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# Chandra X-ray Sources in M101

## 1 Introduction

M101 is a nearby (7.2 Mpc, Stetson et al. (1998)), face-on spiral galaxy that is ideal for studies of the X-ray source population in a galaxy similar to the Milky Way. Since M101 is viewed through a relatively small amount of obscuring foreground Galactic hydrogen gas ($`N_H=1.2\times 10^{20}`$ cm-2, Stark et al. (1992)), it is especially well suited for surveying soft X-ray sources, without the observational biases introduced by the thick absorption in the Galactic plane when studying X-ray sources in our own Galaxy. Although M101 has a slightly later morphological type (Scd vs. Sbc) and a significantly larger D25 isophotal diameter (60 kpc vs. 23 kpc) than the Milky Way (de Vaucouleurs and Pence, 1978; de Vaucouleurs et al., 1991), one would expect that the properties of the X-ray source populations in these 2 galaxies should be quite similar.

M101 was previously observed with the Einstein X-ray observatory (McCammon and Sanders, 1984; Trinchieri et al., 1990), and later with ROSAT to study both the discrete sources (Wang et al., 1999) and the diffuse X-ray emission (Snowden and Pietsch, 1995). M101 was an obvious candidate for follow up studies with the Chandra X-ray observatory, and this paper presents the basic data and analysis of the population of discrete X-ray sources detected in a Cycle-1 Chandra observation. This paper is one in a series which analyze various aspects of this rich dataset. A previous paper (Snowden et al., 2001) reinvestigated some of the hypernova remnant candidates in M101, and 2 other papers currently in preparation will study the brighter black hole X-ray binary candidates in more detail and analyze the diffuse X-ray emission in M101.

## 2 Data Processing

The present data set consists of a 98.2 ks exposure taken on 26–27 March 2000 with the Chandra observatory ACIS imaging spectrometer with the nucleus of M101 centered near the “aim point” of the S3 CCD chip. The analysis in this paper is limited to the sources detected within the 8$`\stackrel{}{\mathrm{.}}`$4 x 8$`\stackrel{}{\mathrm{.}}`$4 (17.6 x 17.6 kpc) field of view of the S3 chip which has much better angular resolution and extended sensitivity to lower X-ray energies than the other chips. This chip covers the central region of M101 out to a minimum distance of 6.3 kpc from the nucleus towards the NW, and a maximum distance of 14.9 kpc at the east corner of the chip. By comparison, the prominent spiral arms extend out to about 14 kpc, and the $`R_{25}`$ isophotal radius (de Vaucouleurs et al., 1991) is 30.2 kpc, so the S3 chip covers about 50% and 11%, respectively, of these circular areas in M101.

The standard CIAO pipeline software system (“Rev 2” as of December 2000) was used to clean and calibrate the data set. In addition to the standard data cleaning, we also excluded the data during a 64 s interval of unusually high background count rate which reduced the exposure duration to 98180 s. Finally, we excluded all photon events which had a nominal pulse invariant (PI) channel energy greater than 8.0 keV where the S3 chip has virtually no sensitivity. The nominal lower energy cutoff in the data set is 0.125 keV.

## 3 Source Detection

The CIAO celldetect111 At the time that we received the Chandra data files the celldetect program appeared to produce the most reliable list of sources. Later, after the release CIAO v2.1, we repeated the source detection procedure using the wavdetect program, but concluded that the final list of sources presented in Table 1 would not change significantly. The $`\mathrm{log}N\mathrm{log}S`$ analysis in §4 was based on the results from wavdetect. program was initially used with a threshold of $`2.5\sigma `$ to generate a preliminary candidate list of X-ray sources in the 0.125 – 8.0 keV band image. At this low threshold setting about 20% of the sources were clearly spurious, mainly located in the wings of brighter sources near the edges of the chip. These spurious sources were rejected by inspecting their positions on an adaptively smoothed image of the S3 chip field of view constructed from all the X-ray events in which sources with as few as 10 net counts are clearly visible. The final adopted set of sources have formal signal to noise ratios close to 3.0 or higher. Note that the detection threshold for faint point sources increases with distance from the “aim point” because of the decreased angular resolution, and as a result the faintest point sources (with $`F_x10^{16}`$ ergs cm-2 s-1) are detectable only within a radius of about 2′ = 4 kpc from the nucleus of M101.

The positions of our final 110 Chandra X-ray sources in M101 are shown in Figures 1 and 2, and listed in Table 1. The source positions derived from the Chandra data are generally accurate to better than 1″. The mean difference between our X-ray positions and the astrometric optical positions of 12 previously identified supernovae remnants catalogued by Matonick and Fesen (1997) is only 0$`\stackrel{}{\mathrm{.}}`$47 $`\pm `$ 0$`\stackrel{}{\mathrm{.}}`$20, about the size of one ACIS CCD pixel.

As can be seen in Figure 2, the X-ray sources are strongly correlated with the position of the optical spiral arms and bright HII regions in M101. There are relatively few X-ray sources in the interarm regions which indicates that most of the X-ray sources are associated with the young stellar population in M101. To quantify this association, we divided the area covered by the S3 chip into either “spiral arm” or “interarm” regions based on the appearance in the blue optical photograph of M101, with the result that 75% of the area of the chip was classified as covering spiral arm regions (also includes the nuclear region) and 25% as covering interarm regions. Using this spatial criteria, only 8 of the X-ray sources (sources 5, 7, 8, 19, 29, 39, 64, and 97) were found to be located in the interarm regions and not associated with optical emission in M101. This gives a mean surface density of 1.9 sources arcmin-2 in the spiral arms compared with only 0.45 sources arcmin-2 in the interarm regions (both before background subtraction).

We calculated the expected number of background sources in our field based on the point source luminosity function determined from a similar Chandra observation of a blank field by Mushotzky et al. (2000), the HI column density map of M101 by Kamphuis (1993), and the Hartmann and Burton (1997) measure of the Galactic HI column. Given that the Chandra response is rather hard and that the AGN spectra are also hard, the diminution of the surface density of AGNs due to the HI absorption in M101 is rather small, only about 8%. From this we estimate that about 27 of the detected sources, only a quarter of our total sample, are likely to be serendipitous background (or perhaps in a few cases, foreground) sources. Based on the above division of the chip area into “spiral arm” and “interarm” regions, about 20 of these background sources should appear to be located in the spiral arm and nuclear regions. This corresponds to a mean background surface density of 0.38 sources arcmin-2 which is remarkably close to the measured density of sources in the “interarm” regions of 0.45 sources arcmin-2. This suggests that most of these interarm sources are background AGNs, and indeed, 6 of the 8 interarm sources do have relatively hard SR1 and HR1 colors (see §6 and Fig. 6) which are consistent with the expected power law spectrum of an AGN. Furthermore, the brightest of these sources (#5) was previously identified as an AGN by Wang et al. (1999). The other 2 sources located in the interarm regions (#7 and #8) have very soft spectra and thus are more likely to be physically associated with M101. Source #8 in fact is one of the Supersoft sources discussed in §9.

## 4 The log N–log S Relation

To create a $`\mathrm{log}N\mathrm{log}S`$ relation for the point sources towards M101 that would be more easily comparable to relations derived for other galaxies, we applied somewhat more restrictive criteria than for the catalogue of sources. We chose all sources where the effective exposure was greater than 75% of the maximum and having a significance greater than 4.5 in the 0.5-2.0 keV energy band (the M2 band defined in §6), where the source counts were measured within the elliptical PSF region containing 75% of the encircled energy, and the background was measured from an annular region 2 to 4 times the size of the 95% encircled energy ellipse. The source rates were corrected for vignetting. (This choice of energy range balances the need to detect the most numerous types of objects in M101, which are soft, with the desire to detect hard objects as well.) The object catalogue was binned into $`\mathrm{\Delta }\mathrm{log}(S/\text{counts s}^1)`$ bins, and each bin was divided by the number of square arcminutes over which such a flux could have been detected.222The point source detection limit is spatially variable, as both the size of the PSF and the background rate vary. Although the variation of the size of the PSF dominates, since some point sources are embedded in diffuse emission, the background rate can be significant in determining the point source detection limit. Both effects, as well as the effect of the vignetting, were included in this analysis. The $`\mathrm{log}N\mathrm{log}S`$ relation is shown in Figure 3 along with the relation due to background AGN seen through the disk of M101 (as calculated from the relation of Mushotzky et al. (2000)). A flux conversion factor equivalent to $`10^{14}`$ ergs cm-2 s-1 = $`3.33\times 10^3`$ counts s-1, which is appropriate for a background AGN with a $`\mathrm{\Gamma }=1.42`$ power-law X-ray spectrum, was used in these calculations. The resulting $`\mathrm{log}N\mathrm{log}S`$ relation for the sources not due to the background AGN is nearly linear with $`N(>S)S^{0.80\pm 0.05}`$. Excluding the 8 interarm sources identified in the previous section from the analysis only makes a slight difference, resulting in a slope of $`0.76\pm 0.05`$. The uncertainty of the slope was calculated following the Lampton et al. (1976) criteria, and is larger than the bootstrap uncertainty ($`\pm 0.02`$) or the variation produced by changing the flux range of the fit ($`\pm 0.02`$). The relatively flat slope derived here implies that the amount of diffuse emission due to unresolved faint point sources will be small.

Figure 4 shows the surface density of point sources as a function of radius from the nucleus. The optical bulge of M101 is visible out to $`0\stackrel{}{\mathrm{.}}75`$ (Okamura et al., 1976), and we do indeed see an increase in the point source surface density in the bulge region. Because the total number of sources within the bulge region is small ($`14`$) it is difficult to determine whether the “bulge sources” follow a different $`\mathrm{log}N\mathrm{log}S`$ relation than the “disk sources”. However, to within the uncertainties, we do not observe a difference in the shapes of the relations between bulge ($`R<1\mathrm{}`$) and disk sources ($`1\mathrm{}<R<4.5\mathrm{}`$).

