I. Studies on bacteriophage DNA's and minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow dichroism of DNA solutions

Part I

Chapter 1.....A physicochemical study of the DNA molecules from the three bacteriophages, N1, N5, and N6, which infect the bacterium, M. lysodeikticus, has been made. The molecular weights, as measured by both electron microscopy and sedimentation velocity, are 23 x 10⁶ for N5 DNA and 31 x 10⁶ for N1 and N6 DNA's. All three DNA's are capable of thermally reversible cyclization. N1 and N6 DNA's have identical or very similar base sequences as judged by membrane filter hybridization and by electron microscope heteroduplex studies. They have identical or similar cohesive ends. These results are in accord with the close biological relation between N1 and N6 phages. N5 DNA is not closely related to N1 or N6 DNA. The denaturation T_m of all three DNA's is the same and corresponds to a (GC) content of 70%. However, the buoyant densities in CsCl of Nl and N6 DNA's are lower than expected, corresponding to predicted GC contents of 64 and 67%. The buoyant densities in Cs₂SO₄ are also somewhat anomalous. The buoyant density anomalies are probably due to the presence of odd bases. However, direct base composition analysis of N1 DNA by anion exchange chromatography confirms a GC content of 70%, and, in the elution system used, no peaks due to odd bases are present.

Chapter 2.....A covalently closed circular DNA form has been observed as an intracellular form during both productive and abortive infection processes in M. lysodeikticus. This species has been isolated by the method of CsC1-ethidium bromide centrifugation and examined with an electron microscope.

Chapter 3.....A minute circular DNA has been discovered as a homogeneous population in M. lysodeikticus. Its length and molecular weight as determined by electron microscopy are 0.445 μ and 0.88 x 10⁶ daltons respectively. There is about one minicircle per bacterium.

Chapter 4.....Several strains of E. coli 15 harbor a prophage. Viral growth can be induced by exposing the host to mitomycin C or to uv irradiation. The coliphage 15 particles from E. coli 15 and E, coli 15 T^- appear as normal phage with head and tail structure; the particles from E. coli 15 TAU are tailless. The complete particles exert a colicinogenic activity on E.coli 15 and 15 T^-, the tailless particles do not. No host for a productive viral infection has been found and the phage may be defective. The properties of the DNA of the virus have been studied, mainly by electron microscopy. After induction but before lysis, a closed circular DNA with a contour length of about 11.9 μ is found in the bacterium; the mature phage DNA is a linear duplex and 7.5% longer than the intracellular circular form. This suggests the hypothesis that the mature phage DNA is terminally repetitious and circularly permuted. The hypothesis was confirmed by observing that denaturation and renaturation of the mature phage DNA produce circular duplexes with two single-stranded branches corresponding to the terminal repetition. The contour length of the mature phage DNA was measured relative to φX RFII DNA and λ DNA; the calculated molecular weight is 27 x 10⁶. The length of the single-stranded terminal repetition was compared to the length of φX 174 DNA under conditions where single-stranded DNA is seen in an extended form in electron micrographs. The length of the terminal repetition is found to be 7.4% of the length of the nonrepetitious part of the coliphage 15 DNA. The number of base pairs in the terminal repetition is variable in different molecules, with a fractional standard deviation of 0.18 of the average number in the terminal repetition. A new phenomenon termed "branch migration" has been discovered in renatured circular molecules; it results in forked branches, with two emerging single strands, at the position of the terminal repetition. The distribution of branch separations between the two terminal repetitions in the population of renatured circular molecules was studied. The observed distribution suggests that there is an excluded volume effect in the renaturation of a population of circularly permuted molecules such that strands with close beginning points preferentially renature with each other. This selective renaturation and the phenomenon of branch migration both affect the distribution of branch separations; the observed distribution does not contradict the hypothesis of a random distribution of beginning points around the chromosome.

