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# Inflationary Attractor from Tachyonic Matter

## I Introduction

The study of non-BPS objects such as non-BPS branes, brane-antibrane configurations and spacelike branes has recently attracted great attention given its implications for string/M-theory and cosmology. The tachyon field associated with unstable D-branes, might be responsible for cosmological inflation at early epochs due to tachyon condensation near the top of the effective potential DDD , and could contribute to some new form of cosmological dark matter at late times SEN . Several authors have investigated the process of rolling of the tachyon in the cosmological background GWG ; GS . In the slow roll limit in FRW cosmology, the exact solution of tachyonic inflation with exponential potential is found MPT .

A question which has not yet been addressed in the literature on tachyonic inflation is the issue of constraints on the phase space of initial conditions for inflation which arise when one takes into account the fact that in the context of cosmology the momenta of the tachyon field cannot be neglected in the early universe. For models of the type of chaotic inflation, the work of HAF  shows that most of the energetically accessible field value space give rise to a sufficiently long period of slow roll inflation. However, for models of the type of new inflation, allowing for non-vanishing initial field momenta may dramatically reduce the phase space of initial conditions for which successful inflation results, and the attractor is the slow rolling solution DSG .

In this paper we investigate the constrains on the initial conditions of inflation with tachyon rolling down an exponential potential in phase space required for successful inflation. We demonstrate the attractor behaviour of the tachyonic inflation using the Hamilton-Jacobi formalism. We else use an explicitly numerical computation of the phase space trajectories and obtain analytical approximations to the trajectories of the tachyon in different regions. We find that in phase space there exists a curve that attracts most of the solutions.

## II Tachyonic Matter Cosmology

According to Sen SEN , the effective action of the tachyon field in the Born-Infeld form can be written as

$$S=d^4x\sqrt{g}\left(\frac{1}{2\kappa ^2}R+V(T)\sqrt{1+g^{\mu \nu }_\mu T_\nu T}\right)$$
(1)
where T is the tachyon field minimally coupled to gravity. The rolling tachyon in a spatially flat FRW cosmological model can be described by a fluid with a positive energy density $`\rho `$ and a negative pressure $`P`$ given by

$`\rho `$ $`=`$ $`{\displaystyle \frac{V(T)}{\sqrt{1\dot{T}^2}}},`$ (2)
$`P`$ $`=`$ $`V(T)\sqrt{1\dot{T}^2},`$ (3)
Thus

$$\omega =\frac{P}{\rho }=(1\dot{T}^2)$$
(4)
Note that $`1\omega 0`$, and a universe dominated by this rolling tachyonic matter will smoothly evolve from a phase of accelerating expansion to a phase dominated by a non-relativistic fluid GWG . The evolution equation of the tachyon field minimally coupled to gravity, and the Friedmann equation are

$`{\displaystyle \frac{\dot{\mathrm{\Pi }}}{1\mathrm{\Pi }^2}}+3H\mathrm{\Pi }+{\displaystyle \frac{V^{}(T)}{V(T)}}=0,`$ (5)
$`H^2={\displaystyle \frac{\kappa ^2}{3}}{\displaystyle \frac{V(T)}{\sqrt{1\mathrm{\Pi }^2}}},`$ (6)
where $`\mathrm{\Pi }\dot{T}`$ denotes the velocity of tachyon. A universe dominated by tachyon field would go under accelerating expansion as long as $`\mathrm{\Pi }^2<2/3`$ which is very different from the condition of inflation for non-tachyonic field, $`\dot{\varphi }^2<V(\varphi )`$. The tachyon potential $`V(T)0`$ as $`T\mathrm{}`$, but its exact form is not known at present AAGS . Sen has argued that the qualitative dynamics of string theory tachyons can be described by (1) with the exponential potential SENN

$$V(T)=V_0e^{\alpha T},$$
(7)
where $`\alpha `$ is the tachyon mass. The cosmological aspects of rolling tachyon with exponential potential are investigated MPT . In what follows we will consider (1) with exponential potential in purely phenomenological context without claiming any identification of $`T`$ with the string tachyon field.

## III Inflationary Attractor

The Hamilton-Jacobi formulation SB  is a powerful way of rewriting the equations of motion, which allows an easier derivation of many inflation results. We concentrate here on the homogeneous situation as applied to spatially flat cosmologies, and demonstrate the attractor behaviour of the tachyonic inflation using the Hamilton-Jacobi formalism LPB .

Differentiating Eq.(6) with respect to $`t`$ and substituting in Eq.(5) gives

$$\dot{T}=\frac{2}{3}\frac{H^{}(T)}{H^2(T)}$$
(8)
where primes denote derivatives with respect to the tachyon field $`T`$, which gives the relation between $`T`$ and $`t`$. This allows us to write the Friedmann equation in the first-order form

$$[H^{}(T)]^2\frac{9}{4}H^4(T)=\frac{\kappa ^4}{4}V^2(T)$$
(9)
Eq.(9) is the Hamilton-Jacobi equation. It allows us to consider $`H(T)`$, rather than $`V(T)`$, as the fundamental quantity to be specified. Suppose $`H_0(T)`$ is any solution to Eq.(9), which can be either inflationary or non-inflationary. Add to this a linear homogeneous perturbation $`\delta H(T)`$; the attractor condition will be satisfied if it becomes small as $`T`$ increases. Substituting $`H(T)=H_0(T)+\delta H(T)`$ into Eq.(9) and linearizing, we find that the perturbation obeys

$$H_0^{}\delta H^{}\frac{9}{2}H_0^3\delta H$$
(10)
which has the general solution

$$\delta H(T)=\delta H(T_i)\mathrm{exp}\left(\frac{9}{2}_{T_i}^T\frac{H_0^3(T)}{H_0^{}(T)}𝑑T\right)$$
(11)
where $`\delta H(T_i)`$ is the value at some initial point $`T_i`$. Because $`H_0^{}`$ and $`dT`$ have opposing signs, the integrand within the exponential term is negative definite, and hence all linear perturbations do indeed die away. If there is an inflationary solution, all linear perturbations approach it at least exponentially fast as the tachyon field rolls.

## IV Phase Portrait and Cosmological Evolution

We choose different initial conditions $`T`$, in the range $`T0`$, and $`\mathrm{\Pi }`$ in the range $`0\mathrm{\Pi }1`$ and we obtain the phase portrait in the $`(T,\mathrm{\Pi })`$ plane. Figure 1 shows that there exists a curve that attracts most of the trajectories, in the $`(x,y)`$ plane where $`x=\alpha T`$ and $`y=\mathrm{\Pi }`$ are dimensionless coordinates. The initial kinetic term decays rapidly and does not prevent the onset of inflation.

The behavior of the trajectories can be also analyzed analytically. To understand the evolution of the tachyon field we define two regions $`P`$ and $`K`$ in the $`(T,\mathrm{\Pi })`$ plane as indicated in Figure 2. The region $`P`$ is the region where the potential dominates over the energy density, and the region $`K`$ is the region where the kinetic energy dominates.

Curve $`\mathrm{\Gamma }`$. This curve describes the slow rolling solution where the evolution Eq. (5) and the Friedman Eq.(6) in expanding universe can be approximated by

$`3H\mathrm{\Pi }+{\displaystyle \frac{V^{}(T)}{V(T)}}=0,`$ (12)
$`H^2={\displaystyle \frac{\kappa ^2}{3}}V(T),`$ (13)
from which it follows that

$`\mathrm{\Pi }`$ $`=`$ $`{\displaystyle \frac{\alpha }{3\beta }}e^{\frac{\alpha }{2}T}`$ (14)
$`T`$ $`=`$ $`{\displaystyle \frac{2}{\alpha }}\mathrm{ln}\left({\displaystyle \frac{3\beta }{\alpha }}\mathrm{\Pi }\right)`$ (15)
where $`\beta \sqrt{\kappa ^2V_0/3}`$. The expression for the number $`N`$ of e-foldings of inflation can be written as

$$N=\mathrm{ln}\frac{a_e}{a_b}=\kappa ^2_{T_e}^{T_b}\frac{V^2}{V^{\prime \prime }}𝑑T=\frac{\kappa ^2}{\alpha ^2}V(T)|_{T_e}^{T_b},$$
(16)
where $`T_b`$ is the value of the field at the point where it reaches curve $`\mathrm{\Gamma }`$ and $`T_e`$ is the value of the field at the end of the slow rolling phase. In order to obtain enough e-foldings of slow roll inflation the value of $`T_b`$ for such a trajectory must satisfy

$$0T_b<T_b^{60}$$
(17)
where $`T_b^{60}`$ is calculated from Eq.(16) with $`N=60`$.

Region $`P`$. In this region, the potential dominates over the energy density. The potential force $`V^{}(T)`$ is negligible compared to the friction term since the friction coefficient is proportional to the potential. The evolution Eq.(5) and Friedman Eq.(6) are approximately

$`\dot{\mathrm{\Pi }}+3H\mathrm{\Pi }=0`$ (18)
$`H^2={\displaystyle \frac{\kappa ^2}{3}}V(T)`$ (19)
so that

$`\mathrm{\Pi }`$ $`=`$ $`\mathrm{\Pi }_{pk}{\displaystyle \frac{6\beta }{\alpha }}\left(e^{\frac{\alpha }{2}T_{pk}}e^{\frac{\alpha }{2}T}\right)`$ (20)
$`T`$ $`=`$ $`{\displaystyle \frac{2}{\alpha }}\mathrm{ln}\left[e^{\frac{\alpha }{2}T_{pk}}{\displaystyle \frac{\alpha }{6\beta }}\left(\mathrm{\Pi }_{pk}\mathrm{\Pi }\right)\right]`$ (21)
where $`T_{pk}`$ and $`\mathrm{\Pi }_{pk}`$ are the values at the boundary between region $`P`$ and region $`K`$. Let us now denote by $`T_b`$ and $`\mathrm{\Pi }_b`$ the values of the inflaton and its momentum when the trajectory reaches the slow roll curve.

$$T_b=\frac{2}{\alpha }\mathrm{ln}\left[e^{\frac{\alpha }{2}T_{pk}}\frac{\alpha }{6\beta }\mathrm{\Pi }_{pk}\right]$$
(22)
where we have neglected $`\mathrm{\Pi }_b`$ since it is exponentially smaller than $`\mathrm{\Pi }_{pk}`$. In general the unconventional forms of the tachyonic energy density and pressure make the cosmology with tachyon field differ from that with a normal scalar field, and make it difficult to separate kinetic term from potential term. We assume that $`V(T)`$ and $`V(T)(\frac{1}{\sqrt{(1\dot{T}^2)}}1)`$ are regarded as potential and kinetic term respectively. Therefore, the boundary value between region $`P`$ and region $`S`$ is $`\mathrm{\Pi }_{pk}=\frac{\sqrt{3}}{2}`$. So

$$T_b=\frac{2}{\alpha }\mathrm{ln}\left[e^{\frac{\alpha }{2}T_{pk}}\frac{\alpha }{4\sqrt{3}\beta }\right]$$
(23)
To lead to sufficient inflation, from (17) such initial conditions must satisfy

$$\frac{2}{\alpha }\mathrm{ln}\left[e^{\frac{\alpha }{2}T_{pk}}\frac{\alpha }{4\sqrt{3}\beta }\right]<T_b^{60}$$
(24)
Region $`K`$. It is the region of kinetic energy domination where $`V^{}(T)`$ is negligible compared to the friction term and (5) and (6) become

$`{\displaystyle \frac{\dot{\mathrm{\Pi }}}{1\mathrm{\Pi }^2}}+3H\mathrm{\Pi }=0`$ (25)
$`H^2={\displaystyle \frac{\kappa ^2}{3}}{\displaystyle \frac{V(T)}{\sqrt{1\mathrm{\Pi }^2}}}`$ (26)
These can be integrated and we find:

$`\mathrm{\Pi }_2F_1({\displaystyle \frac{1}{2}},{\displaystyle \frac{3}{4}},{\displaystyle \frac{3}{2}},\mathrm{\Pi }^2)`$ $`=`$ $`\mathrm{\Pi }_{pk2}F_1({\displaystyle \frac{1}{2}},{\displaystyle \frac{3}{4}},{\displaystyle \frac{3}{2}},\mathrm{\Pi }_{pk}^2)`$ (27)
$`{\displaystyle \frac{6\beta }{\alpha }}e^{\frac{\alpha }{2}T}|_T^{T_{pk}}`$
$`T={\displaystyle \frac{2}{\alpha }}\mathrm{ln}\left[e^{\frac{\alpha }{2}T_{pk}}{\displaystyle \frac{\alpha }{6\beta }}\mathrm{\Pi }_2F_1({\displaystyle \frac{1}{2}},{\displaystyle \frac{3}{4}},{\displaystyle \frac{3}{2}},\mathrm{\Pi }^2)|_\mathrm{\Pi }^{\mathrm{\Pi }_{pk}}\right]`$ (28)
where $`{}_{2}{}^{}F_{1}^{}(\frac{1}{2},\frac{3}{4},\frac{3}{2},\mathrm{\Pi }^2)`$ is Gauss hypergeometric function.