The above analysis could be repeated for the 2.0–8.0 keV band using the 2-10 keV band AGN luminosity function found by Mushotzky et al. (2000), but in this energy range only $`18`$ of the objects detected with $`\sigma >4.5`$ are not background AGN. The slope of the $`\mathrm{log}N\mathrm{log}S`$ relation is quite uncertain ($`0.69\pm 0.18`$, where the quoted uncertainty is no more than a formal uncertainty); to within the uncertainties, the 2.0–8.0 keV band is consistent with the 0.5–2.0 band.

That the slope of our 0.5–2.0 keV luminosity function does not agree with that of Wang et al. (1999) ($`1.9_{0.3}^{+1.3}`$) is hardly surprising; the HRI data was over an order of magnitude less sensitive, many of the sources detected are actually composed of several point sources, and some of the brighter sources are embedded in diffuse emission that would have fallen within the HRI PSF. Further, the Wang et al. (1999) luminosity function was formed over a much larger area (a radius of $`12\mathrm{}`$ compared to our $`6\mathrm{}`$) and thus may be composed of a different population of sources.

## 5 Source Identification

About 1/4 of the Chandra X-ray sources can be cross-identified with previously observed X-ray sources or are positionally coincident with other catalogued objects as listed in Table 2. The previous ROSAT HRI and PSPC observations of M101 (Wang et al., 1999) detected 19 sources within our field of view, and all but 3 of these are detected in the Chandra observation. A 20th source (their source H42) is just visible on the edge of the field, but it is too highly distorted and affected by the edge of the detector to be included in our final list of sources. Of the 3 non-detected sources, 2 of them were classified as variable by Wang et al. (1999) (their sources H28 and H31) so they may have been in a low flux state during our observation. The other non-detected object (their H41 source) is located near the East corner of the S3 chip, where our detection threshold is relatively high.

The nuclear source seen in the ROSAT HRI image (source H23), is resolved into 2 nearly identical point sources in the Chandra image. The northern component (source #40) appears to coincide with the nucleus at $`14^h03^m12.55^s`$, $`54^{}20`$′56$`\stackrel{}{\mathrm{.}}`$5 but is otherwise unremarkable compared to the other X-ray sources in the field. The other nuclear component is 3$`\stackrel{}{\mathrm{.}}`$1 ($`110`$ pc) to the south and coincides with a loose cluster of bright stars as seen in an HST WFPC-I optical image (after applying a $`1`$″ offset to the nominal HST coordinates to co-align the nucleus in both images). The nuclear X-ray source is slightly brighter than the southern component (they are ranked 9th and 12th in relative X-ray count rate in Table 1), and has a slightly softer spectrum, although both sources have fairly neutral X-ray hardness ratios.

Matonick and Fesen (1997) identified 54 optical SNRs within the Chandra field of view and 9 of these were detected in the X-ray band and listed in Table 2. Another 3 SNR sources (their SNR numbers 24, 32, and 43) are faintly visible on the adaptively smoothed Chandra image, but the detections were not significant enough to be included in our final list of 110 sources. All 9 of the X-ray detected SNRs sources have soft X-ray spectra, as would be expected from a hot plasma. The 2 brightest SNR sources (our #85 and #104) were variable during the Chandra observation, so in at least these cases the X-ray flux must be coming from a compact source and not from from the extended SNR itself. In a companion paper (Snowden et al., 2001) we present a more detailed investigation into the properties of several of these SNRs.

To complete the Table 2 list of cross identifications, 2 of the 5 giant HII regions in M101 (Williams and Chu, 1995) are located near the edge of the S3 chip (source #107 is NGC 5461 and source #110 is NGC 5462). The supernova SN1951H was located about $`12^{\prime \prime }`$ SE of NGC 5462 (Israel et al., 1975), but it is not detected in the Chandra observation. Finally, 7 of the Chandra sources are coincident with near-IR objects in the 2MASS catalog and 2 of these are also cross identified with sources in the HST Guide Star Catalog (one being the nucleus, the other being NGC 5458, a bright HII region).

About 10% of globular clusters in our Galaxy and other nearby galaxies contain X-ray emitting neutron stars, so a population of globular clusters might account for some of the X-ray sources in M101. The only published list of globular type clusters in M101 (Bresolin et al., 1996) contains 41 visually identified clusters within one relatively small (2′ square) HST WFPC II observation. It turns out, however, that most of these clusters are very blue and hence presumably young, like those observed in the Magellanic Clouds. Out of the 14 X-ray sources in this same region of M101, only one of them (source #80, one of the Supersoft sources discussed in §9) is located within 2″ of any of the optical clusters, which has a $`40`$% probability of occurring by chance.

## 6 X-ray Colors

The X-ray events located within a circular region around each of the 110 X-ray sources were used to calculate the count rate within standard energy bands and to generate spectra and light curves for each source. The radius of the region was chosen as a function of the distance of the source from the optical axis so as to enclose $`>95`$% of the source flux as predicted from the model PSFs and verified by numerical experiments on the brightest sources. The area of each source region is given by the “Area” column in Table 1, in units of the 0$`\stackrel{}{\mathrm{.}}`$49 Chandra CCD pixels.

Since most of the sources are too faint for detailed spectral analysis, we have characterized the general spectral properties of the sources by using the ratios of the X-ray count rates in 2 sets of soft, medium, and hard energy X-ray bands. The energy ranges for the first set of bands (S1, M1, and H1) were selected to produce roughly equal count rates in each band for the typical sample of sources seen in M101. For the second set of bands (S2, M2, and H2) a more standard set of astrophysically relevant energy ranges were used to facilitate the comparison of our results with those from previous X-ray missions. The adopted energy range for each of these bands is given in Table 3 along with the observed mean background flux level in each band. (The slight variation in background level and diffuse emission across the field is not significant for these purposes). The net counts, after background subtraction, for each source in each of these 6 bands is listed in Table 1. A pair of soft and hard X-ray flux ratios (or X-ray colors) were then calculated from the net counts in the three bands, where SR1 = (M1 - S1) / (S1 + M1), HR1 = (H1 - M1) / (M1 + H1), and similarly for the SR2 and HR2 ratios. In principle, the measured colors will depend on the position of the source in the field because the sensitivity of the ACIS instrument (i.e., the effective area of the telescope) decreases with distance from the aimpoint at slightly different rates depending on the energy band. This effect is small over the area covered by the S1 chip, however, and would cause the apparent X-ray colors to shift by only about 0.01 as the source is moved from the aim point to the far corner of the chip.

We compared the Chandra 0.125-2.0 keV (S2 + M2 band) count rates with the ROSAT HRI count rates as measured by Wang et al. (1999). Figure 5 shows that there is a very good correlation between the HRI and Chandra count rates for 15 of the 16 sources in common, which indicates that they have not varied significantly between the epochs of the observations (80% of the HRI data were obtained in 1996 and 20% in 1992). The one very discrepant point is source #98 which is highly variable (see §7) and is now about 25 times brighter in mean flux level than during the ROSAT observations. It has been plotted at 1/10 of its actual meanChandra count rate in order to fit onto the scale of Figure 5. The other bright source in Figure 5 (NGC 5462) has a slightly higher ROSAT count rate than would be predicted by the relation defined by the other points, but the comparison is complicated because the higher resolution Chandra image shows that it is a blend of several sources. Also shown at the bottom of Figure 5 are the Chandra count rates for 11 sources which were not detected in the ROSAT observations. The brightest 2 of these sources (#93 and #71) were variable during the Chandra observation (and hence could have been in a low state during the HRI observations), and the other sources are close to the ROSAT detection threshold, so it is not particularly surprising that these sources were not previously detected the ROSAT data.

The SR1 and HR1 X-ray colors provide a sensitive discriminator between sources with different types of X-ray spectra as shown in Figure 6. (Note that the SR2 and HR2 colors are less useful for this purpose because most of the flux lies in the M2 band and hence most of the points end up crowded into the lower right quadrant of the HR2 vs. SR2 diagram). The 45 brightest sources, which have more than 40 net X-ray counts, have been plotted with their calculated $`1\sigma `$ error bars. The fainter sources have been omitted for clarity. Any points which have a SR1 or HR1 value lying outside the physically allowed range of -1 to +1 (due to uncertain background subtraction) have been plotted at the limiting value. It can be seen that most of the points in Figure 6 lie within a broad diagonal band ranging from the softest sources in the lower left to the hardest sources in the upper right.

The calculated SR1 and HR1 flux ratios for several model X-ray source distributions are also plotted in Figure 6. The upper 3 curves show models with power law flux distributions with photon index slopes of 1.5, 2.0, and 4.0 respectively, and the 2 lower curves show blackbody models with temperatures of kT = 0.1 and 0.2 keV. In each case the lines connect the calculated SR1 and HR1 values for 4 $`N_H`$ hydrogen column densities of, from left to right, $`10^{20}`$, $`5\times 10^{20}`$, $`10^{21}`$, and $`10^{22}`$ atoms cm-2. These models show that the SR1 color is most sensitive to the $`N_H`$ parameter such that the more heavily obscured sources lie towards the right hand side of the figure. The HR1 color, on the other hand, is a better indicator of the intrinsic shape of the spectral flux distribution such that the flatter spectrum sources lie towards the top of the figure.

The representative models that are plotted in Figure 6, while not unique, provide an indication of the physical nature of the objects that lie in different areas of the color – color diagram. The very soft sources in the lower left corner form a distinct subpopulation which are discussed further in §9. The expected population of obscured background AGNs seen through the disk of M101 will generally have power law spectra with photon index slope in the range $`1.3<\mathrm{\Gamma }<4.0`$ and total HI columns $`>5\times 10^{20}`$. There are more than enough sources within this range of Figure 6 to account for the expected number of AGNs in the field and the remainder are likely to be low mass X-ray binaries in M101 itself. The 6 AGN candidates located in the interarm regions of M101, previously discussed in §3, fall within this region of the figure (although one of them, source #39, lies quite close to the 4.0 slope limit) and are plotted with open triangles. The sources below the $`\mathrm{\Gamma }`$ = 4.0 powerlaw model line are inconsistent with the spectrum of a typical AGN and are therefore more likely to be physically associated with M101.