Chapter 5....Some physicochemical studies on the minicircular DNA species in E. coli 15 (0.670 μ, 1.47 x 10⁶ daltons) have been made. Electron microscopic observations showed multimeric forms of the minicircle which amount to 5% of total DNA species and also showed presumably replicating forms of the minicircle. A renaturation kinetic study showed that the minicircle is a unique DNA species in its size and base sequence. A study on the minicircle replication has been made under condition in which host DNA synthesis is synchronized. Despite experimental uncertainties involved, it seems that the minicircle replication is random and the number of the minicircles increases continuously throughout a generation of the host, regardless of host DNA synchronization.

Part II

The flow dichroism of dilute DNA solutions (A₂₆₀≈0.1) has been studied in a Couette-type apparatus with the outer cylinder rotating and with the light path parallel to the cylinder axis. Shear gradients in the range of 5-160 sec.^-1 were studied. The DNA samples were whole, "half," and "quarter" molecules of T4 bacteriophage DNA, and linear and circular λb₂b₅c DNA. For the linear molecules, the fractional flow dichroism is a linear function of molecular weight. The dichroism for linear A DNA is about 1.8 that of the circular molecule. For a given DNA, the dichroism is an approximately linear function of shear gradient, but with a slight upward curvature at low values of G, and some trend toward saturation at larger values of G. The fractional dichroism increases as the supporting electrolyte concentration decreases.

Chemical and mineralogical characterization of micro-inclusions in diamonds

Secondary-ion mass spectrometry (SIMS), electron probe analysis (EPMA), analytical scanning electron microscopy (SEM) and infrared (IR) spectroscopy were used to determine the chemical composition and the mineralogy of sub-micrometer inclusions in cubic diamonds and in overgrowths (coats) on octahedral diamonds from Zaire, Botswana, and some unknown localities.

The inclusions are sub-micrometer in size. The typical diameter encountered during transmission electron microscope (TEM) examination was 0.1-0.5 µm. The micro-inclusions are sub-rounded and their shape is crystallographically controlled by the diamond. Normally they are not associated with cracks or dislocations and appear to be well isolated within the diamond matrix. The number density of inclusions is highly variable on any scale and may reach 10^(11) inclusions/cm^3 in the most densely populated zones. The total concentration of metal oxides in the diamonds varies between 20 and 1270 ppm (by weight).

SIMS analysis yields the average composition of about 100 inclusions contained in the sputtered volume. Comparison of analyses of different volumes of an individual diamond show roughly uniform composition (typically ±10% relative). The variation among the average compositions of different diamonds is somewhat greater (typically ±30%). Nevertheless, all diamonds exhibit similar characteristics, being rich in water, carbonate, SiO_2, and K_2O, and depleted in MgO. The composition of micro-inclusions in most diamonds vary within the following ranges: SiO_2, 30-53%; K_2O, 12-30%; CaO, 8-19%; FeO, 6-11%; Al_2O_3, 3-6%; MgO, 2-6%; TiO_2, 2-4%; Na_2O, 1-5%; P_2O_5, 1-4%; and Cl, 1-3%. In addition, BaO, 1-4%; SrO, 0.7-1.5%; La_2O_3, 0.1-0.3%; Ce_2O_3, 0.3-0.5%; smaller amounts of other rare-earth elements (REE), as well as Mn, Th, and U were also detected by instrumental neutron activation analysis (INAA). Mg/(Fe+Mg), 0.40-0.62 is low compared with other mantle derived phases; K/ AI ratios of 2-7 are very high, and the chondrite-normalized Ce/Eu ratios of 10-21 are also high, indicating extremely fractionated REE patterns.

SEM analyses indicate that individual inclusions within a single diamond are roughly of similar composition. The average composition of individual inclusions as measured with the SEM is similar to that measured by SIMS. Compositional variations revealed by the SEM are larger than those detected by SIMS and indicate a small variability in the composition of individual inclusions. No compositions of individual inclusions were determined that might correspond to mono-mineralic inclusions.

