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# Science with SIRTF – Some Examples

## 1. Introduction

The Space InfraRed Telescope Facility (SIRTF) (Fanson et al. 1998) is the fourth and final element in NASA’s family of “Great Observatories”. SIRTF consists of a 0.85-meter telescope, cooled to $`T<5.5K`$ and three cryogenically-cooled science instruments capable of performing imaging and spectroscopy in the $`3180\mu `$m wavelength range (Fig. 1). More details are summarized in Table 1.

Incorporating large-format infrared detector arrays, SIRTF offers orders-of-magnitude improvements in capability over existing programs. While SIRTF’s mission lifetime requirement remains 2.5 years, recent programmatic and engineering developments have brought a 5-year cryogenic mission within reach. A fast-track development schedule will lead to a launch in December 2001. SIRTF represents an important scientific and technical bridge to NASA’s new Origins program.

75% of the observing time will be available to the community in form of general science proposals and so-called Legacy proposals (The SIRTF Legacy Science Program is intended to maximize the scientific return from SIRTF early in the mission, and comprises a handful of large-scale observing projects to be executed primarily within the first year of SIRTF’s lifetime.) In addition for the first 2.5 years of SIRTF’s prime mission, 20 percent of observing time will be allocated to the GTO program and an additional 5% is reserved as Director’s discretionary time. More details can be found at http://sirtf.caltech.edu

This paper presents three examples of “typical” SIRTF science, most of which are covered by the GTO program. These examples have been selected to demonstrate SIRTF’s superb capabilities and to match the scientific focus of the 3rd “Three Island Euroconference on Clusters and Associations”. More examples can be found elsewhere, e.g., in Brandl et al. (1999).

## 2. Instruments and Sensitivities

SIRTF’s science payload consists of three cryogenically cooled instruments, which together offer observational capabilities stretching from the near- to the far-infrared. Figure 2 shows a simulation comparing the performance of the latest major IR observatories on deep large area surveys. Following is a brief summary of the characteristics of each instrument. Details are described in the SIRTF Observers Manual (2000).

### 2.1. The InfraRed Array Camera (IRAC)

The IRAC (Giovanni G. Fazio, PI) provides images at 3.6, 4.5, 5.8 and 8.0$`\mu `$m, over two adjacent 5.12 x 5.12 arcminute fields of view. One field of view images simultaneously at 3.6 and 5.8$`\mu `$m and the other at 4.5 and 8.0$`\mu `$m via a dichroic beamsplitter. All four detector arrays are 256x256 with 1.2 arcsecond square pixels. A cold shutter is provided for dark measurements, and also allows the detectors to be illuminated by light from a transmission calibrator. Sensitivities for IRAC are given in Table 2.

### 2.2. The InfraRed Spectrograph(IRS)

The IRS (James R. Houck, PI) performs both low and high-resolution spectroscopy. Low resolution, long slit spectra ($`\lambda /\mathrm{\Delta }\lambda =62124`$) can be obtained from 5.3 to 40$`\mu `$m. High resolution spectra ($`\lambda /\mathrm{\Delta }\lambda =600`$) in Echelle mode can be obtained from 10 to 37$`\mu `$m. The spectrograph consists of four modules, each of which is built around a 128x128 pixel array. The sizes of the slits are summarized in table 3.

One of the modules incorporates a peak-up function that can be used in locating and positioning sources on any of the four spectrometer slits with sub-arcsecond precision. The peak-up array has 1.8 arcsec square pixels and a field of view of 1 arcminute by 1.2 arcminutes. Two filters are available for use with up array, covering 13.5 – 18.5 microns or 18.5 – 26 microns. Sensitivities for the IRS are shown in Figure 3.

### 2.3. The Multiband Imaging Photometer for SIRTF (MIPS)

The MIPS (George H. Rieke, PI) is designed to provide photometry and super resolution imaging as well as high speed mapping capabilities in three wavelength bands centered near 24, 70 and 160 microns. The array materials are Si:As, Ge:Ga, and stressed Ge:Ga with pixel sizes of 2.5, 5, 10, and 16 arcseconds, depending on wavelength and detector. MIPS is also capable of low-resolution spectroscopy ($`\lambda /\mathrm{\Delta }\lambda =1525`$) over the wavelength range 55-96 microns and a Total Power Mode for measuring absolute sky brightness. Sensitivities for MIPS are given in Table 4.

## 3. Science with SIRTF

### 3.1. Example 1: Searches for Brown Dwarfs

During the past two years, ground-based surveys have begun to succeed in identifying large numbers of relatively young, nearby brown dwarfs in star-forming regions, young open clusters and the eld. IRAC will be able to extend those e orts to older and lower mass brown dwarfs and superplanets. In nearby star-forming regions like Taurus, IRAC should be able to detect isolated objects down to near the mass of Jupiter, $`1M_J`$. In the nearest and best-studied open clusters – in particular, the Pleiades and the Hyades – IRAC should be able to detect brown dwarfs down to $`10M_J`$.

As Figure 4 illustrates, the ratio of the IRAC bands at 3.6 and 4.5$`\mu `$m is a very good means of selecting brown dwarfs. The method of observation would be to carry out a large area survey of several open star clusters (e.g. NGC 2264, Pleiades, Hyades). The survey area is approximately 5 square degrees for NGC 2264 and the Pleiades, and approximately 10 square degrees for the Hyades. The integration time would be 30 seconds per position, observing each position three times (90s total), which would achieve a sensitivity of 10$`\mu `$Jy, 5$`\sigma `$ at 4.5$`\mu `$m. The total observing time for all three fields would be about 160 hours. The brown dwarf candidates would be selected by 3.6/4.5$`\mu `$m color, based on model predictions and known objects from the 2MASS and DENIS surveys. The lowest mass objects will be detected only at 4.5$`\mu `$m in 90s. The 4.5$`\mu `$m only objects would need to be re-observed with much longer integrations to provide a detection at 3.6$`\mu `$m.

Figure 5 shows the IRAC color/color diagram for objects with masses of 5, 10, 20, and $`30M_J`$ at various ages. The IRAC color/color diagram for galaxies in the field is shown in the same diagram. The galaxies are well-separated from the brown dwarfs, appearing in the lower left corner of the color/color plot. (Fazio et al. 1999).

### 3.2. Example 2: Protostellar and Protoplanetary Disks

The spectral range covered by the IRS includes most of the important emission and absorption features from interstellar and solar-system-like dust grains (Fig. 6). It also includes many fine structure lines of ions and neutral atoms that are bright in H II regions, phot-dissociation regions and young stellar objects; the lower transitions in pure rotational spectrum of molecular hydrogen; and many other molecular rotational and rotation-vibration lines of abundant species whose emission is important in the energetics or diagnosis of warm molecular gas.

The IRS is particularly sensitive to emission from dust and gas that lies in the inner parts of protostellar, protoplanetary and debris disks, between a few tenths and a few tens of AU from the star. In the nearest regions of star formation, the IRS will be able – in just a few minutes of integration – to take high-quality spectra of disks around protostellar objects with masses down to the hydrogen-burning limit and even beyond. Fig. 6 also illustrates how the mid-IR SEDs varies under different boundary conditions and hence can be used as powerful diagnostics for disk evolution and structure, even if the source is spatially unresolved (Armus et al. 2000).

### 3.3. Example 3: Star Formation in Interacting Galaxies

Collisions between galaxies are one of the most energetic events in the Universe with energies of typically $`10^{53}J`$ – the equivalent of $`10^{89}`$ supernovae – on timescales of about $`3\times 10^8`$ yrs (Struck 1999). The interactions trigger the formation of massive star clusters either directly through the collision of clouds or induce bars which funnel gas and foster wave and resonant ring star formation. The strongest star formation rates are usually observed in the most violently interacting galaxies – the best known example probably is the Antennae galaxy NGC 4038/39.

The young stars within a starburst are extremely enshrouded by dust with typical average extinctions of $`A_V25`$mag (Smith et al. 1996). Hence, observational studies in the mid-IR are the best method to probe the properties of dusty starburst cores and the surrounding interstellar medium. Fig. 7 illustrates the spatial resolution of the IRS spectrographs with their slits overlayed on the HST/WFPC2 picture of the Antennae galaxy (Whitmore et al. 1999). At the distance of 2.8 kpc the width of the short-high slit ($`1021\mu `$m) corresponds to only 500 pc; the length of the short- and long-low slits of $`55^{\prime \prime }`$ and $`151^{\prime \prime }`$, respectively, make it – for the first time – practically possibly to obtain mid-IR spectra of the entire region at relatively high spatial resolution.

Figure 8 shows a simulation of how the spectrum of a low luminosity region in the Antennae galaxy will look when observed with the IRS high-resolution module. The on-source integration time for this simulation is 256s, the flux is normalized to an average 20mJy in the $`1930\mu `$m window, a typical value for a low-luminosity region according to the ISOCAM-CVF map (Mirabel et al. 1998). The instrument simulation is based on the mid-IR spectrum of the starburst galaxy M82 as observed by ISO-SWS (Sturm et al. 2000). Despite the relative faintness and short integration time one can see a variety of important diagnostic lines (see figure caption).

#### Acknowledgments.

This work was supported under JPL contract 960803.

