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# Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures

## I Introduction

The backbone structure of globular proteins displays a notable degree of order and organization resulting in secondary motifs such as $`\alpha `$helices and $`\beta `$sheets and in their optimal arrangement into a compact shape. The special neatness and regularity of native conformations impacts on, or rather reflects, several features that are distinctive of naturally occurring proteins bakernature ; opthelix ; Miche99b ; secstr . Indeed, experimental and theoretical studies have shown that native structures conceal a wealth of information about aspects as diverse as native elastic properties, folding rates and key folding stages bav93 ; Plaxco ; Chan98 ; hiv . A promising graph theoretical approach jacobs01 ; rader02  can be used to ifentify rigid and flexible regions in proteins, and to investigate the emergence of such flexible regions in unfolding processes. Recent topology-based approaches, which are independent of sequence specificity, have revealed that a schematic, coarse-grained structural description is sufficient to obtain results in remarkable qualitative and even quantitative agreement with known experimental facts.

For example, concerning near-native vibrations, one is entitled to replace the detailed interactions among amino acids which are in contact in the native state with springs acting on effective centroids (usually the $`C_\alpha `$ atoms) bav93 ; tir96 . Topological folding models, on the other hand, try to characterize how the loss of configurational entropy contrasts the progressive establishment of native interactions in a folding process Go ; Miche99b ; Finkel ; eaton ; baker ; thirum ; Clem ; hiv .

In the present study, we focus on a topology-based model that incorporates both the aspects mentioned above. It consists of a beads-and-springs model but, at variance with other approaches, the strength of the effective interaction depends on the temperature of the thermal bath gaussian . Since the model is amenable to analytic treatment, it is possible to characterize rigorously both the thermodynamics as well as the vibrational/relaxation dynamics at various equilibrium stages of the folding process (not only near the native state).

The scope of the present study is two-fold. First we examine how the organization of native contacts impacts on fundamental properties of proteins and, hence, to what extent the knowledge of the contact map can be exploited to predict experimentally verifiable quantities. Our second goal is to repeat the same analysis in the context of generic disordered globular structures. From the comparison of the outcomes we aim at finding clues about the criteria adopted by nature in the selection of viable folds.

The vibrational spectrum at finite temperature allows to determine typical relaxation times which, in turn, correlate with high accuracy with experimental folding rates. This is rather surprising and unexpected since the relaxation time refers to near equilibrium situations whereas the folding process is far from equilibrium.

Furthermore, the comparative study of analogous static and vibrational properties of disordered globular structures, or otherwise random graphs, and proteins shows that the latter have very uncommon properties in terms of flexibility and mechanical relaxation times that can be exploited to predict not only folding rates but also the key sites of an enzyme and amino acid vibrational amplitudes in partially folded states. These distinctive mechanical properties reflect the hierarchical assembly of protein native states Baldwin  and, in particular, can be traced back to the presence and organization of secondary elements. Hence, they add to the increasing evidence that the emergence of such motifs was promoted by special criteria operated by nature to select viable folds plato ; Chothia2 ; chan90 ; Socci94 ; opthelix .

The straightforward implementation of concepts presented here, makes the model under consideration a useful tool to characterize the folding properties of a protein, complementing alternative theoretical strategies or more labor-intensive experimental techniques.

## II Theory

The model under consideration incorporates two features that previous theoretical investigations have proved successful for protein modeling. In spirit, it belongs to the class of Go-models Go , since the energy scoring function introduces a bias in structure space favoring the formation of native contacts. This ensures that the native structure under examination has minimum effective energy. Furthermore, we make use of the observation that, near equilibrium, the dynamics resulting from complicated atomic interactions can be well-reproduced by simple harmonic potentials tir96 ; levitt85 ; go\_gauss91  at least for time intervals shorter that 1 ns Amadei93 . The starting point of our analysis is the following effective harmonic Hamiltonian gaussian  (for its derivation, see Appendix A):

$$H=\underset{i,j}{}𝐫_𝐢L_{ij}𝐫_𝐣+f(T),$$
(1)
where $`𝐫_𝐢`$ denotes the distance-vector of site $`i`$ from its position in the native structure, and $`f`$ is a term that only depends on the equilibrium temperature. The entries of the symmetric matrix, $`L`$, incorporate the elastic forces that act on each residue to restore the native separation with its nearest neighbors in sequence (effect of the peptide bonding) and with other amino acids in interaction in the native state. The peptide bond is modeled by springs whose associated Boltzmann weight is independent of temperature. This reflects the little change of the peptide coupling over the range of temperatures where unfolding/refolding transitions are studied. In addition to this contribution, at variance with previous approaches, the energy scoring-function includes temperature-dependent interactions between the pairs of residues contacting in the native state. The list of such interactions is summarized in the contact map, $`\mathrm{\Delta }`$, whose entries, $`\mathrm{\Delta }_{ij}`$, are 1 if residues $`i`$ and $`j`$ are in contact in the native state (i.e. their Cα separation is below the cutoff $`c=7.5`$ Å) and 0 otherwise. For simplicity we refer to these temperature-dependent interactions as non-covalent, although they also act on consecutive residues. The strength of such non-covalent springs is calculated self-consistently according to the method described in Appendix A. This makes the model non-linear but still very tractable. When the temperature of the model is zero (this mathematically-convenient idealization corresponds to a physiological temperature where the protein is stable in its native state), all springs have the same strength. As temperature is switched on, this strength is reduced by a deterministic amount that is larger for springs where the largest stretching is observed (see Appendix A).

## III Results and discussion

### III.1 Vibrational properties of proteins and disordered structures

At zero temperature, when the non-covalent springs are equally strong and dominate in number over the covalent ones, the model is equivalent to the Gaussian Network Model (GNM) of Bahar et al. bah97 ; hal97 ; bah98 , which has been widely used to characterize the mobile regions of the native state from the analysis of the normal modes of the structure. These represent the natural oscillations (independent of each other) of a protein and convey information about which regions are more flexible, and how thermal energy is dissipated in order to restore equilibrium (i.e. the native structure). Although atoms in proteins are as tightly packed as in crystalline solids, the vibrational properties of native structures are very different bav93 . A notable example is given by the density of eigenvalues of the $`L`$ matrix, that is the histogram of vibrational frequencies. This is shown in Fig. 1, where we concentrated on two examples: an individual enzyme, the monomer of the HIV-1 protease, and the average histogram calculated for several proteins known to fold via the simplest possible mechanism (two-state) Jackson . The peculiarities of the protein spectrum can be ascribed to several distinctive protein properties such as the varying degree of site connectivity (burial profile) or the neat hierarchical organization of the native state in terms of secondary motifs.

To identify how the vibrational spectrum is affected by these general features we shall not take the crystalline solids as a reference, but consider several families of disordered contact maps. For example, to isolate the role played by the burial profile from other features we first consider disordered matrices obtained by taking the contact map of a real protein and randomly reshuffling its entries yet preserving the symmetry of the matrix, the burial profile and the contacts between consecutive sites. Successively we shall consider the case of completely disordered maps but with equal connectivity (burial) for each site. It is important to stress that in these two cases of disorder, the $`\mathrm{\Delta }`$ matrices will not, in general, be physically viable. In fact, it is not guaranteed that there exists a viable three-dimensional backbone associated to an arbitrary symmetric contact map. For this reason, we complete our analysis by considering the case of contact matrices of three-dimensional compact self-avoiding structures generated randomly with a computer with the constraint to be as compact as naturally-occurring proteins. This case will provide a useful term of comparison for identifying the spectral properties resulting from the neatly organized three-dimensional shape of naturally occurring protein conformations.

We begin by considering the first instance of disorder, i.e. random reshufflings that preserve both the symmetry of $`\mathrm{\Delta }`$ and also the protein native burial profile, i.e. the native number of contacts to which each site takes part Miche99b . The reshufflings consist in picking randomly a pair of non-zero distinct entries, $`\mathrm{\Delta }_{ij}`$ and $`\mathrm{\Delta }_{kl}`$ and checking if the entries $`\mathrm{\Delta }_{il}`$ and $`\mathrm{\Delta }_{kj}`$ are zero. If this is so, the old pair of entries (and their symmetric counterparts) are set to zero and the new ones to 1. The preservation of the connectivity of each site allows to study the impact of disorder on the vibrational frequency spectrum while keeping burial profiles unaltered. As anticipated above, such randomized contact maps are not necessarily the counterpart of any feasible three-dimensional structure; in fact, a more appropriate view of such matrices is within the framework of graphs bollobas ; Michefr , (the nodes and links corresponding to beads and springs, respectively).

A very important difference shown in Fig. 1 is that proteins have a larger number of low-frequency modes of vibration compared to the spectrum of the reshuffled maps. This difference is made more dramatic by considering the spectrum of loopless regular graphs. The term regular here refers to the fact that all sites have the same connectivity (burial), $`k`$, but the entries of the associated symmetric matrix, $`\mathrm{\Delta }`$, are otherwise random Merris94 .

This limit case of disorder is important because the average spectrum of such ensemble of matrices has been calculated exactly by McKay Mckay81 . The density of eigenfrequencies is given by:

$$f(\omega )=\{\begin{array}{cc}\frac{k\sqrt{4(k1)(\omega k)^2}}{2\pi (k^2(\omega k)^2)}\hfill & \text{for }|\omega k|<2\sqrt{k1}\hfill \\ 0\hfill & \text{otherwise,}\hfill \end{array}$$
(2)
and its distribution is shown in Fig. 1 for the case $`k=8`$, corresponding to the average site connectivity (including peptide bonding) in real proteins (when the interaction cutoff is around 7.5 Å).

It appears that the range of vibrational frequencies is severely limited compared to that of real proteins; in fact, the spectrum of such graphs reproduces only the central part of the frequency histogram of proteins. The outlying tails at both low and high frequency are not captured at all. Previous studies have pointed out how such tails reflect the existence of heterogeneity in site connectivity (burial) mona99 ; biro99 . This fact, and its implications for the mechanical properties of natural biopolymers are examined in detail in the next section.

