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# DV and WDVV

## 1 Introduction

The Witten-Dijkgraaf-Verlinde-Verlinde (WDVV) equations  in the most general form can be written  as system of algebraic relations

$$\begin{array}{c}_I_J^1_K=_K_J^1_I,I,J,K\end{array}$$
(1)
for the third derivatives

$$\begin{array}{c}_I_{JK}=\frac{^3}{T_IT_JT_K}_{IJK}\end{array}$$
(2)
of some function $`(𝐓)`$. Have been appeared first in the context of topological string theories , they were rediscovered later on in much larger class of physical theories where the exact answer for a multidimensional theory could be expressed through a single holomorphic function of several complex variables .

Recently, a new example of similar relations between the superpotentials of $`𝒩=1`$ supersymmetric gauge theories in four dimensions and free energies of matrix models in the planar limit was proposed . It has been realized that superpotentials in some $`𝒩=1`$ four-dimensional Yang-Mills theories can be expressed through a single holomorphic function  that can be further identified with free energy of the multi-support solutions to matrix models in the planar limit . A natural question which immediately arises in this context is whether these functions – the quasiclassical tau-functions, determined by multi-support solutions to matrix models, satisfy the WDVV equations? In the case of positive answer this is rather important, since multi-support solutions to the matrix models can play a role of “bridge” between topological string theories and Seiberg-Witten theories  which give rise to two different classes of solutions to the WDVV equations (see, e.g.,  and ).

This question was already addressed in , where it was shown that the multicut solution to one-matrix model satisfies the WDVV equations. However, this was verified only perturbatively and, what is even more important, for a particular non-canonical! (and rather strange) choice of variables.

In this paper, we demonstrate that the quasiclassical tau-function of the multi-support solution satisfies the WDVV equations as a function of canonical variables identified with the periods and residues of the generating meromorphic one-form $`dS`$ . An exact proof of this statement consists of two steps. The first, most difficult step is to find the residue formula for the third derivatives (2) of the matrix model free energy. Then, using an associative algebra, we immediately prove that free energy of multi-support solution satisfies WDVV equations, upon the number of independent variables is fixed to be equal to the number of critical points in the residue formula.

In sect. 2, we define the free energy of the multi-support matrix model in terms of the quasiclassical tau-function  along the line of . In sect. 3, we derive the residue formula for the third derivatives of the quasiclassical tau-function for the variables associated both with the periods $`\{𝐒\}=\{S_i\}`$ and residues $`\{𝐭\}=\{t_i\}`$ of the generating differential $`dS`$. In sect. 4, we prove that the free energy of the multisupport solution $`(𝐓)`$ solves the WDVV equations (1) as a function of the full set of variables $`\{𝐓\}=\{𝐒,𝐭\}`$ whose total number should be fixed to be equal to the number of critical points in the residue formula for the third derivatives (2). In sect. 5, we verify this statement explicitly for the first nontrivial case where the total number of variables is equal to four. 111Let us point out that the WDVV equations (1) are nontrivial only for the functions of at least three independent variables. However, as we see below, the structure of residue formula for the matrix model free energy requires the minimal number of independent variables to be at least four! From this point of view, the origin of the “experimental observation” of  valid for a function of three variables still remains unclear to us. Finally we present several concluding remarks and discuss possible generalizations.

We restrict ourselves by the $`𝒩=1`$ supersymmetric theories without flavours originally considered in . The results can be easily generalized. Note that the literature on the subject is already quite extensive , and different interesting developments of the issues discussed in this paper can be immediately obtained.

## 2 Tau-function of multi-support matrix model

We first exactly define what we call below the multi-support free energy of the matrix model in the planar limit. We are mostly doing with one-matrix integrals 222The generalization to the two-matrix case  is rather straightforward and will be discussed in the last section. of the form

$$\begin{array}{c}Z=𝑑\mathrm{\Phi }e^{\frac{1}{\mathrm{}}\mathrm{Tr}W(\mathrm{\Phi })}\end{array}$$
(3)
where the potential $`W(\mathrm{\Phi })`$ is supposed to be a polynomial of a degree $`(n+1)`$. The free energy in the planar limit of (3) can be defined as the first term in the expansion

$$\begin{array}{c}F(𝐭,t_0)=lim\left(\mathrm{log}Z\left(𝐭\right)\right)=_{g=0}^{\mathrm{}}\mathrm{}^{2g2}F_g(𝐭,t_0)\end{array}$$
(4)
implying $`N\mathrm{}`$, $`\mathrm{}0`$ with $`N\mathrm{}=t_0`$ being fixed. In what follows we are only interested in the first term of this expansion, $`F_0(𝐭,t_0)`$. In fact, we deal with another quantity, $`(𝐭,t_0,𝐒)`$, where $`S_i=\mathrm{}N_i`$, $`S_i=t_0`$ are extra variables – the filling numbers of (metastable) vacua. In order to get from this quantity $`F_0(𝐭,t_0)`$, one needs to minimize the free energy with respect to the filling numbers, $`\frac{}{S_i}=0`$. However, one can still preserve $`S_i`$ as free parameters introducing the ”chemical potentials”.

The origin of the new variables $`S_i`$ becomes rather transparent after one says that instead of direct computation of (3) this problem is replaced by the saddle point approximation – finding the extremum of the functional $`F_0\left[\rho (\lambda )\right]W\rho \rho (\lambda _1)\mathrm{log}\left|\lambda _1\lambda _2\right|\rho (\lambda _2)+\mathrm{\Pi }_0\left(\rho t_0\right)`$ where $`\mathrm{\Pi }_0`$ is just a Lagrange multiplier to fix the total normalization of the eigenvalue density. This latter condition means the saddle point equation is non-trivial only on the support of $`\rho `$. For one matrix model, this support can be presented as a set $`\{D_i\}`$ of cuts in complex eigenvalue plane, see fig. 1.

Then, one should add to this functional the term $`\mathrm{\Pi }_i\left(_{D_i}\rho S_i\right)`$, which via Lagrange multipliers, controls the filling numbers at each cut, i.e. to consider

$$\begin{array}{c}(𝐭,t_0,𝐒)W\rho \rho (\lambda _1)\mathrm{log}\left|\lambda _1\lambda _2\right|\rho (\lambda _2)+\mathrm{\Pi }_0\left(\rho t_0\right)+^{}\mathrm{\Pi }_i\left(_{D_i}\rho S_i\right)\end{array}$$
(5)
Then, the extra variables appear due to the extra information hidden in (5) compare to (3) – the structure of nontrivial eigenvalue supports. It is well-known that at “critical” densities $`\frac{\delta }{\delta \rho }=0`$, (5) is a (logarithm) of quasiclassical tau-function  (see, e.g., ).

In principle, in order to compare $``$ with the matrix model quantity $`F_0`$, one needs to put further restrictions to get rid of the metastable vacua. This would lead to shrinking part of the cuts into the double points (see discussions of these issues, say, in ). Here we would forget this issue and consider smooth curves (6) with only two marked points at infinities on two $`\lambda `$-sheets of the curve (6).

Note also that in (5) one can make two different natural choices for the set of new independent variables: the first choice corresponds to independent filling of all cuts, then $`t_0=S_i`$, while the second choice corresponds to choosing as independent $`t_0`$ and all $`S_i`$ except of corresponding to one of the cuts (that is why the corresponding sum in (5) is denoted as $`^{}`$). These choices are related by the linear change of variables which does not influence the WDVV equations (see ). The first choice is more “symmetric” while the second one corresponds to the canonical choice of variables in the sense of  or to the homology basis on smooth curve (6) with added marked points at two infinities. We use both of them below depending on convenience.

The complex curve of one-matrix model “comes from” the loop equations (see, for example, ) and can be written in the form

$$\begin{array}{c}y^2=W^{}(\lambda )^2+f(\lambda )R(\lambda )\end{array}$$
(6)
with the matrix model potential (3) parameterized as

$$\begin{array}{c}W(\lambda )=_{l0}t_{l+1}\lambda ^{l+1}\end{array}$$
(7)
or

$$\begin{array}{c}W^{}(\lambda )=_{l=0}^n(l+1)t_{l+1}\lambda ^l\end{array}$$
(8)
being the polynomial of $`n`$-th degree in our conventions. The coefficients of the function

$$\begin{array}{c}f(\lambda )=_{k=0}^{n1}f_k\lambda ^k\end{array}$$
(9)
are related to the extra data (the filling numbers) of the multicut solution. The eigenvalue density $`\rho (\lambda )`$ is the imaginary part of $`y(\lambda )`$ and vanishes outside the cuts. Therefore, the eigenvalue distribution $`𝐒`$ can be fixed by the periods

$$\begin{array}{c}S_i=_{A_i}𝑑S\end{array}$$
(10)
of the generating differential

$$\begin{array}{c}dS=yd\lambda \end{array}$$
(11)
taken around the eigenvalue supports to be identified (except for one of the supports) with the canonical $`𝐀`$-cycles. Then

$$\begin{array}{c}\frac{dS}{S_i}=d\omega _i\\ _{A_i}𝑑\omega _j=\delta _{ij}\end{array}$$
(12)
when the derivatives are taken at fixed coefficients $`\{t_l\}`$ of the potential (8). One can show that the Lagrangian multipliers in (5) are given by integrals of the same generating differential (11) over the dual contours (see fig. 1)

$$\begin{array}{c}\mathrm{\Pi }_i=_{B_i}𝑑S\end{array}$$
(13)
To the set of parameters (10) one should also add 333By the $`\mathrm{}`$-point in what follows we call for short the point $`\mathrm{}_+`$ or $`\lambda =\mathrm{}`$ on the “upper” sheet of hyperelliptic Riemann surface (6) corresponding to the positive sign of the square root, i.e. to $`y=+\sqrt{W^{}(\lambda )^2+f(\lambda )}`$. the total number of eigenvalues $`N\mathrm{}=t_0`$

$$\begin{array}{c}\mathrm{res}_{\mathrm{}}\left(dS\right)=\frac{f_{n1}}{2(n+1)t_{n+1}}t_0\end{array}$$
(14)
and the parameters of the potential (7), (8), which can be equivalently written as

$$\begin{array}{c}t_k=\frac{1}{k}\mathrm{res}_{\mathrm{}}\left(\lambda ^kdS\right)\\ k=1,\mathrm{},n\end{array}$$
(15)
while the leading term coefficient $`t_{n+1}`$ is supposed to be fixed (we will discuss this issue in detail below). Then

$$\begin{array}{c}d\mathrm{\Omega }_0=\frac{dS}{t_0}=(n+1)t_{n+1}\frac{\lambda ^{n1}d\lambda }{y}+\frac{1}{2}_{k=0}^{n2}\frac{f_k}{t_0}\frac{\lambda ^kd\lambda }{y}\end{array}$$
(16)
and the dependence of $`\{f_k\}`$ with $`k=0,1,\mathrm{},n2`$ on $`t_0`$ is fixed by the condition

$$\begin{array}{c}_{A_i}\left((n+1)t_{n+1}\frac{\lambda ^{n1}d\lambda }{y}+_{k=0}^{n2}\frac{f_k}{t_0}\frac{\lambda ^kd\lambda }{y}\right)=0\end{array}$$
(17)
which for $`i=1,\mathrm{},n1`$ gives exactly $`n1`$ relations on the derivatives of $`f_0,f_1,\mathrm{},f_{n2}`$ w.r.t. $`t_0`$. The bipole differential (16) can be also presented as

