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# Rationality of Partial Zeta Functions

## 1 Introduction

Let $`𝐅_q`$ be the finite field of $`q`$ elements of characteristic $`p`$. Let $`\overline{𝐅}_q`$ be a fixed algebraic closure of $`𝐅_q`$. Let $`X`$ be an affine algebraic variety over $`𝐅_q`$, embedded in some affine space $`𝐀^n`$. That is, $`X`$ is defined by a system of polynomial equations

$$F_1(x_1,\mathrm{},x_n)=\mathrm{}=F_m(x_1,\mathrm{},x_n)=0,$$

where each $`F_i`$ is a polynomial defined over $`𝐅_q`$. Let $`d_1,\mathrm{},d_n`$ be positive integers. For each positive integer $`k`$, let

$$X_{d_1,\mathrm{},d_n}(k)=\{xX(\overline{𝐅}_q)|x_1𝐅_{q^{d_1k}},\mathrm{},x_n𝐅_{q^{d_nk}}\}.$$

The number $`\mathrm{\#}X_{d_1,\mathrm{},d_n}(k)`$ counts the points of $`X`$ whose coordinates are in different subfields of $`\overline{𝐅}_q`$. We would like to understand this sequence of integers $`\mathrm{\#}X_{d_1,\mathrm{},d_n}(k)`$ indexed by $`k`$. As usual, it is sufficient to understand the following generating function.

###### Definition 1.1

Given $`X`$ and the $`n`$ positive integers $`d_1,\mathrm{},d_n`$, the associated partial zeta function $`Z_{d_1,\mathrm{},d_n}(X,T)`$ of $`X`$ is defined to be the following formal power series

$$Z_{d_1,\mathrm{},d_n}(X,T)=\mathrm{exp}\left(\underset{k=1}{\overset{\mathrm{}}{}}\frac{\mathrm{\#}X_{d_1,\mathrm{},d_n}(k)}{k}T^k\right)1+T𝐐[[T]].$$

Replacing $`q`$ by a power of $`q`$, without loss of generality, we may assume that the integer $`d_i`$’s are relatively prime. In the special case that $`d_1=\mathrm{}=d_n=1`$, the number $`\mathrm{\#}X_{1,\mathrm{},1}(k)`$ is just the number of $`𝐅_{q^k}`$-rational points on $`X`$. The partial zeta function $`Z_{1,\mathrm{},1}(X,T)`$ then becomes the classical zeta function $`Z(X,T)`$ of the variety $`X`$. Dwork’s rationality theorem  says that $`Z(X,T)`$ is a rational function. Deligne’s theorem  on the Weil conjectures says that the reciprocal zeros and the reciprocal poles of $`Z(X,T)`$ are Weil $`q`$-integers. Recall that a Weil $`q`$-integer $`\alpha `$ is an algebraic integer such that $`\alpha `$ and each of its Galois conjugates have the same complex absolute value $`q^{w/2}`$ for some non-negative integer $`w`$. The integer $`w`$ is called the weight of $`\alpha `$.

One of our motivations to introduce the above more general partial zeta function comes from potential applications in number theory, combinatorics and coding theory. From a theoretic point of view, a special case of the partial zeta function reduces to the geometric moment zeta function  attached to a family of algebraic varieties over $`𝐅_q`$, which was in turn motivated by our work on Dwork’s unit root conjecture . Intuitively, the partial zeta function gives many new ways, parametrized by the integers $`d_i`$’s, to count the geometric points on $`X`$ and thus it contains critical information about the distribution of the geometric points of $`X`$. The partial zeta function also provides a simple diophantine reformulation of many much more technical problems. In , the following two results were proven concerning the possible rationality of the partial zeta function. Recall that for a complex number $`\alpha `$ and a complex power series $`R(T)`$ with constant term $`1`$, we can define the complex power $`R(T)^\alpha `$ in terms of the binomial series $`(1+T\frac{R(T)1}{T})^\alpha `$.

###### Proposition 1.2 (Faltings )

Let $`d=[d_1,\mathrm{},d_n]`$ be the least common multiple of the $`d_i`$. Let $`\zeta _d`$ be a primitive $`d`$-th root of unity. There are $`d`$ rational functions $`R_j(T)`$ ($`1jd`$) with $`R_j(0)=1`$ and with algebraic integer coefficients such that

$$Z_{d_1,\mathrm{},d_n}(X,T)=\underset{j=1}{\overset{d}{}}R_j(T)^{\zeta _d^j}.$$

Furthermore, the reciprocal zeros and reciprocal poles of the $`R_j(T)`$’s are Weil $`q`$-integers.

This result shows that the partial zeta function is nearly rational. It is proved by using a geometric construction of Faltings and the general fixed point theorem in $`\mathrm{}`$-adic cohomology.

###### Proposition 1.3 ()

If the integers $`\{d_1,d_2,\mathrm{},d_n\}`$ can be rearranged such that $`d_1|d_2|\mathrm{}|d_n`$, then the partial zeta function $`Z_{d_1,\mathrm{},d_n}(X,T)`$ is a rational function in $`T`$, who reciprocal zeros and reciprocal poles are Weil $`q`$-integers.

This result shows that the partial zeta function has the stronger property of being a rational function in some non-trivial special cases. It is proved by viewing $`X`$ as a sequence of fibered varieties and inductively using the Adams operation of the relative $`\mathrm{}`$-adic cohomology. Although it was felt that the partial zeta function may not be always rational in general, no counter-examples were found. The aim of this note is to prove the following result.

###### Theorem 1.4

For any variety $`X`$ as above and any positive integers $`\{d_1,\mathrm{},d_n\}`$, the partial zeta function $`Z_{d_1,\mathrm{},d_n}(X,T)`$ is a rational function in $`T`$, who reciprocal zeros and reciprocal poles are Weil $`q`$-integers.

The idea of the proof is to exploit the geometric construction of Faltings and its relation to Galois action. Once the rationality is proved, one main new problem about the partial zeta function is to understand its dependence and variation on the arithmetic parameters $`d_i`$’s. This would raise many interesting new questions to be explored, as already illustrated in the special case of moment zeta functions . The first question one could ask for is about the number of zeros and poles of the partial zeta function. In Fu-Wan , using Katz’s bound  on the $`\mathrm{}`$-adic Betti numbers, an explicit total degree bound for $`Z_{d_1,\mathrm{},d_n}(X,T)`$ is given, which grows exponentially in $`d`$. We conjecture that the true size of the total degree is much smaller and bounded by a polynomial in $`d`$.

###### Conjecture 1.5

There are two positive constants $`c_1(X)`$ and $`c_2(X)`$ depending only on $`X`$ such that the total degree of the partial zeta function $`Z_{d_1,\mathrm{},d_n}(X,T)`$ is uniformly bounded by $`c_1(X)d^{c_2(X)}`$ for all positive integers $`\{d_1,\mathrm{},d_n\}`$.

This conjecture has been proved to be true in Fu-Wan  in the special case that $`d_1=\mathrm{}=d_r=1`$ and $`d_{r+1}=\mathrm{}=d_n=d`$, corresponding to the so-called moment zeta function case which has been studied more extensively in connection to Dwork’s unit root conjecture. We believe that the above conjecture (if true) together with a deeper analysis of the weights of the zeros and poles of the partial zeta function would have many important applications. Under suitable conditions, we would like to have optimal estimates of the form

$$|\mathrm{\#}X_{d_1,\mathrm{},d_n}(k)q^{k(d_1+\mathrm{}+d_ndm)}|c_1d^{c_2}q^{k(d_1+\mathrm{}+d_ndm)/2},$$

see section $`4`$ for some results in the case of Artin-Schreier hypersurfaces ($`m=1`$).

Acknowledgements. Some results of this paper were obtained during the 2001 Lorentz center workshop “L-functions from algebraic geometry” at Leiden University and the 2003 AIM workshop “Future directions in algorithmic number theory”. The author thanks both institutes for their hospitality. The author would also like to thank H. W. Lenstra Jr. for his interests and discussions on this paper.

## 2 Rationality of partial zeta functions

We slightly generalize the setup in the introduction. Let $`f_i:XX_i`$ ($`1in`$) be morphisms of schemes of finite type over $`𝐅_q`$. Assume that the map $`f:XX_1\times \mathrm{}\times X_n`$ defined by

$$f(x)=(f_1(x),\mathrm{},f_n(x))$$

is an embedding. For each positive integer $`k`$, let

$$f_{d_1,\mathrm{},d_n}(k)=\{xX(\overline{𝐅}_q)|f_1(x)X_1(𝐅_{q^{d_1k}}),\mathrm{},f_n(x)X_n(𝐅_{q^{d_nk}})\}.$$

This is a finite set since $`f`$ is an embedding.

