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# 1 Expression of the genes in the set S(GATGAG): The average expression of the genes in the set (solid red line) are compared to the genome-wide average expression (dashed green line) at the seven time points of the diauxic shift experiment. The expression data are the log₂ of the ratio between mRNA levels at each timepoint and the initial mRNA level.

Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

M. Caselle1, F. Di Cunto2 and P. Provero3,1,∗

1 Dipartimento di Fisica Teorica, Università di Torino, and INFN, sezione di Torino, Torino, Italy.

2 Dipartimento di Genetica, Biologia e Biochimica, Università di Torino, Torino, Italy.

3 Dipartimento di Scienze e Tecnologie Avanzate, Università del Piemonte Orientale, Alessandria, Italy.

e-mail addresses:
caselle@to.infn.it, ferdinando.dicunto@unito.it, provero@to.infn.it

corresponding author

Abstract

Background

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation.

Results

The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined.

Conclusions

We have described and successfully tested a simple computational method to identify upstream motifs relevant to gene regulation in eukaryotes by studying the statistical correlation between overepresented upstream motifs and gene expression levels.

Introduction

One of the biggest challenges of modern genetics is to extract biologically meaningful information from the huge mass of raw data that is becoming available. In particular, the availability of complete genome sequences on one hand, and of genome-wide microarray data on the other, provide invaluable tools to elucidate the mechanisms underlying transcriptional regulation. The sheer amount of available data and the complexity of the mechanisms at work require the development of specific data analysis techniques to identify statistical patterns and regularities, that can then be the subject of experimental investigation.

The regulation of gene expression in eukaryotes is known to be mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. One of the main problems in studying regulation of gene expression is to identify the motifs that have transcriptional meaning, and the genes each motif regulates.

The usual approach to this kind of analysis begins by identifying groups of co-regulated genes, for example by applying clustering techniques to the expression profiles obtained from microarray experiments. One then studies the upstream sequences of a set of coregulated genes looking for shared motifs. Examples of this approach as applied to S. cerevisiae are Refs. .

In this paper we suggest an alternative method which somehow follows the inverse route: genes are grouped into (non-disjoint) sets, each set being characterized by a short motif which is overrepresented in the upstream sequence. For each set, the average expression is computed for a certain microarray experiment, and compared to the genome-wide average expression from the same experiment. If a statistically significant difference is found, then the motif that defines the set of genes is a candidate regulatory sequence. The rationale for looking for overrepresented motifs is that, in many instances, regulatory motifs are known to appear repeated many times within a relatively short upstream sequence , so that the number of repetitions turns out to be much bigger than what would be expected from chance alone.

A somehow related approach, which does not require any previous grouping of genes based on their expression profiles, was presented in Ref. , where the effect of upstream motifs on gene expression levels is modeled by a sum of activating and inhibitory terms. Experimental expression levels are then fitted to the model, and statistically significant motifs are identified. Our approach differs in the importance given to overrepresented motifs, thus considering activation and inhibition as an effect that depends on a threshold number of repetitions of a motif rather than on additive contributions from all motifs. Clearly the two mechanisms are far from being mutually exclusive, therefore we expect the candidate regulatory sites found with the two methods to significantly overlap.

However it is important to notice that the kind of statistical correlation between upstream motifs and expression that our algorithm identifies does not depend on any special assumption on the functional dependence of expression levels on the number of motif repetitions, as long as this dependence is strong enough to provide a significant deviation from the average expression when enough copies of the motif are present. A comparison of our results with those obtained in Ref.  is provided in the “Results and discussion” section.

The method

In general the motifs with known regulatory function are not identified with a fixed nucleotide sequence, but rather with sequences where substitutions are allowed, or spaced dyads of fixed sequences, etc. However in this study, in order to test the method while keeping the technical complications to a minimum, we will limit ourselves to fixed short nucleotide sequences, that we call words. While previous studies (see e.g ) show that even this simple analysis can give interesting results, the method we present can easily be generalized to include variable sequences and other more complicated patterns.

The computational method we propose has two main steps: first the open reading frames (ORFs) of an eukaryote genome are grouped in (overlapping) sets based on words that are overrepresented in their upstream region, compared to their frequencies in the reference sample made of all the upstream regions of the whole genome. Each set is labelled by a word. Then for each of these sets the average expression in one or more microarray experiments are compared to the genome-wide average: if a statistically significant difference is found, the word that labels the set is a candidate regulatory site for the genes in the set, either enhancing or inhibiting their expression.

It is worth stressing that the grouping of the genes into sets depends only on the upstream sequences and not on the microarray experiment considered: It needs to be done only once for each organism, and can then be used to analyse an arbitrary number of microarray experiments. It is precisely this fact that should allow the extension of the method to patterns more complex than fixed sequences, while keeping the required computational resources within reasonable limits.

Constructing the sets

We consider the upstream region of each open reading frame (ORF), and we fix the maximum length $`K`$ of the upstream sequence to be considered. The choice of $`K`$ depends on the typical location of most regulatory sites: in general $`K`$ is a number between several hundred and a few thousand. For each ORF $`g`$, the actual length of the sequence we consider is $`K_g`$ defined as the minimum between $`K`$ and the available upstream sequence before the coding region of the previous gene.

For each word $`w`$ of length $`l`$ ($`6l8`$ in this study), and for each ORF $`g`$ we compute the number $`m_g(w)`$ of occurrences of $`w`$ in the upstream region of $`g`$. Non palindromic words are counted on both strands: therefore we define the effective number of occurrences $`n_g(w)`$ as

$`n_g(w)`$ $`=`$ $`m_g(w)+m_g(\stackrel{~}{w})\mathrm{if}w\stackrel{~}{w}`$ (1)
$`n_g(w)`$ $`=`$ $`m_g(w)\mathrm{if}w=\stackrel{~}{w}`$ (2)
where $`\stackrel{~}{w}`$ is the reverse complement of $`w`$.

We define the global frequency $`p(w)`$ of each word $`w`$ as

$$p(w)=\frac{_gn_g(w)}{_gL_g(w)}$$
(3)
where, in order to count correctly the available space for palindromic and non palindromic words,

$`L_g(w)`$ $`=`$ $`2(K_gl+1)\mathrm{if}w\stackrel{~}{w}`$ (4)
$`L_g(w)`$ $`=`$ $`(K_gl+1)\mathrm{if}w=\stackrel{~}{w}`$ (5)
$`p(w)`$ is therefore the frequency with which the word $`w`$ appears in the upstream regions of the whole genome: it is the “background frequency” against which occurrences in the upstream regions of the individual genes are compared to determine which words are overrepresented.

For each ORF $`g`$ and each word $`w`$ we compute the probability $`b_g(w)`$ of finding $`n_g(w)`$ or more occurrences of $`w`$ based on the global frequency $`p(w)`$:

$$b_g(w)=\underset{n=n_g(w)}{\overset{L_g(w)}{}}\left(\genfrac{}{}{0pt}{}{L_g(w)}{n}\right)p(w)^n\left[1p(w)\right]^{L_g(w)n}$$
(6)
We define a maximum probability $`P`$, depending in general on the length $`l`$ of the words under consideration, and consider, for each $`w`$, the set

$$S(w)=\{g:b_g(w)<P\}$$
(7)
of the ORFs in which the word $`w`$ is overepresented compared to the frequency of $`w`$ in the upstream regions of the whole genome. That is, $`w`$ is considered overrepresented in the upstream region of $`g`$ if the probability of finding $`n_g(w)`$ or more instances of $`w`$ based on the global frequency is less than $`P`$.

This completes the construction of the sets $`S(w)`$. Two free parameters have to be fixed: the length $`K`$ of the upstream region to be considered and the probability cutoff $`P`$ for each length $`l`$ of words considered. A result in Ref.  suggests suitable choices of these two numbers: the authors list the 34 ORFs of S. cerevisiae that have 3 or more occurrences of the word GATAAG in their 500 bp upstream region. 23 out of these 34 ORFs correspond to a gene with known function, and 20 out of these 23 are regulated by nitrogen. This result suggests to choose $`K=500`$ for the upstream length, and a value of the probability cutoff such that three or more instances of GATAAG in the 500 bp upstream region of an ORF are considered significant. Any choice of $`P`$ between 0.018 and 0.1 would satisfy this criterion, and we chose $`P=0.02`$. Tentatively, we kept the same value of $`P`$ for all values of $`l`$. With this choice, the number of instances of a word that are necessary to be considered overrepresented in a 500bp upstream sequence can be as high as six for common 6-letter words and as low as one for rare 8-letter words. In particular, our set $`S(GATAAG)`$ almost111Our set is smaller that the one reported in Ref.  because we do not allow the upstream sequence to overlap with the previous gene: this eliminates 7 genes form the set. coincides with the one discussed in . However the word GATAAG will not turn out to be significant in our study.

As noted above, it would be natural to make the probability cutoff $`P`$ depend on the word length, simply because the number of possible words increases with their length: For example one could take the cutoff for each word length to be inversely proportional to the number of independent words of such length. However it turns out that this procedure tends to construct sets that are less significant when tested for correlation with expression. Therefore we chose to fix the cutoff at 0.02 for all word lengths. It is important to keep in mind that no statistical significance whatsoever is attributed to the sets per se: The only sets that are retained at the end of the analysis are the ones that show significant correlation with expression. Therefore the choice of the cutoff in the construction of the sets can be based on such a pragmatic approach without jeopardizing the statistical relevance of the final result.

Studying the average expression level in each set

The second step of our procedure consists in studying, for each set $`S(w)`$ defined as above, the expression profiles of the ORFs belonging to $`S(w)`$ in DNA microarray experiments. The idea is that if the average expression profile in the set $`S(w)`$ for a certain experiment is significantly different from the average expression for the same experiment computed on the whole genome, then it is likely that some of the ORFs in $`S(w)`$ are coregulated and that the word $`w`$ is a binding site for the common regulating factor.