$$\begin{array}{c}d\mathrm{\Omega }_0=d\mathrm{log}\left(\frac{E(P,\mathrm{})}{E(P,\mathrm{}_{})}\right)\end{array}$$
(18)
where $`E(P,P^{})`$ is the Prime form. Differential (18) obviously obey the properties

$$\begin{array}{c}\mathrm{res}_{\mathrm{}}d\mathrm{\Omega }_0=\mathrm{res}_{\mathrm{}_{}}d\mathrm{\Omega }_0=1\\ _{A_i}𝑑\mathrm{\Omega }_0=0,i=1,\mathrm{},n1\end{array}$$
(19)
For the derivatives w.r.t. parameters of the potential (15), one gets

$$\begin{array}{c}d\mathrm{\Omega }_k=\frac{dS}{t_k}=\frac{W^{}(\lambda )k\lambda ^{k1}d\lambda }{y}+\frac{1}{2}_{j=0}^{n2}\frac{f_j}{t_k}\frac{\lambda ^kd\lambda }{y}\end{array}$$
(20)
obeying

$$\begin{array}{c}_{A_i}𝑑\mathrm{\Omega }_k=_{A_i}\frac{W^{}(\lambda )k\lambda ^{k1}d\lambda }{y}+\frac{1}{2}_{j=0}^{n2}\frac{f_j}{t_k}_{A_i}\frac{\lambda ^kd\lambda }{y}=0\end{array}$$
(21)
and this is again a system of linear equations on $`\frac{f_j}{t_k}`$. To complete the setup one should also add to (13) the following formulas 444 Naively understood the integral in (22) is divergent and should be supplemented by some proper regularization. In what follows we ignore this subtlety since it does not influence the residue formulas for the third derivatives, those one really needs for the WDVV equations (1). The simplest way to avoid these complications is to think of the pair of marked points $`\mathrm{}`$ and $`\mathrm{}_{}`$ as of degenerate handle; then the residue (14) comes from degeneration of the extra $`A`$-period, while the integral (22) from degeneration of the extra $`B`$-period.:

$$\begin{array}{c}\mathrm{\Pi }_0=_{\mathrm{}_{}}^\mathrm{}_+𝑑S\end{array}$$
(22)
(we again remind that, instead of $`t_0`$, the parameter $`S_n=t_0_{i=1}^{n1}S_i`$ can be used equivalently) and

$$\begin{array}{c}v_k=\mathrm{res}_{\mathrm{}}\left(\lambda ^kdS\right),k>0\end{array}$$
(23)
On genus $`g=n1`$ smooth Riemann surface (6), there are $`2g=2n2`$ independent noncontractable contours which can be split into the so-called $`𝐀\{A_i\}`$ and $`𝐁\{B_i\}`$, $`i=1,\mathrm{},g`$, cycles with the intersection form $`A_iB_j=\delta _{ij}`$. The canonical holomorphic differentials (12) are normalized to the $`𝐀`$-cycles, and their integrals along the $`𝐁`$-cycles give the period matrix,

$$\begin{array}{c}_{B_j}𝑑\omega _i=T_{ij}\end{array}$$
(24)
To check integrability of (13) and (22) one needs to verify the symmetricity of the second derivatives. For the part related with the derivatives only w.r.t. the variables (10), this is just a symmetricity of the period matrix of (6) and follows from the Riemann bilinear relations for the canonical holomorphic differentials (12)

$$\begin{array}{c}0=_\mathrm{\Sigma }𝑑\omega _id\omega _j=_k\left(_{A_k}𝑑\omega _i_{B_k}𝑑\omega _j_{A_k}𝑑\omega _j_{B_k}𝑑\omega _i\right)=T_{ij}T_{ji}\end{array}$$
(25)
Analogously

$$\begin{array}{c}0=_\mathrm{\Sigma }𝑑\omega _id\mathrm{\Omega }_0=_k\left(_{A_k}𝑑\omega _i_{B_k}𝑑\mathrm{\Omega }_0_{A_k}𝑑\mathrm{\Omega }_0_{B_k}𝑑\omega _i\right)+\\ +\mathrm{res}_{\mathrm{}}(d\omega _i)_{\mathrm{}_{}}^\mathrm{}_+𝑑\mathrm{\Omega }_0\mathrm{res}_{\mathrm{}}(d\mathrm{\Omega }_0)_{\mathrm{}_{}}^\mathrm{}_+𝑑\omega _i=_{B_i}𝑑\mathrm{\Omega }_0_{\mathrm{}_{}}^\mathrm{}_+𝑑\omega _i\end{array}$$
(26)
Formula (25) means that

$$\begin{array}{c}\frac{\mathrm{\Pi }_i}{S_j}=T_{ji}=T_{ij}=\frac{\mathrm{\Pi }_j}{S_i}\end{array}$$
(27)
while from (26) one gets

$$\begin{array}{c}\frac{\mathrm{\Pi }_j}{t_0}=\frac{\mathrm{\Pi }_0}{S_j}\end{array}$$
(28)
This allows one to introduce the function $`(𝐓)=(𝐒,t_0,𝐭)`$ such that

$$\begin{array}{c}\frac{}{S_j}=\mathrm{\Pi }_j,\frac{}{t_0}=\mathrm{\Pi }_0,\frac{}{t_k}=v_k\end{array}$$
(29)
The integrability of the last relation can be checked similar to (27), (28) with the help of Riemann bilinear relations involving the Abelian integrals $`\mathrm{\Omega }_k=^P𝑑\mathrm{\Omega }_k`$, for example (cf. e.g. with , where similar relations were used for the quasiclassical tau-function of the Seiberg-Witten theory):

$$\begin{array}{c}\mathrm{res}_{\mathrm{}}\left(\mathrm{\Omega }_kd\omega _i\right)=_\mathrm{\Sigma }\mathrm{\Omega }_k𝑑\omega _i=_l\left(_{A_l}\mathrm{\Omega }_k^+𝑑\omega _i_{A_l}\mathrm{\Omega }_k^{}𝑑\omega _i\right)_l\left(_{B_l}\mathrm{\Omega }_k^+𝑑\omega _i_{B_l}\mathrm{\Omega }_k^{}𝑑\omega _i\right)=\\ =_l\left(_{B_l}𝑑\mathrm{\Omega }_k_{A_l}𝑑\omega _i_{A_l}𝑑\mathrm{\Omega }_k_{B_l}𝑑\omega _i\right)=_{B_i}𝑑\mathrm{\Omega }_k\end{array}$$
(30)
where $`\mathrm{\Sigma }`$ is the cut Riemann surface (6) (see fig. 2), and in the last equality we used (21).

## 3 Residue formula

### 3.1 Holomorphic differentials

Let us now derive the formulas for the third derivatives of $``$, following the way proposed by I.Krichever . We first note that the derivatives of the elements of period matrix (in this section, for simplicity, we set the coefficients of potential (8) to be fixed) can be expressed through the integral over the “boundary” $`\mathrm{\Sigma }`$ of cut Riemann surface $`\mathrm{\Sigma }`$ (see fig. 2)

$$\begin{array}{c}\frac{T_{ij}}{S_k}_kT_{ij}=_{B_j}_kd\omega _i=_\mathrm{\Sigma }\omega _j_kd\omega _i\end{array}$$
(31)
where $`\omega _j=^P𝑑\omega _j`$ are the Abelian integrals, whose values on two copies of cycles on the cut Riemann surface (see also fig. 2) are denoted below as $`\omega _j^\pm `$. Indeed, the computation of the r.h.s. of (31) gives

$$\begin{array}{c}_\mathrm{\Sigma }\omega _j_kd\omega _i=_l\left(_{B_l}\omega _j^+_kd\omega _i_{B_l}\omega _j^{}_kd\omega _i\right)_l\left(_{A_l}\omega _j^+_kd\omega _i_{A_l}\omega _j^{}_kd\omega _i\right)=\\ =_l_{B_l}\left(_{A_l}𝑑\omega _j\right)_kd\omega _i_l_{A_l}\left(_{B_l}𝑑\omega _j\right)_kd\omega _i=\\ =_l\left(_{A_l}𝑑\omega _j\right)_{B_l}_kd\omega _i_l\left(_{B_l}𝑑\omega _j\right)_{A_l}_kd\omega _i\underset{_{A_i}𝑑\omega _j=\delta _{ij}}{=}_kT_{ij}\end{array}$$
(32)
One can now rewrite (31) as

$$\begin{array}{c}_kT_{ij}=_\mathrm{\Sigma }\omega _j_kd\omega _i=_\mathrm{\Sigma }_k\omega _jd\omega _i=\mathrm{res}_{d\lambda =0}\left(_k\omega _jd\omega _i\right)\end{array}$$
(33)
where the sum is taken over all residues of the integrand, i.e. over all residues of $`_k\omega _j`$ since $`d\omega _i`$ are holomorphic. In order to investigate these singularities and understand the last equality in (33), we discuss first how to take derivatives $`_k`$ w.r.t. moduli, or introduce the corresponding connection.

To this end, we introduce a covariantly constant function – the hyperelliptic co-ordinate $`\lambda `$, i.e. such a connection that $`_k\lambda =0`$. Roughly speaking, the role of covariantly constant function can be played by one of two co-ordinates – in the simplest possible description of complex curve by a single equation on two complex variables. Then, using this equation, one may express the other co-ordinate as a function of $`\lambda `$ and moduli. Any Abelian integral $`\omega _j`$ can be then expressed in terms of $`\lambda `$, and in the vicinity of critical points $`\{\lambda _\alpha \}`$ where $`d\lambda =0`$ (for a general (non-singular) curve this is always true) we get an expansion

$$\begin{array}{c}\omega _j(\lambda )\underset{\lambda \lambda _\alpha }{=}\omega _{j\alpha }+c_{j\alpha }\sqrt{\lambda \lambda _\alpha }+\mathrm{}\end{array}$$
(34)
whose derivative

$$\begin{array}{c}_k\omega _j_k\omega _j|_{\lambda =\mathrm{const}}=\frac{c_{j\alpha }}{2\sqrt{\lambda \lambda _\alpha }}_k\lambda _\alpha +\mathrm{regular}\end{array}$$
(35)
gives first order poles at $`\lambda =\lambda _\alpha `$ up to regular terms which do not contribute to (33). The exact coefficient in (35) can be computed for $`\lambda `$ related with the generating differential $`dS=yd\lambda `$. Then, using

$$\begin{array}{c}y(\lambda )\underset{\lambda \lambda _\alpha }{=}\mathrm{\Gamma }_\alpha \sqrt{\lambda \lambda _\alpha }+\mathrm{}\end{array}$$
(36)
where $`\mathrm{\Gamma }_\alpha =\sqrt{_{\beta \alpha }(\lambda _\alpha \lambda _\beta )}`$ or

$$\begin{array}{c}\frac{}{t_k}y(\lambda )=\frac{\mathrm{\Gamma }_\alpha }{2\sqrt{\lambda \lambda _\alpha }}\frac{\lambda _\alpha }{t_k}+\mathrm{regular}\end{array}$$
(37)
together with

$$\begin{array}{c}dy=\frac{\mathrm{\Gamma }_\alpha }{2\sqrt{\lambda \lambda _\alpha }}d\lambda +\mathrm{regular}\end{array}$$
(38)
and

$$\begin{array}{c}d\omega _j=\frac{c_{j\alpha }}{2\sqrt{\lambda \lambda _\alpha }}d\lambda +\mathrm{}\end{array}$$
(39)
and, following from (11) and (12)

$$\begin{array}{c}d\omega _k=_kdS=\frac{\mathrm{\Gamma }_\alpha _k\lambda _\alpha }{2\sqrt{\lambda \lambda _\alpha }}d\lambda +\mathrm{regular}\end{array}$$
(40)
one finally gets for (33)

$$\begin{array}{c}\mathrm{res}\left(_k\omega _jd\omega _i\right)=_\alpha \mathrm{res}\left(\frac{c_{j\alpha }_k\lambda _\alpha }{2\sqrt{\lambda \lambda _\alpha }}d\omega _i\right)=_\alpha \mathrm{res}\left(\frac{d\omega _j}{d\lambda }d\omega _i_k\lambda _\alpha \right)=_\alpha \mathrm{res}\left(\frac{d\omega _id\omega _jd\omega _k}{d\lambda dy}\right)\end{array}$$
(41)
In hyperelliptic situation, the derivation presented above is equivalent to using the Fay formula

$$\begin{array}{c}\frac{T_{ij}}{\lambda _\alpha }=\widehat{\omega }_i(\lambda _\alpha )\widehat{\omega }_j(\lambda _\alpha )\end{array}$$
(42)
where $`\widehat{\omega }_i(\lambda _\alpha )=\frac{d\omega _i(\lambda )}{d\sqrt{\lambda \lambda _\alpha }}|_{\lambda =\lambda _\alpha }`$ is the ”value” of canonical differential at a critical point.

