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# Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?

## I Introduction

Single-macromolecular manipulation techniques, such as atomic force microscopy and optical tweezer methods, were recently used by many authors to investigate the mechanical properties of double-stranded DNA (dsDNA) and to understand how the tension in dsDNA influences the interactions between DNA and proteins such as DNA/RNA polymerases, type II topoisomerases, and RecA proteins (for a brief review see Ref. ). Many useful insights have been obtained through a detailed analysis of the experimental data generated by these precise measurements (see, for example, Refs. \[2-9\]). These new experimental techniques were recently used also on RNA and single-stranded DNA (ssDNA) to explore the structure formation of these polynucleotides. A RNA or ssDNA is a linear chain of nucleotide bases. At physiological conditions (concentration $``$ $`0.1`$M Na+ and temperature $``$ $`300`$K), RNA molecules in biological cells can fold into stable native configurations (as in the case of proteins) to fulfill their various biological functions. The higher-order structures in RNA and ssDNA are caused by the possibilities to form base-pairs between the complementary nucleotide bases, A and U (T, in the case of ssDNA), and G and C. These structures can be further stabilized by the vertical stacking interactions between nucleotide base-pairs. In a long polynucleotide chain, because there are a great many different ways to form base-pairs, the accessible configurational space is very large, and the equilibrium configurations are determined by the competition between entropy and the interaction energy. To investigate how base-pairing and base-pair stacking influence structure formations of polynucleotide is therefore of both biological and theoretical interest.

Recent measurements demonstrated that the structures of polynucleotides are sensitive to the ionic strength of the aqueous solution. In a high salt environment (for example, 150 mM Na+ or 5 mM Mg2+), electrostatic repulsive forces between the negatively-charged nucleotide phosphate groups are largely shielded and base-pairing is favored; furthermore, experimental observations suggested the formation of hairpinned configurations in ssDNA. To understand the hairpin formation in ssDNA and RNA, Montanari and Mézard suggested very recently a model for these polynucleotides. Base-pairing interaction is considered in their model, and their theoretical calculation can reproduce the experimental force-extension curve measured on a ssDNA chain whose nucleotide bases are arranged in relatively random order. It can be shown (see below and also Ref. ) that the force-induced structural transition in ssDNA is a second-order continuous phase transition process, characterized by a gradual decrease in the number of base-pairs as the external force is increased beyond a certain threshold value.

On the other hand, Rief et al. observed a quite different phenomenon: when they pulled a ssDNA chain made of poly(dA-dT) or poly(dG-dC) sequence apart with an atomic force microscope, they found that the distance between its two ends suddenly changes from nearly zero to a value comparable to its total contour length during a very narrow force range.

A question thus arises: Why is the force-induced structural transition of ssDNA gradual and continuous in one case and highly cooperative in the other case, even though the solution conditions in these two kinds of experiments are comparable? We noticed that there may be strong base-pair stacking interactions in the designed ssDNA chains, while stacking interactions are absent or negligible in the relatively random sequences. We have previously shown that the short-ranged base-pair stacking potential in dsDNA dominates the energy contribution and it is the reason both for the stability of dsDNA and its high extensibility at large forces. Is the dramatically different experimental observation of Rief et al. (compared with those of ) caused by base-pair stacking interaction? Given the fact that the stacking potential is a kind of short-ranged (nearest-neighbor) interaction, does the cooperative transition reported in  for such an 1D system really differ qualitatively from that observed in ?

To address these questions, we extend the work of Montanari and Mézard to include the effect of stacking interactions, and thus obtain a more realistic model for polynucleotides. We find that when the base-pair stacking potential is small, the ssDNA chain is in a hairpinned macro-state with the base-pairs only weakly stacked (hairpin-I), while when the stacking potential is large, the ssDNA is in a hairpinned macro-state with almost complete pairing and stacking (hairpin-II). The force-induced transition between hairpin-II and random coil is first-order, while the transition between hairpin-I and random coil is continuous. There is also a continuous phase transition between hairpin-I and hairpin-II, which may be induced by changing the nucleotide arrangement or by environmental variations in temperature or ionic strength. A simplified treatment of the same question was reported earlier.

The paper is organized as following: Section II introduces the theoretical model of ssDNA; and Sec. III presents some qualitative arguments concerned with the structural transitions in the model of ssDNA; in Sec. IV we perform a direct comparison with experimental observations. The main points of the paper are summarized in Sec. V, accompanied by some qualitative discussions on RNA secondary structure formation. We suggest the possibility to extend the theoretical method in this paper to address the long-range interactions along topologically constrained double-stranded DNA molecules, i.e., dsDNA with fixed linking number.

## II Model of ssDNA with base-pair stacking interaction

The model used in the present study is similar with that developed earlier by Montanari and Mézard, albeit with base-pair stacking potential included. We discuss a fictitious polymer chain made of $`N`$ tiny beads (bases) with index $`i`$ from $`1`$ to $`N`$ (each base in the model may correspond to several bases in a realistic polynucleotide). Between any two adjacent bases ($`i`$ and $`i+1`$) there is an elastic bond of equilibrium length $`b`$ and length variance $`\mathrm{}`$ ($`\mathrm{}b`$, i.e., the bond is considerably rigid). For any two bases $`i`$ and $`j`$, if their mutual distance $`|𝐫_{ij}|`$ is less than an interaction radius $`a`$ there could be a pairing potential $`V_{\mathrm{pair}}^{i,j}(𝐫_{ij})`$ (and we say that an $`i`$-$`j`$ base-pair is formed); and if any two base-pairs are nearest neighbors to each other (that is, $`i`$-$`j`$ and $`(i+1)`$-$`(j1)`$), there is an additional stacking interaction $`J_{i,i+1}^{j,j1}(𝐫_{ij},𝐫_{i+1,j1})`$. In this work, as what is assumed in other previous theoretical treatments, only the secondary pairing patterns are considered, which leads to the following constraints on the pairing between bases: (1) each base can be unpaired or be paired to at most one another base; (2) if base $`i`$ is paired to base $`j`$ (suppose $`i<j`$) and $`k`$ to $`l`$ ($`k<l`$), then either $`i<j<k<l`$ ($`\mathrm{`}\mathrm{`}`$independent”) or $`i<k<l<j`$ ($`\mathrm{`}\mathrm{`}`$nested”).

Because of these restrictions, the partition function can be calculated iteratively. In the case when the pairing interaction radius $`a`$ is far less than bond equilibrium length $`b`$ ($`ab`$), the total statistical weight $`Z_{j,i}(𝐫)`$ for a polynucleotide segment (from base $`i`$ to $`j`$) whose ends being separated by a distance $`𝐫`$ is expressed as

$`Z_{j,i}(𝐫)={\displaystyle 𝑑𝐮\mu (𝐮)Z_{j1,i}(𝐫𝐮)}+f_{ji}(𝐫){\displaystyle 𝑑𝐮_1𝑑𝐮_2\mu (𝐮_1)\mu (𝐮_2)Z_{j1,i+1}(𝐫𝐮_1𝐮_2)}`$ (1)
$`+{\displaystyle \underset{k=i+1}{\overset{j2}{}}}{\displaystyle 𝑑𝐮_1𝑑𝐮_2𝑑𝐮_3𝑑𝐯\mu (𝐮_1)\mu (𝐮_2)\mu (𝐮_3)f_{jk}(𝐯)Z_{k1,i}(𝐫𝐮_1𝐯)Z_{j1,k+1}(𝐯𝐮_2𝐮_3)}`$ (2)
$`+s(a|𝐫|)\mathrm{exp}(\beta V_{\mathrm{pair}}^{j,i}(𝐫)){\displaystyle 𝑑\mathrm{u}_1𝑑\mathrm{u}_2\mu (𝐮_1)\mu (𝐮_2)g_{i,i+1}^{j,j1}(𝐫,𝐫𝐮_1𝐮_2)Z_{j1,i+1}^{(p)}(𝐫𝐮_1𝐮_2)}`$ (3)
$`+{\displaystyle \underset{k=i+1}{\overset{j2}{}}}{\displaystyle }d𝐮_1d𝐮_2d𝐮_3d𝐯s(a|𝐯|)\mathrm{exp}(\beta V_{\mathrm{pair}}^{j,k}(𝐯))g_{k,k+1}^{j,j1}(𝐯,𝐯𝐮_2𝐮_3)\times `$ (4)
$`Z_{k1,i}(𝐫𝐮_1𝐯)Z_{j1,k+1}^{(p)}(𝐯𝐮_2𝐮_3).`$ (5)
Here, $`\mu (𝐫)\mathrm{exp}((|𝐫|b)^2/2\mathrm{}^2)`$ is the probability density for the bond vector $`𝐫`$; $`f_{ji}(𝐫)=\mathrm{exp}[\beta V_{\mathrm{pair}}^{j,i}(𝐫_{ij})]1`$ characterizes the pairing interaction between bases $`i`$ and $`j`$ (this viral expansion form $`f`$ is introduced because that, in the first integral on the right-hand side of the equality in Eq. (5), an vanishing pairing potential between the end base $`j`$ and any another base is assumed and the contributions of all these possible base-paired configurations are included. Such spurious contributions should be removed since the pairing potential is actually nonzero); $`s(x)`$ is a signal function, $`s(x)=1`$ if $`x0`$ and $`0`$ otherwise; $`g_{i,i+1}^{j,j1}(𝐫_{i,j},𝐫_{i+1,j1})=\mathrm{exp}[\beta J_{i,i+1}^{j,j1}(𝐫_{ij},𝐫_{i+1,j1})]1`$ characterizes the base-pair stacking interaction (the reason for the introduction of the viral coefficient $`g`$ can be similarly understood as that for the introduction of the viral coefficient $`f`$). $`Z_{j,i}^{(p)}`$ is the statistical weight for a ssDNA segment whose two end bases ($`i`$ and $`j`$) forming a base pair:

$`Z_{j,i}^{(p)}(𝐫)`$ $`=`$ $`s(a|𝐫|)\mathrm{exp}(\beta V_{\mathrm{pair}}^{j,i}(𝐫)){\displaystyle 𝑑𝐮_1𝑑𝐮_2\mu (𝐮_1)\mu (𝐮_2)Z_{j1,i+1}(𝐫𝐮_1𝐮_2)}`$ (6)
$`+`$ $`s(a|𝐫|)\mathrm{exp}(\beta V_{\mathrm{pair}}^{j,i}(𝐫)){\displaystyle }d𝐮_1d𝐮_2\mu (𝐮_1)\mu (𝐮_2)g_{i,i+1}^{j,j1}(𝐫,𝐫𝐮_1𝐮_2)\times `$ (8)
$`Z_{j1,i+1}^{(p)}(𝐫𝐮_1𝐮_2).`$
The statistical property of this model system is determined by the coupled equations (5) and (8). In the general case where the pairing and stacking potentials are dependent on base index, it is certainly of no hope to investigate the property of the system analytically. Here we simplify our task by assuming that the pairing and stacking potentials between any bases have the same form, i.e., assuming the polymer chain to be homogeneous. Then in Eqs. (5) and (8) all the subscripts specifying specific bases can be dropped, especially we can write $`f_{ji}(𝐫)`$ as $`f(𝐫)`$, $`Z_{j,i}(𝐫)`$ as $`Z_{ji}(𝐫)`$ and $`Z_{j,i}^{(p)}(𝐫)`$ as $`Z_{ji}^{(p)}(𝐫)`$. In the model, the stacking potential is a function of the inter-base distances for the two base-pairs concerned. Since the base-pair’s inter-base distance is usually very small (less than $`a`$), we can approximate the stacking potential to be constant in this range, and hence we just denote the stacking potential to be a constant $`J`$ and denote $`g=g_{i,i+1}^{j,j1}(𝐫_{i,j},𝐫_{i+1,j1})=const.`$

The Fourier transforms of the generating functions (Laplace transforms) of the statistical weights are defined as

$$\mathrm{\Xi }(\zeta ,𝐩)=𝑑𝐫\left(\underset{n=0}{\overset{\mathrm{}}{}}Z_n(𝐫)\zeta ^n\right)\mathrm{exp}(i𝐩𝐫),$$
(9)
and

$$\mathrm{\Xi }^{(p)}(\zeta ,𝐩)=𝑑𝐫\left(\underset{n=0}{\overset{\mathrm{}}{}}Z_n^{(p)}(𝐫)\zeta ^n\right)\mathrm{exp}(i𝐩𝐫).$$
(10)
Considering the iterative expressions for $`Z_n`$ and $`Z_n^{(p)}`$ in Eqs. (5) and (8), we can show that

$`\mathrm{\Xi }(\zeta ,𝐩)`$ $`=`$ $`[1+\zeta \sigma (𝐩)\mathrm{\Xi }(\zeta ,𝐩)]\times `$ (12)
$`\left(1+{\displaystyle \frac{\zeta ^2b^3}{(2\pi )^3}}\left[{\displaystyle 𝑑𝐪\sigma ^2(𝐪)\gamma (𝐩𝐪)\mathrm{\Xi }(\zeta ,𝐪)}+g{\displaystyle 𝑑𝐪\sigma ^2(𝐪)\gamma ^{}(𝐩𝐪)\mathrm{\Xi }^{(p)}(\zeta ,𝐪)}\right]\right),`$
and

$$\mathrm{\Xi }^{(p)}(\zeta ,𝐩)=\frac{\zeta ^2b^3}{(2\pi )^3}𝑑𝐪\sigma ^2(𝐪)\gamma ^{}(𝐩𝐪)\left[\mathrm{\Xi }(\zeta ,𝐩)+g\mathrm{\Xi }^{(p)}(\zeta ,𝐪)\right],$$
(13)
where $`\sigma (𝐩)=𝑑𝐫\mu (𝐫)\mathrm{exp}(i𝐩𝐫)=(\mathrm{sin}pb/pb)\mathrm{exp}(p^2l^2/2)`$, with $`\sigma (\mathrm{𝟎})=1`$; $`\gamma (𝐩)=b^3_{|𝐫|a}𝑑𝐫f(𝐫)\mathrm{exp}(i𝐩𝐫)`$ and $`\gamma ^{}(𝐩)=\gamma (𝐩)+(a/b)^3`$. Since $`ab`$, we have $`\gamma ^{}=\gamma `$ and both $`\gamma `$ and $`\gamma ^{}`$ can be regarded as independent of momentum $`𝐩`$. Then Eqs. (12) and (13) lead to

$$\mathrm{\Xi }(\zeta ,𝐩)=\frac{D(\zeta )}{1\sigma (𝐩)D(\zeta )},$$
(14)
where

$$D(\zeta )=\zeta +\zeta \mathrm{\Xi }^{(p)}(\zeta )=\eta _1\zeta ^3+\eta _2\zeta ^2+\zeta ,$$
(15)
with coefficient $`\eta _1`$ a constant and $`\eta _2`$ related to $`D`$:

$`\eta _1=g\gamma b^3(2\pi )^3{\displaystyle 𝑑𝐪\sigma ^2(𝐪)}=g\gamma (4\pi )^{3/2}(b/\mathrm{}),`$ (16)
$`\eta _2(D)=D\eta _1\left[1+(b^2\mathrm{}/g\pi ^{3/2}){\displaystyle 𝑑𝐪\frac{\sigma ^2(𝐪)}{1\sigma (𝐪)D}}\right].`$ (17)
Equations (14) and (15) are the central equations of this article.

When a external force $`𝐅`$ is applied at the end of the ssDNA chain, the total partition function is $`Z_N^F=𝑑𝐫Z_N(𝐫)\mathrm{exp}(\beta 𝐅𝐫)`$. The Laplace transform of this partition function is calculated to be

$$\underset{N=0}{\overset{\mathrm{}}{}}Z_N^F\zeta ^N=\mathrm{\Xi }(\zeta ,i\beta 𝐅),$$
(18)
where $`\mathrm{\Xi }(\zeta ,i\beta 𝐅)`$ is determined by Eq. (14).

For a linear polymer system, the free energy is an extensive quantity proportional to the number of monomers $`N`$ in the thermodynamic limit. This indicates that the smallest positive singularity point of the function $`\mathrm{\Xi }(\zeta ,i\beta 𝐅)`$ in the variable $`\zeta `$ corresponds to the free energy density of the ssDNA chain. This point is used in the next section.

