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# Evidence for a relativistic iron line in GRS 1915+105

## 1 Introduction

### 1.1 Iron line diagnostics of relativistic accretion discs

Black Hole (BH) accreting systems are expected to exhibit spectral features whose form is determined by reprocessing of primary high-energy photons by gas swirling around the central body. Resulting spectral distortions are of utmost importance because they probe the effects of strong gravity, which are otherwise difficult to reveal. General-relativity (GR) calculations of predicted spectra, and their comparison with observational data, may help to measure physical parameters of BHs, such as their masses and angular momenta (e.g. Martocchia 2000, and references therein).

The iron K$`\alpha `$ fluorescent emission is specially important as a diagnostic of GR effects (e.g. Fabian et al. 1989; Laor 1991; Matt et al. 1992; Martocchia & Matt 1996; Martocchia et al. 2000). In case it is originated in the innermost regions of an accretion disc, it gives the possibility, in principle, of distinguishing between a rotating (Kerr) and a static (Schwarzschild) central BH. This is because the resulting line profile is affected both by Special Relativity (Doppler, including transverse, shifts) and General Relativity (energy shift, lensing) effects. It is very broad and asymmetric, the exact shape critically depending on the geometrical parameters of the emitting region (disc inner and outer radii, inclination angle). For the same set of parameters, differences between Schwarzschild and extreme Kerr line profiles are rather subtle. However, the innermost stable orbits of the disc are different in the two cases - corresponding respectively to 6 and 1.23 gravitational radii - and the profiles are very different for the two values. The measurement of an innermost emitting radius less than 6$`r_\mathrm{g}`$ can therefore be the signature of a spinning BH.

This diagnostic has been successfully used in the case of Seyfert galaxies (e.g. Tanaka et al., 1995, Wilms et al., 2001), while in galactic BH candidates ionization of the inner accretion flow generally prevents fluorescent emission from being effective. Nevertheless, intense, broad Fe K$`\alpha `$ emission has been observed in Cyg X-1 with both BeppoSAX (Frontera et al., 2001) and Chandra (Miller et al., 2002a). Large, possibly relativistic K$`\alpha `$ profiles have been detected also in XTE J1748-288 (Miller et al., 2001) and XTE J1650-500 (Miller et al., 2002b).

### 1.2 GRS 1915+105

GRS 1915+105 is one of the so-called microquasars, Galactic jet sources with properties similar to those of quasars, but on a smaller, stellar scale. It was extensively studied since its discovery by the WATCH experiment on GRANAT in 1992 (Castro-Tirado et al. 1992). Due to very large interstellar absorption, the optical counterpart of this source was not easily found: only recently, Greiner et al. (2001a) reported results of a spectroscopic analysis in the H and K bands, which suggest that the mass-donating star is a K-M III star, i.e. that GRS 1915+105 belongs to the class of low-mass X-ray binaries.

Greiner et al. (2001b) used these infrared spectroscopic observations to infer the companion’s orbital period - which is $`33.5`$ days - and determine the mass function $`f(M_\mathrm{c})9.5M_{}`$. Since the donor’s mass, for K-M III stars of that kind, is known to be $`1.2M_{}`$, and the inclination is known, too, the mass of the central compact object has been constrained to $`M_\mathrm{c}=14\pm 4M_{}`$, i.e. well above the standard neutron star mass limit.

Weak variable radio/IR emission connected with jets has been often detected (Mirabel & Rodriguez 1994). Measurements of the jets’ superluminal motion allowed to estimate the source distance $`D12.5`$ kpc and inclination $`i70^\mathrm{o}`$ (Rodriguez & Mirabel, 1999; Fender et al., 1999).

GRS 1915+105 is well-known for the extremely wide variety of its variability modes, ranging over all possible bands and timescales (e.g. Markwardt et al. 1999, Belloni et al. 1997a,b; Greiner et al. 1996). Time-resolved observations have been intensively performed especially with the Rossi X-ray Timing Explorer (RXTE) satellite mission. Belloni et al. (2000), for instance, managed to classify these observations into 12 separate classes based on count rate and color characteristics. In this way, the source variability could be explained in terms of transitions between three basic states: two soft states with a fully observable disc at two different temperatures (“A” with the lower temperature, “B” with the higher), and a hard state corresponding to the non-observability of the innermost parts of the accretion disc (state “C”). State “C”, with low flux and hard color, can last uninterruptedly for weeks or even months. The most popular model for the source’s large scale variability is the one proposed by Belloni et al. (1997a,b), who invoked the onset of a Lightman-Eardley thermal-viscous instability which blows-off the innermost, radiation-pressure supported part of the (optically thick) disc. The hard state (C) would then correspond to a steady replenishment, which takes place on a viscous timescale. Indeed, evidence of the temporary disappearance and subsequent restoring of the inner portion of the accretion disc comes from simultaneous BeppoSAX and Ryle radiotelescope observations (Feroci et al., 1999).

The iron K$`\alpha `$ emission line in GRS 1915+105 is usually not very intense, and is therefore difficult to study in detail - not to mention the dramatic spectral variability of the source, which requires selecting short time intervals, so reducing the statistical quality of the spectra. Lee et al. (2001) recently reported that neutral Fe K$`\alpha `$ emission is likely present in the high-resolution data of a low-hard state, collected with Chandra HETGS, together with Fe photoelectric edges and absorption lines due to highly ionized matter. These features indicate that ionized iron, probably belonging to the accretion disc itself, is present on the line of sight with abundance larger than solar.

Actually, during the several observational campaigns performed by BeppoSAX, the Fe K$`\alpha `$ line was almost invariably rather weak, with Equivalent Widths (EW) of a few tens of eV at most. Only in the observation of April 19, 1998, the line was strong enough (EW$`\stackrel{>}{}200`$ eV; cp. Fig. 3) for a detailed analysis of its profile to be performed. We have therefore analyzed the spectral data from this observation, further selecting some intervals of relative calmness in the lightcurve (see Fig. 1), to limit the spectral variability as much as possible. In order to model the source emission, we adopted the illumination model, local spectra and emissivities described in Martocchia, Matt & Karas (2001) and Martocchia, Karas & Matt (2000; see also: Martocchia 2000). Finally, we used our own fitting tool, dedicated to GR spectral distortions in Kerr metric, to analyze the data. The tool, named kerrspec, is described in the Appendix.

## 2 Data reduction

BeppoSAX (Boella et al 1997) is composed by several instruments. Here we made use of the two imaging instruments, the LECS and the MECS, and the high energy, passively collimated instrument, the PDS. As customary, we have used the following energy bands: 0.1-4 keV for the LECS; 1.8-10 keV for the MECS; 15-150 keV for the PDS (neglecting higher energy data because of insufficient statistics due to the short integration times). The LECS and MECS spectra have been selected from regions of 8’ radius and centered on the source. The background has been evaluated from similar regions in blank field observations, and then subtracted. The PDS is composed by four units, two of which (switching every 96 s) monitoring the background, which is automatically subtracted in the pipeline producing the spectrum.

We discuss here the BeppoSAX observation of GRS 1915+105 started on April 19, 1998 at 11:33:19 UT and ended on April 20, 1998 at 20:14:52 UT. Among the several BeppoSAX campaigns on GRS 1915+105, we selected this one because the iron line EW was significantly larger than in all other observations.

Out of the entire $`120`$ ks observation, some time intervals were sorted out where the source variability is less pronounced. These are the six satellite orbits starting from 3$`\times `$104 s after the beginning of the observation, see Fig. 1. Analysis of the other parts of the observation would require a finer temporal analysis which is beyond the scope of this paper and is deferred to a future work.

All spectral fits were performed with the xspec v.11 software package. In the following, all errors refer to 90% confidence level for one interesting parameter ($`\mathrm{\Delta }\chi ^2`$=2.71)

At the flux level of GRS 1915+105, it is very likely that systematic errors cannot be neglected with respect to the statistical ones. This may explain the rather large values of the $`\chi ^2`$ reported below.

## 3 Data analysis and results

### 3.1 The best-fit model in a selected time interval

Let us first discuss the fifth interval as an example, being the one in which a low value of $`\chi ^2`$ was found when fitting with simple models. The model for the continuum includes the usual ingredients for this source: a disc thermal emission (diskbb), a powerlaw with exponential cutoff, and a Compton Reflection component (pexrav: Magdziarz & Zdziarski 1995), which is expected to always accompany the iron emission line. All these components are seen through interstellar absorption. The best-fit spectrum and $`\mathrm{\Delta }\chi ^2`$ for the fifth interval, fitting without any iron line, is shown in Fig. 2, left panel ($`\chi _{\mathrm{red}}^2=2.64`$). The presence of an iron line is obvious. To better show the profile of the line, we also fitted the spectrum excluding the energy region which contains this feature (3-7.5 keV), and then reintroduced this energy interval. The residuals are shown in Fig. 3 (fifth panel), after reinserting the data of the 3-7.5 keV interval. The presence of a prominent, broad and red-tailed iron line is clear.