### III.2 Localization properties

In a variety of contexts, from the physics of disordered systems to graph theory, spectra have always attracted considerable attention because of the special localization properties of the associated modes. High frequency normal modes are usually concentrated on sites/regions with high connectivity And58 ; And78 ; mona99 ; biro99 ; levitt85 ; tirion93 . This is intuitive since a larger number of connections leads to an enhanced local stiffness and hence a higher frequency of vibration. Conversely, low frequency modes are centered on sites/regions that, having fewer connections than average, are more flexible mona99 ; bah98 . This overall picture applies remarkably well to the reshuffled contact maps, as visible in Fig. 2. The plots show that the modes at low \[high\] frequency are very localized on sites with low \[high\] connectivity (burial). The degree of localization of a normalized eigenmode of vibration, $`\{v\}`$ is defined as $`_j|v_j|^4`$ (see eg. biro99 ). This measure will take on the largest value, 1, if all entries of $`\{v\}`$ but one are zero (full localization). On the contrary, the localization measure will be minimum when all the vector components are equal in modulus (full delocalization).

It is now interesting to turn to the case of proteins. Fig. 2 shows that high-frequency modes are, as before, highly localized on heavily buried sites. Notice that the highly localized states are not limited to the upper edge of the spectrum. The picture, however, changes for low-frequency modes, which appear to be significantly more delocalized than for the reshuffled case. This denotes a degree of flexibility that is significantly larger than randomly connected graphs (yet with the same burial profile!). This is not a peculiar feature of the HIV-1 Protease monomer, but is more general, as illustrated in the right panel of Fig. 2 displaying averages taken over the two-state folders listed in the caption of Figure 5 and their reshufflements. The averages in Fig. 2 are reported only for the 40 slowest modes, which cover a similar range of frequencies across the two-state folders. The inhomogeneity of the lengths of such proteins prevents from taking straightforward averages over the whole frequency range.

Several previous investigations of normal modes and spectra of proteins levitt85 ; tirion93 ; go\_gauss91 ; bah97b ; lus98 ; Hex98 ; rna98 ; jer99 ; hiv99 ; hal99 ; bah99 ; kes00 ; ani01  had already noted the existence and utility of low-frequency modes in proteins. For example the low-frequency spectrum affects not only the mechanical stability of proteins but also the thermodynamic one cieplak2001 ; hoang2000b ; cieplak ; furthermore it has been argued that the slowly moving regions are the natural candidates for biological functions involving structural rearrangements. It is important, however, to note that also the burial-preserving reshuffled maps have low-frequency vibrations.

The novel message of Fig. 2 is that the slow modes of random graphs are nearly fully localized (as high frequency modes), while in proteins one encounters the slow movement of regions spanning several residues levitt85 . This special property, which does not depend on the burial profile, must result from the special organization of native contacts which provides a remarkable degree of flexibility. This, in turn, is associated with a rate of thermal energy dissipation that is slower compared to disordered graphs. The natural measure for the limiting rate at which mechanical excitations decay is, in fact, given by the smallest frequency (eigenvalue) of $`L`$. Equivalently, the slowest vibrational relaxation (decay) time in the system, which we shall denote as $`\lambda _0`$, is given by the inverse of the smallest vibrational frequency, $`\lambda _0=1/\omega _0`$.

The immediate cause for this further difference is simply described in terms of graph properties bollobas . There is a well-defined relationship between the slowest relaxation time and the average contact-diameter (meaning the average number of native contacts, including those between consecutive sites, that have to be traversed to go from an arbitrary site to another). This relation is neatly visible in Fig. 3, which displays results for the distinct two-state folders and an equal number of their reshufflements.

It is important to see that, among all proteins, the ones with many local contacts (all-$`\alpha `$ family) tend to be at one end of the scatter plot, while proteins belonging to the all-$`\beta `$ family are closer to the case of reshuffled contact maps. The relaxation of real proteins appears to be also slower than randomly-collapsed three-dimensional structures. Within our simplified approach this difference is most visible at finite temperatures, as illustrated in Fig. 3, where the relaxation rates are computed at $`T=2T_F`$.

The slowest relaxation encountered in proteins can be understood from the fact that the establishment of a few random contacts, very rapidly makes the structure rigid, and less susceptible to further rearrangements. The hierarchical organization of contacts in proteins, in terms of secondary motifs further arranged in the tertiary structure, is responsible for the enhanced flexibility visible in Fig. 3. In fact, the relaxation times of isolated secondary motifs, both $`\alpha `$ and $`\beta `$, of equal length is nearly the same and, again, much higher than a corresponding random reshuffling. This is illustrated in Fig. 4. From these facts it is tempting to speculate that $`\alpha `$\- and $`\beta `$-like motifs are among the configurations that, for a given burial profile, have the largest relaxation times. This is particularly intuitive in the case of helices since their periodicity (modulus boundary effects) is immediately associated to the presence of slowly-decaying excitations.

### III.3 Folding rates

In this subsection we shall explore the intimate connection between the relaxation time of slow eigenmodes of protein structures in thermal equilibrium and the protein folding rate. It is tempting, and physically appealing, to speculate that the relaxation rate of partially folded states may be an indicator of the folding velocity. This stems from the observation that low-frequency vibrations involve extended protein segments and require less energy to be activated. Hence, structural rearrangements from the unfolded state to the native one should occur more easily when the relaxation times of partially folded states are higher. This qualitative argument is also supported by a different reasoning where the folding of a protein is viewed as a diffusion in the complicated free-energy landscape until the native-state (at the minimum of the accessible free energy) is reached. Different native shapes will then be associated with landscapes that, despite being biased towards the native conformation, may have significant differences in terms of numbers of metastable minima, height of the barriers between them etc. The corrugation of the landscape will undoubtedly affect the folding rate. The relaxation time of a structure in thermal equilibrium reflects the average ruggedness of the landscape. In a smoother landscape a protein will be able to make larger conformational changes for the same amount of dissipated energy. We can thus conclude that the native state is reached with greater difficulty if, during the folding process, the partially-formed structures have smaller equilibrium relaxation times.

In agreement with this picture, we have found a notable interdependence (see Fig. 5) between the experimental folding rates, $`K_F`$, and the slowest relaxation rate, $`\omega _0`$ (in dimensionless units) which dominates the long-time relaxation kinetics in equilibrium. At temperatures much larger than the folding temperature, $`T_F`$ (identified as the temperature at which the peak of the specific heat is observed), the relaxation time, $`\lambda _0=1/\omega _0`$ conveys little information about the folding rate, since virtually no contacts are formed; this is true also at low $`T`$, where it measures only the rate of thermal dissipation of the fully-folded native structure.

The highest correlation is observed at finite temperatures higher than $`T_F`$ (see Fig. 5). Although we believe that the precise location of the peak of the correlation may be sensitive to the model details, this result is plausible since it is above the folding transition that the significant search in conformation space occurs. The correlation coefficient in the neighborhood of the optimal temperature is $`r=0.73`$. It is possible to assess its statistical significance by comparison with the null case of no correlation between relaxation rates and folding times. In the absence of any pair correlation between variables with converging moments, one expects that the correlation coefficient measured over a finite sample is normally distributed. This allows to calculate exactly the probability to encounter a correlation coefficient higher than $`r=0.73`$ if relaxation and folding times were statistically independent. This probability turns out to be equal to $`210^4`$ which testifies that the observed dependence between the two quantities is truly significant.

These results add to previous studies where folding rates were predicted with analogous level of significance on the basis of contact locality Plaxco  or different topologic indicators (such as the clustering coefficient or cliquishness) based on a graph-theoretical description of a protein’s non-bonded interactions Michefr .

### III.4 B factors

The choice of a simple Gaussian Network Model to investigate the biological function of proteins has been motivated by a striking qualitative agreement between the experimental $`B`$ factors (or temperature factors) measured in X-ray diffraction experiments and the mean square residue displacement calculated theoretically from the expression hal97 ; bah98 ; erm2002 :

$$B_i^{\mathrm{theory}}\underset{k}{}\frac{1}{\omega _k}|v_i^k|^2$$
(3)
where $`i`$ is the residue index, $`v_i^k`$ is the $`i`$-th component of the $`k`$-th mode whose eigenfrequency is $`\omega _k`$. The sum in eqn. (3) is over $`k`$ such that $`\omega _k0`$. Several alternative methods exist to predict (or refine) experimental $`B`$ factors levitt85 ; diamond90 ; tirion93 ; coarse2002 ; halle2002 . The appealing feature of this Gaussian approach is that it is possible to give a good account of the experimental $`B`$ factors by exploiting only the connectivity information contained in the native structure. A recent work by Halle halle2002  has remarked the heavy influence that the native-state topology exerts on the measured $`B`$-factors; in particular, it was shown that the mobility of an amino acid anti-correlates with its degree of burial (estimated as the number of non-covalent bonds to which it takes part). Besides the fundamental effect of the burial profile, the GNM allows to model the influece on $`B`$-factors of other important topogical features, such as the locality of contacts and presence of highly-interconnected clusters of interactions. In addition, the decomposition of dynamical motion into independent modes allows to trace which modes of vibrations are most responsible for the mobility of a given site or protein region, thus providing useful hints about the protein biological function.

In this section we perform an analysis of the correlation between the theoretical and experimental B factors, aimed at investigating the role played by the single vibrational eigenmodes in the overall observed temperature factors.

We stress that in our model, both eigenfrequencies and eigenmodes are temperature-dependent. We begin our analysis by considering the $`T0`$ limit of our model, that corresponds to the GNM studied in refs. bah97 ; hal97 ; jer99 .