## 7 Temporal Variability

Out of the 37 brightest sources which have more than 60 net counts, 4 of them (sources 85, 93, 98, and 104) showed definite intensity variability during the Chandra observation ($`<10^5`$ probability of being a constant source based on the Kolmogorov-Smirnov test), and 4 others (sources 51, 66, 71, and 108) are probably variable (with probabilities ranging from 0.01 – 0.06 of being a constant source). The flux curves for these sources are shown in Figure 7. Two of these variable sources (#93 and #71) are now brighter than the ROSAT detection threshold, but they were not detected in the previous ROSAT observations taken in 1992 and 1996. In addition to these 8 variable sources, there were also 2 variable sources previously observed with ROSAT (sources H28 and H31) which apparently have now faded below the Chandra detection limit.

Object #98 is currently the brightest and also the most dramatically variable source in M101. It has increased by about a factor of 25 in mean flux level from when it was previously observed by ROSAT and the count rate varied by more than a factor of 6 during the Chandra observation alone.

## 8 X-ray Models and Fluxes

The 29 brightest sources have enough flux ($`>100`$ counts) to perform at least crude spectral modeling using the HEASARC XSPEC (Arnaud, 1996) model fitting program. Most of the sources could be satisfactorily fit with a simple absorbed power law spectrum model, however 8 of the softest sources were better fit by an absorbed blackbody model. Table 4 lists the best fitting model parameters for these 29 sources. Also tabulated are the apparent X-ray fluxes calculated by integrating the model spectrum over the energy range of the S2 (0.125 – 0.5 keV), M2 (0.5 – 2.0 keV), and H2 (2.0 – 8.0 keV) energy bands as well as the intrinsic X-ray luminosity of the source in each of the 3 bands, correcting for the model $`N_H`$ absorption and assuming a distance of 7.2 Mpc to M101. In general the models provided a satisfactory fit to the observed spectra, as shown by the reduced $`\chi ^2`$ values given in the table. The main exception to this is the brightest variable source #98 whose integrated spectrum could not be well fit by any simple model. The X-ray flux from this source is generally very soft, but the spectrum changes significantly with the flux level. As a consequence, the flux and luminosity values given for this object are only representative of its true nature. This unusual object will be studied in more detail in a separate paper, but it is already apparent that this is a super-Eddington source with an maximum instantaneous luminosity in the range of $`10^{39}`$ to $`10^{40}`$ergs s-1

The ratio between the total net X-ray counts and the model X-ray flux in the S2, M2, and H2 bands for the 29 brightest sources was used to derive a mean counts-to-flux conversion factor which could be applied to the fainter sources to estimate their fluxes. Figure 8 shows the flux-per-count ratio plotted as a function of the hardness ratio, HR2, for each source. The adopted multiplication factors, which convert from total net counts in our 98.2 ks exposure into units of ergs cm-2 s-1 are

$$C_{S2}=(2.37\pm 0.39)\times 10^{17},$$

$$C_{M2}=((3.5+0.9\times HR2)\pm 0.24)\times 10^{17}$$

and

$$C_{H2}=(1.89\pm 0.34)\times 10^{16}$$

where the M2 band conversion factor has a slight dependence on the hardness ratio of the source. These conversion factors were used to compute the X-ray flux values given in Table 1 for all the sources. Note that all the X-ray flux and luminosity values (but not the net counts values) quoted in this paper have been corrected for several instrumental effects. Every flux and luminosity value has been multiplied by a nominal factor of 1.02 (or 1.05 in the case of the slightly smaller apertures that were used for the 2 nuclear sources) to correct for the flux that was excluded by the circular integration apertures. In addition, 6 of the sources needed a $`5`$% correction factor because they were projected near one of the “warm” columns next to the CCD readout amplifier which were excluded during the initial data cleaning procedure. Finally, 2 of the sources were located near the edge of the chip and required an additional vignetting correction factor because the deliberate wobbling of the telescope pointing axis during the exposure caused the source to periodically move on and off the chip.

Figure 9 shows the distribution of $`\mathrm{log}F_x`$ for all 110 sources (using the values from Table 1), and Figure 10 shows the distribution of $`\mathrm{log}L_x`$ for the 29 brightest sources from Table 4. Note that it is not possible to reliably compute the luminosity for the fainter sources because the individual $`N_H`$ values are unknown. Several of the sources, especially in the softest band, appear to have luminosities greater than the Eddington limit of $`1.3\times 10^{38}`$ ergs s-1 for a one solar mass object, but the uncertainties in the calculated luminosities are sometimes quite large. The brightest S2 band source, #93, for example, has a high luminosity mainly because the best fitting model has a very steep spectrum and a large hydrogen column density of $`7.5\times 10^{21}`$ cm-2 which leads to a large correction factor to the apparent flux. The next most luminous S2 band source is #98 which, as mentioned previously, is highly variable and it’s spectrum is not well fit by simple flux models. It has been plotted at it’s mean Chandra flux level, but it’s instantaneous luminosity has been observed to vary by at least 2 orders of magnitude.

In principle, the observed color dependence of the counts-to-flux conversion factor for the M2 band (Fig. 8) could affect the analysis of the $`\mathrm{log}N\mathrm{log}S`$ relation in §4. In that analysis we assumed a constant conversion factor between counts and flux, but if the mean X-ray color of the sources changes with count rate (i.e., if the fainter sources are significantly harder or softer in the mean than the brighter sources) then this would cause a systematic difference between the slope of the $`\mathrm{log}N\mathrm{log}(counts)`$ and the $`\mathrm{log}N\mathrm{log}(flux)`$ relations. This difference could be important because most observational source population studies have used $`\mathrm{log}N\mathrm{log}(counts)`$, whereas most theoretical interpretation is done in terms of $`\mathrm{log}N\mathrm{log}(flux)`$.

In order to judge the importance of this effect, we computed the mean HR2 color of sources as a function of count rate, as shown in Figure 11. The fact that there is no significant trend in the figure (the best fitting line has a slope of $`0.013\pm 0.16`$) means that our assumption of a constant counts-to-flux conversion factor has not biased the derived slope of the $`\mathrm{log}N\mathrm{log}S`$ relation.

## 9 Super Soft Sources

Ten of the Chandra X-ray sources have very soft spectra similar to the Supersoft sources (SSS) that have been seen in other nearby galaxies. These M101 sources can be divided into 2 distinct subclasses: the brighter class consists of 3 sources (13333 The only source detected in M101 in the Einstein IPC ultrasoft survey, at $`14^h03^m00^s`$, $`54^{}22`$′25″(Thompson et al., 1998) may coincide with our source #13. The positions differ by 1$`\stackrel{}{\mathrm{.}}`$3, which is about twice the typical error in the Einstein source positions, but is still well within the 3′ integration radius that was used to extract the Einstein source counts. , 45, and 99) and the fainter and softer class consists of 7 sources (8, 16, 30, 72, 80, 96, and 101). The brighter class of SSS have a mean count rate of 2.0 counts ks-1 and have a S2 band (0.125 – 0.5 keV) to M2 band count ratio of 3:1. The fainter class of SSS, on the other hand, are an order of magnitude fainter with a mean flux of 0.26 counts ks-1, and have such a soft spectrum that essentially all the flux is emitted in the S2 band.

The 3 brighter SSS have very similar spectra as demonstrated by the good agreement between the blackbody model fits given in Table 4 for the sources: the best fitting model temperatures range from 60 to 100 eV (equivalent to 0.7 to 1.1 million degrees K) and the hydrogen column densities lie in the range of 1.0 to $`8.0\times 10^{20}`$ cm-2, which is consistent with the Galactic column density of $`1.2\times 10^{20}`$ cm-2 in the direction of M101 (Stark et al., 1992; Hartmann and Burton, 1997) plus an additional absorption component local to the sources in M101. Because the spectra are so similar, we combined the counts from the 3 sources to obtain the better signal to noise spectrum shown in Figure 12. The best fitting blackbody model to this combined spectrum has a temperature of $`72\pm 2`$ eV (equivalent to $`8.4\pm 0.2\times 10^5`$ K) and $`N_H=6.0\pm 0.7\times 10^{20}`$ atoms cm-2. Note that the formal errors on the model parameters are unrealistically small, and do not take into account the unknown systematic errors in the calibration of the instrumental response below 0.3 kev. The mean luminosity of these 3 sources over the 0.125 to 2.0 keV band is $`1.4\times 10^{38}`$ ergs s-1 with most of this flux emitted below 0.5 keV. None of these 3 sources showed any obvious signs of variability, either during the Chandra exposure or between the epochs of the ROSAT and Chandra observations.

The combined spectrum of the 7 fainter SSS in M101 is shown in Figure 13. In spite of the statistically large uncertainties in the count rates and the large systematic uncertainties in the energy calibration of the Chandra detector at these low energies, it is clear that this fainter class of SSS has a much softer spectrum than the brighter class shown in Figure 12. Since the $`N_H`$ value is not well constrainted by the model fits, we assumed a conservative value equal to the Galactic column of $`1.2\times 10^{20}`$ cm-2. Under this assumption the best fitting blackbody model to the mean spectrum has a temperature of $`47\pm 2`$ eV and a 0.125 to 2.0 keV luminosity of $`1.1\times 10^{37}`$ erg s-1 (85% of this flux is emitted below 0.3 keV). Assuming a larger $`N_H`$ value decreases the best fitting model temperature only slightly, but it greatly increases the calculated luminosity (by a factor of 7 for $`N_H`$ = $`6\times 10^{20}`$ cm-2) because even a small increase in column density produces a large increase in extinction for these soft sources.