We first tried to model the line with a gaussian. The best–fit is obtained with a rest energy $`E_0=6.38\pm 0.12`$ keV, $`\sigma =0.70\pm 0.15`$ keV and EW$`250`$ eV; the $`\chi _{\mathrm{red}}^2`$ is then 1.48 (see Fig. 2, central panel). The most natural interpretation for a so broad line is emission from a relativistic accretion disc (Fabian et al., 1989), an hypothesis further supported by the asymmetry of the profile (see Fig. 3). The next step was therefore to substitute the gaussian with the relativistic model kerrspec, described in the Appendix. To be self–consistent, we also applied the relativistic corrections to the reflection continuum (using kerrspec) as well as to the disc thermal component (using diskpn, Gierlinski et al. 1999). After having verified, however, that the results are insensitive to the latter corrections, in order to save computer time we adopted the simple, non relativistic models for the continuum in all the following fits. The inclination angle has been always fixed to 70 (Mirabel & Rodriguez 1994), while the inner and outer disc radii were kept free to vary. We tried different emissivity laws, and found the best solution with a rather “flat” dependence on radius ($`r^2`$). With the relativistic line model ($`E_0=6.4`$ keV) the fit is better than with a gaussian: $`\chi _{\mathrm{red}}^2=1.31`$. The spectrum and residuals are shown in Fig. 2, right panel. If $`E_0`$ is instead fixed to 6.7 keV, corresponding to He–like iron, the fit is significantly worse ($`\chi _{\mathrm{red}}^2>>2`$).

We also tried adding a narrow gaussian centered either at $`6.4`$ or at $`6.7`$ keV; no significant improvements in the fits were found.

One problem with the above fits is that the resulting parameters of the thermal emission are rather unplausible. The temperature is very large, $`kT=3.77_{0.43}^{+0.44}`$ keV, and the component’s normalization very low ($`0.41\pm 0.22`$; see Arnaud 1996 for the meaning of this normalization), implying a value of the inner radius of the order of one kilometer. This, in turn, implies an upper limit to the BH mass (obtained assuming the inner emitting radius conciding with the innermost stable orbit for a maximally rotating BH) of less than 1 solar mass, contrary to observations (Greiner et al., 2001b). If the disc blackbody component is neglected in the model, the fit e.g. with the gaussian line yields a worst fit $`\chi _{\mathrm{red}}^2=1.61`$, but the results on the line parameters does not change significantly. Moreover, the fit with a relativistic line is still better than with a gaussian also in this case.

We therefore conclude that the relativistic solution for the iron line, besides being the most natural physical explanation for the very broad line observed, does not depend on the details of the continuum model.

The small relative luminosity of the disc thermal component (if present at all) brings us to interpret the source’s state as a ‘C’-type, in the scheme of Belloni et al. (2000). This interpretation is in agreement with the occurrence of a “plateau” in the light curve (lower flux and variability), although a hard spectrum would be expected, while instead we get a steep powerlaw, and a cutoff at rather low energies (see Table 1.).

### 3.2 Other time intervals

For all other time intervals we found qualitatively similar results: a broad and prominent iron line, which is better fitted by a relativistic line profile than by a gaussian, and a faint disc blackbody component.

An inspection of the residuals often indicates problems both around 1 keV, and above 50 keV. The latter problem may be due to a non–thermal component arising when the Comptonized power law cuts–off, while we have no obvious explanation for the former problem. To overcome these difficulties, and because we are interested here to the iron line properties, we decided from now on to exclude the LECS data in the fits, and to use the PDS up to 50 keV only. With this prescriptions, and assuming as working hypothesis that the iron line arises from a relativistic disc, we analysed all the time intervals with a model which neglects disc thermal emission and includes, besides the line, a power law with exponential cut–off and a Compton reflection continuum. We stress again that the latter component is included more on astrophysical ground (it is supposed to always go along with the iron line) rather than because strongly required by the data. After having verified that the values of the absorbing column densities $`n_\mathrm{H}`$ for the various intervals are all consistent with each another and to the value of 5.4$`\times 10^{22}`$ cm-2, for simplicity we fixed in all fits $`n_\mathrm{H}`$ to this value.

The results for the various time intervals are summarized in Table 1. The larger value of the $`\chi _{\mathrm{red}}^2`$ of the fifth interval with respect to those described above is due to the lower number of spectral bins and to the exclusion of the thermal component. Given the abovementioned uncertainties on the proper modeling of the continuum, we stress that the values in the table should be taken with caution: a different continuum models may result in somewhat different values of the disc parameters. In any case, a general result seems to emerge: the inner radius of the line emitting region is larger than the innermost stable orbit. Whether this means that the innermost regions are absent, or simply that they do not emit the iron line (for instance because the matter is mildly ionized and resonant trapping effective, Matt et al. 1993) we cannot say.

Finally, we tried summing the spectra of all six time intervals together, and fitting with the same model. The very large reduced $`\chi ^2`$, 5.1, indicates that spectral variability is too large over these time scales. In particular, strong residuals at the iron line energies imply that the line parameters change with time, as suggested by the results of the time–dependent spectral analysis.

## 4 Discussion

A strong iron K$`\alpha `$ fluorescent line is present in the April 19, 1998, spectrum of the superluminal galactic source GRS 1915+105. The line is broad and skewed, clearly indicating emission from a relativistic accretion disc. We successfully fitted the line with a fully relativistic profile. To our knowledge, this is the first time that a relativistic iron line is observed in this source, largely due to the fact that we catched the line with an unusually large equivalent width.

While providing evidence that an accretion disc resides in the innermost part of this system, our result confirms that strong gravity is at work in distorting the iron line profile. From the best–fit parameters we conclude that the line is from neutral or low-ionization iron, and likely emitted from a region of the accretion disc which is close but probably does not include the innermost stable orbit, even for a static BH (but the values of the disc parameters are somewhat dependent on the adopted model for the continuum, and must be taken with caution). This may imply either that the disc does not extend down to this radius, or that the line is not emitted in the innermost regions, maybe because the iron there is in the intervals of ionizations in which resonant trapping efficiently destroys line emission (e.g. Matt et al. 1993; 1996). Unfortunately, at these radii differences in the line profile between Kerr and Schwarzschild metrics are too subtle to be detectable, and the question of the angular momentum of the BH - which, from this analysis, is not required to have a large value - actually remains open.

So, no final statement about the spin of the BH in GRS 1915+105 can still be made. Zhang et al. (1997), on the basis of soft state X-ray brightness (which is most likely due to thermal emission), suggested that a fast rotating BH is hosted at the center of this source. Their conclusion was based on a mass value twice that measured by Greiner et al. (2001b). However, even accounting for the correct mass, the BH spin seems to be larger in GRS 1915+105 than in GRO J1655-40, and this does not fit to the results based on QPO diagnostics, as explained below. The accretion disc temperatures of the two sources are nearly identical, and the mass estimate for GRO J1655-40 is $`M7M_{}`$ (Orosz & Bailyn, 1997; Shahbaz et al., 1999). Taking Zhang et al.’s innermost thermally emitting orbit for GRS 1915+105 (at $`40`$ km, i.e. $`r_{\mathrm{ms}}2r_\mathrm{g}`$), one infers a BH spin $`a0.95`$ in this source (Bardeen et al., 1972). Actually, Zhang et al.’s estimates of the BH angular momentum are based on rather simplified models of the continuum, and they do not include GR spectral distortions and effects of radiation transfer through the disc atmosphere (e.g. Merloni et al., 2000; Gierliński et al., 1999 and 2001). In our data analysis, even accounting for GR effects on the thermal component, we got disc temperatures and luminosities which are physically unplausible, and do not allow us to test assumptions regarding either the BH mass nor its spin. Non-standard disc models (e.g. slim-disc) could actually reproduce high temperature discs for non-rotating BHs.

QPO diagnostics could therefore be useful as independent tests. Various models try to explain the occurrence of QPOs, suggesting that the oscillations correspond to the motion on the last stable orbit (Shapiro & Teukolsky, 1983), and sometimes invoking GR effects such as “frame dragging” and relativistic precession (e.g. Merloni et al., 1999; Stella et al., 1999). An interesting possibility is that the highest QPO frequency changes in connection with the variation of the disc innermost radius.

QPOs in GRS 1915+105 have been observed in a wide range of frequencies ($`0.001÷67`$ Hz, e.g. Morgan et al. 1997). In GRS 1915+105 the QPO highest frequency (67 Hz), unlike all the others, does not change much with time, and may therefore be related to the accretion disc innermost stable orbit $`r_{\mathrm{ms}}`$ (Morgan et al. 1997). A similar case is given by the 300 Hz QPO in GRO J1655-40.