## III Qualitative analysis of the hairpin-coil transition

It is evident that $`\mathrm{\Xi }(\zeta ,i\beta 𝐅)`$ has a pole $`\zeta _{\mathrm{pole}}`$ determined by

$$D(\zeta _{\mathrm{pole}})=1/\sigma (i\beta 𝐅)=\frac{\beta Fb}{\mathrm{sinh}(\beta Fb)}\mathrm{exp}(\beta ^2F^2\mathrm{}^2/2),$$
(19)
where $`F=|𝐅|`$. The function at the right side of the equality monotonously decreases with $`F`$ from $`1`$ at $`F=0`$ to $`0`$ as $`F\mathrm{}`$. On the other hand, the function $`D(\zeta )`$ is related to the Laplace transform of the hairpinned configurations as indicated by Eq. (15), therefore $`D(\zeta )`$ has a finite convergence radius, and it is an increasing function of $`\zeta `$ before this radius is reached. The singularity of $`D(\zeta )`$ is related to the roots of Eq. (15). Although analytical expressions for the roots of this third-order equation are available, they are lengthy and here we discuss the statistical property of the system through an alternative routine. First we consider two extreme cases:

Case A: the base-pair stacking potential $`J=0`$. In this case $`g=0`$ and $`\eta _1=0`$ and Eq. (15) reduces to second-order. This situation has been studied by Montanari and Mézard and they found that $`D(\zeta )`$ has a second-order branching point at $`\zeta _{\mathrm{bp}}`$ equaling to the maximum of the expression $`(1+\sqrt{1+4D\eta _2})/2\eta _2`$, which is reached at $`D=D_{\mathrm{bp}}<1`$. When the external force is less than the threshold value $`F_{\mathrm{cr}}`$ determined by Eq. (19) at $`D=D_{\mathrm{bp}}`$, the polymer resides in the hairpinned phase with zero extension, and the free energy density equals to $`\varphi (F)=(1/\beta )\mathrm{ln}\zeta _{\mathrm{bp}}`$ and is force-independent. At $`F=F_{\mathrm{cr}}`$ there is a second-order continuous hairpin-coil phase-transition (because $`d\zeta /dD=0`$ at $`D_{\mathrm{bp}}`$), and the free energy density is changed to $`\varphi (F)=(1/\beta )\mathrm{ln}(\zeta _{\mathrm{pole}})`$.

Case B: the stacking potential $`J`$ so large that $`g1`$. In this case, Eq. (17) indicates that $`\eta _2=D\eta _1`$ and Eq. (15) is equivalent to

$$(\zeta +1/\sqrt{\eta _1})(\zeta D)(\zeta 1/\sqrt{\eta _1})=0.$$
(20)
We readily see that when $`D1/\sqrt{\eta _1}`$ the smallest positive root of this equation is $`\zeta =D`$; and when $`D>1/\sqrt{\eta _1}`$, the smallest positive solution is a constant $`\zeta =1/\sqrt{\eta _1}(g\gamma )^{1/2}`$. Most importantly, we have $`d\zeta /dD=1`$ as $`D`$ approaches $`1/\sqrt{\eta _1}`$ from below. As a consequence, for $`F<F_{\mathrm{cr}}`$ which is determined by Eq. (19) with $`D=1/\sqrt{\eta _1}`$, the polymer is in the hairpinned state and the free energy density is $`\varphi (F)=(1/2\beta )\mathrm{ln}\eta _1(1/2\beta )\mathrm{ln}(g\gamma )`$ (again independent of $`F`$). For $`F>F_{\mathrm{cr}}`$ the system is in the random coil state, and $`\varphi (F)=(1/\beta )\mathrm{ln}(\zeta _{\mathrm{pole}})`$. Here $`\zeta _{\mathrm{pole}}`$ is determined by Eq. (19) (with $`D=\zeta _{\mathrm{pole}}`$). At $`F=F_{\mathrm{cr}}`$ there is a first-order hairpin-coil phase-transition, resulted from the fact that $`d\zeta /dD|_{D=1/\sqrt{\eta _1}}=1`$.

Comparing case A and case B, we have the impression that the inclusion of base-pair stacking interaction may dramatically change the statistical property of the ssDNA system, even the order of the hairpin-coil phase transition. This is understandable qualitatively. The stacking interaction has two effects: (1) it makes base-pairing even more favorable; and (2) it causes the formed base-pairs to aggregate into large stacked blocks. Since the order of the hairpin-coil transition is related to the intensity of the stacking potential, the hairpin macro-state at low stacking intensity is anticipated to be different to the hairpin macro-state at high stacking intensity, and a continuous phase transition between these two hairpin macro-states can be predicted as the average base-pair stacking intensity changes. This insight is confirmed by observing how the order parameter of this system changes with stacking potential, as shown in Fig. 1. Later we will refer to the hairpin macro-state at low stacking intensity as hairpin-I and that at high stacking intensity as hairpin-II.

In the general case, the average number of base-pairs (in units of $`N/2`$) is calculated according to $`N_{\mathrm{bp}}=2\varphi /\mathrm{ln}\gamma ,`$ and the average number of stacked base-pairs (also in units of $`N/2`$) is $`N_{\mathrm{sbp}}=2\varphi /\mathrm{ln}g,`$ and the relative extension of each ssDNA bond along the direction of the external force is obtained by $`Ex=\varphi /F.`$

We demonstrate in Fig. 1 how the values of $`N_{\mathrm{bp}}`$, $`N_{\mathrm{sbp}}`$, and the ratio $`N_{\mathrm{sbp}}/N_{\mathrm{bp}}`$ change with strength of base-pair stacking potential. In this figure $`\gamma `$ is fixed to $`1.9`$ (just serves as an example) and the external force is set to zero. We see that as the stacking potential $`J`$ increases, all these three quantities increases and they approaches $`1`$ as $`J`$ reaches about $`J_{\mathrm{cr}}6k_BT`$. The ratio $`N_{\mathrm{sbp}}/N_{\mathrm{bp}}`$ could serve as an order parameter. Figure 1 shows that when stacking potential is high, almost all the nucleotide bases are paired and stacked; lowering stacking potential from $`J>J_{\mathrm{cr}}`$ to $`J<J_{\mathrm{cr}}`$ there is a continuous phase transition where such a highly stacked configuration is gradually melted out and a growing fraction of bases becomes unpaired and unstacked. This is a structural transition between a highly stacked hairpin macro-state (hairpin-II) and a loosely stacked (or irregular) hairpin macro-state (hairpin-I). This hairpin I-II transition is induced by changing the average effective base-pair stacking interaction in the polymer. Giving a polynucleotide chain, macroscopically the effective base-pairing interaction is determined mainly by its base composition, while the effective stacking potential is determined mainly by the particular arrangement of the bases along the chain. Hence, for different polynucleotides with the same base composition, the folded hairpin configurations may be quite different and fall into two gross catalogue, dependent on their particular base sequence arrangement. This is consistent with the observation that certain RNA chains have unique stable native configurations. The transition between hairpins-I and -II can also be induced by temperature changes or variations in solution ionic concentrations.

It should be mentioned that the critical stacking potential $`J_{\mathrm{cr}}`$ is not sensitive to the pairing potential. This can be seen from the fact that the hairpin I-II transition occurs when the second term in the square brackets of Eq. (17) approaches zero, a condition which is solely satisfied when the stacking potential (and hence $`g`$) becomes large.

The force-induced hairpin-coil transition is then second-order or first-order depending on whether the hairpinned configuration is type I or type II. In Fig. 2 the force vs extension relationship for ssDNA at different pairing and stacking interaction intensities are shown. As is expected, at large stacking intensity, there is a broad force-plateau and this force-plateau disappears as stacking potential is lowered. It is striking to notice that only the inclusion of base-pair stacking interaction can lead to the appearance of a highly cooperative hairpin-coil transition. As shown also in Fig. 2 (the dot-dashed curve), if $`J=0`$ the force-extension curve is always continuous and gradual no matter how strong the base-pairing interaction is.

These theoretical predictions are summarized in the qualitative phase-diagram depicted in Fig. 3.

## IV Quantitative comparison with experimental observations

In the last section we have analyzed the main qualitative predictions of the present polynucleotide elastic model. In this section we apply these results to attain a quantitative understanding of some reported experimental findings.

Bustamante et al. and others  have pulled a plasmid ssDNA fragment of 10.4 kilobases under different ionic concentrations. They found that the elastic response of ssDNA deviates from that of a random coil both at high and at low ionic conditions. It was suspected that in high salt environments there is partial hairpin formation in the ssDNA chain. As is consistent with this insight, Fig. 4 demonstrates that at high salt conditions, the ssDNA made of such a relatively random sequence can be well modeled by the present model with an effective base-pairing interaction characterized by the dimensionless quantity $`\gamma =1.2`$ and Kuhn length $`b=1.7`$nm and bond length variation $`\mathrm{}=0.065b=1.105`$$`\AA `$. The effective base-pair stacking interaction for radom sequences seems to be quite small and is set to $`J=0`$ in the fitting (the thick solid line in Fig. 4). Such a comparison has already been performed by Montanari and Mézard earlier. For random sequences the reason that the effective stacking interaction is negligible may be explained as follows: In the polynucleotide chain whose bases arrange randomly, the formed base-pairs are usually seperated from each other and the possibility for two base-pairs to be adjacent to each other is quite small.