The SSS were first detected in other nearby galaxies by Einstein (Long et al., 1981), and later studied more extensively with ROSAT (Trumpler et al., 1991; Greiner et al., 1991). Supper et al. (1997) classified 3.8% (15 out of 396) of the ROSAT PSPC sources in M31 as being Supersoft sources, This is not necessarily inconsistent with the higher rate of SSS we found in M101 (9%), however, because the higher Galactic $`N_H`$ absorption towards M31 ($`6\times 10^{20}`$ cm-2) compared to M101 will absorb much of the soft flux from these sources. For this same reason, the SSS are difficult to detect in our Galaxy if they are more than $`1`$ kpc away in the plane of the disk. Clearly, it will be of great interest to see how the properties of the SSS population vary between different types of galaxies as more data from the Chandra and XMM observatories become available in the near future.

While the diversity of observed properties argues against lumping all SSS into a single class of object, the generally accepted model for the classical SSS is that they are white dwarf stars with steady nuclear burning in their envelopes (Van den Heuvel, et al., 1992). It is thought that high accretion rates ($`>10^7M_{}`$ yr-1) from a low mass secondary onto the white dwarf primary fuels the burning of the hydrogen near the surface of the white dwarf. The predicted luminosities range from $`6\times 10^{36}`$ ergs s-1 to $`1\times 10^{38}`$ ergs s-1, with peak energy fluxes in the 30 – 50 eV range, in good agreement with the sources seen in M101. The steep drop in flux above about 0.8 keV seen in Figure 12 is typical of most SSS; recent high signal to noise ASCA observations (Asai et al., 1998) have shown that this break can be explained by an absorption edge feature probably due to O VIII at about 0.87 keV. This and other edges originating from hydrogen-like or helium-like ions of carbon, nitrogen and oxygen would be expected for the emission from a hot white dwarf with a stable hydrogen burning envelope.

The SSS are also related to classical novae (CNe) in that SSS are quasi-steady nuclear burning, whereas CNe are the result of thermonuclear runaways. Indeed, many CNe go through a SSS phase several months after the peak of optical outburst. In one case, the SSS phase lasted for nearly a decade (Shanley et al., 1995). We looked for a similar correlation in M101 by comparing the positions of the 7 known optical novae that occurred within our M101 field between 1994 and 1997 (Shafter et al., 2000) with our X-ray source catalog and with the position of even fainter possible sources seen in the adaptively smoothed X-ray image, but found no matches. Thus, at least none of these novae had a long-lasting, bright, SSS phase after their optical outburst.

## 10 Conclusions

This paper provides a preview of what the studies of the X-ray source populations in external galaxies will reveal and what they will teach us about the X-ray sources in our own Galaxy. The main result of this paper is the catalog of 110 X-ray sources seen in the Chandra observation of the face-on spiral galaxy M101. The detection threshold is about $`10^{36}`$ ergs s-1, but depends on position because of the variable angular resolution of the X-ray telescope across the field of view. Since this flux threshold is several orders of magnitude higher than the level of coronal X-ray emission expected from normal stars, most of these sources must be more exotic objects, including X-ray binaries, supersoft sources (SSS), and supernovae remnants. The field of view of the current observation only covers about 50% of the prominent spiral arms in M101, so a complete census of all the X-ray sources visible with Chandra in M101 at this flux limit could contain twice as many objects.

Only about 1/4 of the sources are estimated to be background AGNs, so most of our sources are physically associated with M101. The bulk of the point sources are related to spiral arms, suggesting that the population of X-ray sources is derived from young objects in regions of active star formation, and thus may be dominated by High-Mass X-ray Binaries. Conversely, spiral arms have higher stellar densities for all stellar types, so there may not be an over-abundance of High-Mass X-ray Binaries. Most of the sources seen in the interarm regions are probably AGNs because their surface density is close to the expected number of background sources, and because the X-ray colors of most of the interarm sources are consistent with that from a power law spectrum usually seen in AGNs.

At a distance of 7.2 Mpc Chandra can provide a luminosity function down to $`10^{36}`$ ergs s-1, so measuring the luminosity functions for the nearby galaxies will do much to explore the link between the X-ray source populations and the star-formation history, and will help to interpret the X-ray source luminosity functions being developed for the Milky Way. The derived $`\mathrm{log}N\mathrm{log}S`$ relation for the sources in M101 is nearly linear with a slope of $`0.80\pm 0.05`$ over the flux range $`10^{36}10^{38}`$ ergs s-1. We observed no difference in the slope of the relations between bulge ($`R<1\mathrm{}`$) and disk sources ($`1\mathrm{}<R<4.5\mathrm{}`$), however, there are few sources in the bulge so the uncertainties in the bulge slope are relatively large. Another recently published $`\mathrm{log}N\mathrm{log}S`$ study similar in scope to the present work is that of Tennant et al. (2001) for the galaxy M81 (NGC 3031) at a distance of 3.63 Mpc (Freedman et al., 1994). M81 is an Sab galaxy with a substantially larger bulge than M101. For the 0.2–8.0 keV band Tennant et al. (2001) find the $`\mathrm{log}N\mathrm{log}S`$ of the disk sources to have a slope of -0.50 over the flux range $`4\times 10^{36}2\times 10^{39}`$ ergs s-1, somewhat flatter than our relation. Given the difference in energy range, as well as possible differences in the slope of the AGN luminosity functions used, the two values are consistent with each other. At a limiting flux of $`10^{37}`$ ergs s-1, however, the surface density of X-ray sources is nearly four times greater for M81 (0.2 kpc-2) than for M101 (0.05 kpc-2), presumably reflecting the differences in the star formation rate between the two galaxies.

Eight of the brighter sources show evidence for short term temporal variation over the 98.2 ks period of our observation, and 2 other sources previously observed with ROSAT are no longer visible with Chandra. The brightest Chandra source is also the most variable source, varying by more than a factor of 6 during the observation. The current mean flux level is about 25 times higher than when previously observed with ROSAT. This source has a soft spectrum which varies significantly with the flux level. Simple spectral models do not provide a very good fit to the spectrum, but it is clear that it has a super-Eddington luminosity which sometimes exceeds $`10^{39}`$ ergs s-1. This unusual source will be studied in more detail in a subsequent paper.

The nuclear X-ray source is non-exceptional and looks very much like the other sources in the field. It is not spatially resolved, although there is evidence for enhanced diffuse X-ray emission near the nucleus (to be studied in a separate paper). While this source may well be a weak AGN similar to that detected in most other nearby galaxies (Ho et al., 2001), it could also simply be a typical X-ray binary located in the dense stellar environment close to the nucleus. There is another nearly identical X-ray source just 3$`\stackrel{}{\mathrm{.}}`$1 to the south of the nucleus which coincides with a loose cluster of bright stars. A power-law spectral model gives a resonable fit to both the nuclear source and the southern companion, resulting in photon indices of 2.02 and 1.56, and luminosities of $`4.2\times 10^{37}`$ ergs s-1 and $`3.8\times 10^{37}`$ ergs s-1 in the 0.5 – 2.0 keV band, respectively.

About 9% of the M101 sources have extremely soft spectra similar to the SSS seen in other nearby galaxies. The 10 SSS in M101 can be naturally divided into 2 classes: the 3 brightest SSS have a mean luminosity of $`1.4\times 10^{38}`$ ergs s-1 and a model blackbody temperature of $`72\pm 2`$ eV. The other 7 SSS have an order of magnitude smaller X-ray count rate, most of which is emitted below 300 eV. The model temperature and luminosity of these fainter sources is dependent on the assumed hydrogen column density, but is in the neighborhood of 50 eV and $`1.1\times 10^{37}`$ erg s-1 respectively. The observed luminosities and temperatures of both these classes of SSS are within the range predicted by the standard models of a white dwarf star with steady nuclear burning in its envelope fueled by accretion from a low mass secondary.

We wish thank the referee, Dr Philip Kaaret, for his careful review and useful suggestions that improved this manuscript. This research was supported in part by NASA grant number 01900441. We have made use of data and software obtained from the High Energy Astrophysics Science Archive Research Center (HEASARC), provided by NASA’s Goddard Space Flight Center.


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# Dwarf Galaxies in the Local Group and in the Local Volume

## 1 Introduction

Galaxies cover a vast range of types and properties. The by far most frequent type of galaxy are dwarf galaxies, i.e., galaxies with low mass, low luminosity, low metallicity, and small in size. The terminological distinction between dwarf galaxies and “normal” or giant galaxies is poorly defined and is used in different ways by different authors. For the purpose of this paper we shall use the absolute $`V`$-band magnitude as a simple distinguishing criterion and consider all galaxies fainter than $`M_V=18`$ mag as dwarf galaxies. A potentially more meaningful criterion would be mass rather than luminosity since dwarf galaxies have a range of different mass-to-light ratios. Such a definition would, for instance, consider all galaxies with masses of 1/10 or 1/100 of $`M^{}`$ as dwarf galaxies. However, since masses are unknown for most dwarf galaxies while luminosities are a directly measurable observable, we will use the luminosity criterion here.

In hierarchical structure formation scenarios dwarf galaxies (or more generally: small dark matter halos) are important building blocks of more massive galaxies and should have been even more numerous in the early Universe. Accordingly, the dwarfs we observe today are considered survivors of an initially much richer population. Interestingly, at the low-mass end we observe fewer dwarf galaxies today than the number of predicted surviving dark matter halos (e.g., Klypin et al. 1999). This may imply that we are either missing a large fraction of low-mass galaxies, that these halos do not have optically detectable counterparts, or that the scenarios are wrong.