###### Definition 2.1

Given the morphism $`f`$ and the $`n`$ positive integers $`\{d_1,\mathrm{},d_n\}`$, the associated partial zeta function $`Z_{d_1,\mathrm{},d_n}(f,T)`$ of the morphism $`f`$ is defined to be the following formal power series

$$Z_{d_1,\mathrm{},d_n}(f,T)=\mathrm{exp}\left(\underset{k=1}{\overset{\mathrm{}}{}}\frac{\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)}{k}T^k\right)1+T𝐐[[T]].$$

It is clear that the special case in the introduction corresponds to the case that $`X`$ is affine in $`𝐀^n`$ and $`f_i`$ is the projection of $`x`$ to the $`i`$-th coordinate $`x_i𝐀^1`$.

###### Theorem 2.2

For any morphism $`f`$ and any positive integers $`\{d_1,\mathrm{},d_n\}`$, the partial zeta function $`Z_{d_1,\mathrm{},d_n}(f,T)`$ is a rational function in $`T`$, whose reciprocal zeros and reciprocal poles are Weil $`q`$-integers.

To prove this theorem, we begin with the geometric construction of Faltings. Let $`d=[d_1,\mathrm{},d_n]`$ be the least common multiple. The set of geometric points on the $`d`$-fold product $`X^d`$ of $`X`$ has two commuting actions. One is the $`q^1`$-th power geometric Frobenius action denoted by $`\mathrm{Frob}`$. Another is the automorphism $`\sigma `$ on $`X^d`$ defined by the cyclic shift

$$\sigma (y_1,\mathrm{},y_d)=(y_d,y_1,\mathrm{},y_{d1}),$$

where $`y_j`$ denotes the $`j`$-th component ($`1jd`$) of a point $`y=(y_1,\mathrm{},y_d)`$ on the $`d`$-fold product $`X^d`$. Thus, each component $`y_j`$ is a point on $`X`$. Let $`Y=Y(d_1,\mathrm{},d_n,f)`$ be the subvariety of $`X^d`$ defined by the equations

$$f_i\sigma ^{d_i}=f_i,1in,$$

where $`f_i:X^dX_i^d`$ denotes the map $`f_i(y_1,\mathrm{},y_d)=(f_i(y_1),\mathrm{},f_i(y_d))`$. Thus, a point $`y=(y_1,\mathrm{},y_d)X^d`$ is on the subvariety $`Y`$ if and only if

$$f_i(y_j)=f_i(y_{j+d_i}),1in,1jd,$$
$`(2.1)`$
where $`j+d_i`$ is taken to be the smallest positive residue of $`j+d_i`$ modulo $`d`$. It is clear that $`Y`$ is stable under the action of $`\sigma `$ which commutes with $`\mathrm{Frob}`$.

Now, let $`a`$ be a fixed positive integer relatively prime to $`d`$. Let $`y=(y_1,\mathrm{},y_d)`$ be a geometric point of $`Y`$. One checks that

$$\sigma ^a\mathrm{Frob}^k(y)=y\mathrm{Frob}^k(y_j)=y_{j+a},1jd.$$
$`(2.2)`$
The latter is true if and only if

$$\mathrm{Frob}^k(f_i(y_j))=f_i(y_{j+a}),1in,1jd$$
$`(2.3)`$
as $`f`$ is an embedding. Iterating equation (2.3) $`d_i`$ times, we get

$$\mathrm{Frob}^{d_ik}(f_i(y_j))=f_i(y_{j+ad_i}).$$

Since $`y`$ is on $`Y`$, by (2.1), we deduce that

$$\mathrm{Frob}^{d_ik}(f_i(y_j))=f_i(y_j).$$

Taking $`j=1`$, we see that every fixed point $`yY(\overline{𝐅}_q)`$ of $`\sigma ^a\mathrm{Frob}^k`$ uniquely determines a point $`y_1X(\overline{𝐅}_q)`$ satisfying $`f_i(y_1)X_i(𝐅_{q^{d_ik}})`$ for all $`1in`$.

Conversely, given $`y_1X(\overline{𝐅}_q)`$ such that $`f_i(y_1)X_i(𝐅_{q^{d_ik}})`$ for all $`1in`$, we define

$$y_j=\mathrm{Frob}^{kh_j}(y_1),1jd,$$

where $`h_j`$ is the unique integer between $`0`$ and $`d1`$ such that $`ah_j+1j(\mathrm{mod}d)`$. The integer $`h_j`$ is clearly well defined since $`a`$ and $`d`$ are relatively prime. If $`jj^{}(\mathrm{mod}d_i)`$, then $`h_jh_j^{}(\mathrm{mod}d_i)`$. Since $`f_i(y_1)X_i(𝐅_{q^{d_ik}})`$, we deduce that

$$f_i(y_j)=\mathrm{Frob}^{kh_j}(f_i(y_1))=\mathrm{Frob}^{kh_j^{}}(f_i(y_1))=f_i(y_j^{}).$$

This shows that the point $`y=(y_1,\mathrm{},y_d)`$ is on $`Y`$. Since $`f`$ is an embedding and $`f_i(y_1)X_i(𝐅_{q^{d_ik}})`$ for all $`i`$, we deduce that $`y_1X(𝐅_{q^{dk}})`$. Using the congruence $`a(h_j+1)+1j+a(\mathrm{mod}d)`$, we derive that

$$\mathrm{Frob}^k(y_j)=\mathrm{Frob}^{k(h_j+1)}(y_1)=y_{j+a}.$$

This proves that $`\sigma ^a\mathrm{Frob}^k(y)=y`$. In summary, we have proved the following result.

###### Lemma 2.3

Let $`a`$ be a positive integer relatively prime to $`d`$. Then, for each positive integer $`k1`$, we have the following equality

$$\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)=\mathrm{\#}\mathrm{Fix}(\sigma ^a\mathrm{Frob}^k|Y(\overline{𝐅}_q)).$$
$`(2.4)`$
This lemma was proved in the case $`a=1`$ in . It together with the general $`\mathrm{}`$-adic fixed point theorem gives

$$\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)=\underset{j0}{}(1)^j\mathrm{Tr}(\sigma \mathrm{Frob}^k|H_c^j(Y\overline{\mathrm{F}}_q,𝐐_{\mathrm{}})),$$

where $`\mathrm{}`$ is a prime number different from $`p`$ and $`H_c^j`$ denotes the $`\mathrm{}`$-adic cohomology with compact support. This formula is likely explicitly stated somewhere in SGA. We have not found it. The quasi-projective case is explained in . The general finite type case follows by excision.

Since $`\sigma `$ and $`\mathrm{Frob}`$ commute, $`\sigma ^d=1`$, we can decompose the cohomology space into the eigenspaces of $`\sigma `$. The eigenvalues of $`\sigma `$ are $`d`$-th roots of unity. The eigenvalues of $`\mathrm{Frob}`$ are algebraic integers (in fact, Weil $`q`$-integers by Deligne’s theorem). It follows that there are finitely many $`d`$-th roots of unity $`\alpha _i`$ and finitely many algebraic integers $`\lambda _i`$ such that for all integers $`k1`$, we have

$$\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)=\underset{i}{}\pm \alpha _i\lambda _i^k.$$

We collect similar terms in terms of $`\lambda _i`$ and rewrite the above expression as

$$\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)=\underset{j}{}A_j\lambda _j^k,$$

where the $`\lambda _j`$’s are distinct and $`A_j𝐙[\zeta _d]`$. Replacing $`\sigma `$ by $`\sigma ^a`$ with $`(a,d)=1`$ and using Lemma 2.3, we deduce that for all $`\tau \mathrm{Gal}(𝐐(\zeta _d)/𝐐)`$,

$$\mathrm{\#}f_{d_1,\mathrm{},d_n}(k)=\underset{j}{}\tau (A_j)\lambda _j^k.$$

This sequence of expression is unique since the $`\lambda _j`$’s are distinct. It follows that $`\tau (A_j)=A_j`$ for all $`j`$ and all $`\tau `$. Thus, $`A_j𝐙`$ and

$$Z_{d_1,\mathrm{},d_n}(f,T)=\underset{j}{}(1\lambda _jT)^{A_j}$$

is indeed a rational function. Theorem 2.2 is proved.

