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# Icosahedral packing of RNA viral genomes

## Abstract

Recent studies reveal that certain viruses package a portion of their genome in a manner that mirrors the icosahedral symmetry of the protein container, or capsid. Graph theoretical constraints forbid exact realization of icosahedral symmetry. This paper proposes a model for the determination of quasi-icosahedral genome structures and discusses the connection between genomic structure and viral assembly kinetics.

An essential step in the assembly of any virus is the structural reorganization of the single stranded (ss) or double stranded (ds) RNA and DNA molecules that comprise the genome into a form that fits inside the viral capsid. This involves a well-known structural incongruity; the protein capsid shells of nearly all sphere-like viruses adopt *icosahedral symmetry* while, as discussed below, a viral genome of less than twelve segments fundamentally cannot assume an icosahedral conformation in view of its one-dimensional, chain-like primary structure Bink and Pleij (2002). In fact, microscopy studies of the structure of the ds DNA genome of bacteriophage viruses reveal a completely *non*-icosahedral spool-like organization Odijk (1998). A semi-flexible chain—such as ds DNA—that is confined inside a sphere having an interior surface that repels this chain and a radius comparable or smaller than the chain persistence length will, indeed, adopt such a spool-like structure as its free energy minimum Riemer and Bloomfield (1978); Hud (1995).

The problem of the interior organization of ss RNA viral genomes is more delicate. SS nucleotide chains have a much greater conformational flexibility than duplex chains, so ss RNA chains are better able to adjust to the icosahedral symmetry of the capsid than ds DNA chains. The secondary structure of RNA molecules in solution is characterized by paired segments conntected by branch points, unpaired “bubbles” and “hair pins” (see Fig. 2). The various competing secondary structures can be analyzed by statistical mechanical methods Bundschuh and Hwa (2002). Moreover, unlike the case of the bacteriophage viruses, for a significant number of ss RNA viruses, capsid assembly *requires* the presence of the genome molecules Fisher and Johnson (1993). This “co-assembly,” which can take place spontaneously by self-assembly Fisher and Johnson (1993), is due in part to non-specific electrostatic attraction between RNA molecules and capsid proteins. Attractive interactions between the genome and the interior surface of the icosahedral capsid should promote icosahedral order. X-ray diffraction studies reveal that the outer layer of the genome of a number of ss RNA viruses such as Cowpea Chlorotic Mottle Virus (CCMV) Bink and Pleij (2002); Baker et al. (1999); Speir et al. (1995), Flock House Virus (FHV) Bink and Pleij (2002); Baker et al. (1999); Tsuruta et al. (1998), calicivirus Bink and Pleij (2002); Baker et al. (1999); Prasad et al. (1994), Cowpea Mosaic Virus (CMV) Bink and Pleij (2002); Baker et al. (1999, 1992), Turnip Yellow Mosaic Virus (TYMV) Bink and Pleij (2002); Baker et al. (1999); Böttcher and Crowther (1996), indeed adopt at least partial icosahedral symmetry.

A particularly striking illustration of icosahedral ordering is provided by the *Nodaviridae* group of viruses. The FHV and Pariacoto *Nodaviridae* viruses have so-called “T=3” icosahedral capsids, as shown in Fig. 1.

The genome of these viruses consists of two single-stranded RNA molecules. One of these two molecules, RNA2, consists of about 1,400 (FHV), respectively 1,300 (Pariacoto) base pairs and encodes for “Protein $`\alpha `$,” a precursor of the capsid protein. This molecule plays a key stabilizing role in capsid assembly Fisher and Johnson (1993), and it is probably the part of the genome that is resolved in the diffraction experiments. As shown in Figs. 1b and c, the icosahedral portion of the RNA genome is distributed over a *dodecahedral cage* formed by the low-curvature borders of twelve five-fold pyramids that together make up the T=3 rhombic tricontahedron capsids of the FHV and Pariacoto viruses. Even though the genome is ss RNA, the portions shown in Fig. 1 actually have the form of *double helices* with the two strands oriented in the standard way with opposite 3’ to 5’ directions. These paired double-helical segments have a length per edge of about 10 bases for the FHV structural study and 25 bases for the Pariacoto structural study. Given the 30 edges of a dodecahedron, this means that for FHV about 43% of RNA2 contributes to the double-helical sections, and for Pariocoto *essentially 100% of RNA2*. If we assume that the 20 (unresolved) *vertices* are also structurally identical, we would have to connect together the 30 double-helical segments with 20 identical three-strand branch-points (see Fig. 2A) placed at the vertices of the dodecahedron. The resulting structure has true icosahedral symmetry (apart from the different base-pair sequences for the different segments), but it actually consists of 12 separate, interlocking RNA rings, which is inconsistent with the structure of the *Nodaviridae* genome tan . This structural conflict is closely connected to a classical result of graph theory, which states that it is impossible to construct a one-dimensional path restricted to the edges of either an icosahedral or a dodecahedral structure while visiting every edge just once Bollobás (1990); gra  (a dodecahedron has the same symmetry properties as an icosahedron). The proposition that the 20 vertices obey icosahedral symmetry is thus incorrect. As shown below, information concerning the structural inhomogeneity of the vertices actually provides us with important information on the *formation history* of the virus. It is the aim of the present article to present a statistical mechanical model for quasi-icosahedral ordering of ss RNA viral genomes.

On the basis of the above-mentioned X-ray structure studies, we set the following constraints on the secondary structure of RNA2:

1. the edges of the dodecahedron should be occupied by the rigid duplex segments.
2. the branch points, bubbles, and hair-pins of the secondary structure should be confined to the vertex regions.

Under these constraints, there are only three possible types of vertex structures, which can be represented diagrammatically as follows. The first vertex type (“A”) are pure branch-points, the familiar three-strand junctions of ds RNA and DNA. These vertex types are illustrated in Fig. 2. The arrows in the figure indicate the 3’ to 5’ direction of the RNA2 molecule. Electrostatic repulsion between the duplex branches of the junction favors $`120^{}`$ angles between the branches, which have to be deformed by a moderate amount in order to fit on the vertex of a dodecahedron. Cases A1 (a “right-turn” vertex) and A2 (a “left-turn” vertex) are related by a rotation over 180 degrees along one of their branches. The energy cost, $`\mathrm{\Delta }E_A`$, is the same for the two cases.

Next, a type “B” vertex consists of a combination bubble/hairpin, as shown in Fig. 2B, which has a total of six variations. Note that the presence of the bubble permits the sharp kink between the two connected duplex sections required at a vertex of the dodecahedron. There are now four RNA strands located at the vertex so the electrostatic energy, $`\mathrm{\Delta }E_B`$, of a class B vertex is presumably higher than that of a class A vertex. Finally, for a class C vertex, three hair-pin/stem-loops are located at one vertex

A class C vertex requires that six RNA strands are located at a single vertex and thus has presumably the highest electrostatic energy ($`\mathrm{\Delta }E_c`$).

The energy cost of a particular secondary RNA2 structure is, then,

$$H=E^{\mathrm{sol}}+N_A\mathrm{\Delta }E_A+N_B\mathrm{\Delta }E_B+N_C\mathrm{\Delta }E_C$$
(1)
with $`E^{\mathrm{sol}}`$ the solution energy cost of the secondary structure computed by the existing procedure Bundschuh and Hwa (2002), while $`N_{AC}`$ denotes the number of vertices. The non-specific electrostatic binding energy contributes a constant energy that need not be included.

Since, by assumption, Class A vertices have the lowest free energy it is logical to start by constructing RNA configurations that have *only* A-type junctions, in which case there are no hairpins or stem-loops at all (i.e. $`N_B=N_C=0`$). That does not mean that the genome has to be disconnected. Recall that there are two different possible junctions, related by a $`180^{}`$ rotation. Since we allow for vertex heterogeneity, we can use both junction types and search for a single-connected genome. In order to do this, we represented the dodecahedral cage by a planar graph. A singly-connected RNA molecule must visit every edge of this graph twice, each case in opposite directions, in order to form the double helical segments on the edges. *The existence of this type of path is not forbidden by graph theory*. The problem of identifying a permissible path for a ss RNA molecule is equivalent to a finding particular choice for the A1 and A2 vertices at every node of the dodecahedron such that they can be connected by a continuous path. We will call this a *Modified Euler Path* (MEP). In order to identify MEP’s, we carried out a computer search in which one of the nodes of the dodecahedron was singled out as the starting (and ending) point of the MEP, while all other vertices are either designated as right turn or left turn vertices. This produced 262,144 different candidates for a MEP. Most of the candidate walks were unsuccessful, because the walker arrived at a point at which the conditions for the walk were violated. However, in 54,272 of the cases a MEP was generated with a mean success rate of 53/256=0.207…Two examples of such walks are displayed in Fig. 3.

Although the (3D) symmetry of these RNA structures is very close to icosahedral, it is not exact because the successful MEP s contain a certain number of edges with an extra crossing, as indicated by a cross in Fig. 3. This implies that the double-helical segments that occupy these must have either an extra half turn, or a deficit of one half turn. The MEP s we generated contained a minimum of eleven crossings and a maximum of twenty, corresponding to the two cases shown in Fig. 3. If the energy cost of Type B and Type C vertices are significantly higher than that of a Type A vertex, then the pattern with the minimum number of extra crossings should be the lowest free energy structure.