## V Conclusions and Discussions

To demonstrate the attractor behaviour of the tachyonic inflation, We use the Hamilton-Jacobi formalism, which greatly simplifies the analysis. Adding to any solution to Eq.(9) a linear homogeneous perturbation, we find the perturbation die away exponentially. The attractor behaviour indicates that, regardless of initial conditions, the late-time solutions are the same up to a time shift, which cannot be measured LMS . We else use an explicitly numerical computation of the phase space trajectories and obtain analytical approximations to the trajectories of the tachyon in different regions. One can easily verify from Figure 1 and Figure 2 that these approximations are in very good agreement with the numerical results, and that the slow rolling solution is the late-time attractor. Although the initial kinetic term decays rapidly and does not prevent the onset of inflation, allowing for non-vanishing initial field momenta around $`T=0`$ may dramatically reduce the phase space of initial conditions for which successful inflation results.

According to the picture of tachyonic inflation, the homogeneous tachyon field near the top of the potential rolls down towards the minimum of the potential at $`T\mathrm{}`$. Tachyonic matter behaves at late time as a pressureless gas of massive particles. In most versions of the theory of reheating, production of particles occurs only when the inflaton field oscillates near the minimum of its effective potential. However, the effective potential of the rolling tachyon does not have any minimum at finite $`T`$, so this mechanism does not work. It is unclear how the universe could be reheated in the framework of tachyon cosmology. Recently, some studies pointed out that as the tachyon evolves into the late-time, the coupling to the closed string becomes more and more large GHY . These results motivate us to expect that the tachyon could emit closed string radiation MGAS ; OY , such as graviton and dilation, into the bulk and eventually settles in the finite minimum.

###### Acknowledgements.

It is a pleasure to acknowledge helpful discussions with G.N.Felder and R.S.Tung. This project was in part supported by NNSFC under Grant Nos. 10175070 and 10047004 as well as also by NKBRSF G19990754.


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# A new perspective on the analysis of helix-helix packing preferences in globular proteins

## Introduction

The issue of the pairwise packing between helices in proteins was addressed soon after helical structures had been suggested. A number of models were developed, mostly devoted to surface complementarities upon packing. The “knobs into holes” model, first introduced by Crick  and elaborated by Richmond and Richards , aimed to find the best steric fit between regular helices. Chothia, Levitt and Richardson  recognized the importance of “ridges” and “grooves” formed by residues with different sequential distances (“ridges into grooves” model). Efimov  tried to relate the packing angle between the two helices with the preferred rotational states of the side-chains along them. A comprehensive analysis was eventually carried out by Walther et. al. , by modeling helix packing as the superposition of the two regular lattices that result from unrolling the helix cylinders onto a plane and contain points representing each residue. The six “preferred” angles predicted by this last model are consistent with earlier results and with the histograms of the experimentally observed packing angles (see Fig. 7 of Ref. ). The agreement between theoretical modeling and experimental data was remarkable, although not perfect (see Ref.  for a more detailed discussion).

The success of steric models in providing an explanation for the most prevalent packing angles was however put under discussion after the observation made by Bowie  that statistical corrections must be applied to the values collected from experimentally determined structures before true interaxial angle preferences can be revealed. Indeed, the helix-helix packing is defined to occur only when:

* \[C1\] the segment of closest approach (SCA), of length $`d_R`$, between the two finite helix axes is shorter than a prefixed threshold $`d_c`$;
* \[C2\] this segment intersects both helix axes at a perpendicular angle.

In Ref. , two helices were considered to be in contact if they were satisfying both conditions $`C1`$ and $`C2`$. Note that Walther et al.  selected interacting helical pairs from their database of native protein conformations, by considering distances between all possible inter-helical heavy atom pairs. We used a different selection procedure involving distances between inter-helical $`C_\alpha `$ atom pairs (see Methods for details). None of these particular choices really affects our geometrical analysis, and condition C1, as defined above, is just the simplest way of defining an equivalent distance constraint.

Condition C2 is needed to ensure face-to-face packing of the two helices, justifying thus the use of theoretical modeling based on the steric interdigitation of the helices.

If the SCA is coincident with the global segment of closest approach (GSCA), of length $`d`$, between the two straight lines which are obtained by indefinitely prolonging the helix axes, condition C2 is then automatically satisfied. In such a situation, which corresponds to effectively dealing with helices of infinite length (see Fig. 1a), the reference probability distribution of interaxial angles $`P(\mathrm{\Omega })`$ is simply the spherical-polar distribution between any two random vectors, namely $`P(\mathrm{\Omega })\mathrm{sin}\mathrm{\Omega }`$ .

Walther and co-workers  realized that the finiteness of helix axes is crucial in modifying the angular dependence of $`P(\mathrm{\Omega })`$, because requiring that the SCA intersects both axes at a perpendicular angle introduces new restrictions depending on the packing angle $`\mathrm{\Omega }`$. This can be understood by looking at Fig. 2a, where it is shown that, fixing one helix position, and assuming the GSCA to be orthogonal to the page, the second finite helix axis may then be placed only within a plane parallel to the paper plane and such that its starting point lies inside the dark shaded parallelogram $`A`$.

The probability of placing the starting point of the second helix in A is proportional to its area and therefore to $`\mathrm{sin}\mathrm{\Omega }`$. Consequently the probability $`P(\mathrm{\Omega })`$ for selecting a particular packing angle is proportional to the product of the spherical-polar contribution and of the $`\mathrm{sin}\mathrm{\Omega }`$ effect due to the finite length condition:

$$P(\mathrm{\Omega })\mathrm{sin}^2\mathrm{\Omega }$$
(1)
With this new random reference distribution the actual angular propensities need to be reconsidered. As is clear from Fig. 2 of Ref. , the normalized frequencies reveal a prominent representation of packing angles near $`0^{}`$ and $`180^{}`$ (not expected by theoretical models) whereas the predicted optimal steric packing angles manifest themselves, at most as shoulders in the distribution of propensities. The predictivity of geometrical models is cast under serious doubts after this analysis.

Our first observation is that the random distribution $`P(\mathrm{\Omega })\mathrm{sin}^2\mathrm{\Omega }`$ is correct only and only if the condition of mutual perpendicularity between the SCA and the two axes is strictly fulfilled. But is this the real situation when statistical histograms are derived?

As a matter of fact, condition $`C2`$ was relaxed by Walther et al., by admitting a small tolerance: a total deviation $`\tau =\tau _1+\tau _2`$ ($`\tau _1`$ and $`\tau _2`$ are the complementary angles to the angles $`\theta _1`$ and $`\theta _2`$ formed between the SCA and helix 1 and helix 2, respectively (see Fig. 1b)) was accepted up to a threshold $`\tau _{\mathrm{max}}`$ ($`\tau _{\mathrm{max}}=5^{}`$ in  and $`\tau _{\mathrm{max}}=1^{}`$ in ).

At first, one might wonder why such a threshold needs to be used since it does not effectively increase the number of data contributing to the histograms. However, we believe that this choice is indeed necessary because of the ambiguity in the definition of the axis direction in natural helices, which introduces an intrinsic uncertainty in the computation of the $`\mathrm{\Omega },\theta ,\tau `$ angles (see Methods for a detailed explanation of how the axis is reconstructed in the typical case of a non-ideal bent helix and for an estimation of such uncertainty $`\overline{\mathrm{\Delta }\mathrm{\Omega }}`$). A relaxation of condition $`C2`$ is thus crucial, if we want to analyse correctly data extracted from the database of real native protein structures.

We will show in this paper, by means of partly semi-analytical geometrical arguments and eventually numerical simulations, that such threshold effect does drastically change the random reference distribution. Having measured helix-helix packing angles from a set of $`600`$ proteins representative of the PDB native structures, we will then reanalyse the packing angle distribution after its proper rescaling with the newly found reference distribution.

## Methods

### Databank and helix pair selection

We employed the same ensemble of 600 proteins considered by Chang et. al , which consisted of sequences varying in length from 44 to 1017, with low sequence homology and covering many different three-dimensional folds according to the Structural Classification of Proteins (SCOP) scheme . The structures were monomeric and determined using x-ray crystallography. We collected $`4397`$ helices each with at least four consecutive residues classified as helical in the PDB files. The average number of residues of these helices was $`11.5`$. Two helices were defined to be in close contact, if at least one interhelical contact between $`C^\alpha `$ atoms was present, with a maximal threshold distance of $`5.5\AA `$ (analogous to condition $`C1`$ in the text). Only helix pairs separated in sequence by at least $`40`$ intervening residues were considered, to get rid of possible correlations induced by short loops. The resulting data set consisted of $`1460`$ closely packed helix pairs.

### Helix axis reconstruction

The reconstruction of the helix axis from the coordinates of the $`C^\alpha `$ atoms of the corresponding residues is a critical step in the determination of packing angle preferences. Since real helices can be bent, we adopted the procedure described by Walther et al. in ref. , in which a local axis is associated to every consecutive residue pair along the helix. The overall axis is thus a broken line consisting of short segments.

A good starting approximation for the local axis $`𝐚_i`$, based on the the four $`C^\alpha `$ atom positions $`𝐫_{i1}`$, $`𝐫_i`$, $`𝐫_{i+1}`$, $`𝐫_{i+2}`$, was introduced by Chothia et al. . We employed a sligthly modified definition, where we first define the normalized bond vectors $`𝐛_i=\left(𝐫_{i+1}𝐫_i\right)/\left|𝐫_{i+1}𝐫_i\right|`$. In this way, the set of three orthonormal vectors $`𝐭_i`$, $`𝐯_i`$, $`𝐮_i`$, the natural reference system associated with the $`C^\alpha `$ atom trace, can be defined without the distortions due to the fluctuations of the bond length between consecutive $`C^\alpha `$ atoms in the following way : $`𝐭_i=\left(𝐛_i+𝐛_{i1}\right)/\left|𝐛_i+𝐛_{i1}\right|`$, $`𝐯_i=𝐛_i\times 𝐛_{i1}/\left|𝐛_i\times 𝐛_{i1}\right|`$, $`𝐮_i=𝐭_i\times 𝐯_i`$. If the $`C^\alpha `$ atom trace followed a perfect ideal helix, the vector $`𝐚_i=𝐮_i\times 𝐮_{i+1}`$ would be parallel to the helix axis. We then initially determined the local axis between residues $`i`$, $`i+1`$, as the vector parallel to $`𝐚_i`$, of length $`1.45\AA `$, which has the geometric centre of the closest four consecutive $`C^\alpha `$ atom positions, $`𝐫_{i1}`$, $`𝐫_i`$, $`𝐫_{i+1}`$, $`𝐫_{i+2}`$, as its midpoint. The two local axes at the helix termini were obtained by simply prolonging the neighbouring ones.

We then applied a smoothing procedure similarly to Walther et al. . The ‘new’ local axes $`𝐚_i`$ were obtained by averaging the direction of the closest three ‘old’ ones, $`𝐚_{i1}`$, $`𝐚_i`$, $`𝐚_{i+1}`$, while conserving its midpoints. For the two local axes at the helix termini we averaged over the direction of the closest two available ones. To ensure the continuity of the overall axis, the inner hinges of the broken axial line were computed as the midpoints between extremities of consecutive local vectors obtained from the running average. After repeating the whole procedure twice, the standard deviation of the distances of each $`C^\alpha `$ atom from the reconstructed helix axis was $`0.16\AA `$.