## References

Allard, F. et al. 1996, ApJ, 465, 123

Armus, L. et al. 2000, in The Fourth Tetons Summer Conference: Galactic Structure, Stars, and the Interstellar Medium, ed. C. Woodward & M.D. Bicay, in press

Brandl, B. et al. 1999, astro-ph/9912216

Engelbracht, C. et al. 1999, http://mips.as.arizona.edu/MIPS/Science\_f.html

Fanson, J.L. et al. 1998, SPIE 3356, 478

Fazio, G.G. et al. 1999, in ASP Conf. Ser. Vol. 177, Astrophysics with Infrared Surveys: A Prelude to SIRTF, ed. M.D. Bicay, R.M. Cutri & B.F. Madore, 462

Malfait, K. et al. 1998, A&A, 332, 25

Mirabel, I.F. et al. 1998, A&A, 333, 1

SIRTF Observers Manual – available from the SSC at
http://sirtf.caltech.edu/SciUser/Documents/SOM.html

Smith, D.A. et al. 1996, ApJS, 104, 217

Struck, C. 1999, Phys. Reports 321, 1

Sturm, E. et al. 2000, A&A, 358, 481

Whitmore, B.C. et al. 1999, AJ, 118, 1551


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# A Note on TeV Cerenkov Events as Bose-Einstein Gamma Condensations

## Abstract

The idea that the TeV air showers, thought to be produced by $`>10`$ TeV gamma rays from Mrk 501, can be mimicked by coherent bunches of sub-TeV photons is reexamined, focusing on fundamental considerations. In particular, it is shown that the minimum spot size of the beam of pulsed TeV photons arriving at Earth is on the order of a few kilometers, unless a lens with certain characteristics is placed between the TeV laser and Earth. The viability of the laser production mechanism proposed by Harwit et al. (2000) is also reassessed.

It has been argued recently (e.g., Coppi & Aharonian 1999) that the detection of TeV photons from Mrk 501 at energies well above 10 TeV (Hayashida, et al. 1998; Aharonian et al. 1999) places severe constraints on the diffuse extragalactic IR background, and may be particularly problematic (Protheroe & Meyer, 2000) in view of recent determinations of the IR background by various experiments. Motivated by this consideration, Harwit et al. (1999) proposed that the observed air showers, that are commonly interpreted as due to single $`>10`$ TeV gamma rays, can be produced by coherent bunches of sub-TeV photons that are not absorbed by pair production on the extragalactic IR background. What they envisaged essentially is that some mechanism in the source (Mrk 501) produces pulsed, sub-TeV lasers that, when interacting with the Earth’s atmosphere could mimic TeV air shower events. This hypothesis has been tested subsequently by the HEGRA collaboration (Aharonian et al. 2000), who claimed that it can be rejected on the basis of a comparison of the energy dependent penetration depth in Earth’s atmosphere of TeV photons from Mrk 501 with the penetration depth of photons from the Crab Nebula. In view of the growing interest in this scenario it is worth reexamining its viability. Below, we discuss the fundamental limitations of such a TeV laser.

What are the basic requirements from the system under consideration?

i) A typical Cerenkov flash produced by a TeV air shower lasts for about several ns. This implies that the width of the TeV pulse produced by the laser, $`\mathrm{\Delta }t`$, should not exceed this timescale, and that temporal coherence must be maintained over a time $`>\mathrm{\Delta }t`$. The corresponding light crossing time, $`c\mathrm{\Delta }t`$, is of the order of several meters. In principle, however, the dimension of the system should not be restricted to this scale. In laboratory lasers, for instance, pulse durations as short as the decay time of the lasing substrate (which can be shorter by many orders of magnitude than the light crossing time of the cavity, though typically larger than the beam diameter) can be achieved using e.g., mode locking or Q switching methods (which require modulation of either the pumping rate or the refraction index in the cavity) (e.g., Svelto 1998). Although it is difficult to envisage how this situation can be accomplished under astrophysical conditions, the requirement that the size of the system would not exceed the pulse width does not seem to be fundamental. Moreover, if the laser mechanism involves relativistic motion the pulse can be further compressed, owing to time dilation effects.

ii) The spot size of the TeV laser beam illuminating Earth should be within the angular resolution of current TeV experiments, otherwise the shower image will differ from that expected to be produced by a single TeV photon. (If the spot is resolved, it can give rise to a shower image that may resemble that of a cosmic ray shower. Such an event is likely to be rejected.) For a typical angular resolution of 0.1, and shower hight of say 10 km, this yields a spot size $`<20`$ meters. As shown below this requirement places a stringent constraint on the system.

Harwit et al. argued that the arriving bunched photons would spread over a distance $`\mathrm{\Delta }yh/\mathrm{\Delta }p_y\lambda L/D`$, where $`\mathrm{\Delta }p_y`$ is the uncertainty in transverse momentum, which equals approximately the product of the photon momentum, $`h/\lambda `$, and the angular size of the source subtends at Earth, $`D/L`$, with $`D`$ being the characteristic source dimension and $`L`$ the distance between Earth and the source (Mrk 501). Taking $`D`$ to be on the order of a Schwarzschild radius of a supermassive black hole yields $`\mathrm{\Delta }y`$ in the range between $`10^1`$ to $`10^4`$ cm for the expected range of black hole masses, which, as they argued, is negligible in Cerenkov detection. It should be noted, however, that $`\mathrm{\Delta }y`$ is essentially the size of the diffraction wing of a beam having a diameter $`D`$ at a distance $`L`$ from the beam waist (see Fig. 1) and not the spot size, which for the above parameters is practically $`D`$. Thus, if the dimension of the photon bunch (or Bose Einstein condensate, as termed by those authors) is indeed $`Dr_g`$, then in the absence of an additional optical system (see below), the arriving photon bunch would spread over a similar scale, not $`\lambda L/r_g`$. We suspect though that the picture envisioned by Harwit et al. is that each condensate is well localized, so that the spatial dimension of each bunch at the source is not $`D`$ but very small. In that case the uncertainty in transverse momentum of a photon in the bunch is related to the latter scale and is much larger than that quoted above. The question then is, what is the minimum spot size that can be achieved given the distance between Earth and Mrk 501?

Consider some apparatus that produces a pulsed TeV laser beam having a diameter $`D`$ at the beam waist (see Fig. 1). The diffraction angle of the beam is $`\psi =\lambda /D`$, where $`\lambda =2\times 10^{17}(ϵ/1\mathrm{T}\mathrm{e}\mathrm{V})^1`$ cm is the wavelength of the laser at its spectral peak, and $`ϵ`$ is the corresponding energy. At a distance $`L`$ from the laser the beam spot size, $`a`$, is the sum of the waist spot size and the size of the diffraction wing:

$$a=D+\psi L=D+(\lambda /D)L.$$
(1)
For a target at a fixed distance $`L`$ from the laser, the minimum beam spot size $`a_{min}`$ can be obtained by minimizing $`a`$ with respect to $`D`$; that is taking $`da/dD=0`$. This yields $`D=\sqrt{\lambda L}`$ and

$$a_{min}=2\sqrt{\lambda L}10^5(L/100\mathrm{M}\mathrm{p}\mathrm{c})(ϵ/1\mathrm{T}\mathrm{e}\mathrm{V})^1\mathrm{cm}.$$
(2)
Taking $`L`$ to be the distance from Earth to Mrk 501 ($`L=130`$ Mpc assuming $`h_o=0.65`$), we conclude that the arriving pulse of sub TeV photons would spread over a distance of at least several kilometers.

The spot size can in principle be reduced if a lens is placed between the source and Earth. In the optimal case the radius of the lens should be comparable to the beam radius, and its focal plan should intersect Earth. Unser such conditions the size of the spot illuminated by the TeV laser is diffraction limited (assuming complete coherence). Denoting by $`D_l`$ the lens diameter and by $`L_l`$ its distance from Earth, and requiring a spot size smaller than say 10 meters, yields a minimum lens diameter of

$$D_{lmin}=10^7(L_l/100\mathrm{M}\mathrm{p}\mathrm{c})(ϵ/1\mathrm{T}\mathrm{e}\mathrm{V})^1\mathrm{cm}.$$
(3)
This is larger than the gravitational radius of a stellar mass object. As an illustrative example consider lensing of the TeV beam by a point mass located on the axis of the beam a distance $`L_l`$ from Earth. In that case only rays for which the impact parameter lies in the range between $`b_+`$ and $`b_{}`$, where $`b_\pm 2\sqrt{r_gL_l}\pm d`$, $`d`$ being the diameter of the beam spot on Earth, and $`r_g`$ is the gravitational radius of the lens, will be deflected by the required angle. For typical parameters, this constitutes only a tiny fraction of the beam photons and, therefore, a point mass cannot provide the required lens. What seems to be needed is some extended object with a density profile such that the refraction index of the lens would be independent of the lens radius. Perhaps high velocity clouds?

We conclude by briefly commenting on the TeV laser production mechanism discussed by Harwit et al. These authors suggested that inverse Compton scattering of OH or H2O megamaser photons by a relativistic beam of nonthermal (in the comoving frame) electrons, may provide a mean for producing a coherent TeV pulse. We stress that spontaneous scattering is a process that tends to destroy coherence; a single seed photon has a probability of being scattered into many different directions with different phases. (It is worth noting that the occupation number of scattered photons will be reduced not only by the ratio of bandwidths, as pointed out by Harwit et al., but also by the ratio of angular sizes of the beam of scattered photons and the megamaser beam, which can in principle be large.) The fact that the occupation number may largely exceed unity does not imply that the emission is coherent, unless the phases of emitted photons are somehow correlated. In order to mimic TeV air showers, it is required that several photons will be scattered into a solid angle, henceforth denoted by $`\mathrm{\Delta }\mathrm{\Omega }`$, not larger than that subtends at the source by the maximum spot size allowed in the Earth’s atmosphere, and will have a time spread of no more than several ns. Since the scattering process is unsynchronized, it implies that the characteristic dimension of the emitting volume should not exceed $`\mathrm{\Gamma }^2`$c$`\mathrm{\Delta }t`$, where $`\mathrm{\Delta }t10`$ ns is again the time scale of a typical Cerenkov shower, and $`\mathrm{\Gamma }`$ is the bulk Lorentz factor of the electron beam. Using the number density of maser photons adopted by Harwit etal., $`n_{ph}10^{10}`$ cm-3, yields a scattering rate per electron of $`\nu _{sct}=\sigma _Tcn_{ph}2\times 10^4`$ s-1. The total scattering rate by a beam section of volume $`\mathrm{\Delta }V(\mathrm{\Gamma }^2c\mathrm{\Delta }t)^3`$ containing relativistic electrons having density $`n_e`$ is then $`\nu _{sct}\mathrm{\Delta }Vn_e2\times 10^{16}`$ ($`\mathrm{\Delta }t`$/$`10`$ ns)3($`\mathrm{\Gamma }/100`$)6 ($`n_e`$/$`10^2`$ cm-3) s-1. Now, only a fraction $`\mathrm{\Delta }\mathrm{\Omega }/\mathrm{\Delta }\mathrm{\Omega }_b`$ will be scattered into a solid angle $`\mathrm{\Delta }\mathrm{\Omega }`$, where $`\mathrm{\Delta }\mathrm{\Omega }_b`$ denotes the solid angle of the TeV photon beam, which in the case of scattering by an electron beam having bulk Lorentz factor $`\mathrm{\Gamma }`$ is on the order of $`\mathrm{\Delta }\mathrm{\Omega }_b\pi \mathrm{\Gamma }^2`$. For a maximum spot size $`d`$ we thus obtain: $`\mathrm{\Delta }\mathrm{\Omega }/\mathrm{\Delta }\mathrm{\Omega }_b10^{43}`$ ($`\mathrm{\Gamma }/100`$)2( $`d/10^3`$ cm)2($`L/100`$ Mpc)-2. Consequently, the rate at which the maser photons in the volume $`\mathrm{\Delta }V`$ are scattered into a given direction within a solid angle $`\mathrm{\Delta }\mathrm{\Omega }`$ is approximately $`10^{27}`$ s-1, about 35 orders of magnitudes smaller than what required.