However, it is well known that a path covering a graph with overpasses and underpasses, as shown in Fig. 3, are *knotted* Nechaev (1996). Even the MEP that has the minimum number of crossings still is highly knotted. RNA molecules in solution are never knotted (though viral RNA may have “pseudo-knots” Pleij et al. (1985)), and a knotted RNA molecule released by a virus during infection would not be functional. We thus must exclude knotted RNA structure and hence Class A Quasi-Icosahedral order. Knot-free genomes can be constructed by demanding that, unlike the structures shown in Fig. 3, the secondary structure of RNA molecules inside a virus has the same linearly-branched, circuit-free topology as RNA molecules in solution. When a linearly branched structure decorates a dodecahedral graph, types B and C vertices unavoidably appear. Given the presumed higher free energy cost of a type C vertex, we will construct linearly branched genomes with only type A and B vertices. Linearly-branched RNA secondary structures characteristically contains an equal number of branches and hairpin/stemloop structures. That means that *there must be an equal number of A and B type vertices*, so $`N_A=N_B`$. The simplest example of such an A-B structure involves singly-branched RNA molecules, i.e. the molecule consists of a *main-chain* and a certain number of unbranched *side-chains*. Secondary structures that are nearly singly-branched are indeed encountered in the spectrum of RNA2, with an energy of about 10 kcal/mole above the groundstate Pleij et al. (1985).

To cover the dodecahedral graph with a single-branched structure, every edge of the dodecahedron must be a link between an A type and a B type vertex. If this is the case, then the main chain of the RNA molecule must visit every vertex of the dodecahedral graph once and only once. The construction of such a route is a well-known problem in graph theory, known as a “Hamiltonian Path” Bollobás (1990); not . We will focus on the special case of a Hamiltonian Path that starts and ends on the same vertex of a graph, which is a Hamiltonian Cycle, is shown in the lower right-hand corner of Fig. 4. In this case, any point on the graph can be treated as the starting site. To every edge of the graph that is not part of the Hamiltonian Path, we must assign an A-B or a B-A pair of vertices, so for the Hamiltonian Cycle of relevance to the ordering of RNA on an icosahedral virus, we obtain $`2^{10}`$ different possible configurations. These $`2^{10}`$ configurations form a subset of the allowed secondary RNA stuctures in solution. For a given base-pair sequence, the optimal secondary structure within this subset can, in principle, be determined by minimizing $`H`$.

The biological relevance of the secondary structure of the viral genome is, in fact, intimately connected with the assembly scenario of the virus, and this imposes important constraints on the RNA configuration. It has been well-established for ss RNA cylindrical viruses that the RNA molecule acts as a linear growth template Flint (2000). Growth starts from a specific hairpin structure (the “packaging signal”) and proceeds by successive addition of protein oligomers under the action of the non-specific protein-RNA interaction. The length of the RNA molecule determines the size of the virus. It is currently not known whether main chain type ss-RNA molecules also can act as growth templates for the icosahedral family of viruses, but the only microscopy study of the growth kinetics of RNA/capsid co-assembly of an icosahedral virus does report that growth starts from a three-protein nucleus followed by the successive addition of oligomer units Sorger et al. (1986). The observed co-assembly scenario resmbles the growth of a curved two-dimensional (2D) *protein crystal* that closes in on itself. The characteristic feature of conventional (slowly) growing crystals is that they are compact. New units are predominantly added to those available sites on the surface of the crystal where the new unit can make a maximum number of bonding contacts with units that are already incorporated. The co-assembly condition requires the presence of RNA material when new units are added. The effect of this process is to even out surface roughness, although with increased growth velocities, the growth surface may roughen.

To examine whether the reported growth scenario is consistent with the proposed Hamiltonian path/cycle model developed above, we assume that the Hamitonian Path construction provides the lowest accessible free energy structure as proposed in the previous section. The assembly history for the Hamiltonian Cycle is shown in Fig. 4, in which we show only the main chain part. Edges that are not indicated by heavy lines in the figure below are occupied by a side-chain, ending in a hairpin. Except for the first step, every added pentamer bonds at least to two edges, one occupied by the main chain and one occupied by a side chain. The growth morphology imposed by the Hamiltonian path construction is, then, consistent with compact 2D growth structures.

In summary, on the basis of elementary graph-theoretical arguments, we propose that the quasi-icosahedral organization of unsegmented ss RNA viral genomes is based on the exploitation of the secondary structure of the viral RNA to form a Hamiltonian path or cycle along a subset of the edges of a polyhedron inscribed on the capsid surface, with side-branches covering the remaining edges. The important role for the RNA main-chain structure would be consistent with the main-chain acting as a linear template for the growth of the capsid during the self-assembly process. Our arguments predict that quasi-icosahedral organization should never be encountered for viruses with unsegmented fully duplexed ds DNA or RNA genomes. Experimental tests should be straightforward. For instance, FHV self-assembles under in-vitro conditions. Self-assembly of FHV with a duplexed RNA strand having the same length as the FHV ss RNA should be difficult or impossible. Determining the nature fo the vertex inhomogeneity of actual Nodaviridae would provide a decisive test of the model. Because current structural determination methods impose icosahedral symmetry, this is not yet possible, but we are hopeful that developments in these methods will make such a test feasible in the not-too-distant future.

We would like to thank Professors W. M. Gelbart and J. E. Johnson for helpful discussions. We are also grateful to Professor Johnson for permission to reproduce Fig. 1.


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# Yet MORE PM Survey Discoveries….?

## 1. Introduction

The Parkes Multibeam Survey (PM Survey) has discovered nearly half the known pulsars. Observations started in 1997 and completed in 2002. The PM survey used the 13-beam receiver at the 64-metre Parkes Radio Telescope and covered a strip along the Galactic plane with $`|b|<5^o`$ and $`l=260^o`$ to $`l=50^o`$. The observations were carried out with a 0.25ms sampling time, collecting $`2^{23}`$ samples, in an approximately 35-min observation. The nominal limiting flux density is about 0.2mJy, for dispersion measures (DM) of less than 300 cm<sup>-3</sup>pc. (Further details of the PM system can be found in Manchester et al. (2001)). There are approximately 2670 pointings, each of 13 beams, making a total of 34,710 integrations. The data are stored on some 154 DLT tapes for off-line processing.

Since the start of the survey, improved search techniques have been implemented and there has been some changes to the interference filters used. Consequently, there are more pulsars expected to be discovered using the existing data. With the increased computing power now available, particularly in the form of beowulf clusters such as Cobra at Jodrell Bank, it has been decided to reprocess the entire data set.

## 2. Binary Pulsar Discoveries

There have been 73 binary pulsars discovered, of which 15 have been discovered or re-detected in the PM survey (there are 19 known in the survey area). There is a large number, 25, which have been discovered in searches of Globular Clusters (GC). The reasons for being so many GC binary pulsars discovered is that as well as having a lot of stars in a restricted space, so stars often “capture” each other, the whole of the GC is in a narrow range of dispersion measures. It is, therefore, feasible to use more computationally expensive acceleration searches. This illustrates the benefit of using improved acceleration search algorithms with long integrations as discussed in Friere (2000) and Camilo et al. (2000).

The plot, in figure 1, of pulsar periods and orbits for these systems highlights that PM binary pulsars may have some selection effects. There are four binary pulsars which are within the PM survey area and not reported as detected. Two of the undetected pulsars B1855+09 and B1913+16 have flux levels of 4mJy (DM 13.3) and 0.7mJy (DM 169) respectively at 1400MHz, well above the minimum detectability levels. The other two do not have flux levels recorded for 1400MHz, but have DM’s and periods where the PM survey is reasonably sensitive.

Considering B1913+16, for example, it is a pulsar with a period of 59ms, but with a fast orbital period of 7.7hours. The full FFT would suffer significant smearing of upto 10 Fourier bins, thus limiting sensitivity.

Also, it can be seen that, apart from B1744-24A (a pulsar in GC Terzian 5) and J1141-6545 which are both very bright, there are no pulsars detected with orbits of less than 1 day, which could be partially due to selection effects. There are no binary pulsars with periods of less than 9-ms, however, there is a group with medium - long periods (50 - 500ms) and long orbits ($`>`$230 days), these can be detected using non-accelerated searches.

There is a clear possibility of finding further binary pulsars in the PM data.

## 3. PM Reprocessing Search algorithms

The PM survey has used a long integration of 35 mins for high sensitivity. However, the integration time makes it insensitive to fast binary pulsars due to smearing of received power across a number of Fourier bins. The processing to date has almost all only used a frequency domain search of the full data set for each observation. Consequently, the search has had the predicted sensitivities only for solitary pulsars up to about 2-sec period. The reprocessing of the data includes searches for accelerated (binary) pulsars, long period pulsars and single pulses - looking for “Giant Pulses” at a particular DM (McLaughlin 2001).

* Frequency Domain Search \- Most pulsars found have periods of one second or less and are effectively searched for using the frequency domain. This is due to the great efficiency of the FFT algorithm at separating many different frequencies concurrently.