Even when the effective stacking potential $`J`$ between two consective node-pairs becomes comparable with thermal energy $`k_BT`$ (the thin doshed line in Fig. 4), the gradual force-extension pattern is only slightly changed. It indicates that the stacking interaction still plays a less important role than the pairing interaction. But the fitting deteriarates much for $`J2k_BT`$ if the pairing potential is kept constant (thin dotted line): for example, at $`J=6K_BT`$ (thin solid line) there is a wide plateau in the theoretical force-extension curve.

In another experiment, Rief et al. synthesized single-stranded poly(dG-dC) and poly(dA-dT) DNA chains and investigated their elastic responses under external force field. They observed a highly cooperative elongation process in both these two kinds of sequences, with the transition force being $`20`$ pN for poly(dG-dC) and $`9`$ pN for poly(dA-dT). Figure 5A and Fig. 5B shows the experimental records as well as the theoretical fittings based on the present model.

In the case of poly(dG-dC), the theoretical curve is obtained by calculating the total extension of a polymer connected by a dsDNA segment of $`290.0`$nm (with persistence length $`53.0`$nm and stretch modulus $`S=1000.0`$pN as determined by previous experiments) and a ssDNA segment of $`230.0`$nm (with Kuhn length $`1.7`$nm and bond length variance $`1.105\AA `$ as determined by the data of Fig. 4). (We have included a segment of dsDNA simply because the experiment in  was performed by inserting a ssDNA segment between two dsDNA segments). In the hairpinned state at zero force, the average free energy per Kuhn length is thus determined by the transition force to be $`\varphi =(1/2\beta )\mathrm{ln}(\eta _1)=5.59k_BT`$. Similarly, in the case of poly(dA-dT), the fitting is obtained with a dsDNA segment of $`80.0`$nm and a ssDNA segment of $`445.0`$nm ($`b=1.7`$nm, $`\mathrm{}=1.53`$$`\AA `$) with the average free energy per Kuhn length being $`\varphi =1.763k_BT`$.

Assuming each Kuhn length contains three nucleotide bases (i.e., each base in the model corresponds to three realistic nucleotides), we can infer that the free energy per base-pair in the poly(dG-dC) chain is $`3.72k_BT`$, while in the poly(dA-dT) chain is $`1.18k_BT`$. These values are close to what we estimated earlier and are close to the phenomenological parameters $`E_{GC}3.0k_BT`$ and $`E_{AT}=1.3k_BT`$ chosen by Bochelmann et al. to interpret their experimental results of separating the two strands of a dsDNA apart by mechanical force.

## V Conclusive remarks

In this paper, we have presented an elastic model for single-stranded DNA and RNA polymers, where both the base-pairing and base-pair stacking interactions where considered. The theoretical calculations demonstrated that, depending on the intensity of base-pair stacking potential, ssDNA or RNA can form two kinds of hairpinned structures, hairpin-I and hairpin-II, with the base-pairs in hairpin-I only slightly stacked and those in hairpin-II almost completely stacked. The force-induced hairpin-coil transition is a second-order process if the polymer was originally in hairpin-I macro-state and a first-order process if it was in hairpin-II macro-state. The phase diagram and the force-extension relationship for this polymer system were obtained and the theoretical results achieved good agreement with experimental observations. This work indicates the significance of base-pair stacking interaction to the structural property of polynucleotide chains. The existence of such a hairpin-II macro-state in a designed polynucleotide also justified our previous phenomenological work on the same system by considering only single-looped hairpin structures.

The present work has the following implications. Given a polynucleotide chain, if the nucleotide bases are randomly arranged, then the possibility to forming stacked patterns of base-pairs is very small, since even forming the smallest stack of two base-pairs requires the correlations among four nucleotide bases. Therefore, in random polynucleotide chains, stacking potential is not important. The chains can only form loose hairpins (hairpin-I), and structural fluctuations between these hairpins may be large and quick, making it difficult for the existence of any well-defined stable native configurations. However, things may be dramatically changed if the polynucleotide chain composed of the same bases as the random chain rearranges these nucleotide bases carefully. If the bases in the chain is arranged in such a way that forming of base-pairs results in stacking of base-pairs, then it is very likely that the polymer will fold into certain stable native structures which are much lower in structural energy than other configurations. Is this part of the reason why some polynucleotide sequences are folded in a particular manner (such as transfer RNA or t-RNA)? The nucleotide sequences in RNA molecules of biological cells are the results of millions of years of natural evolution and selection, and therefore in some sense, they should all be well designed.

Finally, we just mention that the theoretical method used in this work to count for the long-range interactions in ssDNA may be applied to investigate the tertiary structures (supercoils) in double-stranded DNA caused by the topological constraint of fixed linking numbers. The topological constraint leads to a long-range interaction along the dsDNA chain and make the polymer to fold into compacted plectonemic structures. Similar force-extension profiles as the theoretical curves in Fig. 4 have been observed.

## VI Acknowledgment

We are grateful to Prof. Z.-C. Ou-Yang. One of the authors (H.Z.) appreciates a helpful correspondence with A. Montanari, the helps of U. Bastolla and Jian-Jun Zhou, as well as the financial support of the Alexander von Humboldt Foundation. H.Z. is also grateful to Prof. R. Lipowsky for a critical reading of the manuscript and comments.


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# 1 Introduction

## 1 Introduction

The possibility that the gauge bosons of the Standard Model(SM) may be sensitive to the existence of extra dimensions near the TeV scale has been entertained for some time; in the literature the cases with both factorizable and non-factorizable metrics(such as in the Randall-Sundrum(RS) model) have been considered. The phenomenology of these models in either case is particularly sensitive to how the SM fermions are treated.

In the simplest scenario, the fermions remain on the wall located at the fixed point $`y_i=0`$ and are not free to experience the extra dimensions. (Here, lower-case Roman indices label the co-ordinates of the additional dimensions while Greek indices label our usual 4-d space-time.) However, since 5-d translational invariance is broken by the wall, the SM fermions interact with the Kaluza-Klein(KK) tower excitations of the SM gauge fields in the usual trilinear manner, i.e., $`gC_n\overline{f}\gamma _\mu fG_{(n)}^\mu `$, with the $`C_n`$ being some geometric factor and $`n`$ labelling the KK tower state with which the fermion is interacting. For simple factorizable models, current low-energy constraints arising from, e.g., $`Z`$-pole data, the $`W`$ boson mass and $`\mu `$-decay generally require the mass of the lightest KK gauge boson to be rather heavy, $`\begin{array}{c}>\hfill \\ \hfill \end{array}4`$ TeV in the case of the 5-d SM. In the case of the RS model, similar analyses have obtained lower bounds as great as 25 TeV.

A second possibility, perhaps the most democratic, allows all of the SM fields to propagate in the $``$ TeV-1 bulk. In this case, there being no matter on the walls, the conservation of momentum in the extra dimensions is restored and one now obtains interactions in the 4-d Lagrangian of the form $`gC_{ijk}\overline{f}^{(i)}\gamma _\mu f^{(j)}G_{(k)}^\mu `$, which for factorizable metrics vanishes unless $`i+j+k=0`$, as a result of the afore mentioned momentum conservation. This implies that pairs of zero-mode fermions, which we identify with those of the SM, cannot directly interact singly with any of the excited modes in the gauge boson KK towers. Such a situation clearly limits any constraints arising from precision measurements since zero mode fermion fields can only interact with pairs of tower gauge boson fields. In addition, at colliders it now follows that KK states must be pair produced, thus significantly reducing the possible direct search reaches for these states. In fact, employing constraints from current experimental data, Appelquist, Cheng and Dobrescu(ACD) find that the KK states in this scenario can be as light as a few hundred GeV. In the RS case, since the bulk is now AdS5, the wave functions for the zero-mode fermions are no longer $`y`$-independent and the higher KK modes are described by Bessel functions, the existence of non-zero $`C_{ijk}`$ does not require the above index sum to vanish. However, one still finds that the low-energy constraints on the gauge boson KK mass scale in this scenario are also weaker than when fermions are forced to lie on the wall—but not to the degree experienced by the factorizable models.