## 3 A graph theoretic generalization

In this section, we give Lenstra’s generalization of the partial zeta function and its rationality in a graph theory setup. Let $`G=(V,E)`$ be a finite directed graph, where $`V`$ is the set of vertices of $`G`$ and $`E`$ is the set of directed edges of $`G`$. For each edge $`eE`$, let $`s(e)`$ (resp. $`t(e)`$) denote the starting (resp. the terminal) vertex of the edge $`e`$. Suppose that for each $`vV`$, we are given a scheme $`X_v`$ of finite type over $`𝐅_q`$. Suppose that for each edge $`eE`$, we are given a morphism $`f_e:X_{s(e)}X_{t(e)}`$ of finite type over $`𝐅_q`$. Let $`d_v`$ ($`vV`$) be positive integers. For each positive integer $`k`$, we define

$$N(k)=\mathrm{\#}\{x=(x_v)_{vV}\underset{vV}{}X(𝐅_{q^{d_vk}})|eE,f_e(x_{s(e)})=x_{t(e)}\}.$$

Define the graph zeta function to be

$$Z_{d_1,\mathrm{},d_n}(G,X,T)=\mathrm{exp}\left(\underset{k=1}{\overset{\mathrm{}}{}}\frac{N(k)}{k}T^k\right)1+T𝐐[[T]].$$

One can ask if this power series is a rational function in $`T`$.

###### Theorem 3.1 (Lenstra)

For any graph $`G`$, any schemes $`X_v`$ and any morphisms $`f_e`$ as above, the graph zeta function $`Z_{d_1,\mathrm{},d_n}(G,X,T)`$ is a rational function in $`T`$, whose reciprocal zeros and reciprocal poles are Weil $`q`$-integers.

To prove this theorem, it suffices to reduce the above graph zeta function to the case of partial zeta functions. For this purpose, let $`X`$ be the fibred product of the schemes $`X_v`$ ($`vV`$) over all morphisms $`f_e`$ ($`eE`$). That is,

$$X=\{x\underset{vV}{}X_v|eE,f_e(x_{s(e)})=x_{t(e)}\}.$$

The scheme $`X`$ is a closed subscheme of the Cartesian product $`_{vV}X_v`$. For each $`vV`$, let $`f_v`$ be the composed map

$$f_v:X\underset{vV}{}X_vX_v,$$

where the last map is the projection to $`X_v`$. With these definitions, it is clear that the graph zeta function $`Z_{d_1,\mathrm{},d_n}(G,X,T)`$ is simply the partial zeta function $`Z_{d_1,\mathrm{},d_n}(f,T)`$ attached to the morphisms $`f_v:XX_v`$. The theorem is proved.

It may be of interest to explore possible graph theoretic applications of this zeta function.

## 4 Artin-Schreier hypersurfaces

To give an example, we consider the case of Artin-Schreier hypersurfaces. Let

$$f(x_1,\mathrm{},x_n,y_1,\mathrm{},y_n^{})𝐅_q[x_1,\mathrm{},x_n,y_1,\mathrm{},y_n^{}],$$

where $`n,n^{}1`$. For each $`d1`$, let

$$N_d(f)=\mathrm{\#}\{(x_0,\mathrm{},x_n,y_1,\mathrm{},y_n^{}):x_0^px_0=f(x_1,\mathrm{},x_n,y_1,\mathrm{},y_n^{})\},$$

where $`x_i𝐅_{q^d}`$ ($`0in`$) and $`y_j𝐅_q`$ ($`1jn^{}`$). Heuristically (for suitable $`f`$), we expect

$$N_d(f)=q^{dn+n^{}}+O(q^{(dn+n^{})/2})$$

where the constant depends on $`p`$, $`f`$, and $`d`$. Deligne’s estimate  on exponential sums implies the following result.

###### Theorem 4.1 (Deligne)

Given $`f`$ as above, we write $`f=f_r+f_{r1}+\mathrm{}+f_0`$, where $`f_i`$ is homogeneous of degree $`i`$. Assume that the leading form $`f_r`$ defines a smooth projective hypersurface in $`𝐏_{𝐅_q}^{n+n^{}1}`$, and assume that $`pr`$. Then for $`d=1`$, we have the following inequality

$$|N_1(f)q^{n+n^{}}|(p1)(r1)^{n+n^{}}q^{(n+n^{})/2}.$$

What can be said about $`d>1`$? To answer this question, we introduce the following terminology.

###### Definition 4.2

Let $`d`$ be a positive integer and let $`f`$ be a polynomial as above. We define the *$`d`$th fibred sum of $`f`$* to be the following new polynomial

$$_y^df=f(x_{11},\mathrm{},x_{1n},y_1,\mathrm{},y_n^{})+\mathrm{}+f(x_{d1},\mathrm{},x_{dn},y_1,\mathrm{},y_n^{}).$$

The following estimate on $`N_d(f)`$ is proved in .

###### Theorem 4.3 (Fu-Wan)

Given $`f`$ as above, we write $`f=f_r+f_{r1}+\mathrm{}+f_0`$, where $`f_i`$ is homogeneous of degree $`i`$. Assume that $`_y^df_r`$ is smooth in $`𝐏_{𝐅_q}^{dn+n^{}1}`$ and assume that $`pr`$. Then, we have the following inequality

$$|N_d(f)q^{dn+n^{}}|(p1)(r1)^{dn+n^{}}q^{(dn+n^{})/2}.$$

Example 4.4 Consider the case that

$$f(x,y)=f_{1,r}(x_1,\mathrm{},x_n)+f_{2,r}(y_1,\mathrm{},y_n^{})+f_{r1}(x,y),$$

where $`f_{1,r}`$ is smooth in $`𝐏_{𝐅_q}^{n1}`$, $`f_{2,r}`$ is smooth in $`𝐏_{𝐅_q}^{n^{}1}`$ and $`f_{r1}`$ is a polynomial of degree at most $`r1`$. It is then straightforward to check that $`_y^df_r`$ is smooth in $`𝐏_{𝐅_q}^{dn+n^{}1}`$ if and only if $`d`$ is not divisible by $`p`$. Since the condition that the fibred sum be smooth is Zariski open, there exist many more examples of such $`f`$ to which the theorem applies if $`d`$ is not divisible by $`p`$.

It would be interesting to prove similar results for the Kummer hypersurface $`x_0^D=f(x_1,\mathrm{},x_n,y_1,\mathrm{},y_n^{})`$; see Katz  for some related weaker results in this direction.

Institute of Mathematics, Chinese Academy of Sciences, Beijing, P.R. China

Department of Mathematics, University of California, Irvine, CA 92697, USA

Email: dwan@math.uci.edu


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# Universal behavior of localization of residue fluctuations in globular proteins

\[

## Abstract

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.

\]

Proteins are important biological macromolecules that control almost all functions of living organisms. It was once believed that proteins are rather amorphous and without well-defined structures. After more and more structures have been determined by crystallographic and NMR methods, it has revealed that protein structures are far from random. They have well-defined secondary and tertiary structures which comprise essential information relating to their functions and mechanisms.

Proteins in the folded states are not static. Instead, the constituent residues fluctuate near their native positions owing to the finite temperature effects. It has been now well accepted that the fluctuations are crucial for enzyme catalysis and for biological activity. Recently, there has been considerable interest in the correlations between protein functions and fluctuations. Intensive theoretical studies on fluctuations of protein have been carried out based on either molecular dynamics simulations or normal mode analyses (NMA) by using all-atom empirical potentials. It has been shown that the NMA is a very useful method to study protein fluctuations. The use of atomic approaches becomes computational demanding when dealing with large proteins. For proteins composed of more than thousand residues, it is difficult to investigate by using the conventional atomic models and potentials. On the other hand, coarse-grained protein models and simplified force fields have revealed a great success in description of the residue fluctuations of proteins. Although there have been intensive studies on residue fluctuations, to our knowledge, there is few study on localization properties of residue fluctuations.

