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# The Vela Pulsar’s Radio Nebula

## 1 Introduction

The observations of the Vela pulsar wind nebula (PWN) made by Chandra X-ray Observatory (Pavlov et al., 2000; Helfand et al., 2001) lead us to examine the published high resolution results of the region (Bietenholz et al., 1991; Bock et al., 1998b; Bock et al., 1998a; Bock et al., 2002) and the archives of the Australia Telescope Compact Array (ATCA) to explore whether there was similar radio emission associated with the pulsar. Prompted by the revealing images obtained from the available (archival) data, we re-observed with four moderately compact configurations, and two closely spaced frequencies. Correlation data in each integration were folded and binned at the pulsar period (pulsar binning) at the highest possible rate (thirty two bins per period). Furthermore we reprocessed archived data at 1.4 and 2.4-GHz.

Previous high resolution observations of this region are reported in Bietenholz et al. (1991) using the VLA, Bock et al. (1998b) using Molonglo Observatory Synthesis Telescope (MOST) and Bock et al. (1998a); Bock et al. (2002) using the ATCA. These final two papers discuss results from the same data as we subsequently accessed from the archive.

Our observations show an extended radio nebula with symmetric morphology surrounding the pulsar and its X-ray nebula. We describe our results, compare them to those in the literature, and consider some of the consequences.

## 2 Observations and Data reduction

All the data were collected at the Australia Telescope Compact Array (ATCA) in Narrabri (latitude -30.3o) (Frater et al., 1992). Observations were made at 5.2-GHz with the Array in the standard configurations 0.375, 0.75D, 1.5D and 6D. The maximum and minimum baselines were 110 and 0.35 k$`\lambda `$ (angular resolutions of $`1.9^{^{\prime \prime }}`$ to $`9.8^{^{}}`$) for a total of 42.7 hours. Observations at 8.5-GHz we used the 0.75D, 1.5D and EW352 configurations with a four pointing mosaic, to get full coverage of the extended source. The maximum and minimum baselines were 130 and 0.6 k$`\lambda `$ ($`1.6^{^{\prime \prime }}`$ to $`5.7^{^{}}`$) and data were collected over a total of 38.3 hours. In both cases we observed in two nearby frequencies, with bandwidths of 128 MHz, to ensure that there would be no ambiguities in the rotation measure (RM) and to maximise the independent uv coverage. We used the ATNF correlator mode that divides each integration data into separate phase bins spanning the pulsar period. This firstly allowed the highly variable pulsar flux to be excluded from the image and secondly allowed us to selfcalibrate (i.e. derive the antennae phases from the observations) on the strong signal from the pulsar (0.6 Jy at 8.5 GHz). Where the interstellar dispersion smeared the pulse arrival time across the band into several bins (significant only for observations below 2.4-GHz) we dedispersed across the multiple spectral channels. The correlator configuration used for our observations separated the received signal between thirty two pulsar bins. The archived data from 1996 was observed as part of a thirty five pointing mosaic with only one observation covering the pulsar. They were made with an eight-bin pulsar mode. The full details are shown in Table 1.

The data reduction was done following the standard procedures using the MIRIAD software package. The antenna gains were calibrated with regular observations of B0823-500. Absolute flux calibration was against B1934-638, observed at the end or the beginning of each observation. The bright FR-II galaxy to the North (centred at 08:35:22.6 -45:07:37.6) has been suppressed by modelling its structure at the highest resolution and subtracting its contribution from the uv visibilities. Details of this source are to be found in Table 2 and the image at 5 GHz in Figure 1. We selfcalibrated on the bin containing the maximum pulsar flux and transferred the phases to the off-pulse data. All images were then produced by grading the uv plane appropriately for an equivalent FWHM beamwidth of $`10^{\prime \prime }`$, except the 1.4-GHz and 2.4-GHz images, which were produced with uniform weighting. Deconvolution was done with the task PMOSMEM, a full polarisation version of the maximum entropy task MOSMEM, for mosaicked images.

## 3 Image analysis

A single pointing was used for the 5 GHz observations and radio emission was found over a region comparable to the primary beam ($`9.3^{}`$). The images are corrected for the primary beam taper and are cut off where the response falls below 25% of the maximum. The most obvious effect of this is the higher noise levels at the edge of the images. We have confirmed that we are producing an accurate representation of this wide field of view using the model from the mosaicked image in an equivalent uv data set. As that model was fully recovered we can be sure that the image produced is not truncated. The phase centre was $`1^{\prime \prime }`$ south of the pulsar.

The next set of observations, at 8.5 GHz, was mosaicked and thus has a greater sky coverage than those for the 5 GHz observations, despite the narrower primary beam. These images are corrected for the combined primary beam taper and have a cutoff at 33% of the maximum.

A similar, pulsar binned, mosaicked observation of the entire Vela X region was made by Bock in 1996 (Bock et al., 1998a; Bock et al., 2002). He kindly made the calibrated 2.4-GHz data available. The 1.4-GHz data from six 128-MHz bands was recovered from the archives with the maximal number of spectral channels. We processed those pointings of these data that covered the pulsar in a similar fashion, with the added step of correction for the pulsar dedispersion across the frequency channels. In these data we suppressed the FR-II galaxy and three other point sources (30 mJy at 08:33:43.8 -45:17:58, 13 mJy at 08:34:52.8 -45:20:07 and 7 mJy at 08:35:29.2 -45:18:25) in the field. The 2.4-GHz data consist of three 128-MHz bands, with poor long baseline coverage. These data were imaged without the 6 km antenna, so it has the lowest resolution; $`36^{\prime \prime }\times 26^{\prime \prime }`$.

The images for both of the lower frequencies also have corrections for the primary beam applied. These, however, are much less significant for the large primary beam at these frequencies. The phase centre for these observations was $`3^{}`$ south of the pulsar.

One of the common problems is in comparing the absolute flux scales between different configurations responding to different sets of spatial frequencies. We have addressed this by making point to point comparisons of images smoothed to a $`20^{\prime \prime }`$ beam size, and fitting a global slope and intercept to this intensity-intensity plot. These showed that the flux scales agreed with each other to within 1 mJy/beam, except for the 5-GHz observations, which suffered a shortfall of 3 mJy/beam (i.e. $`F_{6cm}=F_{3cm}\times 0.78+3`$mJy). Given that the 5 GHz observations were not mosaicked, and therefore could not be expected to fully recover flux on the shortest baselines, this is not surprising. These offsets are corrected for in the spectral index images, and for the integrated flux density measurements.

## 4 Results

### 4.1 The background FR-II galaxy

We have derived the flux density from the background FR-II galaxy at each frequency. Low resolution images of the nebula will need to correct for this, so we provide the fluxes in Table 2 and the 5-GHz image (Figure 1). The galaxy was imaged and deconvolved at maximum resolution, and the deconvolution model subtracted from the uv data before imaging the region around the Vela pulsar.

### 4.2 Images at 8.5 GHz

We find a highly polarised and roughly symmetric region of emission which is centred on the pulsar. The polarised fraction is 30% with a r.m.s. variation of 7% across the nebula. In Figure 2 the flux from the pulsar and the FR-II galaxy has been removed.

We have defined the northern lobe as the area with brightness greater than 1.25 mJy/beam that lies within $`2.5^{}`$ north of the pulsar and $`2.5^{}`$ east to $`2.5^{}`$ west. This covers an area of 5.3 square arcminutes in which we find an integrated flux density of 230 mJy. Altering the cutoff flux by $`\pm 10`$% gives variation of 40 mJy. For the more diffuse southern lobe, we define the region where flux density is greater than 1 mJy, and extending to $`5^{}`$ south of the pulsar, within the band $`1.3^{}`$ east to $`5^{}`$ west. This we found to cover 18 square arcminutes and amount to 650 mJy. Errors in these estimates arise from uncertainty in the definition of the regions and the lack of low spatial frequency information. However, as we have corrected for the offset in the linear fit to flux against frequency, we believe these uncertainties are insignificant. The observed flux values, and those from the other observed bands are listed in Table 3.

The flux emitted in the region of the X-ray emission, which we define as the region where Chandra detected flux greater than 20 $`\sigma `$ above the background (1 count per square arcsecond), is $`25\pm 3`$ mJy. This is a well defined region covering 0.73 square arcminutes. Our error limits are those fluxes measured with a X-ray flux cutoff of $`17\sigma `$ and $`23\sigma `$. We also estimated the flux from the region after the subtraction of a planar background. The residual flux found was within a few sigma of zero. We report both of the total flux and the residual values in table 3.

### 4.3 Images at 5 GHz

We find an even more highly polarised region of emission at this frequency. The mean polarised fraction is 60% with a r.m.s. of 10% across the nebula. Figure 3a shows the total intensity, and 3b the polarised intensity with position angles overlaid. We estimated the integrated flux densities by using the regions defined at 8.5 GHz and offsetting the flux scale as discussed in section 4.6. The results are in Table 3.

The region around Vela was observed previously with the VLA (Bietenholz et al., 1991) at 5 GHz, and their image of the region is Figure 1 in that paper. Their image does not go nearly as deep as ours (stopping at the $`8\sigma `$ contour). Therefore they reported only the sharp, bright, northern edge, and as a result had identified the symmetry axis (and the spin-axis projection) as that bisecting the length of the feature. Whilst the observations have similar resolution and point source sensitivity, our combined configurations have a greater concentration of the shorter baselines that are most sensitive to the low surface brightness structures we find here. The peak fluxes we find for the FR-II galaxy and the edge of the northern lobes are consistent with their observations.