To look for such instances we consider the gene expression profiles during the diauxic shift, i.e. the metabolic shift from fermentation to respiration, as measured with DNA microarrays techniques in Ref. . In the experiment gene expression levels were measured for virtually all the genes of S. Cerevisiae at seven time-points while such metabolic shift took place. The experimental results are publicly available from the web supplement to Ref. .

We considered each time-point as a single experiment, and for each gene $`g`$ we defined the quantity $`r_g(i)(1=1,\mathrm{},7)`$ as the $`\mathrm{log}_2`$ of the ratio between the mRNA levels for the gene $`g`$ at time-point $`i`$ and the initial mRNA level. Therefore e.g. $`r_g(i)=1`$ means a two-fold increase in expression at timepoint $`i`$ compared to initial expression.

For each time-point $`i`$ we computed the genome-wide average expression $`R(i)`$ and its standard deviation $`\sigma (i)`$. These are reported in Tab. 1, where $`N(i)`$ is the number of genes with available expression value for each timepoint. Then for each word $`w`$ we compute the average expression in the subset of $`S_w`$ given by the genes for which an experimental result is available at timepoint $`i`$ (in most cases this coincides with $`S_w`$):

$$R_w(i)=\frac{1}{N(i,w)}\underset{gS_w}{}r_g(i)$$
(8)
where $`N(i,w)`$ is the number of ORFs in $`S_w`$ for which an experimental result at timepoint $`i`$ is available, and the difference

$$\mathrm{\Delta }R_w(i)=R_w(i)R(i)$$
(9)
$`\mathrm{\Delta }R_w(i)`$ is the discrepancy between the genome-wide average expression at time-point $`i`$ and the average expression at the same time-point of the ORFs that share an abundance of the word $`w`$ in their upstream region. A significance index $`\mathrm{sig}(i,w)`$ is defined as

$$\mathrm{sig}(i,w)=\frac{\mathrm{\Delta }R_w(i)}{\sigma (i)}\sqrt{N(i,w)}$$
(10)
and the word $`w`$ is considered significantly correlated with expression at time point $`i`$ if

$$|\mathrm{sig}(i,w)|>\mathrm{\Lambda }$$
(11)
In this work we chose $`\mathrm{\Lambda }=6`$: this means that we consider meaningful a deviation of $`R_w(i)`$ by six s.d.’s from its expected value. The sign of $`\mathrm{sig}(i,w)`$ indicates whether $`w`$ acts as an enhancer or an inhibitor of gene expression.

Results and discussion

We found a total of 29 words of length between 6 and 8 above our significance threshold $`|\mathrm{sig}|>6`$. Most of them are related to known regulatory motifs; two words turned out to be false positives due to the presence, in their sets, of families of identical ORF’s. Finally, one word does not match any known motif and is a candidate new binding site.

The comparison between our significant words and known motifs was performed using the database of regulatory motifs made publicly available by the authors of Ref. , and the CompareACE software  available from the same web source. This package allowed us to compute the Pearson correlation coefficient of the best alignment between each of our significant words and each known regulatory motif (expressed as a set of nucleotide frequencies).

We used the following criterion to associate our significant words to known motifs: a motif is considered as identified if at least one significant word scores better than 0.8 when compared to it. A probability value for this choice of the cutoff can be estimated to be a few percent: out of all the 2080 independent 6-letter words, 66 (that is 3.17%) score better than 0.8 with at least one motif. For 7- and 8-letter words we have respectively 2.21% and 1.51%. Once a motif has been identified, all words which score best with the motif are attributed to it, independently of the score, provided their expression pattern is consistent with the word(s) scoring better than 0.8.

PAC and RRPE motifs

Nine significant words can be associated to the PAC motif , all of them with rather high scores. They are shown in Tab. 2, where, as in all the following tables, significativity indices are shown only for those timepoints where they exceed our threshold $`|\mathrm{sig}|>6`$. Given the perfect alignment of these words, it is not surprising that these sets largely overlap each other: The union af all the nine sets contains a total of 96 genes. As an example, in Fig. 1 we show the average expression for the genes associated with the word GATGAG as a function of the time, compared to the average expression computed over the whole genome. Fig. 2 shows the significance index for the same set. In Tab. 3 we show the set of 24 genes associated to the word GATGAG, together with their expression profiles.

Two words can be associated with confidence to the motif RRPE , and are shown in Tab. 4. The union of the two sets contains 76 genes. We see that genes containing the motifs PAC and RRPE are repressed at the late stage of the diauxic shift compared to the early stages. This result is in agreement with the expression coherence score data available from the web supplement to Ref. : There one can see that (1) of all known regulatory motifs, PAC and RRPE show the highest expression coherence for the diauxic shift and (2) viceversa, of the eight experimental conditions considered in Ref. , the diauxic shift is the one in which both the PAC and RRPE motif show the highest expression coherence score.

STRE and MIG1 motifs

A total of ten significant words can be associated to the motifs STRE  and MIG1 . It is well known that these play an important role in glucose repression (see e.g.  and references therein). Most of these words show comparable scores for the two motifs (due to their similarity) so we decided to show them together in Tab. 5 which shows the two scores for each word. A total of 212 genes belong to the union of all these sets.

The UME6 motif

Two words are associated to the known UME6 motif, a.k.a. URS1 , known to be a pleiotropic regulator implicated in glucose repression . They are shown in Tab. 6. The two sets do not overlap, so that a total of 56 genes are associated to this motif.

Other significant words

Three words, shown in Tab. 7, are of uncertain status: for the first one, the set S(ACTTTC) contains only 2 genes, making the statistical significance of the result questionable. The word CCCCTGAA scores best with the PDR motif (0.58): given the low significance of this score, and the fact that PDR does not seem to be relevant for any other word, this is most likely accidental. The word should probably be considered as belonging to the STRE/MIG1 motif (the scores are STRE: 0.46, MIG1: 0.49). Finally the word GCCCCTGA scores best with UME6 (0.55), but its expression pattern is more similar to the STRE/MIG1 motifs (scores: STRE:0.44, MIG1: 0.46).

False positives due to families of identical or nearly identical ORF’s

The genome of S. cerevisiae contains a few families of genes whose coding and upstream regions are identical or nearly identical. Consider for example the COS1 gene (YNL336W): the seven genes COS2-COS8 have both coding sequence and 500kb upstream sequence coinciding better than 80% with the COS1 sequence. Therefore if the upstream sequence of COS1 contains overerpresented words, they will likely appear in all of the upstream regions. On the other hand, the expression profiles of all the genes in the family will be the same when measured by a microarray experiment, simply because the experimental apparatus cannot distinguish between the mRNA produced by the various members of the family, due to cross-hybridization between their mRNA. Therefore all of the genes of the family are likely to occur in the sets of the words that are overrepresented in their upstream region, and even a small deviation from the genome-averaged expression acquires a statistical significance.

We found two instances of this in our analysis: the words GACGTAGC and GGTCGCAC appear to be associated to significant enhancement of the corresponding sets of genes at late timepoints in the diauxic shift: however the two sets contain respectively seven out of eight and all of the COS1-COS8 genes. Since the COS genes are mildly overexpressed, this creates a false statistical significance. When one corrects for this, by keeping only one representative of the family, the statistical significance of the two sets disappears.

A candidate new motif

Finally, the word ATAAGGG/CCCTTAT is a candidate new binding site, since it does not have good comparison scores with any of the known motifs. It scores best with the AFT1 motif, with a 0.52 score which is practically meaningless since 84.9% of all independent 7-letter words score the same or better with at least one motif. It is associated with 13 genes, as shown in Tab. 8, which are overexpressed at late timepoints. The average expression levels for the set and the significance index are shown as a function of time in Figs. 3 and 4.

Comparison with the results of Ref.

As stated in the introduction, the method proposed in Ref. also allows one to identify regulatory motifs without any previous clustering of gene expression data: a linear dependence of the logarithm of the expression levels on the number of repetitions of each regulatory motifs is postulated, and motifs are ranked according to the reduction in $`\chi ^2`$ obtained when such dependence is subtracted from the experimental expression levels. Iteration of the procedure produces a model, that is a set of relevant regulatory motifs, for each expression data set.

In Ref.  such a model is presented for the 14 min. time point in the $`\alpha `$-synchronized cell-cycle experiment of Spellmann et al., Ref. . We used our algorithm on the same data set to compare the findings. Let us concentrate on the 7-letter words (the longest considered in ). We found 9 significant words, reported in Tab. 9. Of these, five coincide with or are very similar to words found by the authors of Ref. (see their Tab. 2). The remaining four (AGGCTAA, GGCTAAG, GCTAAGC and CTAAGCG, whose similarity clearly suggests the existence of a longer motif) are of particular interest for the purpose of comparing the two methods: If one looks at the dependence of the expression levels on the number of occurrences of these words in the 500 bp upstream region, one clearly sees the existence of an activation threshold (see Fig. 5, where such dependence is shown for GGCTAAG). On the other hand, by looking at these data one hardly expects a significant reduction in $`\chi ^2`$ when trying to describe this dependence with a straight line. This should be compared to the same dependence for the word AAAATTT, shown in Fig. 6, which is found by both algorithms. On the other hand, there are two 7-word motifs found in  that do not pass our significativity threshold, that is CCTCGAC and TAAACAA.

We can conclude that the two methods tend to find motifs with a different effect on gene expression: probably the best results can be obtained by using them both on the same data set.

Conclusions

We have presented a new computational method to identify regulatory motifs in eukaryotes, suitable to identify those motifs that are effective when repeated many times in the upstream sequence of a gene. The main feature that differentiates our method from existing algorithms for motif discovery is the fact that genes are grouped a priori based on similarities in their upstream sequences.

Most of the significant words the algorithm finds can be associated to five known regulatory motifs: This fact consitutes a strong validation of the method. Three of them (STRE, MIG1 and UME6) were previously known to be implicated in glucose suppression, while the fact that PAC and RRPE sites are relevant to regulation during the diauxic shift is in agreement with expression coherence data as reported in the web supplement to Ref. . One of the significant words we find (ATAAGGG) cannot be identified with any known motif, and is a candidate new binding site.