Today’s dwarf galaxies are the closest currently known counterparts of the early galaxy-forming fragments. Their star formation histories may hold the clue to understanding the conditions and evolution of the early Universe. Especially low-mass dwarf galaxies tend to have experienced little enrichment and few star formation episodes, i.e., they are “simple systems” as compared to more massive galaxies. These properties make the study of their evolutionary histories particularly interesting. They are also interesting objects from the point of view of stellar evolution since here we can study star formation histories in low-metallicity environments, investigate mass functions in low-mass, low-density environments, study the impact of neighboring massive galaxies on star formation, find out about preconditions for star cluster formation, etc.

These studies give the most accurate and reliable results where stellar populations can actually be resolved into individual stars. This makes nearby dwarf galaxies in the Local Group and Local Volume excellent targets.

The Local Group is the small group of galaxies around the Milky Way and M31. Within a zero-velocity surface of 1.2 Mpc (Courteau & van den Bergh 1999), the Local Group contains 36 known or suspected member galaxies. Since the orbits of these galaxies are still unknown, it is uncertain whether all of them are members, although one usually assumes that dwarf galaxies within $`200`$ kpc of a more massive galaxy are bound satellites of that galaxy. On the other hand, we may be missing quite a few low-luminosity members that have yet to be discovered. For example, recent searches three to four years ago uncovered four new, faint Local Group dwarfs (Armandroff, Davies, & Jacoby 1998; Karachentsev & Karachentseva 1999; Armandroff, Jacoby, & Davies 1999; Whiting, Hau, & Irwin 1999).

The Local Volume (and Local Void) comprises the volume with a radius of about 5 Mpc. It includes galaxies with velocities $`500`$ km s-1 that are either part of small galaxy groups or field galaxies. The exact number of galaxies and their faint-end census in the Local Volume remain unknown. A recently completed all-sky search led to the detection of $`600`$ dwarf and low-surface-brightness galaxies, whose angular extent indicates that they may belong to the Local Volume (Karachentsev et al. 2000a). More than half of these objects were new discoveries.

## 2 Morphological types of dwarf galaxies

Dwarf spiral galaxies are found among S0, Sa, Sb, Sc, and Sd galaxies. They have central surface brightnesses of $`\mu _V\begin{array}{c}>\\ \end{array}23`$ mag arcsec-2, H i masses of $`M_{\mathrm{HI}}\begin{array}{c}<\\ \end{array}10^9`$ M, and usually large mass-to-light rations inferred from rotation curves (e.g., Schombert et al. 1995; Matthews & Gallagher 1997). Dwarf spirals are at the high-mass end of the dwarf galaxy distribution. Early-type dwarf spirals show rotation curves typical for rotationally supported exponential disks, while late-type dwarf spirals are slow rotators or exhibit solid-body rotation. Dwarf spirals show slow continuous star formation. Later types tend to be more metal-poor and gas-poor than earlier types (McGaugh 1994). Very late-type spirals may be in transition to irregulars. Dwarf spirals are found in clusters and in the field.

Blue compact dwarf galaxies (BCDs) are actively star-forming objects with centrally concentrated starbursts. Both gas and stars show pronounced central concentration, contributing to the compact appearance, fueling the starburst, and leading to high central surface brightnesses (typically $`\mu _V\begin{array}{c}<\\ \end{array}19`$ mag arcsec-2). Various subtypes of dwarf galaxies exhibit BCD characteristics including H ii galaxies, blue amorphous galaxies, and certain types of low-mass Wolf-Rayet galaxies. The H i masses of BCDs are $`10^9`$ M and may exceed the stellar mass. Part of the very extended gas may be kinematically decoupled from the galaxies (van Zee, Skillman, & Salzer 1998). In their inner parts BCDs show solid-body rotation. BCDs are often observed in relative isolation away from the dense centers of clusters or groups.

Dwarf irregular galaxies (dIrrs) are irregular in appearance and appear dominated by scattered bright H ii regions in the optical. In H i these gas-rich galaxies show a complicated fractal pattern full of shells and clumps. In the more massive dIrrs the H i distribution is usually much more extended than even the oldest stellar populations. In some cases evidence for gas accretion has been observed (e.g., Wilcots & Miller 1998). In less massive dIrrs the H i may be displaced with respect to the stellar light distribution, either off-centered or showing a ring-like structure with a central depression (e.g., Young & Lo 1997a). DIrrs are characterized by $`\mu _V\begin{array}{c}<\\ \end{array}23`$ mag arcsec-2, $`M_{\mathrm{HI}}\begin{array}{c}<\\ \end{array}10^9M_{}`$, and $`M_{\mathrm{tot}}\begin{array}{c}<\\ \end{array}10^{10}M_{}`$. The more massive dIrrs show increasing chemical enrichment with decreasing age. In low-mass dIrrs gas and stars may show distinct spatial distributions and kinematics. Solid-body rotation is common among the more massive dIrrs, while low-mass dIrrs occasionally do not show measurable rotation. DIrrs are found in clusters, groups, and in the field. They exhibit little concentration toward massive galaxies. Massive dIrrs may continue to form stars over a Hubble time (Hunter 1997). Very low-mass, gas-poor dIrrs, on the other hand, may be evolving towards dwarf spheroidals.

Dwarf elliptical galaxies (dEs) are spherical or elliptical in appearance, compact, have high central stellar densities and are typically fainter than $`M_V=17`$ mag. Other characteristics include $`\mu _V\begin{array}{c}<\\ \end{array}21`$ mag arcsec-2, $`M_{\mathrm{HI}}\begin{array}{c}<\\ \end{array}10^8M_{}`$, and $`M_{tot}\begin{array}{c}<\\ \end{array}10^9M_{}`$. They tend to be found close to massive galaxies, usually have little or no detectable gas, and are often not rotationally supported. If gas is detected it may show an asymmetric distribution, be less extended than the underlying stellar light, and may be kinematically distinct (Young & Lo 1997b; Sage, Welch, & Mitchell 1998; Welch, Sage, & Mitchell 1998). DEs may show pronounced nuclei that can contribute up to 20% of the galaxy’s light. The fraction of these nucleated dEs (dE(N)) increases among more luminous dEs. The surface density profiles of dEs and dE(N)s are best described by Sérsic’s (1968) generalization of a de Vaucouleurs $`r^{1/4}`$ law and exponential profiles (Jerjen et al. 2000).

Dwarf spheroidal galaxies (dSphs) are diffuse, gas-deficient, low-surface-brightness dwarfs with very little central concentration. They are characterized by $`M_V\begin{array}{c}>\\ \end{array}14`$ mag, $`\mu _V\begin{array}{c}>\\ \end{array}22`$ mag arcsec-2, $`M_{\mathrm{HI}}\begin{array}{c}<\\ \end{array}10^5M_{}`$, and $`M_{tot}10^7M_{}`$. DSphs are the faintest, least massive galaxies known. The upper limits for their H i are usually even below the amounts expected from normal stellar mass loss. DSphs are usually found in close proximity of massive galaxies and do not appear to be supported by rotation. Their velocity dispersions indicate the presence of a significant dark component when virial equilibrium is assumed.

The difference in the spatial distribution of dEs and dSphs on the one hand and dIrrs on the other hand is also known as morphological segregation or as the morphology–density relation for dwarf galaxies and may be a signature of environmental effects on galaxy evolution.

Tidal dwarf galaxies form from the debris torn out of more massive galaxies during interactions and mergers. In contrast to other dwarf galaxies they do not contain dark matter and may have high metallicities for their luminosity depending on the evolutionary stage of the parent galaxy (Duc & Mirabel 1998). Masses, sizes, gas content, etc. of tidal dwarfs depend critically on the conditions during the interaction and on the parent galaxy. It is possible that certain dIrrs and dSphs are tidal dwarfs that formed relatively early. For instance, various authors suggested that the Milky Way dwarf companions may be part of two or more major debris streams in polar orbits (e.g., Majewski 1994; Lynden-Bell & Lynden-Bell 1995). Potential candidates for nearby tidal dwarf galaxies based on their intrinsic properties are discussed by Hunter et al. (2000).

## 3 Dwarf Galaxies in the Local Group

The dwarf galaxies studied most extensively to date are dwarf galaxies within the Local Group. Of the above mentioned types, the Local Group contains dIrrs, dEs, and dSphs as well as galaxies that may be in transition from dIrrs to dSphs.

The results from the detailed studies of Local Group dwarfs can be (incompletely) summarized as follows.

Local Group dwarfs were found to vary widely in their star formation histories, mean metallicity and enrichment histories, times of their major star formation episodes, fractional distribution of ages and subpopulations. Indeed no two dwarf galaxies are alike, not even if they are of the same morphological type or have similar luminosities (Grebel 1997). In part their properties appear to be correlated with galaxy mass and with environment (proximity to massive galaxies).

In many Local Group dwarfs spatial variations in star formation history were detected. In general, there is a tendency for the younger populations to be more centrally concentrated (and possibly more enriched), whereas older populations are more extended. This may in part be an effect of dynamical evolution, but may also indicate that star formation was able to continue over an extended period of time in the central regions since these may have been able to retain gas longer (or may have been rejuvenated by gas inflow in accretion events). For a summary of population gradients in a number of Local Group dSphs, see Harbeck et al. (these proceedings). Harbeck et al. conclude that presence or absence of these gradients does not show a clear correlation with environment.

A common property to all dwarf galaxies studied in sufficient detail so far is the presence of an old population. All claims of discoveries of purely young galaxies have subsequently been refuted once deeper images or data with better coverage of the outskirts of these galaxies became available. Deep ground-based imaging of the “halos” of dIrrs led to the detection of old red giant branches (e.g., Minniti & Zijlstra 1996) All dSphs and dEs for which deep photometry was obtained revealed horizontal branches, a clear indicator of old populations. The nearest candidate for a dwarf spiral, NGC 3109, shows a presumably old red giant branch in its outer regions (Minniti, Zijlstra, & Alonso 1999). Deep imaging of BCDs has revealed the presence of intermediate-age and possibly old populations (e.g., Lynds et al. 1998), as already inferred from integrated colors.