Perhaps the most interesting possibility occurs when the SM fermions experience extra dimensions by being ‘stuck’, i.e., localized or trapped at different specific points in a thick brane away from the conventional fixed points. It has been shown that such a scenario can explain the absence of a number of rare processes, such as proton decay, by geometrically suppressing the size of the Yukawa couplings associated with the relevant higher dimensional operators without resorting to the existence of additional symmetries of any kind. In addition such a scenario may be able to explain the fermion mass hierarchy and the observed CKM mixing structure thus addressing important issues in flavor physics. In order for this scheme to work the field that traps the various fermions must make the width of their wave functions in the extra dimension, $`\sigma `$, both much smaller than the typical separation of the various fermions as well as the size of the extra dimensions themselves $`\pi R_c`$, where $`R_c`$ is the compactification radius. In the original model of Arkani-Hamed and Schmaltz the fermion wave functions were taken to be rather narrow Gaussians, e.g., $`\sigma \frac{1}{10}R_c`$. Previous analyses  have indicated that it may be possible to obtain some information about the specific locations of the various SM fermions in the extra dimensions at future colliders through measurements of cross sections and various asymmetries. In particular it has been demonstrated that future lepton colliders can distinguish the case where quarks and leptons are localized at the same fixed point from where they are separated by a distance $`\pi R_c`$, i.e., they sit at opposite fixed points. In this paper we will address this issue in detail, i.e., whether and/or how well future lepton colliders can be used to determine the locations of all of the SM fermion zero-modes in the extra dimensions.

The outline of this paper is as follows: in Section II we describe our setup in detail and will employ the current precision electroweak data to obtain lower bounds on the masses of the first KK gauge bosons in the Arkani-Hamed-Schmaltz model. Such an analysis has yet to be performed for the case of models with localized fermions with the three generations localized at different points and as a first step is necessary to determine the energy scale that needs to be explored by future lepton colliders. In Section III we will demonstrate the ability of these colliders to determine the various fermion locations in the case of one extra dimension both with and without the added assumption of any family symmetry. We will consider measurements both below and on top of the first gauge KK resonance; we will demonstrate that it is the below resonance measurements that are more directly useful in localizing the SM fermions. This is particularly useful if the center of mass energy of the lepton collider were limited. Finally, our summary and conclusions can be found in Section IV.

## 2 Setup and Bounds from Precision Data

In the Arkani-Hamed-Schmaltz scenario, a fermion (in particular the fermion zero mode) interacts with a new scalar field which generates the thick/fat brane or domain wall and which has a zero determined by its Yukawa coupling at the point at which the fermion is to be trapped. To be specific let us consider the case of one extra dimension. In the region near the zero the scalar field is essentially a linear function of $`y`$ thus leading to an approximately Gaussian-shaped wave function for the trapped fermion. This region of linearity is rather small, $`\sigma `$, in comparison to size of the compactified space $`\pi R_c`$, and its slope in that region sets the scale for the Gaussian width of the fermion wave function. Unlike the fermions, the SM gauge and Higgs fields are free to propagate throughout the brane thickness and it is the zero mode of the Higgs which obtains the usual SM vacuum expectation value(vev) which is therefore $`y`$ independent. Choosing as usual the $`S^1/Z_2`$ orbifold for compactification, the gauge fields can be straightforwardly decomposed into their KK modes(Case I) and we are also free to choose the gauge where the fifth component of the gauge fields vanishes; thus

$$G_\mu (x,y)=G_\mu ^{(0)}(x)+\sqrt{2}\underset{n=1}{}\left[G_\mu ^{+(n)}(x)\mathrm{cos}\frac{ny}{R_c}+G_\mu ^{(n)}(x)\mathrm{sin}\frac{ny}{R_c}\right],$$
(1)
with the $`\pm `$ referring to the $`Z_2`$ parity of the KK tower states. Representing the $`y`$-dependent part of the wave function for the fermion zero modes as a set of normalized Gaussians with a common width $`\sigma `$, $`g(yy_f)`$, centered around the points $`y_f`$, the interaction of the gauge and fermion fields can be described by the action

$$S=d^4x𝑑yg_5\overline{f}(x)g(yy_f)\gamma _\mu f(x)g(yy_f)G^\mu (x,y),$$
(2)
so that the gauge zero modes, the usual SM gauge fields, have couplings which are insensitive to the fermions position, $`y_f`$. In the limit of very narrow Gaussians, $`(n\sigma /\pi R_c)^2<<1`$, the gauge KK excitations do not see the finite width of the fermions in the extra dimension and we are essentially left in the $`\delta `$-function limit. In that case the $`y`$ integration is trivial and we find that the gauge KK tower modes interact with the fermion zero modes via the action

$$S=d^4x\sqrt{2}g_4\overline{f}(x)\gamma ^\mu f(x)\underset{n=1}{}\left[G_\mu ^{+(n)}(x)\mathrm{cos}\frac{ny_f}{R_c}+G_\mu ^{(n)}(x)\mathrm{sin}\frac{ny_f}{R_c}\right].$$
(3)
As discussed in Refs. , when $`n`$ grows sufficiently large the above inequality is no longer satisfied and the gauge fields begin to see the finite size of the fermion wave function and the resulting integrated overlap of the fermion and gauge wave functions results in an exponential suppression of the coupling of the fermion zero modes to the higher KK gauge boson tower members. (Further effects due to the fact that the wave functions are not truely Gaussian in shape will also occur.) This is particularly important in the case of more than one extra dimension where sums over KK states are generally divergent. This exponential suppression of the couplings for large $`n`$ now results in convergent sums over KK states for these cases.

As an aside we note that in the above KK decomposition we have not demanded that the gauge field itself have a fixed $`Z_2`$ parity. In many cases this is useful in model construction and, since the SM fields are to be identified with the zero modes, gauge fields are taken to be $`Z_2`$ even. In this circumstance, which we call case II, the KK decomposition is identical to the above after dropping the terms proportional to $`\mathrm{sin}\frac{ny_f}{R_c}`$.

Since the Higgs field obtains its constant vev in the bulk there is no tree level mixing between the different gauge KK tower levels and after spontaneous symmetry breaking (SSB) it is easiest to employ the conventional SM/mass eigenstate basis for the tower states: $`\gamma ^{\pm (n)},Z^{\pm (n)},W^{\pm (n)}`$, etc. While the $`\gamma ^{\pm (n)}`$ obtain masses $`n/R_c=nM_c`$, the $`Z^{\pm (n)}`$ and $`W^{\pm (n)}`$ states have masses given by $`(n^2M_c^2+M_{Z,W}^2)^{1/2}`$. This implies that, e.g., if $`M_c`$=4 TeV then the difference in mass between the first $`Z`$ and $`\gamma `$ KK excitation is approximately 1 GeV. In the case where both $`Z_2`$ even and odd gauge KK states are present, the two are exactly mass degenerate at the tree level. In the absence of tree-level mixing of any of the KK states, their modifications to the precision electroweak parameters are relatively straightforward to isolate and in doing so we follow the analysis as presented by Rizzo and Wells.

First, we assign the 15 SM chiral fermions specific locations in the extra dimension: $`y_{Q_i},y_{L_i},y_{u_i},y_{d_i}`$ and $`y_{e_i}`$ where $`Q_i^T=(u,d)_{Li}`$, $`L^T=(\nu ,\mathrm{})_{Li}`$, etc. These locations are found to be somewhat more easily analyzed in terms of the dimensionless rescaled variables $`x_a=y_a/\pi R_c`$. Given the fact that the KK gauge boson mass matrix is diagonal, the first place that KK tower exchange will be important is in $`\mu `$-decay through which the Fermi constant is defined. At tree level one can write

$$\frac{G_F}{\sqrt{2}}=\frac{g^2}{8M_W^2}(1+V_G),$$
(4)
where $`V_G`$ sums the W boson tower KK contributions; SM radiative corrections to this expression can be performed in the usual manner and we will assume these are included in what follows. (We note in passing that, in principle, stronger bounds on the scale $`M_c`$ can be obtained by considering constraints on leptonic flavor-changing neutral currents(FCNC) as discussed by Delgado, Pomarol and Quiros. However, in our particular case these bounds will involve all six of the coefficients $`x_{L_i}`$ and $`x_{e_i}`$ as well as the a priori unknown left and right-handed leptonic mixing matrices. This makes it somewhat difficult to extract any useful limits without making further model-dependent assumptions. Of course, if the $`x`$’s were generation independent, FCNC would be avoided at tree level as in the SM. For the moment, however, we will attempt to remain as general as possible.) In the 5-d SM example above, neglecting the possible effects of the Gaussian coupling suppression as previously discussed, we can write