It is easy, at least in principle, to extend the method to a larger class of regulatory sites. According to our knowledge of gene regulation, this should be done at least in two directions: (1) the analysis should not be restricted to fixed sequences, but extended to motifs with controlled variability; in particular the extension to spaced dyads  should be straightforward; (2) the combinatorial analysis of binding sites  could also be performed along the same lines, that is first grouping genes according to which combinations of motifs appear in their upstream region, and then analysing expression profiles within each group.

Acknowledgement

Upstream sequences were downloaded, and many cross-checks were performed, using the impressive collection of packages available from the Regulatory Sequence Analysis Tools (RSAT)  at
http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/ or
http://embnet.cifn.unam.mx/rsa-tools/.


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# Photon vs Energy Magnitude Systems and the Measurement of the Cosmological Parameters

## 1 Introduction

Measurements of the cosmological parameters using distance indicators rely on the redshift-dependent evolution of the distance modulus $`\mu `$. The distance modulus is measured as the difference between observed and absolute magnitudes of a “standard candle” after K-correction (Oke & Sandage, 1968) for the redshifting of its spectrum. The theoretical value for $`\mu `$ is related to the luminosity distance $`d_L(z)`$ defined such that a source with luminosity $`L`$ at redshift $`z`$ has observed energy flux $`f`$ as if the energy has been diluted to the surface of a sphere with radius $`d_L`$, i.e. $`L=4\pi d_L^2f`$ (e.g. Carroll, Press, & Turner (1992)). Cosmological parameters can then be measured from their functional dependence on $`d_L`$; this technique has been used by two groups with Type Ia supernovae \[the High-$`z`$ team (Riess et al., 1998) and the Supernova Cosmology Project (SCP) (Perlmutter et al., 1999)\] and gives evidence for an accelerating universe.

Observations are in fact made with photon counters (CCD’s, photo-multipliers) and the luminosity distance is not the same as the “photon luminosity distance” $`d_\gamma `$; if N is the photon luminosity and n is the observed photon flux, then $`N=4\pi d_\gamma ^2n`$ where $`d_L=d_\gamma (1+z)^{1/2}`$. This has lead to some confusion as to whether a “photon” distance modulus should be used to measure cosmological parameters, whether the magnitude system is photon-based or energy-based, and which K-corrections should be applied. Such distinctions which previously have been unimportant are significant as we move into an era of precision cosmology. In this paper we rederive and expand upon the K-correction results of Schneider, Gunn, & Hoessel (1983). We comment on the magnitude system and the Johnson-Cousins system in particular (§ 2). We find that any ambiguity can be removed with the proper definition of the K-correction for which we derive the equations for both photon and energy systems (§ 3). We conclude that although the differences between the two K-corrections are small, the distinction between energy and photon systems is important for planned future high-precision supernova experiments (§ 4).

## 2 Magnitude Systems

The primary standards of a photometric system can have their magnitudes measured either by their energy or photon flux ratios. Unless a photon–energy conversion correction is later applied, the flux system is determined by the detectors used to measure the primaries. The type of detector used in subsequent observations does not determine whether the magnitude system is photon or energy based; in principle the color and airmass corrections put observed magnitudes into the primary system.

The Johnson-Cousins magnitude system prevalent today is a photon system, what Johnson & Morgan (1953) describe as “a system of photoelectric photometry”. As described in Johnson & Morgan (1951), their observational setup employed a photomultiplier as a detector, with the counts being the number of “deflections” recorded by a potentiometer. After an airmass correction these counts were directly converted to magnitudes. The secondary stars of Landolt (1973, 1983, 1992) (whose raw data also were obtained with photon counters) are calibrated via Johnson and Cousins primary standards and thus must be in the photon system. Observed magnitudes are therefore photon-based and should be analyzed as such.

An illustrative example of where there is a numerical difference between the two magnitude systems is a star that has the same integrated $`B`$-band energy flux as Vega (which for simplicity we consider to be the zero point of the magnitude system) but has a different photon flux since it has a different spectral energy distribution (SED). Relative magnitude measurements with a single filter of a set of stars with similar spectral energy distributions are independent of whether we are photon counting or measuring energy; two stars with the same SED but differing brightness will have

$$\mathrm{\Delta }m=m_2^\gamma m_1^\gamma =m_2^ϵm_1^ϵ$$

where $`m_1`$ and $`m_2`$ are the stars’ magnitudes. It follows that since the zeropoint of magnitude system is based on Vega, the energy and photon magnitudes of A0V stars are identical: $`m_{A0V}^\gamma =m_{A0V}^ϵ`$.

As an aside, one of the Johnson & Morgan (1953) criteria for a photometric system is “a determination of the zero point of the color indices in terms of a certain kind of star which can be accurately defined spectroscopically.” Such knowledge, along with the shapes of the pass-band transmission functions, do allow for calculated transformation between photon and energy magnitude systems. Indeed, much effort has been placed in measuring and modeling the intrinsic SED of Vega (Dreiling & Bell (1980) and references therein).

## 3 The K-correction

We explicitly review the K-correction calculation of Kim, Goobar, & Perlmutter (1996) that has been used in SCP cosmological analysis. to remove any ambiguity. We define the K-correction $`K_{xy}`$ such that

$$m_y^\alpha =M_x^\alpha +\mu (z)+K_{xy}^\alpha $$
(1)
where $`\alpha =\{\gamma ,ϵ\}`$ for photon or energy magnitude systems. The observed magnitude in passband $`y`$ is $`m_y`$ and the absolute magnitude in passband $`x`$ is $`M_x`$. We adopt the theoretical expression for the distance modulus, $`\mu `$, based on luminosity distance. In other words, the functional form of $`\mu (z;H_0,\mathrm{\Omega }_M,\mathrm{\Omega }_\mathrm{\Lambda })`$ in Equation 1 is identical for photon and energy systems. Given $`f_\lambda (\lambda )`$ as the energy flux density of a supernova 10 parsecs away, we can compute the corresponding energy and photon fluxes at high redshift.

$$\begin{array}{cc}f_\lambda (\lambda )d\lambda \hfill & \hfill \text{Energy flux density in d}\lambda \text{ bin of a supernova 10 parsecs away}\\ n_\lambda (\lambda )d\lambda =\frac{\lambda d\lambda }{hc}f_\lambda (\lambda )\hfill & \hfill \text{Photon flux in d}\lambda \text{ bin of a supernova 10 parsecs away}\\ f_\lambda ^z(\lambda )d\lambda =\frac{d\lambda }{1+z}f_\lambda \left(\frac{\lambda }{1+z}\right)\left(\frac{10pc}{d_L(z)}\right)^2\hfill & \hfill \text{Energy flux density in d}\lambda \text{ bin of a supernova at }z\\ n_\lambda ^z(\lambda )d\lambda =\frac{\lambda d\lambda }{hc(1+z)}f_\lambda \left(\frac{\lambda }{1+z}\right)\left(\frac{10pc}{d_L(z)}\right)^2\hfill & \hfill \text{Photon flux density in d}\lambda \text{ bin of a supernova at }z\end{array}$$

The $`(1+z)^1`$ terms in the redshifted flux densities are due to wavelength dilution (Oke & Sandage, 1968). The ratio between high and low-redshift photon flux is a factor $`1+z`$ greater than the corresponding ratio for energy flux which suffers from redshifted energy loss. More precisely

$$\frac{n_\lambda ^z(\lambda )}{n_\lambda (\lambda /(1+z))}=\frac{(1+z)f_\lambda ^z(\lambda )}{f_\lambda (\lambda /(1+z))}.$$
(2)
The fact that the relative photon fluxes of high-redshift supernovae are $`1+z`$ “brighter” than energy fluxes can be interpreted as being due to the latter’s extra energy loss due to redshift.

Using the fact that $`\mu =5\mathrm{log}\left(\frac{10pc}{d_L(z)}\right)`$ we can compute and compare energy and photon K-corrections,

$`K_{xy}^ϵ`$ $`=`$ $`2.5\mathrm{log}\left({\displaystyle \frac{𝒵_x^ϵ(\lambda )S_x(\lambda )𝑑\lambda }{𝒵_y^ϵ(\lambda )S_y(\lambda )𝑑\lambda }}\right)+2.5\mathrm{log}(1+z)+2.5\mathrm{log}\left({\displaystyle \frac{f_\lambda (\lambda )S_x(\lambda )𝑑\lambda }{f_\lambda (\lambda /(1+z))S_y(\lambda )𝑑\lambda }}\right)`$ (3)
$`K_{xy}^\gamma `$ $`=`$ $`2.5\mathrm{log}\left({\displaystyle \frac{\lambda 𝒵_x^\gamma (\lambda )S_x(\lambda )𝑑\lambda }{\lambda 𝒵_y^\gamma (\lambda )S_y(\lambda )𝑑\lambda }}\right)+2.5\mathrm{log}(1+z)+2.5\mathrm{log}\left({\displaystyle \frac{\lambda f_\lambda (\lambda )S_x(\lambda )𝑑\lambda }{\lambda f_\lambda (\lambda /(1+z))S_y(\lambda )𝑑\lambda }}\right).`$ (4)
The filter transmission functions are given as $`S_i(\lambda )`$ where $`S_x`$ is the rest-frame filter and $`S_y`$ is the observer filter. (The transmission functions give the fraction of photons transmitted at a given wavelength where we assume no down-scattering.) For the standard star (i.e. calibrator) SED $`𝒵(\lambda )`$ we assume the existence of a standard star with identical properties as the supernova, i.e. with exactly the same color and observed through the same airmass. Pragmatically, this assumption affirms perfect photometric calibration to all orders of color and airmass. For convenience, we choose these secondary standards to have 0 magnitude. In principle, a different standard will be needed for each filter, choice of photon or energy flux, and each source SED. Each standard is labeled $`𝒵_X^\alpha `$ where $`X=\{U,B,V,R,I,\mathrm{}\}`$ and $`\alpha =\{\gamma ,ϵ\}`$ for photon or energy flux as defined earlier.

