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# Simulation of a semiflexible polymer in a narrow cylindrical pore

## Abstract

The probability that a randomly accelerated particle in two dimensions has not yet left a simply connected domain $`𝒜`$ after a time $`t`$ decays as $`e^{E_0t}`$ for long times. The same quantity $`E_0`$ also determines the confinement free energy per unit length $`\mathrm{\Delta }f=k_BTE_0`$ of a semiflexible polymer in a narrow cylindrical pore with cross section $`𝒜`$. From simulations of a randomly accelerated particle we estimate the universal amplitude of $`\mathrm{\Delta }f`$ for both circular and rectangular cross sections.

PACS 36.20.Ey, 05.10.-a, 05.10.Gg, 05.70.Ce

Submitted to J.Phys. A

Consider a long semiflexible polymer with persistence length $`P`$ fluctuating in a cylindrical pore with diameter $`D`$. In the narrow-pore limit $`D<<P`$ the free energy of confinement per unit length $`\mathrm{\Delta }f`$ is given by

$$\mathrm{\Delta }f=A_{}\frac{k_BT}{P^{1/3}D^{2/3}}.$$
(1)
This follows from simple scaling or dimensional arguments , such as that given below. Similarly, for a pore with a rectangular cross section  with edges $`L_1,L_2<<P`$

$$\mathrm{\Delta }f=A_{}\frac{k_BT}{P^{1/3}}\left(\frac{1}{L_1^{2/3}}+\frac{1}{L_2^{2/3}}\right).$$
(2)
The dimensionless constants $`A_{}`$, $`A_{}`$ in equations (1) and (2) are universal numbers, independent of both macroscopic and microscopic properties of the polymer chain. From computer simulations Dijkstra et al. estimated

$$A_{}=2.46\pm 0.07.$$
(3)
Solving an integral equation numerically that arises in an exact analytical approach, Burkhardt obtained

$$A_{}=1.1036.$$
(4)
In the Monte Carlo simulations of Dijkstra et al. , polymer configurations consistent with the Boltzmann distribution were generated with a Metropolis algorithm incorporating detailed balance. In this Letter we estimate $`A_{}`$, $`A_{}`$ with a precision of about $`1\%`$ using a Langevin dynamics approach, which is simple and efficient. Instead of a confined semiflexible polymer, we simulate a Newtonian particle which is randomly accelerated by Gaussian white noise in two dimensions. In the narrow-pore or tight-confinement limit these two systems have equivalent statistical properties, as discussed in  and reviewed below. The basic idea, illustrated in figure 1, is that each of the possible world lines of a particle, which is randomly accelerated in two dimensions and remains in a domain $`𝒜`$ for a time $`t`$, corresponds to an allowed configuration of a tightly-confined semiflexible polymer in a cylindrical pore or tube with cross section $`𝒜`$.

We now describe the correspondence in more detail. As in , polymer configurations are specified in terms of Cartesian coordinates $`(𝐱,t)=(x_1,x_2,t)`$. The $`t`$ axis is parallel to the axis of the cylindrical pore, as shown in figure 1. In the narrow-pore limit $`D<<P`$ or $`L_1,L_2<<P`$, configurations with overhangs are negligible, i.e. $`𝐱`$ is a single-valued function of $`t`$. The partition function is given by the path integral

$$Z(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};t)=_𝒜D^2x\mathrm{exp}\left[\frac{1}{2}P_0^t𝑑t\left(\frac{d^2𝐱}{dt^2}\right)^2\right]$$
(5)
where $`𝐱`$ and $`𝐮=d𝐱/dt`$ denote the displacement and slope of the polymer at $`t`$, and $`𝐱_\mathrm{𝟎}`$ and $`𝐮_\mathrm{𝟎}`$ the same quantities at $`t=0`$. A hard-wall confining potential is assumed, and the $`𝐱`$ integration is limited to the domain $`𝒜`$.

The path integral implies the the partial differential equation

$$\left[\frac{}{t}+𝐮_𝐱\frac{1}{2P}_{𝐮}^{}{}_{}{}^{2}\right]Z(𝐱,𝐮;𝐱_\mathrm{𝟎}𝐮_\mathrm{𝟎};t)=0$$
(6)
to be solved with the initial condition

$$Z(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};0)=\delta (𝐱𝐱_\mathrm{𝟎})\delta (𝐮𝐮_\mathrm{𝟎}).$$
(7)
Since the polymer is confined to the interior of the pore and configurations with a discontinuity in slope cost an infinite energy, $`Z(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};t)`$ vanishes for $`𝐮𝐧>0`$ as $`𝐱`$ approaches a hard wall. Here $`𝐧`$ is a vector normal to the wall and directed toward the interior of the pore.

As in  we consider exponentially decaying solutions of equation (6) with the form $`\psi (𝐱,𝐮)\mathrm{exp}(Et)`$. The eigenfunctions $`\psi `$ and eigenvalues $`E_n`$ satisfy

$$\left[𝐮_𝐱\frac{1}{2P}_{𝐮}^{}{}_{}{}^{2}E_n\right]\psi _n(𝐱,𝐮)=0$$
(8)
where $`\psi (𝐱,𝐮)`$ also vanishes for $`𝐮𝐧>0`$ as $`𝐱`$ approaches the pore wall. In the long-polymer limit the partition function and the confinement free energy per unit length are given by

$$Z(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};t)\mathrm{const}\times \psi _0(𝐱,𝐮)\psi _0(𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎})e^{E_0t}t\mathrm{}$$
(9)
$$\frac{\mathrm{\Delta }f}{k_BT}=E_0(P,D)$$
(10)
for a pore with a circular cross section of diameter $`D`$, where $`E_0`$ is the smallest of the eigenvalues $`E_n`$.

The $`P`$ and $`D`$ dependence in equation (1) may be derived from (10) by making the scale change $`𝐱=\alpha 𝐱^{}`$, $`𝐮=\beta 𝐮^{}`$ in (8), where $`\alpha `$ and $`\beta `$ are arbitrary positive constants. This leads to the scaling property

$$E_n(P,D)=\alpha ^1\beta E_n(\alpha ^1\beta ^3P,\alpha ^1D)$$
(11)
of the eigenvaues. Setting $`\alpha =D`$ and $`\beta =P^{1/3}D^{1/3}`$ in equation (11) and substituting the result in (10), we obtain

$$\frac{\mathrm{\Delta }f}{k_BT}=\frac{E_0(1,1)}{P^{1/3}D^{2/3}}$$
(12)
This expression is entirely consistent with equation (1) and implies

$$A_{}=E_0(1,1).$$
(13)
Similarly, for a pore with a rectangular cross section

$$2A_{}=E_0(1,1,1)$$
(14)
where $`E_0(P,L_1,L_2)`$ denotes the smallest eigenvalue in equation (8) for a rectangular domain with edges $`L_1`$, $`L_2`$. Equations (13) and (14) allow us to determine the universal amplitudes $`A_{}`$ and $`A_{}`$ from calculations with $`P=D=L_1=L_2=1`$.

For the rectangular domain equation (8) has separable eigenfunctions $`\psi _{m,n}(𝐱,𝐮)=\varphi _m(x_1,u_1)\varphi _n(x_2,u_2)`$, with eigenvalues $`E_{m,n}=E_m^{(1\mathrm{dim})}(P,L_1)+E_n^{(1\mathrm{dim})}(P,L_2)`$, where

$$\left[u\frac{}{x}\frac{1}{2P}\frac{^2}{u^2}E_m^{(1\mathrm{dim})}(P,L)\right]\varphi _m(x,u)=0.$$
(15)
Here $`0<x<L`$, and $`\varphi (x,u)`$ vanishes for $`x=0,u>0`$ and $`x=L,u<0`$. Thus equation (14) may be rewritten as

$$A_{}=E_0^{(1\mathrm{dim})}(1,1)$$
(16)
in terms of the smallest eigenvalue of (15) for $`P=L=1`$. The earlier numerical result for $`A_{}`$, noted in equation (4), was obtained in  by converting (15) to an integral equation, determining the smallest eigenvalue numerically, and substituting the result in (16).