### 3.2 Meromorphic differentials

Almost in the same way the residue formula can be derived for the meromorphic differentials (20). One gets

$$\begin{array}{c}\frac{}{t_k}=\mathrm{res}_{\mathrm{}}\left(\lambda ^kdS\right),k>0\end{array}$$
(43)
therefore

$$\begin{array}{c}\frac{^2}{t_kt_n}=\mathrm{res}_{\mathrm{}}\left(\lambda ^kd\mathrm{\Omega }_n\right)=\mathrm{res}_{\mathrm{}}\left((\mathrm{\Omega }_k)_+d\mathrm{\Omega }_n\right)\end{array}$$
(44)
where $`\left(\mathrm{\Omega }_k\right)_+`$ is the singular part of the integral of 1-form $`d\mathrm{\Omega }_k`$. Further

$$\begin{array}{c}\frac{}{t_m}\mathrm{res}_{\mathrm{}}\left(\lambda ^kd\mathrm{\Omega }_n\right)=\mathrm{res}_{\mathrm{}}\left(\lambda ^k\frac{d\mathrm{\Omega }_n}{t_m}\right)=\mathrm{res}_{\mathrm{}}\left((d\mathrm{\Omega }_k)_+\frac{\mathrm{\Omega }_n}{t_m}\right)=\mathrm{res}_{\mathrm{}}\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)\end{array}$$
(45)
The last expression can be rewritten as

$$\begin{array}{c}\mathrm{res}_{\mathrm{}}\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)=_\mathrm{\Sigma }\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)+\mathrm{res}_{\lambda _\alpha }\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)=\mathrm{res}_{\lambda _\alpha }\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)\end{array}$$
(46)
since $`_\mathrm{\Sigma }\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)=0`$ due to $`_{A_i}𝑑\mathrm{\Omega }_n=0`$, (cf. with (32)):

$$\begin{array}{c}_\mathrm{\Sigma }\mathrm{\Omega }_j\frac{}{t_k}𝑑\mathrm{\Omega }_i=_l\left(_{B_l}\mathrm{\Omega }_j^+\frac{}{t_k}𝑑\mathrm{\Omega }_i_{B_l}\mathrm{\Omega }_j^{}\frac{}{t_k}𝑑\mathrm{\Omega }_i\right)_l\left(_{A_l}\mathrm{\Omega }_j^+\frac{}{t_k}𝑑\mathrm{\Omega }_i_{A_l}\mathrm{\Omega }_j^{}\frac{}{t_k}𝑑\mathrm{\Omega }_i\right)=\\ =_l_{B_l}\left(_{A_l}𝑑\mathrm{\Omega }_j\right)\frac{}{t_k}𝑑\mathrm{\Omega }_i_l_{A_l}\left(_{B_l}𝑑\mathrm{\Omega }_j\right)\frac{}{t_k}𝑑\mathrm{\Omega }_i=\\ =_l\left(_{A_l}𝑑\mathrm{\Omega }_j\right)_{B_l}\frac{}{t_k}𝑑\mathrm{\Omega }_i_l\left(_{B_l}𝑑\mathrm{\Omega }_j\right)_{A_l}\frac{}{t_k}𝑑\mathrm{\Omega }_i\underset{_{A_i}𝑑\mathrm{\Omega }_j=0}{=}0\end{array}$$
(47)
Now, as in the holomorphic case one takes

$$\begin{array}{c}\mathrm{\Omega }_n(\lambda )\underset{\lambda \lambda _\alpha }{=}\mathrm{\Omega }_{n\alpha }+\gamma _{n\alpha }\sqrt{\lambda \lambda _\alpha }+\mathrm{}\end{array}$$
(48)
and, therefore

$$\begin{array}{c}\frac{}{t_k}\mathrm{\Omega }_j\frac{}{t_k}\mathrm{\Omega }_j|_{\lambda =const}=\frac{\gamma _{j\alpha }}{2\sqrt{\lambda \lambda _\alpha }}\frac{\lambda _\alpha }{t_k}+\mathrm{regular}\end{array}$$
(49)
Then, using (36), (37) and (38) together with

$$\begin{array}{c}d\mathrm{\Omega }_j=\frac{\gamma _{j\alpha }}{2\sqrt{\lambda \lambda _\alpha }}d\lambda +\mathrm{}\end{array}$$
(50)
and the relation, following from (20), (37)

$$\begin{array}{c}d\mathrm{\Omega }_k=\frac{}{t_k}dS=\frac{\mathrm{\Gamma }_\alpha d\lambda }{2\sqrt{\lambda \lambda _\alpha }}\frac{\lambda _\alpha }{t_k}+\mathrm{regular}\end{array}$$
(51)
one gets for (46)

$$\begin{array}{c}\frac{^3}{t_kt_nt_m}=\mathrm{res}_{\lambda _\alpha }\left(d\mathrm{\Omega }_k\frac{\mathrm{\Omega }_n}{t_m}\right)=\mathrm{res}_{\lambda _\alpha }\left(d\mathrm{\Omega }_k\frac{\gamma _{n\alpha }}{2\sqrt{\lambda \lambda _\alpha }}\frac{\lambda _\alpha }{t_m}\right)=\\ =\mathrm{res}_{\lambda _\alpha }\left(d\mathrm{\Omega }_k\frac{d\mathrm{\Omega }_n}{d\lambda }\frac{\lambda _\alpha }{t_m}\right)=\mathrm{res}_{\lambda _\alpha }\left(\frac{d\mathrm{\Omega }_kd\mathrm{\Omega }_nd\mathrm{\Omega }_m}{d\lambda dy}\right)\end{array}$$
(52)
In a similar way, one proves the residue formula for the mixed derivatives, so that we finally conclude

$$\begin{array}{c}\frac{^3}{T_IT_JT_K}=_{\lambda _\alpha }\mathrm{res}_{\lambda _\alpha }\left(\frac{dH_IdH_JdH_K}{d\lambda dy}\right)=_{\lambda _\alpha }\mathrm{res}_{\lambda _\alpha }\left(\frac{\varphi _I\varphi _J\varphi _K}{d\lambda /dy}dy\right)=\\ =_{\lambda _\alpha }\mathrm{\Gamma }_\alpha ^2\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )\varphi _K(\lambda _\alpha )=_{\lambda _\alpha }\frac{\widehat{H}_I(\lambda _\alpha )\widehat{H}_J(\lambda _\alpha )\widehat{H}_K(\lambda _\alpha )}{_{\beta \alpha }(\lambda _\alpha \lambda _\beta )^2}\end{array}$$
(53)
for the whole set $`\{T_I\}=\{t_k,t_0,S_i\}`$ and $`\{dH_I\}=\{d\mathrm{\Omega }_k,d\mathrm{\Omega }_0,d\omega _i\}`$. In formula (53) we have introduced the meromorphic functions

$$\begin{array}{c}\varphi _I(\lambda )=\frac{dH_I}{dy}=\frac{\widehat{H}_I(\lambda )}{R^{}(\lambda )}\end{array}$$
(54)
for any (meromorphic or holomorphic) differential $`dH_I=\widehat{H}_I(\lambda )\frac{d\lambda }{y}`$ and $`R(\lambda )=W^{}(\lambda )^2+f(\lambda )`$. The derivation of the residue formula for the set of parameters including $`t_0`$ corresponding to the third-kind Abelian differential (16) can be performed in a similar way.

## 4 Proof of WDVV

Having the residue formula (53), the proof of the WDVV equations (1) is reduced to solving the system of linear equations , which requires only fulfilling the two conditions:

* The “matching” condition

$$\begin{array}{c}\mathrm{\#}(I)=\mathrm{\#}(\alpha )\end{array}$$
(55)
and
* nondegeneracy of the matrix built from (54):

$$\begin{array}{c}det_{I\alpha }\varphi _I(\lambda _\alpha )0\end{array}$$
(56)

Under these conditions, the structure constants $`C_{IJ}^K`$ of the associative algebra

$$\begin{array}{c}\left(C_I\right)_L^K\left(C_J\right)_M^L=\left(C_J\right)_L^K\left(C_I\right)_M^L\\ (C_I)_J^KC_{IJ}^K\end{array}$$
(57)
responsible for the WDVV equations can be found from the system of linear equations

$$\begin{array}{c}\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )=_KC_{IJ}^K\varphi _K(\lambda _\alpha ),\lambda _\alpha \end{array}$$
(58)
with the solution

$$\begin{array}{c}C_{IJ}^K=_\alpha \varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )\left(\varphi _K(\lambda _\alpha )\right)^1\end{array}$$
(59)
To make it as general, as in , one may consider an associative isomorphic algebra (again $`\lambda _\alpha `$)

$$\begin{array}{c}\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )=_KC_{IJ}^K(\xi )\varphi _K(\lambda _\alpha )\xi (\lambda _\alpha )\end{array}$$
(60)
which instead of (59) leads to

$$\begin{array}{c}C_{IJ}^K(\xi )=_\alpha \frac{\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )}{\xi (\lambda _\alpha )}\left(\varphi _K(\lambda _\alpha )\right)^1\end{array}$$
(61)
The rest of the proof is consistency of this algebra with relation

$$\begin{array}{c}_{IJK}=_LC_{IJ}^L(\xi )\eta _{KL}(\xi )\end{array}$$
(62)
with

$$\begin{array}{c}\eta _{KL}(\xi )=_A\xi _A_{KLA}\end{array}$$
(63)
expressing structure constants in terms of the third derivatives and, thus, leading to (1). It is easy to see that (62) is satisfied if $`_{KLA}`$ are given by residue formula (53).