Equations 3 and 4 generalize the K-corrections of Schneider, Gunn, & Hoessel (1983)111Note that in the notation of Schneider, Gunn, & Hoessel (1983), $`f_\nu `$ and $`f_{\nu (1+z)}`$ are the same function evaluated at different frequencies. and are precisely those given and calculated in Kim, Goobar, & Perlmutter (1996). In that paper, it was found that the differences between the two K-corrections are non-zero but small, $`|K_{xy}^ϵK_{xy}^\gamma |<0.07`$ magnitudes. They are a function of redshift, filters, and supernova epoch and thus can cause small systematic shifts in light-curve shapes and magnitude deviations in the Hubble diagram. The use of the incorrect K-correction will have a significant effect on experiments with small $`<0.1`$ targeted magnitude errors.

To illustrate, in Figure 1 we plot $`K_{BZ}^ϵK_{BZ}^\gamma `$ (where $`Z`$ refers to the passband and not redshift) for a standard Type Ia supernova at $`B`$ maximum and 15 rest-frame days after maximum out to $`z=2`$. The differences are close to zero at $`z1.1`$ where $`B(\lambda /(1+z))Z(\lambda )`$. Beyond this optimal redshift, the differences can be $`>0.01`$ magnitudes. The redder color of the supernova at the later epoch gives relatively larger photon K-corrections over almost all redshifts.

The similarity in the two K-corrections is due to two competing terms that nearly cancel. A photon K-correction is $`1+z`$ brighter because the supernova does not suffer redshifting energy loss. However, the zeropoint of the redder filter used to observe the redshifted supernova is larger since an A0V photon spectrum is flatter than its energy spectrum. This makes the observed supernova magnitude numerically fainter. Consider the special case where $`S_y(\lambda )=S_x(\lambda /(1+z))`$. With perfect filter-matching the specifics of the supernova spectrum are unimportant and the K-corrections depend on the zeropoints:

$`K_{xy}^ϵ`$ $`=`$ $`2.5\mathrm{log}\left({\displaystyle \frac{𝒵_x^ϵ(\lambda )S_x(\lambda )𝑑\lambda }{𝒵_y^ϵ(\lambda )S_y(\lambda )𝑑\lambda }}\right)`$ (5)
$`K_{xy}^\gamma `$ $`=`$ $`2.5\mathrm{log}\left({\displaystyle \frac{(1+z)\lambda 𝒵_x^\gamma (\lambda )S_x(\lambda )𝑑\lambda }{\lambda 𝒵_y^\gamma (\lambda )S_y(\lambda )𝑑\lambda }}\right)`$ (6)
$`=`$ $`2.5\mathrm{log}\left({\displaystyle \frac{(1+z)<\lambda _x>𝒵_x^\gamma (\lambda )S_x(\lambda )𝑑\lambda }{<\lambda _y>𝒵_y^\gamma (\lambda )S_y(\lambda )𝑑\lambda }}\right)`$ (7)
where $`<\lambda >`$ is the effective wavelength of the standard through the filter. As long as the standard star is well behaved, we expect the effective wavelength of the redshifted filter to be $`1+z`$ greater then that of the restframe filter $`<\lambda _y>(1+z)<\lambda _x>`$ so that

$$K_{xy}^\gamma 2.5\mathrm{log}\left(\frac{𝒵_x^ϵ(\lambda )S_x(\lambda )𝑑\lambda }{𝒵_y^ϵ(\lambda )S_y(\lambda )𝑑\lambda }\right)=K_{xy}^ϵ.$$
(8)
Choosing filters that accept the same spectral region at both low and high redshifts not only reduce errors but also reduces the difference between energy and photon K-corrections.

The effect of using the “energy” distance modulus in defining the K-correction in Equations 1, 3, and 4 are seen in the open-filter K-corrections. When $`S_x=S_y=1`$, the energy K-correction is unnecessary and indeed $`K_{xy}^ϵ=0`$. For the photon K-correction we find $`K_{xy}^\gamma =2.5\mathrm{log}(1+z)`$, the difference between “energy” and “photon” distance moduli.

A simple measure for the difference between single-filter K-corrections is the ratio in effective wavelength of a redshifted and unredshifted source through that filter. For example, sources with power-law SED’s have identical photon and energy K-corrections. For low-redshift objects the difference in effective wavelength should be very small (unless they have pathological spectra) and thus make little difference in distance determinations. For example, a Type Ia supernova at maximum at $`z=0.1`$ observed through the $`B`$-band would have a distance modulus error of 0.02 magnitudes if the wrong K-correction were applied.

## 4 Conclusion

We have shown that the measurements $`m_Y(z)M_X`$ do depend on whether the magnitude system is based on energy or photon flux. Although the “photon luminosity distance” is shorter than the standard luminosity distance, we can still use the relation $`m_Y(z)=M_X+\mu (z)+K_{XY}`$ with the appropriate definitions of the K-corrections; the ones of Kim, Goobar, & Perlmutter (1996) are appropriate. With this definition, the standard equations linking the energy distance modulus to cosmology are applicable. The Johnson-Cousins magnitude system is in fact photon-based. Therefore, the $`K_{XY}^\gamma `$ K-correction should and has been used in the supernova cosmology analysis of the Supernova Cosmology Project. Although application of the incorrect K-correction would contribute negligibly to the error budget of the current supernova sample, the distinction is important for precision experiments that require 0.02 magnitude accuracies, such as the Supernova Acceleration Probe. With the choice of well-matched filters, differences between energy and photon K-corrections can be minimal.

Using the “count” distance modulus based on $`d_\gamma `$ in Equation 1 would provide a more physically satisfying definition of the count K-correction. Recall that $`\mu ^ϵ=\mu ^\gamma +2.5\mathrm{log}(1+z)`$. Then the extra $`2.5\mathrm{log}(1+z)`$ in the K-correction would give

$$K_{xy}^\gamma =2.5\mathrm{log}\left(\frac{\lambda 𝒵_x^\gamma (\lambda )S_x(\lambda )𝑑\lambda }{\lambda 𝒵_y^\gamma (\lambda )S_y(\lambda )𝑑\lambda }\right)+2.5\mathrm{log}\left(\frac{\lambda f_\lambda (\lambda )S_x(\lambda )𝑑\lambda }{\lambda ^{}f_\lambda (\lambda ^{})S_y((1+z)\lambda ^{})𝑑\lambda ^{}}\right).$$
(9)
In other words, the K-correction would depend simply on the ratio of supernova photons in the rest-frame filter and a blue-shifted observer filter, and the zeropoint. This methodology would preserve the physical meanings that we associate with both distance modulus and K-correction. For simplicity, however, we here adopt the energy distance modulus for both K-corrections to be consistent with the literature and to ensure unambiguity when referring to K-corrected magnitudes and distance moduli.

We would like to thank Arlo Landolt and Saul Perlmutter for reading our manuscript and for their insightful questions and comments. This work was supported by the U.S. Department of Energy under contract No. DE-AC03-76SF00098 and a NASA LTSA grant to PEN.


text:
# The Evolution of Copper in the Globular Cluster 𝜔 Centauri

## 1 Introduction

Omega Centauri is the most massive globular cluster known in the Milky Way. This cluster is also the only one known whose stars display a large range of abundances in all elements, such as Fe, Ca, Ti, Ni or O. The abundance of a standard metallicity indicator, such as Fe, spans a range from \[Fe/H\]$``$ -2.0 up to -0.4 (Pancino et al. 2000). The abundance variations arise from chemical self-enrichment and evolution in $`\omega `$ Cen, with many of these elements produced in supernovae of type II (SN II), e.g. as discussed by Brown et al. (1991) or Brown & Wallerstein (1993). In addition to self-enrichment in elements produced in SN II, $`\omega `$ Cen displays an even larger abundance range in the neutron-capture s-process elements, such as Y, Zr, Ba, or La. Ratios, such as \[Ba/Fe\], increase tremendously as \[Fe/H\] increases in $`\omega `$ Cen: this cluster underwent an enormous increase in s-process abundances during its chemical evolution, with the s-process elements being produced in asymptotic giant branch (AGB) stars (Lloyd Evans 1983).

Other elements, produced in sites other than SN II or AGB stars, can provide additional insights into the chemical evolution and possible progenitor identity of this relatively small stellar system. In this study, we report on copper abundances in 40 red giant stars in $`\omega `$ Cen, (10 of which have already been studied in Smith et al. 2000), as well as in small samples of red giants in the other globular clusters NGC288, NGC362, NGC3201, NGC6752, and M4 (NGC6121). Copper abundances in these various globular cluster giants are then compared to samples of field stars from the literature, in order to explore the behavior of Cu with metallicity in the Galaxy. The \[Cu/Fe\] ratio is not constant in halo stars, as shown by Sneden & Crocker (1988) and Sneden et al. (1991), where \[Cu/Fe\] increases with increasing metallicity as \[Cu/Fe\] $`\alpha `$ 0.4\[Fe/H\] up to \[Fe/H\]=-1, where it then reaches the solar ratio. For higher metallicities, the \[Cu/Fe\] is solar. These trends were seen both in field and globular cluster stars.

Given the somewhat complicated chemical history of copper, both Sneden et al. (1991) and Matteucci et al. (1993) reviewed the nucleosynthetic sites of copper (as well as zinc). Sneden et al. suggested that much of the copper in metal-poor stars was formed in the weak component of the s-process, whereby a neutron capture on Fe-peak elements is produced during the late stages of core He-burning (Couch et al. 1974, Raiteri, et al. 1991) in massive stars. Some copper was also expected to be formed in explosive nucleosynthesis from SN II. At higher metallicities, they expect that most of the copper was formed in Type Ia supernovae (SN Ia). Only a small fraction ( $`<`$ 30%) of the copper abundance in the sun can come from s-process without gross inconsistencies with other elemental and isotopic abundances (Raiteri et al. 1992). Because the weak component of the s-process is a secondary mechanism for nucleosynthesis, this site for the formation of copper agrees qualitatively with a relationship of increasing \[Cu/Fe\] as a function of \[Fe/H\] in metal-poor stars.