Recently, a second high-frequency QPO has been detected in GRS 1915+105 (Strohmayer 2001), with $`\nu _040`$ Hz. In terms of the frame-dragging model, this lower frequency peak could be associated to the radial epicyclic frequency $`\nu _{\mathrm{rad}}`$ through the formula $`\nu _0=\nu _{\mathrm{Kep}}\nu _{\mathrm{rad}}`$ (the nodal precession can be connected to a further low-frequency peak, already detected at $`0.9`$ Hz by Morgan et al., 1997). Strohmayer also reports that the 67 Hz QPO did in fact drift in frequency by as much as 5 percent. If this frequency is associated with the Keplerian motion at the last stable orbit, then - assuming the BH spin is the same in GRS 1915+105 and GRO J1655-40 - it should scale with $`M_\mathrm{c}^1`$. Thus, a factor $`2÷3`$ of discrepancy would remain with respect to Greiner et al.’s estimate. This indicates that the BH spin in the two sources is different. If the QPOs in GRS 1915+105 and GRO J1655-40 are seen in the framework of the frame dragging scheme (e.g. Cui et al., 1998, for details on the model), and using Greiner et al.’s mass estimate, we have $`a0.8`$ and 0.95 for the two sources, respectively. On the other hand, if the QPO frequency had a diskoseismic origin (e.g. Nowak et al., 1997), the model would require a maximally spinning BH in GRO J1655-40, and an almost static BH in GRS 1915+105 (cp. Greiner et al., 2001b, and references therein).

Clearly, further tests for the BH spin would be of extreme importance. Iron line diagnostics may be crucial to solve the puzzle: better resolution and sensitivity spectral data, provided by satellites of the new (e.g. XMM-Newton) and future (e.g. Constellation-X, XEUS) generations, will be probably decisive in this respect.

###### Acknowledgements.

AM and GM acknowledge financial support from MURST under grant cofin-00-02-36, GM also from ASI, VK from GAUK 188/2001 and GACR 202/02/0735. TB thanks the Cariplo Foundation for financial support.

## Appendix: The computational technique

We have computed GR effects acting on both the iron K$`\alpha `$ line emission and the Compton reflection continuum. We adopt the usual assumption of a geometrically thin, optically thick, cold (with respect to X-rays reprocessing) reflector extending over the equatorial plane. We take into account the directional anisotropy of the illuminating flux, caused by aberration, Doppler effect and light focusing. GR anisotropy of the illuminating flux is crucial to distinguish static from spinning BHs, because the primary illumination, as well as the induced emissivity of the reflection component, carry information about the spacetime in the very vicinity of the BH. The iron line profile and, in particular, its intensity and EW are affected by spacetime distortions (Martocchia & Matt, 1996; Martocchia et al., 2000).

The observed line profiles are often obtained from the data by subtracting the Compton-reflected component without taking into account important relativistic effects, such as the iron edge smearing, which may be relevant if the emission occurs down to the innermost stable orbit, in particular for spinning BH. In our computations (e.g. Martocchia et al., 2000), besides using emissivity laws derived from a proper GR treatment of the illuminating flux, we treated at the same time the GR distortions on the iron line together with the underlying continuum hump (Martocchia et al., 2000; Martocchia et al., 2001).

In order to fit real spectra, a ray-tracing code was developed in the form of a user-defined subroutine, kerrspec (Martocchia 2000), which has been linked to the xspec data analysis package (Arnaud 1996). In the adopted scheme, a large set of light rays (null geodesics) in the Kerr BH spacetime is pre-calculated and stored. This allows an efficient access during the fitting loop. The code allows the radial, angular and energy dependencies of the local emissivity to be specified on input in a tabular or semi-analytical form. After fixing the desired grid resolution in the image plane, the required light rays corresponding to all image pixels are retrieved.

The original approach (Karas et al. 1992) was refined in order to improve the resolution around the inner edge of the disc, very near to the BH horizon, and to ensure better confidence in the region where strong focusing occurs. This turned out to be necessary because the computed line profiles are very sensitive to the radius of the innermost emitting orbit, especially if the emissivity varies rapidly with radius. We recall that the innermost emission area is usually identified with a ring located at the marginally stable orbit, $`r_1r_{\mathrm{ms}}`$, the value of which depending on the BH angular momentum.

The local emissivity law, $`F(r)`$, must be specified before running the code. Different choices are available: a power-law dependence $`F_q(r)r^q`$; a “standard” Novikov-Thorne-Page model (Novikov et al. 1974); or the effect of illumination from a central source (Martocchia & Matt 1996). In the latter case, $`h`$ (the primary source height) is a phenomenological parameter which determines the form of the local emissivity law: small $`h`$ corresponds to enhanced concentration of primary X-rays near the horizon, resulting in substantial anisotropy of the reflected component. The local emissivity has an angular dependence, too, including possibly a limb-darkening law. This may be expressed either by the functional forms for fluorescent and Compton-reflected emission given by Ghisellini et al. (1994), or, alternatively, by the numerically-derived tables from the Montecarlo computations by Matt et al. (1991), which yielded the whole spectra of the reflected component.

The local profiles of the emissivity were interpolated by polynomials to save time machine (cp. Martocchia 2000, Martocchia et al., 2001). These emissivity laws are valid between the inner disc edge (assumed to be equal to or greater than the innermost stable orbit) and the outer edge. Because the emission tends to be concentrated in the central parts of the disc, the inner emitting radius is usually better constrained in the fits than the outer radius.

Typically, the code may take up to a few hours, on a common DECalpha workstation, to fit a spectrum using curved geodesics in the very vicinity of the BH, i.e. accounting for radiation emitted at distances of the order of $`r_\mathrm{g}`$ from the event horizon.


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# REFERENCES

Geometry of compact tubes and protein structures

Jayanth R. Banavar†,∗, Alessandro Flammini, Davide Marenduzzo, Amos Maritan‡,∗ & Antonio Trovato§

Department of Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

International School for Advanced Studies (S.I.S.S.A.), Via Beirut 2-4, 34014 Trieste, INFM and the Abdus Salam International Center for Theoretical Physics, Trieste, Italy

§ Niels Bohr Institutet, Blegdamsvej 17, 2100 København Ø, Denmark

* To whom correspondence should be addressed (E-mail: banavar@psu.edu and maritan@sissa.it).

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction – the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.

A revolution  in the understanding of biomolecular structure took place about 50 years ago using the precise geometrical relationships among the atoms and molecules and the rigorous application of the new structural principles enunciated by Linus Pauling . Earlier, in 1939, J. D. Bernal  had noted that the symmetry of protein crystals is much higher than would be expected statistically from compounds of such great complexity. This would seem to indicate that each molecule is built of subunits, themselves unsymmetrical but arranged in a symmetrical way. The protein folding problem, the determination of the structure of the folded state of a protein from knowledge of the sequence of amino acids, has remained unsolved despite a large amount of experimental information on protein structures, the availability of powerful computers and detailed knowledge of the building blocks of proteins and their chemistry. The approach pioneered by Pauling is exceedingly effective for understanding small scale structures in great detail but becomes harder to apply at the scale of full protein structure. The complexity arises from the 20 types of naturally occurring amino acids and the solvent and their mutual interactions.

An independent approach to the study of such complex problems consists of stepping back and adopting a coarse-grained view which incorporates just the most essential elements which capture the important emergent features. For example, given a specific chemical compound, one may use the principles of quantum mechanics and chemistry to determine its crystalline structure. Alternatively, in a coarse-grained sense, one may deduce the existence of several types of crystalline structure based on general symmetry and packing considerations. In this case, the specific chemistry of a material would dictate which one of these candidate structures the material would adopt. A common example is the face-centered-cubic (fcc) arrangement adopted both by common salt with strong electrostatic interactions and hard spheres (oranges packed by a grocer) in order to achieve the most efficient packing.

In order to attack a problem of the magnitude of the structure of complex biomolecules, we suggest that it is necessary to consider both points of view. Even assuming that computational power in the future reaches a point which allows a brute force solution incorporating all details, one might be able to mimic Nature but not necessarily understand her. On adapting a statement by Pauling  (we have added three words of our own), the problem has been examined, in the main, from one point of view only – not the wrong point of view, but one which, unaided, gives a vista insufficient to reveal the simplicity underlying the true complex nature.

The power of the coarse-grained approach is illustrated by considering some of the familiar states of matter. The gas, liquid and solid phases can be understood in terms of atoms and their interactions modelled as hard spheres (there is no distinction between the gas and liquid phases in the absence of any attractive interaction) or Lennard-Jones systems. On varying the nature of interactions and thermodynamic quantities such as temperature and/or pressure, it is possible to obtain these states of matter, which arise from the collective, emergent behavior of a large number of atoms. Glassy behavior ensues when the crystallization is thwarted by dynamical constraints. Entirely new classes of behavior are found on considering anisotropic molecules as in liquid crystals  – the breaking of the symmetry of the building blocks introduces qualitatively new features.

The molecules of life are chain molecules, polymers, which introduce the feature of connectivity along the chain. Indeed, this feature has been exploited by Nature in the DNA molecule to code for genes. Detailed studies of polymers have revealed several phases including a swollen phase (analogous to the gas phase) corresponding to self-avoiding conformations, a highly degenerate compact phase in which different monomers of a chain have an effective attraction to form a dense globule and semi-crystalline phases .