This is the same search as performed previously, using the full length FFT. However, improvements in the “birdie filters” means that less of the spectrum is removed.
* Time Domain Search \- Long period pulsars ( $`>`$ 2 sec period) are most sensitively searched for using a time domain search, efficiently done by using a Fast Folding Algorithm (FFA) (Staelin 1969). This is because at low frequencies the separation of periods becomes relatively coarse using an FFT. By only searching a limited period range the FFA is reasonably efficient computationally.
* Linear Acceleration Search \- An efficient technique to search for linearly accelerating pulsars has been written and tested (e.g Anderson 1992), but has not been used on large quantities of data. Known as a “stack search”, this operates by the relative shifting and summing of independent partial FFT’s of the data (in this case 16 segments). It is very efficient in that many accelerations can be tested with only one set of transformed segments. Its limitations are that there is a loss of approximately 20% in sensitivity (see tests later and Anderson 1992) over a fully coherent search and only pulsars which are in orbits long enough to be accelerating linearly over the time of the observation, will have the maximum sensitivity.
* Phase Acceleration Search \- This approach searches for periodicities in the variations of the observed pulsar period, using the frequency domain - an FFT of an FFT (Ransom 2001). This is capable of identifying pulsars which have completed more than 1.5 orbits over the period of the observation. In the PM survey these would be very fast binaries, having orbits less than 20-mins. Such binaries do have been detected in X-rays, for example X1820-303 (Stella, Priedorsky & White 1987, which has a 685-sec orbit.

## 4. Search algorithm testing

Figure 2 shows the sensitivity of the search algorithms to simulated pulsars with various parameters. Although the segmented search significantly increases sensitivity to relatively fast binaries, it can clearly be seen that there is still a region of low sensitivity for binary pulsars between 20min and 6 hours.

## 5. Cobra Reprocessing

Reprocessing of data at Jodrell Bank will be on Cobra - a cluster of 91 processor boards incorporating 182 processors. A full tape takes approximately 1 day to process, while using 100 processors. It is anticipated that a significant number of new pulsars will be discovered in the PM Survey data; most will be normal solitary pulsars, however, there may be some really exciting objects.

## References

Anderson S. B. 1992, PhD Thesis, California Institute of Technology

Camilo F. et al. 2000, ApJ, 535,975

Freire P. 2000, PhD Thesis, The University of Manchester

Manchester R. N. et al. 2001, MNRAS, 328, 17

McLaughlin, M. 2001, PhD Thesis, Cornell University

Ransom S. M. 2001, PhD Thesis, Harvard University

Staelin D. H. 1969, in IEEE vol. 57, 724

Stella L., Priedorsky W., White N. ER., 1987, ApJ, 312. L17


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# Electromagnetic Fluctuations during Fast Reconnection in a Laboratory Plasma

## Abstract

Clear evidence for a positive correlation is established between the magnitude of magnetic fluctuations in the lower-hybrid frequency range and enhancement of reconnection rates in a well-controlled laboratory plasma. The fluctuations belong to the right-hand polarized whistler wave branch, propagating obliquely to the reconnecting magnetic field, with a phase velocity comparable to the relative drift velocity between electrons and ions. The short coherence length and large variation along the propagation direction indicate their strongly nonlinear nature in three dimensions.

Magnetic reconnection (e.g. biskampbook, ) plays an important role in determining the evolution of magnetic topology in relaxation processes in high-temperature laboratory plasmas, magnetospheric substorms, solar flares, and more distant astrophysical plasmas. Often, magnetic reconnection is invoked to explain the observed rapid release of magnetic energy in these highly conducting plasmas. A central question of magnetic reconnection concerns why the observed reconnection rates are much faster than predictions by the Sweet-Parker model sweet58 ; parker57  based on magnetohydrodynamics (MHD) with the classical Spitzer resistivity. In this two-dimensional (2D) model, the infinitely small resistivity causes magnetic field to dissipate only in very thin current sheets, which impede the outflow of mass leading to significantly slow reconnection rates. The subsequently proposed Petschek model petschek64  is based on standing slow shocks to open up the outflow channel allowing larger mass flows thus the faster reconnection rates. However, it has been shown later biskamp86 ; uzdensky00  that the Petschek solution is not compatible with uniform or smooth resistivity profiles. On the other hand, perhaps not surprisingly, the plasma resistivity can be enhanced due to microinstabilities which are often active only in the reconnection region where plenty of free energy exists in the form of a large relative drift between ions and electrons and large inhomogeneities in pressure and magnetic field. This anomalous resistivity not only can broaden the current sheet to increase the mass flow and the reconnection rate in the context of the Sweet-Parker model kulsrud01  but also its localization is able to open up the outflow channel for the fast reconnection ugai77 ; kulsrud01 ; biskamp01 . Alternatively, a recent theory birn01  attempts to explain fast reconnection rates based on non-dissipative terms, notably the Hall term, in the generalized Ohm’s law in a 2D and laminar fashion.

The underlying microinstabilities biskampbook  for the resistivity enhancement have been considered to be predominantly electrostatic in nature due to their effectiveness in wave-particle interactions. The primary candidate is the Lower-Hybrid Drift Instability (LHDI) krall71 , which has been frequently observed in space plasmas gurnett76 ; cattell86 . Recently this instability has been studied in direct relation with reconnection in laboratory carter02a  and in space shinohara98 ; bale03 . The main conclusion of these studies is that the LHDI is active only at the low-$`\beta `$ edge region of current sheet, but not at the high-$`\beta `$ central region, where the resistivity needs to be enhanced for fast reconnection. This conclusion is consistent with an earlier theory davidson77  which showed stabilization of LHDI by finite plasma $`\beta `$, and also with more recent numerical simulations horiuchi99 ; lapenta02 .

By contrast, much less attention has been paid to electromagnetic fluctuations and their relation with reconnection, although they have been also regularly observed in space gurnett76 . In this Letter, we report the first clear experimental evidence for electromagnetic fluctuations in the lower-hybrid frequency range during fast reconnection in a well-controlled laboratory plasma, Magnetic Reconnection Experiment (MRX) yamada97b . The observed waves are identified as right-hand polarized whistler waves propagating obliquely to the magnetic field. Earlier laboratory experiments stenzelgekelman6  on reconnection have indicated evidence for high-frequency electromagnetic fluctuations in the electron MHD regime where only electrons are magnetized, but their roles in the reconnection process were unclear. On the other hand, most plasmas of interest for the reconnection problem are well into the MHD regime where ions are also magnetized at least outside of the reconnection region, as in MRX. In one case, magnetic fluctuations have been interpreted as byproducts of LHDI in space plasmas shinohara98 .

In the MRX, magnetic reconnection is driven by reducing currents in two flux cores whose toroidally symmetric shape ensures the global 2D geometry, as illustrated in Fig.1. Oppositely directed field lines in the $`Z`$ direction are pulled together radially, forming a current sheet flowing along the $`\theta `$ direction. All essential parameters needed for characterizing reconnection are measured by an extensive set of diagnostics yamada97b . In a previous quantitative study ji98 , it was shown that the observed reconnection rates can be explained by a modified Sweet-Parker model including an effective resistivity, determined experimentally by $`\eta ^{}E_\theta /j_\theta `$ where $`E_\theta `$ and $`j_\theta `$ are toroidal reconnecting electric field and current density, respectively. In highly collisional plasmas, $`\eta ^{}`$ is very close to the classical Spitzer perpendicular resistivity $`\eta _{\text{Spitzer}}`$ trintchouk03  while $`\eta ^{}\eta _{\text{Sptizer}}`$ when the collisionality is reduced ji98 , in correlation with strong nonclassical ion heating hsu00 . High-frequency fluctuations have been measured in MRX in order to explore the possibility of the resistivity enhancement due to microinstabilities in low collisionality regimes. Although the LHDI was identified at the low-$`\beta `$ edge region of the current sheet, electrostatic fluctuations did not correlate well with the reconnection process in their temporal and spatial behavior as well as their collisionality dependence, leading to a conclusion that the electrostatic fluctuations do not play an essential role in the fast reconnection in MRX carter02a ; carter02b .

The experimental results reported here focus on electromagnetic fluctuations, which do correlate well with fast reconnection. The main diagnostics used are based on four small magnetic pickup coils mounted inside an electrostatically shielded glass tube. All three components of magnetic field are measured at almost the same location. The probe outputs are fed into a miniature circuit board, which houses four amplifiers embedded in the probe shaft near the tip in order to provide noise immunity and impedance matching. The integrated bandwidth is up to 30 MHz.