We analyzed 30 protein structures, all obtained in X–ray diffraction experiments, of different size (up to about 200 amino acids). The proteins, listed in the caption of Fig. 6, are chosen among the monomeric representatives of distinct structural classes obtained from high-resolution data oligons . Thermal fluctuations for each amino acid were compared with the corresponding temperature factor reported for the CA atoms in the PDB file pdb . Although a remarkable agreement with experimental data can be obtained for several proteins (correlation coefficients larger than 0.75 for proteins with nearly 200 residues), in some rare instances the correlation was around 0.4 (see Fig. 6). It must be borne in mind, however, that such correlations are never trivial, since they are measured over the entire protein length. Assuming, as before, that in case of no correlation the distribution of $`r`$ is normal, we can calculate the probability to observe higher correlations than the measured ones. Even in the worst case, this probability is never larger than $`t=\mathrm{3\; 10}^4`$ which is an indicator of excellent correlation. This estimate of statistical significance is so small that even if more precise calculations (e.g. accounting for the skewness in the B-factors distributions) modify the estimate of $`t`$ by two orders of magnitude, the correlation significance would be high.

Although statistically relevant, the agreement with temperature factors does not have the same quality for all crystal structures. It is important to remark that the crystallographic $`B`$-factors are not obtained by direct measurement, but from a suitable parametric fit of the measured diffraction pattern. In unfavorable conditions (affected also by crystallographic resolution), the fit may be significantly underdetermined and reliable data can be obtained only imposing additional constraints on the $`B`$ factors (such as their smooth variation along the main- or side-chains). Inspection of the PDB files for which the worst correlations are seen have revealed that, indeed, those proteins lacked the $`B`$-factor smoothness. Another possible source of discrepancy between theoretical and experimental data is the fact that we neglected the proximity effect of the surrounding proteins in the crystal structure. The presence of neighboring proteins might reduce the mobility of some regions (and notably those experiencing a pronounced freedom of movement), as already noted in previous studies levitt85 ; tirion93 ; coarse2002 ; halle2002 .

Equation (3) clearly indicates that most of the contribution to the theoretical $`B`$ factor comes from low-frequency modes, since the fast ones are suppressed by their frequency reciprocal weight. It is sensible to ask how much each individual mode correlates with the experimental $`B`$ factors. If a clear trend of such correlation against the mode frequency is found, one could devise a better (knowledge-based) weighting scheme, alternative to the one of eqn. 3 to improve the theoretical estimates of mean square displacement of residues. To answer this question we have obtained for each mode, $`k`$, the linear correlations between the experimental $`B`$ factors along the chain, $`\{B_i^{exp}\}`$ and the mode amplitudes, $`\{|v_i^k|^2\}`$. Such correlations, computed separately for each mode of the proteins listed in Fig. 6 are reported in Fig. 7a.

The majority of positive correlations are found in the region of slowest eigenmodes (eigenfrequencies up to 6), while there is a negligible correlation for middle frequencies, and a weak anti-correlation for fast eigenmodes (frequencies larger than 12). This is evident in figure 7b where one can compare the histograms of the correlation coefficients cumulated (with equal weights) over fast and slow eigenmodes. The anti-correlation of the experimental $`B`$-factors with the square-amplitudes profile of fast eigenmodes is in agreement with the graph theoretical prediction of a localization of the fastest eigenmodes in nodes of higher connectivity. These nodes are less mobile in the protein structure and hence associated with smaller $`B`$ values. Furthermore, since all eigenmodes are orthogonal, the sites whose vibrational amplitude is large in the slowest eigenmodes, will not be very mobile in the fastest ones, and viceversa.

Following this analysis we can conclude that low eigenmodes cooperate to generate much of the fluctuation pattern of the protein structure, while intermediate modes have little influence and fast modes could be safely excluded from the sum, since they contribute to raise the mobility of highly connected nodes.

Finally, we observe that the theoretical $`B`$’s carry a non trivial dependence on temperature through the eigenmodes (due to the temperature dependence of matrix $`L`$). Fig. 8 summarizes the behaviour of the correlation with experimental data against temperature for four representative proteins. It can be seen that, typically, by working at a temperature around $`2T_F`$ the correlation with experimental data can be increased significantly. As visible, an exception to this trend is given by the few proteins which already have a poor correlation at $`T=0`$.

We have considered also the case of NMR proteins, for which accurate relaxation measurements can directly probe the mobility of local portions of the protein thus providing an effective $`B`$ factor. Strikingly, the correlation between the theoretical and the experimental $`B`$ factors observed in this situation was systematically higher than for the X-ray resolved counterparts, as can be ascertained from Fig. 6. It would be tempting to conclude that this improved agreement is due to the more direct way with which NMR experiments can address local vibrational amplitudes. However, due to the insufficient annotation of PDB files of some NMR-resolved structures, it is not always possible to ascertain whether the reported data follow from precise relaxation measurements or from an a posteriori analysis of the various model structures compatible with measured distance-constraints.

### III.5 B factors and key sites

The analysis of the mobility, in thermal equilibrium, of different protein residues carries significant information about sites that are important in the folding process. We illustrate this important application for the case of the HIV-1 Protease. This enzyme represents an ideal benchmark due to the vast number of clinical studies thanks to which comprehensive tables of key mutating sites have been compiled Condra ; BIOCH88 ; gulnik ; hiv1 ; apr ; tisdale . Molecular dynamics studies have attempted to clarify the special role played by these amino acids either through all-atom simulations of the protease piana2002  or through topological folding models hiv . It appears that a number of key mutating sites form contacts that act as rate limiting steps for the folding process hiv .

One attempt to describe/predict this crucial set of amino acids from the analysis of normal modes was carried out in Refs. bah97 ; hal97 ; jer99  within GNM (to which our model reduces when $`T=0`$), who pointed out that high frequency modes are localized close to key mutating sites hiv99 . Our results, especially those of Fig. 2, support the view that the sites where the high frequency modes concentrate are paramount for native stability; in fact they are among the least exposed ones. However, this property is only related to the native structure, and does not imply that the same sites play the leading role in overcoming the folding rate-limiting steps.

A more direct strategy would be to determine the handful of contacts that form cooperatively at, or in the neighborhood of, the folding transition temperature. The formation of such contacts, which has an all-or-none character, is expected to constrain significantly the mobility of the residues involved in their establishment. This scheme, which has been confirmed a posteriori in simplified folding models of the HIV-1 PR and prion hiv ; goprion , can be naturally adopted in the present case. In fact, a natural and convenient measure of the degree of spatial constraint of a given site is provided by the associated B-factor. Thus, near the folding transition temperature, one expects that the key sites have nearly native like values for the $`B`$ factors, while other residues will have much larger fluctuations than in the native state. Therefore, one may identify the key sites as those with small values of $`B`$ or small derivatives of $`B`$ with respect to temperature. It turns out that both these criteria work well, as illustrated in Fig. 9. Among the top 13 sites ranked according to the smallness of $`B`$ factors there are 5 key residues: 32,33,77,84,30. In the top 13 sites ranked according to the derivative of $`B`$ there is an additional key site, namely residue 82. The probability to observe at least these many matches had we chosen the sites randomly, would have been 3 % and 0.5 % respectively in the two cases. It must be stressed that the present strategy to identify key sites exploits the information on native topology in a non-trivial manner avoiding, for example, the pitfall of selecting the most buried sites as the key ones. In fact, to collect the same number of correct matches found before, one needs to retain about twice as many burial-ranked sites than for the B-factor-ranked case. We have verified that this conclusion holds for all interaction cutoffs in the range 6.5-8 Å. This very good statistical validation shows that the physically appealing identification of the key sites through normal modes analysis can be fruitfully applied in contexts of high practical importance.

## IV Conclusions

We have focused on the characterization of both the folding process and equilibrium physical properties of natural proteins through the normal modes analysis of a suitable topological model. Previous investigations of normal vibrations around the native state have proved a valuable tool to describe the large scale motion of proteins and obtain clues about their biological functionality.

Although we also focus on specific protein instances, such as the HIV-1 protease, our scope is more directed at finding some general characteristics of proteins’ dynamics in thermal equilibrium (at various temperatures) that distinguish these biopolymers from a randomly compact polymer. This comparison has a two-fold objective: one of theoretical interest, the other more practical.

¿From the point of theoretical biophysics, the identification of features that are unique (and common) to proteins provides clues about the special evolutionary criteria that have promoted the selection of the wide repertoire of naturally-occurring proteins yet using only a limited number of fold families plato ; Chothia2 ; secstr . In the detailed account provided here we have shown that proteins are very flexible and have long relaxation times, in thermal equilibrium, compared to globular polymers. In turn, the relaxation time of partially folded states is shown to have a significant correlation with experimental folding times ($`r`$ can be as high as 0.73). We give a quantitative account of the intimate dependence of the relaxation rates with native state topology; thereby providing a novel additional support to the influence of native-state topology over folding rate. It is also found that high-frequency modes involve as many sites in natural proteins as in disordered structures. Despite this, the structural regions involved in slow motions are much more extended in proteins. Without this property (common to the few tens of proteins considered here) it would probably be impossible for a protein to carry out the articulated mechanical tasks necessary for biological functionality bah99 ; hal99 ; hiv99 ; kes00 . The direct investigation of the vibrational properties of individual secondary motifs has shown that their presence and organization are distinctive features of protein structures. This observation adds to previous evidence according to which the ubiquity of secondary motifs in real proteins is due to the very special properties that they confer both to the native state and to the folding process.

¿From a more practical point of view, the knowledge of how these ”special features” have arisen through the selection of certain viable native shapes, can be used as a predictive tool. In particular, the straightforward deterministic analysis of the topologic folding model adopted here allows to predict folding rates with high statistical significance. A further important application is in the ”a priori” determination of the B factors that are essential in the refinement and validation of protein structures resolved by X-ray and NMR. A by-product of the analysis of B factors of partially folded states is the identification of the sites (or contacts) that lock into their relative native position at early stages of the folding process. Taking the case of HIV-1 PR as a reference, we have shown that such sites are among those that are known to be involved in rate-limiting steps of the folding process. Therefore, within this single simple framework it is possible to model various aspects of the folding process and other equilibrium properties obtaining a thorough protein characterization that is consistent with available experimental results.