Proteins are an important class of chain biomolecules made up of amino acids. These molecules fold into a somewhat compact state with the folded structures controlling their functionality. The folding is driven by hydrophobic interactions or the tendency of certain amino acids to avoid water. The structures of folded proteins do not correspond to the generic compact phase of a polymer. First, the total number of protein folds is only a few thousand  instead of the innumerable compact conformations of a generic chain of the same length and second, the building blocks of biomolecular structure are pretty motifs including helices and sheets. Indeed, generic compact conformations are neither suitable for encoding specificity nor are they dynamically accessible in a simple manner. Furthermore, proteins, while stable and able to fold rapidly and reproducibly to their native state structures , are sensitive to the right types of perturbations and are consequently able to perform a dizzying array of functions. Here, we shall argue that this phase adopted by molecules embodying life is a new one distinct from the well-studied polymeric phases.

Let us begin with a set of unconstrained hard spheres with an attraction of a given range. When the attraction has a range smaller than the diameter of the hard sphere, it is ineffective and the ground state is a gas. On increasing the range to a value equal to the hard sphere diameter, the ground state changes from a gas to a fcc crystal – each hard sphere is surrounded by the maximum possible number of other hard spheres. Consider now a polymer chain made up of hard spheres tethered together. When the attraction between the hard spheres is sufficiently short range, the analog of the gas phase is a swollen phase corresponding to self-avoiding conformations of the chain. On turning on the attraction by increasing its range, there is a change in the ground state structure. One now gets a fcc lattice but this time with the tethers running through the hard spheres. There are a huge number of ways of doing this and so the ground state is highly degenerate. Of course, a plethora of other compact states would be obtained if this crystallized state is dynamically inaccessible due to the tethering or other constraints. Such compact states are not good candidates for structures of proteins because there are too many of them and accessing a specific structure is next to impossible. Of course, constraints on the local curvature of the chain could lead to other structures, such as lamellar semi-crystalline phases , at low temperatures.

The model of spheres tethered together to form a chain does capture the notion of connectivity of a chain but it leaves out a second key factor, the inherent anisotropy associated with the local directionality of the chain. In other words, for a given sphere, the adjacent spheres along the chain define a local direction adopted by the chain. This anisotropy is most easily captured by replacing the sphere by an object with axial symmetry, the simplest example of which is a coin or a circular disc. Indeed, an object made up of tethered coins of identical size resembles a tube of uniform thickness such as a garden hose. Such a tube like geometry is a coarse-grained representation of the well-known steric effects  of the basic constituents of proteins. One may then ask what the analog of the fcc crystal phase is for such a tube.

There are two physical consequences of the tube picture. First, there is a local curvature constraint that does not permit radii of curvature smaller than the tube thickness. This feature may equally well be captured for the case of spheres tethered together by an explicit bond-bending energy term. The second consequence, which is unique to the tube description, is the inherent anisotropy which is reflected in the dependence of the potential energy of interaction between two spatially nearby segments of the tube, not only on their distance from each other but also on their mutual orientation (Figure 1). This change in the symmetry of isotropic interactions between spheres (that is conventionally considered in the well-studied polymer case) to the cylindrical symmetry associated with the tube leads to qualitative changes in the nature of the ground state conformations. At high temperatures, for a tube, one expects a swollen phase in which the local directions defining the tube are distributed isotropically. At sufficiently low temperatures, there is a spontaneous symmetry breaking leading to the selection of a preferred tube direction. This transition is analogous to the isotropic-nematic transition in liquid crystals  for tubes. For tube segments, which are thin compared to the range of the attractive interaction and which are near each other, there is a larger flexibility in their relative orientation (see Figure 1). Thus, in this case, a dense globule phase with no significant orientational ordering is expected at intermediate temperatures between the swollen and the orientationally ordered phases.

We now turn to the ground state structures of a simpler situation, one exploited by Nature in proteins, of a short tube when the forces promoting its compaction just set in. Indeed the interaction range and the tube size are matched for proteins because, on the one hand, the effective interactions in the presence of the solvent are short range and the squeezing out of water is facilitated by the outer atoms of nearby side chains coming together and, on the other, it is these same side chains that determine the effective thickness of the tube. Detailed analytic and numerical calculations show that one obtains far fewer conformations than the corresponding generic polymer chain or a thin tube (allowing a protein only relatively few selection choices for its native state conformation) because the different parts of the tube have to position themselves just right relative to each other in order to respect the inherent anisotropy and yet avail of the effective attraction (Figure 1).

Consider the effect of tuning the thickness of the short tube for a given range of attraction. When the tube thickness is bigger than the range of attraction, one obtains a swollen phase because the attraction is ineffective. The other extreme is when the tube thickness is very small compared to this range. In this limit, the greater degrees of freedom for the relative positioning of nearby tube segments due to the longer range of attraction leads to many degenerate conformations.

On varying the tube thickness, near the point when the attractive forces have just set in, as described below, different segments of the tube have to position themselves just right with respect to each other in order to avail of this attraction. This has two important consequences: first, the tube compaction leads to the formation of a hydrophobic core in the interior of the folded structure and, second, this careful relative positioning of the tube segments combined with the anisotropy associated with the tube weeds out all but a few from the list of possible candidate structures for ground state conformations. These conformations may be thought of as being marginally compact and are thus attractive candidates for versatility and flexibility, because they are able to respond to small changes in an effective manner. Furthermore, on lowering the temperature, starting from the swollen phase, one would expect an almost immediate ordering at a relatively low temperature (with respect to a thinner tube) into one of the ground state conformations without any partially folded intermediates. This “two-state” character is an important feature of small globular proteins and arises in the tube context because the scale of the interaction energy goes down as the tube becomes thicker, entropic effects are less important at the low temperatures of ordering and the orientational effects become stronger (see Figure 1).

We show below that the building blocks of these structures are the familiar helix, hairpins and sheets. Furthermore, elementary considerations predict the geometry of an ideal helix, which is very close to that observed in Nature, and the zig-zag appearance of the strands.

We have carried out computer simulations and analytic calculations of short tubes in the marginally compact phase. The resulting structures are shown in Fig. 2. Helices and hairpins (sheets) are of course the well-known building blocks of protein structures  (see Fig. 2 (A1) and (D1) for two examples from a protein and (A2), (D2) and (D3) for the tube structures in our simulations). In addition to the prediction of these motifs in our calculations, it is interesting to note that some of the other marginally compact conformations bear a qualitative resemblance to secondary folds in biopolymers. Helices analogous to Fig. 2 (A3) with an irregular contact map occur, e.g., in the HMG protein NHP6a  with pdb code 1CG7. Fig. 2 (C1) shows the “kissing hairpins”  of RNA (pdb code 1KIS), each of which is a distorted and twisted hairpin structure while Fig. 2 (C2) is the corresponding tube conformation. Fig. 2 (B1) shows a helix of strands found experimentally in Zinc metalloprotease  (pdb code: 1KAP), whereas Fig. 2 (B2) is the corresponding marginally compact conformation obtained in our calculations.

It is possible to understand the results shown in Fig. 2 by means of simple arguments. Let us begin by taking a piece of tube of radius $`R_0`$ and length equal to $`2\pi R_0`$. Gonzalez and Maddocks  have shown that a simple description of a tube is obtained by taking all triplets of points along the axis of the tube and measuring the radii of the circles passing through them with a view of ensuring that none of these radii is smaller than the thickness. In particular, the local radius of curvature of a tube can never be smaller than its thickness. By placing the tube in the form of a donut of radius $`R_0`$, one can effectively fill all the space in the middle of the donut. When the tube is longer than $`2\pi R_0`$, the most efficient means of compactifying it is to place it in a helical conformation with local radius of curvature equal to $`R_0`$ and with the pitch chosen so that the segments of the tube in successive turns lie on top of each other. This is, of course, a valid structure only when the range of attractive interactions allows contacts to be made in this geometry. This ideal space-filling helix has a special pitch to radius ratio (see Fig. 2 (A2)), which is observed not only in $`\alpha `$-helices in globular proteins but also in the helices of collagen . An effective squeezing out of the space between the successive turns of the helix is accomplished by the fact that the orientations of the interacting segments of the tube are parallel to each other. Were this not to be the case, the inherent anisotropy of the tube (imagine a tube made up of discrete coins) would lead to a mismatch, a factor of no consequence in a chain made up of tethered hard spheres. One may show analytically that, on increasing the tube thickness, helices are excluded from being the ground states, when the tube thickness exceeds $`R_0^{max,hel}\left(\sqrt{1+R_1^2}\right)/20.943`$ ($`R_1`$ is the range of the attractive interaction and is chosen to be 1.6 units in Fig. 2 – all lengths in the simulation are measured in units of the distance between successive $`C_\alpha `$ atoms) which is obtained when two parallel straight lines (successive turns of the helix treated as circles with infinite radius) are at a distance of $`R_1`$ from each other. Indeed this structure is one that corresponds to a hairpin.