Indeed, requiring only matching $`\mathrm{\#}(\alpha )=\mathrm{\#}(I)`$, one gets

$$\begin{array}{c}_KC_{IJ}^K(\xi )\eta _{KL}(\xi )=_{K,\alpha ,\beta }\frac{\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )}{\xi (\lambda _\alpha )}\left(\varphi _K(\lambda _\alpha )\right)^1\varphi _K(\lambda _\beta )\varphi _L(\lambda _\beta )\xi (\lambda _\beta )\mathrm{\Gamma }_\beta \end{array}$$
(64)
and finally

$$\begin{array}{c}_KC_{IJ}^K(\xi )\eta _{KL}(\xi )=_\alpha \frac{\varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )}{\xi (\lambda _\alpha )}\varphi _L(\lambda _\alpha )\xi (\lambda _\alpha )\mathrm{\Gamma }_\alpha =_\alpha \mathrm{\Gamma }_\alpha \varphi _I(\lambda _\alpha )\varphi _J(\lambda _\alpha )\varphi _L(\lambda _\alpha )=_{IJL}\end{array}$$
(65)
Hence, for the proof of (1) one has to adjust the number of parameters $`\{T_I\}`$ according to (55). The number of critical points $`\mathrm{\#}(\alpha )=2n`$ since $`d\lambda =0`$ for $`y^2=R(\lambda )=0`$. Thus, one have to take a codimension one subspace in the space of all parameters $`\{T_I\}`$, a natural choice will be to fix the eldest coefficient of (8). Then the total number of parameters $`\mathrm{\#}(I)`$, including the periods $`𝐒`$, residue $`t_0`$ and the rest of the coefficients of the potential will be $`g+1+n=(n1)+1+n=2n`$, i.e. exactly equal to $`\mathrm{\#}(\alpha )`$. In sect. 5 we present an explicit check of the WDVV equations for this choice, using the expansion of free energy computed in .

Note that equations (60) are basically equivalent to the algebra of forms (or differentials) considered in . In this particular case one may take the basis of 1-differentials $`d\omega _i`$, $`d\mathrm{\Omega }_k`$ with multiplication given by usual (not wedge!) multiplication modulo $`dS=yd\lambda `$. Then, one can either directly check that the algebra with this multiplication is associative (similar to how it was done in ), or, using hyperelliptic parameterization, remove the factor $`\frac{d\lambda }{y}`$ in order to reduce the algebra to the ring of polynomials with multiplication modulo the polynomial ideal $`y^2=W^2(\lambda )+f(\lambda )`$, which is obviously associative.

In the proof of the WDVV equations we used in this section, the associativity (57) is absolutely evident, being associativity of the usual multiplication, and the main point to check was to derive (62)-(63). When using instead the algebra of differentials, the main non-trivial point is to check its associativity, while the relations (62)-(63) appear as even more transparent than above corollary of the residue formula.

## 5 Explicit check of the WDVV equations

To convince ourselves that the general proof indeed works and to get some further insights, in this section we consider the explicit check of the WDVV equations (1) perturbatively. To do this, let us take the perturbative expansion of the prepotential (29) at small $`S_i`$’s (here we take the symmetric choice of variables with $`i=1,\mathrm{},n=g+1`$), keeping the coefficients of the matrix model potential $`𝐭`$’s arbitrary, and see if this perturbative expansion of $``$ satisfies the WDVV equations order by order. A general procedure of getting such perturbative expansion was proposed in .

We are going to check here only the simplest non-trivial case of cubic matrix model potential, which is reformulated in terms of elliptic curve (6) with four branch points. According to (55) the corresponding solution to WDVV equations (1) should depend exactly on four independent variables, and we are choosing them to consist of two filling numbers ($`S_1`$ and $`S_2`$) and two coefficients of the potential ($`t_1`$ and $`t_2`$). The perturbative expansion for this case was constructed in  up to the fifth order in $`S_i`$’s and was later discussed in many other places (see, e.g., ). It reads

$$\begin{array}{c}=S_1W(\mu _1)S_2W(\mu _2)+\frac{1}{2}S_1^2\mathrm{log}\left(\frac{S_1}{\mathrm{\Delta }}\right)+\frac{1}{2}S_2^2\mathrm{log}\left(\frac{S_2}{\mathrm{\Delta }}\right)+2S_1S_2\mathrm{log}(\mathrm{\Delta })+\\ +\frac{1}{\mathrm{\Delta }^3}\left(\frac{2}{3}S_1^3\frac{2}{3}S_2^3+5S_1S_2^25S_1^2S_2\right)+\frac{1}{\mathrm{\Delta }^6}\left(\frac{8}{3}S_1^4+\frac{8}{3}S_2^4\frac{91}{3}S_1S_2^3\frac{91}{3}S_1^3S_2+59S_1^2S_2^2\right)+\\ +\frac{1}{\mathrm{\Delta }^9}\left(\frac{56}{3}S_1^5\frac{56}{3}S_2^5\frac{871}{3}S_1^4S_2+\frac{871}{3}S_2^4S_1+\frac{2636}{3}S_1^3S_2^2\frac{2636}{3}S_1^2S_2^3\right)+O(S^6)\end{array}$$
(66)
Here the matrix model potential (7) is fixed to be $`W(\lambda )=\lambda ^3/3+t_2\lambda ^2/2+t_1\lambda `$; and $`\mu _1`$, $`\mu _2`$ are the roots of the equation $`W^{}(\lambda )=0`$, i.e.

$$\begin{array}{c}\mu _1=\frac{1}{2}t_2+\frac{1}{2}\sqrt{t_2^24t_1}\\ \mu _2=\frac{1}{2}t_2\frac{1}{2}\sqrt{t_2^24t_1}\\ \mathrm{\Delta }\mu _1\mu _2=\sqrt{t_2^24t_1}\end{array}$$
(67)
The perturbative expansion of free energy (66) is symmetric with respect to simultaneous transformation $`S_1S_2`$ and $`t_2t_2`$. However, since the whole prepotential but its linear part depends only on $`t_2^2`$, the transformation of $`t_2`$ is only essential for the linear term.

Note that in the context of supersymmetric field theories such formulas usually depend on an additional parameter $`\mathrm{\Lambda }_{QCD}`$ associated with the field theory scale . However, this parameter here emerges only as regularization (see footnote 4) and generally can be omitted within the matrix model approach. Moreover, since the terms depending on $`\mathrm{\Lambda }_{QCD}`$ are at most quadratic in $`S_i`$ and $`t_i`$ (they are logarithmic or polynomial in $`\mathrm{\Lambda }_{QCD}`$, with the latter proportional to $`W(\mathrm{\Lambda }_{QCD})`$), they do not contribute to the WDVV equations and just renormalize the second derivatives of the prepotential (or period matrix of the curve similar to (6) playing the role of the set of effective couplings in the field theory at low energies (cf. with )).

There is one subtlety with the perturbative prepotential (66) – when calculating it the authors of  were interested only in the terms depending on $`S_i`$. There could be, in principle, some terms dependent only on $`t_i`$’s. This does not, however, happen in our case. Indeed, these terms would survive in the limit of all $`S_i=0`$, i.e. when $`f(\lambda )=0`$ in (6) and $`y=W^{}(\lambda )`$ is just a polynomial. Then from (23) it follows that $`v_k=\frac{}{t_k}=0`$ in this limit, hence we miss at most linear in $`t_i`$ terms.

In contrast to the weak coupling expansion of the Seiberg-Witten theory when logarithmic terms do satisfy the WDVV equations themselves exactly (see )555Note that expansion (66) that goes over positive powers of variables, $`S_i`$’s is rather similar not to the weak coupling expansion of the Seiberg-Witten theory but to its strong coupling expansion (see, for example, ). In the latter case, the WDVV equations trivially hold due to the duality argument . , some technical complication with perturbative check of whether the prepotential (66) satisfies the WDVV equations emerges due to different orders of magnitude of different matrix elements of the matrix of third derivatives of the prepotential (2). Say, matrix $`\left(_{t_2}\right)_{JK}`$ has all matrix elements except for $`\left(_{t_2}\right)_{t_j,t_k}`$ of the order $`O(1)`$, while the latter ones of the order of $`O(S_i)`$. (We definitely put all $`S_i`$’s of the same order of magnitude.)

Therefore, a careful calculation in every matrix element is required to determine the order of the WDVV equations where the perturbative expansion contributes to. In practice, one suffices to rescale all $`S_i`$’s with a scale parameter $`\mathrm{\Lambda }`$. Then, all non-trivial matrix elements of same matrix WDVV equation (i.e. for concrete $`IJK`$) are of the same order in $`\mathrm{\Lambda }`$ (choosing other indices $`IJK`$ in (1) changes this order). Say, for the choice $`(I,J,K)=(t_2,S_1,t_1)`$ the leading order of the equation(1) is $`\mathrm{\Lambda }^7`$ and trivially vanishes. It is contributed only by the linear and logarithmic (in $`S_i`$’s) terms of (66). The cubic terms of the prepotential contribute to $`\mathrm{\Lambda }^8`$-order, the quartic terms to $`\mathrm{\Lambda }^9`$-order etc. Using the program MAPLE, we have checked that the WDVV equations (1) are satisfied with the prepotential (66) up to the fifth order in $`S_i`$.

Now, one can consider further non-trivial examples with matrix model potentials being polynomials of higher degree. One technical problem now is that $`W(\mu _i)`$ is getting more and more involved function of $`t_i`$’s, since $`\mu _i`$’s become the roots of polynomial equations of increasing order. Therefore, we lose just a principal possibility of analytic analyzing $`W(\mu _i)`$ if $`W(\lambda )`$ is a polynomial of order 6 and higher. Nevertheless, one can still look at different limiting regimes with some of roots of $`W^{}(\lambda )`$ approaching close to each other.

## 6 Conclusion

In this paper we have proven that the (generalized) free energy of the matrix model in planar limit satisfies the WDVV equations (1). The proof is based on the residue formula for the quasiclassical tau-functions introduced in  which was derived above for the whole basis of the first-kind or holomorphic (12), second-kind (20) and third-kind (16) meromorphic Abelian differentials. The proof of the WDVV equations based on the residue formula requires the matching condition (55) (or associativity of the algebra of differentials), and the first nontrivial example of our statement for the case of four variables we have checked explicitly for its perturbative expansion (66).

The matching condition (55) requires for the quasiclassical tau-function defined by (6) and (11) to satisfy the WDVV equations (1) as a function of the set of parameters involving necessarily the coefficients of the matrix model potential and corresponding to the meromorphic differentials. In other words, we cannot restrict ourselves for the set of only holomorphic differentials, like it happens for the prepotentials of the Seiberg-Witten models , associated as well in the sense of sect. 2 to integrable systems  (see also  and references therein). This is similar to the case of softly broken $`𝒩=4`$ Seiberg-Witten theory, where the WDVV equations are not satisfied by the prepotential, being a function of the Seiberg-Witten periods corresponding to the holomorphic differentials only . In that case one should also necessarily add meromorphic differentials, but any physical sense of the corresponding parameters, in contrast to the situation considered in this paper, remains yet unclear.

Our statement can be generalized straightforwardly to the case of the two-matrix model and the corresponding non-hyperelliptic curve . It was already suggested in  that the WDVV equations should hold for the quasiclassical tau-function of the two-matrix model, whose construction is based on the non-hyperelliptic curve, and similar to (11) meromorphic differential. One can use our line of reasoning of sect. 3 and sect. 4 as a general proof in the two-matrix case either, since our proof does not require any specific of the curve (6) like existence of the hyperelliptic parameterization. The perturbative expansion of the multisupport solution of the two-matrix model is not known yet (it can be computed, say, using the diagrammatic expansion proposed in ) and it would be interesting to calculate the free energy of the two matrix model explicitly and repeat for this case the explicit calculation of sect. 5.