Now consider a particle which is randomly accelerated in the $`d`$-dimensional space $`(x_1,\mathrm{}x_d)`$ by Gaussian white noise with zero mean according to

$$\frac{d^2x_i}{dt^2}=\xi _i(t)\xi _i(t)\xi _j(t^{})=P^1\delta _{ij}\delta (tt^{}).$$
(17)
The probability density in phase space $`(𝐱,𝐮)`$ that the particle remains in the domain $`𝒜`$ for a time $`t`$ while the position and velocity evolve from $`(𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎})`$ to $`(𝐱,𝐮)`$ satisfies a Fokker-Planck equation  with exactly the same form (6), initial condition (7), and boundary condition at the boundary of $`𝒜`$. Thus the probability density of the randomly accelerated particle equals the partition function of a semiflexible polymer in a pore with cross section $`𝒜`$ and decays as $`\mathrm{exp}(E_0t)`$ for long times, as in equation (9).

To estimate $`A_{}`$ using equation (16), we simulated a randomly accelerated particle in one spatial dimension. From simulations in two dimensions we obtained a second estimate of $`A_{}`$ based on (14) and a prediction for $`A_{}`$ from (13). The simulation routine, similar to that in , will now be described briefly.

In an unbounded $`d`$-dimensional space the exact solution of the Fokker-Planck equation (6) with initial condition (7) and with $`P=1`$ is given by

$$Z_{\mathrm{free}}(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};t)=\left(\frac{3^{1/2}}{\pi t^2}\right)^d\mathrm{exp}\left\{\frac{6}{t^3}\left[(𝐱𝐱_\mathrm{𝟎}𝐮_\mathrm{𝟎}t)(𝐱𝐱_\mathrm{𝟎}𝐮t)+\frac{1}{3}(𝐮𝐮_\mathrm{𝟎})^2t^2\right]\right\}$$
(18)
Trajectories with the probability distribution $`Z_{\mathrm{free}}(𝐱_{n+1},𝐮_{n+1};𝐱_n,𝐮_n;\mathrm{\Delta }_{n+1})`$ given by (18) are generated using the algorithm

$`𝐱_{n+1}`$ $`=`$ $`𝐱_n+𝐮_n\mathrm{\Delta }_{n+1}+𝐞_n\mathrm{\Delta }_{n+1}^{3/2}\left(3^{1/2}s_{n+1}+r_{n+1}\right)`$ (19)
$`𝐮_{n+1}`$ $`=`$ $`𝐮_n+𝐞_n\mathrm{\hspace{0.17em}2}\mathrm{\Delta }_{n+1}^{1/2}r_{n+1}`$ (20)
where $`𝐱_n`$ and $`𝐮_n`$ are the position and velocity of the particle at time $`t_n`$, and $`\mathrm{\Delta }_{n+1}=t_{n+1}t_n`$. The quantity $`𝐞_n`$ is a unit vector that points either along the positive $`x_1`$ axis , the positive $`x_2`$ axis, $`\mathrm{}`$, or the positive $`x_d`$ axis with equal probability, and $`r_n`$ and $`s_n`$ are independent Gaussian random numbers satisfying

$$r_n=s_n=0,r_n^2=s_n^2=1.$$
(21)
In the absence of boundaries there is no time-step error in the above algorithm,i.e., the $`\mathrm{\Delta }_n`$ may be chosen arbitrarily. Close to the boundaries small time steps are needed. As in  we performed our simulations with

$$\mathrm{\Delta }_{n+1}=10^5+10^1D_n$$
(22)
where $`D_n`$ is the distance from the particle to the closest point of the domain boundary at time $`t_n`$. This time step fulfills a reliability criterion discussed in .

Some sample simulational results are shown in figure 2. The quantity $`Q(t)`$ is the probability that a particle with a random initial position in a one or two-dimensional domain and with initial velocity zero, which is randomly accelerated according to equation (17) with $`P=1`$, has not yet left the domain after a time $`t`$. The curves labelled ’circle,’ ’square,’ and ’interval’ refer to a circular domain of diameter $`D=1`$, a square with edges $`L_1=L_2=1`$, and a one-dimensional interval of length $`L=1`$. Each of curves is based on 10,000 independent trajectories.

Since $`Q(t)=d^dxd^dud^dx_0Z(𝐱,𝐮;𝐱_\mathrm{𝟎},\mathrm{𝟎};t)`$, it decays as $`e^{E_0t}`$ for long times, with the same decay constant $`E_0`$ as $`Z(𝐱,𝐮;𝐱_\mathrm{𝟎},𝐮_\mathrm{𝟎};t)`$ in equation (9). We determined $`E_0`$ for the circular, square, and one-dimensional domains by fitting $`Q(t)`$ for long times with an exponential function. A surprising result, shown in figure 2, is that the curves for the circular and square domains practically coincide when plotted versus $`E_0t`$ instead of $`t`$.

We also estimated $`E_0`$ for circular, square, and one-dimensional domains from trajectories that all begin at the the center of the domain with initial velocity zero. The results are consistent with the results for random initial positions but have a somewhat greater statistical uncertainty.

Combining our best estimates of $`E_0`$ with equations (13), (14), and (16), we obtain

$`A_{}`$ $`=`$ $`2.375\pm \mathrm{\hspace{0.17em}0.013}`$ (23)
$`A_{}`$ $`=`$ $`1.108\pm \mathrm{\hspace{0.17em}0.013}`$ (24)
The result (23) for $`A_{}`$ is somewhat lower than the estimate (3) of Dijkstra et al.  and has a smaller statistical uncertainty. The result (24) for $`A_{}`$ in equation is consistent with the value (4) obtained by Burkhardt from the numerical solution of an exact integral equation . Bundschuh  has also confirmed (4) to within a few percent with a numerical transfer matrix approach  for semiflexible polymers.

In summary we have found a simple and efficient simulational procedure for calculating the confinement free energy of a semiflexible polymer in a narrow cylindrical pore with cross section $`𝒜`$. We use the equivalent statistical properties of a Newtonian particle which is randomly accelerated by Gaussian white noise in two dimensions. The probability that the particle has not yet left a domain $`𝒜`$ in a time $`t`$ decays as $`e^{E_0t}`$. We determine $`E_0`$ from our simulations and then interpret it, following equation (10), in terms of the polymer free energy. We emphasize that the equivalence between the statistics of the polymer and the randomly accelerated particle is asymptotically exact in the limit in which the pore diameter is much smaller than the polymer persistence length.

TWB appreciates the hospitality of the Institut Laue-Langevin, where this work was begun, and thanks Ralf Bundschuh for helpful correspondence.


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# 1 Introduction

## 1 Introduction

The highest energies are defined, at a given time, by our detector capabilities. Thus the highest energies will be the just measured or soon to be measured energies. To-day, the frontier in cosmic rays reaches $`10^{20}`$ eV. This represents a macroscopic energy, namely 16 J, transported by a microscopic object. For charged particles, the highest energy events seem to necessitate some New Physics, beyond the present understanding of astrophysics and particle physics.

Concerning neutrinos, apart from the low energy ones coming from the explosion of SN1987A, only neutrinos of terrestrial origin have been detected so far. It is a challenge to detect neutrinos which may be witnesses of the most violent phenomena in the Universe. With their very small probability of interactions and their neutral nature, they can come unaffected from the most distant parts of the Universe. Theoretical predictions give two regions of interest: from $`10^{14}`$ eV to $`10^{17}`$ eV for the contribution of AGN’s, and from $`10^{18}`$ eV to $`10^{20}`$ eV for GZK neutrinos, the ones created but the high energy cosmic rays interacting with the CMB.

Moreover, the study of high energy neutrinos may be used, not only to find sources, but also to constrain some properties of these elusive particles. For example, limits on oscillations can be achieved for $`\delta m^2`$ unreachable otherwise, and one can dream of searching for cosmic neutrinos through the Z0 resonant absorption.