In this paper, based on a coarse-grained protein model, we show theoretically that there is a similar behavior in the localization of residue fluctuations for globular proteins, even though their architectures and sizes are rather different. In our study of residue fluctuations, proteins are modeled as elastic networks. The nodes are residues linked by inter-residue potentials that stabilizes the folded conformation. This model has been usually referred as the Gaussian network model (GNM), which can give a satisfactory description of the fluctuation of folded proteins. In this model, residues are assumed to undergo Gaussian-distributed fluctuations about their native positions. No distinction is made between different types of residues. A single generic harmonic force constant is used for the inter-residue interaction potential within a cutoff range. We consider residues as the minimal representative units and the $`\alpha `$-carbons are used as corresponding sites for residues. Considering all contacting residues, the internal Hamiltonian within the GNM is given by

$$H=\frac{1}{2}\gamma \left[\mathrm{\Delta }𝐑^\text{T}\left(𝚪𝐄\right)\mathrm{\Delta }𝐑\right],$$
(1)
where $`\gamma `$ is the harmonic force constant; $`\left\{\mathrm{\Delta }𝐑\right\}`$ represents the $`3N`$-dimensional column vectors of fluctuations $`\mathrm{\Delta }𝐑_1,\mathrm{},\mathrm{\Delta }𝐑_N`$ of the $`C^\alpha `$ atoms, where $`N`$ is the number of residues; $`𝐄`$ is the third order identity matrix; the superscript T denotes the transpose; $``$ stands for the direct product, and $`𝚪`$ is the $`N\times N`$ Kirchhoff matrix with the elements given by

$$\mathrm{\Gamma }_{ij}=\{\begin{array}{cc}H\left(r_\text{c}r_{ij}\right),\hfill & ij,\hfill \\ \underset{i(j)}{\overset{N}{}}\mathrm{\Gamma }_{ij},\hfill & i=j.\hfill \end{array}$$
(2)
Here, $`r_{ij}`$ is the separation between the $`i`$-th and $`j`$-th $`C^\alpha `$ atoms; $`H(x)`$ is the Heaviside step function, and $`r_\text{c}`$ is the cutoff distance outside of which there is no inter-residue interaction. The $`i`$-th diagonal element of $`\mathrm{\Gamma }`$ characterizes the local packing density or the coordination number of residue $`i`$. The inverse of the Kirchhoff matrix can be decomposed as

$$\mathrm{\Gamma }^1=𝐔\mathrm{\Lambda }^1𝐔^\text{T},$$
(3)
where $`𝐔`$ is an orthogonal matrix whose columns $`𝐮_i\left(1iN\right)`$ are the eigenvectors of $`\mathrm{\Gamma }`$, and $`\mathrm{\Lambda }`$ is diagonal matrix of eigenvalue $`\lambda _i`$ of $`\mathrm{\Gamma }`$. Cross-correlations of residue fluctuations between the $`i`$-th and $`j`$-th residues are found from

$$\left[\mathrm{\Delta }𝐑_i\mathrm{\Delta }𝐑_j\right]=\frac{3k_BT}{\gamma }\left[\mathrm{\Gamma }^1\right]_{ij}.$$
(4)
From Eqs. (3) and (4), the mean-square (ms) fluctuations (also called Debye-Waller or B-factors) of the $`i`$-th residue associated with the $`\alpha `$-th mode are given by

$$\left[\mathrm{\Delta }𝐑_i\mathrm{\Delta }𝐑_i\right]_\alpha =\frac{3k_BT}{\gamma }\lambda _\alpha ^1\left[u_\alpha \right]_i\left[u_\alpha \right]_i.$$
(5)
In our calculation, the cutoff distance $`r_\text{c}=7`$ Å is used, as adopted in previous studies. The harmonic force constant $`\gamma `$ is determined by fitting to the experimental ms fluctuations. From this model, one can obtain the fluctuation mode frequencies and eigenvectors for a given protein. The GNM can in general give results in good agreement with the observed B-factors .

The spatial distribution of a given mode is characterized by its eigenvectors. To study the localization properties of protein fluctuations, we have to compute participation ratio (PR) for each mode, defined by

$$P_\alpha =\frac{1}{N}\left(\underset{i}{}\left[u_\alpha \right]_i^4\right)^1.$$
(6)
Values of PR range from $`1/N`$ to unity. PR takes the value of unity if all residues have equal fluctuation. If only one residue fluctuates PR is equal to $`1/N`$. From its definition, it is obvious that PR is a measure of the degree of localization. If the PR is small for a given mode, only a few residues have considerable fluctuations and the mode is a localized one. On the other hand, if the PR is large for a given mode, the mode is delocalized.

It is known that at the physiological temperatures, protein fluctuates among different conformations around its native one. Therefore, in principle, all contributions from these conformations should be considered in the calculation of PR. Unfortunately, only one conformation could be obtained from experiments. However, these conformations could be obtained approximately by the following way. For each residue, it is assumed that it can stay at any position inside the sphere with a radius of half the magnitude of fluctuation centered on the position obtained from experiments. A conformation can be derived by a random choice of the position for each residue while the inter-distance between two adjacent residues is kept unchanged within the framework of the SHAKE algorithm .

The calculated PR for several proteins is shown in Fig. 1. The Brookhaven Protein Databank (PDB) codes and references of the proteins studied are listed in Table I. The modes are numbered starting from the lowest frequency. In the calculations about 100 conformations are adopted. It is found that if more conformations are used, the curves will become smoother eventually.

Based on the Anderson localization theory, Bahar et al.  suggested that modes with larger fluctuation frequencies would be more localized, indicating a monotonous decrease in PR with frequency. As suggested by Onuchic et al.  proteins are neither ordered nor random systems, the localization properties of protein fluctuations should show some intrinsic features from those in ordered or random systems.

It can be seen from Fig. 1 that starting from lowest frequency, PR first decreases with frequency, then increase, and finally decreases with frequency. A large number of globular proteins which have diversified topology, secondary structure arrangement and size are calculated. This behavior of PR seems to be universal, holding for all globular proteins. Other molecular systems such as tRNA are also calculated. But the behavior of PR is qualitatively different from proteins (data not shown). So it is reasonable to conjecture that the different behavior of PR in globular proteins from other systems reflects the intrinsic difference of certain properties. Recently, Micheletti et al.  studied the localization properties of HIV-1 protease. A similar behavior of PR in HIV-1 protease was found.

To study the origin of the behavior of PR in globular proteins, the fluctuation patterns of the protein myoglobin at different frequency regions are given in Fig. 2. The different frequency regions in the figure are labeled by different letters (see Fig. 1). In the low frequency region A, the fluctuations represent a collective motion, characterized by large values of PR. In the region B, the PR is small, implying localized fluctuations. It is interesting to note that in this region the fluctuations occur dominantly at the loops. In the highest frequency region D, the fluctuations are found to be confined to the secondary structures, resulting small PR. In the region C, one can find that motions of both loops and secondary structures are involved. The degree of localization is, however, smaller than that in regions B and D, but it is larger than that in region A. Therefore, it can be concluded from the fluctuation patterns that the dip of PR occurred at lower frequency side (region B) originates from the localized fluctuations at loops that connect the secondary structures. For conventional disordered solids or random coils, there are nearly no well-defined secondary structures and consequently no loops. The resulting PR will show a different behavior. It is obvious that the different behavior of PR in globular proteins from that of conventional random solids or coils originates from the different nature of structures.

To get a deeper insight into how the localization properties are affected by the topology, a lattice model with different length of the loop is adopted. In this model, a protein is represented by a self-avoiding chain of beads placed on a two-dimensional discrete lattice. In construction of this model protein, one must consider the fact that the secondary structure has higher packing density while the loop has lower packing density. A core region is introduced by making two helices contacted each other since cores, with higher packing density, are important to stabilize the whole structure. Our model protein shown in Fig. 3(a) consists of two helices, a connective loop, and a core. All residues (beads) are treated identically. In our calculations only the nearest neighbor interaction is considered.

Advantages of the lattice model are that we can change the structure as desired to get insight into how the residue fluctuations are affected by the changes in structures, which is difficult to do in real proteins. In Fig. 3(b) the calculated PR by the GNM for the model protein with different loop length is shown. The loop length is changed by moving the loop horizontally to the left or right. The curves are smoothed simply by adjacent averaging using 10 points. It is obvious that the PR of fluctuations in the simple model protein shows a similar behavior to that of real globular proteins. With increase in the loop length, the PR values of both the dip (region B in Fig. 1) and the peak (region C in Fig. 1) decrease. It can be seen from Fig. 3(c) that at the dip the fluctuations are dominant in the loop region. Again, the origin of the dip is the cause of the loop. For the highest frequency mode, the fluctuations dominantly occur at the helices, especially at the core region. The broad peak comprises modes which are more delocalized and worse defined. These peaks are relevant to the coupling motions among secondary structures.

In summary, localization properties of fluctuations in globular proteins were studied by using the Gaussian network model. It was found that the participation ratio of fluctuations in globular proteins shows a universal behavior, confirmed by theoretical calculations in both real globular and model proteins. The loops connecting the secondary structures are responsible for this feature.

This work was supported by the NSFC. Partial support from Shanghai Science and Technology Commission, China is acknowledged. Interesting discussions with Dr. Y. Q. Zhou, Dr. C. Tang, and Dr. J. Z. Y. Chen are acknowledged.


text:
# Cavity Light Bullets: 3D Localized Structures in a Nonlinear Optical Resonator

(today)

## Abstract

We consider the paraxial model for a nonlinear resonator with a saturable absorber beyond the mean-field limit and develop a method to study the modulational instabilities leading to pattern formation in all three spatial dimensions. For achievable parametric domains we observe total radiation confinement and the formation of 3D localised bright structures. At difference from freely propagating light bullets, here the self-organization proceeds from the resonator feedback, combined with diffraction and nonlinearity. Such ”cavity” light bullets can be independently excited and erased by appropriate pulses, and once created, they endlessly travel the cavity roundtrip. Also, the pulses can shift in the transverse direction, following external field gradients.