I thank M. Segev, D. Eichler, D. Maoz, and A. Gal Yam for enlightening discussions. Support from the Israel Science Foundation is greatly acknowledged.


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# Fractal Statistics and Quantum Black Hole Entropy

## Abstract

Simple considerations about the fractal characteristic of the quantum-mechanical path give us the opportunity to derive the quantum black hole entropy in connection with the concept of fractal statistics. We show the geometrical origin of the numerical factor of four of the quantum black hole entropy expression and the statistics weight appears as a counting of the quanta of geometry.

The fractal properties of path swept by point-particles are described by the relation $`LR^h`$, i.e. between a closed path of length $`L`$ and size $`R`$, with $`h`$ a fractal parameter or Hausdorff dimension. On the other hand, the values of $`h`$ can be obtained from the propagators of the particles. We have introduced the concept of universal classes of particles or quasiparticles labeled just by this fractal parameter, such that for $`h`$ defined in the interval $`1`$$`<`$$`h`$$`<`$$`2`$, we obtain Fractal Statistics ( fractal distribution function ) given by

$`n={\displaystyle \frac{1}{𝒴[\xi ]h}},`$ (1)
where the function $`𝒴[\xi ]`$ satisfies the equation

$`\xi =\left\{𝒴[\xi ]1\right\}^{h1}\left\{𝒴[\xi ]2\right\}^{2h},`$ (2)
and $`\xi =\mathrm{exp}\left\{(ϵ\mu )/KT\right\}`$ has the usual definition. Thus we generalize in a natural way the fermionic($`h=1`$) and bosonic($`h=2`$) distributions for particles carrying rational or irrational values for the spin quantum number $`s`$. The particles termed fractons ( they live in two-dimensional multiply connected space ) are collected in each class $`h`$ taking into account the fractal spectrum

$`h1=1\nu ,\mathrm{\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}0}<\nu <1;h1=\nu 1,\mathrm{\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}\hspace{0.33em}1}<\nu <2;`$ (3)
$`etc.`$ (4)
and the spin-statistics relation $`\nu =2s`$.

We emphasize that the Fractal Statistics captures the observation about the fractal nature of the quantum-mechanical path, which reflects the Heisenberg uncertainty principle. Besides this, the classes $`h`$ satisfy a duality symmetry defined by $`\stackrel{~}{h}=3h`$ and so, we extract a fractal supersymmetry which defines pairs of particles $`(s,s+\frac{1}{2})`$. In this way, our formulation can be understood as a quantum-geometrical description of the statistical laws of Nature.

In this Letter, we show that simple considerations about the fractal characteristic of the quantum path give us the quantum black hole entropy expression. Following Hausdorff, we define a length $`L`$ The Hausdorff length is scale independent ( self-similar ) and has fractal dimension. as

$`L=l_pR^h,`$ (5)
where $`l_p=\sqrt{\frac{\mathrm{}G}{c^3}}`$ is the Planck length. Squaring the eq.(5) and taking the logarithm, we obtain

$`\mathrm{ln}R={\displaystyle \frac{1}{2h}}\mathrm{ln}{\displaystyle \frac{A}{l_p^2}},`$ (6)
with $`A=L^2`$(area).

Given that the quantum of gravitational field is bosonic, $`h=2`$ and as $`\frac{A}{l_p^2}`$ is a sufficiently large number, we assume that $`\frac{A}{l_p^2}=N!`$ ( $`A10^{66}`$ and $`N`$ is considered as a large number ) and using the Stirlings formula

$`\mathrm{ln}R`$ $`=`$ $`{\displaystyle \frac{1}{4}}\mathrm{ln}N!`$ (7)
$`=`$ $`{\displaystyle \frac{N}{4}}\mathrm{ln}\left[{\displaystyle \frac{N}{e}}\right]`$ (8)
$`=`$ $`{\displaystyle \frac{A}{4l_p^2(N1)!}}\mathrm{ln}\left[{\displaystyle \frac{N}{e}}\right],`$ (9)
and

$`{\displaystyle \frac{\mathrm{ln}R^{N!}}{\mathrm{ln}N!}}\mathrm{ln}𝒲={\displaystyle \frac{A}{4l_p^2}}{\displaystyle \frac{𝒮}{K}},`$ (10)
($`K`$ is the Boltzmann constant), hence $`𝒲=R^{\frac{N!}{\mathrm{ln}N!}}`$, with $`N!=R^4=\frac{A}{l_p^2}`$, i.e.
$`𝒲=\left\{N!\right\}^{\frac{N!}{4\mathrm{ln}N!}}=\left\{\frac{A}{l_p^2}\right\}^{\frac{A}{4l_p^2\mathrm{ln}\left\{\frac{A}{l_p^2}\right\}}}=e^{\frac{A}{4l_p^2}}=e^{\frac{𝒮}{K}}`$,

is the statistics weight of the macroscopic state of entropy $`𝒮`$ or the total number of microscopic states (quanta of geometry ) compatible with this macroscopic state. Thus, we can say that $`𝒲`$ establishes a notion of quantum geometry. Therefore, in this way we identify the quantum black hole entropy as ( quantum here means that the Hausdorff dimension $`h`$ encodes information about the quantum path and the particle associated to it ) Another direction of research, exploiting an analogy between edge states in $`(2+1)`$-dimensional gravity and fractional quantum Hall efffect, also has extracted as result a geometric entropy.

$`𝒮_{BH}`$ $`=`$ $`K\mathrm{ln}𝒲`$ (11)
$`=`$ $`{\displaystyle \frac{Kc^3}{4\mathrm{}G}}A,`$ (12)
where the quantities $`c,G,\mathrm{},`$ are the speed of light, Newtons constant, Plancks constant and we note that the numerical factor of four has a geometrical origin §§§ A discussion about this coefficient by Bekenstein, properly, reinforces our topological interpretation of it.. Finally, in some sense the holographic principle The entropy in the region $`A`$ is bounded by its boundary, i.e. the closed length $`L`$ or the dynamics of a system in $`A`$ can be described by a system which lives in $`L`$. is realized in our approach, since the fractal parameter $`h`$ is related to the boundary($`LR^{h=2}`$) of the area($`AR^{2h=4}`$), so in one phrase all in $`𝒮_{BH}`$ is pure geometry It is possible, classically, that the phase space of a system gravitating a black hole be compact, with volume scaling as area ( external to black hole ) and so, the holographic principle is a consequence of the gravitating system quantization.. It is worth noting that our analysis is supported by the results of another consideration about $`2`$-point function in two-dimensional quantum gravity .


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# On the Effects of a Bulk Perturbation on the Ground State of 3D Ising Spin Glasses

## Abstract

We compute and analyze couples of ground states of $`3D`$ spin glasses before and after applying a volume perturbation which adds to the Hamiltonian a repulsion from the true ground state. The physical picture based on Replica Symmetry Breaking is in excellent agreement with the observed behavior.

Studying the scaling behavior of ground states (GS) of disordered systems  turns out to be a powerful tool. Here by using a powerful technique based on a bulk modification of the Hamiltonian  we are able to give strong numerical evidence of a Replica Symmetry Breaking like behavior of $`3D`$ spin glasses. With this study we believe we vastly enlarge the scope of , where we were changing the boundary conditions to analyze the changes induced in the GS microscopic structure. The open debate is about the role of the exact (Replica Symmetry Breaking, RSB) solution of the Mean Field spin glass model, where field theory is exact by definition , in describing finite dimensional spin glasses: the validity of a possible phenomenological description, the (more or less modified) droplet picture , should probably be taken as an alternative possibility. The RSB picture is characterized by the presence of states (for the terminology we refer to ) that are locally different one from the other.

In this respect equilibrium Monte Carlo simulations are useful , but since it is impossible to thermalize large, low $`T`$ systems, if one is not far enough from $`T_c`$ there is the remote possibility  that the asymptotic physical picture could be disguised because of crossover effects (this criticism does not apply to the off-equilibrium simulations , and very low $`T`$ recent simulations  also claim to disprove it). The remarkable achievement of the work of  has been to realize that one can compute GS for systems of size comparable to the one of finite $`T`$ numerical simulations. The first series of papers  has been computing couples of GS with periodic boundary conditions (PBC) and with anti-periodic boundary conditions (APBC). A different method, based on the use of a bulk perturbation  has been first used by Palassini and Young to detect the inconsistency of a (even modified) droplet picture: large scale excitations with a finite energy cost (first discussed in ) are clearly detected by this approach. In the replica approach we expect that these large scale excitations correspond to the simultaneous reverse of a large non-compact block of spins: the surface to volume ratio of the set of the flipped spins should asymptotically go to a non-zero value. In previous studies  this surface to volume ratio was investigated: it was found that it was slowly decreasing with $`L`$ and its behavior was compatible with a small negative power of $`L`$.