This work was supported by INFM and MURST cofin 2001. GL’s research has been supported by a Marie Curie Fellowship of the European Community Programme “Improving Human Research Potential and the Socio–Economic Knowledge Base” under contract number HPMF–CT–2001–01432. The authors are solely responsible for information communicated and the European Commission is not responsible for any view or results expressed. We are indebted to Jayanth Banavar, Ken Dill, Burak Erman, Doriano Lamba and Henriette Molinari for stimulating discussions and helpful suggestions.

## Appendix A Appendix. Methods: Analytical characterization of the model

The simplified energy functional used to characterize the equilibrium or folding properties of a target structure, $`\mathrm{\Gamma }`$ is:

$$=\frac{KT}{2}\underset{i=1}{\overset{N1}{}}(𝐫_i𝐫_{i+1})^2+\frac{1}{2}\underset{ij}{}\mathrm{\Delta }_{ij}^\mathrm{\Gamma }[(𝐫_i𝐫_j)^2R^2]p_{ij}$$
(4)
where $`𝐫_i`$ denotes the distance-vector of the $`i`$th $`C_\alpha `$ from its position in the native structure, $`\mathrm{\Gamma }`$ (assumed to be $`N`$ residues long). $`K`$ is the strength of the peptide bonds, and $`T`$ is the absolute temperature (incorporating the Boltzmann constant). $`\mathrm{\Delta }^\mathrm{\Gamma }`$ is the contact matrix, whose element $`\mathrm{\Delta }_{ij}`$ is 1 if residues $`i`$ and $`j`$ are in contact in $`\mathrm{\Gamma }`$ (i.e. their Cα separation is below a cutoff $`c`$. (in this study $`c=7.5`$ Å) and 0 otherwise. The matrix $`\mathrm{\Delta }_{ij}^\mathrm{\Gamma }`$ along with the native $`C_\alpha `$ coordinates encodes the topology of the protein. In standard off-lattice approaches, the interaction $`V(d)`$ between non-bonded amino acids at a distance $`d`$, is taken to be a square well potential, or some type of Lennard-Jones interaction. Our choice in Eq. (4) is a sort of “harmonic well” which, while being physically sound and viable, is suitable for a self-consistent treatment, as explained below.

The temperature-dependent term $`p_{ij}`$ is the probability that the separation of amino acids $`i`$ and $`j`$ fall within a distance $`R`$ of the native separation. Therefore $`R`$ plays the role of an effective outer rim of the quadratic potential well and can be set to a few Angstroms ($`R=3`$ Å in the present study) to reflect the fact that, when the separation of two residues exceeds substantially the native one their interaction is negligible. The strength of the peptide bond, $`K`$, is set to $`1/15`$ gaussian . Such choice of values guarantees that close to the folding transition temperature, nearly half of the native contacts are formed, consistently with several unrelated studies karp ; Jackson .

The simple quadratic form of Hamiltonian in Eq. (4) allows to determine exactly the $`p_{ij}`$’s from the self-consistent relation:

$$p_{ij}=\mathrm{\Theta }(|𝐫_i𝐫_j|^2R^2).$$
(5)
where $`\mathrm{\Theta }(x)`$ is the unitary step function and the brackets denote the thermal averaging under the action of Hamiltonian 4, that depends on $`p_{ij}`$ as well. Operatively, one starts from a trial choice of the $`p_{ij}`$, which is used to determine a new set of parameters through eqn. (5). Convergence is obtained in a few tens of iterations at any temperature. Now in such self consistent approach the problem is fully solved and all equilibrium or dynamical quantities can be calculated exactly by evaluating analytical expressions. At $`T=0`$ the model correctly assigns the lowest energy to the native structure (all $`p_{ij}`$’s equal to 1). Upon increasing the temperature, each interacting pair will have increasing mutual separation (in modulus) and correspondingly, the $`p_{ij}`$’s will decrease to reflect the milder binding. In the limit $`T\mathrm{}`$ all $`p_{ij}`$’s tend to 0. It is worth pointing out that our energy functional treats non-native contacts in a neutral way: their formation is not favoured but is not discouraged either. As a consequence, at finite temperatures, non-native contacts have a non-zero probability of formation, which can still be computed through 5.

Simple algebraic operations allow to recast the self-consistent energy function in the following form:

$$=\underset{ij}{}𝐫_𝐢L_{ij}𝐫_𝐣\frac{1}{2}\underset{ij}{}\mathrm{\Delta }_{ij}^\mathrm{\Gamma }R^2p_{ij}$$
(6)
where

$$L_{i,j}=\{\begin{array}{cc}\hfill KT(2\delta _{i,1}\delta _{i,N})/2+_l\mathrm{\Delta }_{i,l}^\mathrm{\Gamma }p_{i,l}& \mathrm{for}i=j\hfill \\ \hfill p_{i,j}\mathrm{\Delta }_{i,j}+KT\left(\delta _{i,j+1}\delta _{i,j1}\right)/2& \mathrm{for}ij.\hfill \end{array}$$
(7)
While the present form of the model does not accurately describe the effects of self-avoidance this does not lead to a qualitatively wrong behaviour in the highly-denatured ensemble (large $`T`$). The treatment of steric effects becomes progressively more accurate as temperature is lowered. In fact, the model guarantees that the native state is the true ground state and therefore protein conformations found at low temperature inherit the native self-avoidance. The connectedness of the chain, as well as its entropy, are captured in a simple but non-trivial manner. The most significant advantage of the model is that it can be used to explore the equilibrium thermodynamics without being hampered by inaccurate or sluggish dynamics.


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# Generalized Benney Lattice and the Heavenly Equation

## 1 Introduction:

The Benney lattice  is defined by a set of equations of the form

$$\frac{A_k}{t}=A_{k+1,x}+kA_{k1}A_{0,x},k=0,1,2,\mathrm{}$$
(1)
where the subscript $`x`$ denotes derivative with respect to the $`x`$ coordinate. Several physical systems can be obtained from the Benney lattice. In particular, note that if we identify

$$A_k=u^kv,k=0,1,2,\mathrm{}$$
(2)
where $`u,v`$ are two independent dynamical variables, then the set of equations in (1) reduces to

$$\frac{v}{t}=(uv)_x,\frac{u}{t}=uu_x+v_x$$
(3)
which is the polytropic gas equation  with $`\gamma =2`$. The Benney lattice defines a dispersionless system of equations  and can be given a Lax description in the following manner. Consider the Lax function

$$L=p+\underset{k=0}{\overset{\mathrm{}}{}}A_kp^{(k+1)}$$
(4)
where the coefficients, $`A_k`$, are functions of $`(x,t)`$ while $`p`$ represents the momentum of the classical phase space. Then, with the usual canonical Poisson brackets of classical mechanics, it is easy to verify that the Benney lattice is obtained from

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_+,L\}$$
(5)
where $`()_+`$ stands for the projection with non-negative powers of $`p`$. This shows that the system of equations in (1) is integrable. Furthermore, it is also known that this system of equations is Hamiltonian with three distinct Hamiltonian structures, much like the system of polytropic gas equations .

In this letter, we will generalize the Benney lattice and obtain a new system of equations which can also be identified with various physical systems. In particular, we will show that this system leads naturally to a generalization of the Chaplygin gas  as well as the heavenly equation . We will give a Lax description of this system and construct two infinite sets of conserved charges. One of the sets of charges follows directly from the Lax description while the connection of the second set to the Lax function remains unclear at the present. Interestingly, both sets of the charges are related to the Legendre polynomials. We also present the generating function for these charges as well as the Riemann invariants of the system. We construct two Hamiltonian structures associated with this system and show that the system is bi-Hamiltonian (is a pencil) . This is quite easily seen in a suitable choice of the dynamical variables. We also show the involution of the charges directly from the structure of the generating functions. The generalized elastic medium equations, associated with this system, are also shown to be bi-Hamiltonian. We discuss the connection of the heavenly equation with this system of equations and conclude with some discussions on various other aspects of this sytem.

## 2 Generalized Benney Lattice

Let us consider a Lax function of the form

$$L=p^1+\underset{k=0}{\overset{\mathrm{}}{}}A_kp^{k+1}$$
(6)
If we assume the Poisson brackets of the classical phase space to be modified as

$$\{A,B\}_m=p^m\{A,B\}$$
(7)
then, it is easy to check that the Lax equation

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_0,L\}_m$$
(8)
does not lead to a consistent set of equations for $`m=0`$ (namely, the standard Poisson bracket relations). For $`m=1`$, we have a set of consistent equations provided all the odd coefficients, $`A_{2k+1}`$, in the Lax function vanish. Thus, taking our Lax function as

$$L=p^1+\underset{k=0}{\overset{\mathrm{}}{}}A_kp^{2k+1}$$
(9)
the Lax equation

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_0,L\}_{m=1}$$
(10)
leads to a system of equations given by

$$\frac{A_k}{t}=A_{k+1,x}+(2k+1)A_kA_{0,x}$$
(11)
This system of equations can be thought of as a generalization of the Benney lattice.

Let us note next that this system of equations can be reduced to a generalized Chaplygin gas in the following manner. Let us identify

$$A_0=u,A_1=\frac{1}{2v^2},A_k=\frac{1}{2}\underset{i=0}{\overset{k1}{}}A_{ki1}A_i,k>1$$
(12)
where $`(u,v)`$ are the independent dynamical variables. Then, it is straightforward to show that the system of generalized Benney lattice equations reduces to

$$\frac{v}{t}=(uv)_x,\frac{u}{t}=uu_x+\frac{v_x}{v^3}$$
(13)
This looks very much like the Chaplygin gas (polytropic gas for $`\gamma =1`$)  except for the relative sign in the two equations. It can be seen easily that there is no transformation which will normalize the sign in both the equations.