Typical raw signals are shown in Fig.2 during a single discharge when reconnection is induced. High-frequency fluctuations appear in all three components of magnetic field right after $`t=260\mu `$s when the current sheet is formed, and persist as long as the reconnection goes on. Spectrograms, which display the fluctuation power in the time-frequency domain, are shown in the right panels of Fig.2. It is seen that discrete peaks exist in the lower-hybrid frequency range and they tend to also vary accordingly with the changes in the local lower-hybrid frequency $`f_{\text{LH}}\sqrt{f_{\text{ce}}f_{\text{ci}}}`$, shown as black lines 111 The local magnetic field (and $`f_{\text{LH}}`$), remains nonzero at the current sheet center due to a residual toroidal field generated during the plasma formation process yamada97b .. The spatial profile of the total fluctuation amplitude $`|\stackrel{~}{B}|`$ is plotted in Fig.3. The fluctuations have large amplitudes consistently near the current sheet center with peak $`|\stackrel{~}{B}|/B_{\text{up}}`$ up to 5%, where $`B_{\text{up}}`$ is the upstream reconnecting magnetic field. It should be noted that both temporal behavior and spatial behavior of the magnetic fluctuations are in sharp contrast with the electrostatic fluctuations carter02a ; carter02b .

In order to identify the observed electromagnetic waves, it is crucial to measure their propagation characteristics. Two techniques have been employed for this purpose. The first one is called the hodogram technique urrutia00 , which is based on the tip trajectories of a fluctuating magnetic field vector measured at a single point in space. For a given frequency, the condition $`\stackrel{~}{𝑩}=0`$ can be translated to $`𝒌\stackrel{~}{𝑩}=0`$ where $`𝒌`$ is the dominant wavenumber vector, the direction of $`𝒌`$ can be determined by the right-hand rule $`\stackrel{~}{𝑩}(t_0)\times \stackrel{~}{𝑩}(t_0+\delta t)`$ when $`ff_{\text{ci}}`$. Power spectra of the fluctuating magnetic field can be constructed in the domain of frequency and the angle between $`𝒌`$ and the background $`𝑩_0`$, as shown in Fig.4(left). It is seen that in the low frequencies, $`𝒌`$ has a rather large angle ($`60^{}`$) to $`𝑩_0`$ with a broad spread while in higher frequencies, $`𝒌`$ has a rather small angle ($`30^{}`$) to $`𝑩_0`$ with a narrow spread. In addition, since the $`𝒌`$ vector has only a small radial component (not shown), $`𝒌`$ remains in the $`Z\theta `$ plane. Therefore, it is concluded that the observed magnetic fluctuations are right-hand polarized whistler-like waves propagating obliquely to the magnetic field while staying within the current sheet.

While the direction of $`𝒌`$ is determined by the hodogram technique, its magnitude or the wavelength is determined by a second technique using the phase shift measured between two spatial points. Two glass tubes, each containing a pickup coil, are mounted to a probe shaft with a distance of 7 mm between their axes. Each signal is fed to a single-channel version of the miniature in-shaft amplifier carter02a . The phase shift along the $`\theta `$ or $`Z`$ direction is measured to construct power spectra in the domain of frequency and $`k_\theta `$ \[Fig.4(right)\] or $`k_Z`$ (not shown). It is found that the magnetic fluctuations propagate mainly in the $`\theta `$ direction, along which electrons drift, but not in the $`Z`$ direction. The phase velocity, $`V_{\text{ph}}=(3.4\pm 0.8)\times 10^5`$m/s calculated from the slope of the black line in Fig.4(right), is reasonably consistent with the relative drift velocity $`V_\text{d}j_\theta /en=(2.5\pm 0.9)\times 10^5`$m/s, where $`n`$ is the plasma density.

The measurements of the propagation characteristics described above are made at the outer edge of the current sheet ($`R`$=40cm) where the fluctuations have only moderate amplitudes (see Fig.3) and stay relatively coherent within the probe separation. At the current sheet center where the fluctuation amplitude peaks, the measurements of $`𝒌`$ have not been so successful due to extremely short coherence lengths. The coherence $`\gamma |\stackrel{~}{B}_1\stackrel{~}{B}_2^{}|/(|\stackrel{~}{B}_1||\stackrel{~}{B}_2|)`$ between signals $`\stackrel{~}{B}_1`$ and $`\stackrel{~}{B}_2`$ rapidly decreases to the noise level when the separation is larger than 0.5$``$1.5 cm, suggesting their strongly nonlinear nature. (For comparison, the wavelength measured at $`R=`$40cm in the same $`\theta `$ direction is $`5`$cm for $`f`$=10MHz.) Furthermore, it is found that the fluctuation amplitude varies substantially along the $`\theta `$ (current) direction, breaking the 2D axisymmetry of the current sheet and consequently the reconnection process. Further detailed measurements indicate that the fluctuation amplitude tends to correlate with the local $`V_\text{d}`$.

The next important question concerns how the observed magnetic fluctuations are related to the resistivity enhancement, and thus the fast reconnection process in MRX. It is consistently found that the fluctuation amplitudes are sensitive to plasma density or equivalently the collisionality. For example, when the density is reduced from $`5\times 10^{19}\text{m}^3`$ to $`2\times 10^{18}\text{m}^3`$, $`|\stackrel{~}{B}_Z|`$ increases from 0.1 G (close to the noise level for the measurements) to $`1`$ G, as shown in Fig.5. Since the resistivity enhancement also strongly depends on the plasma collisionality ji98  (Fig.5), a clear positive correlation between magnetic fluctuations and resistivity enhancement is established, as shown in Fig.6 222The resistivity is calculated by assuming toroidal symmetry of the current sheet ji98 , which does not necessarily hold true in the discharges used for this study. However, the averaged resistivity obtained by a scan over 20 toroidal angles is reasonably consistent with values based on the axisymmetry assumption provided enough numbers of discharges are used for averaging..

Given the experimental data described above, it is clear that the observed electromagnetic waves are caused by microinstabilities driven by free energy stored in the reconnecting current sheet, in the form of large $`V_\text{d}`$ and/or large inhomogeneities. Since essentially no electrostatic fluctuations are detected concurrently, the observed magnetic fluctuations cannot be simply byproducts of LHDI, which is driven by inhomogeneities, propagating primarily perpendicular to the field. In addition, magnetic fluctuations due to LHDI are dominated by their component along $`𝑩_0`$ while experimentally all three components have roughly the same amplitude (see Fig.2). The waves also cannot be described as whistler waves driven by electron temperature anisotropy kennel66 , which propagate mainly along $`𝑩_0`$.

Many observed key features of the magnetic fluctuations, however, are consistent with the so-called Modified Two-Stream Instability (MTSI) in the high-$`\beta `$ limit ross70 ; krall71 ; mcbride72 ; wu83 ; basu92 . In contrast to LHDI, MTSI is driven only by a large relative drift across the magnetic field in homogeneous plasmas. In the low-$`\beta `$ limit, both LHDI and MTSI behave similarly silveira02 . When $`\beta `$ is large ($`1`$), LHDI is stabilized davidson77  while MTSI remains unstable but the Alfvén speed $`V_\text{A}`$ replaces the ion sound (or thermal) speed as the critical speed for $`V_\text{d}`$. The resultant waves are largely electromagnetic and right-hand polarized whistler-like waves propagating obliquely to the field with $`V_{\text{ph}}V_\text{d}`$ ross70 . Under certain conditions similar to those at the current sheet in MRX, such as $`\beta 1`$ and $`V_\text{d}/V_\text{A}5`$, the waves are unstable only at certain propagation angles to the field wu83 ; basu92 . However, the discrete peaks in the frequency spectra (Fig.2) cannot be explained by these theories, which were based on the slab geometry. Global eigenmode calculations taking into account the boundary conditions, as have been done for LHDI yoon02 ; daughton02 , may explain the discrete frequency peaks.

Quantitative estimates of resistivity enhancement due to these fully nonlinear waves as described above are not straightforward. Nonetheless, examinations of each term in the generalized Ohm’s law reveal that the turbulent Hall term due to the magnetic fluctuations could be sufficiently large to balance the reconnecting electric field if the measured coherence lengths are used as the perpendicular scale length. Other candidates, such as off-diagonal terms in the pressure tensor, can also possibly provide required effective friction between electrons and ions as a result of wave-particle interactions.

In summary, a detailed experimental study in MRX has established, for the first time, a clear and positive correlation between magnetic fluctuations in the lower-hybrid frequency range and fast reconnection in the low-collisionality regimes. The waves have been identified as right-hand polarized whistler waves, propagating obliquely to the reconnecting field, with a phase velocity comparable to the relative drift velocity. These waves are consistent with the modified two-stream instability driven by large drift speeds compared to the Alfvén speed in high-$`\beta `$ plasmas. The short coherence length and large variation along the propagation direction indicate their strongly nonlinear nature. Quantitative understanding of the effects of these waves on the resistivity enhancement, and thus reconnection rates, requires further experimental efforts to directly measure relevant terms in the generalized Ohm’s law. Theories and numerical studies of linear and nonlinear characteristics of current-driven microinstabilities using proper models and boundary conditions in 3D should provide much-needed physical insight.

The authors are grateful to D. Cylinder and R. Cutler for their excellent technical support, J. Whitney, K. Shen, and J. Carter for their contributions through a summer program, and T. Carter for useful discussions. This work was jointly supported by DOE, NASA, and NSF.