The zig-zag hairpin of Fig. 2 (D2) is a distorted version of this idealized case due to the discreteness of the protein chain. One can use elementary geometrical considerations to prove that the zig-zag nature accommodates a tube of larger thickness compared to straight segments. For two zig-zag antiparallel strands facing each other, one can show analytically that the maximum thickness is obtained (leaving aside the edge effect of how the strands are connected together in a hairpin) when one has a space-filling conformation. Indeed, this condition leads to the following relationship between the tube thickness $`R_0`$ and the interaction range $`R_1`$

$$R_1^2+2+\frac{R_1}{R_0}4R_0^2=0,$$

which yields a value of $`R_01.2124`$, when $`R_1=1.6`$, in perfect accord with our simulations.

For intermediate tube thicknesses between those corresponding to a helix or a hairpin, we find only a few other structures that may be thought of as interpolating between the two limiting cases. In order of decreasing thickness, one obtains first the kissing hairpin structure (Fig. 2 (C2)), which is a hairpin twisted into three dimensions – a feature allowed for by the slightly smaller thickness compared to the planar hairpin; a helix made up of strands (Fig. 2 (B2)); and irregular, somewhat non-ideal helices (Fig. 1 (A3)). In all cases, nearby parts of the tube are oriented parallel to each other.

It is interesting to consider the ground state of many long tubes subject to compaction. Packing considerations suggest that the tubes become essentially straight and parallel to each other and are arranged (when viewed end on) in a triangular lattice, analogous to the Abrikosov flux lattice phase in superconductors . Returning to the case of a single tube, in the very long length limit, a similar phase would be expected with the additional constraint of the bending of the tube segments at the ends. As stated before, for a discrete chain, a planar placement of zig-zag strands is able to accommodate the largest thickness tube that can yet avail of the attraction – however, the thickness for this limiting case is too large to produce the three dimensional ordering alluded to above. It would be interesting to consider how the ground state structure crosses over from the “flux-lattice” type phase to the familiar planar phase. Indeed, for thick tubes of moderate length, one may expect to form a large sheet-like structure analogous to the cross-$`\beta `$-scaffold observed as a building block of amyloid fibrils . Such fibrils have been implicated in a variety of human disorders including Alzheimer’s disease and spongiform encephalopathies such as Creutzfeldt-Jakob disease. Remarkably, recent findings suggest that the ability of proteins to form amyloid is a generic property of polypeptide chains .

Many strategies for attacking the protein folding problem have been put forward which employ a coarse-grained description . None of the currently used methods has been successful. Our results suggest that a deficiency of all these methods has been that the context provided by the local tube orientation is neglected while considering the interaction between coarse-grained units. The novel phase discussed here arises from the addition of anisotropy to the well-studied polymer problem just as one obtains rich liquid crystal behavior on studying anisotropic molecules. A mapping of the phase behavior of tubes on varying the nature of interactions, the thickness of the tube, the length of the tube and temperature might yield additional surprises.

In 1939, J. D. Bernal  wrote: Any effective picture of protein structure must provide at the same time for the common character of all proteins as exemplified by their many chemical and physical similarities, and for the highly specific nature of each protein type. Our results provide a simple framework for the common character of all proteins. Our analysis is based on just three ingredients – all proteins share a backbone, there are effective forces which promote the folding of a protein and the one and only new idea that a protein can be viewed as a tube (see Fig. 3). We have not introduced any input into our analysis which pertains to the highly specific nature of each protein type  as encoded by the amino acid sequence. It would be interesting to extend our calculations to a tube of non-uniform thickness. For example, the presence of a small amino acid like glycine at backward bends allows for tight turns to be formed to facilitate good packing and lead to low values of local thickness. Also, the wide variety of amino acid properties such as hydrophobicity, charge and ability to form disulfide or hydrogen bonds may be captured in a coarse-grained way by inhomogeneous attractive amino acid specific interactions, which respect the inherent anisotropy of a tube.

It is important to stress that our results are not at odds with or meant as a substitute for the detailed and beautiful work involving the laws of quantum mechanics and biochemistry. The virtue of our approach is that it predicts a novel phase with selected types of structures and the attendant advantages. It is then necessary to complement this information with the principles of quantum chemistry to assess whether a given biomolecule would fit one of these structures. We do not invoke hydrogen bonds as Pauling did in his prediction of protein secondary motifs  and indeed not all the structures in the marginally compact phase are compatible with hydrogen bond placement. What is remarkable, however, is that the lengths of the covalent and hydrogen bonds and the rules of quantum chemistry conspire to provide a perfect fit to the basic structures in this novel phase. One cannot but be amazed at how the evolutionary forces of Nature have shaped the molecules of life  ranging from the DNA molecule, which carries the genetic code and is efficiently copied, to proteins, the work horses of life, whose functionality follows from their form which, in turn, is a novel phase of matter.

Acknowledgements We are indebted to Flavio Seno and Michele Vendruscolo for useful discussions. This work was supported by INFM, MURST cofin2001, NASA and the Penn State MRSEC under NSF grant DMR-0080019.

FIGURE CAPTIONS

Figure 1:

Potential energy of interaction of two straight tubes as a function of their mutual distance and relative orientation.

The top panel shows the simplified geometry that we have considered. Two straight tubes, each of length $`2l`$, are placed a distance $`d`$ from each other with their axes making an angle $`\theta `$ with respect to each other. The line joining the centers of the tubes is perpendicular to both the tube axes. We consider a favorable energy of interaction when a pair of infinitesimal segments of the axes of the two tubes are within a distance $`R_1`$ (chosen to be 1.6 units as in the simulations described in Fig. 2), which is the range of a uniform attractive interaction. The lower panel shows plots of the potential energy both as a function of $`d`$ and $`\theta `$ for $`l=1`$. The left hand figure shows how the tube geometry leads to an anisotropic interaction, reflected by an energy which depends on $`\theta `$, for three values of $`d`$. Note that in each case the energy has been scaled by the energy when the tubes are parallel to each other with the corresponding value of $`d`$. The anisotropy becomes more pronounced as the tubes become thicker because this restricts the possible range of $`d`$ to values closer to $`R_1`$. The weak minimum for the $`d=0`$ case away from $`\theta =0`$ is due to the short length of the tubes. The lower right hand panel shows a plot of the magnitude of the potential energy when the tubes are oriented parallel to each other as a function of $`d`$. (we have chosen units such that the scale of the attractive interaction energy of two segments within the range of attraction is simply given by the product of their lengths.) The potential energy is zero when the value of $`d`$ exceeds that of $`R_1`$. Note that, for a continuum tube, as the tube thickness, $`R_0`$, increases towards $`R_1/2`$, restricting $`d`$ to values close to but smaller than $`R_1`$, there are two simultaneous effects. First the scale of the interaction energy becomes very weak and second, the anisotropy becomes pronounced. As described in the text, both these effects play a crucial role in simplifying the behavior of proteins.

Figure 2:

Building blocks of biomolecules and ground state structures associated with the marginally compact phase of a short tube.

In order to mimic a protein, the axis of the tube of non-zero thickness (radius of cross-section) $`R_0`$ is modelled as a one dimensional discrete chain, whose bonds are of fixed length (set equal to 1 without loss of generality – all other lengths will be measured in these units from now on) and which connect neighboring $`C_\alpha `$ atoms along the chain. The thickness  of the tube is captured by disallowing conformations for which $`R_0>\mathrm{min}_{ijk}R_{i,j,k}`$, where $`R_{i,j,k}`$ is the radius of the circle going through the centers of the atoms $`i`$, $`j`$ and $`k`$:

$$R_{i,j,k}=\frac{r_{i,j}r_{j,k}r_{i,k}}{4A_{i,j,k}}$$

where $`A_{i,j,k}`$ is the area of the triangle through $`i`$, $`j`$ and $`k`$ and $`r_{i,j}`$ is the distance between the centers of the $`i`$-th and the $`j`$-th atoms. Indeed, one may ascribe a local thickness to the tube by measuring all three body radii associated with a given atom and all other pairs and selecting the smallest radius among these. Figure 3 shows the distributions of the local tube thickness for the native state structures of 30 proteins and underscores the excellent approximation of viewing the protein as a tube of uniform thickness.

The interaction between non-consecutive atoms is modeled via a 2-body potential with a hard core and a square well:

$$V(r_{i,j})=\{\begin{array}{cc}\mathrm{}& \text{ if }r_{i,j}<2R_{h.c.}\text{ }\\ 1& \text{ if }2R_{h.c.}<r_{i,j}<R_1\text{ }\\ 0& \text{ if }R_1<r_{i,j}\text{ }\end{array}$$

The three-body interactions capture the inherent anisotropy of a tube, whereas the pairwise potential drives the compaction. For the results shown here, $`R_{h.c.}`$ has been set to $`0.55`$, $`R_1`$ to $`1.6`$ and $`R_0`$ was increased in the vicinity of the transition to the swollen phase until the number of pairwise contacts was reduced to three. While these values have been selected in order to mimic the protein backbone formed by the $`C_\alpha `$ atoms, we have verified that our results are robust to variations in these values.