## 2 Charged cosmic rays

The spectrum of cosmic rays as it is measured to-day, extends over more than 30 orders of magnitude in flux and reaches energies of macroscopic size.

The highest energy events are at the origin of a puzzle. Protons above $`5.10^{19}`$ eV undergo the GZK (Greisen-Zatsepin-Kuzmin) effect, namely their interaction cross-section with the CMB background is such that one interaction length amounts to about 50 Mpc. This is only 1% of the size of the Universe and there are no known sources energetic enough in this close neighbourhood. The GZK effect should show as a pile-up of events followed by a cut-off at the critical energy. Experimentally, a few events are seen above the cut-off, and there is no unique explanation for their existence. In ’top-down’ models, these events are interpreted as traces of topological defects or very high mass remnants of the Big Bang.

In order to shed some light on the problem, it is essential to increase the present statistics. Here comes the difficulty: the flux is extremely low, on the order of 1 cosmic per km2 and century.

The Auger observatory is instrumenting 3000 km2 in the Argentinian pampa, thus hoping to collect some 30 events per year in the interesting energy region. The set-up should be operational in a couple of years.

Euso projects to use an optical telescope on the International Space Station. From 380 km altitude, it is able to watch 150000 km2 of atmosphere and should detect some 800 events par year through the fluorescence light emitted along the showers generated by the passage of the cosmic rays.

## 3 The problems of neutrino detection

Very ambitious projects also exist for neutrino detection. The aim is to instrument large volumes of up to 1 km3 under the ice of the South Pole or deep underwater. However this technique is only efficient for the detection of up-going muons produced in the interactions of $`\nu _\mu `$. The energy resolution on the detected muon is based on catastrophic bremsstrahlung and is limited typically to a factor of 5.

The difficulty of detecting neutrinos comes from their very small cross-section necessitating large targets. Even at an energy of $`10^{20}`$ eV, the cross-section reaches only $`10^{31}`$ cm2. The probability of interacting while traversing the atmosphere is only 10-4 . The most optimistic predictions of neutrino fluxes give no hope of seeing events coming down from the sky. Thus it is necessary to use a denser target. The earth is an obvious candidate but here comes another problem. At very high energies the earth becomes opaque to neutrinos. The cut-off happens at 100 TeV. Above this energy, $`\nu _e`$ and $`\nu _\mu `$ are absorbed if they cross the earth through its center. The case of the $`\nu _\tau `$ is more favorable because of the multibang phenomenon. An effect similar to the GZK one takes place: very high energy $`\nu _\tau `$ can cross the earth but their energy is degraded and they all exit with a few $`10^{14}`$ eV. Of course, $`\nu _\tau `$ detection is only possible if neutrinos oscillate with maximum mixing since only $`\nu _e`$ and $`\nu _\mu `$ are directly produced in known mechanisms, at least in first order.

The Auger observatory will be able to detect a few $`\nu _\tau `$ events, by catching some of the products of the interaction in the mountain close to the apparatus. For Euso the possibility of detecting neutrino interactions by up-coming showers in the atmosphere is hampered by the threshold which is too close to the cut-off coming from earth opacity.

## 4 A novel way to look at neutrinos

In order to alleviate these constrains, it is proposed to search for neutrino interactions in a mountain. This allows a detector closer to the shower and a target thin enough. The leptons generated in the process have a chance to come out of the rock and they subsequently develop a shower through the atmosphere of a valley. The shower is detected by its Cerenkov emission in an optical device. Cerenkov emission has the advantage over fluorescence to give collimated light. For example the Euso threshold is a few $`10^{19}`$ eV for fluorescence, it is only a few $`10^{14}`$ eV for Cerenkov light. But the subtended solid angle in a given set-up reduces to 10-3 srd, because of collimation.

The telescope copies the one of Euso. Its optics covers a large field of view of 60 degrees. It could in principle be a 1 m2 prototype of the final device (Eusino?). The detector must be fast, it is based on multianode photomultipliers. The background fixes the needed number of pixels. The night-glow is measured equal to 200 photoelectrons per m2, ns and srd. In order to get a 10% random occupancy with a 10 ns gate, this requires about 20000 pixels (10% of the full Euso). With a valley 20 km wide, each pixel sees a spot of less than 100 m $`\times `$ 100 m of the opposite face.

Two such telescopes separated by a few 100 m and observing the same area would allow coincidences and stereoscopic information by TOF, thus reducing drastically the background.

## 5 Expectations

There are two ways to look for Cerenkov light: direct observation when the detector lies in the illuminated cone, or reflected light. The first method is adapted to point-like sources, the second to a diffuse flux.

For the direct detection of Cerenkov light, one considers neutrinos traversing the moutain ridge in front of the telescope. Cerenkov intensity for a given electromagnetic shower in the atmosphere has been well studied by the high energy photon telescopes (Cat, Whipple…). A shower of 300 GeV initiated about 10 km above earth generates 2 photoelectrons per m2 over a full area of half a km2. This gives a total of a few 105 photoelectrons. Higher energy showers give a linearly increasing flux of photons. The threshold is dictated by the number of detected photons. If one requires a minimum of 10 photoelectrons over a few adjacent pixels, the energy threshold is 2.1013 eV. At such energy the atmospheric flux starts to die down in front of the predicted AGN contributions. This method is well adapted to search for a neutrino emission coming from our galactic center or from AGN’s like the Markarians.

For the indirect Cerenkov light, the idea is to take advantage of the flash of light reflected on the mountain facing the telescope. The albedo is quite large, specially on a snowy surface. The reflection spreads light over 2$`\pi `$ srd. The set-up is now sensitive to large solid angles, but the telescopes catch a small fraction, 10-10, of the emitted photons due to reflection. This pushes the threshold to higher values. To collect 10 photoelectrons in a telescope, the initial shower energy must be above 1017 eV. This energy range is well adapted to GZK neutrinos.

## 6 Conclusion

The relatively modest experiment discussed here can explore an effective area of 50 km2 due to the large field of view of the optical device. The effective target depends on the nature of the considered neutrino.

For $`\nu _\mu `$, the produced $`\mu `$ can cross large distances in the rock before it exits, but the Cerenkov light emitted along its trajectory in the atmosphere may not be intense enough.

For $`\nu _\tau `$ the situation is the most favourable. The $`\tau `$ can cross several km in the rock, then comes out of the mountain and decays over the valley giving a high energy shower. The effective target is huge, up to 500 km3srd at high enough energies. With the technique of the reflected Cerenkov flash, and with the expectations of GZK neutrinos, a calculation gives some 10 events per year.

For $`\nu _e`$, one can take advantage of the Landau-Pomeranchouk-Migdal effect which suppresses the development of electromagnetic showers in dense materials. At energies of 1020 eV, an electron produced by the interaction of a $`\nu _e`$ can cross up to 100 m of rock. When it reaches the air the shower develops immediately. Thus the effective target has a depth of 100 m.

The present idea is essentially adapted to the detection of $`\nu _e`$ and $`\nu _\tau `$ interactions. This is complementary to the physics reach of volume detectors like Amanda and Antares which are limited to $`\nu _\mu `$ interactions. The angular resolution is quite good reaching 2 mrad. Moreover, this technique allows a decent energy measurement, typically 30$`\%`$, and, if statistics are large enough, spectra can be measured.

## 7 References

For more reading:

The Auger observatory, www.auger.org/admin/

The Euso project, www.ifcai.pa.cnr.it/$``$EUSO/

R.J.Protheroe, astro-ph/9809144

T.J.Weiler, hep-ph/0103023

A.Letessier-Selvon, astro-ph/0009416

X.Bertou et al., astro-ph/0104452

D.Fargion, astro-ph/0101565

S.Iyer Dutta et al., hep-ph/0012350


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# Genetic information and quantum gas

## Abstract

Possible explanation of the 64/20 redundancy of the triplet genetic code based on the assumption of quantum nature of genetic information is proposed.