The competition between transverse diffraction and nonlinearities in optical systems (resonators, systems with feedback mirror or counterpropagating beams) leads to the formation of cavity solitons (CS) appearing as bright pulses on a homogeneous background opf ; ramazza . The possibility of exploiting CS as self-organized micropixels in semiconductor vertical microresonators has been recently proved nature , after previous observations and predictions in various classes of macroscopic optical systems (see e.g. ackemann ; weiss ). Such phenomena occur when the mean-field-limit (MFL) is valid, so that in the propagation direction $`z`$ (coinciding with the resonator axis) there is no spatial modulation of the field envelope. In this work we show how, beyond the MFL, an analogous formation of soliton-like structures confined in the transverse plane and in the longitudinal direction can be predicted. We call these structures Cavity Light Bullets (CLBs). They appear as bright stable pulses, spontaneously stemming and self-organizing from the modulational instability (MI) of a homogeneous field profile, and travelling along the resonator with a definite period.

In the past, the temporal dynamics of a laser field, linked to the competition of longitudinal modes and without the MFL, has been extensively studied ikeda ; squicciarini . Those approaches included a plane wave approximation and could not account for pattern formation. On the other hand there are relatively few works dealing with pattern formation beyond the MFL in an optical resonator. An exact treatment has been proposed in LeBerre1  but negligible field absorption is considered, i.e. the field intensity is assumed constant along the $`z`$-axis. Other approaches proceed from a model proposed in silberberg , where 2nd-order dispersion is the main mechanism for longitudinal self-modulation of propagating pulses , and the adaptation to resonator systems is heuristically provided with a formalism similar to MFL models . There, the formation of light bullets is shown tlidi1 ; rosanov . Other theoretical studies have considered parametric resonators ($`\chi ^2`$ nonlinearities) where, though, the mechanism of structure confinement is due to domain wall locking oppo  rather than pattern localization, and experimental confirmations are still missing.

On the other side, the self-collapse of a pulse, leading to formation of light bullets freely propagating in a medium, has been extensively studied by various authors trapani . Moreover, in this case, the phenomenon does not involve a MI in the sense of Ref. firth2  or the localization of patterns emerging thereof: the formation of one or more bullets involves a single pulse undergoing diffraction and dispersion. The CLBs presented in our work, conversely, are stable solutions of the intracavity field profile, superimposed to a nonmodulated background.

In this Letter, we analyze a well-established model for a resonator with a saturable absorber lugiato  to which diffraction in the transverse plane is added lax . The omission of the atomic dynamics, at difference from LeBerre1 , allows us to simplify the spatiotemporal field behavior avoiding competition between different timescales (field and atoms) note .

After casting the model, we extend an approach developed in the 80s squicciarini  to include diffraction and analyze the MI domains and the pattern formation stemming thereof. We apply checkpoints using existing literature both close and far from MFL conditions. We then find conditions for radiation confinement and report about Cavity Light Bullets in a parametric domain not far (apart from the exclusion of the MFL) from firth2 . Finally, we show how CLBs can be excited and their motion controlled via field gradients.

In the paraxial and Slowly Varying Envelope Approximation (SVEA), but without any hypothesis on the longitudinal profile of the intracavity field, the equations governing the spatiotemporal dynamics of a two level saturable absorber in a nonlinear unidirectional ring resonator driven by a coherent field, can be cast as done in lugiato1  and after adiabatic elimination of the atomic variables (good cavity limit) we have

$$\frac{1}{c}\frac{F}{t}+\frac{F}{z}=\frac{\alpha F\left(1i\mathrm{\Delta }\right)}{1+\mathrm{\Delta }^2+|F|^2}+\frac{i}{2k_0}_{}^2F$$
(1)
(and complex conjugate) with the boundary condition

$$F(x,y,0,t)=TY_{inj}+RF(x,y,L,t)e^{i\delta _0}$$
(2)
where $`Y_{inj}`$, $`F`$ denote respectively the normalized envelope of the input beam (CW and transversely homogeneous) and of the intracavity field; $`\mathrm{\Delta }`$ is the scaled  atomic detuning, $`\delta _0`$ is the scaled  cavity detuning, $`\alpha `$ is the absorption coefficient per unit length at resonance. $`T`$ and $`R`$ are the transmission and reflection coefficients, respectively, of the entrance and the exit mirror, being $`T+R=1`$; $`x`$ and $`y`$ are the transverse Cartesian coordinates and $`z`$ the longitudinal coordinate, being $`z=0`$ and $`z=L`$ the input and the output mirrors, respectively. Here, for simplicity, we consider the equivalence between the cavity ($``$) and the medium’s ($`L`$) lengths, i.e. the active medium completely fills the cavity.

The transverse laplacian $`_{}^2`$ describes diffraction in transverse plane $`(x,y)`$, while $`F/z`$ accounts for the variation of the field envelope along the cavity axis.

The stationary, transversely homogeneous solution is obtained by setting $`_{}^2F=0`$ and $`F/t=0`$ in Eq. (1) and by solving the resulting ODE; it turns out that it can be multivalued. The stationary intracavity intensity $`|F_{st}(z)|^2`$ is monotonically decreasing from input to output mirror ikeda ; NARDUCCI . Then, extending the approach of Lugiato et al. squicciarini  to include diffraction, we can study the stability of the solutions $`F_{st}(z)=\rho _{st}(z)e^{i\theta _{st}(z)}`$, $`(\rho _{st},\theta _{st})`$ against perturbations which are modulated along $`z`$ and in the $`(x,y)`$ plane; i.e. we consider a perturbed field $`F(x,y,z,t)`$ as follows

$$F_{st}(z)+\delta F(x,y,z,t)=F_{st}(z)+\delta f(z)e^{\lambda t}e^{i(k_xx+k_yy)}$$
(3)
with $`\delta f(z)=e^{i\theta _{st}}\left(\delta \rho (z)+i\rho _{st}\delta \theta (z)\right)`$, (to first order, with $`\delta \rho ,\delta \theta `$). $`k_x`$ and $`k_y`$ represent the components of the transverse modulation in the Fourier space. The different ansatz on the spatial dependence of the perturbations reflects the symmetry invariance in the $`(x,y)`$ plane and the lack thereof along the axis. At difference from the MFL treatment, due the $`z`$ dependence of $`\rho _{st}`$ and $`\theta _{st\text{ }}`$, we cannot obtain a simple algebraic equation for the eigenvalues $`\lambda `$ after linearizing Eq. (1) around the imposed solution $`F_{st}(z)`$ for the small perturbation $`\delta F(x,y,z,t)`$. As it turns out, we must first find two linearly independent solutions $`r_1(z)`$, $`r_2(z)`$ and $`u_1(z)`$, $`u_2(z)`$ for the following system of two coupled 1st order ODEs, as obtained from insertion of ansatz (3) into Eq. (1):

$`{\displaystyle \frac{dr}{dX}}`$ $`=r\left({\displaystyle \frac{1}{A}}+{\displaystyle \frac{1}{2X}}\right)+u\left({\displaystyle \frac{k_{}^2A}{4k_0\alpha X}}\right)`$ (4)
$`{\displaystyle \frac{du}{dX}}`$ $`=r\left({\displaystyle \frac{\mathrm{\Delta }}{A}}+{\displaystyle \frac{k_{}^2A}{4k_0\alpha X}}\right)+u\left({\displaystyle \frac{1}{2X}}\right)`$ (5)
where $`X(z)=\rho _{st}^2(z)`$, $`r(z)=`$ $`\delta \rho (z)e^{\frac{\lambda z}{c}}`$, $`u(z)=`$ $`\delta \theta (z)\rho _{st}(z)e^{\frac{\lambda z}{c}}`$, $`A=1+\mathrm{\Delta }^2+X(z)`$ and $`k_{}^2`$ $`=k_x^2+k_y^2`$. As the field must fulfill the constraints imposed by the boundary conditions, once such solutions are found, the perturbed field $`F(x,y,z,t)`$ can be evaluated, and then substituted into Eq. (2). We rehandle the latter equation along the lines of squicciarini  and finally, we obtain a quadratic equation for $`\eta =Re^{\frac{\lambda L}{c}}`$

$$\eta ^2W_1+\eta W_2+W_3=0,$$
(6)
where the $`W_i`$’s depend on $`\delta _0`$, $`\theta _{st}(z)`$ and on $`r_{1,2}(z=0)`$, $`r_{1,2}(z=L)`$, $`u_{1,2}(z=0)`$, $`u_{1,2}(z=L)`$. The eigenvalues can thus be obtained as

$$\lambda _\pm =\left(\frac{c}{L}\right)\left(\mathrm{ln}(\eta _\pm )+\mathrm{ln}(R)i2\pi n\right)\text{}n𝒩$$
(7)
where it is evident that the condition $`Re(\lambda _\pm )>0`$, allows for a numerable set of unstable longitudinal modes to destabilize the stationary solution, for each $`(k_x,k_y)`$ wavevector. From a physical view point we can then expect a complex unstable dynamical behavior of the system associated to a nonlinear competition among transverse and longitudinal modes. A detailed treatment of the stability analysis and of the guidelines for accessing a parametric domain where localization in $`3D`$ could be achieved, fall beyond the letter format: an extended paper is currently in preparation.