The top row shows some of the building blocks of biomolecules, while the second row depicts the corresponding structures obtained for a tube. (A1) is an $`\alpha `$-helix of a naturally occuring protein, while (A2) and (A3) are the helices obtained in our calculations – (A2) has a regular contact map and is obtained when $`R_0=0.80267`$ whereas (A3) ($`R_0=0.833`$) is a distorted helix in which the distance between successive atoms along the helical axis is not constant but has period $`2`$. (B1) is a helix of strands in the alkaline protease of pseudomonas aeruginosa, whereas (B2) shows the corresponding structure ($`R_0=0.88`$) obtained in our computer simulations. (C1) shows the “kissing” hairpins of RNA and (C2) the corresponding conformation obtained in our simulations with $`R_0=0.95`$. Finally (D1) and (D2) are two instances of quasi-planar hairpins. The first structure is from the same protein as before (the alkaline protease of pseudomonas aeruginosa) while the second is a typical conformation found in our simulations when $`R_0>0.98`$. The sheet-like structure (D3) is obtained for a longer tube.

Figure 3:

Distribution of local thicknesses of the native state structures of 30 proteins. The peaked distribution shows that it is a good approximation to think of a protein as a tube of uniform thickness of around $`2.7\AA `$.


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# Regular and Chaotic Dynamics 5, No. 1, 89-91 (2000) A note on geodesics on ellipsoid

## Abstract

The purpose of this note is to show that the Jacobi problem of geodesics on ellipsoid , ,  may be reduced to a more simple case, namely, to the Clebsch problem . The last one is the problem with quadratic nonlinearity and may be solved directly by using of Weber’s approach  in terms of multi-dimensional theta functions.

1. The problem of geodesics on ellipsoid is a classical one. For two-dimensional ellipsoid, its solution was announced by Jacobi on 28 December, 1838  (see Appendix). Using the remarkable substitution, he reduced this problem to quadratures. These results were published in the paper  and then considered in details with the use of elliptic coordinates in his lectures at Königsberg University in 1842/43. They can be found in the book .

Later Weierstrass described another approach and succeeded in integrating of the equations for geodesics explicitely in terms of two-dimensional theta functions  .

Another solution of this problem was given by Moser (, ) who included it to the modern scheme of isospectral deformations and described the relation of this problem with the geometry of quadrics and algebraic geometry of spectral curve. For $`n`$-dimensional case, the algebro-geometrical approach was given by Knörer .

Here we show that this problem may be considered without using elliptic coordinates and algebraic geometry as a projection of a simpler system (for a general description of this method, see , ). Namely, it may be considered as a projection of the system with a larger number of degrees of freedom and with the simplest (quadratic) nonlinearity, the so-called Clebsch system . The equations of motion for this system were integrated in terms of multi-dimensional theta functions by Weber  (for modern exposition, see ).

2. The $`(n1)`$-dimensional ellipsoid in $`n`$-dimensional Euclidean space $`^n`$ is defined by the equation

$$Q_0(x)=\underset{j=1}{\overset{n}{}}\frac{x_j^2}{a_j}=1.$$
(1)
The standard metric in Euclidean space induces the metric on ellipsoid. The free motion of a point particle of unit mass on such an ellipsoid is described by the Hamiltonian

$$H=\frac{1}{2}\underset{j=1}{\overset{n}{}}y_j^2.$$
(2)
The equations of motion have the form

$$\dot{x}_j=y_j,\dot{y}_j=\ddot{x}_j=\nu (x,y)\frac{x_j}{a_j},j=1,\mathrm{},n.$$
(3)
To obtain $`\nu (x,y)`$, we shall differentiate the equation (1) twice with respect to time. As a result, we get

$$\underset{j=1}{\overset{n}{}}\frac{x_jy_j}{a_j}=0$$
(4)
and

$$\nu (x,y)=\frac{B(y)}{A(x)},$$
(5)
where

$$B(y)=\underset{j=1}{\overset{n}{}}\frac{y_j^2}{a_j},A(x)=\underset{j=1}{\overset{n}{}}\frac{x_j^2}{a_j^2}.$$
(6)
Theorem. Equations (3), (5), (6) for geodesics on ellipsoid are equivalent to the equations of motion for the Clebsch system,

$`{\displaystyle \frac{d}{d\tau }}y_j`$ $`=`$ $`{\displaystyle \underset{k}{}}\omega _{jk}y_k,`$
$`{\displaystyle \frac{d}{d\tau }}l_{jk}`$ $`=`$ $`{\displaystyle \underset{m}{}}(l_{jm}\omega _{mk}\omega _{jm}l_{mk})\left(a_j^1a_k^1\right)y_jy_k.`$
Here we introduced additional variables related to angular momentum tensor

$$l_{jk}=x_jy_kx_ky_j\text{and}\omega _{jk}=\frac{1}{a_ja_k}l_{jk}$$
(8)
and $`\tau `$ is a local time defined by the formula

$$d\tau =A^1dt,\frac{d}{d\tau }=A\frac{d}{dt}.$$
(9)
Proof. After the change of a standard time $`t`$ by a local time $`\tau `$, the right-hand side of equations (3) takes a polynomial form

$$\frac{d}{d\tau }x_j=A(x)y_j,\frac{d}{d\tau }y_j=B(y)\frac{x_j}{a_j}.$$
(10)
One can see that there are following identities:

$`B(y){\displaystyle \frac{x_j}{a_j}}`$ $`=`$ $`{\displaystyle \underset{k}{}}\omega _{jk}y_k,B(y)={\displaystyle \underset{j<k}{}}{\displaystyle \frac{1}{a_ja_k}}l_{jk}^2,`$
$`\left(a_j^1a_k^1\right)B(y)x_jx_k`$ $`=`$ $`{\displaystyle \underset{n}{}}(l_{jm}\omega _{mk}\omega _{jm}l_{mk})\left(a_j^1a_k^1\right)y_jy_k.`$
From here, it follows equations (7). They are the equations with the simplest, namely, quadratic nonlinearity and they are exactly equations of motion for the Clebsch system .

3. It is easy to check that equations (7) have $`n`$ independent integrals of motion,

$$F_j=y_j^2+\frac{1}{a_ja_k}l_{jk}^2,j,k=1,\mathrm{},n,$$
(12)
in involution, $`\{F_j,F_k\}=0`$. So, the system under consideration is completely integrable.

The generating function of integrals of motion has the form

$$G_\lambda (y,l)=\underset{j=1}{\overset{n}{}}\frac{1}{a_j\lambda }F_j=\underset{j=1}{\overset{n}{}}\frac{y_j^2}{a_j\lambda }\underset{j=1}{\overset{n}{}}\frac{l_{jk}^2}{(a_j\lambda )(a_k\lambda )},$$

and we have

$$\{G_\lambda ,G_\mu \}=0.$$

Let us rewrite these equations in the Hamiltonian form. For this, we use the Poisson structure related to the Lie algebra $`e(n)`$ of motion of Euclidean space $`^n`$,

$`\{l_{ij},l_{km}\}`$ $`=`$ $`\delta _{ik}l_{jm}\delta _{im}l_{jk}\delta _{jk}l_{im}+\delta _{jm}l_{ik},`$
$`\{l_{ij},y_k\}`$ $`=`$ $`\delta _{jk}y_i\delta _{ik}y_j,\{y_j,y_k\}=0.`$
So, the quantities $`y_j`$, $`l_{km}`$ generate the Lie algebra $`e(n)`$ of motion in $`n`$-dimensional Euclidean space.

The Hamiltonian $`H`$ should be the function of $`F_j`$ and in fact, due to the quadratic form of equations of motion, it should be a linear combination of $`F_j`$,

$$H=\frac{1}{2}b_jF_j.$$
(14)
The simple calculations show that $`b_j=a_j^1`$. Hence

$`\dot{y}_j`$ $`=`$ $`\{H,y_j\},\dot{l}_{jk}=\{H,l_{jk}\},`$
$`H`$ $`=`$ $`{\displaystyle \frac{1}{2}}\left({\displaystyle \underset{j}{}}{\displaystyle \frac{y_j^2}{a_j}}{\displaystyle \underset{i,j}{}}{\displaystyle \frac{l_{ij}^2}{a_ia_j}}\right)=G_0(y,l).`$
Eqs. (15) are the Hamiltonian equations related to the Poisson structure for the Lie algebra $`e(n)`$.

For two-dimensional case these equations were integrated explicitly by Weber  in terms of theta functions of two variables. For multi-dimensional case, see  and .

Note that as it was shown by Joachimsthal , the quantity

$$I(x,y)=A(x)B(y)$$

is an integral of motion, $`I(x,y)=c^2`$.

Now we may obtain the expressions for the quantities $`x_j`$ and $`A(x)`$:

$$x_j(\tau )=B^1(y)a_j\frac{d}{d\tau }y_j,A(x)=\underset{j}{}\frac{x_j^2}{a_j^2}=c^2B^1(y).$$
(16)
Finally, the expression for $`t`$ as the function of $`\tau `$ is given by a quadrature

$$t(\tau )=_0^\tau A(\tau )𝑑\tau .$$
(17)
So, we get the formulae for all dynamical variables.