Matteucci et al. (1993) revised the Sneden et al. (1991) model to force a quantitative fit to the data. As they note, any model is hampered by the poorly understood nucleosynthetic yields of Cu in SN II and SN Ia. The conclusion of their paper is that adequate fits to these elements in metal-poor stars could be made only if there was significant nucleosynthesis from SN Ia in the metallicity range -2 $`<`$ \[Fe/H\] $`<`$ -1. One theoretical prediction that indirectly pertains to the production of copper via SN Ia is the study by Kobayashi et al. (1998) who have revisited the models for the formation of Type Ia supernovae. In the models of single degenerate progenitors, the wind from the accreting white dwarf plays an important role in regulating the slow increase in mass of the white dwarf. The existence of this wind allows a much larger parameter space of single degenerate progenitors to produce Type Ia supernova explosions. Their prediction is that SN Ia will not form for $`[Fe/H]<1`$, apparently contradicting the models of Matteucci et al. (1993).

The origins of the metallicity variations and the details of chemical evolution in $`\omega `$ Cen are not understood. However, it clearly has a different chemical evolution history from the Galactic halo and disk. Moreover, little observational work on copper has been published since Sneden et al. (1991). With this in mind, we set out to explore the copper abundances in $`\omega `$ Cen with its different chemical history to gain insight into the sites of copper nucleosynthesis.

## 2 Observations

The echelle spectra assembled and analyzed in this paper were obtained at two different telescopes: the Blanco 4m at CTIO and the 3.9m Anglo-Australian Telescope (AAT). The CTIO spectra were obtained using the cassegrain echelle spectrograph and the Red Long camera (590 mm focal length). Typical resolutions were 35,000 with wavelength coverage from about 5235 $``$ 8518Å. In this project, 10 red-giant members of $`\omega `$ Cen were observed, along with 4 members each in NGC288 and M4, 3 members in NGC362, and 2 members each in NGC3201 and NGC6752. The $`\omega `$ Cen giant spectra were analyzed in Smith et al. (2000), while the other cluster members are analyzed for the first time in this paper. All red giants observed have effective temperatures in the range of roughly 3800–4500K. The CTIO data were reduced to wavelength-calibrated spectra with the IRAF programs. More details in the data reduction procedures are described in Smith et al. (2000). Final signal-to-noise ratios in these spectra were typically 100 to 250.

In addition to the CTIO spectra, high-resolution (R$``$ 38,000) spectra were analyzed for Cu I from the spectra previously studied by Norris & Da Costa (1995) and Norris, Da Costa, & Tingay (1995). These two papers provided equivalent widths and an abundance analysis of several elements for a sample of 40 $`\omega `$ Cen giants, but the authors did not determine Cu abundances. These spectra were obtained with the University College London Echelle Spectrograph (UCLES), with a CCD detector at the coude focus of the 3.9m Anglo Australian Telescope (AAT). The data were reduced to 1-d spectra using both IRAF and FIGARO routines: more detailed discussion of the data reduction of the UCLES spectra can be found in Norris et al. (1995). Typical signal-to-noise ratios of these final, reduced spectra are S/N$``$ 50.

Examples of spectra showing the Cu I line, as well as their synthetic fits, are discussed and shown in Section 3 (Analysis). Table 1 is a summary of the observing log for the spectra analyzed in this study.

## 3 Analysis

The techniques for model atmosphere abundance analyses of red giants spanning the effective temperature range sampled in this study are well established and more detailed discussions of the techniques adopted here can be found in earlier papers: e.g., Norris & Da Costa (1995), Smith et al. (1995), or Smith et al. (2000). In short, published model atmospheres, based upon the Bell et al. (1976: here BEGN) grid for red giants, are used with basic stellar parameters ($`T_{\mathrm{eff}}`$, log $`g`$, and metallicity) derived from a combination of photometry and spectroscopic analyses.

The abundance analysis was carried out for the program stars under the assumption of LTE, using the most recent version of the spectral analysis code MOOG (Sneden 1973). Model atmospheres were interpolated within the standard grid of BEGN models produced by Gustafsson et al. (1975). For red giants spanning the range of temperatures, gravities, and metallicities that represent the program stars, use of these models, with appropriately selected samples of spectral lines, can produce abundance results that are accurate (on an absolute scale) to within typically 0.1 $``$ 0.2 dex, depending upon the spectral lines and species in question.

The copper abundances derived in this study are based on the single Cu I line at 5782.127Å, and adopting the gf-value used by Sneden & Crocker (1988) (same as in Sneden, Gratton, & Crocker 1991), which itself is from the laboratory determination by Hannaford & Lowe (1983). In addition, hyperfine (hfs) and isotopic splitting is significant for this line and these components were included in the analysis, with the hfs and isotopic data taken from Biehl (1976). The various hyperfine and isotopic components of the 5782Å line, along with their gf-values, are listed in Table 2: the gf-values are weighted by their respective solar system isotopic fractions of 0.69 for 63Cu and 0.31 for 65Cu.

A synthetic fit of the Cu I line in the Solar Flux Atlas (Kurucz et al. 1984) is shown in Figure 1. The overall fit of the synthetic hfs profile with the observed solar line-profile is quite good, although there are some small mismatches near the line center (these will not affect measurably the derived stellar Cu abundances). The resulting solar Cu abundance is log $`ϵ`$ $`=`$ 4.06, compared to the accepted photospheric abundance of 4.21 $`\pm `$ 0.04 (Grevesse & Sauval 1998). It should be noted that the solar Cu abundance quoted by Grevesse & Sauval was derived using the gf-value from Koch & Richter (1968), with log (gf)5782= -1.78 compared to -1.72 from Hannaford & Lowe (1983). This suggests that a comparison of the Grevesse Cu photospheric abundance to the one derived here should include a –0.06 dex offset from the differing gf-values. Also, Grevesse quoted a result based upon the empirical Holweger–Müller model (Holweger & Müller 1974), while we used a theoretical MARCS model: the small remaining difference of 0.09 dex is, thus, entirely reasonable. Of importance for later discussion comparing results derived here with the field-star abundances from Sneden & Crocker (1988) and Sneden et al. (1991), is that these studies and our study used the same gf-value for the 5782Å Cu I line. In their analysis, Sneden & Crocker (1988) derived a solar photospheric copper abundance using the same gf-value as adopted here, and found log $`ϵ`$= 4.12. They used the Holweger–Müller solar model atmosphere and the small difference of 0.06 dex between these respective studies can be attributed to different solar models and slightly different microturbulent velocities (0.8 km s-1 in Sneden & Crocker and 1.0 km s-1 here).

Derived abundances depend upon the adopted values of effective temperature ($`T_{\mathrm{eff}}`$), surface gravity (parameterized by log $`g`$), overall stellar metallicity (typified by \[Fe/H\]), and the microturbulent velocity ($`\xi `$). In the Smith et al. (2000) analysis, the effective temperatures and surface gravities were derived from spectroscopy: the spectroscopic analysis used the numerous Fe I and Fe II lines (with well-determined laboratory $`gf`$-values) measurable in high-resolution spectra. Demanding the simultaneous conditions of zero slope in plots of Fe abundance (from Fe I) versus both excitation potential and equivalent width yield the effective temperature and microturbulent velocity. Enforcing ionization equilibrium, such that both Fe I and Fe II yield the same abundance, provides the model surface gravity. Norris & da Costa (1995) used a different approach to derive stellar parameters, with the effective temperatures determined from the infrared photometry of Persson et al. (1980) and Paltoglou & Norris (1989), using the Teff–IR color scales from Cohen, Frogel, & Persson (1978).

A comparison of the derived stellar parameters in the two independent studies (Norris & Da Costa 1995 and Smith et al. 2000) is useful and is possible for 4 stars in common to both samples: ROA’s 102, 213, 253, and 219. Mean differences and standard deviations of the basic stellar parameters, in the sense of ‘Smith et al. minus Norris & Da Costa’, were computed and these are found to be: $`\mathrm{\Delta }`$Teff= +25$`\pm `$125K, $`\mathrm{\Delta }`$(log g)= -0.02$`\pm `$0.25 dex, $`\mathrm{\Delta }`$$`\xi `$= +0.10$`\pm `$0.27 km s-1, and $`\mathrm{\Delta }`$\[Fe/H\]= -0.05$`\pm `$0.06 dex. Therefore, there are no significant offsets between the stellar parameters derived by Norris & Da Costa (1995) and those from Smith et al. (2000), with the scatter, as measured by the standard deviations, being very close to the estimated uncertainties as discussed in both papers.

An additional check of the Smith et al. (2000) Fe I–Teff scale against IR color scales is possible using data from the Two Micron All Sky Survey (2MASS: http://www.ipac.caltech.edu/2mass/). Infrared J, H, and K magnitudes can be found for 8 of the Smith et al. stars and effective temperatures were computed for these giants using four different (V–K)–Teff calibrations, from Cohen et al. (1978), McWilliam (1990), van Belle et al. (1999), and Alonso, Arribas, & Martinez-Roger (1999). Transformations of the 2MASS colors, to other photometric systems, can be found in Carpenter (2001) and, for the $`\omega `$ Cen stars, are quite small. The four different (V–K) calibrations yield effective temperatures with scatters of about $`\pm `$60K for an inidividual $`\omega `$ Cen giant, and the comparison of the mean difference and standard deviation of Teff(Fe I) – Teff(V–K) is +38$`\pm `$138K: this is very similar to the comparison to the Norris & Da Costa (1995) Teff’s. Due to the lack of any significant offsets, we expect no systematic differences as the previously derived stellar parameters from Norris & Da Costa and Smith et al. are on a consistent scale within the errors. Therefore, the adopted parameters and Fe abundances for the $`\omega `$ Cen sample stars remain the same from the previous studies and these are assembled in Table 3 together with the derived copper abundances for the sample stars studied in this cluster.