We tested this stability analysis by reproducing the instability scenario predicted in Stefani : when the values of $`\mathrm{\Delta }`$, $`\alpha L`$ and $`\delta _0`$ approach the mean field limit (according to definition introduced in lugiato ), the number of longitudinal modes, setting off the instability of the stationary solutions,  reduce to one.

Beyond the MFL, we could use existing literature as a checkpoint, to reproduce some patterns previously reported far from the MFL, e.g. the multiconical character of the MI with a parametric set close to that considered in Patrascu et al. LeBerre1 .

The numerical integration of the dynamical equation Eq.(1) has shown in this case the formation of three dimensional patterns strongly irregular in both space and time; this behavior agrees with the preliminary analyses suggesting chaotic dynamics and spatial decorrelation of patterns as the input field intensity increases beyond the MI threshold.

In order to meet stable global patterns and $`3D`$ localization of light structures, the path we induced from our analyses was to limit the nonlinear radiation-matter coupling, without reducing absorption, and also remaining fairly far from the MFL. A condition we obtained by choosing: $`\mathrm{\Delta }=0`$, $`\alpha L=1.2`$, $`T=0.1`$, $`\delta _0=0.1`$. In Fig. 1 we report for this set of parameters the stationary transversely homogeneous state curve by plotting the intensity of intracavity field on the exit window $`I=|F(L)|^2`$ versus the input filed amplitude, and the instability domain ($`Re(\lambda _\pm )>0`$) obtained using the stability analysis just described.

In this case, the simulations show, for example, a transverse intensity profile of isolated peaks, irregularly distributed in space and oscillating in time . Seen in $`3D`$, we identify a series of structures, emerging from a subcritical bifurcation of the first positive branch of the steady-state curve (see Fig. 1). They are confined in the transverse plane but also have a limited, variable length in the $`z`$ direction and travel the resonator with a period $`\frac{L}{c}`$ (see Fig. 2(a)). This is thus a valid example of spontaneous self-organization of a complex optical system in 3D (and time). Moreover, we can observe a spontaneous reduction of the length of such structures, until a stable (and minimal) limit length is achieved (see Fig.2(b)). These structures are what we call CLBs.

For input field values where structures coexists with the lower stable homogeneous branch, delimited in Fig.1 by the two arrows, by means of the usual technique adopted to switch on/off 2D Cavity Solitons in the mean field regime Stefani , we added to the input field a suitably narrow and short Gaussian pulse, to locally realize a portion of the spatially modulated solution.

By varying the Gaussian pulse duration, intensity and phase, we managed to ”write” and ”erase” the CLBs, i.e. structures confined in all three spatial dimensions (analogous to the ones reported in Fig. 2) which make a round-trip in a period $`\frac{L}{c}`$; when the addressing pulse is much longer, the length of the structure reaches the full resonator’s length and the stable structure emerging thereof becomes the 3D analog of the 2D cavity soliton.

The computational most demanding simulations have been carried on in a simplified system with only one transverse dimension, $`x`$, after checking the coherence of the pattern scenario between the $`3D`$ and $`(z,x)`$ systems. We show that is possible to create several independent CLBs using input Gaussian pulses aimed at any transverse position, provided they are separated at least by a critical distance on the order of the CLB diameter. Moreover, by superimposing to the holding beam a transverse phase modulation, we observe a slow lateral drift of CLBs climbing the intensity hill, induced by the input phase gradients themselves, towards their maxima (see Fig. 3).

We believe that the lower limit in the self-organised CLB length is linked to some characteristic length of the system, but we are still missing an unquestionable analytical result. We report that when longer pulses are applied in the input field, one seems to achieve longer CLBs (in the $`z`$ direction); an organized report about the latter issues will be published elsewhere. The CLB reported in this work can be highly appealing for optical information processing, making possible the architecture of self-clocked, self-organised, reconfigurable pixels, which can encode all-optical information both serially (in the longitudinal trains of CLBs) and parallely (in the transversal arrays of CLBs). With respect to manipulation of 2D arrays of CS (proposed e.g. in spinelli ; spinelli2 ) one can figure out additional controls (e.g. transversely injected fields) to change the phase of CLB trains and thus manipulate information contents, or to increase the ”input” channels, which can also be seen as logical gates’ operands.

On different grounds, CLBs lend themselves to similar applications as usual light bullets do, namely stroboscopes for atomic/molecular dynamics. Presently (because of the SVEA in our model) our timescales are still too long for this, but the benefit unique to cavity-sustained structures is that they can be seen as a coherent state of the radiation in the cavity that may repeatedly interact  with (e.g.) a quantum system (atom/condensate). In this case one could speak of a ”quantum stroboscope” provided the coherences in the system are long compared to the cavity round-trip.

This work was supported by the MIUR National Project ”Formazione e controllo di solitoni di cavità in microrisonatori a semiconduttore”


text:
# On the prime power factorization of 𝑛!

## 1 Introduction

For a prime number $`p`$ and every positive integer $`m`$ let $`e_p(n)`$ be the power at which the prime number $`p`$ appears in the prime factorization of $`n!`$. In , it was asked whether for every fixed positive integer $`k`$ there exists a positive integer $`n`$ so that all the numbers $`e_{p_i}(n)`$ are even, where $`p_1<p_2<\mathrm{}<p_k`$ denote the first $`k`$ prime numbers. The above question was answered in the affirmative by Berend in . In fact, Berend proved more, namely that for a fixed value of $`k1`$ the number of positive integers satisfying the above property has bounded gaps. Specifically, there exists a computable constant $`C(k)`$, depending only on $`k`$, such that every interval of length $`C(k)`$ of positive numbers contains a positive integer $`n`$ satisfying the above property. This result has been extended in  to the following setting: There exists a positive constant $`C(k)`$ depending only on $`k`$, such that if $`\epsilon _i\{0,1\}`$ (for $`i=1,\mathrm{},k`$) are such that there exists at least one positive integer $`n`$ satisfying the congruences $`e_{p_i}(n)\epsilon _i(mod2)`$ for all $`i=1,\mathrm{},k`$, then there exist infinitely many such positive integers $`n`$, and the set of such positive integers has gaps bounded by $`C(k)`$. This extends the result of Berend on the original problem addressed by Erdős and Graham, because there $`n=1`$ clearly satisfies the above congruences with $`\epsilon _i=0`$ for all $`i=1,\mathrm{},k`$. The authors of  mention that for $`2k5`$ every pattern $`\epsilon _i\{0,1\}`$ for $`1ik`$ appears at least once (hence, infinitely often by the above result), and they conjectured that every pattern of length $`k`$ appears for all values of $`k1`$. This conjecture was recently proved by Chen .

In , a stronger conjecture is stated, and this conjecture was mentioned by Yong-Gao Chen in his talk at the ICM2002 in Beijing.

###### Conjecture 1 (Sander ).

Let $`p_1,\mathrm{},p_k`$ be distinct primes, and let $`\epsilon _1,\mathrm{},\epsilon _k\{0,1\}`$. Then

$$|\{0n<N:e_{p_i}(n)\epsilon _i(mod2),1ik\}|\frac{N}{2^k}\mathrm{as}N\mathrm{}.$$

In , it is shown that the above conjecture holds for $`k=1`$, and it is also shown that every pattern of length $`2`$ appears with two arbitrary primes $`p_1`$ and $`p_2`$.

In this paper, we first address the following more general conjecture:

###### Conjecture 2.

Let $`p_1,\mathrm{},p_k`$ be distinct primes, $`m_1,\mathrm{},m_k`$ be arbitrary positive integers $`(2)`$, and $`0a_im_i1`$ for $`i=1,\mathrm{},k`$ be arbitrary residue classes modulo $`m_i`$. Then

$$|\{0n<N:e_{p_i}(n)a_i(modm_i),1ik\}|\frac{N}{m_1\mathrm{}m_k}\mathrm{as}N\mathrm{}.$$

Thus, Conjecture 2 says that for fixed prime numbers $`p_1,\mathrm{},p_k`$ and for fixed integers $`m_1,\mathrm{},m_k`$ the numbers $`(e_{p_1}(n),\mathrm{},e_{p_i}(n))`$ should be uniformly distributed modulo $`(m_1,\mathrm{},m_k)`$, which is just a natural extension of Conjecture 1.