The redundancy of the genetic code, where 64 possible nucleotide triplets code only 20 amino acids used as building blocks for all proteins, is well known. For a non-degenerate triplet code written in a four letter nucleotide alphabet (ATCG), the naive expectation of the possible coding repertoire is equal to the number of all sequences of $`r`$ elements ($`r=3`$, triplet) with each element taken from a set containing $`k`$ elements ($`k=4`$, number of bases):

$$A_r^k=k^r,orA_3^4=64.$$
(1)
In reality, only 20 amino acids are encoded, thus the code is degenerate because different triplets code the same amino acid. In each triplet the first two letters are more significant than the third one, but without full degeneracy: otherwise we would have only $`4^2=16`$ amino acids instead of 20. The endeavor of answering the question on the origin of $`64/20`$ degeneracy utmost inevitably leads to the conclusion that on the early stages of evolution codon was functioning as a set of nucleotides, rather than an ordered sequence. If it is the case, the total number of functionally different combinations (functional keys) should be equal to the number of sets equivalent with respect to permutations of $`r`$ elements with each element taken from a $`k`$-element set:

$$C_r^k=\frac{(k+r1)!}{r!(k1)!},orC_3^4=\frac{(4+31)!}{3!(41)!}=20.$$
(2)
The coincidence between combinatoric rule (2) and the redundancy $`64/20`$ was noted long ago by Gamov , who stressed it as a question to be answered in the future. Recently Patel , in relation to quantum computations, suggested that the choice of 20 amino acids is a result of optimization with respect to a quantum search algorithm, like that proposed by Grover. The Grover’s algorithm relates the number of objects $`N`$ that can be distinguished by a number of yes/no queries, $`Q`$, according to

$$(2Q+1)\mathrm{sin}^1(1/\sqrt{N})=\pi /2.$$
(3)
For $`Q=3`$ the exact solution is $`N=20.2`$. Thus, from the standpoint of quantum information theory, $`N=20`$, being very close to $`20.2`$, provides a quantum database search with minimal possible errors asking 3 questions only.

We would like to propose another interpretation of the genetic code redundancy 64/20. The formula (2) exactly coincides with the number of quantum states of a Bose gas of $`r=3`$ particles with $`k=4`$ possible quantum states, i.e. with the number of arrangements of $`r`$ indistinguishable particles into $`k`$ states.

The concept of an ideal Bose gas is an idealization used for adiabatically isolated systems of identical quantum particles. To some extent, we can suggest that this idealization works for the transcription and translation of genetic information. Taking into account that the typical codon size is about 0.5 nm, from the Heisenberg uncertainty principle

$$\mathrm{\Delta }x\mathrm{\Delta }p\mathrm{},$$
(4)
we can easily infer that for the typical size of a nucleotide

$$\mathrm{\Delta }p\frac{1.0510^{27}ergsec}{1.710^8cm}6.210^{20}\frac{gcm}{sec}.$$

For the typical mass of a hydrogen atom the energy associated with $`\mathrm{\Delta }p`$ is

$$\mathrm{\Delta }E=\frac{(\mathrm{\Delta }p)^2}{2m}\frac{(6.210^{20}\frac{gcm}{sec})^2}{21.6710^{24}g}1.210^{15}erg$$
(5)
For comparison, the typical energy of the hydrogen bond (in water) is $`1\frac{kkal}{mole}710^{14}erg`$ . Thus, the difference between the quantum fluctuations energy and the typical energy of hydrogen bond is one order only, and this small contribution might be significant for the formation of fine molecular structures. Due to the quantum fluctuation contribution, the processing by any biological agent of a single nucleotide by means of formation of hydrogen bonds is less reliable than the simultaneous processing of a nucleotide complex. For a codon, the size of which is roughly 3 times larger than that of a nucleotide, the quantum fluctuation energy is one order less, and that provides a reliable transmission of information. In other words, we can say that reading/writing of genetic information occurs by means quantum transitions of adiabatically isolated codon-anticodon pairs, i.e. in the quantum system of 6 nucleotides, three of those carry information content.

For complete analogy with quantum Bose gas, one could expect the codons with same nucleotide content (but different order of nucleotides) to code the same nucleic acid. The possible explanation for this does not happen is, that at early stages of the evolution this was really so, and each triplet was functioning as just a set of proto-nucleotides without any internal ordering, but later in course of the evolution with changing structure of nucleotides the symmetry with respect to permutation was spontaneously broken: the system evolved to a new ground state with less energy. What we observe now might be a result of this symmetry breaking. If so, this symmetry breaking should be non-degenerate: it maps 20 quantum states before the breaking to 20 states after it. It is important that if the proposed concept of adiabatically isolated quantum gas of nucleotides is valid, it guarantees exactly 20 possible states: not less, not more.

Aknowledgement

The authors are thankful to Dr. D. Chakalov for some bibliographical references related to this subject.

This work was supported in part by ISTC project 1813p/2001.


text:
# U, B and r band luminosity functions of galaxies in the Coma clusterBased on observations made with the Isaac Newton Telescope, operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias

## 1 Introduction

Clusters of galaxies are important laboratories for studies of galaxy evolution. The galaxy population in clusters is very different from the population in the field, suggesting that galaxy formation and evolution are a strong function of the environment.

The galaxy luminosity function (LF) should be an excellent tracer of environmental effects. Knowledge of the shape of the LF (in different bands) is a powerful tool for studies of galaxy evolution. Specifically, one can look for correlations between the shape of the general LF and environmental or cluster properties. In general the LF drops steeply at bright magnitudes and rises gradually at fainter magnitudes as described by a Schechter function . Sometimes, however, features such as bumps and a steeply rising faint part are found, which cannot be adequately fitted by a single Schechter function. Galaxies in the cluster core region are expected to have a different merger history than the galaxies populating the cluster outskirts where it blends into the field. This should be reflected in differently shaped LFs for dense and less dense regions within a cluster. López-Cruz et al.  propose that the flat faint end slopes found in rich clusters result from the disruption of dwarf galaxies. Biviano et al.  report a dip in the bright part of the general LF for rich clusters which is not seen in LFs of poor clusters or in the field. Andreon  verified the invariance of the shape of the bright part of the type-dependent LF in a large range of environments from the field to the cores of clusters several orders of magnitude denser. The determination of the exact shapes of LFs is difficult as the faint ends suffer from uncertainties in the contamination by field galaxies.

The Coma cluster ($`z=0.023`$, richness class 2) is the richest of the nearby clusters and ideal to study environmental effects (for a detailed overview of research on the Coma cluster see Mazure et al. 1998). Previous large field studies of the photometric properties of the galaxies in the Coma cluster have been based on photographic plates (e.g. Godwin, Metcalfe & Peach 1983; Lugger 1989). CCD studies yield better photometric precision, but have hitherto been limited to relatively small areas, mainly focused on the central regions (e.g. Thompson & Gregory 1993; Biviano et al. 1995; Bernstein et al. 1995; López-Cruz et al. 1997; Secker et al. 1997; Lobo et al. 1997; de Propris et al. 1998; Trentham 1998a, 1998b; Mobasher & Trentham 1998; Andreon 1999). We combine the benefits of wide field coverage with the photometric accuracy attainable with CCDs, by using the Wide Field Camera (WFC) on the Isaac Newton Telescope (INT) to image a large part of the Coma cluster from the dense core to the outskirts of the cluster. Our data offers the interesting possibility to study the LF for a large range of environments within the cluster. The primary goals of our survey are to study the LF, the colour-magnitude relation and to complement a large HI survey conducted with the Westerbork Synthesis Radio Telescope (WSRT).

In this paper we present our data and use our catalogue to construct *U*, *B* and *r* band LFs for various regions of the Coma cluster area. Our study complements previous studies of the LF of the Coma cluster by providing accurate, deep CCD photometry in three bands, covering an area of 5.2 deg2. Our wide field $`U`$ band data is of particular importance, because the $`UR`$ colour is a sensitive indicator of the presence of young stellar populations. Furthermore, the rest frame $`U`$ band remains in the optical window out to $`z1.3`$, which makes the $`U`$ band observations very useful for comparison to high redshift clusters. Previous $`U`$ band studies of Coma were limited to small samples of individual galaxies . Our mosaic has similar resolution (in kpc) and size (in Mpc) as large HST WFPC2 mosaics of high redshift clusters (e.g. van Dokkum et al. 1998) and provides a valuable low *z* zeropoint for studies of the evolution of galaxy morphology, colour and luminosity. For the first time a $`U`$ band LF for such a large area of the Coma cluster is determined. In addition we study the dependence of the LF on passband and projected distance from the cluster centre.