The interaxial packing angle between two helices was computed bewteen the local axis pair for which the minimum distance of closest approach was achieved. In case the segment of closest approach (SCA) intersected an inner hinge of the broken global axis, the local axis direction was defined as the average of the two corresponding local vectors. The whole discussion concerning the perpendicularity of both local axis direction with the SCA applies only to cases involving a terminal local axis, since face-to-face packing is anyway ensured in case of contact between inner local axes. Packing angles are positive if the background helix is rotated clockwise with respect to the frontal helix when facing them. The angle $`\mathrm{\Omega }=0^{}`$ ($`\mathrm{\Omega }=\pm 180^{}`$) corresponds to parallel (antiparallel) helices with respect to their sequence direction.

Imposing the further requirement that the SCA intersected both local axis directions at a perpendicular angle within a threshold $`\tau _{\mathrm{max}}`$ plays a critical role, as discussed in the text. For the three different $`\tau _{\mathrm{max}}`$ values considered in this work, $`\tau _{\mathrm{max}}=7^{},11^{},15^{}`$, we collected datasets of $`765`$, $`837`$, $`899`$ closely packed helix pairs, respectively.

As a final remark we report the mean value of the angle $`\mathrm{\Delta }\mathrm{\Omega }`$ which is formed between consecutive local directions averaged over all inner hinges of all helical axes which were reconstructed using the procedure discussed above. We found $`\overline{\mathrm{\Delta }\mathrm{\Omega }}=6.7^{}\pm 4.0^{}`$, strongly supporting the necessity of allowing a similar threshold when imposing angular constraints as in condition $`C2`$.

## Results and Discussion

### Geometrical analysis

We will now sketch the geometrical consequences of relaxing condition $`C2`$ within a given threshold, in order to understand by means of a simple argument how this effects the random reference distribution. A comprehensive analytical treatment is in principle feasible but quite cumbersome. Numerical simulation will ultimately be the preferential approach to extract the corrected random reference distribution for interaxial angles.

Within the admitted threshold $`\tau _{\mathrm{max}}`$, cases similar to the one described in Fig. 1b may now occur. The SCA between the two helices, which intersects helix 1 at one of its axis ends and helix 2 at some internal point, forms an angle $`\theta _1`$ which deviates from $`\frac{\pi }{2}`$ by less than $`\tau _{\mathrm{max}}`$, whereas the GSCA does not intersect both helices (in this situation $`\tau _10,\tau _2=0`$). If $`d<d_c`$, the two helices are considered to be in contact. The condition $`\tau _1<\tau _{\mathrm{max}}`$ is equivalent to the condition that GSCA intersects helix 1 within a distance $`\mathrm{\Delta }l_{\mathrm{max}}`$ from the end of its axis. This limit is reached when $`\theta _1=\theta _{\mathrm{min}}\frac{\pi }{2}\tau _{\mathrm{max}}`$.

There are also cases in which $`\tau _1=0`$ and $`\tau _20`$, when the SCA intersects helix 2 at one of its axis ends and helix 1 at some internal point, and cases in which both $`\tau _1`$ and $`\tau _2`$ are not zero, and the SCA intersects both helices at one of their axes ends (Fig. 1c). In this last case, the geometrical condition implied by $`\tau _1+\tau _2<\tau _{\mathrm{max}}`$, and involving the distances $`\mathrm{\Delta }l_1`$, $`\mathrm{\Delta }l_2`$ from the end of both helix axes to their intersection with the GSCA, is more complicated (and is discussed in the caption of Fig. 1).

Using the visual representation of Fig. 2b, we can say that allowing condition $`C2`$ to be satisfied within the threshold $`\tau \tau _1+\tau _2<\tau _{\mathrm{max}}`$, opens up the possibility for the starting point of helix 2 to lie in the portion of space ($`𝒢`$) formed by the four lightly shaded parallelograms (two parallel to helix 1 with sides $`h_1`$ and $`\mathrm{\Delta }\mathrm{\Delta }l_{\mathrm{max}}\mathrm{sin}\mathrm{\Omega }`$, and two parallel to helix 2 with sides $`h_2`$ and $`\mathrm{\Delta }`$) and by the four remaining white corner regions ( whose boundaries are defined by hyperboles, see Figure 2 caption for details), which surround parallelogram $`A`$.

To compute the area of $`𝒢`$ is not trivial, because of the hyperbole-shaped regions, but the result is obviously $`\mathrm{\Omega }`$ dependent. For example a simple trigonometric calculation shows that:

$$\mathrm{\Delta }=\{\begin{array}{cc}\frac{d\mathrm{sin}\tau _{\mathrm{max}}}{\sqrt{\mathrm{sin}^2\mathrm{\Omega }\mathrm{sin}^2\tau _{\mathrm{max}}}}& \left|\mathrm{sin}\mathrm{\Omega }\right|>\mathrm{sin}\tau _{\mathrm{max}}\hfill \\ \mathrm{}& \left|\mathrm{sin}\mathrm{\Omega }\right|\mathrm{sin}\tau _{\mathrm{max}}\hfill \end{array}$$
(2)
This implies that the area of $`𝒢`$ diverges for $`\left|\mathrm{sin}\mathrm{\Omega }\right|\mathrm{sin}\tau _{\mathrm{max}}`$, which already points towards the fact that relevant corrections are possible even for small values of $`\tau _{\mathrm{max}}`$.

To conclude our analysis we need to enforce also condition $`C1`$. By using the pythagorean theorem it is easy to see that for any fixed $`d<d_c`$, $`C1`$ is satisfied for any point (thought as starting point of helix 2) whose distance $`\mathrm{\Delta }s(d_R)=\sqrt{d_R^2d^2}`$ from parallelogram $`A`$ is less than $`\mathrm{\Gamma }=\mathrm{\Delta }s(d_c)=\sqrt{d_c^2d^2}`$. These points belong to the region $`𝒢^{}`$, shown in Fig. 2c, formed by the 4 parallelograms (two of sides $`h_1`$ and $`\mathrm{\Gamma }`$ and two of sides $`h_2`$ and $`\mathrm{\Gamma }`$) and the four circular sectors (of radius $`\mathrm{\Gamma }`$) surrounding A. The area of $`𝒢^{^{}}`$ is independent on $`\mathrm{\Omega }`$ (see caption of Fig. 2c).

All the points in the portion of space $`=𝒢𝒢^{^{}}`$ resulting from the intersection of $`𝒢`$ and $`𝒢^{^{}}`$ satisfy both condition $`C1`$ and $`C2`$.

Therefore, the probability $`P^{\tau _{\mathrm{max}}}(d)`$ of selecting a particular angle $`\mathrm{\Omega }`$ with a tolerance $`\tau _{\mathrm{max}}`$, at a given distance $`d<d_c`$, is given by the product of the spherical polar term $`\mathrm{sin}\mathrm{\Omega }`$  and a term proportional to the area of parallelogram $`A`$ plus the area of $``$.

When $`|\mathrm{sin}\mathrm{\Omega }|<\mathrm{sin}\tau _{\mathrm{max}}`$, Eq.2 shows that $`\mathrm{\Delta }`$ diverges and thus:

$$P^{\tau _{\mathrm{max}}}(d)\mathrm{sin}\mathrm{\Omega }\left(h_1h_2\mathrm{sin}\mathrm{\Omega }+2(h_1+h_2)\mathrm{\Gamma }+B\right)$$
(3)
where $`B`$ is the area of the corner regions in $``$.

Since $`\mathrm{\Gamma }`$ does not depend on $`\mathrm{\Omega }`$, the second term in the bracket will eventually dominate the small $`|\mathrm{sin}\mathrm{\Omega }|`$ behaviour of $`P^{\tau _{\mathrm{max}}}(d)`$. In practice, the actual relevance of this effect can be appreciated only after integrating $`P^{\tau _{\mathrm{max}}}(d)`$ over $`d`$, since the relative weights of the different terms in the bracket vary with $`d`$. Such computation is quite cumbersome and we have rather chosen to get $`P^{\tau _{\mathrm{max}}}`$ by simulating random helices which satisfy the contact conditions within a threshold $`\tau _{\mathrm{max}}`$, and to extract numerically the normalized histograms.

### Numerical simulations

In order to compute the reference distribution $`P^{\tau _{\mathrm{max}}}\left(\mathrm{\Omega }\right)`$ for interaxial packing angles we generated random helix pairs by means of computer simulations, and then selected them with the same conditions, $`C1`$ and $`C2`$, used in extracting histograms from real helices in native protein structures. Note that when computing the reference distribution we did not take steric effects into account; in other words random helices might overlap.

More specifically, we constructed ideal discretized helices with the same geometrical properties of $`\alpha `$-helices in real proteins, i.e. twist per residue $`99.1^{}`$, rise per residue $`1.45\AA `$, radius $`2.3\AA `$ (as is the case when considering $`C_\alpha `$ atoms). We chose to generate helices consisting of $`11`$ residues, the average length in the dataset of real helices that we collected from the PDB. Keeping fixed the position of the first helix, the second helix was placed by firstly choosing randomly the midpoint of its axis within a sphere of radius $`15\AA `$ centred in the midpoint of the first helix axis, and then selecting, again randomly, both the direction of its axis and the twist of its first residue.

Boundary effects might be relevant, when the radius of the sphere in which the second helix is generated is too small with respect to the helix length and helix finiteness is effectively reduced. We made sure that our results did not change when increasing the radius of the sphere in which the second helix axis is placed.

We generated $`510^7`$ random helix pairs, $`29915472`$ out of which satisfied condition $`C1`$ of having at least one pair of residues distant less then $`5.5\AA `$. Condition $`C2`$ was then applied, in the same way as explained in Methods for the real helices data set, with the whole axis being now a segment in the ideal case. In this way we generated $`11467456`$, $`13033815`$, $`14553626`$ helix pairs, respectively, for the three different $`\tau _{\mathrm{max}}`$ values considered in this work, $`\tau _{\mathrm{max}}=7^{},11^{},15^{}`$.

In Fig. 3 we plot the corresponding random reference distributions $`P^{\tau _{\mathrm{max}}}\left(\mathrm{\Omega }\right)`$, comparing them with the ideal ($`\tau _{\mathrm{max}}=0`$) case: $`P(\mathrm{\Omega })\mathrm{sin}^2\mathrm{\Omega }`$. The difference, although due to a very subtle effect is substantial, and it is clearly seen that a new regime is present for $`|\mathrm{sin}\mathrm{\Omega }|<\mathrm{sin}\tau _{\mathrm{max}}`$, as expected from the previous discussion.

### Reanalysing experimental results

To test the effect of this new reference distribution we have recomputed an experimental distribution of interaxial angles (see Methods for details) by analysing a databank of 600 proteins and using a contact threshold $`d_c=5.5\AA `$ and a tolerance $`\tau _{\mathrm{max}}=7^{}`$, corresponding the intrinsic uncertainty $`\overline{\mathrm{\Delta }\mathrm{\Omega }}=6.7^{}`$ estimated when determining local axis directions (see Methods). The histogram is reported in the upper panel of Fig. 4: in order to obtain good statistics for each single bin, we gathered results every $`15^{}`$. The histogram is consistent with previous analysis . In the middle panel of Fig. 4 we plot $`P^7^{}(\mathrm{\Omega })`$ and, for reference, $`P(\mathrm{\Omega })`$ normalized with the same binning as in the previous panel. Finally, in the lower panel of Fig. 4 we present the histogram both rescaled with $`P^7^{}(\mathrm{\Omega })`$ and with $`P(\mathrm{\Omega })`$. The results are clear and striking: the correct distribution $`P^7^{}(\mathrm{\Omega })`$ removes the spurious peaks at $`0^{}`$ and $`\pm 180^{}`$, whereas $`4`$ out of the $`6`$ predicted packing angles  arise as clean local maxima in the expected positions. Only two of the predicted packing angles are clearly not favoured according to our analysis. Remarkably, the two peaks theoretically predicted at $`143.9^{}`$ and $`158^{}`$, that were seen as shoulders in the unrescaled histogram, are instead placed in the correct position (within binning uncertainty) in the rescaled histogram. We also note that a residual preference for parallel and antiparallel alignment of two contacting helices cannot be ruled out even after proper rescaling. Because of small statistics, it is difficult to ascertain whether this is a genuine effect or is just due to the tail superposition of different preferential angle peaks. In order to further test both the robustness of the results and the full procedure we have obtained statistical histograms from the experimental data using three different thresholds, $`\tau _{\mathrm{max}}`$. Since we can compare them with the corresponding random distribution we should expect three similar rescaled histograms. This is nicely confirmed by Fig. 5, where the three rescaled histograms show a very good overlap, within the statistical uncertainty. We also note that generally, the greater the threshold used to relax condition $`C2`$, the more blurred the peaks corresponding to the sterically preferred angles. This confirms that condition $`C2`$ is needed to ensure face-to-face packing and the applicability of steric models.