Appendix

Lettre de M. Jacobi à M. Arago, concernant les lignes géodésiques tracées sur un ellipsoide à trois axes .

Königsberg, le 28 décembre 1838

Monsieur,

Je suis parvenu à ramener aux quadratures la ligne géodésique sur un ellipsoide à trois axes inégaux. Ce sont des formules extrémement simples, des intégrales abéliennes qui se changent dans les intégrales elliptiques connues, en égalant entre eux deux de ces trois axes. Ce probleme m’ayant paru long-temps très difficile, je crois que sa solution pourra intéresser peut-ètre quelques-uns des illustres membres de l’Académie des Sciences.

Acknowledgements I am grateful to Max–Planck–Institut für Mathematik in Bonn, where this paper was prepared, for the hospitality.


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# X-ray Variability of Blazars

## 1 Introduction

The multiwavelength continuum emission of blazar type AGN is dominated by non-thermal radiation in a relativistic jet pointing close to the line of sight. Magnification of the light intensity and variation amplitude, and foreshortening of intrinsic variability time scales, due to aberration effects, make blazars the most luminous and variable AGN at all frequencies and the most direct probe of galactic nuclear continuum emission. The amplitude of flux density variations increases as a function of frequency. Sensitive X-ray observations of bright blazars are therefore effective in measuring temporal and spectral properties on time scales as short as hours or even minutes. X-ray variability on the shortest time scales allows us to derive the sizes of the inner nuclear regions and to trace the kinematics of the jet, and thereby study how the relativistic particles are accelerated and injected in the emission region and how efficiently they cool thereafter and escape. Combined with simultaneous observations at other wavelengths, X-ray light curves carry information on multiwavelength spectral variability and on temporal delays of emission at different frequencies. These can be used to test the models for the production of the blazar continuum.

The spectral energy distributions (SEDs) of blazars are typically double-peaked (in a $`\nu f_\nu `$ representation), with a first component attributed to synchrotron radiation, the maximum of which is located at IR to soft X-ray frequencies, and a second component correspondingly peaking at GeV to TeV energies, produced through inverse Compton scattering (Figure 1, left). According to whether the peak of their first component is at IR or UV/soft X-ray wavelengths, the sources have been defined as Low-Energy or High-Energy Peaked Blazars (Padovani & Giommi 1995), or as ‘red’ or ‘blue’ blazars (Fossati et al. 1998). However, rather than exhibiting a neat distinction between red and blue sources, the blazar population presents a continuity of properties between these two extrema, all correlating with the bolometric luminosity.

High energy peaked blazars have lower bolometric luminosities and smaller ratios between high energy and low energy components (i.e. smaller inverse Compton dominance). Ghisellini et al. (1998) identify the ambient (broad emission line region or accretion disk) photon density as the parameter governing these correlations: in sources with lower ambient photon densities (blue blazars) the high energy electrons cool via scattering off synchrotron photons (synchrotron self-Compton mechanism, SSC), while for high ambient photon densities the inverse Compton scattering off external radiation prevails (red blazars).

In blue blazars the radiation efficiency is smaller than in red ones, and therefore in the former sources electrons can attain higher energies, thus synchrotron spectra peak at higher frequencies, and the overall luminosity is lower than in red blazars (however, Urry 1999 discusses some caveats against this scenario; see also Giommi, Menna, & Padovani 1999a). The difference in synchrotron luminosities may be determined by different degrees of relativistic beaming. Boettcher & Dermer (2002) interpret the increasing spectral hardness with decreasing luminosity of blazars in an evolutionary scenario of increasing reduction of the black hole accretion power with time (see also Maraschi 2001).

In the X-ray spectral range the two contributions from synchrotron and inverse Compton components overlap, with the former dominating in blue blazars, and the latter in red blazars (see Donato et al. 2001 for a recent comprehensive review of blazar X-ray spectra). Therefore, in blue blazars photons up to 10 keV, and occasionally 100 keV or more, especially in outburst, represent the highest energy tail of the synchrotron radiation. Being produced by the most energetic electrons, they are most sensitive to variations in the acceleration and cooling processes, and are thus expected to exhibit the most rapid and largest amplitude variability. In a few of these blazars the inverse Compton component, produced through SSC, is detected up to TeV energies.

In red blazars, the X-ray spectrum is still due to SSC, while external Compton dominates at the higher frequencies (Takahashi, Madejski, & Kubo 1999). In the last 10 years, the blazar monitoring by X-ray satellites ROSAT, ASCA, RXTE, BeppoSAX, and recently XMM, has produced many results on variability, as reviewed, e.g. by Ulrich, Maraschi, & Urry (1997), Urry (1999), Sambruna (1999), McHardy (1999), Maraschi et al. (2000), and Maraschi & Tavecchio (2001). The best studied red blazars present X-ray variability correlated with optical and gamma rays, although the variation amplitude is usually smaller than in gamma rays (e.g., Wehrle et al. 1998; Ghisellini et al. 1999). The hard X-ray spectral variability is modest (Sambruna et al. 1997; Lawson, McHardy, & Marscher 1999; Hartman et al. 2001; Ballo et al. 2002). For some objects (intermediate blazars) the X-ray observations have simultaneously sampled the synchrotron and the SSC components at soft and hard X-rays, respectively (Giommi et al. 1999b; Tagliaferri et al. 2000; Ravasio et al. 2002; Tanihata et al. 2000).

Blue blazars present a higher amplitude X-ray emission variability than red blazars (factors of up to 30 with respect to quiescence), accompanied by different spectral variability (compare the remarkable changes of spectral slope and synchrotron peak frequency in Mkn 501, Pian et al. 1998, with the modest peak frequency variations in PKS 2005–489, Perlman et al. 1999; Tagliaferri et al. 2001). In the present paper I will summarise some of the most recent results obtained for the brightest and best monitored BL Lacs Mkn 501, Mkn 421, and PKS 2155–304, all of which belong to the class of blue blazars.

## 2 Mkn 501

This source has been observed by BeppoSAX in April 1997, April–May 1998, and June 1999. On the first occasion it exhibited an outburst accompanied by dramatic spectral hardening: the synchrotron peak energy was observed to reach 100 keV or more, i.e. almost three orders of magnitude larger than in its quiescent state (Catanese et al. 1997; Pian et al. 1998). The following year, the peak energy was found at 20 keV and the emission intensity above 1 keV was lower. The fact that, despite the radiation losses, the synchrotron peak was still at such high energies one year after the outburst indicates the presence of efficient, continuously active mechanisms of particle acceleration in this source.

In June 1999 BeppoSAX recorded an ‘inactive’ state, i.e. similar to the historical one, both in emission level and synchrotron peak energy ($``$0.5 keV), and characterised by modest (amplitude of 10-20%) intraday flux variability (Tavecchio et al. 2001). In Figure 1, right, the X-ray spectra are shown together with the simultaneous TeV observations. The X-ray spectra are best described by curved and continuously steepening laws. Their variability can be reproduced by changes of the electron break energy only (i.e. the energy of the electrons which emit at the spectral maximum). As frequently noted in blazars (see also Section 3), the X-ray spectral index and peak energy correlate well with the source intensity, flatter index and higher peak energy corresponding to brighter states.

The good correlation between intensity and spectral index holds also when previous GINGA and ASCA observations are considered together with BeppoSAX data (Kataoka et al. 1999). The X-ray and TeV intensities correlate well with no measurable time lag larger than one day. This suggests that the same electron population is responsible for the X- and gamma-ray emission through the SSC mechanism in a homogeneous region (Tavecchio, Maraschi, & Ghisellini 1998; Tavecchio et al. 2001; Petry et al. 2000). The ensuing prediction for the correlated behaviour of X-ray and TeV flux densities in different states (Tavecchio et al. 2001) is in good agreement with the simultaneous RXTE and TeV HEGRA observations in 1997 (see Figure 6 in Krawczynski et al. 2000).

Strong correlation between spectral hardness and intensity has been observed by RXTE as well in June 1998, when a rapid shift in synchrotron peak energy was also detected during a brightening. The simultaneous X-ray and TeV flux and spectral variability points, again, to the SSC origin of the multiwavelength emission (Sambruna et al. 2000).

In July 1997, when Mkn 501 was close to its historically largest X-ray intensity, RXTE observations of the source revealed unusual anti-correlation between spectral hardness and intensity (i.e. flatter spectrum for dimmer intensity). At that epoch the source exhibited variations of up to 30% over a few hours (Lamer & Wagner 1998). Remarkably rapid variability has been detected during the May 1998 RXTE campaign, when the blazar flared by factors 1.6 and 2 in $``$200 seconds in the 2–10 keV range and 10–15 keV, respectively (Catanese & Sambruna 2000). With the event is associated significant spectral variability.