IR spectra of inclusion- bearing zones exhibit characteristic absorption due to: (1) pure diamonds, (2) nitrogen and hydrogen in the diamond matrix; and (3) mineral phases in the micro-inclusions. Nitrogen concentrations of 500-1100 ppm, typical of the micro-inclusion-bearing zones, are higher than the average nitrogen content of diamonds. Only type IaA centers were detected by IR. A yellow coloration may indicate small concentration of type IB centers.

The absorption due to the micro-inclusions in all diamonds produces similar spectra and indicates the presence of hydrated sheet silicates (most likely, Fe-rich clay minerals), carbonates (most likely calcite), and apatite. Small quantities of molecular CO_2 are also present in most diamonds. Water is probably associated with the silicates but the possibility of its presence as a fluid phase cannot be excluded. Characteristic lines of olivine, pyroxene and garnet were not detected and these phases cannot be significant components of the inclusions. Preliminary quantification of the IR data suggests that water and carbonate account for, on average, 20-40 wt% of the micro-inclusions.

The composition and mineralogy of the micro-inclusions are completely different from those of the more common, larger inclusions of the peridotitic or eclogitic assemblages. Their bulk composition resembles that of potassic magmas, such as kimberlites and lamproites, but is enriched in H_2O, CO_3, K_2O, and incompatible elements, and depleted in MgO.

It is suggested that the composition of the micro-inclusions represents a volatile-rich fluid or a melt trapped by the diamond during its growth. The high content of K, Na, P, and incompatible elements suggests that the trapped material found in the micro-inclusions may represent an effective metasomatizing agent. It may also be possible that fluids of similar composition are responsible for the extreme enrichment of incompatible elements documented in garnet and pyroxene inclusions in diamonds.

The origin of the fluid trapped in the micro-inclusions is still uncertain. It may have been formed by incipient melting of a highly metasomatized mantle rocks. More likely, it is the result of fractional crystallization of a potassic parental magma at depth. In either case, the micro-inclusions document the presence of highly potassic fluids or melts at depths corresponding to the diamond stability field in the upper mantle. The phases presently identified in the inclusions are believed to be the result of closed system reactions at lower pressures.

Toward Understanding Astrophysical Phenomena

Fast radio bursts (FRBs), a novel type of radio pulse, whose physics is not yet understood at all. Only a handful of FRBs had been detected when we started this project. Taking account of the scant observations, we put physical constraints on FRBs. We excluded proposals of a galactic origin for their extraordinarily high dispersion measures (DM), in particular stellar coronas and HII regions. Therefore our work supports an extragalactic origin for FRBs. We show that the resolved scattering tail of FRB 110220 is unlikely to be due to propagation through the intergalactic plasma. Instead the scattering is probably caused by the interstellar medium in the FRB's host galaxy, and indicates that this burst sits in the central region of that galaxy. Pulse durations of order $\ms$ constrain source sizes of FRBs implying enormous brightness temperatures and thus coherent emission. Electric fields near FRBs at cosmological distances would be so strong that they could accelerate free electrons from rest to relativistic energies in a single wave period. When we worked on FRBs, it was unclear whether they were genuine astronomical signals as distinct from `perytons', clearly terrestrial radio bursts, sharing some common properties with FRBs. Recently, in April 2015, astronomers discovered that perytons were emitted by microwave ovens. Radio chirps similar to FRBs were emitted when their doors opened while they were still heating. Evidence for the astronomical nature of FRBs has strengthened since our paper was published. Some bursts have been found to show linear and circular polarizations and Faraday rotation of the linear polarization has also been detected. I hope to resume working on FRBs in the near future. But after we completed our FRB paper, I decided to pause this project because of the lack of observational constraints.