### 4.4 Images at 2.4 GHz

We found the same double lobed structure in these lower resolution observations. The Southern lobe is more nebulous than at 5 cm, but clearly does not connect to the bar of emission seen in radio and X-rays (Frail et al., 1997) in the Vela X region (Figure 4). The fluxes from the three regions defined are listed in Table 3.

### 4.5 Images at 1.4 GHz

The data presented here are a subset of the observations of the whole Vela SNR region, which are published by Bock et al. (1998a); Bock et al. (2002). The best of these images were made at $`22^{\prime \prime }\times 23^{\prime \prime }`$ resolution. Figure 3 in Bock et al. (1998a) covers a slightly larger region than our Figure 5. Our images were made at the maximum resolution and then smoothed to match the resolution of the other images ($`20^{\prime \prime }\times 20^{\prime \prime }`$), but have the strong background sources removed.

Two sources were found (1.1 & 0.9 mJy) exactly one beam width away to the North and the South of the pulsar position. They are only found in the lowest or highest frequency channels of the pulsar bins after or before the pulsar signal. The pulsar is so strong at these frequencies that we are seeing the images from the bandpass sidelobes (i.e. about 128 MHz above and below our band edges) which of course have a phase change of $`180^o`$. Excluding these the integrated flux from this region is 33 mJy. The spectral index calculations using the 1.4-GHz data have these point sources subtracted. The flux from within this region is 2.8 mJy if we fit and subtract a planar background. 1 mJy of this is at the position of the pulsar and probably is flux from the pulse unsuccessfully excluded in the bin selection.

These images are complicated by other strong steep spectrum emission. However the polarised total intensity images, Figure 6, do show a double lobed structure. We have confirmed that the variation of the polarised emission is not associated with bandwidth depolarisation by processing sub-bands separately then recombining them. In particular the measured RM at the edge of the southern lobe (less than 70 rad m-2) is too small to cause any significant losses in intensity and thus produce a false edge.

### 4.6 Spectral Index and rotation measure

Comparisons between the images were done after smoothing them to $`20^{\prime \prime }`$. The lower resolution spectral index images made using the 2.4-GHz are not presented. The comparisons between the other three frequencies are shown in Figure 7. The mean spectral index was calculated across the whole region and is listed in Table 4. The errors are the one sigma variation across the image, not that of each independent point. The spectral index was calculated after comparing the data at different frequencies in an ‘intensity-intensity’ plot, to find the offset in the flux scales between the frequencies. This avoids the perennial problem in comparing interferometric images with different uv sampling. It was found that the dominant offset was for 5-GHz which was underestimated by 3 mJy/beam (at $`20^{\prime \prime }`$). The formal errors are dominated by the error in the flux scale offset, and are not uniform. They are typically $`\pm 0.03`$ in regions with significant flux density.

In most cases the spectral index is uncorrelated with known features, except for between 5-GHz and 1.4-GHz where $`\alpha =0.3\pm 0.1`$ (where $`F\nu ^\alpha `$) across the image, but with a noticeable flattening around the X-ray region. Further observations to investigate this are required. The edges of the lobes in the 5/8-GHz spectral index are remarkably high, but have the poorest signal to noise.

Faraday rotation along the sight line from the nebula has been deduced from the multi-frequency observations. Figure 8 shows its variation across the source. After correction for this propagation effect, the intrinsic orientation of the linearly polarised component (Figure 10) shows a symmetric pattern about the pulsar spin axis projection.

The above rotation measure values imply that there would be some bandwidth depolarisation (a differential Faraday rotation of $`56^o`$) across the 20 cm band. Averaging across the band, however, would only produce a 5% fall in the integrated polarised flux. This effect could be dealt with, but would add little to our results, and has not been attempted.

### 4.7 Polarised intensity

Polarisation fraction and angle provides one of the greatest diagnostics as to the underlying processes and conditions. We see in the 5 and 8-GHz observations that the polarisation fraction is high, and approaches the theoretical maximum for synchrotron emission. The polarisation position angles (associated with the electric field vectors) are first corrected for Faraday rotation, then are rotated further by 90 degrees to view (as shown in Figure 10) the corresponding magnetic field structure in the emission regions. A clear signature of toroidal magnetic field with respect to the spin axis of the pulsar is apparent.

A more detailed model of the emission, combining the X-ray and radio data, will be presented in the next paper.

### 4.8 Pulsar Wind Nebula surface brightness

Using the latest estimated distance of 0.3 kpc (Caraveo et al., 2001; Dodson et al., 2003) and using equation 4 from Frail & Scharringhausen (1997) we find the radio luminosity to be $`6.8\times 10^{30}`$ ergs/s, or $`1\times 10^6`$ of the spin down energy, $`\dot{E}`$. This is below the upper limit for twenty seven of the thirty one non-detections of PWN discussed in Gaensler et al. (2000). It may be that the lack of PWN is not due to their intrinsic rarity, but their inefficiency in converting the spin down power into detectable radio emission. Furthermore the assumption of a proper motion powered shock front clearly breaks down as the bright radio emission features are approximately parallel to the proper motion direction and there is no ‘wake-like’ feature that can be associated with the known proper motion direction (which is close to the projected spin axis of the star).

## 5 Conclusions

We believe we have observed the true extent and morphology of the radio wind nebula associated with the Vela pulsar. The toroidal magnetic field structure revealed by the polarisation data and the symmetric morphology around the projected spin axis of the star (as in the X-ray case) argue strongly for the nebula to be pulsar (rotation) driven, in terms of both, the recent and continued injection of particles and the (possibly wound-up) magnetic fields in the regions of radio emission. The extension towards the south, seen in the 2.4 and 1.4 GHz images, is unpolarised and thus has a different character from that of the nebula. The rotation measure along these sight-lines appears insufficient to cause significant depolarisation.

This allows the much more complex region, Vela X, to be unambiguously identified with the integrated history of Vela’s emission, but not driven by the current particle population. This affects all the estimates of expected PWN brightness based on the Vela-X region (e.g. Frail & Scharringhausen (1997)).

The most striking feature in comparing the X-ray and radio emissions is that the radio emission starts at a distance from the centre where X-ray emission stops. Given the remarkable similarity in the morphologies in the two bands, it is tempting to model the radio nebula on the lines of the available models for the X-ray data. Results of our preliminary attempts (Lewis et al., 2002) to extend the model of Radhakrishnan & Deshpande (2001) for the radio data have been very encouraging. A more detailed modelling of the radio data is in progress and will be reported later separately.

## 6 Acknowledgements

The Australia Telescope Compact Array is part of the Australia Telescope, funded by the Commonwealth of Australia for operation as a National Facility, and managed by CSIRO. The access of data from the archive was assisted by Robin Wark. Dr Bock made the calibrated 2.4-GHz data available. The pulsar binning mode required the timing observations made at Mount Pleasant. This research has made use of NASA’s Astrophysics Data System Abstract Service. The X-ray data for the Chandra observations were downloaded from the public access site, the Chandra Data Archive (CDA). This is part of the Chandra X-Ray Observatory Science Centre (CXC) which is operated for NASA by the Smithsonian Astrophysical Observatory.

The 1.4 GHz data was partially processed by Godfrey and See-Toh for their 3rd-year astronomy practical.


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# Oscillator Models for the Universe and Dark Energy

## 1 Planck Scale Oscillators

In an earlier communication , it was argued that a typical elementary particle like a pion could be considered to be the result of $`10^{40}`$ evanescent Planck scale particles. The argument was based on random motions and also on the modification to the Uncertainity Principle. We will now consider the problem from a totally different point of view, which not only reconfirms the above result, but also enables an elegant extension to the case of the entire universe itself.
We first consider an array of $`N`$ particles, spaced a distance $`\mathrm{\Delta }x`$ apart, which behave like oscillators, that is as if they were connected by springs. We then have

$$r=\sqrt{N\mathrm{\Delta }x^2}$$
(1)
$$ka^2k\mathrm{\Delta }x^2=\frac{1}{2}k_BT$$
(2)
where $`k_B`$ is the Boltzmann constant, $`T`$ the temperature, $`r`$ the extent and $`k`$ is the spring constant given by

$$\omega _0^2=\frac{k}{m}$$
(3)
$$\omega =\left(\frac{k}{m}a^2\right)^{\frac{1}{2}}\frac{1}{r}=\omega _0\frac{a}{r}$$
(4)
We now identify the particles with Planck masses, set $`\mathrm{\Delta }xa=l_P`$, the Planck length. It may be immediately observed that use of (3) and (2) gives $`k_BTm_Pc^2`$, which ofcourse agrees with the temperature of a black hole of Planck mass. Indeed Rosen had shown that a Planck mass particle at the Planck scale can be considered to be a universe in itself .
We now use the fact alluded to that a typical elementary particle like the pion can be considered to be the result of $`N10^{40}`$ Planck masses (Cf.ref.). Using this in (1), we get $`rl`$, the pion Compton wavelength as required. Further, using (2), (3) and (4), we get for a pion,

$$k_BT=\frac{m^3c^4l^2}{\mathrm{}}=mc^2,$$

which ofcourse is the well known formula for the Hagedorn temperature for elementary particles like pions. In other words, this confirms the conclusions in , that we can treat an elementary particle as a series of some $`10^{40}`$ Planck mass oscillators.
However it must be observed from (2) and (3), that while the Planck mass gives the highest energy state, an elementary particle like the pion is in the lowest energy state. This explains why we encounter elementary particles, rather than Planck mass particles in nature. Infact as already noted , a Planck mass particle decays via the Bekenstein radiation within a Planck time $`10^{42}secs`$. On the other hand, the lifetime of an elementary particle would be very much higher.
Using the fact that the universe consists of $`n10^{80}`$ elementary particles like the pions, the question is, can we think of the universe as a collection of $`10^{120}`$ Planck mass oscillators? This is what we will now show. Infact if we use equation (1) with

$$N10^{120},$$

we can see that the extent $`r10^{28}cms`$ which is of the order of the diametre of the universe itself. Next using (4) we get

$$n\mathrm{}\omega _0^{(min)}\frac{l_P}{10^{28}}m_Pc^2\times 10^{60}$$
(5)
which gives the correct mass of the universe. In other words the universe itself can be considered to be a normal mode of Planck scale oscillators.