Throughout this paper we use $`H_0=100h_{100}`$ km s-1 Mpc-1 and coordinates are given in equinox J2000.0.

## 2 Observations

The data were collected during the nights of March 19–22 1999 with the Wide Field Camera (WFC) on the Isaac Newton Telescope (INT), on Rogue de Los Muchachos on the island of La Palma (Spain). The WFC consists of four $`2048\times 4100`$ pixels EEV CCDs and a fifth CCD for autoguiding. The layout of the chips is shown in Fig. 1. It is designed to provide a large field survey capability for the prime focus of the INT. The sky coverage is $`4\times 259\mathrm{}^2`$ with a plate scale of $`0\stackrel{}{.}333`$ pixel-1. The camera covers 80 per cent of the unvignetted field of the INT.

We have imaged a mosaic of 25 overlapping pointings covering a total area of $`5.2`$ deg2 or $`2.8\times 2.8h_{100}^1`$ Mpc. Broadband filters RGO *U*, Harris *B* and Sloan *r* were used for the 6 pointings covering the core and the south-west group (containing NGC 4839). The other 19 pointings were observed with Harris B and Sloan r. For each pointing two exposures, offset by $`1\mathrm{}`$, were taken. This ensured that we would be able to determine the relative zeropoint offsets between exposures and chips and there would be very few gaps in the final mosaic. Furthermore, galaxies in the overlapping regions give us good estimates of the errors due to photon noise and flatfielding. Integration times were $`2\times 300`$ s in $`B`$, $`2\times 600`$ s in $`r`$ and $`2\times 900`$ s in $`U`$. The layout of the field is shown in Fig. 2. Thick lines delineate pointings which were observed in the $`U`$ band, as well as $`B`$ and $`r`$.

The overall weather was good with an average seeing during the first two nights of $`1.4\mathrm{}`$ and $`1.9\mathrm{}`$ during the last two nights in the *r* band. The strategy was to observe the central parts of the cluster in *U*, *B* and *r* under photometric conditions. During the first night the standard Landolt  fields Sa107-602 and Sa101-427 were also observed at similar airmasses as the central fields. These standard fields contain many standard stars and give a good spread over the four CCD chips. This is important for the absolute calibration, since no two chips have exactly the same characteristics. In fact it is known that the WFC is non-linear.

The Coma fields were observed when the cluster had risen to an airmass $`<1.8`$. At the start of nights 3 and 4 we took exposures of an empty field (see Section 4.4). This field was later used to correct *U* band galaxy counts for foreground/background contamination.

## 3 Initial reduction

### 3.1 Flatfielding

Prior to any reduction the images were inspected to judge their quality. For each chip the bias frames per night were checked for repeating structures and count levels. The bias-structures were also visible in the science images. We combined all bias frames to create an average master bias frame for each night and each chip. After several tests we decided that the bias subtraction had to be performed in two steps; we first subtracted the overscan level by fitting a second order polynomial to the columns and then subtracted the (overscan subtracted) master bias frames. The second step successfully removed the remaining bias structures for chips 1,2 and 4. Chip 3 suffered from a few bad columns. These were removed by interpolation or by aligning and combining the images taken with a small offset. The rms noise level in the master bias frame was negligible compared to the rms noise in the science frames.

Accurate flat field images were created from the science frames. We have obtained 52 science images of the Coma area per chip per band for the  *B* and *r* bands. For the *U* band we have 23 science images, including the empty fields. We constructed a  *B* and *r* band masterflat by scaling these images by the mode, rejecting the lowest 10 and highest 15 pixelvalues, followed by median filtering. The *U* band masterflats were constructed in the same way, but there we rejected the lowest 5 and highest 10 pixelvalues before median filtering.

As a test we compared our flatfields to the ones of the Wide Field Imaging Survey which are available from the WFC archive111http://archive.ast.cam.ac.uk/wfsurvey/wfsurvey.html. Differences between the flat fields were at the level of $`10^4`$ or less, assuring that we have good quality flats.

After flatfielding, approximately 2.5 per cent of the area of chip 3 still suffers from $`3`$ per cent variations in the background, because this chip is partly vignetted. Because of the overlap between neighbouring pointings this has very little impact on our final mosaic. On average, the images are very flat with less than 0.8 per cent variations in the background.

### 3.2 Photometric calibration

The ultimate aim was to obtain a homogeneous photometric scale over the whole area covered. We dedicated the photometric anchor point to be chip 4 of pointing 11 (Fig. 2) at airmass 1.000. This field was observed during the first night under photometric conditions at a time close to when the standards were taken. First, we determined the photometric offsets between the four chips of the WFC, using objects in overlapping regions between the two offset exposures for each pointing. For the *U* band the number of bright objects in overlapping areas was low. Therefore, we could not use objects to determine the offsets, since this would have given unreliable results. Instead, we used the skylevel to determine photometric offsets. First, we made sky-images by filtering out all objects of the science images in the same way as for the flatfields. Comparison of the mean skylevels of the sky images gave the offsets. The resulting offsets are listed in Table 1. Errors indicate the uncertainty in the mean of all independent measurements. The $`1\sigma `$ spread between independent measurements of pairs of different pointings is much larger, and is caused by varying conditions between observations of neighbouring pointings. The offsets depend on the passband, because the response curves of the four CCDs are not identical.

We applied these offsets to bring all chips to the same scale. Only the first two nights were photometric and we proceeded by determining the photometric offsets between neighbouring pointings. The mean offset values are based on the 8 (or more) brightest objects in the overlapping areas in order to guarantee a reliable determination. We found differences of a few hundredths of a magnitude between fields taken at significantly different times (airmasses, conditions) in *B* and *r* up to more than a tenth of a magnitude in *U*. We mapped all the photometric offsets per pointing per band and scaled all pointings in such a way that the errors were spread over the total observed region and did not accumulate towards the edges of the covered area. The final result is that all *B* and *r* band images have the same zero-point to $`0.04`$ mag and the *U* band images to $`0.06`$ mag. This is shown for the $`r`$ and $`U`$ bands in the right panels of Fig. 3.

The photometric calibration was done using Landolt  standard stars. We did not have sufficient standard stars on all the chips to solve for the extinction coefficients so we set the extinction coefficients to constant values. We used average extinction coefficients at the effective wavelengths of the filter+CCD system, as listed in Table 2, to derive the colour terms and zero-points. The zero-points are listed in Table 3. The colour terms were found to be very small ($`0.01`$) and are neglected. Since Coma lies close to the galactic pole the extinction is insignificant for our purposes (0.043, 0.034 and 0.021 mag in the *U*, *B* and *r* bands respectively). Hence, we did not apply extinction corrections.

## 4 Object catalogues

The data volume is considerable and requires a fully automated pipeline for data handling. After the standard reduction steps the processed images were presented to software implemented at the Leiden Data Analysis Center (LDAC) for pipeline processing of overlapping images . The processing software is a series of programmes that, when run in a chain, derive source parameters for any given set of input frames of a given passband. Only the first step is an actual data *reduction* task in that it reduces the information to be processed from image data to catalogue data (an object list). All but the last of the following pipeline routines add information to the catalogue(s) increasing its size and information content. The final step merges the catalogues to create a multi-colour object catalogue with astronomically meaningful source information. The pipeline processing is performed on the full data set. Along the way we must decide on values for various parameters. We describe the pipeline steps in more detail below.