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# Thermal-timescale mass transfer and magnetic CVs

## 1. Introduction

The evolutionary relations among subclasses of magnetic and non-magnetic cataclysmic variables (mCVs and CVs respectively) have been studied for quite some time. Nevertheless, our understanding of these relations remains incomplete, caused largely by serious selection effects which prevent completeness of the samples. Here we consider the future evolution of the peculiar mCV AE Aqr. Its future spin evolution and equilibrium states could clear much of the current confusion, as this binary has been identified as member of a potentially large group of post-thermal timescale mass transfer systems (Schenker et al., 2002). One consequence of this is the prediction of a relatively large population of mCVs at long orbital periods. Such a population has not been detected. We consider the possibility that this could be because these long period mCVs occupy spin equilibria which significantly hamper accretion onto the white dwarf (WD), causing them to have been overlooked or misclassified.

### 1.1. Thermal-timescale mass transfer

We first consider the origin of CVs (Fig. 1). The progenitor of the WD starts off as the more massive star in a relatively wide binary, which has evolved through various stages of (single) stellar evolution forming a degenerate core in its centre. During the AGB phase the star swells and fills its Roche lobe. A subsequent phase of common envelope evolution leaves the system with the exposed core (pre-WD) and the largely unaffected secondary in a close orbit. In order to be a future CV this system has to become semi-detached. This can be achieved by angular momentum loss (AML) shrinking the orbit or nuclear evolution increasing the secondary’s radius. The latter channel can lead to a large fraction of systems with a secondary more massive than the WD primary leading to thermal-timescale mass transfer (TTMT).

Examples of TTMT evolution are the various model tracks for AE Aqr presented in Schenker et al. (2002). In contrast to standard CVs (which have low mass donors and stable, AML-driven mass transfer) this subclass passes through an initial phase of high mass transfer prior to become an AML-driven CV. If we consider CVs which have suffered TTMT, we expect there to be differences to standard CVs at the onset of mass transfer: (i) The WDs are likely to have large rotation rates and masses. This is a consequence of the high mass transfer rates during the supersoft phase (during TTMT) which allows significant accretion onto the WD. (ii) Instead of low-mass MS stars, the donors are the evolved cores of more massive stars. Their different internal structure, manifesting itself e.g. in a different mass-radius exponent $`\zeta `$, leads to smaller $`M_2`$ at the same $`P_{\mathrm{orb}}`$, and even to different mass transfer rates. (iii) The magnetic fields on either or both the donor and the WD may be different (cf. Cumming, 2002, and this volume, on $`\mathrm{B}`$–field suppression in rapidly accreting WDs).

### 1.2. Non-synchronous mCVs

The majority of known mCVs (Fig. 2) are either polars (mostly below the period gap) or intermediate polars (IPs, above the gap up to $`6`$ h). There are only a few, mostly peculiar systems longwards of $`6`$ h, one of which is AE Aqr. If many other systems like it have passed through a similar phase, where do they appear on the period distribution? This lack of magnetic systems between 6 and 10 h we termed the “IP gap”, well aware of the sparse observational data to establish its existence (cf. recently reheated discussions on evidence for a period gap in mCVs).

## 2. White Dwarf spin and magnetosphere

We use a simplified description for the magnetic drag on gas streaming past a spinning WD (King, 1993), where the magnetic acceleration $`a_{\mathrm{mag}}`$ is proportional to the velocity shear $`\left(v_{\mathrm{B}\mathrm{field}}v_{\mathrm{flow}}\right)`$. After splitting off the radial power dependency in the drag and replacing the $`\mathrm{B}`$–field and flow velocities with the WD rotation and Keplerian motion respectively we obtain

$$a_{\mathrm{mag}}=k_0R^n(R\mathrm{\Omega }_{\mathrm{spin}}\sqrt{\mathrm{G}M_1/R}).$$
(1)
Different interaction models are reduced to variations in the drag coefficient $`k_0`$ and the radial power $`n0`$. Propelling and accreting states are possible depending on the WD spin, which determines the sign of the velocity shear.

Extending the usual definition of the magnetospheric radius (e.g. Warner, 1995; Frank et al., 2002) we compare the timescale of the magnetic interaction to the dynamical timescale (in the disk-less case, I) and to the viscous timescale (in the truncated disk case, II). Fig. 3 shows the resulting critical radii (shaded for $`n=6`$, and an additional set of lines for $`n=0,2,3`$). For $`n=6`$ there is a critical spin period

$$P_{\mathrm{max}}=18\mathrm{s}\mu _{33}^{2/3}\dot{\mathrm{M}}_{16}^{1/3}m_1^{2/3}\sigma _9^{1/3}c_6^{1/3}$$
(2)
marking the maximum of the propelling branch in case I. Such a maximum exists for all $`n<3`$ for both cases. Additionally the asymptotic radius of the accreting branch in the limit of slow rotation can be written as

$$R_{\mathrm{asym}}=1.6\times 10^9\mathrm{cm}\mu _{33}^{4/9}\dot{\mathrm{M}}_{16}^{2/9}m_1^{1/9}\sigma _9^{2/9}c_6^{2/9},$$
(3)
which corresponds to the radius where the stream becomes threaded in an ordinary polar. Both of these expressions describe case I where the mass transfer stream is specified by $`\dot{\mathrm{M}}`$ (in $`10^{16}\mathrm{g}\mathrm{s}^1`$), a stream width $`\sigma `$ (in $`10^9\mathrm{cm}`$), and the sound speed at the L1 point $`c`$ (in $`10^6\mathrm{cm}\mathrm{s}^1`$). The WD mass is $`m_1`$ (in $`\mathrm{M}_{}`$) and its magnetic moment is $`\mu `$ (in $`10^{33}\mathrm{G}\mathrm{cm}^3`$). The corresponding expressions for case II are

$$P_{\mathrm{max}}=124\mathrm{s}\alpha ^{18/125}\mu _{33}^{24/25}\dot{\mathrm{M}}_{16}^{33/125}m_1^{32/25}$$
(4)
and

$$R_{\mathrm{asym}}=5.9\times 10^9\mathrm{cm}\alpha ^{12/125}\mu _{33}^{16/25}\dot{\mathrm{M}}_{16}^{22/125}m_1^{13/25},$$
(5)
with $`\alpha `$ describing the usual disk viscosity.

Spin equilibria IPs are achieved when torques on the WD cancel. Comparing $`R_{\mathrm{mag}}`$ to various other important radii identifies such states (Warner, 1995; King & Wynn, 1999). We are now able to analyse the various spin equilibria in mCVs provided we have good measurements of the periods (easy), magnetic moments (difficult), masses and mass transfer rates (even more so).

## 3. The Future of AE Aqr

### 3.1. Truncated disk due to weak propeller?

Results of our most recent simulation are presented in Fig. 4. Extending previous attempts (Wynn et al., 1997) to model the current status of AE Aqr, this calculation follows the spin evolution through the next few $`10^7\mathrm{yr}`$. During this time the spin-down continues at roughly the current rate. We can clearly see that at $`P_{\mathrm{spin}}>100\mathrm{s}`$ a truncated disk forms with a large inner hole of $`R_{\mathrm{in}}2\times 10^{10}\mathrm{cm}`$.

We compare this result in Fig. 5 to an analysis using critical radii. In the left-hand panel the situation for AE Aqr in its current state is shown: at the observed spin period of 33 sec and a strong propeller (lower curve, as labelled), $`R_{\mathrm{mag}}`$ is large enough to prevent disk formation in the circularization region. As the WD slows down, a disk will form and the effective $`R_{\mathrm{mag}}`$ will switch to the truncated disk case (pair of curves for hot and cold $`\alpha `$). As long as this happens at $`P_{\mathrm{spin}}<P_{\mathrm{max}}`$ (given by eq. (4)), the next stage of spin evolution is a weak propeller in a truncated disk. In the final state of the computation in Fig. 4 we indeed find $`R_{\mathrm{in}}R_{\mathrm{mag}}`$. For $`P_{\mathrm{max},\mathrm{hot}}<P_{\mathrm{spin}}<P_{\mathrm{max},\mathrm{cold}}`$ a stable equilibrium is possible where the propeller slows the WD down during quiescence, while it is spun up by an equal amount during outbursts. This equilibrium can be maintained over secular timescales. Such a system will not be visible as a mCV during its rather long quiescent stage between outbursts. We can now construct a sequence of diagrams for AE Aqr with parameters taken from the post-TTMT evolution by Schenker et al. (2002). The right-hand panel of Fig. 5 (showing only the truncated disk pair of curves) is taken at $`P_{\mathrm{orb}}=5\mathrm{h}`$: the $`R_{\mathrm{mag}}`$ curves are shifted upwards along the corotation radius, i.e. the central hole has grown to the point that spin equilibrium is impossible. Further slow down of the WD ends the weak propeller phase, and for the first time AE Aqr will appear as a normal IP: with a typical $`P_{\mathrm{spin}}/P_{\mathrm{orb}}`$ ratio and $`P_{\mathrm{orb}}`$ in the range where the bulk of IPs are found (Fig. 2).