We use here the same method to make stronger the evidence of the existence of these large scale excitations, and we present a detailed quantitative study of their properties. We show that they behave in agreement with RSB, and that the surface to volume ratio extrapolates to a non-zero value in the limit $`L\mathrm{}`$.

We work in three spatial dimensions ($`D=3`$) on simple cubic lattices of linear size $`L`$, containing $`N=L^3`$ spins with PBC (we have taken $`L=4`$, $`6`$, $`8`$, $`10`$, $`12`$, $`14`$). We consider quenched random couplings $`J`$ extracted from a Gaussian probability distribution with zero expectation value and unit variance. We study the behavior of the GS after changing the Hamiltonian to include a term which repels from the true GS. The Hamiltonian of the first system is

$$H_0(\{\sigma \})\underset{i,\mu }{}\sigma (i)J(i,\mu )\sigma (i+\widehat{\mu }),$$

where the sum is over the $`N`$ sites $`i`$ and the $`D`$ directions $`\mu `$ ($`\widehat{\mu }`$ is the versor in the $`\mu `$ direction). The Hamiltonian of the second system is

$$H_1(\{\tau \})H_0(\{\tau \})\frac{ϵ}{ND}\underset{i,\mu }{}\sigma _0(i)\sigma _0(i+\widehat{\mu })\tau (i)\tau (i+\widehat{\mu }),$$

where the $`\sigma _0(i)`$ are the spins in the GS of $`H_0`$. Let $`\tau _0(i)`$ be the spins in the GS of $`H_1`$: we are interested in studying the differences among $`\sigma _0`$ and $`\tau _0`$ when $`N`$ goes to infinity at fixed $`ϵ`$ (in this limit the perturbation is of order 1, while the total Hamiltonian is of order $`N`$). At this end we define the local site overlap on site $`i`$ as $`q(i)\sigma _0(i)\tau _0(i)`$, and the local link overlap is defined among nearest neighbor sites (or equivalently on links) as $`q_l(i,\mu )q(i)q(i+\mu )`$. If two spin configurations differ by a global spin flip their link overlap is identically equal to $`+1`$ (while their overlap is equal to $`1`$). We also define the average over the system sites and links of the previous quantities: $`qN^1_iq(i)`$, $`q_l(DN)^1_{i,\mu }q_l(i,\mu )`$. With these definitions we have that $`H_1(\{\tau \})=H_0(\{\tau \})ϵq_l`$. We are considering this type of perturbation because the quantity $`q_l`$ is sensitive only to local changes of the configuration, i.e. it is different from 1 only on the interface among the clusters of flipped and non-flipped spins.

The main effect of the perturbation is to generate excited states. It is reasonable to assume that for $`L\mathrm{}`$ the value of the observables computed for fixed value of the site overlap are weakly dependent on the value of $`ϵ`$. This is also suggested by the results of , and will be discussed in more details in . For this reason we will consider the link overlap (and also other quantities) as a function of the (square) site overlap, i.e. $`q_l(q^2)`$. This quantity is defined as the average of the link overlap over those systems for which the square site overlaps of the two ground state is $`q^2`$. We will indicate the link overlap summed over all the systems by $`\overline{q}_l𝑑q^2q_l(q^2)P(q^2)`$, where $`P(q^2)`$ is the probability distribution of $`q^2`$. We have computed $`10^4`$ GS at $`L=4`$ and $`6`$, $`2000`$ at $`L=8`$, $`1500`$ at $`L=10`$, $`500`$ at $`L=12`$ and $`14`$, with $`ϵ=4\sqrt{6}`$, using a genetic algorithm which will be described in .

Given the importance of the issue, we start by discussing the dependence of $`q_l(q^2)`$ over $`q`$ and $`L`$. If we plot $`q_l(q^2)`$ versus $`q^2`$, we notice that $`q_l(q^2)`$ and $`q^2`$ are very strongly correlated. In order to clarify this effect we define the quantity (for all systems such that $`q1`$) $`R_L(q^2)(1q_l(q^2))/(1q^2)`$. For fixed $`L`$ $`R_L(q^2)`$ is nearly $`q^2`$ independent in a large region where $`q`$ is not too large (only close to $`q=1`$ the dependence becomes slightly more noticeable). The $`q^2`$ dependence of $`R(q)`$ in this large $`q`$ region becomes milder with increasing $`L`$. We fit $`R_L(q^2)`$ to the form $`A(L)+B(L)q^2`$ using the data in the range $`q^2(0,0.3)`$: the fits are very good, and the extrapolations are all very smooth. $`B(L)`$ is in all cases a few percent of $`A(L)`$. In fig. 1 the upper points are for $`A(L)R_L(0)=1q_l(0)`$ versus $`L^1`$. Both a linear fit (which extrapolates to a non zero value) and a power fit to the form $`CL^\alpha `$, where $`\alpha `$ turns out to be $`0.44`$, follow the data in a qualitative way, but they are unacceptable because they lead to a very high value of $`\chi ^2`$ (i.e. to a normalized $`\chi ^2=O(20)`$). In fig. 1 we plot a second order polynomial fit that is very good (it has a normalized $`\chi ^20.6`$) and leads to a value of $`A(L=\mathrm{})=0.30\pm 0.01`$. We also plot a fit to the form $`A(L)=a+bL^\lambda `$, that is also good (it has a normalized $`\chi ^2=0.3`$) and leads to a value of of $`A(L=\mathrm{})=0.24\pm 0.01`$ and $`\lambda =0.72\pm 0.02`$. The difference with the $`0.30`$ obtained by the polynomial fit gives an idea of the size of the systematic error over the extrapolation.

The values extrapolated to $`L=\mathrm{}`$ are an estimate of $`1q_l(0)`$, and they have to be compared with the value $`0.245\pm 0.015`$ that we have estimated in : the agreement is good, even if here the systematic error is large. We can conclude that there is evidence that $`1q_l(0)`$ does not extrapolate to zero in the infinite volume limit and the dependence of $`q_l(q^2)`$ is well approximated (for $`q^2`$ not too close to $`1`$) by the form $`q_l(q^2)=1A(1q^2)`$. The previous formula holds in the infinite range SK model, with $`A=1`$. The fact that in $`3D`$ we find a low value ($`A0.3`$) suggests that $`A`$ goes to zero when one approaches the lower critical dimension.

The lower points and curves of fig. 1 are for the expectation value of the link overlap $`\overline{q}_l`$, averaged over all $`q^2`$ values. The curves are again a polynomial and a power law best fits, that here extrapolate to a lower value ($`0.07\pm 0.04`$ for the power law and $`0.155\pm 0.015`$ for the polynomial fit). The error is larger than in $`A(L)`$ (of a factor close to $`2`$) but apart from a shift (since $`\overline{q}_lq_l(0)`$) the two curves are similar.

Let us stress that $`A(L)`$ is important also since $`q_l(q^2)`$ is not expected to depend on $`ϵ`$ when $`L\mathrm{}`$. The $`ϵ`$-perturbation allows to explore low energy states with an energy gap of order $`1`$. The function $`P(q^2)`$ changes with $`ϵ`$  and consequently also the value $`\overline{q_l}`$ changes: still the functional relation that relates $`q_l`$ to $`q^2`$ is unchanged.

It is also interesting to look at the variance squared of $`R_L(q^2)`$, i.e. to $`\sigma _{(R)L}^2(q^2)R_L^2(q^2)R_L(q^2)^2`$. We proceed as for the the best fit of $`R_L(q^2)`$. First we fit $`\sigma _{(R)L}^2(q^2)`$ to the form $`A_W(L)+B_W(L)q^2`$, using the data with $`q^20.3`$: the extrapolations are very good. Also here for a given value of $`L`$ we find that $`\sigma _{(R)L}^2(q^2)`$ is nearly $`q^2`$ independent apart from the region close to $`q^2=1`$. Also the $`q^2`$ dependence of $`\sigma _{(R)L}^2(q^2)`$ in this region becomes weaker mild with increasing $`L`$.

We plot $`A_W(L)`$ versus $`1/L`$ in fig. 2. Together with the data we show a best fit to the form $`A_W(L)CL^\delta `$, that has a low $`\chi ^2`$, and $`\delta =1.35\pm 0.03`$. The fact that a fit to a zero asymptotic value is very good shows that $`q_l`$ as a function of $`q`$ does not fluctuate as $`L\mathrm{}`$: this is the same situation that we find in the mean field RSB theory, with a more complex dependence of $`q_l(q^2)`$ over $`q^2`$. The asymptotically vanishing value of $`A_W(L)`$ explains why the errors on $`q_l(q^2)`$ are smaller that those on $`\overline{q_l}`$.

We discuss next the overlap-overlap correlation functions. The difference among a droplet and a RSB scenario becomes very clear if we consider the overlap-overlap correlation function at fixed value of $`q^2`$ in a system of side $`L`$, i.e. the correlation function obtained by selecting those systems which have a ground state with a fixed value of the mutual overlap:

$$C(x,L|q^2)q(x)q(0)_{(q^2)}.$$

In the RSB case we expect that for large $`L`$ and fixed $`x`$ $`C(x,L|q^2)G(x|q^2)+q^2`$, where the function $`G(x|q^2)`$ depends on $`q^2`$ and for large $`x`$ should behave as $`G(x|q^2)x^{\varphi (q^2)}`$. $`\varphi (q^2)`$ may depend on $`q^2`$, although there are indications that it takes at most only two different values, one at $`q=0`$ and one at $`q0`$ . In the region where $`x`$ and $`L`$ are large we expect that

$$C(x,L|q^2)g(r|q^2)(\frac{1}{x}+\frac{1}{Lx})^{\varphi (q^2)}+q^2,$$
(1)
where $`rxL^1`$. We have used the factor $`(\frac{1}{x}+\frac{1}{Lx})`$ instead of the simpler $`\frac{1}{x}`$ in order to implement the symmetry implied by the presence of PBC.