$$V_G=\frac{2M_W^2}{M_c^2}\underset{n=1}{}\frac{1}{n^2}(\mathrm{cos}\pi nx_{L_1}\mathrm{cos}\pi nx_{L_2}+\mathrm{sin}\pi nx_{L_1}\mathrm{sin}\pi nx_{L_2}),$$
(5)
with $`x_{L_{1,2}}`$ being the locations of the left-handed lepton doublets of the first two generations. In the case where gauge fields are $`Z_2`$ odd the last term can be dropped otherwise the two terms can be combined into a single term : $`\mathrm{cos}\pi n(x_{L_1}x_{L_2})`$, which means that the correction due to tower exchanges depends only upon the relative positions of the two lepton doublets. In this case we find that we can write $`V_G`$ as

$$V_G=\frac{\pi ^2M_W^2}{3M_c^2}F(\mathrm{\Delta }),$$
(6)
with $`\mathrm{\Delta }=x_{L_1}x_{L_2}`$ and $`F(\mathrm{\Delta })`$ shown in Fig.1. With the help of Ref.  one finds that $`F(\mathrm{\Delta })`$ can be obtained analytically: $`F(\mathrm{\Delta })=13\mathrm{\Delta }+\frac{3}{2}\mathrm{\Delta }^2`$. Note that in the limit where the $`x`$’s are generation independent, $`\mathrm{\Delta }=0`$ so that $`F=1`$ and cases I and II yield identical results. It is very important to observe that, unlike the parameter $`V`$ introduced into the Rizzo and Wells analysis, $`V_G`$ can have either sign and even vanishes when $`\mathrm{\Delta }0.423`$. In the case where the $`Z_2`$ odd pieces are dropped we can still re-write $`V_G`$ into a form similar to the above with the replacement $`F(\mathrm{\Delta })\stackrel{~}{F}(x_{L_1},x_{L_2})`$ which remains a function of two variables. Scanning over the $`x_{L_i}`$, however, we again find that the sum, i.e., $`\stackrel{~}{F}`$ is bounded to the region $`\frac{1}{2}\stackrel{~}{F}1`$ as was $`F(\mathrm{\Delta })`$.

Given the shift in $`G_F`$ due to KK exchange it is straightforward to calculate the first order shifts in other electroweak observables due to $`V_G`$ which we imagine (due to the great success of the SM) to be rather small, i.e., of order $`10^3`$ or less. Thus we are free in our analysis below to drop terms in $`V_G`$ that are of more than linear order; this assumption is justified by our final results. We find that

$`\delta x_0`$ $`=`$ $`{\displaystyle \frac{x_0(1x_0)}{(12x_0)}}V_G`$
$`\delta M_W`$ $`=`$ $`{\displaystyle \frac{1}{2}}M_W{\displaystyle \frac{x_0}{(12x_0)}}V_G`$
$`{\displaystyle \frac{\delta \mathrm{\Gamma }_f}{\mathrm{\Gamma }_f}}`$ $`=`$ $`\left[1+{\displaystyle \frac{8Q_f(2T_{3f}4x_0Q_f)}{1+(2T_{3f}4x_0Q_f)^2}}{\displaystyle \frac{x_0(1x_0)}{(12x_0)}}\right]V_G,`$ (7)
where $`x_0(M_W)`$ is the value of the effective weak mixing angle, $`\mathrm{sin}^2\theta _{eff}`$ ($`W`$ boson mass) and $`\mathrm{\Gamma }_f`$ is the decay width for $`Z\overline{f}f`$ in the SM after all of the SM QED, QCD and electroweak radiative corrections have been included. Here $`T_{3f}`$ and $`Q_f`$ are the third component of weak isospin and the electric charge of the fermion, $`f`$, respectively. For $`f=b,c`$, the widths are usually quoted through the ratios $`R_f=\mathrm{\Gamma }(Z\overline{f}f)/\mathrm{\Gamma }(Zhadrons)`$; the shifts in these ratios are given by

$$\frac{\delta R_i}{R_i}=\frac{\delta \mathrm{\Gamma }_i}{\mathrm{\Gamma }_i}\frac{\underset{j}{}\delta \mathrm{\Gamma }_j}{_j\mathrm{\Gamma }_j},$$
(8)
where both sums in the last expression extend over all hadrons. These are the electroweak variables we will employ in our fit. Unlike in the case of Rizzo and Wells, we cannot make use of other observables, such as weak charge $`Q_W`$ measured in atomic parity violation or data arising from deep inelastic neutrino scattering, since they necessarily involve five of the $`x_i`$ for the neutrino/electron and the $`u`$ and $`d`$ quarks.

Using the latest precision electroweak data as well as the updated estimate of $`\alpha (M_Z)`$ obtained from the new low energy data on $`R`$ from the BES-II Collaboration, we find the $`95\%`$ CL allowed region in the $`V_G`$-Higgs mass($`m_h`$) plane shown in Fig.2 for Case I. (All electroweak radiative correction calculations are performed with ZFITTER6.23.) We recall that this same fit in the SM requires $`m_h<200`$ GeV at this level of confidence; here we see that the extra degree of freedom present in $`V_G`$ allows the SM Higgs mass to be as heavy as 350 GeV. Note that for $`m_h>200`$ GeV the $`95\%`$ CL plot requires $`V_G<0`$. Since $`F(\mathrm{\Delta })`$ is known we can use these results to obtain a bound on $`M_c`$ as a function of $`\mathrm{\Delta }`$ for fixed values of $`m_h`$ which is also shown in Fig.2 for Case I. The first thing to note is that in the case where the $`x`$’s are family independent, i.e., $`\mathrm{\Delta }=0`$ the value of $`M_c`$ must be larger than about 4 TeV given the current lower bound on the Higgs mass $`113`$ GeV. (This same result applies also for Case II.) We see that as we vary both $`m_h`$ and $`\mathrm{\Delta }`$ the resulting bounds range from zero to over 6 TeV with typical values of order 2-5 TeV. A scan of the model parameters for Case II gives qualitatively very similar results. From this analysis it is clear that a bound of $`M_c=4`$ TeV is rather typical and we will use this value in our analysis below. To reach such KK resonance mass scales will either require CLIC technology or a muon collider either of which should have integrated luminosities in excess of 1 ab-1=1000 fb-1. Thus it is of particular importance what we can learn from data available below the first KK peak.

## 3 Localizing Fermions at Lepton Colliders

### 3.1 Bhabha Scattering

In order to localize the various SM fermions we must first determine the positions of the particles in the initial state, i.e., for an $`e^+e^{}(\mu ^+\mu ^{})`$ collider we must determine the values of $`x_{L_{1(2)}}`$ and $`x_{e_{1(2)}}`$. (From now on we will drop the family index except where such labels are important and we will denote $`c_{L(R)}=\mathrm{cos}n\pi x_{L(e)}`$ and $`s_{L(R)}=\mathrm{sin}n\pi x_{L(e)}`$.) This can best be done via Bhabha scattering for which the cross section is given by

$`{\displaystyle \frac{d\sigma }{d\mathrm{cos}\theta }}`$ $`=`$ $`{\displaystyle \frac{2\pi \alpha }{s}}{\displaystyle \underset{i,j}{}}[([LL](\mathrm{}_i\mathrm{}_j)^2+[RR](r_ir_j)^2){\displaystyle \frac{u^2}{s^2}}(P_{ij}^{ss}+2P_{ij}^{st}+P_{ij}^{tt})`$ (9)
$`+`$ $`(\mathrm{}_i\mathrm{}_j)(r_ir_j)(([LL]+[RR]){\displaystyle \frac{t^2}{s^2}}P_{ij}^{ss}+[LR]P_{ij}^{tt})],`$
where $`\mathrm{}_i`$ and $`r_i`$ are the couplings of the electron(or muon) to the various gauge bosons, e.g., $`\mathrm{}_Z=\frac{g}{\mathrm{cos}\theta _w}(\frac{1}{2}+\mathrm{sin}^2\theta _w)`$. Here we have employed the usual Mandelstam variables and have made use of the notation

$$P_{ij}^{qr}=s^2\frac{(qm_i^2)(rm_j^2)+\mathrm{\Gamma }_i\mathrm{\Gamma }_jm_im_j}{[(qm_i^2)^2+(\mathrm{\Gamma }_im_i)^2][(rm_j^2)^2+(\mathrm{\Gamma }_jm_j)^2]},$$
(10)
with $`m_i(\mathrm{\Gamma }_i)`$ being the mass (width) of the $`i^{th}`$ gauge boson and where we have defined the polarization projectors ,

$`[LL]`$ $`=`$ $`{\displaystyle \frac{1}{4}}[1+P_1+P_2+P_1P_2],`$
$`[RR]`$ $`=`$ $`{\displaystyle \frac{1}{4}}[1P_1P_2+P_1P_2],`$
$`[LR]`$ $`=`$ $`{\displaystyle \frac{1}{2}}[1P_1P_2],`$ (11)
with $`P_{1,2}`$ being the polarizations of the incoming electron and positron beam respectively.