## Conclusion

In this paper we have shown that the calculation of the probability distribution of interaxial angles between random finite helices which are in contact is not a trivial geometric problem, because of the approximations introduced to ensure face-to-face packing between contacting helices. Such approximations are unavoidable, due to the imperfect shape of natural occurring helices which do not have well defined axes. Although analytical results can be found to estimate the correct random distribution, the simplest way to obtain it consists in using numerical simulations. We have presented a re-analysis of the distribution of packing angles rescaled with our new reference distribution and we have found a remarkable agreement with the packing angles predicted by steric models .

## Acknowledgments

We are indebted to Amos Maritan for stimulating discussions and advice, Giuseppe Zanotti for helpful suggestions and Iksoo Chang for his invaluable help in providing us with the protein databank used in ref. . We thank Harvey Dobbs for a critical reading of the manuscript. This work was supported by INFM, MIUR COFIN-2001 and FISR 2002.

## Figure Legends

### Figure 1

a) The global segment of closest approach (GSCA), of length $`d`$, between two straight lines is, by definition, perpendicular to both of them. The segment of closest approach (SCA), of length $`d_r`$, between two helices (schematically represented by cylinders) surely coincides with the global one if it intersects both helices within their axis length. This fact is always guaranteed if the two helices are assumed to have infinite length (hypothesis of Ref. ).

b) The two finite helices have a SCA that is not coincident with the GCSA. The latter intersects helix 1 at a distance $`\mathrm{\Delta }l_1`$ from its end and may (as in the picture) or may not intersect helix 2. The former joins the end point of helix 1 to a point inside helix 2. The angle formed with helix 1 ($`\theta _1`$) is deviating from $`\pi /2`$ by an amount $`\tau _1`$. Instead $`\theta _2=\frac{\pi }{2}`$ and $`\tau _2=0`$. The trigonometric relation expressing $`\mathrm{\Delta }l_1`$ as an increasing function of $`\tau _1`$ can be easily obtained: $`\mathrm{\Delta }l_1(\tau )=\frac{d\mathrm{sin}\tau _1}{\mathrm{sin}\mathrm{\Omega }\sqrt{\mathrm{sin}^2\mathrm{\Omega }\mathrm{sin}^2\tau _1}}`$. When $`\tau _1<\tau _{\mathrm{max}}`$, condition $`C2`$, defined in the text, is still fulfilled. This is equivalent to require that $`\mathrm{\Delta }l_1\mathrm{\Delta }l_{\mathrm{max}}\mathrm{\Delta }l_1(\tau _{\mathrm{max}})`$. Notice that $`\mathrm{\Delta }l_1(\tau _1)`$ diverges when $`\tau _1`$ approaches $`\mathrm{\Omega }`$ from below, and consequently, when $`\left|\mathrm{sin}\mathrm{\Omega }\right|<\mathrm{sin}\tau _{\mathrm{max}}`$, $`\mathrm{\Delta }l_{\mathrm{max}}`$ diverges. In such regime the condition C2 (but obviously not C1 because $`d_r`$ may also diverge) is always satisfied within the allowed tolerance. A similar situation and a similar analysis can be done for $`\tau _1=0`$ and $`\tau _20`$.

c) GSCA is neither intersecting helix 1 nor helix 2 and the SCA is joining two endpoints. In the case depicted in the figure the two helices are placed in opposite sides with respect to the GSCA. The threshold condition $`\tau _1+\tau _2<\tau _{\mathrm{max}}`$ may be translated into the following one involving $`\mathrm{\Delta }l_1`$ and $`\mathrm{\Delta }l_2`$: $`((\mathrm{\Delta }l_1+\mathrm{\Delta }l_2\mathrm{cos}\mathrm{\Omega })(\mathrm{\Delta }l_2+\mathrm{\Delta }l_1\mathrm{cos}\mathrm{\Omega })\sqrt{(d^2+\mathrm{\Delta }l_1^2\mathrm{sin}^2\mathrm{\Omega })(d^2+\mathrm{\Delta }l_2^2\mathrm{sin}^2\mathrm{\Omega })})`$ $`/`$ $`((\mathrm{\Delta }l_1+\mathrm{\Delta }l_2\mathrm{cos}\mathrm{\Omega })\sqrt{d^2+\mathrm{\Delta }l_1^2\mathrm{sin}^2\mathrm{\Omega }}+(\mathrm{\Delta }l_2+\mathrm{\Delta }l_1\mathrm{cos}\mathrm{\Omega })\sqrt{d^2+\mathrm{\Delta }l_2^2\mathrm{sin}^2\mathrm{\Omega }})>\mathrm{cot}\tau _{\mathrm{max}}`$. Situations in which the two helices are placed on the same side with respect to the GSCA are also possible. In this case the condition becomes $`((\mathrm{\Delta }l_1\mathrm{\Delta }l_2\mathrm{cos}\mathrm{\Omega })(\mathrm{\Delta }l_2\mathrm{\Delta }l_1\mathrm{cos}\mathrm{\Omega })\sqrt{(d^2+\mathrm{\Delta }l_1^2\mathrm{sin}^2\mathrm{\Omega })(d^2+\mathrm{\Delta }l_2^2\mathrm{sin}^2\mathrm{\Omega })})`$ $`/`$ $`((\mathrm{\Delta }l_1\mathrm{\Delta }l_2\mathrm{cos}\mathrm{\Omega })\sqrt{d^2+\mathrm{\Delta }l_1^2\mathrm{sin}^2\mathrm{\Omega }}+(\mathrm{\Delta }l_2\mathrm{\Delta }l_1\mathrm{cos}\mathrm{\Omega })\sqrt{d^2+\mathrm{\Delta }l_2^2\mathrm{sin}^2\mathrm{\Omega }})>\mathrm{cot}\tau _{\mathrm{max}}`$.

### Figure 2

a) In this figure, the position of helix 1 (represented by a vector of length $`h_1`$) and a vector orthogonal to the paper plane, determining the direction of the GSCA to a second helix, are fixed. Given a particular packing angle $`\mathrm{\Omega }`$, in order to satisfy condition C2 without any tolerance $`\tau _{\mathrm{max}}`$, a second finite helix axis (of length $`h_2`$) may then be placed only within a plane parallel to the paper plane and such that its starting point is inside the dark shaded parallelogram $`A`$, Otherwise the SCA between the two finite axes would no longer be perpendicular to both of them. The area of parallelogram $`A`$ is $`h_1h_2\mathrm{sin}(\mathrm{\Omega })`$.

b) The tolerance $`\tau _{\mathrm{max}}`$ with which the condition of perpendicularity between the SCA and the two helices is implemented enlarges the portion of space where the starting point of helix 2 can be placed. The region $`𝒢`$ formed by the four lightly shaded parallelograms and the four white corner regions, which together surround parallelogram $`A`$, can now be exploited. The two parallelograms parallel to helix 2, whose sides are $`h_2`$ and $`\mathrm{\Delta }=\mathrm{\Delta }l_{\mathrm{max}}\mathrm{sin}\mathrm{\Omega }`$, are due to the geometric arrangement described in Fig. 1b with $`\tau _10`$ and $`\tau _2=0`$ (the vector with the dashed starting point represent the possible location of helix 2 in such context). The two other parallelograms, parallel to helix 1, with sides $`h_1`$ and $`\mathrm{\Delta }`$, correspond to the similar case $`\tau _1=0`$ and $`\tau _20`$. The four remaining white regions, corresponding to the case $`\tau _10`$ and $`\tau _20`$, are all limited by hyperbola-like curves. The two of them subtending an obtuse angle are due to the geometric arrangement described in Fig. 1c, corresponding to the two helices being placed in opposite sides with respect to the GSCA (the vector with the white starting point represent the possible location of helix 2 in such context). The two of them subtending an acute angle correspond to the two helices being placed in the same side with respect to the GSCA. In both cases it is possible to find the equation describing such boundary curves, which we omit here for the sake of simplicity. The area of $`𝒢`$ is $`2(h_1+h_2)\mathrm{\Delta }`$ plus a non trivial contribution coming from the four corner regions.

c) The distance constraint C1 limits by itself the portion of plane surrounding parallelogram $`A`$ where the starting point of the second helix can be placed. This region $`𝒢^{^{}}`$ is simply the locus of points whose Euclidean distance from $`A`$ in the paper plane is less than $`\mathrm{\Gamma }\sqrt{d_c^2d^2}`$. For given values of $`d`$ and the distance threshold $`d_c`$, this region is thus formed by the four lightly shaded parallelograms and by the four white circular sectors. The area of $`𝒢^{^{}}`$ is $`2(h_1+h_2)\mathrm{\Gamma }+\pi \mathrm{\Gamma }^2`$.

### Figure 3

Ideal ‘random’ distribution of interaxial packing angles for four different values of the angle threshold $`\tau _{\mathrm{max}}`$ used in applying condition $`C2`$; $`\tau _{\mathrm{max}}=0^{}`$ (upper left panel), $`\tau _{\mathrm{max}}=7^{}`$ (upper right panel), $`\tau _{\mathrm{max}}=11^{}`$ (lower left panel), $`\tau _{\mathrm{max}}=15^{}`$ (lower right panel). The four distributions were computed by means of numerical simulations described in Methods. Since ideal helices do not have a preferential order, the histograms show in this figure have been restricted to the $`90^{}<\mathrm{\Omega }<90^{}`$ region. The $`14553626`$ packing angle values collected in the $`\tau _{\mathrm{max}}=15^{}`$ histogram were then successively filtered out by the more and more restrictive $`\tau _{\mathrm{max}}=11^{}`$, $`\tau _{\mathrm{max}}=7^{}`$, $`\tau _{\mathrm{max}}=0^{}`$ threshold conditions to generate the $`13033815`$, $`11467456`$, $`8646994`$ data, respectively, collected in the corresponding histograms. The dashed line is the fit of the $`\tau _{\mathrm{max}}=0^{}`$ data, obtained enforcing condition $`C2`$ in a strict way, to the expected $`P(\mathrm{\Omega })\mathrm{sin}^2\mathrm{\Omega }`$ distribution, which is then reported for comparison in all other histograms. All histograms were constructed with a bin width of $`1.5^{}`$. Histograms are normalized in such a way that a flat distribution would correspond to a constant $`1`$ height.

### Figure 4

Upper Panel. Experimental ‘bare’ unrescaled distribution of interaxial packing angles between contacting helices. Data were obtained with a distance threshold $`d=5.5\AA `$ for interhelical $`C_\alpha `$ atom pairs and an angular threshold $`\tau _{\mathrm{max}}=7^{}`$ for condition $`C2`$. The histogram is normalized in such a way that a flat distribution would correspond to a constant $`1`$ height.

Middle Panel. Ideal ‘random’ distribution which have to be used to rescale the ‘bare’ experimental distribution, in order to reveal true packing angle preferences. The two different distributions obtained with either $`\tau _{\mathrm{max}}=0^{}`$ (thick line) or $`\tau _{\mathrm{max}}=7^{}`$ (filled columns) are shown. Histograms are normalized in such a way that a flat distribution would correspond to a constant $`1`$ height.

Lower Panel. Rescaled distribution of interaxial packing angles. The experimental ‘bare’ distribution in the upper panel is divided by the ideal ‘random’ one in the middle panel, obtained with either $`\tau _{\mathrm{max}}=0^{}`$ (blue line) or $`\tau _{\mathrm{max}}=7^{}`$ (filled columns). Histogram heights greater than $`1`$ correspond to preferential packing angles, whereas heights lower than $`1`$ correspond to disfavoured packing angles.

All histograms were constructed with a bin width of $`15^{}`$. Arrows in the upper and lower panels mark the values of the six preferred packing angles predicted by Walther et al. ; $`\mathrm{\Omega }_{\mathrm{abc}}=37.1^{},97.4^{},22.0^{}`$, each represented twice with a periodicity of $`180^{}`$.