### 3.2. Stable strong propeller??

We also identified a potentially stable configuration for a strong (disk-less) propeller. The velocity of a stream reaches its maximum value near the point of closest approach to the WD, the point at which the rotational velocity of the magnetic field is lowest. So for given $`P_{\mathrm{orb}}`$ and $`q`$ a critical spin period $`P_{\mathrm{crit}}`$ can be found at which the sign of the drag force between the stream and the rotating WD field changes. As the force depends strongly on radius even a small inversion may be sufficient to balance the angular momentum transferred from the WD to the stream while further away. This may lead to a stable propeller, i.e. a situation where the mass transfer stream is leaving the system yet the WD spin does not change. In order to test this new idea, we have performed SPH simulations to investigate the possibility of a stable strong propeller. As can be seen in Fig. 6, it is possible to construct a strong propeller at this critical spin state. Near the point of closest approach the velocity shear reverses and the stream returns angular momentum to the WD. However, it would appear that this can only happen at spin periods well above $`P_{\mathrm{max}}`$ found for AE Aqr.

## 4. Conclusion

In summary both the critical radius analysis and numerical work indicate that AE Aqr will continue to be a strong propeller for a short time. Afterwards it is likely to become a weak propeller system with a truncated disk. At least theoretically, a stable strong propeller is possible, although most probably not feasible for AE Aqr. As long as the system can avoid accreting in a stable, IP-like manner, any descendant of AE Aqr may easily be overlooked as a mCV.

Overall we conclude that TTMT evolution forces us to re-evaluate ideas about magnetic binary evolution. The various spin states of magnetic WDs can lead to drastically different behaviour of otherwise similar systems. In particular, stable states may exist with or without a disk, propelling or accreting. Not all of these states would currently be considered to be magnetic systems on observational grounds.

## References

Cumming, A.: 2002, MNRAS 333, 589

Frank, J., King, A. R., & Raine, D.: 2002, Accretion Power in Astrophysics, Cambridge Univ. Press, Cambridge, 3rd edition

King, A. R.: 1993, MNRAS 261, 144

King, A. R. & Wynn, G. A.: 1999, MNRAS 310, 203

Ritter, H. & Kolb, U.: 1998, A&AS 129, 83

Schenker, K., King, A. R., Kolb, U., Wynn, G. A., & Zhang, Z.: 2002, MNRAS 337, 1105

Warner, B.: 1995, Cataclysmic Variable Stars, Cambridge Univ. Press, Cambridge

Wynn, G. A., King, A. R., & Horne, K.: 1997, MNRAS 286, 436


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# 𝐽/𝜓𝑐𝑐̄ production in 𝑒⁺𝑒⁻ and hadronic interactions

## Acknowledgments

I would like to thank K. Boreskov, O.V. Kancheli for useful duscussions. I am especially grateful to M.V. Danilov for drawing my attention to this problem and discussion of results of Belle Collaboration.
This work is supported in part by the grants: INTAS 00-00366, NATO PSTCLG- 977275, RFBR 00-15-96786, 01-02-17383

## References


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# Large-scale H I structures and the origin of radio galaxies

## 1 Why neutral hydrogen?

The study of the formation and the evolution of massive ellipticals is attracting, at present, a lot of attention. Among these systems, an interesting sub-class is represented by those hosting powerful radio sources. The presence of such activity is telling us that the galaxy is in a particular phase in its evolution. Indeed, the increasing evidence given that super-massive black holes reside in the centres of many elliptical galaxies suggests that the period of activity, turning a “normal” elliptical in a radio galaxy, could be a – relatively short – phase in the life of many (or all?) ellipticals. When in the life of the host galaxy this phase takes place and how it is related to the actual formation of the host galaxy and to its evolution, are questions that are still unanswered.
The importance of mergers/interactions in the formation and triggering of radio galaxies has been brought forward already a long time ago. The peculiarities often observed in the optical morphology of radio galaxies (e.g. tails, bridges, shells and dust-lanes, see He1 ) is one of the main arguments that has led to this conclusion.
However, new results have been recently obtained from the study of the optical continuum in radio galaxies (with the main goal of investigating the nature of the UV excess). It has been found Ta1 ; Wi1  that a young stellar population component is present in at least 30% of radio galaxies. Interestingly, the galaxies showing this component are also the most luminous in the far-IR, indicating a link between an optical starburst and far-IR activity. These results support the idea of a merger origin for radio galaxies and suggest that, at least some of them, had an (ultra-)luminous far-IR galaxy as progenitor Ta1 . The results also indicate that the activity starts late after the merger event. The existence of galaxies where this young stellar component is not observed indicates that either they are observed at a later stage and/or they originate from other type of mergers.
Thus, the study of the stellar population appears to provide some important clues about the origin of radio galaxies. However, some of the information derived in this way is still quite uncertain and it is important to be able to investigate the origin and evolution of these systems in a complementary way. This can be done through the study of large-scale structures of neutral hydrogen around radio galaxies. Indeed, H I has been successfully used to study the fate of the gas in a number of cases where interaction/merger is present. The main advantage of the study of neutral hydrogen is, given the long timescales involved, its capability of retaining old signatures of the merger/accretion. Thus, it can be used to derive key information about the age, size and type of the merger and about when the AGN phase takes place compared to the starburst phase.
Neutral hydrogen has recently given interesting results also for “normal” (i.e. not necessarily radio-loud) elliptical galaxies (see To1 ; To2 ; S1  and refs therein). Interestingly, a small, but significant, fraction, in particular outside clusters of galaxies, contains a sometimes very large amount of H I (i.e. $`M_{\mathrm{HI}}>10^9`$ $`M_{}`$111For $`H_{}=50`$ km s-1 Mpc-1 and $`q=0.0`$, $`M_{\mathrm{HI}}/L_B`$ 0.02) distributed in very extended (tens of kpc in size, see e.g. Fig. 1), and often kinematically regular, structures (see e.g. Mo1 ; To1 ). These structures are long-lived (no major star-formation is going on) and, because of their large amount of H I and the large size, they are believed to originate from major mergers between two disk galaxies. In addition to this, the often observed decoupling between the gas and stellar content and kinematics is taken as a further indication of the external origin of the H I in ellipticals Kn1 . One obvious question is whether there is any connection between radio galaxies, these gas-rich “normal” elliptical galaxies and other major mergers (like the ultra-luminous far-IR galaxies, ULIRGs).

## 2 Large-scale H I structures in radio galaxies: new results

For all these reasons, we have begun a study of large-scale H I structures (tens of kpc in size) in and around radio galaxies. The presence of neutral hydrogen around radio galaxies was known only for a handful of objects. With this study we plan not only to increase the known number of cases, but also to reach a more complete statistics of its occurrence in order to compare with the situation for “normal” ellipticals.
In our search for large-scale H I structures in radio galaxies, we have already at least three interesting new detections (Coma A, B2 0648+27 and 3C 433). This is quite remarkable given that so far only two radio galaxies of comparable radio power (Centaurus A and PKS B1718-649, see Mo3  for an overview) were known to have large-scale H I. For the first time, some of the large-scale H I structures are detected in absorption against the extended radio lobes.

In the radio galaxy Coma A, $`10^9`$ $`M_{}`$ of H I was detected in a disk-like structure of at least 60 kpc in diameter in absorption against the radio lobes (see Mo2 ). The structure of the gas disk (and the amount of H I) suggests that a merger occurred, involving at least one large gas-rich galaxy, at least a few times $`10^8`$ yr ago. Another example is the nearby radio galaxy B2 0648+27 where H I both in emission and in absorption has been detected Mo3 . In emission, we detect a very large amount of H I ($`M_{\mathrm{HI}}=1.110^{10}`$ $`M_{}`$) distributed in a very extended disk, or ring-like structure, of about 160 kpc in size as shown in Fig. 2 Mo3 . We also detect H I absorption against the central radio continuum component. The characteristics of the detected H I and the similarities with some of the “normal” elliptical mentioned above, are explained as the result of a major merger event that is likely to have occurred $`\stackrel{<}{}10^9`$ yr ago.
Extended H I in absorption against the radio lobes has been observed also is 3C 433. In this radio galaxy (Fig. 3), the preliminary analysis of the data shows that $`5\times 10^8`$ $`M_{}`$ of (extended) H I is detected at about 60 kpc from the radio core. The gas shows a velocity gradient, but at the moment it is not clear whether the detected H I is part of an extended gas disk/tail or whether it corresponds to a region of interaction between the ISM and the radio lobe. Given the lower amount of H I detected so far in this object, the origin of this galaxy might be different from the major-merger suggested in the two previous cases. Finally, it is important to notice that both B2 0648+27 and 3C 433 have a clear young stellar population component visible in their optical spectra. The final goal will be to compare the information obtained from the H I data and those obtained from the stellar population.