In addition, the other sample stars from the globular clusters NGC’s 288, 362, 3201, 6752, and M4 are analyzed such that their stellar parameters are derived in the same way as by Smith et al. (2000) and therefore rely on the spectral lines of Fe I and Fe II present in their spectra. Tables 4 and 5 list the Fe I and Fe II measured equivalent widths for these 15 giants (as they have not been published previously). Their corresponding stellar parameters and resulting Fe and Cu abundances are presented in Table 6.

We note that some of the stars from our globular clusters sample have been examined previously (using the same spectra) by Ivans et al. (1999), for M4, and Gonzalez & Wallerstein (1998), for NGC3201 (with neither study including copper in their analyses). These authors used either a different technique (Ivans et al. used line-depth ratios), or a somewhat different set of Fe I and Fe II lines (Gonzalez & Wallerstein 1998) to derive parameters. A comparison of their adopted parameters is useful as an indication of the magnitude of the uncertainties involved in different spectroscopic determinations. For the four M4 giants, differences of (This Study - Ivans et al.) results in $`\mathrm{\Delta }`$Teff= +105$`\pm `$43K, $`\mathrm{\Delta }`$(log g)= -0.06$`\pm `$0.16 dex, $`\mathrm{\Delta }`$$`\xi `$= +0.02$`\pm `$0.10 km s-1, and $`\mathrm{\Delta }`$(\[Fe/H\])= +0.04$`\pm `$0.07. The comparison between (This Study - Gonzalez & Wallerstein) finds (with only average differences listed, as there are only 2 stars in the comparison) $`\mathrm{\Delta }`$Teff= +125K, $`\mathrm{\Delta }`$(log g)= +0.25 dex, $`\mathrm{\Delta }`$$`\xi `$= +0.10 km s-1, and $`\mathrm{\Delta }`$(\[Fe/H\])= -0.08 dex.

In general terms, these various comparisons between independent studies indicate that, for these red giants, effective temperatures can be defined to within $``$100K, surface gravities to about 0.1-0.2 dex, microturbulent velocities within 0.1-0.2 km s-1, and metallicities to within about 0.05 dex. In terms of copper abundances, typical errors of 100K in Teff, 0.2 dex in log g, and 0.2 km s-1 in $`\xi `$ would lead to expected uncertainties of 0.18 dex in derived Cu abundances.

Sample spectral fits of the Cu I line regions are shown in Figures 2, 3, and 4. The star pe75 from NGC362 is shown in Figure 2, illustrating one of the globular cluster giants (other than $`\omega `$ Cen) observed from CTIO. Note that the Cu I line is blended with a Cr I line, although the Cu I line itself is well-defined. Synthetic spectra are plotted for three different Cu abundances: the best-fit value, plus-or-minus 0.1 dex values. Figure 3 also shows a CTIO spectrum, but for the $`\omega `$ Cen star ROA 324 (a star with a rather low \[Cu/Fe\] ratio). Finally, Figure 4 shows an AAT spectrum and resulting synthetic fits for the $`\omega `$ Cen giant ROA 252 (with \[Fe/H\]= -1.74).

Because some of the $`\omega `$ Cen giants are fairly cool (Teff as low as 3750K), a check on the model atmospheres was performed using the latest version of the MARCS code, OSMARCS (Plez, Brett, & Nordlund 1992; Edvardsson et al. 1993; Asplund et al. 1997), that contains more extensive and up-to-date molecular opacities. An OSMARCS model was computed for the coolest giant, ROA201, and the Cu I region was synthesized and analyzed with the newer model as a comparison to the older MARCS model. Virtually no differences were found in the respective synthetic spectra and the same copper abundance was found from both models. This exercise demonstrates that over the temperature range of giants studied here the Cu abundance scale is insensitive to the older MARCS versus newer OSMARCS atmospheres.

As a final check on the copper and iron abundance presented here, possible systematic effects, especially with temperature, were investigated. In low-mass red-giant branches (RGB’s), the position of the giant branch in a Teff–luminosity plane is a function of metallicity, with the more metal-rich red giants being cooler. Since both the Norris & Da Costa (1995) and Smith et al. (2000) samples were observed, essentially, at near-constant V-magnitudes while crossing the RGB in color, the more metal-rich stars tend to be cooler in both samples. Such a correlation could lead to systematic effects in \[Cu/Fe\] versus \[Fe/H\]. Possible systematic trends correlated with stellar parameters are investigated via Figure 5. In the top panel is a spectroscopically derived HR-Diagram, with log g versus Teff: it is clear that the lower surface gravity stars tend to be cooler, as would be expected for low-mass stars ascending the RGB. Superimposed on the observationally derived points are two sample isochrones from Bergbusch & Vandenberg (1992) for 12 Gyr populations with \[Fe/H\]= -2.0 and -1.0, respectively. These iron abundances should nearly bracket the $`\omega `$ Cen stars and, indeed, this is the case. The close match between the derived stellar parameters and those from stellar models suggests that there are not large systematic offsets in the temperatures and gravities used to derive the abundances.

The middle panel of Figure 5 shows \[Fe/H\] versus Teff and demonstrates that the coolest red giants in both samples tend to be found among the most metal-rich stars (with these \[Fe/H\] values being those derived spectroscopically): this is the expected result. Finally, the bottom panel shows \[Cu/Fe\] versus effective temperature and no significant trend exists. The straight line is a least-squares fit to the points and has but an insignificant non-zero slope; there is no evidence that there are measurable systematic abundance trends created by the derivation of stellar parameters or the abundance analysis. It should be noted that if $`\omega `$ Cen stars followed the behavior of the halo one would expect a trend, i.e. the more metal rich (and cooler) giants would have larger values of \[Cu/Fe\]. It would be unlikely that a systematic temperature error would just conspire to provide the observed zero slope of \[Cu/Fe\] with effective tempetarure. It is more likely that the stellar parameters are not affected by significant systematic errors and that the \[Cu/Fe\] ratio in $`\omega `$ Cen is quite constant from \[Fe/H\]=-2.0 to -0.8. A combination of all of the \[Cu/Fe\] values for the $`\omega `$ Cen stars results in a mean and standard deviation of -0.50 $`\pm `$ 0.11: this indicates no evolution in the copper to iron yields over much of the chemical evolution within $`\omega `$ Cen.

## 4 Discussion

The abundances of copper discussed in this paper are assembled in the different panels of Figure 6 as \[Cu/Fe\] versus \[Fe/H\]. As a reference point, we adopt log $`ϵ`$(Fe)= 7.50 and log $`ϵ`$(Cu)= 4.06 as the corresponding solar abundances. All three samples of stars are shown in Figure 6: the field star results, the “mono-metallicity” globular clusters (NGC’s 288, 362, 3201, 6752, and M4), and $`\omega `$ Cen.

In the top panel of Figure 6 are shown the results from Sneden & Crocker (1988) and Sneden et al. (1991) for the field stars, with their corresponding error estimates in \[Cu/Fe\] and \[Fe/H\] plotted. The straight lines are least-squares fits to two metallicity regimes (\[Fe/H\]$``$ -1 and \[Fe/H\]$``$ -1) and are meant only to serve as guides to the eye in order to more easily identify the behavior of copper with metallicity (\[Fe/H\]). It is found that \[Cu/Fe\] is effectively constant in the high-metallicity regime while clearly decreasing towards lower metallicities in those stars having \[Fe/H\]$``$ -1.4 (as discussed in Sneden et al. 1991), with an approximate slope of 0.4 in \[Cu/Fe\] versus \[Fe/H\].

The middle panel of Figure 6 again shows the field-star results (with error bars suppressed for clarity), upon which are plotted our abundances for the globular clusters M4, NGC’s 288, 362, 3201, and 6752. Note that the individual scatter, in both \[Fe/H\] and \[Cu/Fe\], within each globular cluster is quite small; thus, for example, the small differences in \[Cu/Fe\] between NGC362 and the clusters M4 and NGC288, at similar values of \[Fe/H\], are probably real, with the three studied stars in NGC 362 falling slightly below the straight line that represents the field behavior. (Although there is a gap in the sample field population at roughly this metallicity). Except for NGC362, that may have a somewhat low \[Cu/Fe\] ratio for its value of \[Fe/H\], the other 4 globular clusters fall quite close to the mean trend of the field stars.

The general trend for the $`\omega `$ Cen stars is shown in the bottom panel of Figure 6, again with the field-star results overplotted for comparison. Unlike the field, the $`\omega `$ Cen members show a constant \[Cu/Fe\] ratio of about -0.5 in the interval from \[Fe/H\] of $``$ -2.0 up to -0.8: there may be a hint that the scatter in \[Cu/Fe\] increases towards the highest metallicities. The values of \[Cu/Fe\] in the field halo stars and $`\omega `$ Cen are in agreement at \[Fe/H\]$``$ -2, where the two samples overlap, but are clearly different at \[Fe/H\]$``$ -1, with the $`\omega `$ Cen stars falling below the field in \[Cu/Fe\]. In particular, over the upper range of metallicities of the $`\omega `$ Cen sample studied here (with -1.2 $``$ \[Fe/H\] $``$ -0.8) the mean value of \[Cu/Fe\] and standard deviation is -0.52 $`\pm `$0.17 (for 9 stars). For the same \[Fe/H\] range in the field-star sample, \[Cu/Fe\]=-0.05 $`\pm `$0.18 (for 8 stars). The nearly horizontal line in this panel is a least-squares fit to the $`\omega `$ Cen points that has a near-zero slope. The 8-pointed stars are the results for $`\omega `$ Cen from Pancino et al. (2002), and include two members that are significantly more metal-rich than those in our sample. For the stars with \[Fe/H\]$``$ -0.8, the Pancino et al. (2002) results overlap those found in this study; however, $`\mathrm{𝑜𝑛𝑒}`$ of the metal-rich Pancino et al. (2002) stars (with \[Fe/H\]$``$ -0.5) has a \[Cu/Fe\] value that is nearly equal to those found in the field stars at this metallicity. A more rigorous comparison between $`\omega `$ Cen and field behavior will be aided by an increased sample of galactic field stars allowing for a complete elucidation of the behavior of copper in the metallicity range between \[Fe/H\] -2.0 and -0.5.

