that has the potential to be embedded into both natural and synthetic biological systems. To achieve this, NitroBIPS was embedded in a (PDMS) polymer matrix and an optomechanical setup was built in order to expose the sample to optical stimulation and record fluorescent emission. NitroBIPS has two stable forms - one fluorescent and one non-fluorescent - and can be switched between the two via illumination with ultraviolet or visible light. By exposing NitroBIPS samples to specific stimulus pulse sequences and recording the intensity of fluorescence emission, data could be stored in registers and logic gates and circuits implemented. In addition, by moving the area of illumination, sub-regions of the sample could be addressed. This enabled parallel registers, Turing machine tapes and elementary cellular automata to be implemented. It has been demonstrated, therefore, that photochromic molecular memory can be used to implement conventional universal computation in an unconventional manner. Furthermore, because registers, Turing machine tapes, logic gates, logic circuits and elementary cellular automata all utilise the same samples and same hardware, it has been shown that photochromic computational devices can be dynamically repurposed. NitroBIPS and related molecules have been shown elsewhere to be capable of modifying many biological processes. This includes inhibiting protein binding, perturbing lipid membranes and binding to DNA in a manner that is dependent on the molecule's form. The implementation of universal computation demonstrated in this thesis could, therefore, be used in combination with these biological manipulations as key components within synthetic biology systems or in order to monitor and control natural biological processes

Kepler-68: Three Planets, One With a Density Between That of Earth and Ice Giants

NASA's Kepler Mission has revealed two transiting planets orbiting Kepler-68. Follow-up Doppler measurements have established the mass of the innermost planet and revealed a third jovian-mass planet orbiting beyond the two transiting planets. Kepler-68b, in a 5.4 day orbit has mass 8.3 +/- 2.3 Earth, radius 2.31 +/- 0.07 Earth radii, and a density of 3.32 +/- 0.92 (cgs), giving Kepler-68b a density intermediate between that of the ice giants and Earth. Kepler-68c is Earth-sized with a radius of 0.953 Earth and transits on a 9.6 day orbit; validation of Kepler-68c posed unique challenges. Kepler-68d has an orbital period of 580 +/- 15 days and minimum mass of Msin(i) = 0.947 Jupiter. Power spectra of the Kepler photometry at 1-minute cadence exhibit a rich and strong set of asteroseismic pulsation modes enabling detailed analysis of the stellar interior. Spectroscopy of the star coupled with asteroseismic modeling of the multiple pulsation modes yield precise measurements of stellar properties, notably Teff = 5793 +/- 74 K, M = 1.079 +/- 0.051 Msun, R = 1.243 +/- 0.019 Rsun, and density 0.7903 +/- 0.0054 (cgs), all measured with fractional uncertainties of only a few percent. Models of Kepler-68b suggest it is likely composed of rock and water, or has a H and He envelope to yield its density of about 3 (cgs).Comment: 32 pages, 13 figures, Accepted to Ap

Fundamental Properties of Kepler Planet-Candidate Host Stars using Asteroseismology

We have used asteroseismology to determine fundamental properties for 66 Kepler planet-candidate host stars, with typical uncertainties of 3% and 7% in radius and mass, respectively. The results include new asteroseismic solutions for four host stars with confirmed planets (Kepler-4, Kepler-14, Kepler-23 and Kepler-25) and increase the total number of Kepler host stars with asteroseismic solutions to 77. A comparison with stellar properties in the planet-candidate catalog by Batalha et al. shows that radii for subgiants and giants obtained from spectroscopic follow-up are systematically too low by up to a factor of 1.5, while the properties for unevolved stars are in good agreement. We furthermore apply asteroseismology to confirm that a large majority of cool main-sequence hosts are indeed dwarfs and not misclassified giants. Using the revised stellar properties, we recalculate the radii for 107 planet candidates in our sample, and comment on candidates for which the radii change from a previously giant-planet/brown-dwarf/stellar regime to a sub-Jupiter size, or vice versa. A comparison of stellar densities from asteroseismology with densities derived from transit models in Batalha et al. assuming circular orbits shows significant disagreement for more than half of the sample due to systematics in the modeled impact parameters, or due to planet candidates which may be in eccentric orbits. Finally, we investigate tentative correlations between host-star masses and planet candidate radii, orbital periods, and multiplicity, but caution that these results may be influenced by the small sample size and detection biases.Comment: 19 pages, 10 figures, 4 tables; accepted for publication in ApJ; machine-readable versions of tables 1-3 are available as ancillary files or in the source code; v2: minor changes to match published versio