The generalized Chaplygin equations have two infinite sets of conserved charges which can be constructed as follows. First, let us note that any conserved density, $`h(u,v)`$, of hydrodynamic type (namely, not depending on derivatives) must satisfy

$$\frac{dh}{dt}=\frac{h}{u}u_t+\frac{h}{v}v_t=\frac{dG}{dx}=\frac{G}{u}u_x+\frac{G}{v}v_x$$
(14)
From the forms of the equations as well as the integrability condition $`G_{uv}=G_{vu}`$, it follows that any conserved density of hydrodynamic type associated with the system must satisfy the relation

$$2u\frac{^2h}{uv}=v^3\frac{^2h}{uu}+v\frac{^2h}{vv}$$
(15)
where the conserved charges are defined as

$$H=𝑑xh$$
(16)
Let us also note from the structure of the Lax function that we can assign the canonical dimensions $`[v]=2,[u]=2`$ to the variables so that $`[uv]=0`$. As a result, we can construct two independent sets of polynomials of the forms

$$h_k=u^kf_k(uv),\stackrel{~}{h}_k=v^k\stackrel{~}{f}_k(uv)$$
(17)
They must satisfy eq. (15) if they are to correspond to conserved densities of the system and it is not hard to check that this is indeed the case provided the functions $`f(uv)`$ and $`\stackrel{~}{f}(uv)`$ are related to the Legendre polynomials. Explicitly, $`f`$ and $`\stackrel{~}{f}`$ have to satisfy the equations

$`z^2(1z^2)f_k^{\prime \prime }+2z(k(k+1)z^2)f_k^{}+k(k1)f_k`$ $`=`$ $`0`$
$`(1z^2)\stackrel{~}{f}_k^{\prime \prime }2z\stackrel{~}{f}_k^{}+k(k1)\stackrel{~}{f}_k`$ $`=`$ $`0`$ (18)
where we have identified $`z=uv`$ and the primes denote derivatives with respect to $`z`$. The second equation is easily seen to correspond to the Legendre equation. With a change of variables, the first equation can also be seen to be related to the Legendre equation. The two infinite sets of conserved densities are obtained, in this way, to be

$`h_k`$ $`=`$ $`2^ku^k{\displaystyle \frac{1}{(uv)^k}}P_k(uv)=\left({\displaystyle \frac{v}{2}}\right)^kP_k(uv)`$
$`\stackrel{~}{h}_k`$ $`=`$ $`\left({\displaystyle \frac{v}{2}}\right)^{k+1}P_k(uv)`$ (19)
where $`k=0,1,2,\mathrm{}`$ and $`P_k(uv)`$ represent the Legendre polynomials of order $`k`$. The first few densities in the two series have the explicit forms

$`h_0`$ $`=`$ $`1`$
$`h_1`$ $`=`$ $`2u`$
$`h_2`$ $`=`$ $`6\left(u^2{\displaystyle \frac{1}{3v^2}}\right)`$ (20)
and

$`\stackrel{~}{h}_0`$ $`=`$ $`{\displaystyle \frac{v}{2}}`$
$`\stackrel{~}{h}_1`$ $`=`$ $`{\displaystyle \frac{1}{4}}uv^3`$
$`\stackrel{~}{h}_2`$ $`=`$ $`{\displaystyle \frac{1}{16}}\left(3u^2v^5v^3\right)`$ (21)
We will show next that the first set of conserved densities in (19) can be obtained from the Lax function. Let us note that, with the identification in eq. (12), we can sum the infinite series in (9) and the Lax function can also be written in the closed form

$$L=p^1\left(1+2up^2+(u^2\frac{1}{v^2})p^4\right)^{\frac{1}{2}}$$
(22)
There are several interesting things to note from this form of the Lax function. First of all, it is almost trivial to check from this form that we can write

$$\mathrm{Residue}(p^1L^{2n})=\left(\frac{v}{2}\right)^nP_n(uv)=h_n$$
(23)
Let us note that since the Lax function in (22) involves both positive and negative powers of $`p`$, as in the case of a non-standard Lax description of the polytropic gas , it is natural to expect that the residues calculated around $`p=0`$ and $`p=\mathrm{}`$ may provide the two sets of conserved densities. However, in this case, residues calculated at both these points yield the same conserved densities and we do not know yet how to relate the second set of conserved densities to the Lax function.

We also note here that the Lax function can also be expanded around $`p=\mathrm{}`$ so that we can write it in the form

$$L=\underset{k=1}{}A_kp^{(2k+1)}$$
(24)
which has the same form as the Lax for the Benney lattice in (4). However, because of the difference in the classical Poisson brackets, the two systems are inequivalent. It is also interesting to point out here that the system of equations in (13) has a second Lax description. Consider, for example, the Lax function

$$L=p\left(1+2up^2+(u^2\frac{1}{v^2})p^4\right)^{\frac{1}{2}}$$
(25)
Then, it can be verified in a simple manner that the Lax equation

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_+,L\}_{m=1}$$
(26)
also leads to the equations in (13). However, even this second Lax function yields only the first set of conserved densities.

Once we have the conserved densities in closed form and we know that they are related to the Legendre polynomials, we can write generating functions for these conserved densities in closed form. For example, it is easy to check that

$$T(u,v;\lambda )=\frac{v}{\sqrt{v^24uv^2\lambda +4\lambda ^2}}$$
(27)
where $`\lambda `$ is an arbitrary constant parameter, generates the first set of conserved densities as

$$h_n=\frac{^nT(u,v;\lambda )}{\lambda ^n}|_{\lambda =0}$$
(28)
Similarly, the generating function for the second set of conserved densities has the closed form

$$\stackrel{~}{T}(u,v;\stackrel{~}{\lambda })=\frac{v}{\sqrt{44uv^2\stackrel{~}{\lambda }+v^2\stackrel{~}{\lambda }^2}}$$
(29)
where $`\stackrel{~}{\lambda }`$ is an arbitrary constant parameter and we have

$$\stackrel{~}{h}_n=\frac{^n\stackrel{~}{T}(u,v;\stackrel{~}{\lambda })}{\stackrel{~}{\lambda }^n}|_{\stackrel{~}{\lambda }=0}$$
(30)
As in the case of the polytropic gas, we find that the quantity inside the radical determines the Riemann invariants for the system . In this case, the two Riemann invariants have the forms

$$\lambda _\pm =\frac{v}{2}\left(uv\pm \sqrt{u^2v^21}\right)$$
(31)
The generalized Chaplygin gas is a bi-Hamiltonian system. We find that the system has the following two compatible Hamiltonian structures,

$`𝒟_2`$ $`=`$ $`{\displaystyle \frac{1}{8}}\left(\begin{array}{cc}0& v(u^2v^21)\\ v(u^2v^21)& v(u^2v^21)uv^3uv^3v(u^2v^21)\end{array}\right)`$ (34)
$`𝒟_3`$ $`=`$ $`{\displaystyle \frac{1}{2}}\left(\begin{array}{cc}(u^2v^2)+(u^2v^2)& 2(uv)_x\\ 2(uv)_x& (v^2u^2v^4)+(v^2u^2v^4)\end{array}\right)`$ (37)
The equations (13) can be written in the Hamiltonian form with these structures as

$$\left(\begin{array}{c}u_t\\ v_t\end{array}\right)=𝒟_3\left(\begin{array}{c}\frac{\delta H_1}{\delta u}\\ \\ \frac{\delta H_1}{\delta v}\end{array}\right)=𝒟_2\left(\begin{array}{c}\frac{\delta H_2}{\delta u}\\ \\ \frac{\delta H_2}{\delta v}\end{array}\right)$$
(38)
The compatibility of these two Hamiltonian structures can also be checked. However, it involves a lengthy calculation in these variables and takes a much simpler form in an alternate choice of variables. Therefore, we will discuss this question in the next section. However, we note here that, unlike the polytropic gas where there are three Hamiltonian structures, in this case, we have not been able to find the analog of the first Hamiltonian structure.

With these two Hamiltonian structures, the involution of the conserved charges can now be shown easily. In fact, it is much simpler to study the involution of the generating functions for the conserved densities themselves and show that, with respect to either of the structures,

$`\{T(u,v;\lambda ),T(u,v;\lambda ^{})\}`$ $`=`$ $`K_x`$
$`\{\stackrel{~}{T}(u,v;\stackrel{~}{\lambda }),\stackrel{~}{T}(u,v;\stackrel{~}{\lambda }^{})\}`$ $`=`$ $`L_x`$
$`\{T(u,v;\lambda ),\stackrel{~}{T}(u,v;\stackrel{~}{\lambda })\}`$ $`=`$ $`M_x`$ (39)
where $`K,L,M`$ are complicated (but uninteresting) polynomials. This shows that the conserved charges (which are integrals of the densities), are in involution and, therefore, the system is completely integrable with respect to both the Hamiltonian structures.

We conclude this section by pointing out another interesting feature of these equations. We know that the polytropic gas and the elastic medium equations share the same Lax function, the same conserved charges and both these systems are bi-Hamiltonian with the same Hamiltonian structures . In the present case, we also note that if we take the second series of conserved charges from (19) or (21), it is easy to verify that

$$\left(\begin{array}{c}u_t\\ v_t\end{array}\right)=\frac{1}{8}𝒟_3\left(\begin{array}{c}\frac{\delta \stackrel{~}{H}_1}{\delta u}\\ \\ \frac{\delta \stackrel{~}{H}_1}{\delta v}\end{array}\right)=𝒟_2\left(\begin{array}{c}\frac{\delta \stackrel{~}{H}_0}{\delta u}\\ \\ \frac{\delta \stackrel{~}{H}_0}{\delta v}\end{array}\right)=\frac{1}{2}\left(\begin{array}{c}(u^2v^3v)_x\\ \\ (u^3v^6uv^4)_x\end{array}\right)$$
(40)
It is clear, therefore, that the modified elastic medium equations, in this case, are also bi-Hamiltonian.