The situation described by a droplet picture is different: in this case, for large $`L`$ and fixed $`x`$, $`C(x,L|q^2)1`$. One can argue that in the droplet model one should have $`\varphi (q^2)=0`$ and $`g(0|q^2)+q^21`$, i.e $`C(x,L|q^2)D(xL^1|q^2)`$ with $`D(0|q^2)=1`$.

We will discuss our results for small values of $`q`$: we consider the $`q`$ range $`qq_{max}=0.1`$. The results are not very sensitive to the exact position of the $`q_{max}`$ cut (of course if $`q_{max}`$ is too small the statistics fades). In fig. 3 we present our data for $`g(r)`$ as a function of $`wr(1r)`$ for $`\varphi =0.4`$ (we prefer to plot $`g`$ versus $`w`$ since because of the PBC both $`g`$ and $`w`$ are left invariant when $`r`$ goes in $`1r`$). The value of $`q^2`$ we use to subtract the disconnected part is the average of $`q^2`$ in the interval $`qq_{max}`$. We have selected $`\varphi `$ such to optimize the quality of the scaling behavior. The line is for the best fit to a second order polynomial.

The scaling is very good, and the estimate of $`\varphi 0.4`$ reliable. A droplet-like scaling is excluded by our data. We notice that $`C(x,L|0)|_{x=1}=q_l(0)`$ and the scaling form (1) accounts for the $`L`$-dependence of $`q_l(0)`$. If we assume that (1) is exact also for $`x=1`$ (a too strong assumption) we get that $`C(1,\mathrm{}|0)=g(0|0)`$. Using the quadratic fit in fig. 3 to extrapolate the data at $`r=0`$ we get in the infinite volume limit $`1q_l(0)=.33\pm .02`$, which is in reasonable agreement with the previous estimates, given the crudeness of the approximation.

When we analyze the correlation function of the link overlap we also select events at a fixed value of $`q^2`$: as in the previous case we will consider a cut of the form $`|q|<q_{max}=.1`$. We only measure a simple correlation function of $`1q_l(i)`$ (we only look at correlations in a given plane, and average the two contributions coming from separating in the direction $`2`$ links in the direction $`1`$ and in the direction $`1`$ links in the direction $`2`$ ), that we call $`\mathrm{\Omega }(x,L)`$, which we plot in fig. 4 for various $`L`$ ($`x1`$). The different sets of points are plotted versus $`s(x,L)(1/x+1/(Lx))^\lambda `$. If we chose the value $`\lambda =2.1`$ the data at given $`L`$ can be very well fitted by a linear functions, i.e. the lines in fig. 4:

$$\mathrm{\Omega }(x,L)=a(L)+b(L)s(x,L).$$
(2)
We plot in fig. 5 $`a(L)`$ and $`b(L)`$ from (2) and the best linear fits. If for $`L\mathrm{}`$ $`1q_l(0)`$ would go to zero, this correlation function should become identically zero and consequently the two functions, $`a(L)`$ and $`b(L)`$, should extrapolate to zero when $`L\mathrm{}`$. However the slope $`b(L)`$ does not show any tendency to go to zero: the fact that it increases (slightly) with $`L`$ is a substantial indication that it does not converge to zero in the infinite volume limit. The intercept is fitted very well by a $`1/L`$ behavior without corrections and it extrapolates to a non zero value. Moreover the correlation function at large distances should be the square of the expectation values and consequently we have the relation $`a(L)|_{L=\mathrm{}}=(1q_l(0))^2`$. This relation gives a value of $`1q_l(0)=0.26\pm 0.02`$, that compares very nicely to the values we have discussed earlier.

Let us start summarizing our results. We have applied a bulk perturbation, and shown that the results substantiate in a perfect way the ones obtained by changing the boundary conditions . The quantity $`1q_l(0)`$ has a non-zero value that compares very well to the one determined in . We have also determined that $`\overline{q_l}`$ behaves very similarly, and we have estimated its value in the infinite volume limit (four different estimates, affected by different systematic errors are $`.24\pm .01`$, $`.26\pm .02`$, $`.30\pm .01`$, $`.33\pm .02`$, the errors being purely statistical). We have shown that very plausibly in the limit $`L\mathrm{}`$ $`q_l`$ is a well behaved function of $`q^2`$, in strict analogy to what happens in the mean field RSB theory. We have analyzed site overlap and link overlap spatial correlation functions, and we have shown they perfectly obey scaling laws implied by a RSB scenario. Again, this results is quantitative, in which it leads to an estimate of $`q_l(0)`$ coherent with the ones given before.

The RSB scenario is perfectly compatible with the whole set of data. These results are consistent with the recent detection of large scale excitations in spin glass ground states . The behavior we find connects smoothly with the results obtained by simulations at finite temperature  (e.g. the overlap-overlap correlation decays as the distance to a power $`\varphi =.4`$, which is not far from the value obtained from simulation at finite temperature). We think that we have conclusively shown that the ground state structure of $`3D`$ Ising spin glasses with Gaussian quenched random couplings is not trivial.

EM thanks for the very nice hospitality the SPhT of Saclay CEA and the LPTMS of Université Paris Sud, Orsay, where part of this work has been done. We are grateful to O. Martin, M. Palassini and P. Young for useful correspondences and conversations.


text:
# 1 Introduction

## 1 Introduction

The observational view of the universe has drastically changed during the last ten years. Until a decade ago, the universe was supposed to be matter dominated and the cosmic expansion was understood to be slowing down; consequently, the Einstein de Sitter model was taken to be the standard model of the observable universe. The latest cosmological observations reveal a low mass density, spatially flat universe with accelerating expansion. We shall briefly survey the current observations and apply them to investigate the ’missing mass’ problem in cosmology.

In cosmological theories, the Hubble Constant is one of the most important observational parameters due to its sensitivity to the variations in the cosmic energy density and the spatial curvature of the universe. According to the current estimates , $`H_o=65\pm 10km/Mpc/s`$. As regards the curvature of the universe, it was long predicted by the inflationary scenarios that the observable universe must be spatially flat. In the angular power spectrum of CMB , the location of the first Doppler peak near $`l200`$ fortifies this view. At the same time the precise measurements  of the density of matter derived from cluster abundances, baryon fraction in clustered matter indicate a low mass density with $`\mathrm{\Omega }_m0.35`$. It gives rise to the question as to how to account for $`65\%`$ ’missing mass’ in the universe, sometimes, referred to as ’dark energy’. The recent studies undertaken by Supernova Cosmology Project Team  and High Red-shift Search Team  reveal that the distant SNe are fainter and thus more distant than expected for a decelerating universe. It implies that the rate of cosmic expansion is accelerating which in turn provides empirical evidence of the existence of dark energy with negative pressure. For a spatially flat universe, the best values derived from the analysis of combined results of  are approximately $`\mathrm{\Omega }_m=0.25\pm 0.1`$ and for dark energy $`\mathrm{\Omega }_X=0.75\pm 0.1(1\sigma )`$. These values are in excellent agreement with $`\mathrm{\Omega }_m`$ derived from the baryon fraction in clustered matter as discussed above. The most probable candidates for the dark energy are the cosmological constant $`\mathrm{\Lambda }`$ and the Quintessence fields – the scalar fields with evolving equation of state which, during the matter dominated phase, acquire negative pressure and behave like $`\mathrm{\Lambda }_{eff}`$.

As for the break-up of the material content of the universe, the baryonic matter (BM) contributes only $`\mathrm{\Omega }_{BM}=0.05`$ as determined from the precise measurement of deuterium abundance  in very distant hydrogen clouds. The neutrinos might contribute a small fraction $`\mathrm{\Omega }_\nu 0.003`$. The remaining contribution $`\mathrm{\Omega }_{DM}0.29`$ comes from the dark matter (DM) which determines the hierarchy of the structure formation in the universe. The cold dark matter (CDM) consists of particles like axions and neutralinos which move slowly and cannot remove lumpiness on small scale; as such in CDM cosmology, the structure formation follows bottom-up sequence i.e. the galaxies are formed first followed by clusters and super-clusters. On the contrary, the fast moving particles like neutrinos constitute hot dark matter (HDM) which can remove lumpiness on small scale; as such HDM supports top-down sequence of structure formation in the universe. The astronomical observations made by the Keck 10-meter Telescope and the Hubble Space Telescope reveal that most of the galaxies in the universe formed between redshifts 2 to 4, that clusters formed at redshift $`z1`$ and the superclusters are forming to-day. These observations rule out HDM cosmology, restrict the contribution of neutrinos to about $`0.3\%`$ as stated above and favour a CDM cosmology for the observable universe.

It is important to distinguish between the dark matter and dark energy. The dark matter may consist of exotic particles like axions and neutralinos but it attracts and clumps like ordinary matter whereas the dark energy does not clump; it repels matter. In the present paper, we consider the role of two leading candidates of dark energy under the sections QCDM cosmology and $`\mathrm{\Lambda }`$CDM cosmology and discuss those astrophysical/cosmological observations which constrain the magnitude of the dark energy at the nucleosynthesis epoch, during galaxy formation era and at the end of matter dominated (i.e. at the onset of acceleration) era and their implications for the quintessence field and their tracking behaviour. These constraints have also been used to put theoretical limits on the magnitude of the cosmological constant $`\mathrm{\Lambda }`$.

## 2  QCDM Cosmology

Let us first consider CDM cosmology with Quintessence – the rolling scalar fields, with evolving equation of state, which acquire repulsive character (owing to negative pressure) during the late evolution of the universe. The quintessence in the present day observable universe, behaves like $`\mathrm{\Lambda }_{eff}`$ and may turn out to be the most likely form of dark energy which induces acceleration in the cosmic expansion.