## 2 Oscillators and Dark Energy

The existence of the Zero Point Field (ZPF) was realised even by Max Planck. In its later version it has come to be known as Quantum Vaccuum, and lately it has been possible to identify it with the mysterious dark energy. The Zero Point Field arises because of the fact that though classically, an oscillator in the ground state has zero energy, Quantum Mechanically, owing to the uncertainity principle, there is an energy fluctuation about the zero energy level.
Interestingly there have been two schools of thought. Zero Point Field, according to Quantum theoriests is a secondary effect arising from the already present oscilaltors. However according to what has come to be known as Stochastic Electrodynamics, the ZPF is primary, and infact Quantum Mechanics can be deduced therefrom. This is a chicken and egg situation.
Recently the ZPF has come into focus once again because of the observed ever expanding, accelerating feature of the universe. In other words there is a large scale repulsion represented by a cosmological constant $`\mathrm{\Lambda }`$ once invented and then rejected by Einstein, and this cosmic repulsion could be attributed to a mysterious all pervading dark energy, which can be identified with the ZPF: this could be the mechanism which drives the cosmic expansion and acceleration (Cf.ref.) for a review).
Two of the earliest realisations of the ZPF were in the form of the Lamb shift and the Casimir effect.
In the case of the Lamb shift, as is well known, the motion of an orbiting electron gets affected by the background ZPF. Effectively there is an additioinal field, over and above that of the nucleus. This additional potential, as is well known is given by

$$\mathrm{\Delta }V(\stackrel{}{r})=\frac{1}{2}(\mathrm{\Delta }r)^2^2V(\stackrel{}{r})$$

The additional energy

$$\mathrm{\Delta }E=\mathrm{\Delta }V(\stackrel{}{r})$$

contributes to the observed Lamb shift which is $`1000mc/sec`$.
The essential idea of the Casimir effect is that the interaction between the ZPF and matter leads to macroscopic consequences. For example if we consider two parallel metallic plates in a conducting box, then we should have a Casimir force given by

$$F=\frac{\pi ^2}{240}\frac{\mathrm{}cA}{l^4}$$

where $`A`$ is the area of the plates and $`l`$ is the distance between them. More generally, the Casimir force is a result of the boundedness or deviation from a Euclidean topology of or in the Quantum Vaccuum. These Casimir forces have been experimentally demonstrated .
Returning to the ZPF as the ubiquitous dark energy, we observe that , a fluctuating electromagnetic field can be modelled as an infinite collection of independent harmonic oscillators. Quantum Mechanically, the ground state of the harmonic oscillators is described by

$$\psi (x)=\left(\frac{m\omega }{\pi \mathrm{}}\right)^{1/4}e^{(m\omega /2\mathrm{})x^2}$$

which exhibits the probability for the oscillator to fluctuate, mostly in the region given by

$$\mathrm{\Delta }x(\mathrm{}/m\omega )^{1/2}$$

An infinite collection of such oscillators can be modelled by

$$\psi (\xi _1,\xi _2,\mathrm{})=const.\mathrm{exp}[(\xi _1^2+\xi _2^2+\mathrm{})],$$

which gives the probability amplitude for an electromagnetic field configuration $`B(x,y,z),\xi _1`$, etc. being the Fourier coefficients. Finally, as a consequence there is a fluctuating magnetic field given by

$$B=\frac{\sqrt{\mathrm{}c}}{l^2}$$
(6)
where $`l`$ is the extent over which the fluctuation is measured. Further these fluctuations typically take place within the time $`\tau `$, a typical elementary particle Compton time (Cf.ref.). This begs the question whether such ubiquotous fields could be tapped for terrestrial applications or otherwise.
We now invoke the well known result from macroscopic physics that the current in a coil is given by

$$ı=\frac{NBA}{R\mathrm{\Delta }t}$$
(7)
where $`N`$ is the numer of turns of the coil, $`A`$ is its area and $`R`$ the resistance.
Introducing (6) into (7) we deduce that a coil in the ZPF would have a fluctuating electric current given by

$$ı\frac{NA}{R}\frac{e}{l^2\tau }$$
(8)
In principle it should be possible to harness the current (8). While this current is small, if we have a superconductor, then $`R`$ would be very small and the current would be much larger. The question is, whether such an application is possible, on the earth or in an orbiting space craft, for example.
Finally, it may be remarked that the usual ZPF of Quantum Theory leads to an unduly large cosmological constant . However, in the model described in , we get the observed small cosmological constant.


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# A Survey for H2O Megamasers III. Monitoring Water Vapor Masers in Active Galaxies

## 1 Introduction

VLBI mapping of water masers towards the nucleus of the low luminosity active galaxy NGC 4258 reveals a thin, edge-on disk 0.28 pc in radius (Herrnstein et al., 1999). The maser spectrum has a characteristic profile with three clusters of features: the strongest cluster is within 50 km s-1 of the systemic velocity of the galaxy (“systemic features”) while the others are red- and blue-shifted by $``$ 1000 km s-1 w.r.t systemic (“high velocity features”). The three clusters are associated with three loci in the rotating gas disk; each locus corresponds to a peak in the line-of-sight velocity coherence in the disk, thus producing the longest path lengths for maser amplification. The systemic features are associated with gas on the near side of the disk, close to the line of sight to the nucleus and radio continuum jets. The high velocity features are found along the “edges” of the disk, where the rotational velocity vector points approximately along our line of sight.

VLBA observations have been performed on those other megamaser galaxies which are bright enough for self-calibration on the maser features themselves (e.g. NGC 4945 – (Greenhill et al., 1997c), NGC 1068 – (Greenhill and Gwinn, 1997), NGC 3079 – (Trotter et al., 1998), IC 2560 – (Ishihara et al., 2001)). The results suggest that a gas disk is usually present but, in those sources which contain one, the dynamical structure of the masing disk is not as clean as in NGC 4258 (i.e. the disk is not in strictly Keplerian rotation, or maser emission is detected away from the disk).

The maser spectrum of NGC 4258 changes with time in a fashion which can be understood in the context of the rotating nuclear disk model. Narrow lines among the systemic features drift redward through a $``$ 100 km s-1 wide “envelope” at a rate of $``$ 9 km s-1 yr-1 (Haschick et al., 1994; Greenhill et al., 1995). This velocity drift reflects the gravitational acceleration of gas on the near side of the disk as it orbits the central black hole. The acceleration vector of such gas points directly away from the observer. For the high velocity features, the acceleration is directed in the plane of the sky and the maser lines remain at almost constant velocities, although complexities in the gaseous disk and deviations in the positions of the masers from the midline may lead to small velocity changes ($`<`$ 0.8 km s-1 yr-1) in these components (Bragg et al., 2000).

In this paper we investigate the time dependent behavior of water vapor masers in 13 galaxies and present recent sensitive spectra of 7 additional galaxies. We also report a search for water vapor masers towards the nuclei of 58 highly inclined, nearby galaxies.

## 2 Observations

We have monitored the 22 GHz water maser line of 13 galaxies between October 1993 and November 2002. Observations were made at Effelsberg using the 100 m telescope, at Parkes using the 64 m telescope, and at Green Bank using the 140-foot telescope and the 100 m Green Bank Telescope (GBT). Table 1 lists the dates and locations of the observing runs. The velocity scale recorded by the on-line software in Effelsberg uses the optical convention while the spectral data reduction program CLASS expects the radio convention, so a correction must be made to those data. Afterwards, the velocities of individual maser features were checked between the four telescopes and found to be consistent to better than 1 km s-1. Observing conditions varied drastically, and uncertainties in absolute flux densities are 10% to 30%. Thus, while our data are excellent for investigating time dependent velocity variations, uncertain flux calibration and sometimes infrequent sampling make detailed flux variability studies difficult.