There is another, very important direction where one can easily extend the consideration of the present paper. In  there was shown how one can introduce more Whitham times, preserving the same number of moduli $`S_i`$. It is based on using potential $`W(\lambda )`$ of higher degree and fixing some of the coefficients of $`f(\lambda )`$ by the double point conditions. This procedure allows one to make the number of Whitham times and moduli independent in the WDVV equations. It would be interesting to check if the WDVV equations are satisfied in this case, and to construct the perturbative expansion for such a case.

Finally, let us point out that the fact that free energy of multi-support solution of matrix model does satisfy the WDVV equations (1) can be thought of as a first step to write down the generalization of the (quasiclassical) Hirota equations which are known up to now only for the one-support solutions. A link between the WDVV equations and (generalized) Hirota relations  together with the statement of our paper allows one to believe that the counterpart of the Hirota relations for nontrivial quasiclassical tau-functions can be written in an explicit form.

## Acknowledgements

We are grateful to V.Kazakov, I.Krichever, A.Morozov and V.Rubtsov for valuable discussions. The work was partly supported by INTAS grant 00-561 (A.Mar, A.Mir. and D.V.), RFBR grants 01-01-00549 (L.Ch.), 02-02-16946 (A.Mar.), 01-01-00548 (A.Mir.) and 01-02-17488 (D.V.), by the Grants of Support of the Scientific Schools 00-15-96046 (L.Ch.), 00-15-96566 (A.Mar) and 96-15-96798 (A.Mir.), by Russian President’s grant 00-15-99296 (D.V.), by the Volkswagen-Stiftung (A.Mir. and D.V.) and by the program “Solitons” (L.Ch.). A.Mar. would like to thank the support of CNRS, Lab. de Physique Theorique of ENS, Paris, and IHES where an essential part of this work has been done.


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# Correlation between mutation pressure, selection pressure and occurrence of amino acids

## 1 Introduction

Determining the evolutionary distances between two protein sequences requires the knowledge of the substitution rates of amino-acids. It is generally accepted that the more substitutions are necessary to change one sequence into another, the more unrelated they are and the larger their distance to the common ancestor. The most widely used method for the calculation of distances between sequences is based on the mutation data matrix, $`M_{ij}`$, published by Dayhoff et al. , where $`i,j`$ represent amino acids, and an element $`M_{ij}`$ of the matrix gives the probability that the amino acid in column $`j`$ will be replaced by the amino acid in row $`i`$ after a given evolutionary time interval. The interval corresponding to $`1`$ percent of substitutions between two compared sequences is called one PAM (Percent of Accepted Mutations), and the corresponding matrix is denoted as PAM$`1`$ matrix. There is assumed a Markov model of sequence evolution and a simple power $`M^k`$ of the PAM$`1`$ matrix (multiplied by itself $`k`$ times) denotes a matrix, PAM$`k`$, that gives the amino acid substitution probability after $`k`$ PAMs. Today, a much more accurate PAM matrix is available, generated from 16130 protein sequences, published by Jones et al. . The large number of compared genes guarantees that the matrix has negligible statistical errors and it can be considered to be the reference matrix during the calculations of the phylogenetic distances. The matrix is also known as PET$`91`$ matrix.

Recently, by comparing intergenic sequences being remnants of coding sequences with homologous sequences of genes, we have constructed an empirical table of the nucleotide substitution rates in the case of the leading DNA strand of the B. burgdorferi genome ,,. We have found that substitution rates, which determine the evolutionary turnover time of a given kind of nucleotide in third codon positions of coding sequences, are highly correlated with the frequency of the occurrence of that nucleotide in the sequences. There is a compositional bias produced by replication process, introducing long-range correlation among nucleotides in the third positions in codons, which is very similar to the bias seen in the intergenic sequences .

We have used the empirical table of nucleotide substitution rates to simulate mutational pressure on the genes lying on the leading DNA strand of the B.burgdorferi genome and we have constructed MPM$`1`$ matrix (Mutation Probability Matrix) for amino acid substitutions in the evolving genes. Thus the resulting table represents the percent of amino acid substitutions introduced by mutational pressure and not by selection. Next, we compared the survival times of the amino acids in the case without any selection with the effective survival times of the amino acids, counted with the help of the PAM1 PET91 matrix.

## 2 Mutation Table for Nucleotides

DNA sequence of the B.burgdorferi genome was downloaded from the website
www.ncbi.nlm.nih.gov. The empirical mutation table for nucleotides in third positions in codons, which we used in the paper, is the following ,:

$$M=\left(\begin{array}{cccc}1uW_A\hfill & uW_{AT}\hfill & uW_{AG}\hfill & uW_{AC}\hfill \\ uW_{TA}\hfill & 1uW_T\hfill & uW_{TG}\hfill & uW_{TC}\hfill \\ uW_{GA}\hfill & uW_{GT}\hfill & 1uW_G\hfill & uW_{GC}\hfill \\ uW_{CA}\hfill & uW_{CT}\hfill & uW_{CG}\hfill & 1uW_C\hfill \end{array}\right)$$
(1)
where 111The transpose matrix convention has been chosen in .

$$\begin{array}{c}W_{GA}=0.0667W_{GT}=0.0347W_{GC}=0.0470W_{AG}=0.1637\hfill \\ W_{AT}=0.0655W_{AC}=0.0702W_{TG}=0.1157W_{TA}=0.1027\hfill \\ W_{TC}=0.2613W_{CG}=0.0147W_{CA}=0.0228W_{CT}=0.0350\hfill \end{array}$$
(2)
and the elements of the matrix give the probability that nucleotide in column $`j`$ will mutate to the nucleotide in row $`i`$ during one replication cycle. The symbols $`W_{ij}`$ represent relative substitution probability of nucleotide $`j`$ by nucleotide $`i`$, and $`u`$ represents mutation rate. The symbols $`W_j`$ in the diagonal represent relative substitution probability of nucleotide $`j`$:

$$W_j=\underset{ij}{}W_{ij},$$
(3)
and $`W_A+W_T+W_G+W_C=1`$.

The expression for the mean survival time of the nucleotide $`j`$ depends on $`W_j`$ as follows (derivation can be found in )

$$\tau _j=\frac{1}{ln(1uW_j)}\frac{1}{uW_j}.$$
(4)
The above approximated formula is true for small values of the mutation rate $`u`$.

In papers ,,, we concluded that in a natural genome the frequency of occurrence $`f_j`$ of the nucleotides, in the third position in codons, is linearly related to the respective mean survival time $`\tau _j`$,

$$f_j=m_0\tau _j+c_0,$$
(5)
with the same coefficients, $`m_0`$ and $`c_0`$, for each nucleotide. The Kimura’s neutral theory  of evolution assumes the constancy of the evolution rate, where the mutations are random events, much the same as the random decay events of the radioactive decay. However, the linear law in (5) is not contrary to the Kimura’s theory. Still, the mutations represent random decay events but they are correlated with the DNA composition.

## 3 Mutational Pressure MPM$`1`$ Matrix Construction for Amino Acids

We used computer random number generator to generate random deviates with a distribution defined by the elements of the mutation matrix in (1). With the help of the random deviates we were mutating nucleotide sequences of 564 genes from the leading DNA strand of the B. burdorferi genome. The applied value of the mutation pressure was $`u=0.01`$.

For each gene, considered to be an ancestral one in this simulated evolution, we prepared $`10^5`$ pairs of homologous sequences, which diverged from this gene. The gene evolution was stopped when the number of substitutions between the homologous protein sequences reached 1%. All the sequences were translated into amino acids and we constructed a mutation probability matrix MPM$`1`$ according to the procedure of Dayhoff et al. and Jones et al. . The resulting mutation table, with substitution probabilities $`M_{ij}`$, the amino acid mutability $`m_j`$, and the fraction $`f_j`$ of amino-acid in the compared sequences have been presented, respectively, in Table 1 and Table 2.

The elements $`M_{ij}`$ of the MPM$`1`$ matrix in Table 1 have been scaled with the parameter $`\lambda `$, which related them to the evolutionary distance of one percent of substitutions and it is equal to 0.00009731 in our simulations. We introduced the parameter $`\lambda `$ following the equation (3) in the paper by Jones et al.). Therefore,

the diagonal elements of the MPM1 table have been defined with the help of the following formula,

$$M_{jj}=1\lambda m_j,$$
(6)
and the value of the parameter $`\lambda `$ has been calculated from the condition that, in the case of 1% of amino acid substitutions, the total fraction of the unchanged amino acids is equal to

$$\underset{j=1}{\overset{20}{}}f_jM_{jj}=0.99.$$
(7)
## 4 Discussion of results

The major qualitative difference between the MPM matrix introduced in the previous section and the PAM1 PET91 matrix published in the paper by Jones et al. is that the first one is a result of pure mutational pressure whereas the second one is a result of both mutational and selection pressures. Thus, we have two evolutionary mechanisms responsible for the resulting PAM matrices.

With the help of formula (4) (extended to amino acids) we have calculated effective survival times of amino acids in the case of the MPM$`1`$ matrix (Table 1) and the mutational/selectional PAM$`1`$ PET$`91`$ matrix (). The value of the parameter $`\lambda `$ is a counterpart of $`u`$ in (4). In Fig.1, we presented the relation between the calculated survival time o amino acids and their fractions in the B. burgdorferi proteins, in the pairs of diverged genes, in a log-log scale. One can observe that the data are highly correlated and in both cases the dependence of the mean survival time of amino acid on the fraction of the amino acid represents a power law:

$$\tau _jF_j^\alpha $$
(8)
with a negative value of $`\alpha 1.3`$ in the case of selection and a positive value of $`\alpha 0.3`$ in the case of mutation pressure on the leading DNA strand of the B. burgdorferi genome. The value of $`\alpha `$ for the analogous mutational PAM1 matrix calculated in the case of the lagging DNA strand of the B. burgdorferi genome is about twice as small. It is worth to underline that the slopes $`\alpha `$ are the same for the matrices PAM$`k`$ with high values of $`k`$, and thus, they are universal with respect to evolution.

In Fig.1 we may observe a kind of evolutional scissors acting on amino acids. Once the less frequent amino acids, like $`W`$ (tryptophane), $`C`$ (cysteine), have much shorter turn over time compared with other amino acids (as can be seen from the lower line) the selection pressure (upper line) counteracts with the effect. On the other hand, the most mutable amino acids, like $`L`$ (leucine) or $`I`$ (isoleucine) , which are very frequent in genes, seem to be much weakly influenced by selection.

In genes the fraction of the amino acids most protected by selection strongly depends on gene size, it is diminishing when gene’s size is increasing. The effect weakens if we go into right the direction of the evolutionary scissors in Fig.1.