### Figure 5

Rescaled distribution of interaxial packing angles between contacting helices for three different values of the angle threshold $`\tau _{\mathrm{max}}`$ used in enforcing condition $`C2`$; $`\tau _{\mathrm{max}}=7^{}`$ (light grey filled columns), $`\tau _{\mathrm{max}}=11^{}`$ (dark grey line), $`\tau _{\mathrm{max}}=15^{}`$ (black line). Each histogram was obtained by dividing the experimental unrescaled distribution by the corresponding ideal reference one (we used the three distributions represented in Fig. 3 with a different binning). All histograms were constructed with a bin width of $`15^{}`$. Note that the histograms are not normalized, being computed as the ratio of two normalized histograms. The arrows mark the values of the the six optimal packing angles predicted by Walther et al. .

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5


text:
# Evidence for Hydro-Gravitational Structure Formation Theory versus Cold-Dark-Matter, Hierarchical-Clustering, and Jeans 1902

## 1 Introduction

Observations are accumulating about the early universe and the interstellar medium that challenge the standard models of cosmology, galaxy formation, star formation, planet formation and comet formation. For many years no data were available to contradict the Jeans 1902 gravitational structure formation criterion that in a gas of uniform density $`\rho `$, gravitational condensation cannot occur on scales smaller than $`L_J`$ where

$$L_JV_S/(\rho G)^{1/2}(p/\rho ^2G)^{1/2}(RT/\rho G)^{1/2}L_{JHS},$$
(1)
$`G`$ is Newton’s gravitational constant, $`R=k/m`$ is the gas constant, $`k`$ is Boltzmann’s constant, $`m`$ is the gas particle mass, and $`T`$ is the temperature. Because $`V_S(p/\rho )^{1/2}(RT)^{1/2}`$ is $`V_S`$ for an ideal gas, Jeans 1902 and others have assumed that the Jeans acoustic scale $`L_J`$ defined on the left and the Jeans hydrostatic scale $`L_{JHS}`$ defined on the right of (1) are equivalent. They are not. It has been shown that the Jeans criterion is unreliable (Gibson, 1996): non-acoustic density fluctuations are absolutely unstable to structure formation. Hydrostatic equilibrium is achieved only at small scales $`L_{JHS}`$ determined by the largest viscous, turbulent, or diffusive Schwarz scale (Table 1) of HGT and various planetary and star formation processes that are induced at positive non-acoustic nuclei, with $`L_JL_{JHS}`$. Using viscous forces, turbulent forces and diffusion it was shown from HGT-cosmology that the baryonic dark matter is dominated by small frozen planets ($`10^6M_{\mathrm{}}`$ primordial fog particles, or PFPs) that fragmented by self gravity at the plasma to gas transition 300,000 years after the big bang, $`\mathrm{\S }2`$. This theoretical prediction was immediately and independently supported by observations of twinkling frequencies of a lensed quasar, suggesting the lensing galaxy mass is dominated by rogue planets “likely to be the missing mass” (Schild, 1996). The Gibson $`\&`$ Schild 1996 prediction and observational demonstration that the baryonic dark matter is primordial micro-brown-dwarfs has since been confirmed by independent observations in the same and other lensed quasars, and by other observational evidence, $`\mathrm{\S }3`$.

HGT describes the formation of structure by self-gravitational condensations and rarefactions for cosmology, astrophysics and astronomy. The first gravitational structures to form were proto-supercluster-voids in the plasma epoch by fragmentation at 30,000 years after the big bang when viscous and weak turbulent forces first matched gravity forces at the horizon scale $`L_H`$, followed by proto-cluster-voids and proto-galaxy-voids filled with the weakly collisional non-baryonic-dark-matter (NBDM) by diffusion (Gibson, 2000). Cold dark matter condensations (CDM-halos) are excluded by HGT for scales smaller than $`L_{SD}L_H`$ in the plasma epoch, and are not necessary to make structure in the gas epoch (after 300,000 years) by hierarchical-clustering-cosmology (HCC), which is also excluded by HGT. Gravitational clustering of collisionless CDM-halos would produce steep core cusps in galaxies that are not observed (Sand et al., 2002). The most distant galaxies observed are clustered (Steidel et al., 2000) and the closest clusters observed are fragmenting (Gibson & Schild 2003c, ), contrary to HCC. The early clusters predicted by HGT serve as gravitational lenses and produce arcs and multiple arcs of background galaxies at high rates of incidence that contradict all the flat-CDM cosmologies by orders of magnitude (Bartelmann et al., 1998). It is necessary to invent special “super-lensing” clusters to explain the multiple arcs observed in the recent Red-Sequence Cluster Survey and other studies, which would otherwise exclude the presently popular flat-$`\mathrm{\Lambda }`$CDM cosmology by orders of magnitude (Gladders et al., 2003). Drag forces from the expansion of the universe rapidly separated proto-galaxies and helped fragment proto-galaxy-clusters at the plasma-gas transition (Gibson 1999a, ), making galaxy mergers quite rare rather than mandatory as in HCC, and explaining alignments of bright central supercluster galaxies with background QSOs by perspective that otherwise would confute CDMHCC, the big bang, and standard physics (Hoyle et al., 2000) without HGT (Gibson & Schild 2003a, ). Two of these rare galaxy mergers were imaged by the new HST/ACS wide angle camera in the Tadpole complex VV29abcdef (Gibson & Schild 2003b, ) and in Mice, showing star trails of young-globular-clusters (YGCs) produced as star formation is triggered from PGC-PFPs by the mergers of galaxies and their baryonic-dark-matter (BDM) halos. High resolution wide angle images by HST/ACS in the Helix planetary nebula and other nearby PNe in the Galaxy support the HGT prediction that galaxy disks are formed by accreted PGCs, and that the ISM has the high primordial PGC-PFP density fossilized at the time of first structure and expected in star forming regions (Gibson & Schild 2003c, ).

From HGT, density perturbations $`\delta \rho (t)`$ on scales $`L<L_J`$ in a uniform density gas are absolutely unstable to the formation of gravitational structure, and grow or decrease exponentially with time depending on the sign of the perturbation (see Reyden 2003 $`\mathrm{\S }12.1`$ but ignore $`\mathrm{\S }12.2`$). Let $`\rho (t)=\rho +\delta \rho (t)`$ inside a sphere of radius $`\stackrel{}{r}`$ and constant $`\rho `$ outside, where $`\delta \rho (0)=\delta \rho (t=0)`$ and $`L_C|\stackrel{}{r}|L_J`$ with $`L_C`$ the particle collision length. As correctly shown in $`\mathrm{\S }12.1`$, self gravitation causes the density perturbation to either increase in magnitude and shrink in size (gravitational condensation, $`\delta \rho (t)=\delta \rho (0)exp(t\sqrt{[4\pi G\rho ]})`$, with $`\delta \rho (0)>0`$), or increase in magnitude and grow in size (gravitational void formation, $`\delta \rho (t)=\delta \rho (0)exp(t\sqrt{[4\pi G\rho ]})`$, with $`\delta \rho (0)<0`$). Non-acoustic density fluctuations are absolutely unstable to self-gravitational formation of structure, just as shear layers are absolutely unstable to the formation of turbulence due to inertial-vortex forces $`\stackrel{}{v}\times \stackrel{}{\omega }`$, where $`\stackrel{}{v}`$ is velocity and $`\stackrel{}{\omega }`$ is vorticity (Gibson 1999b, ). Both processes are highly non-linear so neither can be reliably described by linear perturbation stability analysis, and both couple very large scales to very small scales so they are difficult to simulate numerically. It is stated without proof in $`\mathrm{\S }12.2`$ (Reyden, 2003) that pressure will prevent the exponential growth of density perturbations on length scales $`LL_J`$. This is not true. The idea that “pressure support” or “thermal support” prevents structure formation on scales smaller than $`L_J`$ is an unfortunate legacy of the erroneous Jeans 1902 criterion for structure formation.

The time $`t_S`$ required for pressure waves (sound) to move a distance $`L`$ is $`t_S=L/V_S`$, where $`V_S`$ is the speed of sound. For $`t_S=t_{FF}(G\rho )^{1/2}`$, $`L=L_J`$, so $`p0`$ for $`|\stackrel{}{r}|L_J`$ and $`t_Stt_{FF}`$. Density perturbations $`\delta \rho (rr_0,t=0)`$ of size $`r_0`$ grow to large values for $`tt_{FF}`$ as we have seen. Pressure forces have the wrong sign to resist gravitational condensation except near the gravitational stagnation point because they arise from Bernoulli’s equation, where $`p/\rho +v^2/2constant`$. Pressure forces overcome condensational self gravitational forces $`G\rho \delta \rho L`$ on scales $`L_{JHS}<r_0L_J`$ only at late stages in a collapse ($`\delta \rho >0`$) due to local irreversible processes (eg: turbulence stresses, viscous heating, condensation of the gas to liquid form, freezing of the liquid, star formation), and have no effect on small scale self gravitational void formation forces ($`\delta \rho <0`$) until the void size reaches $`L_J`$. The maximum speed of void growth is the maximum speed of a rarefaction wave, which is the speed of sound. Self-gravity has the effect of a negative density diffusivity $`D_{\rho G}(L)L^2(\rho G)^{1/2}`$ in the vicinity $`LL_{SD}`$ (see Table 1 and $`\mathrm{\S }2`$) of a non-acoustic density maximum or density minimum, with the resulting absolute instability.

High resolution numerical simulations of stagnant gas show fragmentation and condensation at scales smaller than the Jeans scale, but in calculations to date these have been systematically filtered out as numerical artifacts (Truelove et al., 1997). The authors assume that pressure support or thermal support prevent sub-Jeans-scale self-gravitational condensations and fragmentations in astrophysical fluids and adjust their numerical simulations to conform to these assumptions.

The large gassy Jovian planets beyond Mars in the solar system are a mystery from the Jeans criterion because they violate the Jeans limit $`M_J0.1M_{\mathrm{}}`$ (Larson, 1985). If we compute the Jeans mass $`M_J=L_J^3\rho `$ and solve for the Jeans temperature $`T_J`$ we find

$$T_JM_J^{2/3}\rho ^{1/3}GR^1,$$
(2)
where $`R=8314/M_{mol}`$ m2 s-2 K-1 is the gas constant and $`M_{mol}`$ is the gas molecular weight. Substituting a primordial H-He gas constant $`R_{PM}3612`$ m2 s-2K-1 and the primordial (first structure) gas density $`\rho =10^{17}`$ kg m-3 for Jupiter mass $`10^{27}`$ kg with $`G=6.7\times 10^{11}`$ m3 kg-1 s-2 gives a Jeans temperature $`T_J3.9\times 10^2`$ K that is impossibly cold. Why are Jupiter, Saturn, Uranus and Neptune all contrary to the Jeans limit? Numerous extra-solar planets with Jupiter mass have now been detected that must also be composed of H-He gas. How are these possible? How are rocky planets possible? How are rocks possible? All are impossible by the Jeans criterion, and all are easily explained by HGT, $`\mathrm{\S }2`$. According to HGT, all large planets are formed by a hierarchical clustering of PFPs to form Jovian-PFP-Planets (JPPs) and all stars are formed by further accretion of PFP-JPPs and from their fragments and gas formed by the close proximity to the proto-star. Dust from supernovas is collected by numerous PFP-JPPs in the ISM and turned into rocks near their cores and the cores of the numerous large planets and brown dwarfs (JPPs) formed as the PFPs accrete. Multiple hydrogen freeze-thaw cycles of wandering PFP-JPPs produces many crushing central pressure episodes and layerings. Rocky planets like Earth are thus rocky cores of Jupiters evaporated as the star grows by JPP accretion.

Long period comets with random Oort cloud orbits $`10^{16}`$ m matching a typical PNe radius suggest that the trillions of Oort comets are from a few hundred PFPs constantly drizzling in from the sun’s accretion hole in the ISM (its Oort cloud inner radius according to HGT) that were not captured by the sun and its Jovians in their first accretional attempt and have not yet been completely fragmented by tidal forces and evaporated by radiation (Gibson & Schild 2003c, ). Orbit perturbations of 82 new (first-entry) class I (accurate) Oort comets imply the existence of a SIRTF-infrared and VLA-radio detectable $`10^{28}`$ kg JPP at $`4\times 10^{15}`$ m (Matese et al., 1999). From HGT the inner radius of the Oort cloud is $`3\times 10^{15}`$ m, corresponding to a solar mass accreted from a PGC, and the outer radius is $`3\times 10^{17}`$ m, corresponding to the average extent of a PGC. Without HGT the origin of the huge numbers of fragile, frozen, Oort comets with their eccentric orbits, specific distance scale, and random directions is mysterious.