The GBT data shown here were taken during commissioning and testing of the telescope, and are part of the first K-band experiment performed with the GBT. An 800 MHz bandwidth mode of the spectrometer and the active surface were being tested for the first time during this experiment as well. The active surface was running in an open loop mode and was programmed to counter the effects of gravitational deformations as determined by a finite element model. Aperture efficiencies ranged between 50% and 60% over elevation ranges from 15 to 85 with the active surface on, roughly a factor of two improvement over the efficiency with the active surface off. Because of the test nature of these observations, not all components of the GBT were available. We used only one polarization and only half of the available integrations due to testing of a new mode of the spectrometer. The effective integration times are therefore shorter with the GBT (10 minutes – 1 hour) than the other telescopes; nevertheless, the GBT spectra represent, in most cases, the most sensitive taken on these galaxies. System temperatures for the GBT data ranged from 37K to 60K.

For the Effelsberg and Green Bank 140 ft observations, a pointing calibrator was observed prior to each source, resulting in a pointing accuracy of about 10$`\mathrm{}`$. Pointing at Parkes, using the Master Equatorial System, has similar accuracy. Local pointing calibrators were used with the GBT observations as well. The pointing uncertainty there was 6$`\mathrm{}`$ – 8$`\mathrm{}`$ before applying the local corrections and $``$ 2$`\mathrm{}`$ afterwards. All observations prior to October 1999 utilized position switching to subtract the background. The autocorrelators were typically used in a wide bandwidth mode (50 MHz at Effelsberg, 64 MHz at Parkes, and 40 MHz for the Green Bank 140 ft) to maximize the velocity coverage. Observations since October 1999 at Effelsberg made use of the new dual beam system and new autocorrelator, running in an 8 $`\times `$ 40 MHz mode with polarizations overlapped, resulting in $``$ 150 MHz effective coverage. The GBT data were also taken with a dual beam system using beam switching to remove the background. Baseline curves were removed from the spectra by fitting a polynomial function, and a sinusoidal term as well for a few 140 ft observations. A second or third order polynomial across the 40 MHz – 64 MHz bandwidths generally provided a satisfactory description of the baseline. With the 140 ft, the focus was modulated and a double switching mode was used, with excellent baselines resulting. When fitting a baseline to the full 800 MHz of the GBT spectra, a higher order polynomial was generally required. For the purposes of this program, baseline waviness introduces a problem only when the width of the emission line feature is a significant fraction of the wavelength of the baseline artifacts. NGC 1052 and TXS 2226-184 are thus most seriously affected. The K-band receiver used with the Green Bank 140 ft telescope was upgraded after November 1994, providing a significant improvement in sensitivity. Additional observing details are given in Braatz et al. (1996).

The velocities in this paper follow the optical definition and are calculated with respect to the Local Standard of Rest (LSR). Galaxy recession velocities quoted here are taken from the HI velocities in de Vaucouleurs et al. (1991) and are converted to LSR for comparison with the maser spectra. Data were reduced using the software packages UNIPOPS (NRAO 140 ft), CLASS (Effelsberg 100 m), SPC (Parkes) and AIPS++ (GBT).

## 3 Line Widths and Intensities

The width of observed megamaser lines ranges from $``$ 1 km s-1 (e.g. NGC 5506 and the Circinus Galaxy) to several hundred km s-1 (NGC 1052 and TXS 2226-184). For some sources (e.g. NGC 4945) a broad maser feature is resolved into a group of closely spaced narrow spikes, but not so for NGC 1052 and TXS 2226-184. The width of the maser emission feature in NGC 1052 varies (Figure 1), and although the baselines were occasionally difficult to determine, variations in the maser profile are clearly seen.

One of the characteristic features of cosmic masers, both Galactic and extragalactic, is rapid variability of their observed intensities. The timescale and amount of variability, though, differs drastically for the individual sources we have monitored. The maser in NGC 1386, for example, has remained mostly unchanged during our 8 years of monitoring, while the maser in the Circinus Galaxy has changed its profile entirely between each observation. Indeed, variability in the Circinus maser is reported on timescales as short as several minutes (Greenhill et al., 1997a), possibly due to interstellar scintillation. Variability revealed by the present observations, though, is likely to have an intrinsic component as well (e.g. Kartje et al. (1999)). We have detected strong and short-lived (several month timescale) flares. In some cases, flares seem to arise from previously dimmer features, as in NGC 5506 starting March 1995 and IC 2560, which was seen to be bright in August 1997. In other cases, flares rise up from below the noise level. The sensitivity improvements due to the upgrades of the Effelsberg telescope and the construction of the GBT reveal a wealth of fainter features, as highlighted by the GBT spectrum of NGC 5506 (Figure 2).

Intrinsic variability in maser intensity might result from either a change in the pumping source or a change in the gain path. Some AGN are known to have rapidly variable X-ray sources which might ultimately provide the pumping energy. X-ray variability is stronger for Seyfert 1 galaxies, in which the X-ray source is thought to be seen directly, than for Seyfert 2s, in which a scattered or intrinsically extended component of the X-rays dominates at soft X-ray energies. The difference is believed to be purely one of viewing angle (e.g. Antonucci (1993)) so even though water megamasers are detected in only Seyfert 2s and LINERs, the relevant X-ray variability timescale is that of Seyfert 1s. NGC 1068 is an interesting case when considering this type of behavior. Over the past decade, several prominent maser features in NGC 1068 have disappeared and “new” ones appeared at later times (Baan and Haschick, 1996) having the same velocity. The reappearance suggests that each of these maser features is associated with a molecular gas complex which does not disappear over the monitoring interval, so the variability might be partly due to a changing pumping source. Flares from previously dimmer features, seen in several instances in Figure 1, may have a similar origin.

In NGC 4258, at least some of the maser variability is due to the orbital motion of molecular clouds. The maser associated with a given systemic cloud is only detectable while that cloud is in a small range of its orbit on the near side of the disk. However, the timescale for clouds to pass through this range ($``$ 10 years) is much longer than the observed variability of individual features. More likely, the strength and structure of maser features in this source and most others depend strongly on the geometry and orientation of orbiting molecular complexes.

## 4 GBT Results

Because faint features evident in the GBT data are poorly represented on the flux scales in Figure 1, we reproduce a GBT spectrum (Figure 2) of 10 of the sources monitored as well as 8 others visible in the northern sky. Although the GBT spectrometer covered 800 MHz of simultaneous bandwidth, no maser lines were detected beyond $``$ 80 MHz from the systemic velocity in any of the sources. The spectra in Figure 2 show 1600 km s-1 coverage for all sources except NGC 4258, for which the coverage is expanded to 2600 km s-1 to show the high velocity features, and Mrk 1419 (see Henkel et al. (2002)), which covers 2000 km s-1. The insets to the spectra for NGC 1386 and NGC 4258 are correctly matched to the velocity scale but show an expanded (and offset) flux scale to emphasize the detections of faint features.

## 5 Comments on Individual Sources

The maser in ESO 103-G35 was detected only once (Braatz et al., 1996) in June 1994, and will not be discussed here. Mrk 348 (Falcke et al., 2000) was not detected in H2O during the GBT test observations and has not been monitored during this program. Masers in NGC 3735 (Greenhill et al., 1997b) and NGC 5793 (Hagiwara et al., 1997) have also not been monitored by us but were observed with the GBT, and the resulting spectra are shown in Figure 2. No significant new features are detected in these sources, but the signal-to-noise is better than in previous data. Comments on other maser-detected galaxies follow.

Flux densities in Figure 1 are calibrated in Jy but the spectra are shifted from each other for clarity. Rather than showing the full spectra, a limited velocity window is shown for each source to facilitate comparisons of the maser velocities from one epoch to the next. No maser components were detected outside of the windows shown, except where noted in Mrk 1210. Line velocities used to measure maser drift rates have been determined by fitting Gaussian curves to each line, where possible.

### 5.1 Mrk 1

A single faint ($``$ 0.1 Jy) maser feature near 4868 km s-1 has been seen over 8 years of monitoring, and shows no detectable velocity drift during that period (–0.15 $`\pm `$ 0.13 km s-1 yr-1). This maser line is redshifted from the 21 cm HI velocity (4825 km s-1) by 43 km s-1. The more sensitive spectra of this source reveal that the line is the strongest feature of a cluster of maser features extending some 60 km s-1 and centered near 4860 km s-1. Weaker blueshifted features are evident near 4583 and 4620 km s-1 and likewise show no detectable drift during the monitoring period (0.00 $`\pm `$ 0.16 km s-1 yr-1 and 0.02 $`\pm `$ 0.17 km s-1 yr-1, respectively).

### 5.2 NGC 1052

NGC 1052 is the only elliptical galaxy detected in H2O, and the maser in this source is clearly unlike those in disk galaxies (but, see also the discussion for TXS 2226-184). The broad maser in NGC 1052 seemed to drift redward between March 1994 and December 1995, and subsequently showed complex structure, with an apparent bifurcation of the broad peak evident in the November 1997 spectrum. Several of the spectra, especially those in November 1994 and February 1998, are adversely affected by baseline structure. Nevertheless, the maser profile clearly changed during the monitoring period.