Consider the homogeneous scalar field $`\varphi (t)`$ which interacts with matter only through gravity. The energy density $`\rho _\varphi `$ and the pressure $`p_\varphi `$ of the field are given by

$$\rho _\varphi =\frac{1}{2}\dot{\varphi }^2+V(\varphi )$$
(1)
$$p_\varphi =\frac{1}{2}\dot{\varphi }^2V(\varphi )$$
(2)
The equation of motion of the scalar field

$$\ddot{\varphi }+3H\dot{\varphi }+V^{}(\varphi )=0,V^{}(\varphi )\frac{dV}{d\varphi }$$
(3)
leads to the energy conservation equation

$$\dot{\rho }_\varphi +3H(1+w_\varphi )\rho _\varphi =0$$
(4)
where $`w_\varphi \frac{p_\varphi }{\rho _\varphi }`$ and $`H\frac{\dot{a}}{a}`$ is the Hubble constant. Accordingly, $`\rho _\varphi `$ scales down as

$$\rho _\varphi a^{3(1+w_\varphi )},1w_\varphi <\frac{1}{3}$$
(5)
Obviously, the scaling of $`\rho _\varphi `$ gets slower as the potential energy $`V(\varphi )`$ starts dominating over the kinetic energy $`\frac{1}{2}\dot{\varphi }^2`$ of the scalar field and $`w_\varphi `$ turns negative.

Since there is minimal interaction of the scalar field with matter and radiation, It follows from Eq.(4) that the energy of matter and radiation is conserved separately as

$$\dot{\rho }_n+3H(1+w_n)\rho _n=0$$
(6)
Accordingly

$$\rho _na^{3(1+w_n)}$$
(7)
where $`\rho _n`$ is the energy density of the dominant constituent (matter or radiation) in the universe with the equation of state $`p_n=w_n\rho _n`$ where $`w_n=\frac{1}{3}`$ for radiation and $`w_n=0`$ for matter.

Although, the scalar field is non-interactive with matter, it affects the dynamics of cosmic expansion through the Einstein field equations. Assuming large scale spatial homogeneity and isotropy of the universe, the field equations for a flat Friedmann model are

$$H^2=\frac{\rho _n+\rho _\varphi }{3M_p^2}$$
(8)
and

$$\frac{2\ddot{a}}{a}=\frac{\rho _n+\rho _\varphi +3p_n+3p_\varphi }{3M_p^2}$$
(9)
where $`M_p=2.4\times 10^{18}`$ GeV is the reduced Planck mass.

Denoting the fractional density of the scalar field by $`\mathrm{\Omega }_\varphi \frac{\rho _\varphi }{\rho _n+\rho _\varphi }`$ and that of the matter/radiation field by $`\mathrm{\Omega }_n\frac{\rho _n}{\rho _n+\rho _\varphi }`$, equations (8) and (9) may be rewritten as

$$\mathrm{\Omega }_n+\mathrm{\Omega }_\varphi =\mathrm{\hspace{0.17em}1}$$
(10)
and

$$2\frac{\ddot{a}}{a}=\frac{\rho _n}{3M_p^2}[(1+3w_n)+(1+3w_\varphi )\frac{\mathrm{\Omega }_\varphi }{\mathrm{\Omega }_n}]$$
(11)
The relative growth of $`\mathrm{\Omega }_\varphi `$ versus $`\mathrm{\Omega }_n`$ during the cosmic evolution is given by

$$\frac{\mathrm{\Omega }_\varphi }{\mathrm{\Omega }_n}=\frac{\mathrm{\Omega }_\varphi ^0}{\mathrm{\Omega }_n^0}\left(\frac{a}{a_0}\right)^{3ϵ}$$
(12)
where the tracking parameter $`ϵw_nw_\varphi `$ and $`\mathrm{\Omega }_\varphi ^0`$, $`\mathrm{\Omega }_n^0`$ denote the values of $`\mathrm{\Omega }_\varphi `$ and $`\mathrm{\Omega }_n`$ at the present epoch $`(a=a_0)`$. As discussed in section 1, the $`SNeI_a`$ observations suggest that $`\mathrm{\Omega }_\varphi ^02\mathrm{\Omega }_n^0`$; consequently Eq.(12) may be expressed in terms of the red-shift $`z`$ as below

$$2(\mathrm{\Omega }_\varphi ^11)=(1+z)^{3ϵ}$$
(13)
If we insist that the scalar field, regardless of its initial value, should behave like $`\mathrm{\Lambda }_{eff}`$ today, it must obey tracking conditions  with wide ramifications for quintessence fields already discussed in detail -. In nutshell, tracking consists in synchronised scaling of $`\rho _\varphi `$ and $`\rho _n`$ along a common evolutionary track so as to ensure the restricted growth of $`\mathrm{\Omega }_\varphi `$ during the cosmic evolution in accordance with the observational (both astrophysical and cosmological) constraints. As discussed in , the tracking parameter $`ϵ`$ plays a vital role in monitoring the desired growth of $`\mathrm{\Omega }_\varphi `$. The existence theorem for tracker fields  requires $`ϵ`$ to satisfy the condition $`\frac{ϵ\mathrm{\Omega }_n}{2(1+w_\varphi )}<1`$ and also to conform to cosmological constraints mentioned therein. Here we investigate the consequent limits on the tracking parameter $`ϵ`$ imposed by these constraints to ensure tracking by a quintessence field.

According to the Eq. (13), $`\mathrm{\Omega }_\varphi `$ depends both upon the redshift $`z`$ and the tracking parameter $`ϵ`$. From a general functional form $`\mathrm{\Omega }_\varphi =f(z,ϵ)`$, it is difficult to chart out $`\mathrm{\Omega }_\varphi z`$ variation through tracking unless we are able to fix the value of $`ϵ`$ corresponding to known $`\mathrm{\Omega }_\varphi `$ at certain points in the phase space of $`zϵ`$. This is achieved with the help of the astrophysical constraints discussed in this paper. Having evaluated $`\mathrm{\Omega }_\varphi `$ at some typical points $`(z_0,ϵ_0)`$, we can interpolate $`\mathrm{\Delta }\mathrm{\Omega }_\varphi `$ at neighbouring points $`(z_0+\mathrm{\Delta }z_0,ϵ_0+\mathrm{\Delta }ϵ_0)`$. Using this technique, realistic tracking diagrams of $`\mathrm{\Omega }_\varphi z`$ variation, $`w_\varphi z`$ variation and $`ϵz`$ variation may be drawn as shown in the figures 1,2 and 3.

In this connection, the following differential relation, derived from Eq. (13)

$$\frac{\mathrm{\Delta }\mathrm{\Omega }_\varphi }{3ϵ\mathrm{\Omega }_n\mathrm{\Omega }_\varphi }=\frac{\mathrm{\Delta }z}{1+z}+\frac{\mathrm{\Delta }ϵ}{ϵ}\mathrm{ln}(1+z).$$
(14)
is found quite useful in interpolating the increment $`\mathrm{\Delta }\mathrm{\Omega }_\varphi `$ in terms of the increments $`\mathrm{\Delta }z`$ and $`\mathrm{\Delta }ϵ`$. It is noteworthy that the contribution of the term $`\frac{\mathrm{\Delta }z}{1+z}`$ is very small compared to the contribution of $`\frac{\mathrm{\Delta }ϵ}{ϵ}`$ at high redshifts.

Let us now reconsider the astrophysical constraints discussed in our previous paper , try to refine them and examine their implications for quintessence fields.

1. The Nucleosynthesis Constraint. The first constraint on $`\mathrm{\Omega }_\varphi `$ during the cosmic evolution comes from the helium abundance at the nucleosynthesis epoch $`(z10^{10})`$. The presence of an additional component of energy in the form of quintessence field with energy density $`\rho _\varphi `$ results in an increase in the value of the Hubble constant $`H`$ as given by the differential of the Friedmann equation

$$\frac{2\delta H}{H}=\frac{\delta \rho }{\rho }=\frac{\rho _\varphi }{\rho }.$$
(15)
This, in turn, yields a higher ratio of neutrons to protons at the freeze-out temperature (1 MeV) of the weak interactions and a consequent higher percentage of the helium abundance in the universe. Assuming the existence of three known species of neutrinos, the nucleosynthesis calculation  yields

$$\frac{\delta \rho }{\rho }=\frac{7(N_\nu 3)}{43}$$
(16)
Since the number of neutrino species $`N_\nu <4`$, we arrive at the constraint $`\frac{\delta \rho }{\rho }<\frac{7}{43}`$. If the contribution $`\delta \rho `$ comes from the quintessence field instead, the above constraint translates into nucleosynthesis constraint on $`\mathrm{\Omega }_\varphi `$ as follows

$$\mathrm{\Omega }_\varphi =\frac{\rho _\varphi }{\rho _n+\rho _\varphi }<\frac{7}{50}=0.14$$
(17)
The corresponding value of the tracking parameter is $`ϵ0.035`$.

2. Galaxy Formation Constraint. According to the current estimates in CDM cosmology, the galactic structure formation takes place between the redshift $`z=4`$ and $`z=2`$. The clumping of matter into galaxies demands the dominance of gravitational attraction during this period. Therefore, the repulsive force of quintessence must be relatively weak and $`\mathrm{\Omega }_\varphi `$ must be reasonably less than 0.5 during the galaxy formation era. Interpolation from Eqs. (13) and (14) shows that $`0.33ϵ0.5`$ during the galaxy formation era.

3. Present Epoch. Two recent surveys  based on $`SN_eI_a`$ measurements predict accelerating cosmic expansion with $`\mathrm{\Omega }_\varphi 0.65\pm 0.05`$ at the present epoch (z=0). The constraint $`\ddot{a}>0`$ inserted in Eq. (11) leads to $`ϵ>0.5`$ at the present epoch. Interpolation with the help of Eq.(14) places $`ϵ`$ around 0.75.