What about the inter-stellar-medium (ISM)? If there are really 30,000,000 PFPs per star in the average galaxy, shouldn’t some of these be revealed by their evaporated gas near very hot objects; for example, near carbon white dwarfs formed when ordinary stars have burned most of their H-He gas to form planetary nebulae, or in the ISM after novas and supernovas? Evidence that mysterious “free-floating planets pepper our galaxy” (June 2003 Astronomy cover page) is rapidly accumulating (Naeye, 2003). The number of rogue Jupiters greatly exceeds predictions of “failed brown dwarf” and star expulsion models. Why do mysterious knots, comets and Herbig-Haro objects appear from the dark ISM whenever young stars form plasma jets? Where does the huge amount of gas in the halos of planetary nebulae come from? Are ordinary stars really so inefficient that most of their mass is wasted forming PNe halos? See $`\mathrm{\S }3`$ for a discussion of HST images of the Helix Planetary Nebula (Gibson & Schild 2003c, ), which is the closest PNe to earth, and its thousands of cometary globule PFP and JPP candidates.

HGT contradicts cold-dark-matter hierarchical-clustering-cosmologies (CDMHCC). CDM “halos” cannot remain gravitationally bound because the weakly collisional CDM particles are intrinsically much too diffusive, with $`(L_{SD})_{CDM}L_H`$ during the plasma epoch. Hence, small primordial CDM “halos” (the key misconception) cannot cluster to provide massive gravitational potential wells to collect the baryonic matter and hierarchically form galaxies, clusters and superclusters with ever increasing mass as proposed by CDMHCC. Instead, HGT forms protosuperclusters first in the hot plasma epoch and these gently fragment to proto-clusters and then proto-galaxies as the plasma cools, starting at 30,000 years and finishing at the plasma to gas transition at 300,000 years. The gentle fragmentation from viscous-gravitational beginnings in a uniformly expanding universe explains the remarkable angular and geometric correlations observed between galaxies and quasi-stellar-objects (QSOs) with highly discordant red shifts that are used to contradict the big bang hypothesis (Hoyle et al., 2000).

Compact galaxy clusters like Stephan’s Quintet (SQ) with highly discordant redshifts support the hypothesis that redshifts may be intrinsic (Arp, 1973) and that all the SQ galaxies are at the same distance and were ejected by galaxy NGC 7331 located at the same redshift $`z=0.0027`$ as the nearest member NGC 7320 of the SQ cluster. No physical explanation has been put forth for intrinsic redshifts and QSO ejections. The observations supporting these hypotheses can be easily explained by HGT without inventing new physics by recognizing that the galaxies and QSOs are aligned by perspective, and stay aligned along narrow lines of sight as the universe expands because their sticky beginnings allow only small transverse velocities. CDMHCCs are contradicted by the accumulation of evidence showing strong angular coincidences of QSOs and bright galaxies (Burbidge, 2003). Stephan’s Quintet is presented as an example in $`\mathrm{\S }3`$.

## 2 Hydro-Gravitational Theory

Standard CDM cosmologies are flawed by their adoption of simplistic fluid mechanical equations that fail to incorporate significant forces, and by their inappropriate use of collisionless fluid mechanics. The ill-posed Jeans 1902 theory (neglecting non-acoustic density perturbations) is far too limited a basis for discussion of structure formation because it neglects viscous forces, turbulence forces, non-acoustic density fluctuations, particle collisions, and the effects of diffusion on gravitational structure formation. Jeans did linear perturbation stability analysis (neglecting turbulence) of Euler’s equations (neglecting viscous forces) to reduce the problem of gravitational instability of a nearly uniform ideal gas with density $`\rho `$ only a function of pressure (the barotropic assumption) to one of gravitational acoustics. Furthermore, to reconcile his equations with the linearized collisionless Boltzmann’s equations and the resulting Poisson’s equation for the gravitational potential (Binney & Tremaine, 1987), Jeans assumed the density was zero in a maneuver appropriately known as the “Jeans swindle”. The critical wave length for stability with all these questionable assumptions is the Jeans length scale $`L_J`$ given in Eq. 1 (see Table 1).

Density fluctuations in natural fluids are generally not barotropic as assumed by Jeans 1902 except in small regions and short times near powerful sound sources, but are dominated by non-acoustic (non-barotropic) density variations from turbulent mixing of temperature or chemical species concentrations (Gibson, 2001). Even in the context of Jeans’ theory (without the Jeans swindle), any gravitational condensation on an acoustical density maximum rapidly converts to a non-acoustical density maximum because the accreted mass retains the momentum of the presumed motionless ambient gas. At this point one faces the more realistic problem of gravitational structure formation in a moving, viscous, diffusive, possibly turbulent gas that was addressed by Gibson 1996. Turbulence or viscous forces will dominate gravitational forces at small distances from a non-acoustic point of maximum or minimum density, but gravitational forces will dominate turbulent or viscous forces at larger distances if the gas does not diffuse away faster than it can condense or rarify due to gravity.

The Jeans 1902 analysis fails because the problem was ill posed. Self-gravitational structure formation in nature occurs on non-acoustic density maxima and minima, not sound wave crests, but Jeans started by assuming a uniform density, and was forced to set the density to zero in the Jeans swindle to avoid the nonlinear problems of non-acoustic density maxima forming at acoustic wavecrests. The geometry of evolving non-acoustic density fields at scales $`LL_J`$ is shown in Figure 1, with (top) and without (bottom) self-gravitational instability. Without self-gravity a quasi-equilibrium at the Batchelor length scale (Table 1) exists, where the competition between diffusive smoothing of density gradients and strain rate steepening produces a universal turbulent mixing scale $`L_B(D/\gamma )^{1/2}`$ at points of maximum and minimum density (Gibson, 1968) that begin to decay by diffusion as soon as turbulence scrambles a uniform density gradient to form such extrema with zero density gradients, as shown by experiments and numerical simulations (Gibson et al., 1988). Without gravity, points of maximum density always decrease by diffusion and points of minimum density increase, always moving and diffusing back toward the original configuration with uniform gradient and no density extrema.

Evidence of primordial turbulence in CMB anisotropies (Bershadskii & Sreenivasan, 2002) suggests non-acoustic density maxima necessary to seed primordial gravitational structures were available in the plasma epoch. Assuming the same initial density conditions as Fig. 1 (top), the evolution of density with self gravity (bottom) is very different. The reason is that gravity has the effect of causing a negative diffusivity $`D_{\rho G}(L)=L^2(\rho G)^{1/2}`$ for distances $`L<(D^2/\rho G)^{1/4}`$ close to the points of zero density gradient and maximum or minimum density value. Negative density diffusivity causes absolute gravitational instability at non-acoustic density extrema. With self gravity (bottom) density maxima increase their density values toward infinity and density minima decrease their density values toward zero. Both experience exponential growth to form condensates and voids for all length scales $`LL_J`$ unless limited by turbulent, viscous or diffusive effects at the appropriate Schwarz length scales.

Consider a well posed problem in self-gravitation. A mass perturbation $`M(0)`$ with scale $`LL_J`$ suddenly placed in a motionless fluid of constant density $`\rho `$ at time $`t=0`$ will increase as $`M(t)=M(0)exp[2\pi \rho Gt^2]`$ unless viscous, turbulent, other forces or diffusion arise to prevent the exponential growth (Gibson, 2000). Everything slowly begins to move toward or away from the mass perturbation for $`t>0`$ and everything happens at once at $`tt_{FF}=(\rho G)^{1/2}`$. For $`t<t_{FF}`$ the radial velocity $`v_rGM(0)t/r^2`$ from Newton’s law of gravity, so the mass flow $`dM(t)/dt\rho 4\pi r^2v_r4\pi \rho GM(t)t`$ and density $`\rho `$ are independent of radius. Thus, $`dM(t)/M(t)4\pi \rho Gt`$, so $`M(t)=M(0)exp(2\pi \rho Gt^2)`$. Since everything happens within $`L`$ of the perturbation at $`tt_{FF}`$, any “pressure support” mechanism is confined to this small space-time region and has no affect on the weakly accelerated fluid that slowly gains momentum at scales $`LL_Jxct`$ and $`LxL_J`$ for times $`tt_{FF}`$. Since it takes a time $`tt_{FF}`$ for a sound wave to reach a distance $`xL_J`$ in time $`tt_{FF}`$, any hypothetical acoustic “pressure support” mechanism of the Jeans criterion would be too late to prevent the exponential density singularity at $`tt_{FF}`$. Note that the time required for self-gravitational structure formation depends almost entirely on the mean density $`\rho `$ and only very slightly on the size of the density perturbation $`\delta \rho M(0)L^3`$.

The diffusion velocity is $`D/L`$ for diffusivity $`D`$ at distance $`L`$ and the gravitational velocity is $`L(\rho G)^{1/2}`$. The two velocities are equal at the diffusive Schwarz length scale

$$L_{SD}[D^2/\rho G]^{1/4}.$$
(3)
Weakly collisional particles such as the hypothetical cold-dark-matter (CDM) material cannot possibly form potential wells for baryonic matter collection because such particles have large diffusivity and will disperse, consistent with observations (Sand et al., 2002). Diffusivity $`DV_p\times L_C`$, where $`V_p`$ is the particle speed and $`L_C1/n\sigma `$ is the collision distance for particles with number density $`n=\rho /m`$, $`\sigma `$ is the collision cross section, and $`m`$ is the particle mass. CDM particles have $`\sigma _{CDM}10^{40}`$ m2 or less compared to baryonic $`\sigma _B10^{20}`$ m2 values. Weakly collisional particles thus have large collision distances $`L_C`$ and therefore large diffusivities $`D`$ and large diffusive Schwarz lengths $`L_{SD}`$. Therefore, the non-baryonic dark matter (possibly neutrinos) must be the last material to fragment by self gravity and not the first as assumed by CDM cosmologies. In HGT galaxy formation (Gibson, 1996), the NBDM diffuses to form either an outer halo of the galaxy if the galaxy is isolated, or diffuses completely away from the baryonic galaxy to become part of a galaxy cluster halo or galaxy supercluster halo at Mpc scales $`3\times 10^{22}`$ m or more.

The baryonic matter is subject to large viscous forces, especially in the hot primordial plasma from photon viscosity and gas states from large $`V_p`$ values existing when most gravitational structures first formed, where $`\nu V_p\times L_C`$ if $`L_CL_H`$. The viscous forces per unit volume $`\rho \nu \gamma L^2`$ dominate gravitational forces $`\rho ^2GL^4`$ at small scales, where $`\nu `$ is the kinematic viscosity and $`\gamma `$ is the rate of strain of the fluid. The forces match at the viscous Schwarz length

$$L_{SV}(\nu \gamma /\rho G)^{1/2},$$
(4)
which is the smallest size for self gravitational condensation or void formation in such a flow. Turbulent forces may require even larger scales of gravitational structures. Turbulent forces $`\rho \epsilon ^{2/3}L^{8/3}`$ match gravitational forces at the turbulent Schwarz scale

$$L_{ST}\epsilon ^{1/2}/(\rho G)^{3/4},$$
(5)
where $`\epsilon `$ is the viscous dissipation rate of the turbulence. Thus in strongly turbulent regions with large $`\epsilon `$ values one expects large stars to form because the turbulent Schwarz scales are larger than any other hydro-gravitational scale. In the cold, turbulent, dense molecular clouds of the Milky Way Galaxy disk where the Jeans mass is near $`M_{\mathrm{}}`$ or less, few stars form compared to the rate expected by the Jeans criterion because $`L_{ST}L_J`$.

The Jeans criterion is nearly irrelevant to gravitational structure formation triggered by non-acoustic density maxima and minima where structures can form at scales that are either larger or smaller than $`L_J`$. By Jeans’ criterion no structures can form in the primordial plasma because $`L_J`$ during this hot, dense, epoch is always larger than the scale of causal connection $`L_Hct`$, where $`c`$ is the speed of light and $`t`$ is the time since the big bang. However, the viscous and turbulent Schwarz scales $`L_{SV}L_{ST}`$ became smaller than $`L_J`$ during this period, and first matched the more rapidly increasing $`L_H`$ at time $`t10^{12}`$ seconds (Gibson, 1996), well before $`10^{13}`$ seconds which is the time of plasma to gas transition (300,000 years). Because the expansion of the universe inhibited condensation but enhanced void formation in the weakly turbulent plasma, the first structures were proto-supercluster-voids. At $`10^{12}`$ s the Reynolds number was near critical so that

$$(L_{SD})_{NBDM}L_{SV}L_{ST}5\times L_KL_H=3\times 10^{20}\mathrm{m},$$
(6)
where $`L_{SD}`$ applies to the non-baryonic component and $`L_{SV}`$, $`L_{ST}`$, and $`L_K`$ apply to the baryonic component.