## 3 Mkn 421

A 1 day flare was detected in this source simultaneously in X-rays by BeppoSAX and at TeV energies by the Whipple Cerenkov telescope in April 1998 at the beginning of a 10 day multiwavelength monitoring campaign, involving also the ASCA, EUVE, and RXTE satellites (Takahashi et al. 2000). The X-ray and TeV light curves are well correlated with no temporal lag larger than 1.5 hours (Figure 2, left), indicating that the radiation at the two frequencies is produced by the same electron population via SSC (Maraschi et al. 1999). The observed difference in the flare decay times in X-rays and TeV may be due to light travel time effects adding to radiative time scales (Chiaberge & Ghisellini 1999), or to the inhomogeneity of the emitting region (see also the simultaneous RXTE and TeV observations of June 2000 by Krawczynski et al. 2001).

Within the X-ray band the flare decay is achromatic, if a stationary underlying emission component is postulated (Fossati et al. 2000a). The temporally resolved spectra during the X-ray flare allowed Fossati et al. (2000b) to fully map, for the first time in any blazar, the increase of the synchrotron peak energy during the rising part of the flare and its subsequent decrease during the decay (Figure 2, right). Unlike in Mkn 501, where the synchrotron peak during the outburst can reach 100 keV or more, in Mkn 421 the maximum energy reached by the synchrotron peak is 1 keV. An indication that it may have shifted up to 10 keV or beyond is present in May 2000 BeppoSAX data, when the source was also detected in its historical maximum X-ray brightness ($`F_{210keV}=1.2\times 10^9`$ erg s-1 cm-2, Fossati 2001). It is interesting to note that Mkn 421 presents larger amplitude short term variability than Mkn 501, which suggests that maximum synchrotron peak energy and short time scale variability may have complementary roles in dissipating the jet energy.

It is generally observed that the X-ray intensity and spectral index variations in blazars are correlated, in the sense of spectral hardening during brightening. It has been noted for some time (see e.g. Sembay et al. 1993) that the changes describe different paths in the index–intensity plane, according to whether they refer to the increasing or decreasing portion of a flare. This is seen also during the April 1998 flare of Mkn 421, which exhibits an ‘anti-clockwise’ pattern of intensity vs spectral index (middle and bottom panels of the right side of Figure 2, right). For Mkn 421 this is less common than the opposite ‘clockwise’ pattern (Takahashi et al. 1996; Malizia et al. 2000).

The emission of soft X-rays ($`\stackrel{<}{}`$2 keV) is generally well correlated with and lags that of hard X-rays ($`\stackrel{>}{}`$4 keV) by a variable interval (from 3–4 ks down to $``$300 s) as determined with cross-correlation methods (Malizia et al. 2000; Takahashi et al. 2000; Brinkmann et al. 2001). The soft lag is interpreted as a consequence of the synchrotron cooling, which is more rapid at higher energies. The reversal of this temporal correlation has been observed in 1997 and April 1998 (Treves et al. 1999; Fossati et al. 2000a), suggesting that hard lags may be associated with anti-clockwise intensity spectrum patterns, while soft lags are associated with clockwise patterns. Hard lags may originate when the acceleration time scale approaches the cooling time scale, so that electrons appear first at low energies and gradually build up at higher energies (Kirk, Rieger, & Mastichiadis 1998; Takahashi et al. 2000).

We note however that Edelson et al. (2001) have put into question temporal lags of the order of $``$1 hour, when obtained by applying cross-correlation methods to light curves measured by satellites with low Earth orbits (like ASCA and BeppoSAX).

Mkn 421 flares daily, with a characteristic time scale of 12 hours, as determined from the structure function analysis of the ASCA data in April 1998 (Takahashi et al. 2000; a similar result has been obtained with previous ASCA observations in 1994, Takahashi et al. 1996, and with XMM observations in May 2000, Brinkmann et al. 2001). However, 50% variations of 4–5 hours time scale are typical (Guainazzi et al. 1999; Fossati et al. 2000a; Krawczynski et al. 2001). The symmetric shape of the X-ray flares detected by BeppoSAX and ASCA imply that the cooling time scales are shorter than the light crossing time through the emitting region, so that the latter dominates the variability.

## 4 PKS 2155–304

A blue, relatively nearby ($`z0.1`$) blazar, and one of the brightest at UV and X-ray frequencies, PKS 2155–304 was expected to be a TeV emitter and has indeed been detected at these energies in September–November 1996 by the Cerenkov telescope Mark 6 (Narrabri, Australia) and, with a larger intensity, simultaneously with EGRET and BeppoSAX in November 1997 (Chadwick et al. 1999; Chiappetti et al. 1999; Vestrand & Sreekumar 1999). The X-ray state observed by BeppoSAX is one of the highest ever detected, though lower than that observed by RXTE before the start of the BeppoSAX campaign. A pure SSC model in a homogeneous region accounts well for the X-ray and higher energy radiation, with variability produced solely by changes in electron break energy (Figure 3).

A comparative temporal analysis on the X-ray light curves of PKS 2155–304 in 1994 (ASCA, Kataoka et al. 2000), 1996, and 1997 (BeppoSAX, Giommi et al. 1998; Chiappetti et al. 1999) has been accomplished by Zhang et al. (1999), who found power density spectra of slope similar to those of Seyfert galaxies ($`f^{1.7}`$, e.g. Edelson & Nandra 1999). The minimum variability time scale determined by the power density spectrum analysis in the 1.5–10 keV range is $``$1000 s, consistent with the minimum measured doubling time of the flux.

The degree of variability is found to be a function of brightness, with shorter doubling times and larger fractional variability parameter for brighter states. Similarly, the temporal delays between soft and hard X-rays, determined with different correlation methods, are shorter for higher source intensity (see however Section 3 and Edelson et al. 2001).

Both positive and negative temporal lags between soft and hard X-rays have been measured by RXTE for PKS 2155–304 during successive flares in May 1996, and correspondingly a clockwise or anti-clockwise loop, respectively, is seen in the intensity vs hardness ratio plane (Sambruna 1999). This, as in the case of Mkn 421, can be interpreted in terms of a different duration of the acceleration process with respect to the electron cooling (Kirk et al. 1998).

The variable temporal lags between soft and hard X-ray emission may be related to a different geometry of the emitting region in different states of the source (Zhang et al. 1999), requiring a time-dependent SSC model to reproduce the SED (Kataoka et al. 2000). Alternatively, Georganopoulos & Marscher (1998) have proposed that the different temporal lags observed in 1991 and 1994 between light curves of PKS 2155–304 at UV and X-ray frequencies (Edelson et al. 1995; Urry et al. 1997) can be reproduced by flaring components superimposed on a similar steady state of the jet, and produced by different energy distributions of freshly injected electrons.

It is striking that in this source, similar patterns of X-ray variability are seen, spaced apart by many years (Brinkmann et al. 2000), suggesting recurrent conditions in the mechanism of jet powering and activity development. This also weakens the microlensing hypothesis as the origin of intraday variability in this source (Urry et al. 1993).

## 5 Conclusions

The X-ray campaigns, coordinated with TeV telescopes, have determined a crucial progress toward our understanding of blazars and have shown the importance of X-ray instruments with wide spectral range and good temporal resolution. The correlated variability at X-ray and TeV energies can be reproduced by the changes of a single parameter, namely the break energy of the relativistic electron distribution. In some sources, especially (but not necessarily) during outburst, this parameter can attain extremely high values ($`\gamma _b>10^6`$), resulting in synchrotron peaks beyond 1 keV (Mkn 421), and even up to 50–100 keV, as in Mkn 501, 1ES 2344+514 (Giommi, Padovani, & Perlman 2000), and 1ES 1426+428 (Costamante et al. 2001).

More detections of these ‘extreme synchrotron blazars’ are expected with the advent of the INTEGRAL satellite for soft gamma-ray astronomy. These sources are expected to be TeV emitters, and therefore should be suitable targets for the next generation of sensitive Cerenkov telescopes. Simultaneous observations at X-ray and TeV energies should allow us to measure the correlation of the light curves on shorter time scales than it has been possible so far and identify the relation between source intensity and variable temporal lags. Similar coordinated observations of red blazars, which are not expected to be strong TeV emitters, will receive renewed interest after the launch in the near future of satellites sensitive in the MeV–GeV range, i.e. AGILE and GLAST.

Finally, longer and denser monitoring of blazars will allow a better test of the hadronic models of blazar emission. These predict gamma rays to be due to proton synchrotron radiation (Aharonian 2000), or to pion production by accelerated protons interacting with turbulent fluctuations in the magnetic field (Mannheim 1998), or with ambient radiation fields (Donea & Protheroe 2002). In hadronic models, correlated variability at X-ray and TeV energies may arise from less restrictive sets of parameters than in leptonic models (SSC, or synchrotron and external Compton). However, hadronic and leptonic models are clearly separated in the parameter space, so that it should be possible to distinguish them via a model-independent estimate of the magnetic field and plasma Doppler factor (Rachen 2000).

## Acknowledgments

I thank A. Celotti, L. Chiappetti, G. Fossati, G. Ghisellini, F. Tavecchio, and A. Treves for valuable input, L. Maraschi for a careful reading of the manuscript, and the workshop organisers for a pleasant, stimulating, and constructive meeting.

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