It is instructive to conveniently bin the contributions to the above sum so they can be individually examined. First, we know that the pure SM terms are independent of the $`x_i`$. Next, let us consider the sum of the contributions from a single gauge boson KK level due to a specific type of gauge boson, e.g., $`\gamma ^{\pm (n)}`$ for fixed $`n`$. In case I, summing over the $`Z_2`$ even and odd fields yields an effective rescaling

$`(\mathrm{}_i\mathrm{}_j)^2`$ $``$ $`(\mathrm{}_i\mathrm{}_j)^2(c_L^2+s_L^2)^2,`$
$`(r_ir_j)^2`$ $``$ $`(r_ir_j)^2(c_R^2+s_R^2)^2,`$
$`(\mathrm{}_i\mathrm{}_j)(r_ir_j)`$ $``$ $`(\mathrm{}_i\mathrm{}_j)(r_ir_j)(c_Lc_R+s_Ls_R)^2.`$ (12)
For the first two coupling combinations, the resulting scale factor is just unity while in the last combination we obtain a factor of $`\mathrm{cos}^2n\pi (x_Lx_e)`$. This shows that the pure KK tower terms are either independent of the $`x_i`$ or will only depend upon the absolute value of the difference $`x_Lx_e`$ since cosine is an even function. In case II the corresponding rescaling factors are $`c_L^4,c_R^4`$ and $`c_L^2c_R^2`$ thus showing the separate dependence on both $`x_L`$ and $`x_e`$. The last set of terms are those due to interference between, e.g., the SM $`\gamma `$ and $`\gamma ^{\pm (n)}`$ for fixed $`n`$, again summing over $`\pm `$ states. This set of terms scale similarly to the pure KK contribution except that they are not squared. Putting this all together demonstrates that for case I Bhabha scattering will only probe the quantity $`|x_Lx_e|`$ while for case II it will probe $`x_L`$ and $`x_e`$ independently.

To get a feeling for these cross sections we show in Fig.3 the integrated cross section and the Left-Right Polarization asymmetry, $`A_{LR}`$ as a function of energy assuming $`M=4`$ TeV for the common degenerate masses of $`\gamma ^{\pm (1)}`$ and $`Z^{\pm (1)}`$, for three different models. In all cases we assume an angular cut $`0.985z=\mathrm{cos}\theta 0.8`$; the stronger cut for positive $`z`$ is to remove a significant amount of the SM photon pole. In this plot and in the rest of the analysis below neither initial state radiation nor beamstrahlung corrections have been applied; for more realistic simulations these will need to be included but we know that these corrections will not change our results qualitatively. To generate the curves in the resonance region, family independence was assumed along with the specific values $`x_Q=x_u=x_d=0.5`$.

How well can we extract $`x_{L,e}`$ information from Bhabha scattering? Clearly at low energies below $`1`$ TeV neither the cross section nor $`A_{LR}`$ appears to have any analyzing power. Once the 4 TeV pole is approached, say within a few widths, we become sensitive to the fact that we have assumed generation independence and the particular values above for all the other $`x_i`$. Clearly the mass region near the pole should not be included in this fit. Thus we propose slicing up the region $`1000\sqrt{s}3400`$ GeV into 25 points and accumulating 100 fb-1 of luminosity at each point, determining at each both $`\sigma `$ and $`A_{LR}`$ as well as the Forward-Backward asymmetry, $`A_{FB}`$, and the Polarized Forward-Backward asymmetry, $`A_{FB}^{pol}`$. (This approach is certainly not optimized but will give us a flavor of what we may expect.) We now employ symmetrized cuts $`0.985z0.985`$, assume a single beam polarization, $`P`$, of $`80\%`$, with an error of $`\delta P/P=0.003`$ and we will also assume an error of $`0.3\%`$ on the integrated luminosity. For various input choices of $`x_{L,e}`$ we can ask what the extracted allowed region may be; as typical examples to cover the whole parameter space we will assume that $`(x_L,x_e)`$= (0.2,0.8), (0.5,0.2), or (0.8,0.7). Fig.4 shows the results of performing this fit for case I while Fig.5 shows the corresponding results for case II. In case I, since we have already demonstrated that only the absolute value of the difference between $`x_L`$ and $`x_e`$ can be determined, we should not be surprised to see that that allowed regions take the form of pairs of stripe-like narrow bands. For example, when $`x_L=0.2`$ and $`x_e=0.8`$, the resulting allowed regions should surround the lines $`x_L=x_e\pm 0.6`$ and this is indeed what we find. The allowed regions in each of the examples lie between the narrowly separated pairs of lines; the typical separation of these two lines in the vertical direction is $`0.01`$ but varies somewhat from case to case by as much as a factor of two. This is the best that one can do for case I using data from Bhabha scattering alone. For case II the $`x_{L,e}`$ can be individually determined quite precisely without ambiguity for all three examples as shown in Fig.5. One sees that the size of the allowed regions are about the same or smaller than the the symbol marking the input values themselves.

### 3.2 Fermion Pair Production

To go further with our analysis we need turn our attention to the $`s`$-channel fermion pair production process $`e^+e^{}\overline{f}f`$ which has a cross section given by

$`{\displaystyle \frac{d\sigma }{d\mathrm{cos}\theta }}`$ $`=`$ $`{\displaystyle \frac{2\pi \alpha }{s}}{\displaystyle \underset{i,j}{}}P_{ij}^{ss}[{\displaystyle \frac{u^2}{s^2}}([LL](\mathrm{}_i\mathrm{}_j)_e(\mathrm{}_i\mathrm{}_j)_f+[RR](r_ir_j)_e(r_ir_j)_f)`$ (13)
$`+`$ $`{\displaystyle \frac{t^2}{s^2}}([LL](\mathrm{}_i\mathrm{}_j)_e(r_ir_j)_f+[RR](r_ir_j)_e(\mathrm{}_i\mathrm{}_j)_f)],`$
using the same notation as above. Fig.6 shows that, indeed, the cross section and $`A_{LR}`$ are quite sensitive to variations in the $`x_i`$ in the same $`\sqrt{s}`$ region employed in the case of the Bhabha scattering data fit.

By examining the various pieces that contribute to the cross section as above we can learn the structure of its sensitivity to the $`x_i`$. If we concentrate on the pure KK contributions we obtain the effective rescalings

$`(\mathrm{}_i\mathrm{}_j)_e(\mathrm{}_i\mathrm{}_j)_f`$ $``$ $`(\mathrm{}_i\mathrm{}_j)_e(\mathrm{}_i\mathrm{}_j)_f(c_L^ec_L^f+s_L^es_L^f)^2,`$
$`(r_ir_j)_e(r_ir_j)_f`$ $``$ $`(r_ir_j)_e(r_ir_j)_f(c_R^ec_R^f+s_R^es_L^f)^2,`$
$`(\mathrm{}_i\mathrm{}_j)_e(r_ir_j)_f`$ $``$ $`(\mathrm{}_i\mathrm{}_j)_e(r_ir_j)_f(c_L^ec_R^f+s_L^es_R^f)^2,`$
$`(r_ir_j)_e(\mathrm{}_i\mathrm{}_j)_f`$ $``$ $`(r_ir_j)_e(\mathrm{}_i\mathrm{}_j)_f(c_R^ec_L^f+s_R^es_L^f)^2,`$ (14)
which for case I means that at least this part of the cross section depends only upon the absolute values of four distinct differences that one can form between the various $`x_i`$. The SM-KK tower interference terms are found to scale exactly as above without squaring the factors on the right making this conclusion valid for almost the entire cross section. Note that unlike the case of Bhabha scattering, there are no terms in the cross section which are $`x_i`$ independent beyond those arising from the SM. For case II the same expressions as above are found to hold but with all the terms proportional to $`s_{L,R}^{e,f}`$ set to zero.