We give the following partial result which resolves the above Conjecture 2 under some technical assumptions.

Theorem 1. Let $`p_1,\mathrm{},p_k`$ be distinct primes, $`m_1,\mathrm{},m_k`$ be arbitrary positive integers $`(2)`$ and $`0a_im_i1`$ for $`i=1,\mathrm{},k`$ be arbitrary residue classes modulo $`m_i`$. Assume further that $`p_im_i`$ for $`i=1,\mathrm{},k`$. Then

$$|\{0n<N:e_{p_i}(n)a_i(modm_i),1ik\}|=\frac{N}{m_1\mathrm{}m_k}+O(N^{1\delta }),$$

with $`\delta :=1/(120k^2p^{3m}m^2)`$, where $`m:=\mathrm{max}\{m_i:1ik\}`$, and $`p:=\mathrm{max}\{p_i:1ik\}`$.

Notice that Theorem 1 not only proves Conjecture 2 under the particular assumptions that $`p_im_i`$ for $`i=1,\mathrm{},k`$, but it even gives an upper bound on the size of the error term. In particular, Theorem 1 proves Conjecture 1 for all finite sets of prime numbers not containing the prime number $`2`$.

In the last section of his paper , Berend asks the following question: Assume that $`2=p_1<p_2<\mathrm{}`$ is the increasing sequence of all the prime numbers. Given $`k1`$ and an arbitrary pattern $`\epsilon _i\{0,1\}`$ for $`i=1,2,\mathrm{},k`$, how far does one need to go (as a function of $`k`$) in order to insure that one finds a number $`n`$ so that $`e_{p_i}(n)\epsilon _i(\mathrm{mod}2)`$. Since there are exactly $`2^k`$ such patterns, we expect such a number to be larger than $`2^k`$. Put it differently, find the fastest growing function $`f(x)`$ such that for large $`x`$ there exists $`n<x`$ such that the congruences $`e_{p_i}(n)\epsilon _i(mod2)`$ hold for all $`if(x)`$, where $`\epsilon _i`$ is an arbitrary function defined on the set of positive integers with values in $`\{0,1\}`$. While we are unable to prove that $`f(x)`$ can be taken of the form $`c\mathrm{log}x`$ with some constant $`c`$ (the optimal one being $`1/\mathrm{log}2`$), we can give the following lower bound for $`f(x)`$.

Theorem 2. Let $`3=p_1<p_2<\mathrm{}`$ be the sequence of odd prime numbers and let $`(\epsilon _i)_{i1}`$ be an arbitrary sequence taking only the values $`0`$ and $`1`$. Then there exists an absolute constant $`c_1`$ such that for each large positive real number $`x`$, there exists a positive integer $`n<x`$ such that all congruences

$$e_{p_i}(n)\epsilon _i(mod2),i=1,\mathrm{},k(x)$$

hold with $`k(x):=c_1\left({\displaystyle \frac{\mathrm{log}x}{\left(\mathrm{log}\mathrm{log}x\right)^6}}\right)^{1/9}`$.

## 2  The Proofs

In 1999, D.H. Kim (see ) published a very important paper in which he generalized results of Gelfond , Bésineau , and others, concerning the joint distribution of completely $`q`$-additive functions in residue classes. The results from Kim’s paper found immediate applications, an example of such being a paper by Thuswaldner and Tichy (see ), in which these two authors use Kim’s results to prove a version of the Erdős-Kac theorem for sets described by congruence properties of systems of completely $`q`$-additive functions.

In this paper, we point out that our theorems are immediate applications of Kim’s main result.

We now describe Kim’s main result, and explain how it can be used to prove our results.

Let $`q2`$ be any integer. A function $`f`$ defined on $`𝐍\{0\}`$ satisfying $`f(0)=0`$ and $`f(aq^k+b)=f(a)+f(b)`$ for all integers $`a1`$, $`k1`$, and $`0b<q^k`$ is called completely $`q`$-additive. Note that a completely $`q`$-additive function may be characterized also as given by the sum of the values of some function, taken over the base $`q`$ digits of the argument.

Let $`𝐪:=(q_1,\mathrm{},q_k)`$, and $`𝐦:=(m_1,\mathrm{},m_k)`$ be $`k`$-tuples of integers satisfying $`q_i,m_i2`$ for $`i=1,\mathrm{},k`$, and $`\mathrm{gcd}(q_i,q_j)=1`$ for $`ij`$. For each $`i`$, let $`f_i`$ be a completely $`q_i`$-additive function with integer values, and write $`𝐟:=(f_1,\mathrm{},f_k)`$. Define

$$F_i:=f_i(1),$$
$`(1)`$
$$d_i:=\mathrm{gcd}(m_i,(q_i1)F_i,f_i(r)rF_i(2rq_i1)),$$
$`(2)`$
and let $`𝐅:=(F_1,\mathrm{},F_k)`$ and $`𝐝:=(d_1,\mathrm{},d_k)`$. For brevity, we write $`𝐟(n)𝐚(mod𝐦)`$ if the congruence $`f_i(n)a_i(modm_i)`$ holds for all $`i=1,\mathrm{},k`$. Assume further that $`\mathrm{gcd}(F_i,d_i)=1`$ for all $`i=1,\mathrm{},k`$, and that $`\mathrm{gcd}(d_i,d_j)=1`$ for all $`ij`$. Kim’s theorem says the following:

Theorem K . With the previous assumptions and notations, the estimate

$$|\{0n<N:𝐟(n)𝐚(mod𝐦)\}|=\frac{N}{m_1\mathrm{}m_k}+O(N^{1\delta _1})$$
$`(3)`$
holds as $`N`$ goes to infinity, and for all $`k`$-tuples of residue classes $`𝐚`$ modulo $`𝐦`$, where $`\delta _1:=1/(120k^2q^3m^2)`$, with $`q:=\mathrm{max}\{q_i:1ik\}`$, and $`m:=\mathrm{max}\{m_i:1ik\}.`$

###### Proof of Theorem $`1`$.

To apply Kim’s theorem, let $`i`$ be any fixed index in $`\{1,\mathrm{},k\}`$. Let $`\lambda _i`$ be the minimal positive integer such that the congruence $`{\displaystyle \frac{p_i^{\lambda _i}1}{p_i1}}0(modm_i)`$ holds. Such a value $`\lambda _i`$ exists because $`p_im_i`$. Clearly, $`\lambda _i2`$ because $`m_i2`$. To estimate $`\lambda _i`$ from above, write $`m_i:=m_i^{}m_i^{\prime \prime }`$, where $`m_i^{}`$ and $`m_i^{\prime \prime }`$ are coprime, all the prime factors of $`m_i^{}`$ divide $`p_i1`$, and $`m_i^{\prime \prime }`$ is coprime to $`p_i1`$. It is clear that $`m_i^{}`$ and $`m_i^{\prime \prime }`$ are uniquely determined. By the well-known divisibility properties of Lucas sequences (see ), it follows easily that the number $`\mu _i:=m_i^{}\varphi (m_i^{\prime \prime })`$ satisfies the condition that $`{\displaystyle \frac{p_i^{\mu _i}1}{p_i1}}0(modm_i)`$. Here, for an arbitrary positive integer $`n`$ we used $`\varphi (n)`$ to denote the Euler $`\varphi `$ function of $`n`$. It is easy to see that $`m_i^{}\varphi (m_i^{\prime \prime })2`$ holds for all positive integers $`m_i2`$ (if $`m_i=2`$, then $`p_i`$ is odd, in which case $`\lambda _i=m_i^{}=m_i=2`$, while if $`m_i>2`$, then either $`m_i^{}2`$, or $`\varphi (m_i^{\prime \prime })=\varphi (m_i)2`$). In particular, $`\lambda _im_im`$, where the number $`m`$ is defined in the statement of Theorem 1.

We now write $`q_i:=p_i^{\lambda _i}`$. Notice that $`\mathrm{gcd}(q_i,q_j)=1`$ holds for all $`ij`$, and that $`q:=\mathrm{max}\{q_i:1ik\}p^m`$, where $`p`$ and $`m`$ are defined in the statement of Theorem 1.