To show this, we ordered all 564 genes under consideration with respect to fraction of an examined amino acid and the genes have been assigned a rank number. Next, we plotted the dependence of both the gene size on the rank and the dependence of the amino acid fraction in the gene on the rank. The resulting plots in Figs.2 correspond to two evolutionary extreme cases, representing tryptophan and leucine. It is evident that in the case of tryptophan the fraction of that amino acid in genes is anti-correlated with the gene’s size (notice, that about $`1/3`$ genes do not posses tryptophan). In the case of leucine there is a crossover and the effect of selection is evident only for the genes which have more than 10% of that amino acid. When the fraction of leucine is less than 10% there is even a reverse effect, i.e., the increasing fraction is correlated with the increasing gene’s size. If we look at the evolutionary scissors in Fig.1, we can see that in the case of leucine the survival time, which originates from pure mutational pressure is longer than its selectional counterpart. Recently, there has appeared a paper by Xia and Li  discussing which amino acid properties (like polarity, isoelectric point, volume etc.) affect protein evolution. Thus, there is a possibility to relate these properties to our discussion of the evolutionary scissors.

## 5 Conclusions

We have shown that the amino acids which experience the highest selectional pressure have the shortest turn over time with respect to mutation pressure. The fraction of these amino acids in genes depends on the gene’s size. Much different is the selectional role of the amino acids, like leucine, from the right hand side of the selectional scissors. Although they have long turn over time with respect to the mutational pressure, their fraction cannot be too high. This could be considered as an effect of optimisation of the genetic information on coding with processes of mutagenesis and phenotype selection for protein functions.

Acknowledgemets
The work was supported by the grant number 1016/S/IMi/02.


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# Comment on “Anomalous proximity effect in underdoped YBa2Cu3O6+x Josephson junctions”

Recently Decca et al. have reported an unusually long-ranged proximity effect (PE) between the superconducting and insulating phases of YBCO decca . These beautiful experiments have received lots of attention because they may help to discriminate between alternative scenarios for cuprate superconductivity decca ; scenarios . However, later work scenarios  took for granted the claim decca  that such long range is anomalous. Here we point out that this is not warranted.

At the heart of our argument is the formula used in decca  to estimate the expected range of the PE, $`\zeta \zeta _0\sqrt{\mathrm{}D/2\pi k_BT}`$, where $`D`$ is the diffusion constant. Using this expression decca  obtains $`\zeta =15\text{nm}`$, which is indeed much smaller than the experimental value $`\zeta ^{exp}=90\text{nm}`$. However, the same formula agrees with earlier experiments on YBCO exper , which poses the question why it fails to account for the data of decca . To answer we first note that $`\zeta \zeta _0`$ is only the $`V_N0`$ limit of the more general expression deutscher

$$\frac{\zeta }{\zeta _0}=_0^{\mathrm{}}\frac{d\eta }{\pi \eta }\left[\frac{\mathrm{\Sigma }^{}}{\mathrm{\Sigma }}+\frac{NV_N\mathrm{\Sigma }^{}}{1V_N/V_S+NV_N\mathrm{\Sigma }}+\frac{2}{\eta }\right]$$
(1)
for an interface of a superconductor and a normal conductor with coupling constants $`V_S`$ and $`V_N`$, respectively. $`\mathrm{\Sigma }`$ is a function defined in deutscher  and $`N`$ is the density of states at the Fermi level. A numerical evaluation of Eq. (1) is presented in Fig. 1. The key point is that in the experiments of decca  superconductivity is induced in part of an underdoped sample by photodoping. The PE thus takes place not between two different materials (as in standard experiments), or in an inhomogeneous material a region of which has been severely damaged in the creation of the normal region (as in exper ), but between two differently doped parts of one and the same material. The limit $`V_NV_S`$ is then more appropriate than $`V_N0`$. In this limit Eq. (1) does predict $`\zeta \zeta _0`$, suggesting that the long range is not an unconventional feature of YBCO.

At $`V_N=V_S`$ Eq. (1) predicts $`\zeta \mathrm{}`$. This infinity reflects the fact that in Eq. (1) the density of states is assumed to be the same on both sides of the interface ($`N_N=N_S=N`$), so that for $`V_N=V_S`$ both materials are identical. The restriction to $`N_N=N_S`$ can be overcome in the one-frequency approximation degennes . Numerical evaluation of Eq. (4.15b) of degennes  yields the dashed curves in Fig. 1. Clearly, a large, but finite value of $`\zeta /\zeta _0`$ is obtained, e.g., if $`V_NV_S`$ and $`N_SN_N`$ foot .

In summary, although there are unconventional features in the experiments, the claim that the long range of the PE is one of them decca  seems presently unfounded. Conventional theory deutscher ; degennes  predicts comparably long ranges, once the novel nature of the experiments is accounted for. We thus recommend performing similar experiments on conventional superconductors. The lines of thought on cuprate superconductivity stemming from the assumption that $`\zeta ^{exp}`$ is anomalously large decca ; scenarios  must also be critically reexamined.

This work was funded by FAPESP and CNPq.


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# Hydrostatic pressure dependence of the luminescence and Raman frequencies in polyfluorene

## I Introduction

Polyfluorenes (PF) have emerged as attractive alternativesleclerc ; scherf  to other conjugated polymers for display applications due to their efficient blue emission and high hole mobility at room temperature.grice ; redecker  Blue electroluminescent materials are of particular interest for organic displays since blue light can be converted into red and green quite easily by color-changing media (fluorescent dyes).tasch  PFs have been very efficiently utilized in organic light emitting diodes (OLEDs).bernius  They have been found to exhibit complex morphological behavior that has interesting implications due to their rich photophysics. The liquid crystallinity of PF derivatives with long alkyl substituents allows fabrication of electroluminescent devices with highly polarized emissionmiteva  that is of potential use for backlighting in liquid crystalline displays.grell

OLEDs fabricated from the PF family of materials are known to degrade under operation. The desired blue electroluminescence from the singlet excitons changes to an undesirable 2.1-2.6 eV greenish/reddish emission. Photo-oxidation produces a similar broad emission band in the photoluminescence (PL) spectrum. This red shifted emission has been attributed to aggregation and/or excimer formation in the material.carter ; fujikawa  Recently, List et al.list  have conclusively shown that the 2.3 eV band is related to emission from keto defect sites (9-fluorenone) in the sample. These defect sites act as guest emitters that can efficiently trap singlet excitons created on the conjugated polyfluorene backbone. Time-resolved PL measurements further show different temporal dynamics for the various peaks in the 2.1-2.6 eV region, indicating that the origin of some of the peaks is due to on-chain emissive defects while other peaks are from aggregates and excimers.lupton ; herz

In this work we probe the optical properties of poly\[2,7-(9,9’-bis(2-ethylhexyl))fluorene\] (PF2/6) via PL, absorption, and Raman scattering as a function of hydrostatic pressure. Hydrostatic pressure enhances intermolecular interaction and changes the molecular geometry without producing chemical changes. An understanding of the influence of the intermolecular interactions is crucial since the photoluminescence quantum yield (PLQY) of polymers is known to decrease in the solid state. For example, in methylated ladder-type poly para-phenylene (m-LPPP), the PLQY of solution and film are (100%) and (30%), respectively.tasch2  In decyloxy PPP (DOPPP) PLQY values of 85% in solution and 35% in film are observed.heeger  In the solid state the electronic properties of organic materials depend significantly on the three-dimensional interactions. Recent theoretical methods of quantum-chemistry and solid-state physics in conjunction with experimental measurements have provided valuable insight into the electronic and optical properties of both isolated and interacting conjugated chains (oligomers and polymers).beljonne ; cornil ; spano ; puschnig  Hydrostatic pressure studies also allow us to probe the effects of enhanced interaction on the aggregate and defect-related emissions in these systems.

An additional interesting feature of PF2/6 is that its backbone conformation is intermediate to that of planar and non-planar conjugated solids. It thus provides an interesting contrast to the planar polymer m-LPPP and the non-planar oligophenyls such as para hexaphenyl (PHP). Our previous studies indicate that enhanced intermolecular interactions under the impact of pressure in conjugated solids typically produce an increased degree of conjugation, destabilization of localized states as in m-LPPP, yang ; meerapressure  and changes in the ring torsional motion as in PHP.guha  These changes in geometry can be deduced from their influence on electronic and vibrational spectra. PFs also show rich morphological behavior as a function of temperature: the glass-rubber transition and the liquid crystalline phase are induced at elevated temperatures. It therefore makes it an interesting system to study under high pressure since one can test whether any of the high-temperature phases can be induced by the application of pressure alone at room temperature, thus allowing the study of the corresponding changes in their electronic and vibrational properties in a different region of phase space.

## II Experimental Details

### II.1 Methodology

Pressure studies were conducted in a Merrill-Bassett type diamond anvil cell (DAC) with cryogenically loaded argon as the pressure medium. A small chip of ruby was included in the sample chamber, thus allowing the determination of pressure by measuring the shift of the luminescence spectrum of the ruby. For ambient pressure measurements the samples were loaded in a cryostat that was evacuated to below 100 mTorr to prevent any photo-oxidative damage.

PL and absorption spectra were recorded using an Ocean Optics PC2000 spectrometer with 25-$`\mu `$m slits. The 351.1nm line from an $`\mathrm{Ar}^+`$ laser was used in a backscattering configuration for PL. Raman measurements were performed using a Spex triplemate spectrometer and the 647.1 nm line of a $`\mathrm{Kr}^+`$ laser with 10 mW incident power in a backscattering configuration. The scattered light was detected using a cryogenically cooled CCD array detector and a holographic super-notch filter to block the elastically scattered light. Measurement of the spectrum of a chip of ruby outside the pressure chamber before each Raman measurement ensured that the calibration of the spectrometer was consistent from one day to the next. The low temperature measurements were conducted in a closed cycle helium refrigerator. The spectral data was analyzed using PeakFit and Origin to determine the position, area, and full width at half maximum (FWHM) of the peaks.

### II.2 Sample Details

PF2/6 forms planar monomer units but has a torsional degree of freedom between adjacent monomer units as shown in the inset of Figure 1 (b); its synthesis is described in Ref. (scherf, ). The torsional freedom in PF2/6 makes the structure an intermediate case between non-planar oligophenyls and planar m-LPPP. PF2/6 is semi-crystalline at room temperature, with a glass-rubber transition temperature (Tg) of the amorphous component at 80 oC, and a crystalline to nematic liquid crystalline phase transition at 167 oC (reverse transition at 132 oC upon cooling).scherf  The molecules have been shown to have a C5 helical conformation at room temperature. scherf  Upon further processing some polyfluorene films display a $`\beta `$ phase, which has a more extended intrachain $`\pi `$-conjugation, in addition to the regular glassy $`\alpha `$ phase. The $`\beta `$ phase has been detected in 9,9-di-n-octyl-PF (PF8 or PFO)grell ; cadby  and shows a distinct red shift of absorption and emission peaks with a well-resolved vibronic progression both in absorption and emission. In contrast, the $`\alpha `$ phase shows a well-resolved vibronic progression only in the emission spectrum. Due to the branched alkyl side groups this material is not expected to easily form a $`\beta `$ phase, however, it has been shown that a highly aligned state can be achieved with solvent treatment and thermal cycling .lieser

The PL and Raman spectra were measured from a powder sample of PF2/6, which has both amorphous and crystalline components, while the absorption and PL were measured from a film. The film was prepared by drop-casting PF2/6 dissolved in spectroscopic grade dichloromethane directly onto the surface of the bottom diamond of the DAC. While the film is loosely attached to the diamond surface, it is not bonded onto it, and therefore experiences hydrostatic pressure in the DAC.

All the Raman measurements were carried out with a bulk (powder) sample. This was necessary because the Raman signal from a film is very weak due to the drastically reduced scattering volume.