4. Transition to Accelerated Expansion (Quintessence Dominated Era). The onset of acceleration( $`\ddot{a}>0`$) in the observable universe takes place around the value of $`\mathrm{\Omega }_\varphi 0.5`$ which corresponds to $`ϵ0.66`$ from Eq.(11) at a redshift of $`z=0.419`$ from Eq.(13).

In figure 4, the cosmic events are depicted sequentially by the thick line in the $`\mathrm{\Omega }_n\mathrm{\Omega }_\varphi `$ diagram. The events corresponding to the above constraints are marked by circles.

## 3  $`\mathrm{\Lambda }CDM`$ Cosmology

In this section , we regard the universe to be filled up with a mixture of cold dark matter and the vacuum energy represented by the cosmological constant $`\mathrm{\Lambda }`$ which plays the role of dark energy and tends to accelerate the expansion of the universe.

In the presence of $`\mathrm{\Lambda }`$ term, the Einstein field equations for a spatially flat Friedmann universe are given by

$$H^2=\frac{8\pi G}{3}(\rho _n+\rho _\mathrm{\Lambda })$$
(18)
and

$$\frac{2\ddot{a}}{a}=\frac{8\pi G}{3}(\rho _n+3p_n/c^22\rho _\mathrm{\Lambda })$$
(19)
where $`\rho _\mathrm{\Lambda }=\frac{\mathrm{\Lambda }c^2}{8\pi G}`$ and the Newtonian Gravitational constant $`G=6.6\times 10^8`$ cgs units. In case of matter dominated universe $`(p_n0)`$, the Eqs. (18) and (19) may be rewritten as

$$\mathrm{\Omega }_n+\mathrm{\Omega }_\mathrm{\Lambda }=1$$
(20)
and

$$q=\frac{1}{2}\mathrm{\Omega }_n\mathrm{\Omega }_\mathrm{\Lambda }$$
(21)
where $`q\frac{\ddot{a}}{aH^2}`$ is the deceleration parameter and $`\mathrm{\Omega }_\mathrm{\Lambda }\frac{\rho _\mathrm{\Lambda }}{\rho _\mathrm{\Lambda }+\rho _n}=\frac{\mathrm{\Lambda }c^2}{3H^2}`$.

It is obvious from Eq. (21) that the cosmic expansion slows down as long as $`\mathrm{\Omega }_n>2\mathrm{\Omega }_\mathrm{\Lambda }`$ (i.e $`\rho _n>2\rho _\mathrm{\Lambda }`$); the clumping of matter into galaxies takes place during this period. Transition to accelerated expansion occurs when the deceleration parameter $`q0`$ which corresponds to $`\mathrm{\Omega }_\mathrm{\Lambda }\frac{1}{3}`$. It marks the beginning of the $`\mathrm{\Lambda }`$-dominated phase during which the universe goes on expanding faster and faster and ultimately enters the de Sitter phase of exponential expansion. This is borne out clearly from the analytical solution of the field equations (18) and (19) during matter dominated phase

$$a\mathrm{sinh}^{2/3}(\frac{3}{2}\sqrt{\mathrm{\Lambda }/3}ct)$$
(22)
It is noteworthy that this solution reduces to Einstein de Sitter solution $`at^{2/3}`$ in the limit $`\mathrm{\Lambda }0`$ and goes back to de Sitter expansion as $`\rho _n0`$.

It leads to

$$H=c\sqrt{\mathrm{\Lambda }/3}\mathrm{coth}(\frac{3}{2}\sqrt{\mathrm{\Lambda }/3}ct)$$
(23)
and

$$q=\frac{1}{3}\mathrm{tanh}^2(\frac{3}{2}\sqrt{\mathrm{\Lambda }/3}ct)$$
(24)
The astrophysical constraints discussed in the previous section apply to $`\mathrm{\Lambda }`$ as well. Since $`\mathrm{\Lambda }`$ remains constant throughout, these constraints put theoretical limits on the plausible values of $`\mathrm{\Lambda }`$. For instance, the clumping of matter into galaxies can take place during the cosmic deceleration phase ($`q>0`$) when the gravitational attraction is dominant over cosmic repulsion. It follows from Eq. (24) that during the galaxy formation era

$$\mathrm{tanh}^2\left(\frac{3}{2}\sqrt{\mathrm{\Lambda }/3}ct\right)<\frac{1}{3}$$
(25)
Expressed in terms of redshift $`z`$ with age $`t_0`$ of the universe taken as 13 billion years, we get

$$\mathrm{\Lambda }<4.2\times 10^{57}(1+z)^3$$
(26)
Assuming that the galaxy formation continues up to redshift $`z=2`$, we derive the upper limit of $`\mathrm{\Lambda }`$

$$\mathrm{\Lambda }<33.5\times 10^{57}$$
(27)
The transition to accelerated expansion takes place at $`t=t_c`$ corresponding to redshift $`z=z_c`$ as given by Eq. (24) with $`q=0`$. At the present epoch $`(z=0)`$, the cosmic expansion is accelerating ($`q<0`$). This yields the lower limit of $`\mathrm{\Lambda }`$ as given by

$$\mathrm{\Lambda }>4.2\times 10^{57}$$
(28)
According to the constraint 4 in Section 2, it was found that the transition to accelerated expansion (scalar field dominated) phase in QCDM cosmology occurs at $`z_c0.419`$. Since the transition in $`\mathrm{\Lambda }`$CDM cosmology takes place earlier, we can take $`z_c0.5`$. This corresponds to material density $`\rho _n=7.415\times 10^{30}`$ gm/cm3. At the point of onset of acceleration ($`q=0`$), we have by Eq. (21)

$$2\rho _\mathrm{\Lambda }=\rho _n=8.43\times 10^{30}gm/cm^3$$
(29)
It yields the value

$$\mathrm{\Lambda }=6.99\times 10^{57}$$
(30)
which is in good agreement with the observational estimate $`\mathrm{\Lambda }=\frac{3H_0^2\mathrm{\Omega }_\mathrm{\Lambda }}{c^2}=7.74\times 10^{57}`$ based on the value of the Hubble constant $`H_0=65`$ km/Mpc/s and $`\mathrm{\Omega }_\mathrm{\Lambda }=0.65`$.

## 4 Conclusions

The astrophysical constraints on $`\mathrm{\Omega }_\varphi `$, discussed in Section 2, enable us to present a realistic picture of the scaling of the quintessence energy during tracking and plot the variation of $`\mathrm{\Omega }_\varphi `$ versus $`ϵ,w_\varphi `$ and z (redshift). Whereas both QCDM cosmology and $`\mathrm{\Lambda }`$CDM cosmology are fairly compatible with the recent CMB observations and power spectrum of galaxy clustering, QCDM has the advantage in fitting constraints from high redshift supernovae, gravitational lensing and structure formation at large redshifts . Another distinguishing feature of QCDM cosmology is that the onset of cosmic acceleration takes place when $`\mathrm{\Omega }_\varphi =0.5`$ whereas in $`\mathrm{\Lambda }`$CDM cosmology, $`\mathrm{\Omega }_\mathrm{\Lambda }=\frac{1}{3}`$ marks the onset of acceleration. Taking the observational value $`\mathrm{\Lambda }=7.74\times 10^{57}`$, the transition to the accelerating expansion phase in $`\mathrm{\Lambda }`$CDM cosmology occurs when $`\rho _m=9.3\times 10^{30}gm/cm^3`$ which corresponds to $`z_c0.54`$. In QCDM cosmology, as discussed in Section 2, the transition occurs at $`z_c=0.419`$. It means that the transition to accelerating expansion occurs earlier in $`\mathrm{\Lambda }`$CDM cosmology than in QCDM cosmology. Again, in $`\mathrm{\Lambda }`$CDM cosmology, the universe ends up in inflationary phase with exponential expansion whereas in QCDM cosmology, the ultimate fate of the universe is inflation with exponential or hyperbolic expansion, depending upon the form of the scalar potential.

Acknowledgments This work was supported in part by UGC grant from India. The author acknowledges useful discussions and valuable help of Keith Olive and Panagiota Kanti and hospitality of Theoretical Physics Institute, University of Minnesota.

* Permanent Address: Department of Mathematics and Astronomy, Lucknow University, Lucknow 226007. India.


text:
# Understanding conserved amino acids in proteins

It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a sequence conservatism pattern that is in remarkable agreement with that found in natural proteins. Based on the physical properties of amino acids, we propose a model of evolution that explains conserved amino acids across protein families sharing the same fold.

Molecular evolution is a sumptuous natural laboratory that provides an invaluable source of information about the structure, dynamics and function(s) of biomolecules. This information has already been widely used to understand the folding kinetics, thermodynamics, and function of proteins (e.g. ). The basic belief behind the majority of such studies is that evolution optimizes, to a certain extent, the properties of proteins, so that they become more sufficiently stable, and have better folding and functional properties.

Recent studies  identified positions in several common protein folds where amino acids are universally conserved within each family of proteins having that fold. Such positions are localized in structure, and their unusually strong conservatism may be due to functional reason (e.g. super-site), or folding kinetics (folding nucleus) . In contrast to function and folding kinetics, evolutionary pressure to maintain stability may be applied “more evenly” because all amino acids contribute, to a lesser or greater extent, to protein stability via their interaction with other amino acid residues and with water.

In this letter we develop a model that provides a rationale for conservatism patterns caused by selection for stability. Our model is of equilibrium evolution that maintains stability and other properties achieved at an earlier, prebiotic stage. To this end we propose that stability selection accepts only those mutations that keep energy of the native protein, $`E`$, below a certain threshold $`E_0`$ necessary to maintain an energy gap . The requirement to maintain an energy threshold for the viable sequences makes the equilibrium ensemble of sequences analogous to a microcanonical ensemble. In analogy with statistical mechanics, a more convenient and realistic description of the sequence ensemble is a canonical ensemble, whereby strict requirements on energy of the native state is replaced by a “soft” evolutionary pressure that allows energy fluctuations from sequence to sequence but makes sequences with high energy in the native state unlikely. In the canonical ensemble of sequences, the probability of finding a particular sequence, $`\{\sigma \}`$, in the ensemble follows the Boltzmann distribution

$$P(\{\sigma \})=\frac{\mathrm{exp}(E\{\sigma \}/T)}{Z},$$
(1)
where $`T`$ is the effective temperature of the canonical ensemble of sequences that serves as a measure of evolutionary pressure and $`Z=_{\{\sigma \}}\mathrm{exp}(E\{\sigma \}/T)`$ is the partition function taken in sequence space.