From the point of view of observations, the behavior of \[Cu/Fe\] is different between the field halo stars and the stars in $`\omega `$ Cen over the studied metallicity range. Can this different behavior in the two samples be understood within some simple context? It is safe to assume that the production site(s) for Cu involve either massive stars and Type II supernovae, or Type Ia supernovae (which result from binary-star evolution), and do not involve nucleosynthesis in low-mass AGB stars. Within this context, $`\omega `$ Cen shows clear evidence of enormous elemental contributions from low-mass AGB stars via s-process nucleosynthesis (e.g. Norris & Da Costa 1995), thus, the observed constant values of \[Cu/Fe\] found here do not fit a picture in which Cu synthesis arises in AGB stars. Addressing the point of whether Cu production is associated with either SN II or SN Ia, there are conflicting ideas. As mentioned in the Introduction, based on their observed trend of \[Cu/Fe\] $`\alpha `$ 0.4\[Fe/H\], Sneden et al. (1991) favor a production model for Cu in metal-poor stars (\[Fe/H\] $``$ -1.0) which has two sources, both occurring in massive stars: the weak s-process, operating during core He burning, plus the e-process of Si burning during Type II supernovae. In the more metal-rich disk stars, an additional source of Cu appears from Type Ia supernovae. On the other hand, Matteucci et al. (1993) use the Cu–Fe relation from Sneden et al. (1991) to reach somewhat different conclusions about the origin of Cu. Their chemical models are best fit with Cu being produced predominantly in Type Ia supernovae, even down to metallicities well below -1.0 in \[Fe/H\]. One of the main points of their study is to assume that there is already a SN Ia contribution between metallicities \[Fe/H\] -2.0 and -1.0.

A number of previous studies of $`\omega `$ Cen (e.g. Brown & Wallerstein 1993; Norris & Da Costa 1995; Smith et al. 1995, 2000) find that elements such as Si, Ca, or Ti exhibit the same behavior as observed in the halo field, i.e. that their abundances are enhanced relative to Fe. This is interpreted to result from chemical enrichment from Type II supernovae. Since the halo field and $`\omega `$ Cen are identical in this respect, there is evidence that $`\omega `$ Cen was enriched by SN II ejecta. Thus, the fact that \[Cu/Fe\] exhibits different behavior between the field-halo stars and $`\omega `$ Cen could suggest that the main source of Cu within this metallicity range is not massive stars. Of course, one could speculate that, for example, the weak s-process operates over some restricted mass range and that the mass function of $`\omega `$ Cen was deficient in stars over this range. This speculation, however, introduces additional parameters and will not be explored further here.

If the \[Cu/Fe\] ratios in $`\omega `$ Cen do indeed eliminate massive stars as the dominant Cu producers, this leaves Type Ia supernovae, as suggested by Matteucci et al. (1993). This winnowing of Cu sources still leaves the problem of why the field halo and $`\omega `$ Cen exhibit different behaviors of \[Cu/Fe\] versus \[Fe/H\], but there are a number of possible explanations: 1) The timescale for SN Ia progenitor evolution exceeds the timescale of chemical evolution within $`\omega `$ Cen, 2) SN Ia systems do not form in metal-poor environments, as suggested by Kobayahsi et al. (1998), 3) SN Ia progenitor systems (presumed to be binaries) are sufficiently rare, that none would be expected to form in a small system, such as $`\omega `$ Cen, 4) SN Ia binary progenitor systems form, but are subsequently disrupted in the dense environment of a globular cluster, or, 5) the negligible contribution from SN Ia’s over much of $`\omega `$ Cen’s chemical evolution may result from the selective retention of stellar ejecta in low-mass systems (where AGB winds are more efficiently retained than SN II ejecta, and, in the case here, SN Ia ejecta almost not retained at all).

Concerning option (1), photometric studies by Hilker & Richtler (2000) and Hughes & Wallerstein (2000), as well as the s-process spectroscopic analyses by Smith et al. (2000), indicate that it took $``$ 1-3 Gyr for $`\omega `$ Cen to evolve from \[Fe/H\]$``$ -2.0 to -1.0. The nucleosynthesis from Type II supernovae and from the weak component of the s-process will happen on time scales of 107 years. The timescale for the formation of Type Ia supernovae is not clear mostly due to the lack of a definite progenitor model. The discussion by Kobayashi et al. (1998) gives typical time scales for the double degenerate model as 0.3 Gyr and for single degenerate models of 0.6 Gyrs. A discussion of a larger set of possible Type Ia models gives rough timescales from 0.1 to 4 Gyrs (Branch et al. 1995). It has been long established that the rates of Type Ia supernovae are higher in late-type galaxies (Oemler & Tinsley 1979) than in early types, which would support a shorter time scale for formation of Type Ia events. It therefore seems safe to assume that the age spread measured in the stellar population $`\omega `$ Cen is significantly longer than the time needed to form the typical Type Ia supernovae.

Concerning option (2), Kobayashi et al. (1998) develop models for binary SN Ia progenitors in which the wind from the white dwarf plays a key role in determining whether a Chandrasekhar mass limit is reached. The strength of the wind is a function of the metallicity, and Kobayashi et al. (1998) conclude that Type Ia supernovae are quenched below metallicities of -1.0. In this type of picture, it might be expected that SN Ia’s would be inhibited in all low metallicity environments and thus the field halo and $`\omega `$ Cen would exhibit the same type of behavior. However, this is not what is observed. But of course, this contention resides on the assumption that Ia’s are the main producers of Cu.

Concerning possibility (3) from above, Pagel (1997) estimates that the SN Ia rate in the Milky Way is 0.33 per century. Taking a Galactic stellar mass of $``$ 1011M, this translates to a “mass specific rate” of 3 x 10-14 SN Ia events per year per solar mass of stars. Given an $`\omega `$ Cen protomass of $``$107M, it can be estimated that the SN Ia rate in the cluster would be 10-7 events per year once the time has passed for SN Ia events to turn on. Over some 109 years of chemical evolution, $`\omega `$ Cen would have $``$ 100 SN Ia’s occur. As each SN Ia can eject up to $``$0.6M of Fe (Pagel 1997), these events would have a measurable impact on the abundances, if such ejecta were retained. Of course, this simple argument assumes that the rate of binary formation in a globular cluster is the same as in the Galaxy as a whole. There is no observational evidence concerning the initial fraction of binary systems formed in globular clusters; however, there is evidence that binary sytems can be disrupted in the environment of a globular cluster. In fact, Côté et al. (1996) find that $`\omega `$ Cen has a smaller fraction of binary systems than other globular clusters studied by them (e.g. M71, M4 and NGC3201 among others). This could be a possible explanation for the lack of SN Ia enrichment over much of the \[Fe/H\] evolution in $`\omega `$ Cen, as suggested by possibility (4) from above. In this context, perhaps the incidence of Type Ia supernovae is simply lower in $`\omega `$ Cen compared to the field due to some destruction of SN Ia progenitor systems. This might explain the delayed, but eventual appearence of SN Ia enrichment in the most metal-rich stars in $`\omega `$ Cen (\[Fe/H\] $``$ -0.5) as derived by Pancino et al. (2002).

Another possibility (number 5 from above) in understanding these peculiar chemical traits in $`\omega `$ Cen comes from Smith et al. (2000). The observation that $`\omega `$ Cen contains such a large s-process component led to the speculation that in a relatively low-mass stellar system AGB ejecta, because of their low velocity winds, might be more efficiently retained relative to the much faster moving Type II supernova ejecta. The AGB ejecta would then be mixed with a relatively small amount of SN II ejecta that was retained, as well as with the residual gas of initial composition. The same sort of speculative explanation could hold for explosions of Type Ia supernovae. Differing retention efficiencies between SN II and SN Ia ejecta might be caused by the differing interstellar environments where the explosions occur. For example, Recchi, Matteucci & D’Ercole (2001) model chemical and dynamical evolution in a low-mass, starburst dwarf galaxy and find that a metal-enriched galactic wind is driven out of the galaxy by SN II and SN Ia explosions. They also find that the SN Ia ejecta are preferentially ejected relative to SN II ejecta. Gnedin et al. (2002) have pointed out, however, that the current escape velocity from $`\omega `$ Cen is not that different from the other globular clusters. The hypothesis of selective mass loss or retention, on the other hand, applies to the progenitor object (proto $`\omega `$ Cen) before it was captured into its current retrograde orbit around the Milky Way; the nature of that progenitor object remains unknown. Distinguishing whether possibility (4) or (5) best pertains to understanding the chemical evolution within $`\omega `$ Cen can probably be constrained by determining abundance ratios in a wide variety of stellar environments, such as other types of small galaxies within the Local Group, as well as in a larger sample of $`\omega `$ Cen members from the most metal-rich population identified by Pancino et al. (2000).

Our abundance results lead us to the conclusion that the copper to iron ratio in $`\omega `$ Cen is nearly constant over about a factor of 10-15 range in iron abundance (-2.0 $``$ \[Fe/H\] $``$ -0.8). Over this same range of \[Fe/H\] in the field stars, \[Cu/Fe\] increases by about 0.5 dex. This demonstrates yet another peculiar trait of the chemical evolution found within $`\omega `$ Cen when compared to the Galactic halo field stars at comparable metallicities (the other peculiar chemical trait being the large s-process abundance component in $`\omega `$ Cen).