VLBI spectral line observations in November 1995 (Claussen et al., 1998) show that the maser in NGC 1052 arises primarily from two clumps of gas having distinct but overlapping velocities. The two clumps align parallel to the long known nuclear radio jet. The maser gas may be entrained along the jet or perhaps a disk lies in front of one side of the jet, in which case the masers may originate in gas amplifying the background continuum emission of the jet (in NGC 4258 the maser disk projects perpendicular to the radio continuum jet). It is not clear whether the broad line emission represents gas being accelerated by the jet or whether it is unrelated to the gas dynamics. It is possible that the profile changes result simply from gas at different line-of-sight velocities being lit up with maser emission at different times.

The GBT spectrum shows that in April 2002, after a lengthy gap from the previous spectrum, the maser had dimmed and possibly broadened. That the emission lacks narrow lines is counter to the typical maser profile, and the reason for the smooth, broad profile remains unknown.

### 5.3 NGC 1068

The maser source in NGC 1068 has been studied extensively by Baan and Haschick (1996) and Gallimore et al. (2001), and has not been part of our long-term monitoring program. We do present a GBT spectrum in Figure 2.

### 5.4 NGC 1386

This nearby Seyfert 2 galaxy has two prominent narrow features near 967 and 977 km s-1 and a broad feature at $``$ 860 km s-1, near the galaxy’s systemic velocity of 847 km s-1. The drift in the narrow features is measured to be –0.07 $`\pm `$ 0.14 km s-1 yr-1 (967) and –0.12 $`\pm `$ 0.14 km s-1 yr-1 (977). Individual features in the broad systemic component have not been traceable from one epoch to the next because of the signal-to-noise limitations and blending of the lines, but it is clear that future studies making use of the GBT will be able to track such features. The GBT spectrum also reveals several blueshifted components near 600 km s-1. It is possible that the features near 600 and 970 km s-1 are analogous to the high velocity features, and those near 860 km s-1 to the systemic features, in NGC 4258. Except for flux variability in the narrow redshifted features, the maser profile in this galaxy appears remarkably unchanged over the monitoring period.

### 5.5 Mrk 1210

Narrow maser features were first detected near velocities 4214 and 4247 km s-1, redshifted from the systemic velocity of this galaxy (4032 km s-1). The drifts in these lines are measured to be –0.18 $`\pm `$ 0.11 km s-1 yr-1 and –0.12 $`\pm `$ 0.16 km s-1 yr-1, respectively. If the blueshifted line at $``$ 4091 km s-1 detected in April 2002 is associated with the line at $``$ 4094 during 1998, then it had a blueward velocity drift of –0.93 $`\pm `$ 0.30 km s-1 yr-1. Another line is found at 4226 km s-1 and has no detectable drift (–0.17 $`\pm `$ 0.42 km s-1 yr-1). The GBT spectrum (Figure 2) shows a blueshifted feature centered near 3780 km s-1. This feature was also detected (but not shown in Figure 1 in order to see other features clearly) in Effelsberg spectra from March 2000 and January 2001. The measured velocity drift for this feature is 0.81 $`\pm `$ 0.57 km s-1 yr-1.

### 5.6 NGC 2639

Wilson et al. (1995) discussed the initial results of the monitoring program on NGC 2639, arguing that the galaxy and its maser share a number of similarities with NGC 4258. Most significantly, the strongest maser feature detected between October 1993 and March 1995 drifted redward at a rate of 6.6 km s-1 yr-1. The galaxy was observed several times with the Effelsberg 100 m telescope during the next two years but the maser was not detected, apparently due to a combination of poor weather conditions during the observing and diminishing maser brightness. The maser was detected again in 1997 and 1998. The drift of the line initially seen at 3307 km s-1 over the period Apr 1997 – Feb 1998 is 6.5 $`\pm `$ 1.6 km s-1 yr-1, consistent with the results of Wilson et al. (1995). A pair of 14 mJy lines was detected with the GBT in April 2002 (Figure 2).

The maser emission was observed to be much brighter in April 1997. At that time, broad emission was seen between about 3220 and 3310 km s-1, which is slightly to the blue of the systemic HI velocity, 3335 km s-1. If the masers detected in April 1997 delimit the envelope of systemic maser features (see also the February 1994 spectrum), analogous to the masers in NGC 4258, then the disappearance of the maser feature tracked between October 1993 and March 1995 may be understood in terms of the masing gas drifting beyond the envelope of observable systemic features (cf. Greenhill et al. (1995) for NGC 4258).

### 5.7 Mrk 1419

Henkel et al. (2002) report the discovery of a triply-peaked H2O maser towards the nucleus of Mrk 1419. The authors find that the maser source has properties similar to those seen in NGC 4258, including an acceleration in the “systemic” masers (2.8 $`\pm `$ 0.5 km s-1 yr-1) and no acceleration in the “high velocity” lines. In Figure 2 we present a sensitive spectrum of Mrk 1419 taken with the GBT in April 2002. No features were detected outside of the velocity range reported by Henkel et al. (2002).

### 5.8 NGC 3079

The water maser source in NGC 3079 has been studied extensively by Baan and Haschick (1996) and Hagiwara et al. (2002b) and has not been part of our monitoring program. However, we present a GBT spectrum of this maser (Figure 2) which is shown with a flux range chosen to emphasize the weak features. Our spectrum confirms the redshifted structure detected by Hagiwara et al. (2002b) as well as the narrow gap at the systemic velocity, though the flux in the April 2002 spectrum does not drop to zero at the systemic velocity, as in their December 2001 data.

### 5.9 IC 2560

Observations of the maser in this galaxy clearly benefit from the high sensitivity of the GBT. Since the discovery of the maser in June 1994 (Braatz et al., 1996) with the Parkes telescope, this source has been observed several more times at Parkes and with the NRAO 140 ft. As with NGC 1386, monitoring of this source is sparse because it is too far south for observation with the Effelsberg telescope. A flare in August 1997 resulted in roughly a factor of two increase over the typical flux, but the flare had subsided by December 1997. Although our data show no velocity drift over the 4 years of monitoring, it is clear that from 1994 to 1998 we were not distinguishing individual components in the systemic clump. Ishihara et al. (2001) have observed this source with both the NRO 45 m and Parkes 64 m telescopes, and have attained a greater sensitivity than the 1994 – 1998 spectra shown here. Ishihara et al. (2001) resolve 4 – 6 systemic features at each epoch and find a redward velocity drift in each of 2.6 km s-1 yr-1. They also report the discovery of numerous high velocity components, which are confirmed by our April 2002 spectrum (Figure 2). Note that the velocity scale appears different between the spectra here and those presented by Ishihara et al. (2001) because of the difference between the optical and radio velocity conventions.

### 5.10 NGC 4258

The maser in NGC 4258 has been monitored by Haschick et al. (1994), Greenhill et al. (1995) and Bragg et al. (2000). We have not monitored this source as part of our program, but we do present a GBT spectrum in Figure 2. In the triply-peaked structure of the maser in NGC 4258, the systemic masers are clearly the brightest. A similar relative strength of components is apparent in IC 2560. However, if the negligible velocity drifts in the masers of other detected galaxies indicate that they are analogous to the high velocity lines in NGC 4258, then the high velocity lines are dominant in these galaxies.

### 5.11 M51

The kilomaser in the mildly active nucleus of M51 was first detected by Ho et al. (1987) and has been studied more recently by Hagiwara et al. (2001). This maser has not been a part of our monitoring program, but we present a sensitive GBT spectrum in Figure 2. The blueshifted feature evident in the January 2001 spectrum (Hagiwara et al., 2001) had diminished by the April 2002 spectrum shown here. A new feature appears at 546 km s-1 and two equal intensity ($``$ 0.1 Jy) components are found at 564 and 567 km s-1.

### 5.12 NGC 4945

In NGC 4945 we detected maser emission near the systemic velocity of 556 km s-1 and redshifted from systemic, between about 630 and 740 km s-1. Greenhill et al. (1997c) mapped the features in this source using the subset of VLBA antennas to which NGC 4945 is accessible. They detect blueshifted emission not seen in our spectra (and not shown in the velocity range displayed in Figure 1). Greenhill et al. (1997c) find an elongated maser distribution possibly revealing a disk. The systemic and redshifted features are separated by $``$ 0.15 mas (0.3 pc). One might then expect that the maser features near 556 km s-1 are analogous to the systemic features of NGC 4258. Similarly, the cluster of features to the red might be associated with the “edge” of the disk (i.e. be “high velocity features”). Although Gaussian fits to individual components are difficult in the redshifted features, it is possible to trace local maser peaks throughout the monitoring period. Drifts are negligible, as expected for high velocity lines. We measure drifts of 0.20 $`\pm `$ 0.31 , 0.16 $`\pm `$ 0.31, and 0.25 $`\pm `$ 0.31 km s-1 yr-1 for peaks at 705, 716 and 732 km s-1. The equality of the error estimates results from using channel widths as error estimates for each individual epoch. The strongest systemic line also shows no discernible drift. By resolving the strong systemic peak into two Gaussian components at each epoch, we find that those lines (centered at 553 and 555 km s-1) drift by 0.07 $`\pm `$ 0.35 and –0.07 $`\pm `$ 0.46 km s-1 yr-1. Assuming the disk model fits, a constraint on the black hole mass can be made. Taking a nominal upper limit for the acceleration of $`<`$ 0.1 km s-1 yr-1 and rotation of 130 km s-1, the central black hole mass must be $`>`$ 7 $`\times `$ 105 $`M_{}`$.