As proto-supercluster fragments formed the voids between filled with non-baryonic matter by diffusion, inhibiting further structure formation by decreasing the gravitational driving force. The baryonic mass density $`\rho 2\times 10^{17}`$ kg/$`\mathrm{m}^3`$ and rate of strain $`\gamma 10^{12}`$ $`\mathrm{s}^1`$ were preserved as hydrodynamic fossils within the proto-supercluster fragments and within proto-cluster and proto-galaxy objects resulting from subsequent fragmentation as the photon viscosity and $`L_{SV}`$ decreased prior to the plasma-gas transition and photon decoupling (Gibson, 2000). As shown in Eq. 5, the Kolmogorov scale $`L_K[\nu ^3/\epsilon ]^{1/4}`$ at the time of first structure nearly matched the horizon scale $`L_Hct`$ and the viscous and turbulent Schwarz scales, freezing in the density, strain-rate, and spin magnitudes and directions of the proto-cluster and proto-galaxy fragments of proto-superclusters. Remnants of the strain-rate and spin magnitudes and directions of the weak turbulence at the time of first structure formation are forms of fossil vorticity turbulence (Gibson 1999b, ). Thus HGT naturally explains observed bright galaxy spin alignments and close angular associations with each other and quasars without assuming intrinsic red shifts and mutual ejections.

The quiet condition of the primordial gas is revealed by measurements of temperature fluctuations of the cosmic microwave background radiation, which show an average $`\delta T/T10^5`$, much too small for any turbulence to have existed at that time of plasma-gas transition. This is to be expected because any turbulent plasma motions would have been strongly damped by buoyancy forces after the first gravitational fragmentation time $`10^{12}`$ s. Viscous forces in the plasma are inadequate to explain the lack of primordial turbulence (kinematic viscosity $`\nu `$ $`10^{30}`$ m2 s-1 is required versus only $`4\times 10^{26}`$ m2 s-1 from Gibson 2000). The gas temperature, density, viscosity, and rate of strain are all precisely known at transition, so the gas viscous Schwarz mass $`L_{SV}^3\rho `$ is $`10^{24}`$ kg, the mass of a small planet, or $`10^6M_{\mathrm{}}`$. From HGT, soon after the cooling primordial plasma turned to gas at $`10^{13}`$ s (300,000 yr), the entire baryonic universe condensed to a fog of planetary-mass primordial-fog-particles (PFPs). These gas-cloud objects gradually cooled, formed H-He rain, and eventually froze solid to become the baryonic dark matter and the basic material of construction for stars and everything else, $`30\times 10^6`$ rogue planets per star. The PFP mass $`10^6M_{\mathrm{}}`$ is above the evaporation stability limit $`10^7M_{\mathrm{}}`$ (De Rujula et al., 1992).

The Jeans mass $`L_J^3\rho `$ of the primordial gas at transition was $`10^6M_{\mathrm{}}`$, the mass of a globular star cluster. Proto-galaxies fragmented at the PFP scale but also at this proto-globular-star-cluster PGC scale $`L_J`$, although not for the reason given by the Jeans 1902 theory. Density fluctuations in the gaseous proto-galaxies were absolutely unstable to void formation at all scales larger than the viscous Schwarz scale $`L_{SV}`$. Pressure can only remain in equilibrium with density without temperature changes in a gravitationally expanding void on scales smaller than the Jeans scale. From the second law of thermodynamics, rarefaction wave speeds that develop as density minima expand due to gravity to form voids are limited to speeds less than the sonic velocity. Cooling would therefore occur and be compensated by radiation in the otherwise isothermal primordial gas when the expanding voids approached the Jeans scale. Gravitational fragmentation of proto-galaxies will then be accelerated by radiative heat transfer to these cooler regions, resulting in fragmentation at the Jeans scale and isolation of proto-globular-star-clusters (PGCs) with the primordial-gas-Jeans-mass.

These $`10^{36}`$ kg PGC objects were not able to collapse from their own self gravity because of their internal fragmentation at the viscous Schwarz scale to form $`10^{24}`$ kg PFPs. The fact that globular star clusters have precisely the same density and primordial-gas-Jeans-mass from galaxy to galaxy proves they were all formed simultaneously soon after the time of the plasma to gas transition $`10^{13}`$ s. The gas has never been so uniform since, and no mechanism exists to recover such a high density, let alone such a high uniform density, as the fossil turbulent density value $`\rho 2\times 10^{17}`$ kg/$`\mathrm{m}^3`$. Young globular cluster formation in BDM halos in the Tadpole, Mice, and Antennae galaxy mergers show that dark PGC clusters of PFPs are remarkably stable structures, persisting without disruption or star formation for more than ten billion years.

So the proto-galaxies (PGs) before stars were rapidly fragmented at both the Jeans and viscous Schwarz scales to form PGCs, a million per galaxy, with embedded PFPs, a trillion per PGC and $`10^{18}`$ per PG. Viscous forces inhibited the formation of larger planetoids by accretion of the PFPs except at the cores of the PGCs and the cores of the PGs. It was a very quiet and gentle time. The gentleness of this time of first star formation is reflected in the small, uniformly distributed, long-lived, Population II stars of the ancient globular-star-clusters observed in the Milky Way Galaxy. The time to form the first of these stars was probably one million years (the primordial density free fall time), not the 275 million “dark age” years required by the standard CDM model while the CDM halos formed by frictionless clustering of CDM seeds. Open star clusters formed from captured and disrupted PGCs in the Galaxy disk are exposed to higher levels of radiation and tidal friction than PGCs in the BDM halo, and form large irregularly distributed stars. The large sizes of the disk stars and their slow rate of formation reflect the high turbulence levels of disk star forming regions (from supernovas) compared to the low turbulence levels existing where stars are formed in isolated PGCs. From HGT, the thin disks of spiral galaxies are accretion disks forming within large, massive, spherical BDM halos surrounding the original smaller denser $`10^{20}`$ m galaxy cores from which the PGCs diffused, rather than collapsed gaseous pancakes in CDM halos as envisaged in CDM standard models. Relatively low gas levels are observed in spiral galaxy cores according to HGT, where excess gas is frozen out on the ambient PFPs.

With the expansion of the universe and further cooling, the PGCs and PFPs cooled as well, reaching the 14 K freezing point of hydrogen at about a redshift of 30 at a time about 80 My. Because most of the gas is isolated in individual PFPs separated from their neighbors by distances of about $`10^{14}`$ m corresponding to the primordial density, and because most PFPs within a PGC are initially surrounded homogeneously by identical objects with the same spacing, the tendency without external forcing would be for them to slow down due to friction from the inter-PFP gas and remain isolated indefinitely. After freezing, the PFP collision cross section will decrease but the inter-PFP gas density and friction will also decrease, permitting speedup of the PFPs and a new meta-stable state of equilibrium. The Gunn-Peterson trough phenomenon shows intergalactic gas effectively vanishes for red shifts smaller than 6 ($`t`$ 700 My) in quasar spectra with their Lyman-$`\alpha `$ forests of intervening galaxies. This suggests that most baryonic-dark-matter galaxy halo gas has frozen out on PFPs embedded in the BDM halos at times less than a billion years after the big bang.

As the inter-PGC gas density decreases with time since PFP creation, these PGC clumps of condensing baryonic dark matter become increasingly collisionless and diffusional. Those formed near the core of the proto-galaxy have a higher likelihood of mutual capture, interaction, disruption, and conversion to stars, but those formed on the periphery of the proto-galaxy will tend to either capture each other to form proto-dwarf-galaxies or diffuse to larger and larger orbits. The inner PGCs should be the most agitated by tidal forces and therefore the most likely to form stars and eventually the full population of $`10^6`$ stars observed in a globular star cluster. Those further out might form only a few thousand stars and drift to the outskirts of the luminous portion of the galaxy, sometimes being captured or disrupted by the disk, but the largest number diffusing farther out to form the baryonic-dark-matter (BDM) halo of the galaxy, invisible unless disturbed by intruders as in the case of the Tadpole merging galaxy system (VV29=Arp 188=UGC 10214). Figure 3 shows the HST/ACS image with its combination of wide field and high resolution, which clearly reveals the existence of star wakes, a dark dwarf galaxy and young-globular-clusters triggered into existence from the dark baryonic-dark-matter halo by the merging cluster of galaxy components VV29cdef as they spiral in to the central galaxy VV29a and merge (Gibson & Schild 2003b, ).

Sparse globular clusters such as Palomar 5 with luminous mass $`10^4M_{\mathrm{}}`$ and Palomar 13 with luminous mass $`10^3M_{\mathrm{}}`$ observed in the Milky Way are likely dim rather than disrupted PGCs with 98% to 99.9% of their mass intact as dark-matter PFPs. Nearly half of the stars of Pal 5 are observed as long tidal tails along its orbit about the Galaxy center (Rockosi et al., 2002), suggesting that the same tidal forces that produced the tails may also be producing the stars from a large supply of remaining PFPs. The amount of dark matter in dim globular clusters like Pal 5 and Pal 13 in the Milky Way, and in Galactic dwarf spherical galaxies (dSphs), is likely underestimated in virial estimates $`M(Rv^2/G)`$ of the dark mass $`M`$ because friction from PFP gas is neglected that reduces the velocity variance $`v^2`$ of the stars within radius $`R`$. A mass-to-light ratio $`\mathrm{{\rm Y}}40`$ for Palomar 13 was recently reported (Cote et al., 2002), which is the first estimate from $`v^2`$ measurements in dim globular star clusters and is much higher than $`\mathrm{{\rm Y}}2`$ expected. In another estimate (Cote et al. 2002 Fig. 14b) $`\mathrm{{\rm Y}}7000`$ fitting to the luminosity relation for dSphs which is closer to the value $`\mathrm{{\rm Y}}1000`$ expected from HGT. Large $`\mathrm{{\rm Y}}`$ values measured in dSph galaxies have been assumed to reflect non-baryonic CDM halos (Cote et al., 2002), but from Tadpole we see PGC and dSph dark matter is mostly baryonic because it forms stars when agitated.

The hydro-gravitation-theory (HGT) scenario presented here is significantly different from standard CDMHC cosmology based on Jeans 1902 precepts. Gravitational structures in the baryonic matter fragmented during the plasma epoch with supercluster to galaxy masses. The protosuperclusters have the observed uniform supercluster mass of about $`10^{47}`$ kg (including their non-baryonic halos), with a uniformity not expected for hierarchical clustering of CDM halos assumed in the standard CDMHC model. Weak primordial turbulence is damped by buoyancy forces of the first structures to form fossil vorticity turbulence (Gibson 1999b, ). The density and rate-of-strain values at the time of first structure ($`10^{12}`$ s) are preserved (fossilized), and can still be detected in the density of globular star clusters and the masses of PFPs. The non-baryonic matter diffused to fill the protosuperclustervoids, limiting the amplitude of the density contrast formed to the small values observed in the CMB. Superclusters, clusters and galaxies never contracted or collapsed but continue to fragment and gently expand at slower rates than the rest of the universe.

## 3 Evidence Supporting the Hydro-Gravitational Theory

Evidence supporting the hydro-gravitational theory of structure formation is gradually accumulating. High resolution telescope images in star forming regions and supernova remnants are full of poorly explained small objects, knots and “ejecta” that are likely to be evaporating PFPs. Cometary globules and the huge masses of gas observed by the HST near hot dying stars in planetary nebulae are much more easily explained as the result of evaporating ambient PFPs in the interstellar medium than they are as ejecta. Plasma beams from young stars produce Herbig-Haro objects with cometary tails, and the plasma beams themselves pulsate as though the accreted material forming the star contained planetary mass chunks. Numerous brown dwarfs and Jupiters have been detected whose origin is mysterious without HGT. The total mass of extra-solar planets discovered increases with decreasing planet-mass, even though low mass extra-solar planets are more difficult to detect, as expected if extra-solar planets are formed by accretion of ambient PFPs before their capture by stars.