## 3 Heavenly Equation

Let us consider the Lax function in eq. (22) and identify

$$a=(u^2\frac{1}{v^2}),b=2u$$
(41)
so that we can write

$$L=p^1(1+bp^2+ap^4)^{\frac{1}{2}}$$
(42)
It is straightforward to check that the Lax equation,

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_0,L\}_{m=1}$$
(43)
leads, in these variables, to the equations

$$a_t=ab_x,b_t=a_x$$
(44)
These coupled set of first order equations can also be written as a second order equation of the form

$`\left(\mathrm{ln}a\right)_{tt}`$ $`=`$ $`a_{xx}`$
$`\mathrm{or},X_{tt}`$ $`=`$ $`\left(e^X\right)_{xx}`$ (45)
where we have defined $`X=\mathrm{ln}a`$. This is known as the heavenly equation (in $`1+1`$ dimensions)  and can be obtained as a continuum limit of the Toda lattice. This equation appears in the study of gravitational instantons  and can be linked to the Schröder equation which arises in the bootstrap models as well as in renormalization theory .

The description of the dynamical equations in terms of the variables, $`a,b`$, is simpler and brings out many features rather nicely. For example, the two Hamiltonian structures (37) can be written in these variables to be

$`𝒟_2`$ $`=`$ $`{\displaystyle \frac{1}{2}}\left(\begin{array}{cc}0& a\\ & \\ a& 0\end{array}\right)`$ (48)
$`𝒟_3`$ $`=`$ $`2\left(\begin{array}{cc}a^2+a^2& ab\\ & \\ ba& a+a\end{array}\right)`$ (51)
We note that the first two nontrivial Hamiltonian densities of eq. (20) take the forms, in these variables, as

$$h_1=\frac{b}{2},h_2=b^2+2a$$
(52)
and it is straightforward to check that the above equations can be written in the Hamiltonian forms

$$\left(\begin{array}{c}a_t\\ b_t\end{array}\right)=𝒟_3\left(\begin{array}{c}\frac{\delta H_1}{\delta a}\\ \\ \frac{\delta H_1}{\delta b}\end{array}\right)=𝒟_2\left(\begin{array}{c}\frac{\delta H_2}{\delta a}\\ \\ \frac{\delta H_2}{\delta b}\end{array}\right)$$
(53)
It is clear that these Hamiltonian structures have a much simpler form than the ones given in the last section, although they are equivalent to these. More importantly, we note now that under a shift $`aa,bb+\lambda `$, where $`\lambda `$ is an arbitrary constant parameter

$$𝒟_3𝒟_3+4\lambda 𝒟_2$$
(54)
This shows that the two structures are compatible and that the system is bi-Hamiltonian (otherwise also known as a pencil system). The integrability of this system, therefore, follows. This also brings out why it is more involved to explicitly see the compatibility of the two structures in the old variables, namely, the appropriate shift is highly nontrivial in the $`(u,v)`$ variables.

Furthermore, since the Hamiltonian structures have a simpler form in these variables, the recursion operator can also be constructed easily. It has the form

$$=𝒟_2^1𝒟_3=4\left(\begin{array}{cc}ba^1^1ab_x& 2a^1^1a_x\\ \multicolumn{2}{c}{}\\ 2a& b\end{array}\right)$$
(55)
The recursion operator, in the old variables can, of course, be obtained from this through a coordinate redefinition. However, the form is much more complicated and is uninteresting to list here.

## 4 Summary and Discussions

In this letter, we have generalized the Benney lattice which can describe a generalized Chaplygin gas equation. We have constructed the Lax representation for this system and have constructed two infinite sets of conserved charges which are related to the Legendre polynomials. We can relate one of these two sets to the residues of the Lax function and the relation of the second set to the Lax is unclear at the present. We have given closed form expressions for the generating functions for these densities which also leads to the two Riemann invariants for the system. We have shown that the system is bi-Hamiltonian (a pencil system) and have shown the involution of charges thereby proving complete integrability of the system. We have also shown that the associated generalized elastic medium equations are bi-Hamiltonian as well. This system of generalized Chaplygin gas equations can be transformed to the heavenly equation which arises in many branches of physics. Many features of the system take a simpler form in this description.

We would now like to make some general comments on some other aspects of our system. First, we note that the higher order equations of the hierarchy of generalized Chaplygin gas can be obtained from

$$\frac{L}{t_n}=\frac{1}{2n}\{(L^{2n})_0,L\}_{m=1},n=1,2,\mathrm{}$$
(56)
where $`L`$ is the Lax function in (9) or (22). However, in addition, we have also found that the system of equations

$$\frac{L}{t}=\frac{1}{2n+1}\{(L^{2n+1})_0,L\}_{m=2}$$
(57)
also leads to consistent equations. However, we have not analyzed integrability properties of such systems completely. It is also worth noting that the Lax function in (6) leads through

$$\frac{L}{t}=\frac{1}{2}\{(L^2)_0,L\}_{m=2}$$
(58)
to the Benney lattice. Finally, without going into details, we would like to note that we can generalize the Lax function in (22) to

$$L=p^{1n}\left(1+A_1p^n+A_2p^{2n}\right)^{\frac{1}{n}}$$
(59)
This will lead to a generalized set of equations

$`A_{1,t}`$ $`=`$ $`{\displaystyle \frac{2(n1)}{n}}\left(A_{2,x}{\displaystyle \frac{(n2)}{n}}A_1A_{1,x}\right)`$
$`A_{2,t}`$ $`=`$ $`2\left({\displaystyle \frac{(n3)}{n}}A_2A_{1,x}+{\displaystyle \frac{(n2)}{n^2}}A_1A_{2,x}\right)`$ (60)
following from the Lax equation

$$\frac{L}{t}=\frac{1}{n}\{(L^2)_0,L\}_{m=n1}$$
(61)
All these equations are likely to be integrable since they follow from a Lax description. However, we have not studied these systems in more detail.

## Acknowledgments

This work was supported in part by US DOE grant no. DE-FG-02-91ER40685 as well as by NSF-INT-0089589.


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# Summary Talk on Cosmology and Gravitation XXII Brazilian National Meeting on Particles and Fields

## I Overview and Introduction

After four days of listening to two plenary lectures, two parallel talks, a general public lecture, seventeen oral presentations, and reading more than fifty panels related to Cosmology and Gravitation, my chief impression is that the XXII Brazilian National Meeting on Particles and Fields (XXII BNMPF) was an noticeable scientific meeting, which covered a great variety of issues on Gravitation and Cosmology. It brought together perhaps most of the researchers and graduate students that have worked in this area in Brazilian Universities and Research Institutes. The sessions were very well attended with a fair number of clarifying questions. In general the speakers explained the underlying ground, approaches and results in a clear manner and kept to the time limits. I thank to them all for their quite good talks.

From this and the previous meetings I support the view that if one considers the contributions presented in, e.g., two successive BNMPF meetings they are rather representative of the researches that have been done in this area in Brazil, and most of the contributions reveal a clear emphasis on theoretical and (or) mathematical aspects of Gravitation and Cosmology .

The researches in modern cosmology can be broadly grouped in five domains:

1. Astrophysical cosmology;
2. Observational cosmology;
3. The early universe;
4. Theoretical and mathematical cosmology;
5. Cosmic topology (more recently).

Most of the contributions to the XXII BNMPF (organized by the Brazilian Physical Society - SBF) were in the last three wide families. On the other hand, as far as I am aware a great number of the observationally-oriented works on cosmology are often presented in the annual meeting of the Brazilian Astronomical Society (SAB).

I do not share the view that theoretical (and mathematical) cosmology should be strictly related to the observed universe, otherwise it becomes a pointless exercise. In my evaluation the frontier between theoretical (and mathematical) cosmology and more observationally-oriented cosmology is not and should not be well-defined, and it is very important that we have people working on both general aspects of modern cosmology. However, I understand that a closer interaction between theoretical and observationally-oriented cosmologists is more than desirable — in my view it is recommendable — for the benefit of both (physicist and astophysicist) communities. The recent workshop called New Physics in the Space is certainly a good example in this direction .

A considerable number of abstracts were submitted to the organizers. I envisage how hard was to select between oral and panel presentations. A number of relevant subjects seemed to them to be of interest to motivate oral presentations, but no doubt other organizers would have made a quite different, and perhaps equally good, selection. I will summarize the presented contributions below, with apologies to their authors for any unintentional misapprehension and (or) misrepresentation.

## II Plenary and Parallel Talks

The General Relativity (GR) predicts the existence of gravitational waves, and analyses of experimental data obtained from observations of binary star systems seem to give a clear evidence that these systems loose energy through gravitational radiation .

Gravitational waves are predicted not only by GR but also by other metric gravitational theories of some generality and scope. However, the characteristics of gravitational waves such as propagation speed, multipolar structures and polarization states vary from one theory to another. Thus, it is expected that its detection will provide a rather relevant tool to select the most suitable theory of gravitation . Further, the direct observation of gravitational waves also offer the possibility of testing GR (as well as other metric theories) in a strong field limit, where the effects are not merely a correction of Newtonian Gravitation. Obviously at Earth the waves are expected to be weak perturbations, however they can in principle provide information on the conditions at their strong field sources . Further, the technology needed to detect as well as the analysis of gravitational waves is expected to open a new window for observation of the universe, thus giving rise to a remarkable period in astronomy and cosmology.

Barry C. Barish (California Institute of Technology) delivered a clear plenary lecture in the XXII BNMPF, in which he presented a good review of the new generation of detectors with suitable sensitivities for detecting gravitational waves from a variety of catastrophic events, such as the gravitational collapse of stars or coalescence of compact binary systems. He pointed out that more than forty years after the beginning of the search for gravitational waves, several resonant-mass wave detectors are monitoring the most strong potential sources of such waves (in the $`kHz`$ band) in our galaxy and in our local group. The gravitational wave detection of low frequencies (in the $`mHz`$ band) from space was also briefly discussed in his talk. Contrarily to the earth based detectors, for this type of detection there is a natural advantage which is the fact that essentially all the noises due to the ground are eliminated (for more detail see ).