## 3 Can we use the H I to define an evolutionary sequence?

For B2 0648+27 we have attempted, using the information obtained from the H I, to include this object in an evolutionary sequence, partly already proposed for other gas-rich systems (see e.g. Hi2 ). This could provide a possible scenario for the origin of at least some radio galaxies.
The sequence, depicted in Fig. 5, begins with systems like The Antennae (left) as representative of an ongoing merger where two galaxies are still identifiable and where a starburst is occurring. NGC 7252 (2nd from left) represents a somewhat later stage where the central remnant has already more or less taken the shape of an elliptical galaxy Hi2 . The H I is mainly in large tails at large radii, while the gas in the centre, where much star formation is still occurring, is mainly molecular. NGC 7252 is a strong emitter in the far infrared. The $`3^{\mathrm{rd}}`$ stage with AGN activity is represented in the sequence by B2 0648+27. From the time-scale derived both from the H I and from the stellar population, (and given the shorter time-scale of the AGN phase compared to mergers) the AGN activity must occur at a late stage of the merger while a young stellar population is still observable in the optical spectrum. The final stage (NGC 5266; 4th panel), shows a galaxy that has become a genuine early-type galaxy Mo1 . In NGC 5266 the H I is falling back from the large tidal tails to the galaxy and is in the process of forming a large disk or ring-like structure of low surface density. Star formation is occurring at a much reduced rate and no AGN is detected.
This is, of course, likely to be an oversimplified scenario as a number of other “free parameters” are also playing a role. For example, the genesis of the merger depends also on the type of encounter (e.g. prograde vs retrograde) and the relative size of the two galaxies is making the story more complicated. The environment is also likely to play a very important role.

## 4 Implication for nearby and high-z radio galaxies

The initial results obtained in the study of extended structures of neutral hydrogen in and around radio galaxies indicate that these structures may actually be more common than thought so far. Thus, the H I can be used to study the likely origin of these systems and the time scales involved. Two of the three galaxies described above show a young stellar population components. The parameters obtained from the study of the optical continuum and from the H I can be therefore complementary in order to obtain a full picture. It is important to note that galaxies with a young stellar population appear to be the best candidates for detecting H I. This may further support the idea that they come from particularly gas-rich mergers or they are mergers that occurred recently.
Finally, an important connection is between nearby and high-$`z`$ galaxies. Although interactions and mergers are likely to occur more frequently and more efficiently at high redshifts, in the H I-rich, low redshift radio galaxies we may witnessing similar phenomena. Particularly relevant is the finding (V1  and Villar-Martiń these Proceedings) of a low surface brightness Ly$`\alpha `$ halo with quiescent kinematics in the case of the high-$`z`$ radio galaxy USS 0828+193. One possible way suggested to explain this structure is that the low surface brightness Ly$`\alpha `$ halo is the progenitor of the H I discs found in low redshift galaxies.
If this is the case, the wealth of details that we can learn at low-$`z`$ may be crucial for understanding the structures at high-$`z`$.


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# Spectroscopy of Dark Soliton States in Bose-Einstein Condensates

## 1 Introduction

With the realization of Bose-Einstein condensation (BEC) in dilute atomic gases , a well controllable and easily observable macroscopic wavefunction has become accessible for a wide variety of fundamental experiments. Since the early experiments on oscillations of the condensate  and phonons , excitations of the condensate wavefunction have been subject to intense investigation. Signatures of superfluidity in Bose-Einstein condensates were first observed in the suppression of excitations below a critical excitation velocity  and in the analysis of scissors mode excitations . Recently another striking aspect of superfluidity in BEC has been studied by exciting vortices in two-component condensates  and vortices and vortex arrays in stirred condensates . Vortices as topological excitations of the condensate wavefunction represent particularly interesting phenomena and are still a very active area of research. Dark solitons in Bose-Einstein condensates are in several respects the one-dimensional counterpart to vortices. While the phase of the vortex wavefunction winds up around a zero density ’core’, in a dark soliton state regions of constant phase are separated by a minimum in density and a steep phase gradient. Dark solitons are fundamental excitations in one dimensional systems described by nonlinear wave equations and thus a solution of the Gross Pitaevskii equation, which describes the condensate wave function . In Bose-Einstein condensates, the creation of dark solitons using a phase imprinting method  has been investigated in a strongly elongated geometry in BECs of 87Rb  and in nearly spherical BECs of 23Na . Recently bright solitons in Bose-Einstein condensates with attractive interactions  and filled solitons  have also been observed .

The experiments on dark solitons have so far concentrated on the temporal evolution of the density distribution of the Bose-Einstein condensate, which showed the motion and decay of these excitations. In this article we extend these investigations to the velocity field which underlies a dark soliton state in a Bose-Einstein condensate.

## 2 Properties of dark solitons

In general Solitons are fundamental wave-packet-like excitations of one dimensional nonlinear systems. One characteristic of them is that they do not disperse but preserve their shape due to a balance between dispersive and stabilizing effects in these systems. Dark solitons in Bose-Einstein condensates form density minima, which self stabilize due to a balance of the repulsive mean field interaction which would be minimized by compressing the minimum and quantum pressure. The quantum pressure is related to the kinetic energy associated with the dark soliton velocity field, which is minimized by widening the minimum.

More formally a dark soliton in a homogeneous Bose-Einstein condensate of density $`n_0`$ is described by the one dimensional wavefunction

$$\mathrm{\Psi }_k(x)=\sqrt{n_0}\left(i\frac{v_k}{c_s}+\sqrt{1\frac{v_k^2}{c_s^2}}\mathrm{tanh}\left[\frac{xx_k}{l_0}\sqrt{1\frac{v_k^2}{c_s^2}}\right]\right),$$
(1)
with the position $`x_k`$ and velocity $`v_k`$ of the dark soliton, the correlation length $`l_0=(4\pi an_0)^{1/2}`$, and the speed of sound $`c_s=\sqrt{4\pi an_0}\mathrm{}/m`$, where $`m`$ is the atom mass. Note that a so called black soliton with zero density at the minimum and a $`\pi `$ phase jump is obtained for $`v_k=0`$, while for all other cases the condensate wave function has nonzero amplitude at the position of the density minimum which now moves along the condensate and is associated with a finite phase gradient.

Consequently dark solitons in Bose-Einstein condensates are density minima associated with a steep phase gradient of the condensate wavefunction. This gradient of the phase distribution $`\mathrm{\Phi }(\stackrel{}{r})`$ of the macroscopic Bose-Einstein condensate wavefunction defines a probability current density, which can be interpreted as a superfluid velocity field $`v(\stackrel{}{r})=\frac{\mathrm{}}{m}\mathrm{\Phi }(\stackrel{}{r})`$. Thus, the steep gradient of the phase at the dark soliton leads to a localized peak in the velocity distribution of the BEC. The corresponding BEC density, phase and velocity distributions are shown schematically in Fig. 1.

Equation 1 is strictly valid only for infinite homogeneous one-dimensional systems but many qualitative features remain valid in more realistic experimental cases. However the effect of the trapping potential, the formation process and the dynamics during time-of-flight expansion are not included. In order to model these cases more accurately, we numerically solve the Gross-Pitaevski equation for the case of inhomogenous condensates, trapped in static potentials. Deviations from the 1D behaviour in elongated and nearly spherical traps are treated e.g. in .

## 3 Creation of dark solitons

For the experimental investigation of the dark soliton velocity field we first produce ground state Bose-Einstein condensates of 87Rb as described in . The condensates typically contain $`1.5\times 10^5`$ atoms in the ($`F`$=2, $`m_F`$=+2) state, with less than $`10\%`$ of the atoms being in the thermal cloud. The fundamental frequencies of our static magnetic trap are $`\omega _x=2\pi \times 14`$Hz and $`\omega _{}=2\pi \times 425`$Hz along the axial and radial directions. The condensates are cigar-shaped with the long axis ($`x`$-axis) oriented horizontally and an aspect ratio of $`\lambda 30`$, providing an essentially one dimensional potential for the evolution of the dark soliton on the time scale of the experiment.

In our experimental setup we create dark solitons using a phase imprinting method . The phase distribution of the condensate is changed by using the dipole potential of a far detuned light field ($`\lambda =`$532 nm, $`I20`$W/mm2), illuminating one half of the condensate for a time $`t_p`$ on the order of $`20\mu `$s. Note that this time has to be shorter than the correlation time of the condensate, $`t_c=\mathrm{}/\mu `$, in order to obtain pure phase imprinting, where $`\mu `$ is the chemical potential and in our case $`t_c55\mu `$s. This procedure creates a moving dark soliton and a counterpropagating density wave, which become well separated after some time, $`t_{ev}`$, of further nonlinear evolution in the trapped Bose-Einstein condensate, as shown in Fig. 2 a).

Figure 2 b) shows a typical density-distribution of a dark soliton state created by phase imprinting after some evolution time in a trapped BEC obtained by the numerical solution of the GPE in 1D using the split operator method . This simulation contains a finite optical resolution for the phase imprinting field, leading to a potential gradient with a width of $`2\mu `$m at the edge of the illuminated area, as realized experimentally. Due to this gradient a density wave and some higher order excitations moving to the right are created in addition to the dark soliton. The dark soliton and the density wave move in opposite directions, however the dark soliton is much narrower due to its self stabilization in the nonlinear medium. Note that the velocity field in the region of the dark soliton has only components of negative velocities, $`v(x)<0`$ for a positive soliton velocity $`v_k>0`$. This can be intuitively understood by the fact that a movement of the density minimum necessitates a transfer of matter in the opposite direction.