The oldest populations in the majority of nearby dIrrs and dSphs are indistinguishable in age from the oldest globular clusters in the Galactic halo and bulge (for a full list and references, see Grebel 2000). This indicates a common epoch of the oldest measurable star formation episode. Relative ages were derived from deep photometry extending below the main-sequence turn-off. In at least one dIrr (the Small Magellanic Cloud), however, significant star formation appears to have started with a delay of 2–3 Gyr. Data of sufficient depth and quality to carry out differential age-dating of the oldest populations are so far only available for Milky Way companions, i.e., dwarf galaxies within $`300`$ kpc.

Nearby dwarf galaxies typically show one of two modes of star formation: Continuous or episodic. High-mass dwarf galaxies tend to form stars fairly continuously with amplitude variations of up to a factor of three. They can continue to form stars over another Hubble time without exhausting their gas supply. They exhibit gradual enrichment, since many of the metals produced in star formation episodes are recycled later on. This mode of star formation is observed in high-mass dIrrs and dwarf spirals. Lower-mass dIrrs, dEs, and dSphs show continuous star formation with decreasing star formation rates. In dEs and dSphs, only little gas or no gas at all is observed, and star formation has ceased at the present time. One dSph in the Local Group, Carina, shows episodic or repetitive star formation: This galaxy underwent star formation episodes separated by 2 Gyr long episodes of quiescence. Yet no significant enrichment appears to have occurred if one interprets the narrowness of the red giant branch as an indication of a narrow metallicity range. This may suggest that the later episodes took place with accreted gas. Alternatively, age and metallicity may conspire to form one narrow red giant branch. The resolution of this question requires spectroscopy. It is not yet understood what caused the periods of quiescence and the renewed onset of star formation lateron.

DSphs around the Milky Way tend to have increasing fractions of intermediate-age populations with increasing distance from the Milky Way, suggestive of the impact of environmental effects: Tidal and ram pressure stripping may have removed most of the gas from nearby dSphs very early on, whereas more distant dSphs were able to retain their star-forming material for longer periods of time (e.g., van den Bergh 1994). The two dSph galaxies with the shortest Galactocentric distances (Ursa Minor and Draco) are essentially entirely old. These two are also the two least massive dwarfs. The second most massive dSph in the Local Group, Fornax, ceased to form stars only about 200 Myr ago (Grebel & Stetson 1999). (Here the term “mass” assumes that luminosity traces mass.) Hence the star formation history depends on parent galaxy mass. There are a number of uncertainties with this simplified picture though. Firstly, we do not know the orbits of the Milky Way companions and cannot tell whether their present-day positions are typical for their past distances from the Milky Way. We also do not know how close they came to the Milky Way in the past, and what role interactions played. Secondly, no fully satisfactory mechanism for the gas loss has been found so far. Simulations indicate that internal effects such as supernovae winds are insufficient to rid a dwarf galaxy of its gas (Mac Low & Ferrara 1999). Mayer et al. (2001) suggest that tidal shocks during perigalactic passages close to a massive galaxy may convert dIrrs into dSphs. They show that their simulations can reproduce the observed global properties of the Milky Way dSph companions as well as the morphology-density relation. Taking this model one step further, we would not expect to find isolated dSphs. Thus thirdly, if environmental effects determine the evolution of low-mass dwarfs, the existence of the dSph Tucana in the distant outskirts of the Local Group is hard to explain. This isolated dSph does not show evidence for gas or young or intermediate-age populations.

The M31 dSph companions, which span a similar range of distances around M31 as the Milky Way dSphs around the Galaxy provide a valuable source for testing the ram pressure/tidal stripping scenario. Interestingly, these galaxies do not show evidence for the presence of young or intermediate-age populations as traced by extended blue main sequences or pronounced concentrations of red clump stars. Our preliminary analysis shows little indication for evolutionary trends and present-day distance to M31.

We may be observing ongoing evolution from low-mass dIrrs to dSphs. Low-mass dIrrs show little or no rotation and have low current star formation rates. Their H i is not necessarily concentrated on the optical center of the dwarf. The so-called transition-type galaxies may be in an advanced phase of evolution from dIrrs to dSphs. The measured stellar velocity dispersion of the dIrr/dSph galaxy LGS 3 is comparable to that of dSphs (Cook et al. 1998). Mateo (1998) argues that the three transition-type galaxies LGS 3, Phoenix, and GR 8 lie on the same branch as dSphs when plotting \[O/H\] or \[Fe/H\] versus absolute magnitude. The recent stellar radial velocity determination for Phoenix by Gallart et al. (2001) argues in favor of the H i detected in the vicinity of Phoenix being associated with this dIrr/dSph galaxy, which experienced star formation as recently as 100 Myr ago (Holtzman et al. 2000). The dSph Fornax, which still formed stars some 200 Myr ago (Grebel & Stetson 1999) while being devoid of gas at present (Young 1999), may be a former dIrr that only recently finished its transition to a dSph.

## 4 Dwarf galaxies in the Local Volume

Nearby dwarf galaxies outside of the Local Group have been studied in much less detail. We are currently carrying out an HST WFPC2 snapshot survey to obtain upper red giant branch photometry of 200 nearby dwarf galaxies, and supporting ground-based observations to obtain surface photometry, spectroscopic abundances, and velocities (Grebel et al. 2000). At the same time, we are working on extending the census of dwarf and low-surface-brightness galaxies to fainter magnitudes using the Sloan Digital Sky Survey.

Our HST snapshot program yields information about the recent star formation history and qualitative information about intermediate-age populations. It allows us to determine distances based on the tip of the red giant branch. The slope of the red giant branch can be used for photometric metallicity estimates (see Figure 1 for a schematic color-magnitude diagram). This allows us to derive both projected distances to the target galaxies and deprojected distances between galaxies within galaxy groups. We can thus study the morphology–density relation in galaxy groups in three dimensions rather than only in projection. Studies using projected distributions of dwarf galaxies in nearby groups suggest that dSphs and dEs tend to lie near massive galaxies, whereas dIrrs appear to be more widely distributed (e.g., Jerjen, Binggeli, & Freeman 2000). In Figure 2a we show the the deprojected distances of dwarf galaxies around the Milky Way, M31, and M81. The majority of these dwarfs are dSphs and dEs. In all three cases, we see the qualitatively similar tendency for the dSphs and dEs to concentrate around the closest massive galaxy.

Considering our knowledge of the recent star formation history (based on the observed presence or absence of young and intermediate-age populations) and of galaxy metallicity (through photometry or spectroscopy) we can furthermore study the influence of environment on galaxy evolution. Moreover, we can test the validity of global relationships such as the metallicity–surface brightness–luminosity relation (first illustrated for oxygen abundances and luminosities by Skillman, Kennicutt, & Hodge 1989). In Figure 2b this relation is shown for dwarf galaxies in the Local Group and for dSphs in the M81 group. The mean metallicities for the M81 dSphs are at present purely based on photometry. In spite of the significant scatter, dwarf galaxies in both groups show the expected positive correlation between luminosity, surface brightness, and metallicity.

That dwarf galaxies show common trends for their integrated properties in spite of their individual differences and irrespective of environment may indicate that galaxy mass is a determining factor in dwarf galaxy evolution. On the other hand, the morphology–density relation illustrates that environment is an important factor. Clearly, many important questions require further research, including the mechanisms governing dwarf galaxy evolution, the origin of the morphology–density relation, delayed evolution versus an ancient common epoch of early star formation, gas loss mechanisms, metal loss versus metal retention, enrichment as a function of time, presence and nature of dark matter, and satellite orbits, the uniqueness or generality of the Local Group, and differences between groups of galaxies. We are only at the beginning of the exploration of the properties and evolution of the most frequent type of galaxy, the dwarf galaxies. The new era of large telescopes and a multi-wavelength approach promises to help us solve many of these fundamental questions.

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text:
# Transition Events in Butane Simulations: Similarities Across Models

## 1 Introduction

Ensuring appropriate behavior in molecular simulations has long been a topic of interest, and butane has been an important test molecule as the simplest alkane with a dihedral degree of freedom. In early work on united-atom models Rebertus, Berne and Chandler considered solvent effects on butane conformational equilibrium , while Levy, Karplus and McCammon studied stochastic butane dynamics . Pastor and Karplus later investigated the importance of inertial effects in Langevin dynamics, also using a united atom model of butane . Tobias and Brooks discussed the importance of including hydrogen atoms when considering solvent effects .

One focus of molecular studies has been the dependence of transition rates on the choice of dynamics. In a study of ethylene glycol, which is polar but also possesses a single dihedral angle, Widmalm and Pastor compared rates and other timescales in molecular and Langevin dynamics . Similarly, Loncharich, Brooks and Pastor explored the effects of the Langevin friction constant on transitions rates in the larger “NAMA” molecule with an eye toward speeding up the generation of conformational ensembles in peptides and proteins .

Work in one-dimensional systems, in addition to considering the effects of stochastic dynamics on reaction rates (e.g., ), has explored transition phenomena on still-shorter “microscopic” timescales. Dykman and coworkers have extensively investigated the effects of different noise types and non-equilibrium driving forces on *transition events themselves* in stochastic settings . The present authors previously considered the influence of the local, non-uniform speed along the reaction coordinate on a “dynamic importance sampling” approach to rate computations .

Many “microscopic” questions have remained unanswered regarding *molecular* transition events. What is their duration? Is the reaction coordinate traversed at a uniform speed, or is progress more rapid in some regions?

Is there sensitivity to the choice of dynamics or potential? The need for detailed answers is more pressing in molecular systems because dynamic importance sampling  and “transition path sampling” methods  for computing reaction rates require ensembles of transition event trajectories. A quantitative understanding of transition events could accelerate ensemble generation in these approaches, making larger systems amenable to study. Moreover, because ensembles of transition events are required for rate estimates, the durations set a fundamental minimum on the computer time required to perform such calculations .