Define the completely $`q_i`$-additive function $`f_i`$ as follows. Let $`a`$ be an integer in the interval $`0aq_i1`$, and write it in base $`p_i`$ as

$$a:=a_0+a_1p_i+\mathrm{}+a_{\lambda _i1}p_i^{\lambda _i1}\mathrm{with}0a_jp_i1\mathrm{for}j=0,\mathrm{},\lambda _i1.$$
$`(4)`$
Set

$$f_i(a):=a_0\frac{p_i^01}{p_i1}+a_1\frac{p_i1}{p_i1}+\mathrm{}+a_{\lambda _i1}\frac{p_i^{\lambda _i1}1}{p_i1},$$
$`(5)`$
and extend $`f_i`$ in the obvious way to all the non-negative integers in such a way that it becomes completely $`q_i`$-additive. A compact formula of $`f_i`$ in all non-negative integers is obtained as follows. Let $`n0`$, and write it in base $`p_i`$ as

$$n:=n_0+n_1p_i+\mathrm{}+n_tp_i^t\mathrm{with}0n_jp_i1\mathrm{for}\mathrm{all}j=0,\mathrm{},t.$$
$`(6)`$
For every non-negative integer $`j`$ write $`\overline{j}j(mod\lambda _i)`$ (the least residue). Then

$$f_i(n)=\underset{j=0}{\overset{t}{}}n_j\frac{p_i^{\overline{j}}1}{p_i1}.$$
$`(7)`$
The next observation is that $`f_i(n)e_{p_i}(n)(modm_i)`$. Indeed, it is well-known that, if the base $`p_i`$ representation of $`n`$ is given by (6), then

$$e_{p_i}(n)=\underset{j=0}{\overset{t}{}}n_j\frac{p_i^j1}{p_i1}.$$
$`(8)`$
Thus, comparing (7) with (8), it suffices to show that

$$\frac{p_i^j1}{p_i1}\frac{p_i^{\overline{j}}1}{p_i1}(modm_i),$$

which is equivalent to

$$\frac{p_i^{j\overline{j}}1}{p_i1}0(modm_i),$$

and the last congruence is obvious by the definition of $`\lambda _i`$ and by the fact that $`j\overline{j}`$ is a multiple of $`\lambda _i`$.

Having concluded that the completely $`q_i`$-additive function $`f_i`$ represents precisely $`e_{p_i}`$ modulo $`m_i`$, in order to complete the proof of Theorem 1, it suffices, via Theorem K, to verify that the functions $`f_i`$ satisfy the assumptions of Theorem K. But it is clear that by choosing $`r:=p_i`$, then $`2rq_i1`$ (because $`\lambda _i2`$), and with such an $`r`$ we have $`f_i(r)rF_i=f_i(p_i)=1`$ (notice that $`F_i=f_i(1)=0`$). Thus, formula (2) tells us that $`d_i=1`$, therefore that all the relations $`\mathrm{gcd}(F_i,d_i)=1`$ for $`i=1,\mathrm{},k`$, and $`\mathrm{gcd}(d_i,d_j)=1`$ for $`ij`$ hold. All the assertions of Theorem 1 can now be read off from Theorem K. ∎

###### Proof of Theorem $`2`$.

Given $`k`$, we shall apply Kim’s theorem with the error term to find $`N:=N(k)`$ in such a way as to make sure that there exists $`n<N`$ such that $`e_{p_i}(n)\epsilon _i(mod2)`$. In order to do so, we shall need first to find the dependence of the constants understood in $`O`$ from Theorem K as a function of the data $`k,m,`$ and $`q`$. A close analysis of Kim’s arguments points out that the error term appearing in Theorem K can be made explicit by going through the arguments from Proposition 1 and Proposition 2 in . In both Propositions 1 and 2 in , the constant understood in the error term can be taken to be of the type $`c_2k^{1/2}q`$, where $`c_2`$ is an absolute constant. Thus, with Theorem 1, we have that $`m:=2`$, $`p_k`$ is the $`k`$th odd prime, $`q:=p_k^2`$, and $`\delta :=1/(480k^2p_k^6)`$. By Theorem 1 and Kim’s theorem with the explicit dependence of $`O`$ on the initial data, it follows that there exists an absolute constant $`c_3`$ such that whenever the inequality

$$\frac{N}{2^k}>c_3k^{1/2}p_k^2N^{1\delta }$$
$`(9)`$
holds, then there must exist a positive integer $`n<N`$ such that $`e_{p_i}(n)\epsilon _i(\mathrm{mod}2)`$ holds for all $`i=1,2,\mathrm{},k`$. Inequality (9) is equivalent to

$$\mathrm{log}N>\frac{1}{\delta }\mathrm{log}(c_32^kk^{1/2}p_k^2)=480k^2p_k^6(\mathrm{log}c_3+k\mathrm{log}2+0.5\mathrm{log}k+2\mathrm{log}p_k).$$
$`(10)`$
With the Prime Number Theorem, we have $`p_k=(1+o(1))k\mathrm{log}k`$, and so inequality (10) yields

$$\mathrm{log}N>480(\mathrm{log}2)(1+o(1))k^9\mathrm{log}^6k.$$
$`(11)`$
Setting $`x=N`$ in the left hand side of the above inequality, and expressing $`k`$ as a function of $`x`$, we see that there exists indeed an absolute constant $`c_1`$ so that by setting $`k`$ to be the largest integer less than or equal than $`c_1\left({\displaystyle \frac{\mathrm{log}x}{(\mathrm{log}\mathrm{log}x)^6}}\right)^{1/9}`$ then inequality (11) holds. ∎

## 3 Comments

In this note, we just pointed out how problems about the distributions of exponents of (fixed) primes appearing in the prime power factorization of $`n!`$ in residue classes should be tackled via the general theory of joint distributions of completely $`q`$-additive functions in residue classes. Indeed, by the simple observation of treating this problem in this way, we pointed out that a result far more general than any other results available in the literature on this topic can be inferred in a straightforward way from Kim’s results. In this spirit, we assert that it is probably not too hard to prove Conjecture 2 in its full generality. However, in order to do so, it is probably far more interesting and worthwhile to try to prove an extension of Kim’s results to the following setting.

Let $`𝐪=(q_1,\mathrm{},q_k)`$, $`𝐦:=(m_1,\mathrm{},m_k)`$, and $`𝐟=(f_1,\mathrm{},f_k)`$ be as in Kim’s Theorem. Let further $`𝐮=(u_1,\mathrm{},u_k)`$ and $`𝐯=(v_1,\mathrm{},v_k)`$, where $`u_i1`$ and $`v_i`$ are non-negative integers for $`i=1,\mathrm{},k`$. Write $`𝐟(𝐮n+𝐯)=(f_1(u_1n+v_1),\mathrm{},f_k(u_kn+v_k))`$. We argue that it would be worthwhile to study the distribution of the positive integers $`n`$ such that $`𝐟(𝐮n+𝐯)𝐚(mod𝐦)`$, and to conclude that, under certain natural arithmetical conditions on $`𝐪,𝐦,𝐮,𝐯`$ and $`𝐟`$, the numbers $`𝐟(𝐮n+𝐯)`$ are uniformly distributed in arithmetical progressions. For example, let us see how one would attempt to include the number $`2`$ into the picture in order to prove Conjecture 1 in its full generality. If $`p_i`$ is an odd prime, then define the completely $`q_i`$-additive function $`f_i`$ as in the present paper. When $`p_i=2`$, then if one writes $`n`$ binary as $`n:=n_0+2n_1+\mathrm{}+2^tn_t`$, with $`n_i\{0,1\}`$ for $`i=0,\mathrm{},t`$, then $`e_{p_i}(n)n_1+\mathrm{}+n_t(mod2)`$. Fix $`\epsilon _i\{0,1\}`$, and assume that $`p_1=2`$. For $`i=1`$, define $`f_1(n)`$ to be the sum of the digits of $`n`$ in base $`2`$. Consider the system of congruences:

$$f_i(2n)\epsilon _i\mathrm{for}i=1,\mathrm{},k,$$
$`(12)`$
and

$$f_1(2n+1)\epsilon _1+1,f_i(2n+1)\epsilon _i\mathrm{for}i=2,\mathrm{},k.$$
$`(13)`$
If Kim’s Theorem could be extended as we pointed out above under pertinent assumptions on $`𝐪,𝐦,𝐮,𝐯`$ and $`𝐟`$, and if such pertinent assumptions were fulfilled for the systems of congruences (12) and (13), (with the obvious choices on $`𝐪,𝐦,𝐮,𝐯`$ and $`𝐟`$), then one would get a positive answer to Conjecture 1. By a procedure similar to the one indicated above, one could also get a positive answer to Conjecture 2 via such an extension of Kim’s results.

Acknowledgements. We thank Jean-Marie de Koninck and the referee for suggestions which improved the presentation of this paper. The first author was supported in part by grants SEP-CONACYT 37259-E and 37260-E. The second author was partially supported by a research grant from the School of Sciences at his institution.