### 4.1 Detection of objects

We used SExtractor to automatically detect objects on each chip individually. The complete analysis of an image is done in six steps. First, a model of the sky background is built and parameters describing the global statistics are estimated. Then the image is background-subtracted, filtered and thresholded. Detections are then deblended, cleaned, photometered, classified and written to the final catalogue. For specific details of each of these steps the reader is referred to Bertin & Arnouts  or the SExtractor user’s guide.

Objects were identified as the peaks in the (background subtracted) convolved images that were higher than a given threshold above the local background. We used most of the standard SExtractor settings except for the memory parameters which had to be increased in order to detect the large cD galaxies successfully. The seeing parameter had to be adjusted for each image individually for a good star/galaxy separation. For all objects positions, magnitudes, basic shape parameters and star/galaxy (S/G) classifiers were determined and written to a catalogue. SExtractor produced a catalogue for each image which was subsequently converted to a format suitable for pipeline reduction. As a first pipeline processing step, all information of the individual image source extractions plus all original FITS image header information is combined into one single output catalogue per band.

### 4.2 Astrometry

Astrometric calibration was performed by pairing the input position catalogue (USNO-A2) with the extracted object information. For multiple band processing intercolour pairing is done first and between frames in overlap, overlap pairing is performed as well. The derived astrometric solution is then applied to all the objects in the set of frames. Sky coordinates (RA and Dec), as well as corrected geometric parameters are calculated. The final precision of this calibration depends on the accuracy of the source extractions, input catalogue accuracies and the correctness of the functional description of the distortions. We find $`\sigma _\mathrm{r}0.3\mathrm{}`$ as shown in the left panels of Fig. 3.

### 4.3 Final object catalogue

The final step in creating a catalogue containing useful multi-colour astronomical data is to merge all catalogues to get one source per position on the sky. All information referring to the same astronomical object is gathered and merged. Position information is a weighted mean of all detections where the weighting is based on detection signal-to-noise and detection environment conditions. Details of the merging are configurable. When the brightness contrast between overlapping galaxies is too low the software is not able to deblend them correctly, resulting in an erroneous catalogue entry. On the other hand, setting the deblend contrast parameter too low causes SExtractor to consider bright star forming regions in a galaxy as separate objects. Then, there is the possibility that deblended objects are merged by the pipeline software when creating the final object catalogue. This can happen in cases where objects are small compared to the errors in position and shape parameters. We carefully inspected dense regions in our mosaic and conclude that erroneous catalogue entries are rare and consequently do not affect our results.

Star/galaxy separation was performed based on SExtractor’s stellarity index. For bright objects stars and galaxies are easily separated, but towards fainter magnitudes and for bad seeing the division is not so clear. For most purposes we consider the objects with a S/G classifier value smaller than 0.8 in the *r* band (best seeing) to be galaxies. Bright (saturated) stars tend to have a S/G classifier smaller than this. We filtered these out by demanding a S/G classifier $`<0.1`$ for the brightest magnitudes. We visually inspected all bright objects to conclude that there is no contamination by stars up to at least $`m_\mathrm{r}=15`$. Beyond $`m19`$ mag we probably still have a fraction of stars in the sample, but for most purposes it is better to be contaminated by a (small) fraction of stars than to reject compact galaxies. Histograms of the catalogue’s raw number counts are shown in the panels of Fig. 4. Troughout this paper we use SExtractor’s MAG\_BEST as magnitude estimator. The final mosaic, composed of all pointings observed in the $`B`$ and $`r`$ bands, is shown in Fig. 5.

### 4.4 Control fields

For a survey as large and deep as ours, foreground/background subtraction can only be treated statistically, since only the brightest galaxies have measured redshifts. The main source of uncertainty in the determination of LFs comes from number statistics and background variance. Usually, flanking fields are used to get an estimate of the foreground/background correction and its variance. We expect that over the large area of the WFC the effects of cosmic variance are not important.

For the *U* band we have used $`4\times 900`$ s observations of an empty field located at $`\alpha =8^h00^m00^s,\delta =+50\mathrm{°}00\mathrm{}00\mathrm{}`$ spanning $`980`$ arcmin2. For both the *B* and *r* bands we have made use of the Wide Field Survey (WFS) data archive to get images of random fields. The *B* band control images are eight 600 s exposures, spanning $`2000`$ arcmin2 and centered at $`\alpha =12^h55^m55^s,\delta =+27\mathrm{°}01\mathrm{}40\mathrm{}`$ and $`\alpha =12^h53^m40^s,\delta =+26\mathrm{°}20\mathrm{}00\mathrm{}`$. The *r* band control images are four 600 s exposures, spanning $`1000`$ arcmin2 centered at $`\alpha =16^h04^m26^s,\delta =+54\mathrm{°}49\mathrm{}59\mathrm{}`$. For the *B* and *r* band control fields we rely on the (photometric) reduction of the four chips by the WFS team.

All control images were pipeline reduced to give control catalogues which were filtered with the same criteria as the Coma fields. We applied relative extinction corrections  to bring the extinction in the control fields into agreement with the Coma extinction, not zero extinction.

### 4.5 Completeness

The histograms shown in Fig. 4 suggest that the limiting magnitude is $`22.5`$ mag for all bands. However, due to less than perfect conditions in the last two nights this limit does not apply to the total observed area. To have uniform completeness for the total mosaic we compute LFs up to $`m_{lim}=21.73`$. The positions of these objects, relative to the cluster centre, are plotted in Fig. 6. The cluster is visible as a density enhancement on top of a uniform background. We have only considered clean detections (with good extraction flags) with more than 5 connected pixels above the background threshold.

Detection limits in general depend on the interplay between scale length/effective radius, magnitude and inclination, i.e. surface brightness. Edge-on galaxies of a certain magnitude are easier to detect than their face-on counterparts. Deep surveys have shown the existence of galaxies with surface brightnesses fainter than the night sky. These low surface brightness (LSB) galaxies are more likely to be missed at a given magnitude and inclination than their high surface brightness counterparts. Most of the LSB galaxies investigated in any detail are either late-type and disk dominated (de Blok et al. 1995; McGaugh & Bothun 1994), or giant, Malin-1-like galaxies (Sprayberry et al. 1995; Pickering et al. 1997).

In order to estimate these effects we followed two approaches. First we generated a $`r`$ band luminosity-surface brightness plot for all objects (mostly galaxies) in our catalogue. The data in our catalogue do not contain estimates of the central surface brightnesses, but we can compute mean surface brightnesses for all objects based on total flux and area above the analysis threshold. In Fig. 7 we show the resulting luminosity-surface brightness plot along with the relevant magnitude and surface brightness selection boundaries we used. The dashed lines represent the luminosity-surface brightness relations for objects with the minimum detectable size (the seeing disk). We show minimum size detection lines for a seeing of $`1.5\mathrm{}`$ and $`1\mathrm{}`$, from left to right, and it can be seen that occasionally the seeing drops even below $`1\mathrm{}`$. The mean isophotal limits for the $`U`$ and $`B`$ bands are 25.10 and 25.42 mag arcsec-2 respectively. From this figure it is evident that we are not likely to miss galaxies due to their low surface brightness. Second we generated artificial elliptical galaxies with de Vaucouleurs’ law  light profiles and spiral galaxies with exponential light profiles. We then added these galaxies into empty regions of our Coma images and verified whether SExtractor could recover these using the same selection criteria as for Coma fields. From our simulations we estimate that we are able to detect ellipticals with effective radii $`r_\mathrm{e}3h_{100}^1`$ kpc or $`r_\mathrm{e}9\mathrm{}`$ down to $`19.5`$, $`19.5`$ and $`19`$ mag in the *U*, *B* and *r* band respectively. Furthermore, we are able to detect dwarf galaxies modelled as exponential disks with $`h_\mathrm{d}1`$ kpc down to $`19.5`$, $`20`$ and $`20`$ mag or $`\mu _0=23.8,24.3`$ and 24.3 mag arcsec-2 in the *U*, *B* and *r* band respectively. At the distance of Coma, $`m=20`$ corresponds to $`M=14.2`$. Disk dominated LSB galaxies typically have $`h_\mathrm{d}3`$ kpc and $`\mu _{0,\mathrm{B}}23.2`$ mag arcsec-2. Assuming typical colours as in the de Blok et al.  sample, this corresponds to $`\mu _{0,\mathrm{U}}23.1`$ and $`\mu _{0,\mathrm{r}}22.4`$ mag arcsec-2. Our simulations show that such LSB galaxies are within our detection limits.