The pulsar triple system, J0733+1715, has its orbital parameters fitted to high accuracy owing to the precise timing of the central $\ms$ pulsar. The two orbits are highly hierarchical, namely $P_{\mathrm{orb,1}}\ll P_{\mathrm{orb,2}}$, where 1 and 2 label the inner and outer white dwarf (WD) companions respectively. Moreover, their orbital planes almost coincide, providing a unique opportunity to study secular interaction associated purely with eccentricity beyond the solar system. Secular interaction only involves effect averaged over many orbits. Thus each companion can be represented by an elliptical wire with its mass distributed inversely proportional to its local orbital speed. Generally there exists a mutual torque, which vanishes only when their apsidal lines are parallel or anti-parallel. To maintain either mode, the eccentricity ratio, $e_1/e_2$, must be of the proper value, so that both apsidal lines precess together. For J0733+1715, $e_1\ll e_2$ for the parallel mode, while $e_1\gg e_2$ for the anti-parallel one. We show that the former precesses $\sim 10$ times slower than the latter. Currently the system is dominated by the parallel mode. Although only a little anti-parallel mode survives, both eccentricities especially $e_1$ oscillate on $\sim 10^3\yr$ timescale. Detectable changes would occur within $\sim 1\yr$. We demonstrate that the anti-parallel mode gets damped $\sim 10^4$ times faster than its parallel brother by any dissipative process diminishing $e_1$. If it is the tidal damping in the inner WD, we proceed to estimate its tidal quantity parameter ($Q$) to be $\sim 10^6$, which was poorly constrained by observations. However, tidal damping may also happen during the preceding low-mass X-ray binary (LMXB) phase or hydrogen thermal nuclear flashes. But, in both cases, the inner companion fills its Roche lobe and probably suffers mass/angular momentum loss, which might cause $e_1$ to grow rather than decay.

Several pairs of solar system satellites occupy mean motion resonances (MMRs). We divide these into two groups according to their proximity to exact resonance. Proximity is measured by the existence of a separatrix in phase space. MMRs between Io-Europa, Europa-Ganymede and Enceladus-Dione are too distant from exact resonance for a separatrix to appear. A separatrix is present only in the phase spaces of the Mimas-Tethys and Titan-Hyperion MMRs and their resonant arguments are the only ones to exhibit substantial librations. When a separatrix is present, tidal damping of eccentricity or inclination excites overstable librations that can lead to passage through resonance on the damping timescale. However, after investigation, we conclude that the librations in the Mimas-Tethys and Titan-Hyperion MMRs are fossils and do not result from overstability.

Rubble piles are common in the solar system. Monolithic elements touch their neighbors in small localized areas. Voids occupy a significant fraction of the volume. In a fluid-free environment, heat cannot conduct through voids; only radiation can transfer energy across them. We model the effective thermal conductivity of a rubble pile and show that it is proportional the square root of the pressure, $P$, for $P\leq \epsy^3\mu$ where $\epsy$ is the material's yield strain and $\mu$ its shear modulus. Our model provides an excellent fit to the depth dependence of the thermal conductivity in the top $140\,\mathrm{cm}$ of the lunar regolith. It also offers an explanation for the low thermal inertias of rocky asteroids and icy satellites. Lastly, we discuss how rubble piles slow down the cooling of small bodies such as asteroids.

Electromagnetic (EM) follow-up observations of gravitational wave (GW) events will help shed light on the nature of the sources, and more can be learned if the EM follow-ups can start as soon as the GW event becomes observable. In this paper, we propose a computationally efficient time-domain algorithm capable of detecting gravitational waves (GWs) from coalescing binaries of compact objects with nearly zero time delay. In case when the signal is strong enough, our algorithm also has the flexibility to trigger EM observation {\it before} the merger. The key to the efficiency of our algorithm arises from the use of chains of so-called Infinite Impulse Response (IIR) filters, which filter time-series data recursively. Computational cost is further reduced by a template interpolation technique that requires filtering to be done only for a much coarser template bank than otherwise required to sufficiently recover optimal signal-to-noise ratio. Towards future detectors with sensitivity extending to lower frequencies, our algorithm's computational cost is shown to increase rather insignificantly compared to the conventional time-domain correlation method. Moreover, at latencies of less than hundreds to thousands of seconds, this method is expected to be computationally more efficient than the straightforward frequency-domain method.