## III Steady-State Photoluminescence and Absorption

### III.1 Experimental Results

Figure 1 shows the PL spectra from two PF2/6 films (panel (a) thick film, $``$3000nm; panel (b) thin film, $``$100nm) for a few selected values of temperature. Vibronic progressions are seen in the PL emission of both films, indicating a coupling of the backbone carbon-carbon stretch vibration to the electronic transitions. The vibronic peaks result from a non-zero overlap of different vibronic wavefunctions of the electronic ground and excited states. The transition highest in energy is the 0-0 transition, which takes place between the zeroth vibronic level in the excited state and the zeroth vibronic level in the ground state. The 0-1 transition involves the creation of one phonon. The relative intensity of the 0-0 peak to the 0-1 peak in the thick film (Figure 1(a)) is lower than that in the thin film (Figure 1(b)) indicating a higher self-absorption in the thick film. The peak positions were determined by fitting the spectra to Gaussian lineshapes. In the thin film, the main vibronic peaks that are observed at 30 K are the 0-0 peak at 2.93 eV, the 0-1 at 2.77 eV and the 0-2 transition at 2.59 eV. An additional vibronic replica is observed at 2.86 eV between the 0-1 and 0-2 peaks. These values are very close to the energies observed in the thick film.

With increasing temperatures a broad peak is seen to emerge at 2.3 eV around 150 K for the thick film. Recent work suggests that this peak is related to emission from keto defect sites, list ; scherf  which are due to the inclusion of fluorenone units along the PF backbone. Keto defects (shown in the inset of Figure 1(b)) can be accidentally incorporated into the $`\pi `$-conjugated PF backbone either during synthesis, by direct inclusion of a fluorenone unit, due to oxidization of non-alkylated or monosubstituted fluorene sites, or as a result of a photo-oxidative degradation process. The concentration of these defect sites is quite low in our PF2/6 sample since the 2.3 eV emission is absent in the thin film (Figure 1(b)). Also, it is a thermally activated process; a weak defect-related emission is only observed for temperatures above 150 K for the thick film (Figure 1(a)).

Figure 2 shows the 300 K PL spectrum of a bulk powder sample of PF2/6 at selected values of pressure. The 0-0 transition (2.9 eV) at ambient pressure is barely visible due to self-absorption effects. However, the other vibronics at ambient pressure correlate with the film data in Figure 1. The most remarkable feature is the emergence of a strong orange emission above $``$20 kbar at 2.4 eV, which dominates the spectrum and completely overwhelms the PL from the backbone. This peak is attributed to a combination of emissions from aggregates and keto defect sites (discussed in greater detail in Section III.2). The broad emission, which is comprised of at least 3 peaks, clearly red shifts with increasing pressures. The pressure dependence of the backbone PL transitions is difficult to quantify. The apparent position of the 0-0 transition is affected by changes in the absorption spectrum, and the relative intensities of the backbone and aggregate/defect emissions change dramatically as pressure is increased. The vibronic peaks are clearly observable up to 20 kbar above which pressure they appear to remain relatively constant in energy with increasing pressure. This behavior is contrary to the observations in other $`\pi `$-conjugated molecules and polymers where the backbone emission clearly red shifts under increasing pressures as, for example, in polyacetylene,moses  polythiophene,hess  m-LPPP,yang  PHP,guha2  poly (p-phenylene vinylene) (PPV)webster  and MEH-PPV.drickamer

In order to clarify the behavior of the backbone emission which, as seen from Figure 1, is less affected by the keto defect in thin films, we studied the pressure dependence of the PL from a film of PF2/6 that was drop-cast onto the surface of one of the diamonds of the DAC. We systematically measured the PL both for increasing and decreasing pressures. The backbone emission is clearly defined up to 30 kbar, as shown in Figure 3 (a). Above 30 kbar the 0-1 and 0-2 can no longer be clearly distinguished; instead a broad peak appears at 2.5 eV with a shoulder at 2.4 eV. The 0-0 vibronic peak is clearly observed up to 42 kbar as shown in Figure 3 (a). As the pressure increases further the 2.5 eV peak dominates the spectrum up to the highest pressures ($``$100 kbar). Figure 3 (b) shows the PL spectra taken while lowering the pressure. Some hysteresis is observed in recovering the low-pressure spectra. In the mid-range (30-45 kbar) the emission in the 2.2-2.5 eV is still dominant and the backbone emission recovers very slowly. Full recovery is not observed until $``$10 kbar. We note that our results for the PF2/6 film under hydrostatic pressure conditions in the DAC are quite different from that observed by Rothe et al.rothe , where they observe no hysteresis. In their work a film of PF2/6 was sandwiched between two glass slides: the pressure in their case should be substantially lower than that in a DAC, and is uniaxial as well.

The absorption spectrum as a function of pressure was measured from the same film (at the same pressures as the PL) and is shown in the inset of Figure 4. The spectra were taken at room temperature by dividing the sample transmission by the transmission of the empty diamond cell. Such a broad absorption spectrum is characteristic of the $`\alpha `$ phase. With increasing pressure, the overall absorbance increases and the spectrum red shifts. Increased absorbance in the 2.7 eV region may be indicative of $`\beta `$ phase formation. Although the $`\alpha `$ phase of PF does not show any absorption below 2.90 eV, one cannot rule out a red shift of the absorption edge from the $`\alpha `$ phase itself with increasing pressures. Such effects have been observed in m-LPPP under pressure. meerapressure  The sharp peak at 2.95 eV is from the type II diamond of the pressure cell.

### III.2 Discussion of PL Results

The PL spectrum of the film, was fit using six Gaussian peaks. In the insert of Figure 4 (b) we show a spectrum at 14.8 kbar, where the vibronics, keto, and aggregate emissions are all clearly observed. The highest two are the 0-0 and 0-1 vibronics. The 2.53 eV peak is close to the 0-2 position. The 2.39 eV peak arises from an aggregate, as does the 2.07 peak. The 2.24 eV peak arises from the keto defect. The peak positions of the keto and the aggregate emissions versus pressure for the film sample are plotted in Figure 4 (b), and they red shift by 0.6 and 0.3 meV/kbar, respectively, with increasing pressure. The 0-0 and the 0-1 backbone vibronics are clearly visible up to 40 kbar and shift by about an order of magnitude faster (Figure 4 (a)). Similar systematic fitting of the backbone vibronic peaks is difficult for the powder sample, due to the increasing absorbance and the broad keto emission at higher pressures.

The main impact of pressure on the PL spectrum is the enhanced emission in the 2.1-2.6 eV range which overwhelms the backbone emission of PF2/6 beyond a certain pressure value. Emission in this region has been observed in other works on PF at ambient pressure. Under photodegradation in 9,9-di-n-hexyl-2,7-dibromofluorene (PDHF), three peaks at 2.2 eV, 2.4 eV and 2.6 eV are observed and have been identified as excimer peaks.carter  Using time-resolved PL spectroscopy, Herz and Phillipsherz  find a longer decay time for the 2.15 eV peak, also attributed to an excimer type emission, as compared with other peaks in this region. This result has led to a picture that intermolecular interactions dominate the bulk material properties in PFs.

Work by List et al.list  conclusively shows that the 2.2-2.3 eV emission is from keto defect sites in PFs. This assignment has been confirmed in a recent work by Lupton et al.lupton  using time-resolved PL on a range of poly-and oligofluorene samples. They attribute the 2.3 eV emission to an on-chain emissive defect, in agreement with the keto-type defect. Further, they observe an enhancement of the 2.6 eV emission with increasing sample concentration concluding that the origin of this peak is due to the formation of interchain aggregates.

In our work here, the enhancement of the 2.1-2.6 eV emission for the bulk sample occurs at $``$ 20 kbar and for the film at a slightly higher pressure of $``$ 35 kbar. The relative intensities of the various peaks in the 2.1-2.6 eV band under pressure are different in the film and in a powder sample. In bulk PF2/6 (see Figure 2) both the keto and aggregate emission are equally enhanced at 20 kbar: the keto peak ($``$ 2.3 eV) gains intensity over the aggregate peak ($``$ 2.4 eV) beyond 42 kbar. Although the concentration of the keto defects is quite small in our PF2/6 sample (as shown in Figure 1), increasing the intermolecular interaction causes the emission from the defect sites to be considerably enhanced. This scenario is somewhat similar to the guest-host polyfluorene system where a small concentration of a chromophore with an absorption spectrum closely matching the emission of PFO drastically changes the PL emission.virgili ; cerullo  In these systems there is an efficient Förster energy transfer to the host molecules that allows conversion of the blue emission from PFO into red emission of the guest chromophore. In our case the enhanced intermolecular interaction allows transfer from the backbone to the keto defect making that emission more and more prominent as pressure increases.

In the PF2/6 film, beyond 35 kbar the 2.1-2.6 eV emission dominates the backbone emission. The aggregate emission is stronger than the keto emission which appears as a weak shoulder at higher pressures. The higher aggregation in the film may result from a more compact and ordered morphology in the film. This ordering may also explain the hysteresis of the PL spectra observed between increasing and decreasing pressures. The absence or weak intensity of keto-related peaks in the film may result from a ”pinning” of excitations in ordered regions that prevents diffusion of the excited carriers to the defect states.

A weak shoulder at 1.9 eV is observed both in the film and powder samples of PF2/6 (see Figures 2 and 3). The exact origin of this peak is not understood but most probably it is also due to aggregate emission. In Section IV we discuss how this PL emission at higher pressures results in an antiresonance effect of the Raman phonons.

The overall PL intensity, due to aggregate and keto emission, increases noticeably at 42 kbar in the powder sample. A temperature scan was taken at this pressure since cooling the sample decreases the pressure by $``$ 2 kbar, and thus allows us to cycle through any morphological changes. The relative intensity of the backbone transitions was observed to decrease with increasing temperature. A significant change occurs between 150 K and 250 K. Above 250 K the 0-0 transition is almost completely quenched and the broadband emission increases in intensity by more than a factor of three. These changes in the PL are most likely due to morphological changes in PF2/6.michael  Transport measurements show that polymers in a liquid crystalline state exhibit greatly enhanced interchain charge carrier mobility.redecker2  Since PF2/6 does exhibit a crystalline to nematic liquid crystalline phase transition, it is possible that such a transition causes the sudden change in the relative intensities of the PL emission with increasing pressures.

The rate of red-shift of the 0-0 and 0-1 backbone emission peaks in the PF2/6 film under pressure is similar to shifts observed in m-LPPP film and PHP powder, as shown in Table 1. Future work on copolymers of PF2/6 and with other side-group substitutions (that minimize the incorporation of keto defects) are required to understand the dynamics of the backbone vibronics in the bulk PF2/6 sample, which barely appear to shift. This effect may well be an artifact due to the higher self-absorption in the powder or due to a different morphology of the powder as compared with the film under hydrostatic pressure. The shifts of the aggregate and keto emissions with pressure are similar in film and powder samples.