### 5.13 NGC 5347

The maser in this galaxy was tentatively detected in October 1993 and confirmed by several successive observations, which show a group of weak masers spanning $``$ 100 km s-1 centered near the recession velocity of the galaxy, 2398 km s-1. Although there are hints of redward drifts in the recent spectra, a more finely sampled set of observations is required for confirmation. The GBT spectrum reveals multiple distinguishable components in the systemic clump but no unambiguous detections of high velocity features.

### 5.14 The Circinus Galaxy

Because of the complexity of the maser emission in the Circinus Galaxy it has been divided into two segments for Figure 1, each covering a different velocity range. Maser emission is distributed over a range of 400 km s-1 bracketing the systemic velocity, 433 km s-1. Greenhill et al. (1997a) have shown that the flux of the maser lines in this galaxy vary on timescales of minutes to hours. They suggest that such intraday flux variations may be caused by interstellar scintillation from the ISM of our Galaxy. As evident in Figure 1, strong variability exists over longer timescales as well (note that each of the Circinus spectra shown is the result of a $``$ 2 hour integration, thereby smoothing over much of the 5 – 10 minute timescale variability). While several narrow features do appear to persist from one epoch to the next, most change so much that it is difficult to track velocity drifts. Unlike the narrow lines, though, the broad feature between 325 and 400 km s-1 persists throughout the series of spectra. Uncertainty in the baseline in October 1995 may account for the weakened broad feature for that epoch. Several clumps of maser features seem to persist as well, particularly in the redshifted segment where features grouped near 512, 560, and 600 km s-1 exist throughout the 4.3 year period, though the detailed structure within those clumps changes.

### 5.15 NGC 5506

The maser in the edge-on Seyfert 1.9 galaxy NGC 5506 has been marked by several flares which have lasted roughly a year, and then disappeared. A flare near 1730 km s-1 was detected during 1993 – 1994 and a feature near 1800 km s-1 flared spectacularly through 1995. The numbers in Figure 1 printed adjacent to the flaring features indicate the peak intensity in Jy for the maser spike in cases where the plots overlap. Velocity drifts of lines at 1731 and 1799 km s-1 are measured to be 0.36 $`\pm `$ 0.71 km s-1 yr-1 and 0.00 $`\pm `$ 0.29 km s-1 yr-1, respectively. The isolation and narrow profiles of these lines inspire confidence that each originates from a single, persistent feature rather than a blend. The GBT spectrum (Figure 2) shows a group of weak, narrow features centered near the systemic velocity of the galaxy, 1824 km s-1.

### 5.16 NGC 6240

Although observed many times and tentatively detected by Henkel et al. (1984), H2O maser emission was not conclusively detected in NGC 6240 until 2001. Both Hagiwara et al. (2002a) and Nakai et al. (2002) reported the detection in late spring 2001. Figure 1 shows a tentative detection of this feature in March 2000 and clear detections in January and December 2001 and April 2002. We did not detect the feature at a 3$`\sigma `$ level of 30 mJy (channel spacing: 1.11 km s-1) in November 2002. Velocities, determined by Gaussian fit, were 7565.0 $`\pm `$ 0.8 km s-1 in March 2000, 7565.6 $`\pm `$ 0.5 km s-1 in January 2001, 7568.6 $`\pm `$ 0.7 km s-1 in December 2001, and (two lines) 7567.6 $`\pm `$ 0.1 km s-1 and 7612.1 $`\pm `$ 0.1 km s-1 in April 2002. The feature seen at 7567.6 km s-1 in April 2002 drifted by 1.4 $`\pm `$ 0.3 km s-1 yr-1 between March 2000 and April 2002. In Figure 2 we reproduce the sensitive GBT spectrum from April 2002 showing a 1600 km s-1 velocity range.

### 5.17 TXS 2226-184

TXS 2226-184 has the largest apparent isotropic luminosity of the known water masers, $``$ 6000 $`L_{}`$ (Koekemoer et al., 1995). While the profile resembles that of NGC 1052 in breadth, the maser in TXS 2226-184 has been much less variable during the 7 years it has been monitored. The emission spans $``$ 400 km s-1. The excellent spectra from February 1998 and April 2002 show that the maser profile has complex structure including a bifurcated peak and a tail of emission extending to the blue. These features may exist but be unseen in the less sensitive spectra.

The host galaxy, originally thought to be an elliptical, has recently been observed with HST (Falcke et al., 2000). These authors argue that the presence of an apparent dust lane and the shape of the isophotes are indicative of a spiral host.

### 5.18 IC 1481

Maser emission near 6236 km s-1 has been detected in IC 1481 since the discovery of the maser in April 1995. A second maser spike near 6251 km s-1 appeared in the July 1996 spectrum and has been detected through April 2002. The velocities of these two maser peaks show no discernible drift, with accelerations measured at 0.17 $`\pm `$ 0.12 km s-1 yr-1 (6236) and –0.08 $`\pm `$ 0.18 km s-1 yr-1 (6251). These lines are redshifted from the systemic velocity, 6122 km s-1. A flare appeared around 6310 km s-1 on the 3 November 1997 spectrum, and was not seen on 12 December 1997 or afterwards. Sand et al. (1999) observed this galaxy with the VLA in order to measure the relative positions of the maser and continuum emission. They find a tentative offset of the maser from the continuum of 14 $`\pm `$ 4 mas, a projected distance of 5 pc. This extent is significantly greater than that measured for other nuclear maser sources. If we were to assume that the masers come from the edge of a disk which has an orbital velocity of 120 km s-1 (representative of the displacement of the maser lines from the systemic velocity) then we can infer a black hole mass of 1.7 $`\times `$ 10$`{}_{}{}^{7}M_{}^{}`$. We caution that this measurement is extremely speculative, but it does demonstrate a powerful technique for measuring black hole masses as more sensitive observations become available.

## 6 Masers in Inclined Galaxies

Braatz et al. (1997) show that water masers tend to be detected in those Seyfert 2 or LINER galaxies which are highly inclined, and the reclassification of TXS 2226-184 as an inclined disk galaxy by Falcke et al. (2000) strengthens that trend. One reason for this relation might be that the orientation of the nuclear disk is tied to that of the galactic disk so that maser detections, which favor edge-on nuclear geometries, would also favor highly inclined galactic disks. There is weak evidence that such a coupling may exist in late-type spirals, but not early-type (Wilson and Tsvetanov, 1994). Another reason that highly inclined galaxies appear to be favored might be that an appreciable fraction of the maser amplification arises from non-nuclear gas in the galactic disk. This would explain not only the tendency to find masers in highly inclined galaxies, but also the tendency we have found in this paper for maser lines to remain at a constant velocity. The acceleration of gas towards the galactic center would be very small for masers in the galactic disk, so no velocity drift would be detectable.

The most successful searches for H2O masers have been those which target known AGNs, but AGN catalogs are deficient in highly inclined galaxies. A survey of nearby, bright galaxies indicates that a large fraction (43%) have nuclear emission lines characteristic of an AGN, although their power is generally weaker than “classical” AGNs (Ho et al., 1997). We might expect that a similar fraction of bright, highly inclined galaxies would have some level of nuclear activity, but that such activity has gone undetected due to obscuration. A luminous AGN is not a requirement for strong maser emission, as exemplified by the strong maser emission in the low-luminosity AGN of NGC 4258. Hence it is reasonable to search for water vapor masers in nearby, highly inclined galaxies even if they are not known to be AGNs. We searched 58 nearby galaxies with galactic disk inclinations $`>`$ 80. Table 2 shows the source list. Observations were made in February 1998 with the Effelsberg 100 m, and in August 1998 with the Parkes 64 m. No maser sources were detected. These observations suggest that clouds in the large scale galactic disks do not contribute to the gain of masers originating in the nuclear region and/or these galaxies do not possess nuclear activity required to produce the megamaser. We note that precise Hubble classifications are uncertain for many of the sample because of the high inclinations, but more than half are late-type galaxies, which are less likely to have nuclear activity.

## 7 Discussion

The spectral profile of water masers in NGC 4258 and the velocity changes of the individual narrow features exemplify gas in a thin, edge-on disk: the systemic features drift through a window of velocities about 100 km s-1 wide while masers associated with the projected extremities of the disk remain stationary. NGC 2639 is the only source revealed by this study to partly duplicate this pattern, and only then in its systemic features; there is not yet a detection of high velocity lines from this galaxy. Indeed, H2O maser lines in other galaxies more commonly have constant velocities, regardless of whether they are near the systemic velocity of the galaxy or separated from it (by up to 120 km s-1 in these cases). The current emergence of much more sensitive instruments will be used to test this trend further. Individual systemic features in NGC 1386, for example, can be distinguished now with the GBT.