For some decades since the discovery of the cosmic expansion by Hubble  it was taken for granted that the matter content of the universe was composed by the forms of energy we can readily detect, i.e., the ordinary matter and radiation. Such universe would expand with a negative expansion rate due to gravitational self-attraction of the matter. However, some years later, theoretical aspects of the stability of galaxies and some observations (motion of cluster of galaxies and stars and surrounding galaxies) indicated that most of the matter of the universe does not emit or absorb light (dark matter). The dark matter clear indication found resonance in the 1980’s by the inflationary universe scenario in which the universe is taken to be flat — the total energy density equal to the critical density $`\rho _c=3H_0^2/8\pi G\mathrm{1.7\hspace{0.17em}\hspace{0.17em}10}^{29}g/cm^3`$. However, measurements made by that time offered a clear indication that the ordinary matter and the radiation could only account for about $`10\%`$ of this value — inflation seemed to require dark matter. The new consensus model became that in which the universe contains primarily cold, nonbaryonic dark matter, and although observations at that time indicated that the total mass density was smaller than the critical density, many cosmologists assumed that the flat model was reasonably well-established. However, further observations strongly indicated that the total matter density was indeed less than half of the critical density. The only way of having such a low mass density and a flat universe is if an additional, nonluminous and nonclustering “dark energy” component dominates the universe today, although it must have been negligible in the past so as to permit structure formation. The general relativity Friedmann-Lemaître-Robertson-Walker (FLRW) standard modeling approach requires that this dark energy has a negative pressure, and the recent measurements of distant exploding stars (supernovae) support the existence of a negative-pressure dark energy such that the (total) energy density $`\rho `$ and the (total) pressure $`p`$ obey the relation $`\rho +3p<0`$, which leads to an accelerating expansion for the universe today (for a fair list of basic references on the topics I have briefly mentioned here, see the very good review by Bahcall et al. ).

Luca Amendola (Osservatorio Astronomico di Roma) presented a quite good plenary talk in which he reviewed how the recent independent cosmological observations constrain the values of the cosmological density parameters, and have indicated that the universe is filled with dark matter and dark energy and undergoes an accelerating expansion. He pointed out how recent supernovae Ia observations  call for an acceleration expansion of the universe, which together with recent cosmic microwave, large-scale structure and lensing data give a rather strong indication that the matter (energy) content of the universe is basically composed of dark matter ($`30\%`$), dark energy ($`70\%`$), baryonic matter (very few percent). For more details and references see his review paper in this issue .

Odylio D. Aguiar (INPE) told us about the status of the Mario Schenberg gravitation wave detector, which is being constructed in the Institute of Physics of the University of São Paulo, and is expected to start to operate in 2002. This detector has a spherical antenna, will operate at temperature of less than $`0.1K`$, and will be sensitive to signals of amplitude $`h>10^{21}Hz^{1/2}`$ in the bandwidth $`3.0`$ – $`3.4kHz`$ (for more details on this talk see Aguiar’s paper in this issue ).

It is well known that general relativity is a local metrical theory and therefore its field equations do not fix the topology of the spacetime, since geometry does not in general dictate the topology. This freedom has resulted in a great deal of recent works in which the possibility that the universe may possess a spatial section with a non-trivial topology is examined. Whether we live in a finite or infinite space and what is the size and the shape of the universe are open problems of topological nature. In his talk Helio V. Fagundes presented a brief introduction to cosmic topology in the context of FLRW models, and reviewed the work done by his group and collaborators at IFT/UNESP. The works he described range from early attempts to solve a controversy about quasars through the multiple images produced by nontrivial topologies, to more recent issues such as cosmic crystallography and on quantum cosmology in compact universe models (for more details on this talk see Fagundes’ paper in this issue ).

Before reviewing the oral presentations I remark that one particular objective of the organizers was to involve as far as possible the local general public with the meeting. To this end they invited I. Waga to give a public general lecture on cosmology, and he presented a clear and motivating lecture on the expansion of the universe .

## III Oral Presentations I

The first oral presentation was of an observationally-oriented paper by M.O. Calvão, J.R.T. de Mello Neto and I. Waga , where it was discussed, through Monte Carlo simulations, how the Alcock-Paczyński test, as applied to quasar clustering, can be used to probe the cosmological density parameters space, and also the equation of state parameter. The approach discussed in this contribution may become a relevant strategy to narrow down the cosmological parameter space.

H.P. de Oliveira and S.E. Jorás presented an early universe contribution, where they studied the evolution of the entropy and adiabatic perturbations and showed that for a small amount of dissipation the entropy perturbations can be neglected, and so the purely adiabatic perturbations will be responsible for the primordial spectrum of inhomogeneities .

In a work presented by Sandra Roveda (M.E. Araújo, S.R.M.M. Roveda and W. Stoeger ) spherically symmetric perturbations of FLRW models in the so-called observational coordinates were examined. The FLRW (spherical) models are used as the background spacetime and a particular case of spherical deviation from this background is studied (for more details on this “observational program” I refer the reader to the paper by Ellis et al. ).

Using recent observational constraints on cosmological density parameters, together with recent mathematical results concerning small volume hyperbolic manifolds and a topological detectability indicator introduced in , G.I. Gomero reported on a contribution on cosmic topology in which it is argued that, by employing pattern repetitions, the topology of nearly flat small hyperbolic universes can be observationally undetectable . This is an important result in view of the fact that quantum cosmology seems to favour universes with small volumes, and from the expectation, coming from inflationary scenarios, that the total density $`\mathrm{\Omega }_0`$ is likely to be very close to one.

By considering that the current expanding era is preceded by a contracting phase, in other words by assuming the existence of one bounce, N. Pinto-Neto showed how one can conclude that no observable bounce could possibly have taken place in the early universe if GR together with hydrodynamical fluids describe the evolution of the universe, thus under these conditions the universe has always expanded (see  for more details).

The first set of oral presentation was closed with the presentation by S.E. Jorás of a article by R.H. Brandenberger, S.E. Jorás and J. Martin, in which the spectrum of scalar field fluctuations in a bouncing asymptotically flat universe was calculated, and the dependence of this result on length scales shorter than the Planck length was investigated (for more details see ).

## IV Oral Presentations II

Topological defects such as monopoles, strings and domain walls have been studied in different contexts such as to understand the primordial universe and structure formation in the early universe. Their nature depends upon the topology of the vacuum manifold of the field theory under consideration. The second set of oral presentations began with a contribution by R.M. Teixeira Filho and V.B. Barbosa , where they have obtained in the context of scalar tensor theories the gravitational field of a global monopole, in the weak-field approximation, extending the Barriola and Vilenkin monopole solution found in the context of GR.

S.S. e Costa delivered a contribution related to cosmic topology in which general solutions of the Helmholtz equation, in several coordinates systems for two and three-dimensional hyperbolic, spaces were presented .

Another contribution related to cosmic topology was an article by D. Müller, H.V. Fagundes and R. Opher , where they have studied, through numerical calculations, the Casimir (vacuum) energy for a conformally coupled, massive scalar field in a static universe whose spatial sections are endowed with the topology of the smallest known hyperbolic three-manifold (Weeks manifold). They have concluded that there is a spontaneous vacuum excitation of low multipolar components.

A. Bernui also presented a cosmic topology contribution in which the cosmic crystallography statistical approach to the topological signature of the universe was used in his numerical simulations with incomplete catalogs.

R. Androvandi presented an interesting contribution (R. Aldrovandi, J. Gariel and G. Marcilhacy) on what they call the pre-nucleosynthesis period (PNS period), between $`z10^{10}`$ and $`z10^{15}`$, and where our local physics does not necessarily hold. A general overview of physical problems appearing in the PNS period was given, and possible meaning for the striking outcomes were discussed. For more details see .

## V Oral Presentations III

Condensed matter systems such as light in moving dielectrics and quasiparticles in a moving superfluid can be used to mimic kinematic aspects of general relativity. The comparative study between the kinematical aspects of GR and other kinds of interactions has been called analog model for gravitation or simply analog gravity. These types of analog models are rather important in that, e.g., they provide black hole analogs and may lead to experimental test of quantum field theory in curved space. The last set of oral presentations began with a brief review talk, delivered by R. Klippert (a work in collaboration with V.A. de Lorenci) where it was discussed analog gravity models in several contexts, ranging from electrodynamic in non-linear media  to moving dielectrics and acoustic perturbations (for a fair number of references on this topic see ).

A work by J.M.F Maia and J.A.S. Lima in which a procedure to generate cosmological solutions in the context of GR whose matter content is given by a scalar field plus a perfect fluid was presented. Applications to inflationary and quintessence cosmologies were also considered in specific models (see ).

A.Y. Miguelote reported on the results of an article in collaboration with M.F.A. Silva, A.A. Wang and N.O. Santos, in which some properties of the Levi-Civita (LC) type of solutions of coupled Einstein-Maxwell equations are studied, and some limits of this type of solution are obtained together with an interpretation of the free parameters involved in LC type of spacetimes .

I.D. Soares presented a interesting paper (homoclinic chaos in the dynamics of a general Bianchi IX) of a work in collaboration with H.P. Oliveira, A.M.O. Almeida, and E.V. Tonini, in which they have studied the dynamics of anisotropic (three scale factors) Bianchi type IX model with dust and cosmological constant (positive). They have examined the existence of chaos in this model, and have shown that it is chaotic, and that the chaos has a homoclinic nature. The role played by the cosmological constant in the phase space is shown to be crucial in that it determines both the existence of a saddle-center-center critical point, and the critical points at infinity corresponding to the De-Sitter configuration. For more details I refer the reader to ref. .

The interaction of Hawking radiation and a static electric charge was a contribution delivered by L.C.B. Crispino of a work in collaboration with A. Higuchi and G.E.A. Matsas, in which they have investigated in two interacting situations whether the equality found for the response of a static scalar field is maintained in the case of electric charges (see ).

The last oral presentation was presented by J. Castiñeiras (a work in collaboration with L.C.B Crispino, G.E.A. Matsas and D.A.T. Vanzella). They have studied “free particles” for which $`E<mc^2`$ outside Reissner-Nordstrom blackholes and in a spacetime of a star (for more details see ).