To illustrate the data quality we show examples of galaxies in Fig. 8. These have been drawn from our catalogue for magnitude bins $`M_\mathrm{B}`$= -21 to -13 in steps of one magnitude, two examples per bin.

## 5 Total luminosity functions

We constructed foreground/background corrected LFs by subtracting counts in the control catalogues from the Coma counts. From Fig. 4 it is obvious that the number of foreground/background counts is a strongly varying function of magnitude. Especially the faintest points of the LFs are largely influenced by an inaccurate determination of the amount of contaminating galaxies. We used very large control fields, and large bin-widths compared to the photometric uncertainties. Therefore, effects caused by errors in the determination of foreground/background counts will be suppressed. Furthermore, we carefully calculated effective areas for all control fields and the Coma mosaic by counting unblotted pixels on each frame. Pixels which reduced the area for object detection, e.g. dead columns, saturated stars etc., were blotted prior to the pixelcounting. The total cluster counts and the field counts estimates are listed in Table 4.

In Fig. 9 the LFs for the complete data set are shown. Solid lines represent best-fitting Schechter functions with parameters as listed in Table 5. The faint end slopes increase towards shorter wavelengths. The best-fitting Schechter functions are rather poor representations of the data for all bands, with several points lying more than $`1\sigma `$ away from the best-fitting values. The $`\chi ^2`$ statistic confirms the eye’s impression that the LFs for the complete data set cannot be represented by single Schechter functions. These are the first accurate determinations of LFs for such large areas of a cluster. Furthermore, to our knowledge the *U* band LFs presented here are the first ever published for the Coma cluster.

## 6 Dependence of luminosity functions on radial distance from the cluster centre

In order to study the dependence of the LF on radial distance from the cluster centre we defined five areas as annuli with varying widths and radii projected on the cluster centre, as shown in Fig. 5. For each of these areas we carefully determined the effective area for galaxy detection and constructed the corresponding LFs. The contamination by foreground/background galaxies becomes severe towards the outskirts of the cluster. Their numbers become equal or greater than the Coma counts at $`r>19`$, $`r>18`$ and $`r>17`$ in annulus I, III and IV, respectively.

We arbitrarily defined the core of the Coma cluster as the area with $`r<245h_{100}^1`$ kpc (area I). This is comparable in size to the *total* observed areas in previous studies. In Fig. 10 we show the central LFs with best-fitting Schechter functions overplotted as solid lines. The insets show the 68, 95 and 99 per cent confidence levels for the $`M^{}`$ and $`\alpha `$ parameters resulting from the fit to the binned data. The best-fitting parameters are listed in Table 6. The bright end of the *B* band central LF is not adequately represented by the Schechter function. The faint end, however, is well represented by the Schechter fit. We do not confirm the dip, located at $`M_\mathrm{B}17.2`$, reported by Biviano et al. . We stress that our LF has been determined with completely different data and methods, complicating any direct comparison of results. Their estimate of the faint end slope ($`\alpha _\mathrm{B}=1.3\pm 0.1`$) is, however, in agreement with our result. Comparison of our *B* band LF with the typical richness class 2 composite cluster LF \[1998b\] shows that the faint ends are consistent up to the completeness limit. Beyond the completeness limit the composite LF rises more steeply than the LF we have derived. Our value of the faint end slope of the central *r* band LF is in agreement with Lugger  ($`\alpha _\mathrm{R}1.19\pm 0.17`$), but somewhat shallower than the slopes derived for Coma by e.g. Bernstein et al. , López-Cruz et al.  and Secker et al.  who all find $`\alpha _\mathrm{R}1.4`$. We stress that a direct comparison is hampered by the fact that these authors use different areas or composite LFs. To demonstrate more clearly that the LF is mainly shaped by the area we extracted Trentham’s \[1998a\] area and constructed $`B`$ and $`r`$ band LFs. In Fig. 11 we compare the results of both determinations of the LFs. Up to the completeness limits the LFs are very similar showing that not the methodology employed, but the area chosen has the most crucial effect on the shape of the LF.

In general a single Schechter function is a reasonable representation of all the central LFs with 2 points lying $`1\sigma `$ or more from the best-fitting value for all bands. It is expected from LF studies of *composite* dense and loose clusters and of single rich and poor clusters that the LF shape depends on environment. Below, we study the change in the shape of the LF as function of position *in* the cluster. We will examine whether differences can be attributed to effects of the local environment.

In the panels of Fig. 12 the LFs corresponding to the annuli II to V of Fig. 5 are shown for all bands. It is clear that these LFs are not simply scaled versions of the central LFs.

The $`U`$ band LFs are sensitive to star forming galaxies, and are therefore a poor indicator of the underlying mass distribution. They show significant curvature and at some radii dips, as reported for other bands (e.g. Biviano et al. 1995; Andreon & Pello 1999). Because of these dips these LFs cannot be adequately fitted by single Schechter functions.

The $`B`$ band LF of annulus II still resembles the central LF, but in annuli III and IV the faint end behaves differently. Even further out, in annulus V, the galaxies with $`M_\mathrm{B}19`$ or brighter become very rare and the faint end seems to steepen again, but only marginally.

The $`r`$ band LF of annulus II is relatively flat. At larger radial distances from the cluster centre the LFs become much steeper.

We quantified these trends as follows. We fitted a power law function ($`b10^{aM}`$) to the faint ends of the LFs in order to study their dependence on radial distance from the cluster centre. The LFs were fitted for $`M_\mathrm{U}>`$ -18, $`M_\mathrm{B}>`$ -19 and $`M_\mathrm{r}>`$ -20, respectively. In Fig. 13 we plot the power law slopes as function of cluster radius. We omitted the slope of the $`B`$ band LF for area IV: the value of the slope is extremely sensitive to the fitting region, and hence not well constrained. In general, the faint end slopes become steeper towards larger cluster radii.

## 7 Comparison with field luminosity functions

In the field the galaxy density is orders of magnitudes lower than in the cores of clusters like Coma. Galaxies in a dense cluster environment are likely to follow different evolutionary paths than galaxies in low density fields. It is therefore interesting to investigate whether this is reflected in their LF shapes. LFs of the field population have recently been measured by a number of surveys (e.g. Loveday et al. 1992; Lin et al. 1996; Lin et al. 1997; Geller et al. 1997; Marzke et al. 1998; Lin et al. 1999). Despite the large samples that were used to measure the LFs, controversy on the shape remains. One of the largest local redshift samples of galaxies selected from CCD images is provided by the Sloan Digital Sky Survey (SDSS) (Blanton et al. 2001). The SDSS survey has multicolour $`u^{},g^{},r^{},i^{},z^{}`$ photometry, whereas most of the older surveys measure LFs only for the $`B`$ and $`R`$ bands. We transformed the SDSS LFs to our photometric system using the transformations given in Fukugita et al. . Similarly, values for the slopes in $`U`$, $`B`$, and $`r`$ were obtained by interpolating between the nearest SDSS filters. The resulting SDSS LFs are shown in Fig. 9 as dashed lines. For clarity the LFs were renormalized by adding 2.8 to log $`\varphi (\mathrm{M})`$ in all bands. The faint end slopes of the field LFs increase towards shorter wavelengths, although less significantly than in Coma. The faint end slopes of the $`r`$ and $`B`$ band LFs of field and Coma galaxies are very similar. Interestingly, the faint end of the Coma $`U`$ band LF appears to be steeper than that of the field LF. This may indicate that dwarf galaxies at $`M_\mathrm{B}13`$ in Coma have similar colours as dwarf galaxies in the field.