Identification of FBXL4 as a Metastasis Associated Gene in Prostate Cancer

Prostate cancer is the most common cancer among western men, with a significant mortality and morbidity reported for advanced metastatic disease. Current understanding of metastatic disease is limited due to difficulty of sampling as prostate cancer mainly metastasizes to bone. By analysing prostate cancer bone metastases using high density microarrays, we found a common genomic copy number loss at 6q16.1–16.2, containing the FBXL4 gene, which was confirmed in larger series of bone metastases by fluorescence in situ hybridisation (FISH). Loss of FBXL4 was also detected in primary tumours and it was highly associated with prognostic factors including high Gleason score, clinical stage, prostate-specific antigen (PSA) and extent of disease, as well as poor patient survival, suggesting that FBXL4 loss contributes to prostate cancer progression. We also demonstrated that FBXL4 deletion is detectable in circulating tumour cells (CTCs), making it a potential prognostic biomarker by ‘liquid biopsy’. In vitro analysis showed that FBXL4 plays a role in regulating the migration and invasion of prostate cancer cells. FBXL4 potentially controls cancer metastasis through regulation of ERLEC1 levels. Therefore, FBXL4 could be a potential novel prostate cancer suppressor gene, which may prevent cancer progression and metastasis through controlling cell invasion

Planetary Candidates Observed by Kepler. VIII. A Fully Automated Catalog With Measured Completeness and Reliability Based on Data Release 25

We present the Kepler Object of Interest (KOI) catalog of transiting exoplanets based on searching four years of Kepler time series photometry (Data Release 25, Q1-Q17). The catalog contains 8054 KOIs of which 4034 are planet candidates with periods between 0.25 and 632 days. Of these candidates, 219 are new and include two in multi-planet systems (KOI-82.06 and KOI-2926.05), and ten high-reliability, terrestrial-size, habitable zone candidates. This catalog was created using a tool called the Robovetter which automatically vets the DR25 Threshold Crossing Events (TCEs, Twicken et al. 2016). The Robovetter also vetted simulated data sets and measured how well it was able to separate TCEs caused by noise from those caused by low signal-to-noise transits. We discusses the Robovetter and the metrics it uses to sort TCEs. For orbital periods less than 100 days the Robovetter completeness (the fraction of simulated transits that are determined to be planet candidates) across all observed stars is greater than 85%. For the same period range, the catalog reliability (the fraction of candidates that are not due to instrumental or stellar noise) is greater than 98%. However, for low signal-to-noise candidates between 200 and 500 days around FGK dwarf stars, the Robovetter is 76.7% complete and the catalog is 50.5% reliable. The KOI catalog, the transit fits and all of the simulated data used to characterize this catalog are available at the NASA Exoplanet Archive.Comment: 61 pages, 23 Figures, 9 Tables, Accepted to The Astrophysical Journal Supplement Serie

Planetary Candidates Observed by Kepler VI: Planet Sample from Q1-Q16 (47 Months)

\We present the sixth catalog of Kepler candidate planets based on nearly 4 years of high precision photometry. This catalog builds on the legacy of previous catalogs released by the Kepler project and includes 1493 new Kepler Objects of Interest (KOIs) of which 554 are planet candidates, and 131 of these candidates have best fit radii <1.5 R_earth. This brings the total number of KOIs and planet candidates to 7305 and 4173 respectively. We suspect that many of these new candidates at the low signal-to-noise limit may be false alarms created by instrumental noise, and discuss our efforts to identify such objects. We re-evaluate all previously published KOIs with orbital periods of >50 days to provide a consistently vetted sample that can be used to improve planet occurrence rate calculations. We discuss the performance of our planet detection algorithms, and the consistency of our vetting products. The full catalog is publicly available at the NASA Exoplanet Archive.Comment: 18 pages, to be published in the Astrophysical Journal Supplement Serie