The present study provides answers to these questions, using a spectrum of simulations. First, using the CHARMM potential, all-atom butane is studied in explicit water and acetic acid. Low- and high-friction Langevin simulations are also performed with CHARMM, along with a separate high-friction run using the AMBER potential. We compare the butane event-duration distributions and reaction-coordinate speed profiles with those for one dimensional stochastic systems with white and colored noise.

Two interesting generic features emerge. First, after a simple linear re-scaling by the average, the distribution of transition event durations appears to be *universal* across dynamics, solvent, and potential type — regardless of whether butane or a one-dimensional system is considered. The distribution embodies behaviors predicted analytically from a simple one-dimensional model. Second, the reaction-coordinate speed profiles of butane transitions also display a common, accelerating trend, which matches that of colored-noise, one-dimensional simulations.

In the next section, 2, we discuss simulation models and methods. Section 3 presents an analytic prediction for the distribution of event durations. Sec. 4 contains the simulation results, and we give a summary and some conclusions in Section 5.

## 2 Simulation Models and Set-Up

Transition behavior was studied in a variety of settings — from all-atom, fully solvated molecular dynamics to one-dimensional Langevin dynamics. This section describes the protocols and parameters used.

### 2.1 Fully-Solvated All-Atom Models of Butane

To examine solvent effects on barrier crossing behavior, and to ensure a good standard of comparison for stochastic simulations, we performed two explicit solvent simulations of butane. In one case the solvent was water and in the other it was acetic acid. In both cases the CHARMM program and parameters was used. The butane molecule was lightly restrained to the center of the simulation cell using a harmonic, molecule-specific, center-of-mass energy term. The simulations were performed with constant pressure and temperature and a non-bonded list cut-off of 12 Å. The non-bonded list was generated to 15 Å and the van der Waals force switched to zero over a 12 Å distance. Electrostatics were shifted over the full 15 Å range to cut-off. Dynamics used the leapfrog algorithm (e.g., ) in CHARMM, which for each particle’s position $`𝐱`$ and velocity $`𝐯`$ is given by

$`𝐱(t+\mathrm{\Delta }t)`$ $`=`$ $`𝐱(t)+\mathrm{\Delta }t𝐯(t+\frac{1}{2}\mathrm{\Delta }t)`$ (1)
$`𝐯(t+\frac{1}{2}\mathrm{\Delta }t)`$ $`=`$ $`𝐯(t\frac{1}{2}\mathrm{\Delta }t)+\mathrm{\Delta }t𝐟(t)/m,`$ (2)
where $`𝐟=_𝐱U`$ for potential energy $`U`$ and $`m`$ is the particle’s mass.

The acetic acid simulations consisted of 253 explicit molecules of acetic acid and box dimensions of roughly 65 Å on a side. This created the appropriate density of solvent for a temperature of 300 $`K`$. The water simulations contained 861 TIP3 water molecules and used a box size of roughly 30 Å.

### 2.2 All-Atom Butane in a Stochastic “Solvent”

To maintain as much consistency as possible between the explicit solvent and the implicit solvent simulations, the stochastic simulations used similar options to the explicit solvent simulations. In particular, the non-bonded energies were cut off at 12 Å, and a center-of-mass restraint was again used on the butane molecule. Temperature was maintained at 300 $`K`$. As would be expected, no periodic images were used and there is no pressure control in these stochastic simulations. Dynamics were performed with the leapfrog Langevin dynamics integrator in CHARMM, namely ,

$`𝐱(t+\mathrm{\Delta }t)`$ $`=`$ $`𝐱(t)+\mathrm{\Delta }t𝐯(t+\frac{1}{2}\mathrm{\Delta }t)`$ (3)
$`𝐯(t+\frac{1}{2}\mathrm{\Delta }t)`$ $`=`$ $`𝐯(t\frac{1}{2}\mathrm{\Delta }t)+{\displaystyle \frac{𝐱(t)𝐱(t\mathrm{\Delta }t)}{\mathrm{\Delta }t}}{\displaystyle \frac{1\frac{1}{2}\gamma \mathrm{\Delta }t}{1+\frac{1}{2}\gamma \mathrm{\Delta }t}}`$ (4)
$`+(\mathrm{\Delta }t/m){\displaystyle \frac{𝐟(t)+𝐑(t)}{1+\frac{1}{2}\gamma \mathrm{\Delta }t}}`$
$`𝐯(t)`$ $`=`$ $`\sqrt{1+\frac{1}{2}\gamma \mathrm{\Delta }t}[𝐯(t+\frac{1}{2}\mathrm{\Delta }t)+𝐯(t\frac{1}{2}\mathrm{\Delta }t)]/2,`$ (5)
where $`𝐑`$ is a white-noise frictional force, every component of which is chosen from a Gaussian distribution of zero mean and variance $`2m\gamma k_BT/\mathrm{\Delta }t`$. We used two values of the friction parameter ($`\gamma =5,50\text{ ps}^1`$) to implicitly model solvent effects; only the carbon atoms were treated stochastically, while the hydrogen dynamics were governed by the ordinary ($`\gamma =0`$) leapfrog Verlet algorithm (1).

An additional Langevin simulation was performed using the AMBER potential within the Molecular Modeling Tool Kit (MMTK) . For this “overdamped” (“Brownian”) simulation, dynamics were governed by

$$𝐱(t+\mathrm{\Delta }t)=𝐱(t)+(𝐟/m\gamma )\mathrm{\Delta }t+\mathrm{\Delta }𝐱_R$$
(6)
The noise term $`\mathrm{\Delta }𝐱_R`$ was also chosen to be “white” — in this case, selected independently at every time step from a Gaussian of zero mean and variance

$$\sigma ^2=2\mathrm{\Delta }tk_BT/m\gamma .$$
(7)
All atoms were treated stochastically using the convenient, but we note that overdamped dynamics only make predictions relative to an arbitrary overall timescale  embodied here in the (convenient) choice $`\gamma =150`$.

### 2.3 One-Dimensional Models

We also studied the simple bistable potential discussed in  and many other places, namely,

$$U(x)=E_b\left[(x/l)^21\right]^2,$$
(8)
where $`E_b`$ is the barrier height and $`l`$ the length scale. This potential is shown in Fig. 2. All one-dimensional simulations used overdamped Langevin dynamics (6) with — for simplicity — mass, friction, and the thermal energy scale set to unity: $`m=\gamma =k_BT1`$.

Two types of noise were studied. The first was uncorrelated “white” noise, as discussed above. We also employed exponentially-correlated noise simulated via an Ornstein-Uhlenbeck process , in which $`\mathrm{\Delta }x_Ry`$ is considered a position variable executing *independent* overdamped dynamics (6) in a harmonic potential $`U(y)=(m\gamma /2\tau )y^2`$ subject to white noise with fluctuations given by $`\sigma _y^2=(2\mathrm{\Delta }t/\tau )`$. This formulation yields the auto-correlation function $`y(0)y(t)=\sigma ^2\mathrm{exp}(t/\tau )`$, so that the magnitude of the correlated noise fluctuations is unchanged from the white-noise case.

## 3 Theoretical Analysis of a Simple Model

This section discusses an extremely idealized potential characterized by a transition-event-duration distribution with *features common among all of the models studied*. The reader solely interested in the simulation results could safely pass over this discussion and refer to the asymptotic results quoted later.

The one-dimensional potential is shown in Fig. 3, and the initial state A is defined to be $`x<2`$ and state B is $`x>3`$. The motivation for studying such an unphysical model is based on the fundamental observation made in the present report (see next section): because the distribution of durations appears to be universal, it should be derivable from even a trivial model.

The analysis is based on the simulation-step probabilities governing the overdamped dynamics (6) with white noise. Explicitly, the potential of Fig. 3 is given by

$`U(x)`$ $`=`$ $`0(x<2)`$
$`=`$ $`(E_b/L)(x2)(2<x<3)`$
$`=`$ $`E_b(x>3).`$
For convenience, we introduce the notation $`\delta xf\mathrm{\Delta }t/m\gamma =E_b\mathrm{\Delta }t/m\gamma L`$ for the inclined region $`2<x/L<3`$. Because fluctuation increments $`\mathrm{\Delta }x_R`$ are chosen from a Gaussian distribution, the probability density for choosing an increment $`\mathrm{\Delta }x_j=x_{j+1}x_j`$ in the inclined region is given by

$$T(\mathrm{\Delta }x_j)=\frac{1}{\sqrt{2\pi }\sigma }\mathrm{exp}\left[(\mathrm{\Delta }x_j\delta x)^2/2\sigma ^2\right].$$
(10)
The probability density of a trajectory of $`n_bt_b/\mathrm{\Delta }t`$ steps, $`\zeta ^{n_b}=(x_0,x_1,\mathrm{},x_{n_b})`$, is simply the product of single-step densities:

$$Q(\zeta ^{n_b})=\underset{j=0}{\overset{n_b1}{}}T(\mathrm{\Delta }x_j),$$
(11)
which, because each of the Gaussian form (10), is properly normalized according to

$$d\zeta ^{n_b}Q(\zeta ^{n_b})=1,$$
(12)
where $`\mathrm{d}\zeta ^{n_b}=_{j=0}^{n_b1}\mathrm{d}\mathrm{\Delta }x_j`$.