## 4 Bragg spectroscopy

Bragg diffraction has been used as a tool to manipulate Bose-Einstein condensates  in a number of experiments. It was used to evaluate the velocity distribution of a BEC within the magnetic trap and during time-of-flight experiments . It has also served as a beam-splitter in an interferometer , for interferometric studies of the phase evolution of BECs  and even as an outcoupling mechanism for an atom laser . In addition Bragg diffraction was employed as a tool for the realization of exciting experiments on non-linear effects in BECs  and their possible application to create entanglement . However, a complete review of the use of Bragg spectroscopy in experiments on BEC is beyond the scope of this paper.

Fig. 3 schematically shows the Bragg diffraction process used in the experiments described here (a more detailed explanation can be found in ). Two counterpropagating laser beams induce a two photon transition between two momentum states which differ by two photon momenta, $`2\mathrm{}k`$. Thus the atoms which have been in resonance with the Bragg-transition will be separated from the remaining atoms by $`\mathrm{\Delta }x=\frac{2\mathrm{}kt_{\mathrm{tof}}}{m}`$, where $`t_{\mathrm{tof}}`$ is the time-of-flight after the Bragg pulse. Since the resonance conditon depends on the initial velocity of the atom, a given difference frequency of the laser beams addresses a specific velocity class within the condensate. The width of this resonance corresponds to the Fourier transform of the applied laser pulse envelope. For 87Rb and counterpropagating laser beams the velocity dependence of the resonance condition is given by $`\frac{\mathrm{\Delta }v}{\delta /2\pi }0.39\frac{\mathrm{mm}/\mathrm{s}}{\mathrm{kHz}}`$.

Experiments employing Bragg diffraction on BEC can be divided in two general areas. By using short, intense pulses all velocity classes within a BEC can be accessed and transferred into a moving state. This process corresponds to a variable, coherent beamsplitter for matterwaves. On the other hand, long pulses are selective to the velocity in the BEC and distinct velocity classes can be addressed. This process is used to examine the flux underlying dark solitons in Bose-Einstein condensates. We show that it is also possible to extract spatially resolved information from these measurements, rather than only counting the outcoupled number of atoms.

The experimental sequence starts with the creation of a Bose-Einstein condensate in the magnetic trap followed by phase imprinting for the creation of the soliton (as discussed above). After phase imprinting the condensate evolves in the magnetic trap for a time $`t_{ev}`$ which is varied in order to observe the soliton excitation during formation and later propagation. The Bragg scattering takes place after switching off the magnetic trapping potential. For the experiments a free expansion time, $`t_{exp}=2`$ms, is used after release from the trap in order to reduce the atomic density before applying the Bragg pulse. Collisions between atoms in different Bragg orders are thus negligible. In order to suppress spontaneous processes the frequencies of the Bragg lasers are detuned from the transition $`|F=2|F^{}`$ by 6.8 GHz. The Bragg pulse is usually applied for a duration of $`t_{Bragg}=250\mu `$s, and a time-of-flight of $`t_{TOF}=13`$ms after the pulse is used before detection ($`t_{Bragg}=500\mu `$s and $`t_{TOF}=11`$ms for the BEC spectroscopy in Fig. 7).

## 5 Velocity selective spectroscopy

The velocity selective Bragg scattering process described above is a widely applicable tool to investigate the behaviour of Bose-Einstein condensates. In the following we first observe the formation process of dark solitons due to the phase imprinting method. This is achieved by monitoring the spatial velocity almost immediately after the phase has been imprinted. In a second set of experiments the soliton is observed after a longer evolution time, $`t_{ev}`$, in the magnetic trap, in order to investigate the associated matter flux.

### 5.1 Soliton formation

Fig. 4 shows absorption images of atomic clouds after the above Bragg spectroscopy scheme has been applied with $`t_{ev}=0.2`$ms and different resonance conditions. The upper image (i) was obtained for an off-resonant Bragg pulse and thus just corresponds to a time-of-flight image of the BEC after phase imprinting. Image (ii) shows the case of a Bragg pulse resonant with the resting atoms, which thus obtain a velocity, $`2\mathrm{}k`$, and appear to the right of their position in image (i) due to their horizontal movement during the time-of-flight period of $`13`$ms after phase imprinting. The moving atoms within the cloud are not resonant with the Bragg pulse and remain on the left. They correspond to the density wave and dark soliton. The velocity of these atoms can be determined to be negative, as expected, by scanning the Bragg frequency difference. The density distributions corresponding to Bragg scattering resonant with negative velocity atoms are shown in image (iii), with the resting atoms on the left and the moving atoms on the right.

The simulations show that the velocity field in the Bose-Einstein condensate after the short evolution time, $`t_{ev}=0.2`$ms corresponds almost exclusively to the velocity field induced by the phase imprinting pulse. Fig. 5 shows calculated density and phase distributions in the magnetic trap for various times after the phase imprinting pulse. At $`t_{ev}=0`$ there is no density change but only a phase gradient in the center of the condensate, which corresponds to a velocity field. The associated flow quickly leads to the formation of a density maximum, moving to the left and a density minimum moving to the right. These two start to separate after approximately $`t_{ev}=0.5`$ms with a subsequent dispersive spreading of the density maximum and a narrowing of the density minimum which leads to the dark soliton state. Note that the initial phase gradient is split between the density wave and the dark soliton since both are associated with some flow of matter.

The evolution of the wavefunction in Fig. 5 clearly shows that the mechanism of phase imprinting with finite resolution relies on the joint action of a phase shift and a local removal of atoms due to a momentum transfer. The momentum imparted on some parts of the wave function, assists in the later formation of a dark soliton due to the removal of density from the region of the soliton. The images in Fig. 4 confirm these numerical results. The imparted momentum can be explained classically by the finite width of the edge of the phase imprinting field, which produces a classical force due to the gradient of the light induced AC-Stark shift potential.

### 5.2 Flux associated with a dark soliton

At short evolution times the dark soliton is masked by other excitations induced by the phase imprinting pulse, but after a few ms it becomes apparent due to its self stabilization and slow propagation. An evolution time of $`t_{ev}=3.5`$ms is sufficient to fully seperate the soliton and the density wave as shown by the Bragg scattering experiments and the numerical simulation in Fig. 6.

From the numerical simulation one expects to find local negative velocity components around $`v0.5`$m/s at the positions of the density wave as well as of the dark soliton. The top right image shows nearly resting atoms scattered to the right, while two distinct lines of moving atoms remain on the left: the atoms associated with the dark soliton and the density wave. This scattering behaviour is inverted for a negative velocity Bragg resonance, now scattering the two lines to the right and leaving the resting atoms on the left. No atom is effected by a Bragg pulse resonant with larger negative velocities in the bottom image, showing the limited range of the velocity field in the matter wave. This is clear evidence of the matter wave flux associated with a moving dark soliton.

## 6 Mapping the velocity field

In addition to the above examples of Bragg scattering for a few distinct resonance velocities, which clearly show the signature of dark soliton excitations, we use this method to fully map the underlying velocity field.

We first explain and verify the scheme by mapping the spatial velocity distribution of a pure Bose-Einstein condensate before applying it to a dark soliton excitation. The starting point is a systematic series of Bragg scattering data of a Bose-Einstein condensate after 2 ms of time of flight, as shown in Fig. 7. By taking a vertical cut through the data sets in the region of the scattered peak one obtains the amount of scattered atoms at a fixed position as a function of Bragg detuning. The maximum of this distribution then directly leads to the mean velocity of the atoms scattered to this position. Their original position in the condensate is then retrieved by accounting for their time-of-flight displacement due to the imparted momentum and their original velocity. Repeating this procedure for the position range of the scattered peak this procedure directly gives the velocity field of the condensate wavefunction. In addition to analyzing the scattered peak, we cross check the velocity field data by generating the same data from the inverse behaviour of the non-scattered cloud.

Fig. 8 shows the extracted velocity as a function of position in the Bose condensate. The result is fitted with a linear velocity distribution according to the expected behaviour in the Thomas-Fermi limit. The good agreement confirms the validity of this analysis.

By applying the above method to the dark soliton excitation discussed in section 5.2 we find the underlying velocity field as shown in Fig. 9.

The comparison of the experimental data to the theoretical curve shows good agreement within the finite experimental resolution, which demonstrates the applicability of position resolved Bragg spectroscopy to the investigation of excitations in Bose-Einstein condensates.

## 7 Conclusions

In conclusion we have investigated the matter wave dynamics due to phase imprinting and the matter wave flux underlying a moving dark soliton. Both experiments and theoretical predictions clearly show that the dark soliton movement is associated with a particle flux in the opposite direction. It was demonstrated that Bragg diffraction methods can be used to analyse the spatial phase and the density distribution of dark soliton states in Bose-Einstein condensates.

Future improvements of the tool of the position resolved Bragg spectroscopy technique rely on the use of longer pulses and higher resolution in the detection system. This should allow for precision measurements on many kinds of excitations in Bose-Einstein condensates. In this respect the investigation of the interplay between the imprinted phase and the associated imparted momentum promises important advances in the creation and study of excitations in Bose-Einstein condensates.

We gratefully acknowledge Anna Sanpera for help with the numerical simulations and thank the DFG for support in the Sonderforschungsbereich 407 as well as the European Union for support in the RTN network ”Preparation and application of quantum-degenerate cold atomic/molecular gases” contract no: HPRN-CT-2000-00125.