Next, we apply a mean-field approximation that replaces all multiparticle interactions between amino acids by interaction of each amino acid with an effective field $`\mathrm{\Phi }`$ acting on this amino acid from the rest of the protein. This approximation presents $`P(\{\sigma \})`$ in a multiplicative form as $`_{k=1}^Np(\sigma _k)`$ of probabilities to find an amino acid $`\sigma `$ at position $`k`$. $`p(\sigma _k)`$ also obeys Boltzmann statistics

$$p(\sigma _k)=\frac{\mathrm{exp}(\mathrm{\Phi }(\sigma _k)/T)}{_\sigma \mathrm{exp}(\mathrm{\Phi }(\sigma _k)/T)}.$$
(2)
The mean field potential $`\mathrm{\Phi }(\sigma _k)`$ is the effective potential energy between amino acid $`\sigma `$ and all amino acids interacting with it, i. e.

$$\mathrm{\Phi }(\sigma _k)=\underset{ik}{\overset{N}{}}U(\sigma _k,\sigma _i)\mathrm{\Delta }_{ki}.$$
(3)
Matrix $`U`$ describes energy parameters in contact approximation and matrix $`\mathrm{\Delta }`$ is a contact matrix for protein native structure (see Methods for more detail). The potential $`\mathrm{\Phi }`$ is similar in spirit to the protein profile introduced by Bowie et al.  to identify protein sequences that fold into a specific 3D structure.

For each member, $`m`$, of the fold family (FSSP database ) we compute the mean-field probability, $`p_m(\sigma _k)`$, using Eq. (2) and then, we compute the average mean-field probability,

$$p_{MF}(\sigma _k)=\frac{1}{N_s}\underset{m=1}{\overset{N_s}{}}p_m(\sigma _k).$$
(4)
Eqs. (2) — (4), along with properly selected energy function, $`U`$, make it possible to predict probabilities of all amino acid types and sequence entropy $`S_{MF}(k)`$ at each position $`k`$

$$S_{MF}(k)=\underset{\sigma }{}p_{MF}(\sigma _k)\mathrm{ln}p_{MF}(\sigma _k)$$
(5)
from the native structure of a protein. The summation is taken over all possible values of $`\sigma `$.

Theoretical predictions from statistical-mechanical analysis can be compared with data on real proteins. In order to determine conservatism in real proteins we note that the space of sequences that fold into the same protein structure presents a two-tier system, where homologous sequences are grouped into families and there is no recognizable sequence homology between families despite the fact that they fold into closely related structures .

Using the database of protein families with close sequence similarity (HSSP database ), we compute frequencies of amino acids at each position, $`k`$, of aligned sequences, $`P_m(\sigma _k)`$, for a given, $`m`$th, family of proteins. We average these frequencies across all $`N_s`$ families sharing the same fold that are present in FSSP database :

$$P_{acr}(\sigma _k)=\frac{1}{N_s}\underset{m=1}{\overset{N_s}{}}P_m(\sigma _k).$$
(6)
Next, we determine the sequence entropy, $`S_{acr}(k)`$, at each position, $`k`$, of structurally aligned protein analogs:

$$S_{acr}(k)=\underset{\sigma }{}P_{acr}(\sigma _k)\mathrm{ln}P_{acr}(\sigma _k).$$
(7)
If the stability selection were a factor in evolution of proteins and our model captures it, then we should observe correlation between predicted mean field based sequence entropies, $`S_{MF}(k)`$, and actual sequence entropies $`S_{acr}(k)`$ in real proteins. Thus, the question is: “Can we find such $`T`$, so that predicted conservatism profile $`S_{MF}(k)`$ matches the real one $`S_{acr}(k)`$?”

By varying the values of the temperature, $`T`$ in the range $`0.1T4.0`$, we minimize the distance, $`D^2_{k=1}^N(S_{MF}(k)S_{acr}(k))^2`$, between the predicted and observed conservatism profiles. We exclude from this sum such positions in structurally aligned sequences that have more than 50% gaps in the structural (FSSP) alignment. We denote by $`T_{sel}`$ the temperature that minimizes $`D`$.

We study three folds: Immunoglobulin fold (Ig), Oligonucleotide-binding fold (OB), and Rossman fold (R). We compute correlation coefficient  between values of $`S_{MF}(k)`$, obtained at $`T_{sel}`$, and $`S_{acr}(k)`$ for all three folds. The results are summarized in Table I. The plots of $`S_{MF}(k)`$ and $`S_{acr}(k)`$ versus $`k`$ as well as their scatter plots are shown in Figs. 13(a,b).

The correlation between $`S_{MF}(k)`$ and $`S_{acr}(k)`$ is remarkable for all three folds and indicates that our mean field model is able to select the conserved amino acids in protein fold families. It is fully expected that the correlation coefficient is smaller than 1. The reason for this is that computation of $`S_{MF}(k)`$ takes into account evolutionary selection for stability only and it does not take into account possible additional pressure to optimize kinetic or functional properties.

The additional evolutionary pressure due to kinetic or functional importance of amino acids results in pronounced deviations of $`S_{MF}`$ from $`S_{acr}`$ for few amino acids that may be kinetically or functionally important. A number of amino acids whose conservatism is much greater than predicted by our model form a group of “outliers”, from otherwise very close correspondence between $`S_{MF}`$ and $`S_{acr}`$. To demonstrate that some of those amino acids are important for folding kinetics and as such they can be under additional evolutionary pressure, we color data points on $`S_{MF}`$ versus $`S_{acr}`$ scatter plot according to the range of $`\varphi `$-values  that corresponding amino acids fall into. Thermodynamics and kinetic role of individual amino acids was studied extensively (i) by Hamill et al.  for the TNfn3 (1TEN) protein, and (ii) by López-Hernández and Serrano  for the CheY protein. We use the $`\varphi `$-values for individual amino acids obtained in . We observe that (i) for TNfn3 protein most of the points on Fig. 1(b) that belong to the outlier group have $`\varphi `$-values ranging from 0.2 to 1, and (ii) for CheY protein most of the points (for which $`\varphi `$-values are known) on Fig. 3(b) that belong to the outlier have $`\varphi `$-values ranging from 0.3 to 1.

To conclude, we presented a theory that explains sequence conservation caused by the most basic and universal evolutionary pressure in proteins to maintain stability. The theory predicts very well sequence entropy for the majority of amino acids, but not all of them. The amino acids that exhibit considerably higher conservatism than predicted from stability pressure alone are likely to be important for function and/or folding. Comparison of the “base-level” stability conservatism $`S_{MF}(k)`$ with $`S_{acr}(k)`$ \- actual conservatism profile of a protein fold - allows to identify functionally and kinetically important amino acid residues and potentially gain specific insights into folding and function of a protein.

Methods

Protein model

We represent interactions in a protein in a $`C_\beta `$ approximation — each pair of amino acids interact if their $`C_\beta `$s ($`C_\alpha `$ in the case of Gly) are within the contact distance 7.5Å . The total potential energy of the protein can be written as follows:

$$E=\frac{1}{2}\underset{ij}{\overset{N}{}}U(\sigma _i,\sigma _j)\mathrm{\Delta }_{ij},$$
(8)
where $`N`$ is the length of the protein, and $`\sigma _i`$ is the amino acid type at the position $`i=1,\mathrm{},N`$. $`U(\sigma _i,\sigma _j)`$ is the corresponding element of the matrix of pairwise interactions between amino acids $`\sigma _i`$ and $`\sigma _j`$. $`\mathrm{\Delta }_{ij}`$ is the element of the contact matrix that is defined to be 1 if there is a contact between amino acids $`i`$ and $`j`$, and is 0 otherwise.

Six-letter code potential

Due to the similarities in the properties of the 20 types of amino acids one can classify these amino acids into 6 distinct groups: aliphatic $`\{AVLIMC\}`$, aromatic $`\{FWYH\}`$, polar $`\{STNQ\}`$, positive $`\{KR\}`$, negative $`\{DE\}`$, and special (reflecting their special conformational properties) $`\{GP\}`$. We construct the effective potential of interaction, $`U_6(\widehat{\sigma }_i,\widehat{\sigma }_j)`$, between six groups of amino acids, $`\widehat{\sigma }`$, by computing the average interaction between these groups, i. e.

$$U_6(\widehat{\sigma }_i,\widehat{\sigma }_j)=\frac{1}{N_{\widehat{\sigma }_i}N_{\widehat{\sigma }_j}}\underset{\sigma _k\widehat{\sigma }_i,\sigma _l\widehat{\sigma }_j}{}U_{20}(\sigma _k,\sigma _l),$$
(9)
where $`\sigma `$ denotes amino acids in the 20-letter representation, and $`U_{20}(\sigma _k,\sigma _l)`$ is the 20-letter Miyazawa-Jernigan matrix of interaction ; $`\widehat{\sigma }`$ denotes amino acids in the 6-letter representation. $`N_{\widehat{\sigma }}`$ is the number of actual amino acids of type $`\widehat{\sigma }`$, e. g. for the aliphatic group, $`N_{\widehat{\sigma }}=6`$.

We thank R. S. Dokholyan for careful reading of the manuscript and H. Angerman, S. V. Buldyrev, E. Kussell, L. Li, J. Shimada for helpful discussions. NVD is supported by NIH postdoctoral fellowship. EIS is supported by NIH.