That we do not detect an acceleration in most of the sources indicates that either the gravitational force on the maser clouds is weaker than that in NGC 4258, or that we are preferentially detecting masers whose gravitational acceleration vector is close to the plane of the sky, as is the case for the high velocity masers in NGC 4258. If the masers amplify nuclear continuum emission, which originates nearer the nucleus than the masers themselves, then the maser gas necessarily must have a gravitational acceleration directed away from the observer, regardless of the detailed geometry of the masing gas. For the resulting acceleration to go undetected by our observations, the gas producing systemic maser features would have to be several times more distant from the central mass than in NGC 4258 (0.14 pc), assuming a similar black hole mass (3.9 $`\times 10^7M_{}`$, Herrnstein et al. (1999)). If, instead, the masers are self-amplified structures analogous to the high velocity features in NGC 4258, then the relatively small separations between maser velocities and systemic velocities (40 – 120 km s-1) indicate more slowly rotating structures than the 1000 km s-1 rotating disk in NGC 4258. This might then suggest that there has been a strong selection effect in past surveys used to find new masers, because they were limited in the bandwidth of the spectra. Typically 40 – 64 MHz bands have been used, corresponding to a velocity range of 540 – 863 km s-1. We would only detect high velocity features in those sources with larger, slowly rotating nuclear disks. The absence of systemic features in this case might be caused by the seed radio continuum source being very weak, absent, or offset from the plane of the maser disk.

We thank the telescope operators and staff at Effelsberg and Green Bank and the staff at Parkes for expert assistance throughout this project. We thank Lincoln Greenhill and Jim Moran for stimulating discussions, and Ron Maddalena for his talents with the GBT. We have made extensive use of the NASA/IPAC Extragalactic Database (NED) which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. This research was supported in part by the National Science Foundation through grant AST 95-27289 to the University of Maryland.


text:
# 1 Standard deviation of 𝑘-mer distributions: for the genome of T. pallidum; averaged over 14 microbial genomes with unbiased base composition; of a random sequence with Poisson distribution; of the model genome described in text. In the third column, the number after the ± sign gives the s.d. associated with the average s.d. The last column is the length (𝐿_{𝑒𝑓𝑓}) of a random sequence with the genomic ratio of mean count to s.d..

Evidence for growth of microbial genomes by short segmental duplications

Li-Ching Hsieh, Liaofu Luo and H.C. Lee222Correspondence and requests for material should be addressed to HCL at Physics, NCU; hclee@phy.ncu.edu.tw.§

Department of Physics and Department of Life Science, National Central University, Chungli, Taiwan 320; Department of Physics, Inner Mongolia University, Hohot, China; §Centre de Recherches Mathématiques, Université de Montréal, Montréal, QC, Canada

We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to obey Poisson distributions. It is noticed that for words less than nine letters the average width of the distributions for complete microbial genomes is many times that of a Poisson distribution. We interpret this phenomenon as follows: the genome is a large system that possesses the statistical characteristics of a much smaller “random” system, and certain textual statistical properties of genomes we now see are remnants of those of their ancestral genomes, which were much shorter than the genomes are now. This interpretation suggests a simple biologically plausible model for the growth of genomes: the genome first grows randomly to an initial length of approximately one thousand nucleotides (1k nt), or about one thousandth of its final length, thereafter mainly grows by random segmental duplication. We show that using duplicated segments averaging around 25 nt, the model sequences generated possess statistical properties characteristic of present day genomes. Both the initial length and the duplicated segment length support an RNA world at the time duplication began. Random segmental duplication would greatly enhance the ability of a genome to use its hard-to-acquire codes repeatedly, and a genome that practiced it would have evolved enormously faster than those that did not.

The genome is a highly complex network of embedded codes generated in a very long process of evolution co-driven by chance mutations and misreplications on the one hand and natural selection on the other. The fact that both processes are stochastic makes it that much harder to uncover what the the earliest genome looked like when life first arose. Adding the extreme diversity of organisms to the complexity of each genome would seemingly render the task of unmasking the early genome even more daunting. It is therefore significant when a large set of diverse and complex genomes share an unexpected common or universal property. Here we report one kind of universality in the textual property of the genomes that allows us to deduce a mode of growth which could be common to all early genomes.

Frequency of occurrence of oligonucleotides in microbial genomes

It is a general rule of statistics that very large systems have sharply defined average properties. When apples are randomly dropped into barrels, the distribution of apples in the barrels is governed by the Poisson distribution. If 1,024 apples were dropped into sixty-four barrels, in 95 of 100 cases, each barrel will have between eight and twenty-four apples. In comparison, if 1 million apples were dropped into sixty-four barrels, in 95 of 100 cases, each barrel will have between 15,875 and 15,375 apples. There is a less than one in $`10^{830}`$ ($`10^{980}`$, respectively) chance that one barrel would get as many (few) as twenty-four (eight) thousand apples.

Microbial genomes are seemingly random systems when viewed as texts of the four nucleotides represented by A, C, G and T. To count the number of times each of the sixty-four trinucleotides, or 3-mers, occur in a genome-as-text is similar to counting apples in barrels. The genome of the bacterium Treponema pallidum, the causative agent of syphilis is about 1M base pairs long and has almost even base composition . In an astonishing departure from what is expected of a system of its size, the genome has six 3-mers (CGC, GCG, AAA, TTT, GCA, TGC) occurring more than 24,000 times per 1M nt and two (CTA, TAG) less than 8,000 times. Scrambling the genome sequence thoroughly restores it to a random sequence obeying Poisson distribution and the large-system rule.

T. pallidum is not exceptional in disobeying the large-system rule. For the fourteen complete microbial genome sequences with approximately even base composition (see Methods), the observed standard deviation (s.d.) of the distribution of the frequency of occurrence (hereafter, simply distribution) of 3-mers per 1M nt is 4,080$`\pm `$630 around the mean of 15,625. This is about 32 times the s.d. of a Poisson distribution typifying a random sequence with the same mean.

Nor is the 3-mer exceptional in the $`k`$-mer-statistics of genomic sequences. In Table 1, column 3 gives the average s.d. of the distribution of $`k`$-mers per 1M nt, $`k`$ = 2 to 10, for the fourteen genomic sequences and the s.d. of the average (number given after the $`\pm `$ sign) and column 4 gives the s.d. for a Poisson distribution (that describes a random sequence) with mean value 106/4k. The s.d.’s of the genomic and random sequence have about the same magnitude when $`k`$ is equal to or greater than 10 (not shown in the Table). But with decreasing values of $`k`$ the Poisson s.d. increases as $`2^k`$ whereas the genomic s.d. increases at a much higher rate, such that for $`k8`$ the Poisson s.d. is many times less than the genomic s.d. Moreover, the uncertainty in the genomic s.d. is typically much smaller than the difference between the genomic and Poisson s.d.’s. For example, at $`k`$=2 ($`k`$=6) the genomic s.d. is 40$`\pm `$8 (9.0$`\pm `$1.3) times greater than the Poisson s.d. Thus the genomic distribution differs from the Poisson distribution in a universal fashion, and in this sense we shall speak of a universal genome.

Microbial genomes are large systems with small-system statistics

The universal genome has the statistical property of a random sequence much smaller than itself. To see this, we define the effective random-sequence length $`L_{eff}`$ of the universal genome as the length of a random sequence that has a $`k`$-mer distribution with a mean to s.d. ratio equal to that of the corresponding genomic ratio $`r`$. Then $`L_{eff}`$=$`4^kr^2`$, and its values for the various $`k`$’s are given in the last column of Table 1. One notices that the $`L_{eff}`$ of the universal genome is very short for the smaller $`k`$’s - of the order of 1k nt for $`k`$$``$3 - and grows with $`k`$. When $`k`$=10, it is essentially the same length as the real genome.

A signature of the universal genome is that compared to a random sequence, the former has very large numbers of both overrepresented and underrepresented oligonucleotides. As a typical representative of the universal genome, the genome of E. coli  has 500 and 510 6-mers whose frequency of occurrences are greater than 400 and 100 per 1M nt, respectively, while a random sequence has none in either category. There are many known examples of individual oligonucleotide that exhibit extreme relative abundance. For dinucleotides this was noted to be common and has genome-wide consistency ; tetra- and hexapalindromes are almost always underrepresented in bacteriophages and are underrepresented systematically in bacteria where 4-cutting and/or 6-cutting restriction enzymes are common ; an 8-mer that appears as Chi sites, hotspots of homologous recombination, is highly overrepresented in E. coli ; in the human pathogens Haemophilus influenzae  and Neisseria  there are 9- and 10-mers functioning as uptake signal sequences that are vastly overrepresented. The causes for these extreme cases are generally not known and, with the exception of the dinucleotides, these individual cases do not much affect the statistical properties of the genome.

What caused a genome to have statistical characteristics so starkly distinct from those of a random sequence? Natural selection suggests itself as a prime explanatory candidate. For instance, the 64 frequencies of codons, 3-mers used by the genome to code proteins in genes, exhibit very wide distributions. But natural selection by itself does not directly cause any change in a genome. Such changes are caused by mutation and other mechanisms, all believed to occur at random. Natural selection may account for what changes come to pass; if, however, such changes always tend to promote or retain a randomness that exhibits Poisson distribution, then the ability of natural selection to push the genome very far in a non-Poisson direction would seem to have its limits.

Model for early genome growth

Here we propose a biologically plausible model for the growth and evolution of a universal genome that can generate the observed statistical characteristics of genomic sequences. The model is very simple and consists of two phases. In the first phase the genome initially grows to a random sequence whose size is much smaller than the final size of the genome. In the second phase the genome grows by random duplications modulated by random single mutations. In this work a snapshot is taken of the model genome shortly after it reaches a length of 1M nt. The key in the model is growth by duplication; it is most straightforward way for the universal genome to become what it appears to be: a large system that exhibits small-system statistical characteristics.