## 5 Conclusions

In this work we discuss Cu abundances in 40 red-giant members of $`\omega `$ Cen, as well as 15 red-giant members of 5 other globular clusters that overlap the range of \[Fe/H\] found in $`\omega `$ Cen. Abundances from field stars already published in the literature by Sneden & Crocker (1988) and Sneden et al. (1991) are included in the discussion. It is found that both the field star sample and 4 of the 5 “mono-metallicity” Galactic globular clusters display similar values of \[Cu/Fe\] at a given \[Fe/H\]. The $`\omega `$ Cen members, however, tend to have smaller and nearly-constant values of \[Cu/Fe\] ratios, when compared to the other globulars and the field, as \[Fe/H\] increases. If copper is produced preferentially in SN Ia, relative to SN II, this indicates that $`\omega `$ Cen stars show little, if any, enrichment from SN Ia’s up to a cluster metallicity of \[Fe/H\]$``$ -0.8. A lag in SN Ia chemical enrichment in $`\omega `$ Cen could result either from the disruption of binary SN Ia progenitor systems in $`\omega `$ Cen, or from a higher fraction of SN Ia ejecta being lost from $`\omega `$ Cen.

This work is supported in part by the National Science Foundation through AST99-87374 (VVS).


text:
# Multiwavelength Rotation Curves to Test Dark Halo Central Shapes

## 1. Introduction

The dynamical masses of spiral galaxies are known to differ significantly from their visible masses. The commonly accepted cause is the existence of a ellipsoidal halo of unseen matter in addition to the stars and gas. The exact density distribution of these halos have become an increasingly important issue. On one side, N-body simulations of the cosmological evolution of the Cold Dark Matter (CDM) have now reached a sufficient resolution to predict the dark halo density profiles down to a scale corresponding to the inner parts of the spiral galaxies (Fukushige et al. 1997; Navarro et al. 1997; Moore et al. 1998; Ghigna et al. 2000). They almost always predict dense cuspy halos. On the other side, observations of dwarf spiral galaxies show shallow inner rotation curves, compatible with a flat density core (Blais-Ouellette et al. 2000, hereafter paper II).

The first step in showing the reality of this discrepancy is to eliminate the known possibilities of systematic observational biases. Two classes of errors could contribute to underestimate the velocities, hence the computed density, in the inner parts of spiral galaxies. The prime culprit in radio observations is the “beam smearing” effect due to the relatively low angular resolution of 21 cm data with sufficient sensitivity to detect H I in the outer part of spiral galaxies. Combining the H I density gradient with the velocity gradient will lead to underestimate the velocity at a given radius.

H$`\alpha `$ observations always easily reach an angular resolution where any beam smearing effect can be neglected. A less often commented source of uncertainties though is found in long slit observations, where most of H$`\alpha `$ data come from. The lack of 2D coverage makes the alignment of the slit crucial to retrieve the real kinematics of a galaxy. Missing the kinematical center, which is not always the photometric center (paper II), or just a few degrees between the slit and the galaxy position angle will also lead to an underestimation of the velocities. Inclination estimation, which has to be photometrically determined, is another major source of uncertainties. In addition, the presence of a bar would hardly be noticed and its effect would most probably be confounded with the rotational kinematics.

In order to hedge ourselves against these biases, we use Fabry-Perot high resolution H$`\alpha `$ spectroscopy combined with published radio synthesis observations to study the mass distribution of 8 dwarf and spiral galaxies. In paper II, with a smaller sample, we focused on modeling the mass distribution using different shape of dark matter halos. Here, in addition, we address the more precise question of what inner density slope ($`\gamma `$) halo can have for a given galaxy type or mass.

In section 2, we first briefly review the mass modeling used in the study. Then, in section 3, we look at detailed mass models of a few galaxies. In section 4, the relation between $`\gamma `$ and galaxy mass is discussed followed by concluding remarks.

## 2. Modeling the Mass Distribution

To investigate in details the mass distribution of dark matter halos without a few assumptions on the matter content of spiral galaxies, one would have to adjust a good dozen of parameters. First, the luminous matter distribution depends on the disk and bulge mass-to-light ratios (and their radial gradient), and on the bulge-to-disk ratio. The H I contribution have to be corrected for helium fraction. The dark halos can be non-spherical, in addition to the five parameters usually used to describe the radial density distribution. This general distribution function can be expressed as (see Paper II for details):

$$\rho (r)=\frac{\rho _0}{(c+(r/r_0)^\gamma )\left(1+(r/r_0)^\alpha \right)^{(\beta \gamma )/\alpha }}$$
(1)
where $`\rho _0`$ and $`r_0`$ are characteristic density and radius, where c, included for ease of comparison with other works, can force the presence of a flat density core, where $`\alpha `$ and $`\gamma `$ are respectively the inverse outer and inner logarithmic slopes, and $`\beta `$ the transition parameter.

One could add the distance that is used to calculate the light distribution, and a central mass which is suspected to exist in most spirals.

For some of these constraints, a fixed value is well accepted. The mild or absent color gradient in spiral galaxies lead to a radially constant mass-to-light ratio. The helium fraction can be approximate to its primordial abundance. Distances are hopefully well constrained by independent means.

Otherwise, essentially three data sets can be used to constraint these parameters: luminosity distributions (visible an H I ) and velocity field or, assuming axisymmetry, light profiles and rotation curve. The visible light profile, is used to determine the bulge to disk ratio. The other parameters are all to the charge of the rotation curve. Most of the luminous contributions are heavily constrained by the most inner parts of the curve leading to a possible degeneracy between central mass, bulge, inner disk and halo contributions. That is why, many studies including this one, tend to focus on dwarf galaxies where bulges are negligible and large central masses excluded by the rotation curve. Only there, can one put strong limits on the inner slope of dark halo density distribution. For these galaxies, luminous matter is dependent only on the disk mass-to-light ratio, and dark matter from the central density, the core radius, and the three shape parameters. From the latter, only $`\gamma `$, the inner slope, has a significant impact on halo shape at the scale of dwarf galaxies, $`\alpha `$ and $`\beta `$ being very poorly constrained.

In our procedure, the visible light profile (eventually decomposed in its bulge and disk components) is inverted in a mass profile scaled by the mass-to-light ratios. The H I contribution is estimated from its distribution and multiply by 1.33 to account for helium. The halo shape is, in general, fixed to a known profile. We choose four profiles, widely used in the literature, that span, with some redundancy, through most possibilities. The cuspy profile from Navarro et al. (1997) is a canonical example of CDM simulation prediction, the pseudo-isothermal sphere, the profile from Kravtsov et al. (1998), and Burkert’s profile (Burkert et al. 1995) are all cusp-less profile with different shape parameters. Rotational velocities from all the contributions are then added in quadrature and compare to the rotation curve using a standard $`\chi ^2`$ minimization.

## 3. Mass Models

### 3.1. The Sample

Beside the dwarf galaxies NGC 3109 and IC 2574 from paper II, the whole sample includes 3 fairly bulge-less spirals (UGC 2259, NGC 2403, and NGC 6946), and 3 earlier type spirals (NGC 5055, NGC 2841, and NGC 5985) from paper III. Details are given in Table 1.

### 3.2. The Results

Complete modeling, using the four models, of the most relevant cases are presented here. NGC 3109 and IC 2574 (from paper II) are re-analyze to correct for a numerical problem which underestimated the central density. They are good examples of CDM incompatible dwarfs. Are also modeled, NGC 2403, as an example of bulge-less small spiral compatible with any model, and NGC 5055, as an earlier type spiral with a bulge. Analysis of the whole sample will be presented in a future paper (paper IV). Error bars are the quadratic sum of: half the velocity difference between receding and approaching sides, half the correction for asymmetric drift, error cause by uncertainty on inclination, and statistical error($`\sigma /\sqrt{N}`$).

It is rather clear that NFW profile is incompatible with the two dwarf galaxies. These results are in line with most similar studies using H I (e.g. Côté et al. 2000) or long slit observations (e.g. Swaters et al. 2000, de Blok et al. 2001) but without the related uncertainties (van den Bosch et al. 2000). It has to be noticed that higher resolution N-body simulations tend to give even steeper inner density slopes. The present discrepancy is therefore genuine and probably involve subtle phenomena or new physics.

Mass-to-light ratios tend to be unrealistically low for the smallest galaxies. Halo contributions are therefore an upper limit and are in fact probably shallower.

## 4. Halo Density Gradient

The range of possible observational biases that could explain the core-cusp problem is now significantly reduced, rather close to nil. The question of the physical cause of this shallow inner density distribution have been addressed many times leading to proposals ranging from multi-component dark matter (Burkert & Silk 1997) to self-interacting dark matter (Spergel & Steinhardt) and baryonic feedback processes. These scenarios are though to behave differently under different gravitational potentials. For example, feedback processes can hardly have an impact in galaxies with very deep potential. Plotting $`\gamma `$, the density profile inner slope, against the asymptotic rotational velocity would precisely show the evolution of this behavior. Figure 3 plots $`\gamma `$ against the observe maximum velocity which, for NGC 3109 and IC 2574, is lower than the true asymptotic velocity.

The steepness of NGC 5055 rotation curve leads to an important degeneracy between $`\gamma `$, r0 and $`rho_0`$. It is therefore not clear from the plot if there is a canonic value of $`\gamma `$ around 1.2 that breaks down below 100 km/s or if $`\gamma `$ is intrinsically increasing in massive galaxies.

## 5. Conclusion

We have modeled 8 dwarf and spiral galaxies using cusp-less and cuspy halos. The latter, predicted by CDM N-body simulations are clearly incompatible with dwarf galaxy kinematics. More precisely, galaxies with less than 100 km/s of maximum rotation velocity have a inner density logarithmic slope ($`\gamma `$) of less than .7 as opposed to $`\gamma 1`$ predicted by the N-body simulations.

Presently, $`\alpha `$, the outer density slope is poorly constrained by rotation curves. One need to reach a radius where the luminous disk contribution is negligible while the rotation curve is flat or decreasing (Carignan & Purton 1998). In our sample, UGC 2259 is a good candidate.

Future studies should in part extend to massive bulge-less galaxies to see if $`\gamma `$ is intrinsically rising with galaxy mass or if it is constant, with a break down at low mass. The GHASP survey (Garrido & Amram 2002) should allow this kind of study.

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