## VI Panel Contributions

More than fifty contributions were presented as posters. About twenty per cent were related to the physics of the early universe. F.G. Alvarenga, J.C. Fabris, G.A. Monerat and N.A. Lemos presented two contributions on quantum cosmology . N. Pinto-Neto and E.S. Santini also presented a poster related to quantum cosmology (see in this connection the article ). Three works connected to the preheating process were presented as panels: one by S.E. Jorás and V.H. Cárdenas ; a second by A.H. Campos, R. Rosenfeld and J.M.F. Maia; and another by R.O. Ramos and S.E. Jorás. Three posters were related to inflation one by H.P. de Oliveira and I. Damião Soares, a second by H.P. de Oliveira alone , and a third by J.C. Fabris, A.M. Pelinson and I.L. Shapiro . A.H. Campos, R. Rosenfeld, J.M.F. Maia and H. Reis discussed in a poster the possible production of superheavy primordial particles. R. Aldrovandi, A.L. Barbosa, M. Cançada and J.G. Pereira presented a poster on kinematics of a spacetime with infinite cosmological constant ($`\mathrm{\Lambda }\mathrm{}`$) and speed of light ($`c\mathrm{}`$), whose results may be of some interest to early universe cosmology . A poster with some contact with the early universe was also brought to the meeting by M.G.C. Batista.

Nine contributions related to topological defects in different contexts were presented as posters. Three of them treated these defects in scalar-tensor theories: one by V.B. Bezerra, L.P. Colatto, M.E.X. Guimarães and R.M. Teixeira Filho ; another by V.B. Bezerra and C.N. Ferreira ; and a third by V.B. Bezerra, R.M. Teixeira Filho, G. Grebot and M.E.X. Guimarães . The behaviour of nonrelativistic quantum particles interacting with different potentials in the spacetimes generated by a cosmic string and also by a global monopole were discussed in a panel by G. de A. Marques and V.B. Bezerra . Two posters on cosmic strings were presented: one by A.A. Morégula in collaboration with M.M. Som, and another by V.A. de Lorenci and E.S. Moreira Jr (see ). The solutions of Schrödinger equations for the Coulomb and harmonic oscillator potential in the cosmic-string conical spacetimes of $`N`$ dimensions were presented in a poster by J.L.A. Coelho and R.L.P.G. Amaral . Topological defects in the context of (or related to) condensed matter were discussed in two posters: one by C.A.L. Ribeiro, C. Furtado and F. Moraes, and another by J.F de Assis, V.B. Bezerra and C. Furtado.

Besides Fagundes’ parallel talk and the oral presentations by G.I. Gomero, S.S. e Costa, D. Müller et al., and A. Bernui, we had an additional panel presentation by G.I. Gomero of a work in collaboration with M.J. Rebouças and R. Tavakol  on the detectability of cosmic topology of nearly flat FLRW universes in the light of the most recent observations (Sne Ia, large scale structure (LSS) observations, MAXIMA and BOOMERANG).

In addition to Barry C. Barish’s plenary talk, and O.D. Aguiar’s parallel talk, four posters related to gravitational waves were presented: K.L. Ribeiro and O.D. Aguiar; S.R. Furtado and O.D. Aguiar; and L.A. de Andrade, O.D. Aguiar and K.L. Ribeiro; and also C. Frajuca, N.S. Magalhães, O.D. Aguiar, K.L. Ribeiro, L.A. de Andrade, W.F. Velloso Jr and J.L. Melo (see ).

Three posters were presented on parallel gravity. One by T. Vargas on Regge Calculus in teleparallel gravity, and three others by A.A. Sousa and J.W. Maluf (for more details see ).

It seems indisputable that most of theoretical physicists spend a large amount of their time in carrying out nonnumeric calculation of one sort or another, most of which are algorithmic or semi-algorithmic. Today the computer algebra (CA) systems are standard tools of theoretical physicists for performing symbolic, although in most cases perhaps they simply do not mention this fact. We had three CA poster contributions in the meeting, all related to the Maple system. One dealt with the symmetry groups in GR (by J.A.F. Roveda and J.E.F. Skea), which is a relevant piece of information needed in the invariant (local) characterization of spacetime; and another was about the usage of Maple to calculate quasi-normal modes of radiating systems (by P.C.C. Monteiro Jr and J.E.F. Skea). F.D. Sasse delivered a contribution in collaboration with R.F. McLenaghan and S.R. Czapor where the Maple package NPspinor was used to prove the Hadamard’s conjecture for the scalar wave equation in Petrov type III backgrounds.

Different aspects and contexts of black holes were discussed in a series of four posters. G. de Oliveira Neto studied exact solutions of Einstein’s equations in ($`2+1`$)-dimensions which, depending on the values of certain parameters, may represent the formation of black holes . A.A. Sobreira and V.B. Bezerra examined rotating black hole in Einstein-Fokker theory in ($`2+1`$)-dimensions. Holonomies in the ($`2+1`$)-dimensional geometry of black holes were the content of a poster by A. Carvalho, C. Furtado and F. Moraes. A black hole type solution of Einstein equations in $`2`$-dimensions was discussed by D.G. Delfrate.

There were four posters which I broadly grouped as gravitational-related works. M. Calçada presented a panel on gravitation and the local symmetry group of spacetime . A.A. Sousa and J.W. Maluf presented a poster where they proposed an experimental test for the gravito-magnetic effect. R.C. Rigitano discussed in an interesting poster the geometric representation of general linear transformations, and the possibilities and limitations of the representation of covariant transformations. C.R. Muniz examined geometric properties of the spin in the context of GR.

Two posters were related to Astrophysics. In one the third post-Newtonian dynamics of compact binaries equations of motion was discussed by V. Andrade, L. Blanchet and G. Faye (for detail see ). In another by K. Sau Fa and I.T. Pedron it is used Tsallis’ distribution functions to examine the galaxies in equilibrium configurations with spherical symmetry (King models) .

M.D. Maia presented an interesting panel (related to two works in collaboration with E.M. Monte ) in which he showed how brane-world cosmology offers a quite simple explanation for dark energy.

M.E.X. Guimarães, L.P. Colatto and F.B. Tourinho presented a poster in which they extended to the context of scalar-tensor theories  (where the parameter $`\omega `$ in no longer constant) a procedure, devised by A. Barros and C. Romero , which makes clear how to obtain solutions in the Brans-Dicke theory from solutions in GR for the same matter content when one considers the weak-field approximations in both theories.

In an interesting panel by S.O. Mendes and R. Opher it was discussed how the $`1/r^2`$ gravitational law on submillimetric scale can be used to test the modified Newtonian dynamic theory (MOND) .

Besides the brief review talk, presented by R. Klippert as an oral presentation, Analog Gravity also appeared in a poster by V.A. De Lorenci and R. Klippert .

An interesting panel was presented by F.P. Devecchi and G. Kremer in which the kinetic theory of relativistic gases in two-dimensional space was developed to obtain thermodynamical quantities in $`2`$-dimensional cosmological models .

H.P. de Oliveira and I. Damião Soares presented in a contribution the results of their studies of the dynamics of spherically symmetric gravitational collapse of a massless scalar field . H. P. de Oliveira, I. Damião Soares and E.V. Tonini also had a panel where they presented an analytical method to describe the unstable periodic orbits of the center manifold for Hamiltonian systems. Another poster with some relation to this was presented by O.C. Castellani, G.A. Monerat and J.F.V. Rocha.

M.M. de Souza claimed in a panel that the constant anomalous radial acceleration observed in the Pioneer 10 and 11 spacecrafts can be explained in terms of discrete interactions (for detail see ).

J.F. Villas da Rocha presented a poster in which it was discussed solutions to Einstein’s field equations in $`N`$-dimensions with spherical symmetry .

L. Sandoval Jr considered in a contribution the constraints on generalized metrics (with both symmetric and antisymmetric parts) described through vierbeins imposed by bosonic strings in curved spacetimes.

M.L. Bedran presented an interesting pedagogical panel comparing the Doppler (special relativity) effects with the cosmological redshift of general relativity.

F.D. Sasse reviewed the different interpretations of the Mashhoon effect, and discussed a description of fermions in a storage ring in a Serret-Frenet tetrad frame, instead of the usual Hehl-Ni frame.

M.J. Lazo and S. Ragusa showed in how to calculate the electromagnetic angular momentum emission of fourth order, extending therefore the calculations made in the Landau-Lifchitz book for electric dipole. They intend to use similar scheme to examine analogous gravitational emission.

To close this section I remark that a considerable number of extended versions of the works presented in the XXII BNMPF will be available in a CD (proceedings of the meeting), and can fairly soon be obtained from the Brazilian Physical Society (SBF). So, for more details on some of works briefly reviewed here, I refer the readers to this CD ROM .

## VII Closing Remarks

The large number of abstracts submitted to the Cosmology and Gravitation sessions of the XXII BNMPF is certainly an indicative of the robust level of interest in the area. The meeting was a lively one and demonstrates the vitality of a extensive set of research topics. It also was very informative and many discussions took place in the regular sessions, and also in the coffee and others breaks. The spirit of collaboration, essential to the progress of science, was present in the sessions and discussions.

Let me close my review by strengthening a point I have indicated in the introduction, which is that the interaction and collaboration between theoretical and observationally-oriented gravito-cosmologists is strongly advisable for the advance of the area, the benefit of our community as well as for the formation of Brazilian young scientists in Cosmology and Gravitation.

###### Acknowledgements.

I would like to thank the Organizing Committee for the invitation to deliver the summary talk on Gravitation and Cosmology of the XXII BNMPF. I also thank them for the large amounts of effort put into the organization of a very successful meeting. I thank Ioav Waga for his help in the classification of the topics for my summary talk. Some authors provided me with preprints, reprints or references related to their submitted abstracts. The additional information material proved to be very useful for me, and I thank all these colleagues for their helpful gesture. I also thank Antonio F.F. Teixeira and G.I. Gomero for reading the manuscript and for the useful suggestions. Finally, I thank CNPq for the grant under which this work was carried out.