We found it comparatively easy to generate a sequence that could faithfully reproduce the genomic $`k`$-mer distribution of a particular $`k`$ but not those of other $`k`$’s. Typically such a sequence had an excessively rigid effective random-sequence length and, consequently, a distribution too narrow (broad) for smaller (greater) $`k`$’s. Several such examples are given in the Methods. Generating a sequence that would emulate a real genome was a much more exacting task.

Result

After extensive experimentation, it was found that sequences having the statistical characteristics sought after could be generated from an initial random sequence approximately 1k nt long ($`L_0`$) which was then grown to 1M nt by random duplication of segments of length ($`\overline{l}`$) averaging 25 nt with a spread ($`\mathrm{\Delta }_l`$) of approximately 11 nt (see Methods for detail).

The s.d. of the $`k`$-mer distribution of a good model sequence are given in column five of Table 1. They agree quite well with the observed genomic values in columns two and three although their $`k`$-dependence is slightly too strong. Histograms in Fig. 1 show comparisons between the $`k`$-mer distributions for $`k`$=2, 3 and 4 of the genome of T. pallidum (black) and those of the model sequence (green/gray). In all three cases, the histogram for a random sequence would be represented by a single tower located at the mean frequency. For $`k`$=2 and to a lesser extent $`k`$=3, the histograms for both genomic and model sequences display large fluctuations. The model sequence is not expected to exactly reproduce the counts of the genomic sequence. Indeed, generated stochastically, another (good) model sequence would give distributions indistinguishable from those shown in Fig. 2 but something rather different than those shown in the $`k`$=2 and 3 panels of Fig. 1. In any case, all model sequences would show patterns of fluctuation similar to those exhibited by the genomic sequence and have s.d.’s similar to those given in column 5 of Table 1. Fig. 2 shows comparisons for $`k`$=5 to 9. The panel at the top-left corner compares the 6-mer distribution from T. pallidum with that of a random sequence obtained by scrambling the T. pallidum genome. The strong agreement between the microbial genome and the model sequence contrasts sharply with the glaring differences between the genome and the random sequence.

The model sequence is parameter-sensitive: If $`L_0`$ was much longer than 1k nt no good model sequence could be found (this is expected because $`L_0`$ cannot be much longer than the shortest $`L_{eff}`$ in Table 1); if either $`\overline{l}`$ or $`\mathrm{\Delta }_l`$ was was changed by more than 10% from their optimal values of 25 nt and 11 nt respectively the agreement between the genomic and model sequences would worsen noticeably (see Methods). No mutations were imposed on the model sequence whose properties are shown here; twenty thousand mutation fixations reduces the s.d. of the $`k`$-mer distributions of the model sequence by 4% (for $`k`$=2) to 10% ($`k`$=10) but under casual inspection the model sequence - with or without mutation - has the appearance of a random sequence. Results showing the model reproducing the $`k`$-mer distributions of microbial genomes with highly biased compositions will be presented elsewhere.

In bacterial genomes, typically about 12% of genes represent recent duplication events - 12% in T. pallidum , 11.2% in H. influenzae  and 12.8% in V. cholerae . Our model sequence as presented here does not yet fully explain the pattern of all such duplications, many of which would involve segments up to several k nt long. Work is under way to extend the model to account for the genomic pattern of repeat sequences of all lengths.

Discussion

We mention some biological and evolutionary implications assuming our model does capture the essence of the early growth mechanism of microbial genomes and, by extension, perhaps of all genomes. Setting the initial length of our model universal genome before it began the growth by duplication process to about 1k nt but not much longer (as required by observed data) necessarily implies that the universal genome began its life in an RNA world  in which there were no proteins and RNAs had the dual roles of genotype and phenotype (see  for a review). This view of the origin of life  gained much credence when RNA was discovered to exhibit self-splicing and enzymatic activities . Some RNA enzymes, or ribozymes, are very small; the hammerhead ribozyme is only 31 to 42 nt long  and the hairpin ribozyme is only 50 nt long . Thus the 1k nt initial universal genome was certainly of sufficient size to possess a machinery for sustained evolution and duplication. Our model does not address the origin of this initial genome. The likelihood of its being the evolutionary product of something that arose spontaneously is enhanced by the succcessful isolation of artificial ribozymes from pools of random RNA sequences . The average duplicated segment length of 25 nt is very short compared to a present-day gene that codes for a protein, but likely represents a good portion of the length of a typical ribozyme encoded in the early universal genome.

Shifting the burden away from natural selection onto segmental duplication as the main force driving the universal genomes so far in a non-Poisson direction implies a much higher evolution rate than it might have been if natural selection were the only driving force. The model suggests that uneven codon usage was not the primary cause of the very broad distribution of the 3-mer counts seen in the universal genomes. Rather, the rise of codon was the consequence of an opportunistic evolutionary adaptation to the already-wide 3-mer distribution that had resulted from growth by duplication. Similarly, many - but not all \- of the highly under- or overrepresented oligonucleotides we see now must have been recruited for their respective biological functions after they already had (the suitable beginnings of) biased frequencies of occurrence.

That some statistical characteristics of a present day genome are determined by the charateristics of the genome when it first began to grow by duplication means that we should be able to learn something about such early genomes, and each such ancestral genome should be common to a group of present day genomes that are phylogentically close. Detailed analyses made along this line of reasoning may bring us a step nearer in understanding the univeral ancestor .

Being a natural way to repeatedly utilize hard-to-come-by codes, growth by duplication is in itself a brilliant strategy and must have increased the rates of evolution and species diversion enormously. The continuity of this strategy after the rise of codons and proteins is bundantly in evidence. In higher organisms a large number of repeat sequences with lengths ranging from 1 base to many kilobases are believed to have resulted from at least five modes of duplication . This strategy should provide part of the answer to the questions : how have genes been duplicated at the high rate of about 1% per gene per million years ? and why are there so many duplicate genes in all life forms ? The fact that duplicate genes (after they have diverged) contribute to genetic robustness by protecting the genome against harmful mutations  is likely not what caused the proliferation of duplicate genes, but is rather another example of an adaptation to an existing situation by natural selection for a beneficial function.

Methods

The fourteen microbial genome sequences (length ($`L`$) in M nt and G+C probability ($`p`$) in brackets) E. coli K12 (4.64, .50), E. coli 0157 (5.52, .50), M. thermoautotrophicum (1.75, .50), A. fulgidus (2.18, .49), T. pallidum (1.14, .53), X. fastidiosa (2.67, 0.53), V. cholerae chromosomes I (2.96, .48) and II (1.07, .47), Synechococcus sp. (3.57, .48), N. meningitidis serogroup B strain MC58 (1.57, .52), Y. pestis (4.65, .48), S. typhimurium (4.86, .52), S. enterica (4.81, .52) and P. aerophilum (2.22, .51) are obtained from the GenBank . Counting of $`k`$-mers is done by reading through a $`k`$-base wide window that is slid around the (circular) genome once. Counts are normalized to per 1M nt and bias in base composition is corrected for by dividing the actual counts by the factor $`L2^kp^n\left(1p\right)^{kn}`$, where $`n`$ is the total number of G’s and C’s in each $`k`$-mer.

Generation of model sequence. A random sequence of length $`L_0`$ is first generated. Thereafter the sequence is altered by single mutations (replacements only) and duplications, with a fixed average mutation to duplication event ratio. In duplication events, a segment of length $`l`$, chosen according to the Erlang probability density function $`f\left(l\right)=1/\left(\sigma m!\right)\left(l/\sigma \right)^me^{l/\sigma }`$, is copied from one site and pasted onto another site, both randomly selected. In the above $`m`$ is an integer and $`\sigma `$ is a length scale in bases. The function gives a mean duplicated segment length $`\overline{l}=\left(m+1\right)\sigma `$ with s.d. $`\mathrm{\Delta }_l=\left(m+1\right)^{1/2}\sigma `$. The values $`m=0`$ to 8 and selected values for $`\sigma `$ from 3 to 15,000 were used. The model sequence compared with genomic sequences in the Figures 1 and 2 and in Table 1 was generated with $`L_0=1000`$, $`m=4`$, $`\sigma =5`$ and without mutation events. Fine-tuning to find the best parameters was not attempted. The following are some examples that gave very good distributions for specific $`k`$-mers but not generally; all were generated with $`L_0=1000`$ and $`m=0`$: for 6-mer, $`\sigma =13,000\pm 2,000`$ and on average 0.04$`\sigma `$ mutations per duplication (these parameters also work for genomes with biased base compositions) ; for 2-mer, $`\sigma =50`$, no mutation; for 5-mer, $`\sigma =30`$, no mutation; for 9-mer, $`\sigma =15`$, no mutation.

Presentation of data. In Fig. 2 the curves shown are the result of a small amount of forward and backward averaging - to remove excessive fluctuations. In Fig. 1 data bunching was used to produce the towers shown.

HCL thanks the National Science Council (ROC) for the grant NSC 91-2119-M-008-012 and members of the Redfield Lab and the Otto Lab, Department of Zoology, University of British Columbia, for discussion and the Institute for Theoretical Physics, Chinese Academy of Science, Beijing, and the Center for Theoretical Biology, Beijing University, for hosting visits.