Kepler-21b: A 1.6REarth Planet Transiting the Bright Oscillating F Subgiant Star HD 179070

We present Kepler observations of the bright (V=8.3), oscillating star HD 179070. The observations show transit-like events which reveal that the star is orbited every 2.8 days by a small, 1.6 R_Earth object. Seismic studies of HD 179070 using short cadence Kepler observations show that HD 179070 has a frequencypower spectrum consistent with solar-like oscillations that are acoustic p-modes. Asteroseismic analysis provides robust values for the mass and radius of HD 179070, 1.34{\pm}0.06 M{\circ} and 1.86{\pm}0.04 R{\circ} respectively, as well as yielding an age of 2.84{\pm}0.34 Gyr for this F5 subgiant. Together with ground-based follow-up observations, analysis of the Kepler light curves and image data, and blend scenario models, we conservatively show at the >99.7% confidence level (3{\sigma}) that the transit event is caused by a 1.64{\pm}0.04 R_Earth exoplanet in a 2.785755{\pm}0.000032 day orbit. The exoplanet is only 0.04 AU away from the star and our spectroscopic observations provide an upper limit to its mass of ~10 M_Earth (2-{\sigma}). HD 179070 is the brightest exoplanet host star yet discovered by Kepler.Comment: Accepted to Ap

Planetary Candidates Observed by Kepler, III: Analysis of the First 16 Months of Data

New transiting planet candidates are identified in sixteen months (May 2009 - September 2010) of data from the Kepler spacecraft. Nearly five thousand periodic transit-like signals are vetted against astrophysical and instrumental false positives yielding 1,091 viable new planet candidates, bringing the total count up to over 2,300. Improved vetting metrics are employed, contributing to higher catalog reliability. Most notable is the noise-weighted robust averaging of multi-quarter photo-center offsets derived from difference image analysis which identifies likely background eclipsing binaries. Twenty-two months of photometry are used for the purpose of characterizing each of the new candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are tabulated as well as the products of light curve modeling: reduced radius (Rp/R*), reduced semi-major axis (d/R*), and impact parameter (b). The largest fractional increases are seen for the smallest planet candidates (197% for candidates smaller than 2Re compared to 52% for candidates larger than 2Re) and those at longer orbital periods (123% for candidates outside of 50-day orbits versus 85% for candidates inside of 50-day orbits). The gains are larger than expected from increasing the observing window from thirteen months (Quarter 1-- Quarter 5) to sixteen months (Quarter 1 -- Quarter 6). This demonstrates the benefit of continued development of pipeline analysis software. The fraction of all host stars with multiple candidates has grown from 17% to 20%, and the paucity of short-period giant planets in multiple systems is still evident. The progression toward smaller planets at longer orbital periods with each new catalog release suggests that Earth-size planets in the Habitable Zone are forthcoming if, indeed, such planets are abundant.Comment: Submitted to ApJS. Machine-readable tables are available at http://kepler.nasa.gov, http://archive.stsci.edu/kepler/results.html, and the NASA Exoplanet Archiv

Masses, radii, and orbits of small Kepler planets : The transition from gaseous to rocky planets

We report on the masses, sizes, and orbits of the planets orbiting 22 Kepler stars. There are 49 planet candidates around these stars, including 42 detected through transits and 7 revealed by precise Doppler measurements of the host stars. Based on an analysis of the Kepler brightness measurements, along with high-resolution imaging and spectroscopy, Doppler spectroscopy, and (for 11 stars) asteroseismology, we establish low false-positive probabilities (FPPs) for all of the transiting planets (41 of 42 have an FPP under 1%), and we constrain their sizes and masses. Most of the transiting planets are smaller than three times the size of Earth. For 16 planets, the Doppler signal was securely detected, providing a direct measurement of the planet's mass. For the other 26 planets we provide either marginal mass measurements or upper limits to their masses and densities; in many cases we can rule out a rocky composition. We identify six planets with densities above 5 g cm-3, suggesting a mostly rocky interior for them. Indeed, the only planets that are compatible with a purely rocky composition are smaller than 2 R ⊕. Larger planets evidently contain a larger fraction of low-density material (H, He, and H2O).Peer reviewedFinal Accepted Versio