The relative probability of a given event duration, $`t_b=n_b\mathrm{\Delta }t`$, is a product of two factors: (i) the total number of probable $`n_b`$-step trajectories — whether crossing or not — multiplied by (ii) the fraction of $`n_b`$-step trajectories which cross the barrier (i.e., reach the barrier top at $`x3`$; see Fig. 3). Factor (i) is proportional to $`\sigma ^{n_b}`$, because the fluctuation width in (10) measures the extent of probable steps. The second factor, the fraction of successful trajectories, may be written formally as

$$f_bd\zeta ^{n_b}Q(\zeta ^{n_b})h_A(x_0)h_B(x_{n_b}),$$
(13)
where the indicator function $`h_Y(x)`$ is unity when $`x`$ is in state Y and zero otherwise. That is, the probability of a transition event occurring in $`n_b=t_b/\mathrm{\Delta }t`$ steps is proportional to $`\sigma ^{n_b}f_b`$.

We estimate the fraction of successful trajectories, $`f_b`$, by considering only those trajectories near to the optimal $`n_b`$-step crossing trajectory (which differs from the unique, overall-optimal trajectory — for the the optimal $`n_b`$ — discussed in ). The optimal $`n_b`$-step trajectory for the constant-force potential of Fig. 3 consists of uniform steps of length $`L/n_b`$, and we estimate the number of nearby trajectories as those occurring in a “fluctuation volume” $`\sigma ^{n_b}`$ about the optimal; that is, we estimate

$$f_bc_{0}^{}{}_{}{}^{t_b/\mathrm{\Delta }t}\mathrm{exp}\left[\frac{m\gamma }{2k_BT}t_b\left(\frac{L}{t_b}+\frac{E_b}{m\gamma L}\right)^2\right],$$
(14)
where $`c_0`$ is an unknown constant, presumably of order unity.

Finally, the estimate for the probability distribution of event durations is proportional to the product of $`\sigma ^{n_b}`$ and $`f_b`$, namely,

$$\rho (t_b)(c_1\sigma )^{t_b/\mathrm{\Delta }t}\mathrm{exp}\left[\frac{m\gamma }{2k_BT}t_b\left(\frac{L}{t_b}+\frac{E_b}{m\gamma L}\right)^2\right],$$
(15)
where $`c_1`$ is again an unknown constant. Using the identity $`a^n=e^{n\mathrm{log}a}`$, we can rewrite this approximation as a two-parameter form for purposes of understanding its behavior,

$$\rho (t_b)\mathrm{exp}\left[t_b\left(\frac{c}{t_b}+d\right)^2\right].$$
(16)
The asymptotic behavior is of particular interest and is given by

$`\rho (t_b0)`$ $``$ $`\mathrm{exp}(c^2/t_b),`$ (17)
$`\rho (t_b\mathrm{})`$ $``$ $`\mathrm{exp}(d^2t_b).`$ (18)
It is worth noting that all derivatives of $`\rho `$ vanish as $`t_b0`$.

## 4 Results

### 4.1 Transition-Event Durations

We here present results regarding the durations of transition events, $`t_b`$; see Fig. 1. The universal behavior of the distribution of durations is demonstrated, and limiting behavior is discussed by comparison to the analysis of the previous section. The average durations are also compared to other timescales which distinguish each system, the correlation time and inverse reaction rate.

The definition of a transition duration is necessarily somewhat arbitrary. Here we used the time between the last exit from the initial state and the first entrance to the final state; in other words, $`t_b`$ is the amount of time spent continuously by a trajectory in the transition region. For transitions between the *gauche*$``$ and *trans* states in butane, we chose the the transition region to be $`100<\varphi <150`$; considering symmetry, the region $`210<\varphi <260`$ was chosen for *gauche*$`+`$ and *trans*. Following convention, the *trans* state is centered at $`\varphi =180`$.

The principal results for the distributions of event durations are embodied in Fig. 4. The simple linear rescalings, by the system-specific average durations $`t_b`$, cause the data to collapse onto a fairly well-determined universal curve. The empirical fit to the data, detailed below, confirms the asymptotic behaviors predicted analytically in Eqs. (17) and (18): the gap at small $`t_b`$ is clearly consistent with $`e^{1/t_b}`$ behavior (but not with a more common form like $`t_{b}^{}{}_{}{}^{q}e^{t_b}`$ with exponent $`q>0`$), and the logarithmic scale of Fig. 4(b) reveals the large $`t_b`$ behavior to be a simple exponential decay.

The empirical fit shown in Fig. 4 depicts the form

$$\stackrel{~}{\rho }(t_b)=𝒩^1\mathrm{exp}\left[t_b\left(\frac{2t_{b}^{}{}_{}{}^{r}}{\stackrel{~}{b}+t_{b}^{}{}_{}{}^{r}}+\frac{\stackrel{~}{c}}{t_{b}^{}{}_{}{}^{2}}\right)\right],$$
(19)
where $`𝒩`$ is a normalization factor and the three parameters used are $`\stackrel{~}{b}=1.5`$, $`\stackrel{~}{c}=1.4`$, $`r=5`$. The form was designed, by trial and error, both to display the correct asymptotic behaviors and to capture the inflection point to the right of the peak visible on the logarithmic plot, Fig. 4(b).

### 4.2 Timescales

Another question that can be answered based on our data is whether the crossing event durations in a particular system are correlated with other fundamental timescales, like the correlation time and the (inverse) reaction rates. Table 1 apparently answers this question in the negative. Note that, in the table, the dihedral correlation time is defined by

$$\tau _{\mathrm{corr}}=\varphi (0)\varphi (0)^1_0^{\mathrm{}}dt\varphi (0)\varphi (t),$$
(20)
where the angular brackets refer here to time averages within the *trans* state only. Since the dihedral-angle correlation function of the integrand exhibits strong oscillations in molecular dynamics simulations, Table 1 also includes the decay time of the exponential “envelope,” $`\tau _{\mathrm{decay}}`$. The data also suggest that the rates are not simply related to correlation times.

### 4.3 Reaction-Coordinate Speed Profiles

The reaction-coordinate speed profile  depicts the local speed of progress along the reaction coordinate, as exemplified in Fig. 5. This sub-picosecond behavior (see Table 1) is uniquely available from simulations, and critically important for dynamic importance sampling methods for rate calculations: see Ref. .

As in the case of the the crossing time distributions, the results tell a simple and consistent story. All of the butane simulations show a characteristic “accelerating” speed profile during transitions, as indicated by Fig. 5. Absolute speeds do differ, as is evident from the average crossing times of Table 1. The consistent, accelerating profiles from the butane simulations contrast sharply with the white-noise profile of a one-dimensional simulation discussed in detail in Ref.  and also shown in Fig. 6.

Because even the Langevin butane simulations — *which were performed with white noise* — exhibit the accelerating behavior, one can also conclude that molecular fluctuations are inherently colored (i.e., correlated). The reason is straightforward. If one focuses on the dynamics of particular butane atom, say a methyl carbon, then according to Eq. (6) that atom moves based on the force it feels and a white noise increment. The force itself, however, reflects the relatively long-timescale motions executed by the whole molecule. Hence the molecule acts as its own memory, and correlations are not surprising regardless of the type of noise modeled in $`\mathrm{\Delta }x_R`$.

## 5 Summary and Conclusions

By comparing butane simulations with explicit and implicit solvents, along with simple white- and colored-noise one-dimensional (1D) systems, we have found a remarkable degree of commonality in short-timescale kinetic properties. The distributions of transition-event durations $`t_b`$ *from all systems studied* substantially “collapse” onto a single universal function after a simple linear rescaling (Fig. 4). Similarly, all the profiles of average local speeds during traversal of the reaction coordinate — the “reaction-coordinate speed profiles” — of the butane systems behave similarly (Fig. 5). These profiles, furthermore, qualitatively match those from 1D colored-noise systems, but are clearly distinct from the 1D white-noise behavior (Fig. 6).

Despite this universal short-time behavior, quantitative estimates for reaction-rate, correlation, and event-duration timescales (Table 1) reveals no obvious relationship between butane systems with explicit solvents and those with implicit, stochastic “solvent.” This suggests that stochastic simulations, at least at the level considered here, cannot be used for quantitative estimates of timescales in fully-solvated computations. While this assessment may be more pessimistic than that of Widmalm and Pastor , it is not surprising that consideration of an additional timescale, namely $`t_b`$, makes agreement more difficult. Perhaps more important are two other issues: Do simple stochastic representations become better or worse as larger molecules are considered? What quantity of explicit solvent, say in combination with stochastic boundary conditions , provides a good level of agreement with the array of kinetic quantities in fully-solvated systems?

Further theoretical consideration of the connection between simple and molecular systems would also prove valuable. In particular, the study of simple models possessing a one-dimensional reaction coordinate coupled nontrivially to simple orthogonal degrees of freedom (based on, e.g., ) should permit a better understanding of the effects of noise color on the short-time transition behavior considered here. In a molecular system, as noted in Sec. 4.3, the effective noise on any atom *must* be colored because of the coupling to the non-trivial “bath” of other particles.

Following up on the motivation for the investigation reported here, we believe that an appreciation of the results can inform improved sampling approaches for reaction rate computations within the “transition path sampling”  and “dynamic importance sampling”  methods. These approaches require ensembles of transition-event trajectories. At a simple level, understanding the transition event duration $`t_b`$ in molecular systems is critical: as noted in , the duration of molecular crossing events sets, in part, the minimum computation time required to generate a realistic ensemble of transition-event trajectories. Furthermore, given the universal behavior uncovered here, stochastic simulations evidently reproduce key aspects of explicitly-solvated transition behavior. Despite the clear importance of solvent effects, this study suggests that trajectories harvested in a computationally inexpensive stochastic context should — at a minimum — provide good starting points for refinement in a solvated context.

## Acknowledgments

A number of people contributed to this project with helpful comments and discussions. The authors would like to thank Mark Dykman, Lucy Forrest, Hirsh Nanda, Richard Pastor, Horia Petrache, and Jonathan Sachs. Bernard Brooks provided a useful clarification regarding the Langevin leapfrog algorithm. Funding for this work was provided by the NIH (Grant GM54782), the Bard Foundation, and the Department of Physiology. D.M.Z. is the recipient of a National Research Service Award (GM20394).