## IV Raman scattering

### IV.1 Experimental Results

Figure 5 shows the Raman spectra of powder PF2/6 at 13 K and 300 K at ambient pressure. With increasing temperatures all the Raman peaks in the 1200-1600 cm-1 soften by $``$ 2 cm-1, a value comparable to several known conjugated materials.guha

The Raman frequencies in the 1050-1200 cm-1 region are sensitive to side group substitution; they arise from the C-H bending modes of the ethyl-hexyl side group in PF2/6. The 1290 cm-1, 1342 cm-1 and the 1417 cm-1 are associated with the backbone C-C stretch modes. The Raman peaks in the 1600 cm-1 region arise from the intra-ring C-C stretch mode. This region of the spectrum is best fit with two peaks, a weak peak at 1582 cm-1 and a strong peak at 1605 cm-1. These peak assignments are similar to those of Ariu et al.ariu  in their work on PFO, where the Raman peaks in the 1200-1400 cm-1 region are attributed to the C-C stretch mode between adjacent phenyl rings. It has been assumed that the higher frequency modes in this region are due to the C-C stretch from within the more rigid monomer unit, while the C-C stretch modes between adjacent monomer units are expected to have a lower frequency due to the torsional degree of freedom allowed.ariu

Figure 6 is a plot of Raman spectra from PF2/6 at various pressures. Each frequency region of the graph has been scaled individually so that key features in each spectrum are clearly observed. The break in the $`x`$-axis at 1300 cm-1 denotes the region where the Raman peak from the diamond has been removed for clarity. Most of the phonon frequencies corresponding to the backbone C-C stretch modes are not observable as a function of pressure due to the presence of the strong 1330 cm-1 Raman peak from diamonds in the DAC.

As pressure is increased, all of the Raman frequencies analyzed tend to increase in frequency. Concurrently, the PL tail gains intensity, obscuring the Raman signal beginning with the lower frequency peaks. The region below $``$ 1300 cm-1 is observable up to $``$ 20 kbar and the 1417 cm-1 peak is observed up to about 40 kbar. We note that these Raman measurements were taken using the 647.1 nm (1.92 eV) line of a Kr+ laser. Despite being well below the PL peaks of both the backbone and the keto emissions, the laser line still excites the low energy tail of the PL spectrum (see Figure 3). We believe that this tail most likely arises from aggregate emissions but possibly could also be due to the keto defects.

The rising PL tail above 20 kbar causes several of the Raman peaks to exhibit asymmetric lineshapes and an antiresonance effect characteristic of a Breit-Wigner Fano (BWF) resonance. Such effects have been observed in inorganic semiconductors, for example in p- and n-doped Si and Ge.meera ; cardona  This effect is indicative of a strong electron-phonon interaction between the Raman phonons and the electronic continuum.klein  We find that the most consistent development of the BWF resonance is observed in the 1605 cm-1 peak with the development of asymmetry and increased broadening with increasing pressures is seen in Figure 6. We have conducted a detailed lineshape analysis for this peak in terms of the BWF resonance, discussed in detail in section IV.2.

Along with the asymmetry of the 1605 cm-1 peak, new peaks exhibiting antiresonance effects appear near 1230 cm-1 and 1530 cm-1 (as seen in Figure 6). These peaks appear in the Raman spectra both with increasing and decreasing pressure. Although their signals are weak, their spectra are reproducible. Some of them may be infrared (IR) active modes that become Raman active at higher pressures. In Ref. (list, ) it is seen that there are a number of IR peaks in the 1000-1500 cm-1 range in PF with the strongest IR peak appearing at 1500 cm-1. The 1530 cm-1 feature observed around 40 kbar is most likely the 1500 cm-1 IR active peak shifted to higher frequencies due to the applied pressure. This IR frequency shows a weak signature even in the 1 bar Raman spectrum (Figures 5 and 6), and the magnitude of the shift is consistent with the pressure shifts of the other Raman peaks, as seen in Figure 7.

### IV.2 Discussion of Raman Results

The Raman peaks have been fit with Lorentzian lineshapes to determine their frequency positions. Their peak positions as a function of pressure are plotted in Figure 7. The 1417 cm-1 mode is seen clearly up to 40 kbar. The 1500 cm-1 peak is too weak in intensity to track below 40 kbar, but can be seen as a marked antiresonance and can be tracked reliably for a few data points above 40 kbar. The 34 kbar data point for this peak was taken as the pressure was being decreased, and due to a hysteresis effect the peak was still visible. As the pressure was decreased further the PL background dropped in intensity and the low pressure spectra were fully recovered. All of the peaks shift with fairly similar pressure coefficients.

The positions of the 1605 cm-1 and the shoulder peak at 1582 cm-1 are included up to 60 kbar in Figure 7. Above about 40 kbar the increase of the asymmetry of the 1605 cm-1 peak made fitting to the Lorentzian lineshape difficult. Since the interaction of the main 1605 cm-1 peak with the electronic continuum makes the lineshape broader and asymmetric it was more accurately determined by a BWF fit. It is possible only to resolve one peak using a BWF lineshape. We have fit the entire pressure range using both fits (see Figure 7). At lower pressures there is good agreement between the peak frequencies determined by both the Lorentzian and the BWF fits, however the values deviate at higher pressures. Our linear fits to the frequency vs pressure data for the Lorentzian fits are shown in Figure 7 up to 40 kbar.

Since the PL emission from the aggregates and the keto defects red shift, at higher pressures the 647.1 nm Raman excitation line (1.92 eV) excites the tail of the emission (Figure 3), which couples strongly to the phonons. We therefore directly excite the emission without exciting the backbone PL emission, excluding the possibility of this emission being from excimers.

To determine the peak position, asymmetry parameter and linewidth as a function of pressure, we fit the 1605 cm-1 peak with a BWF lineshape given byzhou

$$I(\omega )=I_0\frac{[(\omega \omega _0)/q+\mathrm{\Gamma }]^2}{(\omega \omega _0)^2+\mathrm{\Gamma }^2},$$
(1)
where $`\omega _0`$ is the discrete phonon frequency, and $`\mathrm{\Gamma }`$ is the width of the resonant interference between the continuum and discrete scattering channels. The asymmetry parameter $`(1/q)`$ depends on the average electron-phonon matrix element $`M`$ and the Raman matrix elements between the ground and excited states of the phonon and electron.meera  The broadening parameter is given by

$$\mathrm{\Gamma }=\pi M^2D(\omega ),$$
(2)
where $`D(\omega )`$ is the combined density of states for the electronic transitions. For non-zero density of states it turns out that when $`q=(\omega \omega _0)/\mathrm{\Gamma }`$, the spectral function $`I(\omega )`$ will reveal an ”antiresonance” close to the value of phonon frequency.klein

Figure 8 shows the asymmetry parameter versus pressure for the 1605 cm-1 Raman mode. The asymmetry is relatively small up to about 35 kbar, with a 1/q value between -0.005 and 0.1. Beyond 40 kbar however, the asymmetry increases rapidly and 1/q varies from -0.3 to -0.6. The inset shows a sample BWF fit to Eq. 1 (bold line) to the experimental data (open triangles) for data at 42 kbar. The peak position and the linewidths from the BWF fits as a function of pressure are plotted in Figure 9. The linewidth shows a square law dependence with pressure ($`\mathrm{\Gamma }P^2`$ ) (solid line in Figure 9). The frequency positions vary almost linearly with pressure. The inset of Figure 9 shows $`1/q`$ to linearly vary with the linewidth $`\mathrm{\Gamma }`$.

Recently, optical techniques based on photoinduced infrared-active vibrational (IRAV) modes have been used to study the photogeneration and recombination dynamics of charged polarons in conjugated polymers.miranda  Österbacka et al. have observed Fano-type antiresonances in the IRAV modes in a series of $`\pi `$-conjugated polymers that are explained well by extending the amplitude model beyond the adiabatic limit.osterbacka  Our observation here is somewhat different; the electronic continuum is from a combination of aggregate and defect emissions that shift to lower energies with increasing pressure. Figure 8 shows that q is negative, indicating that the center frequency of the continuum lies below the discrete mode frequency of 1605 cm-1 (0.2 eV). It is interesting to point out that in $`M_3C_{60}`$ and superconducting cuprates, $`1/q`$ value lies between -0.2 to -0.5,zhou  similar to our results beyond 40 kbar. The high background and the interference from the diamond Raman peak makes it difficult to analyze the asymmetry of the other Raman peaks as a function of pressure. The systematic appearance of the inverted 1530 cm-1 peak at higher pressures makes it a viable candidate for the IR-active frequency that gets activated in the Raman spectrum due to a lowering of the symmetry. Most probably the peak shows an S-like behavior due to the antiresonance effect and therefore appears as a negative peak.

Since the vibrational frequencies of a harmonic solid are independent of compression, pressure induced changes in the Raman spectrum provide insight into the anharmonicity of the solid state potential.ferraro  In this light the linear shift of the 1605 cm-1 peak as a function of pressure is not surprising. The rate of shift is similar to other Raman-active frequencies in PF2/6 which is an indication of the anharmonic potential. Although one expects an additional shift in phonon frequency due to the BWF interaction (the real part of the self energy) we cannot infer any information about this parameter from our data. In materials where the BWF interaction can be tuned, e.g. using uniaxial stress in both n-typemeera  and p-type Si, cardona  the real part of the self energy due to interaction between the phonon and the electronic continuum is determined by comparison with the pure material. In this work, such a comparison is not possible owing to a lack of a defect-free but identical material. Had this parameter been large one would expect a significant deviation in the peak position vs pressure behavior above 40 kbar where the BWF character of the mode is pronounced.

However, the imaginary part of the self-energy, $`\mathrm{\Gamma }`$, does show a quadratic dependence with pressure. Furthermore, the asymmetry parameter should be directly proportional to $`\mathrm{\Gamma }`$ if the average electron-phonon matrix element and the Raman matrix elements between the ground and excited states are assumed to be roughly constant.sathpathy  Indeed, this is what we find, as shown in the inset of Figure 9. The negative slope here is due to the negative q values that we obtain from the fit. At present we are unclear of the physical significance of the quadratic dependence of $`\mathrm{\Gamma }`$ on pressure, which reflects on the density of states of the continuum. A full-scale band-structure calculation incorporating aggregate and defect states should reveal the nature of the electronic density of states.

## V CONCLUSION

In conclusion, we have shown that hydrostatic pressure induces very efficient energy transfer of the singlet excitons to the keto defect sites mainly in bulk PF2/6. Enhanced intermolecular interaction induces a strong aggregate-type emission in the film sample, in addition to a keto emission. This may result from a pinning of excitations in ordered regions in the film that prevents excitation diffusion to the defect states. The Raman modes harden with increasing pressures. The 1605 cm-1 peak exhibits an asymmetric lineshape, characteristic of a Breit-Wigner Fano resonance, and some of the other peaks show an antiresonance effect. This is indicative of a strong electron-phonon interaction between the Raman phonons and the electronic continuum. We have carried out a detailed BWF lineshape analysis for the 1605 cm-1 peak as a function of pressure.

Both the PL and Raman studies from bulk PF2/6 show significant changes at 40 kbar. The aggregate and defect related emission increases significantly and the asymmetry of the 1605 cm-1 Raman peak becomes higher. This may be related to a phase transition. Future work on different side-group substituted PFs that have extraordinarily small keto defect concentration are in progress to obtain insight into the morphological changes that occur in PFs as a function of hydrostatic pressure.

###### Acknowledgements.

S.G. acknowledges the donors of the American Chemical Society Petroleum Research Fund (#35735-GB5) for partial support of this research. U.S. thanks SONY International Europe, Stuttgart, and the Deutsche Forschungsgemeinschaft (DFG) for financial support. One of us (S.G.) thanks Michael Winokur for many valuable insights and discussions.