## 8 Galaxy distribution

The best indicator of the underlying mass distribution in our data set is the *r* band, since it is least influenced by episodic star formation. We use this band to investigate the projected galaxy density distributions. Following Driver et al.  we separate our sample into giant and dwarf galaxies. We define giant galaxies as objects with $`23.5<M_\mathrm{r}<19.5`$ and dwarf galaxies as objects with $`19.5<M_\mathrm{r}<16.5`$. In Fig. 14 we plot the projected distributions of these two types on the sky. In panels (a) and (b) of Fig. 15 we plot their foreground/background corrected projected densities and in panel (c) their ratio as function of distance from the cluster centre. In panels (a) and (b) we also show isothermal profiles for comparison. The giant galaxies have a relatively small, sharply defined, area of high overdensity limited to the central cluster area. At a distance of 0.37 $`h_{100}^1`$ Mpc from the cluster centre their density abruptly drops by $`70`$ per cent and then decreases continuously. At distances from the cluster centre larger than 0.37 $`h_{100}^1`$ Mpc the dwarf-to-giant ratio (D/G) could become somewhat larger than in the core of the cluster, but this is not significant given the large uncertainties.

### 8.1 NGC 4839 group

It has long been known that at $`40\mathrm{}`$ south-west of the cluster centre a secondary concentration of galaxies exists (e.g. Wolf 1901). This is the group associated with the cD galaxy NGC 4839. The presence of this group is clearly visible in Fig. 15: the group’s density lies well above the average density at that cluster radius and is comparable to the central densities. We used a circular area of 255 arcmin2 centered on NGC 4839 (Fig. 5) to determine LFs. The LFs, shown in Fig. 16, are found to have different shapes than the central LFs (solid lines). Mobasher & Trentham  have derived a $`K`$ band LF for the field around NGC 4839. However, due to a small field size (9.9 arcmin2) and large uncertainties in background subtraction, their LF is essentially unconstrained. Lobo et al.  have derived a *V* band LF with a faint end slope comparable to their central LF, using an area of 117 arcmin2. We find a $`B`$ band LF which is much shallower than the central LF. The faint end of the $`U`$ band LF is also flatter, except for the last point. In the $`r`$ band we have a lack of galaxies fainter than $`M_\mathrm{R}=16`$, but the faint end slope is comparable to the slope of the central LF.

## 9 Discussion

In this paper we have used a statistical method to determine in $`U`$, $`B`$ and $`r`$ the LF of the galaxies in the Coma cluster and the dependence of the LF on projected distance from the cluster centre. We did find changes in shape as a function of radius indicating changes in the galaxy population in the cluster. At the same time this implies that comparison with other work is difficult as the LF shape depends critically on the area chosen for study. The changes in the LF shapes are very likely related to the local environment. We will accordingly discuss this possibility in more detail here.

The $`\alpha `$ parameter of the Schechter function measures effectively the faint end slope of the luminosity distribution and characterizes the intermediate and dwarf galaxy populations. A flat faint end slope implies a lack of these low luminosity galaxies. López-Cruz et al.  observe the trend that steep faint end slopes are detected in poorer clusters and the flatter slopes are, on average, found in richer clusters. This suggests that environmental properties could dictate the faint galaxy population. In a scenario in which mergers, interactions, tidal stripping, destruction of dwarfs, infall etc. play a role we expect to see a lack of faint galaxies towards the regions of higher galaxy density. This then should be reflected in a flattening of the low luminosity end of the LF. We do observe this effect; e.g. the slope of the faint end of the $`U`$ band LF decreases from $`a=0.20`$ at $`0.7h_{100}^1`$ Mpc to $`a=0.13`$ in the centre. In terms of the slope of the Schechter function these values correspond to $`\alpha =1.5`$ and $`\alpha =1.32`$. The effect is also present in the $`B`$ and $`r`$ band LFs, and measured out to a larger radius of $`r=1.3h_{100}^1`$ Mpc.

When comparing the faint end slopes of the Coma LFs with those from the SDSS the most striking result is that the $`r`$ and $`B`$ band LFs are very similar. This is remarkable given the differences in environment and galaxy populations. However, the $`U`$ band slopes of Coma are steeper than in the field so apparently there is a relation between the relative increase in low luminosity systems in Coma and the colour of the band. A possible interpretation is that the (infalling?) dwarf galaxies in the outer parts of Coma are undergoing bursts of star formation triggered by interactions with neighbour galaxies and/or the intra-cluster medium. As a result the galaxies brighten, preferentially in the $`U`$ band, causing a steepening of the faint end slopes of the LFs. If correct, this is a clear sign that the Coma cluster is not a relaxed system, but that, especially in its periphery, the cluster is still forming and inducing strong evolution to the galaxy population. The flattening of all Coma LFs towards the cluster centre hints that there the galaxies have already lost most of their gas and enhanced star formation has long ceased.

The group around NGC 4839 has been subject of debate in the literature, because it is not clear whether it is falling into the cluster for the first time or has already made one pass through (for scenarios see e.g. Colless & Dunn 1996; White et al. 1993; Burns et al. 1994). Bravo-Alfaro et al.  have done H i imaging of the Coma cluster and the NGC 4839 group. From the nondetections in the close vicinity of NGC 4839 and the presence of several starburts and post-starbust galaxies with very low H i content in that zone they conclude that it passed at least once through the core. The LF of the field around NGC 4839 has a different faint end slope than the central LFs which could be related to the dynamical history of this group. The observed shape differences could be explained if during the passage a large fraction of the dwarf galaxies has been stripped from the group and redistributed throughout the cluster potential.

To explain the dependence of the shape of the LF on projected distance from the cluster centre we would need much more information. Knowledge of the galaxy morphologies, redshifts, the morphology-density relation (Dressler 1980; Whitmore et al. 1983), the type-dependent LFs, H i observations etc. are necessary to derive a complete scenario in which mergers, tidal stripping, infall etc. play a role. For instance, the observed dips and increasing faint end slopes could be the combined result of Coma’s morphological composition together with the shapes of the type-dependent LFs.

## 10 Summary and conclusions

We have presented the first results of a wide field photometric survey of the Coma cluster in the *U*, *B* and *r* bands. The derivation of the source catalogue, along with the steps concerning the pipeline reduction, have been discussed. Our high quality data provides a valuable low $`z`$ comparison sample for studies of galaxy morphology, colour and luminosity at higher $`z`$.

In this paper we have used the data to study the dependence of the galaxy LF on passband and projected distance from the cluster centre. The LFs of the complete data set cannot be represented by single Schechter functions. The central *U*, *B* and *r* band LFs can be represented by Schechter functions with parameters as listed in Table 6. The expectation that the shape of the LF depends on environment is confirmed. The LFs as a function of distance from the cluster centre have (very) different shapes than the central LFs and, therefore, no universal general LF exists. The faint ends of the LFs become steeper towards the outskirts of the cluster. A steepening of the faint ends of the LFs towards less dense regions clearly supports the existence of environmental effects. The difference in faint end slopes of the overall LFs and those of the field is colour dependent (strongest in $`U`$) and can be attributed to enhanced star formation in the dwarf galaxy population in the outer parts of Coma where evolution apparently is still very strong. The LFs of the field around NGC 4839 support the idea that this group has passed through the cluster centre at least once.

We are in the process of creating a catalogue of all spectroscopically confirmed cluster members. This will enable us to revise the Coma LFs and to check the quality of the statistical method to determine LFs. We have also obtained Westerbork Synthesis Radio Telescope (WSRT) H i mosaic data covering an total area of $`2.94\mathrm{°}\times 2.05\mathrm{°}`$ in order to study the H i properties as function of environment and assess the importance of merging and stripping. Combined with our optical data set this will greatly enhance the ability to study the structure and dynamics of Coma, using a data set that is unrivalled by what is available for any other cluster.

## Acknowledgements

We thank the referee for detailed and constructive comments. Part of the data was made publically available through the Isaac Newton Groups’ Wide Field Camera Survey Programme. P. G. v. D. acknowledges support by NASA through Hubble Fellowship grant HF-01126.01-99A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA under contract NAS 5-26555.