The closest planetary nebula is Helix, Figure 2, where some 6500 cometary globules have been identified, each with mass about $`10^{25}`$ kg and size $`10^{13}`$ m, and separated by about $`10^{14}`$ m (O’Dell & Handron, 1996). Radial tails point away from the hot, central, white dwarf star at $`4\times 10^{15}`$ m. The mass $`2\times 10^{25}`$ kg and separation distances $`10^{14}`$ m of the Helix cometary globules give a halo density $`\rho 10^{17}`$ kg m-3, suggesting that PFPs originally in a sphere with radius $`4\times 10^{15}`$ m have accreted to form the central star out of an ISM with mass dominated by PFPs, with primordial density $`\rho 10^{17}`$ kg m-3, leaving PFPs at the hole boundary (Oort Cloud) evaporated and illuminated by the hot dying star. Measured evaporation rates (Meaburn et al., 1998) are too high for the globules shown in Figure 2 to be PFPs, so they must be JPPs with at least Jupiter mass to have survived this long (Gibson & Schild 2003c, ). If the ISM surrounding the Helix represents a dark proto-globular-star-cluster (PGC), the PN represents the luminous boundary of a hole formed by accreted PFPs to form the illuminating central star, with mass $`10^5`$ of the surrounding ISM PGC baryonic dark matter cloud of PFPs. The gas in the nebula is of order the mass of the star, but the total mass of the atmosphere of the dying star before it is ejected should be less than about $`10^7M_{\mathrm{}}`$.

The mass density for the Helix globules $`10^{14}`$ kg/$`\mathrm{m}^3`$ is three orders of magnitude larger than the density of any atmosphere ejected by the white dwarf star. Shock waves can increase densities by no more than factors $`6`$, not the factors $`10^7`$ required to explain the objects of Figure 2. These cometary globules are usually explained as due to Rayleigh-Taylor instability, where a dense gas shell ejected first is accelerated by a lighter shell ejected more rapidly later, but RT instability cannot increase the density of the dense shell by many orders of magnitude or decrease the density in the RT fingers to form wakes as observed. RT fingers only form in a narrow range of Reynolds numbers near critical, but this is not the case for the Helix objects. If the cometary globule separations in Helix reflects that of the ambient PFP population, the mass density of PFPs is near the value $`10^{17}`$ kg/$`\mathrm{m}^3`$ expected for a PGC. The PGC may have supplied the PFPs from which the Helix star was formed, consistent with the size of the $`4\times 10^{15}`$ m region surrounding the white dwarf that is observed to be empty of cometary globules (Gibson & Schild 2003c, ).

However, the most conclusive and convincing evidence for the PGC-PFP HGT scenario is still the technically challenging one of quasar microlensing. The Schild 1996 interpretation that the QSO 0957+561A,B quasar lens galaxy must be dominated by planetary mass objects is based on the observed high twinkling frequency of the two quasar images A,B. The initially controversial Schild time delay has now been confirmed by several independent observers, and is in the process of further refinement by an international team of observers using telescopes at sufficient points on the Earth to provide continuous coverage and independent confirmation of the twinkling QSO 0957+561A,B light curves (Colley et al. 2002, 2003). At this time four other lensed quasars have been observed with sufficiently precise time delays of the mirage images to extract the planetary mass twinkling frequencies, and these have been observed and reported (Burud et al. 2000, 2002; Hjorthe et al. 2002, Schechter et al. 2002). The specific microlensing profile discovered in Q0957 by Colley and Schild (2003) with high statistical significance shows that the lens galaxy G1 halo population has a significant optical depth of planetary mass objects, and the double-ring halo model of Schild and Vakulik (2003) shows how such rapid microlensing plausibly follows from simulations.

Evidence of substructure in several lensing galaxies is reported by Dalal and Kochanek 2002 from the difference in brightness of the background source mirages, with substructure masses in the range $`10^610^9M_{\mathrm{}}`$. This evidence is presented to suggest that the missing CDM halos of the local group of galaxies is not a crisis for the hierarchical CDM model of galaxy formation that overestimates the numbers of dwarf galaxies by orders of magnitude compared to observations because the actual galaxy substructures may be dark. However, the substructure evidence (Dalal and Kochanek, 2002) of dark non-baryonic CDM halos may also be interpreted as evidence that significant fractions of the lens galaxies central masses are in dark baryonic clumps. Dark PGC clumps of PFPs dominating central galaxy masses is predicted by HGT. Clumps of dark PGCs triggered to form clumps of YGCs by the star formation wake of VV29c are indicated in the VV29b filament of Tadpole by the HST/ACS images (Tran et al., 2003), Figure 3.

Merging galaxy systems such as the Tadpole, Mice, and Antennae are characterized by the appearance out of the dark of young-globular-clusters (YGCs) and large quantities of gas. Using the HST and a wide variety of other telescopes to cover a broad range of frequencies (Zhang et al., 2001), nearly a thousand YGCs have been identified and studied in the Antennae system (NGC 4038/9), which is the closest merging galaxy system at only $`6\times 10^{23}`$ m. At this distance the clusters are well resolved. The mass function inferred from the luminosity for the young (5 Myr) globular clusters in Antennae (Fall and Zhang, 2001) is very different than that for old ($`10`$ Gyr) globular clusters (OGCs), falling with power law slope -2 from a maximum near $`10^4M_{\mathrm{}}`$ rather than showing the narrow lognormal peak near $`2\times 10^5M_{\mathrm{}}`$ widely observed for OGCs. The brightest YGCs have the same mass as the OGCs. We suggest that the low masses of the most numerous YGCs is simply because most of the mass of the PGCs from which these YGCs are forming is still tied up in dark matter PFPs that are rapidly accreting to form stars under the influence of the tidal merger.

Figure 4 shows an HST image of Stephan’s Quintet (SQ, HGC 92, Arp 319, VV 288) which is number 92 in the Hickson catalog of compact clusters. Like over 40$`\%`$ of the HGCs, the SQ galaxies (Burbidge and Burbidge, 1961) have highly discordant redshifts. These are easily explained by HGT, where the SQ and other HGC galaxies with discordant redshifts represent galaxy clusters that have gently separated only recently due to the expansion of the universe (Gibson & Schild 2003a, ). The star wakes in Figure 4 show luminous evidence of the baryonic dark matter cluster halo and its boundary. No evidence of a galaxy merger is shown, in contrast to the Tadpole merger in Figure 3 where the merged galaxy is revealed. Numerous young globular clusters (YGCs) have been identified in SQ (Gallagher et al., 2001), confirming the HGT prediction that the baryonic dark matter consists of PGC clumps of PFPs that can be triggered to form stars by radiation and tidal forces.

Figure 5 shows the tomographic mass distribution of the rich galaxy cluster Abell 1689 determined from the gravitational distortion of 6000 background galaxy images by 4000 foreground galaxies in the cluster (Tyson & Fischer, 1995). A mass to light ratio of about 400 suggests the cluster halo is non-baryonic dark matter with an extent determined by the NBDM particle diffusivity $`D_{NBDM}`$ and the large cluster density. The Schwarz diffusive scale $`L_{SD}(D_{NBDM}^2/\rho G)^{1/4}`$ from the mass profile is $`10^{22}`$ m, giving $`D_{NBDM}6\times 10^{28}`$ m2 s-1 from the cluster density $`5\times 10^{21}`$ kg m-3. Such a large diffusivity excludes any possibility that the outer dark matter halo is baryonic. It fixes the value of the $`m/\sigma `$ ratio to a value $`\rho D(r/GM)^{1/2}10^3`$ kg m-2. Because the maximum collision cross section $`\sigma `$ for non-baryonic matter is about $`10^{36}`$ m2, the maximum particle mass for the NBDM is $`10^{33}`$ kg, excluding WIMPs with $`m10^{27}`$ kg as NBDM candidates by large factors. For example, the neutralino mass is about $`10^{24}`$ kg, giving a $`\sigma `$ value of $`10^{27}`$ m2, which is so large that neutralino-NBDM would be easily detected. The NBDM becomes unstable to gravitational fragmentation when $`L_{SD}`$ becomes less than the horizon scale $`L_H`$. This occurs at $`t(D^2/\rho G)^{1/4}c^1`$, soon after the plasma-gas transition at 300,000 years, for the indicated diffusivity. Outer halos scale with $`M^{1/4}`$ so the galaxy NBDM outer-halo-radius is $`1.5\times 10^{22}`$ m, or about four times the observed BDM inner-halo-radius for the Tadpole galaxy (Gibson & Schild 2003b, ). Since baryons can be no more than $`1/30`$ of the mass of a flat universe from nucleosynthesis, non-baryons can be no more than $`30`$ times the mass of baryons. Thus (neglecting any $`\mathrm{\Lambda }`$ contribution) galaxy outer halo densities are dominated by non-baryons and galaxy inner halo densities are dominated by baryons.

## 4 Conclusions

High resolution images of the Helix Nebula, the Tadpole merger and the Stephan Quintet (SQ) compact cluster support the hydro-gravitational theory (HGT) prediction that primordial-fog-particles (PFPs) in proto-globular-star-clusters (PGCs) dominate baryonic dark matter (BDM) inner-galaxy-halos and the interstellar medium (ISM). Young globular clusters and star wake alignments in Tadpole and SQ are explained by HGT and are not explained by previous models. Evidence accumulates showing high frequency twinkling of quasar images lensed by foreground galaxies, confirming that the galaxy missing baryonic mass is dominated by PFP mass “rogue planets” (Schild, 1996).

Large numbers of extra-solar planets have been discovered with Jupiter mass which must be made of H-He gas, but which are shown to be impossible by the Jeans 1902 gravitational structure formation criterion in $`\mathrm{\S }1`$. Such planets cannot be formed by condensation on rocky cores because the formation of rocks is also impossible by the Jeans criterion. Jupiters and rocks form naturally using hydro-gravitational theory (Gibson, 1996) by accretion of PFPs to form larger planets and stars, and by gravitational accumulation of the dust of supernovas by PFPs and larger planets to form rocky cores. The Helix Nebula and other planetary nebula show evidence that the ISM mass is dominated by PFPs as predicted by HGT. These accrete to form JPPs; Jupiters, brown dwarfs and stars. Evidence that the total mass of small extra-solar JPPs exceeds the total mass of larger extra-solar JPPs, as expected from HGT, suggests that the total mass of brown dwarfs in a galaxy exceeds the mass of stars. This prediction of HGT can be tested by the Space InfraRed Telescope Facility (SIRTF) when it is launched, possibly this year.

Stephan’s Quintet is an example of many compact clusters of galaxies with discordant red shifts that refute CDMHCC and support HGT. HST images confirm the PGC-PFP baryonic dark matter halo model indicated by the Tadpole merger, but show star wakes of cluster galaxies separating through the BDM cluster halo rather than merging as shown by Tadpole and as predicted by HGT. Angular clustering of QSOs and bright galaxies (Burbidge, 2003) also rule out CDMHCC and support either HGT without new physics or intrinsic red shifts and QSO ejection by AGN galaxies (Arp et al., 2001) and a possible failure of the big bang hypothesis (Hoyle et al., 2000). The forty year authoritative accumulation of inexplicable angular clustering of galaxies, clusters and QSOs with anomalous red shifts are readily explained by HGT as the result of perspective and gentle straining along lines of sight by the expansion of the universe, with small transverse velocities reflecting the viscous origins and frictional effects of fragmenting clusters in gassy, baryonic, galaxy and cluster halos.

From HGT and the mass distribution (Tyson & Fischer, 1995) computed for a rich galaxy cluster we find the NBDM particle mass is too small to be a CDM candidate, with fragmentation scales for non-baryonic-dominated outer-galaxy-halos larger than radius values observed for baryon-dominated inner-galaxy-halos. Cusps at galaxy cores expected from small, clustered, collisionless, CDM-halos are not observed (Sand et al., 2002). Hierarchical clustering cosmologies are contradicted by the incidence of strong-lensing clusters (Gladders et al., 2003). The most distant observable galaxies are already clustered (Steidel et al., 2000) and the closest clusters (Gibson & Schild 2003c, ) are fragmenting. HGT and the preponderance of accumulated evidence suggest that cold-dark-matter, hierarchical-clustering-cosmologies (CDMHCCs), and the Jeans 1902 gravitational structure formation criterion are physically incorrect and contrary to observation, and should be abandoned.

The authors are grateful for many constructive suggestions by the Editor and Referee.