One might believe that since the cross section for case I now depends upon four absolute values of $`x_i`$ differences while Bhabha scattering provides a fifth absolute difference, it may be possible to uniquely determine all the $`x_i`$’s when the two sets of data are combined. Unfortunately, this is not the case as a simple example shows. Imagine the $`x_i`$ take on the particular set of values $`x_i^0`$; certainly if one adds or subtracts a common value, $`\delta `$, to all of the $`x_i^0`$ the absolute values of the differences upon which the cross sections depend will be left invariant as long as none of the $`x_i`$ exceed unity or is less than zero as a result of this shift. This implies that the size and location of the $`95\%`$ CL allowed region on the $`x_Lx_e`$ projection for case I will critically depend, e.g., in the case of $`b`$-quarks, on both $`x_Q`$ and $`x_d`$. An example of this is shown in Figs.7 and 8 where Bhabha scattering and $`e^+e^{}\overline{b}b`$ data are combined in an effort to extract the four parameters $`x_L`$, $`x_e`$, $`x_Q`$ and $`x_d`$. (Here a b-tagging efficiency of $`60\%`$ has been used and QCD corrections have been included; we fit to the data taken at the same energy points with the same integrated luminosity as we have already done for the Bhabha analysis.)

As we can see from these figures the inclusion of $`e^+e^{}\overline{b}b`$ data does decrease the size of the stripe-shaped allowed range extracted for $`x_{e,L}`$ from Bhabha scattering but not by a very great amount. We also see that the locations of the allowed regions do depend on the assumed values of $`x_{d,Q}`$. We should be reminded that since these plots are 2-dimensional projections of the 4-dimensional fits, the various points in the allowed regions shown in Figs. 7 and 8 are highly correlated.

In case II there are no ambiguities in any of the couplings and, as in the case of Bhabha scattering, only a very small allowed region is found from the fit. The size of the allowed region on the $`x_ex_L`$ plane is this case is found to be independent of the values of $`x_{d,Q}`$ and not much different than that obtained from Bhabha scattering alone. All three examples are compared in Fig.9.

From this analysis it is clear that for case II precision measurements of the various fermion SM locations is relatively easy to achieve and is quite probably dominated by systematic uncertainties. For case I precision measurements of fermion locations may be possible as well although it would seem that fits to only one or two processes leads to bounded, striped-shape regions. Clearly as more and more final state fermion locations are probed the lengths and locations of these stipes will be reduced. It may be possible that if data on a sufficient number of final states can be collected the allowed striped-shaped regions will be cut down to a sufficient size so that a precise location determination is achievable. Such an analysis is, however, beyond the scope of the present paper so that we must for the moment be satisfied with our rather narrow striped allowed regions for the fermions’ locations.

### 3.3 On-Resonance Observables

In our earlier work it was shown that once we determine that the spin of a resonance in lepton-pair collisions is one (from decay angular distributions) it will be straightforward to determine whether or not it is a KK state or a more typical $`Z^{}`$ provided beam polarization is available. This rests on the use of factorization tests, i.e., linear relationships between measurements of observables made atop the resonance. As is well-known, on a $`Z^{}`$ resonance the tree-level coupling factorization relationship $`A_{FB}=A_{LR}A_{FB}^{pol}`$ is known to hold for any final state fermion $`f`$. However, in the KK case, a single particle resonance is not what is produced. In case I(II) a coherent, resonating combination of 4(2) states is produced simultaneously so we expect relations such as the above to fail. (In earlier work this was explicitly shown to happen for the rather simple case II so that it is rather obvious that it also happens for more complex case I. In this discussion we omit the possibility of any tiny mass splittings of order 1 GeV between the $`Z`$ and $`\gamma `$ states.) This can clearly be seen as follows: a short exercise shows that the above observables on resonance can be written as

$`A_{FB}^f`$ $`=`$ $`{\displaystyle \frac{3}{4}}{\displaystyle \frac{A_1}{D}}`$
$`A_{FB}^{pol}(f)`$ $`=`$ $`{\displaystyle \frac{3}{4}}{\displaystyle \frac{A_2}{D}}`$
$`A_{LR}^f`$ $`=`$ $`{\displaystyle \frac{A_3}{D}},`$ (15)
where $`f`$ labels the final state fermion and we have defined the coupling combinations

$`D`$ $`=`$ $`{\displaystyle \underset{i,j}{}}\mathrm{\Gamma }_i^1\mathrm{\Gamma }_j^1(\mathrm{}_i\mathrm{}_j+r_ir_j)_e(\mathrm{}_i\mathrm{}_j+r_ir_j)_f`$
$`A_1`$ $`=`$ $`{\displaystyle \underset{i,j}{}}\mathrm{\Gamma }_i^1\mathrm{\Gamma }_j^1(\mathrm{}_i\mathrm{}_jr_ir_j)_e(\mathrm{}_i\mathrm{}_jr_ir_j)_f`$
$`A_2`$ $`=`$ $`{\displaystyle \underset{i,j}{}}\mathrm{\Gamma }_i^1\mathrm{\Gamma }_j^1(\mathrm{}_i\mathrm{}_j+r_ir_j)_e(\mathrm{}_i\mathrm{}_jr_ir_j)_f`$
$`A_3`$ $`=`$ $`{\displaystyle \underset{i,j}{}}\mathrm{\Gamma }_i^1\mathrm{\Gamma }_j^1(\mathrm{}_i\mathrm{}_jr_ir_j)_e(\mathrm{}_i\mathrm{}_j+r_ir_j)_f,`$ (16)
with $`\mathrm{\Gamma }_i`$ the individual widths of the contributing KK states. For case I, the sum extends over $`\gamma ^{\pm (1)}`$ and $`Z^{\pm (1)}`$ while for case II only the states $`\gamma ^{+(1)}`$ and $`Z^{+(1)}`$ are included. Note that as long as all of the $`\mathrm{\Gamma }_i`$ are of comparable magnitude factorization relations of the type above are impossible to satisfy. Only in the limit where one of the $`\mathrm{\Gamma }_i`$ dominates the sum (or, of course, when only one state is produced) will factorization be obtainable. Once factorization fails we then know that we are producing more than a simple single resonance.

We note in passing that it is often asked whether it may also be possible to distinguish a single $`Z^{}`$-like resonance from a KK state by the shape of the excitation spectrum. Such an analysis would need to include the effects of both the slight mass difference in the $`\gamma `$ and $`Z`$ states, initial state radiation, finite mass resolution, as well as the appropriate beamstrahlung spectrum corrections and has yet to be performed. Fig.10 shows what a comparison of a KK excitation and a single fitted Breit-Wigner(BW) may look like after ISR and beamstrahlung have been de-convoluted. Near the peak the BW is somewhat more narrow than the actual distribution and overestimates the cross sections in the tails. The actual KK distribution is also seen to be somewhat narrower above than below the resonance peak. Given these small differences it is clear that a detailed analysis must be performed to demonstrate whether or not a KK state can be distinguished from a single BW due to the importance of systematic uncertainties.

With the above discussion, we may ask what information can be obtained on the $`x_i`$ from resonance measurements; certainly statistics is not problem with more than $`10^{67}`$ events expected per ab-1. With these huge statistics it is clear that any such a determination of couplings will be systematics limited for either case I or case II. The simplest case to analyze, in the absence of any family symmetry and in analogy with Bhabha scattering, is the $`e^+e^{}`$ final state. In this case, the couplings in Eqs. (15) and (16) only depend upon the two unknowns $`x_{e,L}`$; however, the asymmetry observables also depend on the three(one) independent ratios of widths, $`\mathrm{\Gamma }_i/\mathrm{\Gamma }_j=R_{ij}`$, in case I(II). Thus for case I, there are not enough observables in this sector alone to fix all of the parameters while a unique solution seems to be obtainable in case II. For case I it is clear that one must combine the data from several flavor sectors in order to obtain a sufficient number of constraints to determine the relevant $`R_{ij}`$ and $`x_i`$ from a rather large simultaneous fit. Such an analysis is beyond the scope of this paper. For case II, knowing $`x_{e,L}`$, and the single width ratio $`R_{12}`$, it would appear that we can proceed to all the other sectors and determine the corresponding $`x_i`$ without much difficulty. However in the case of electrons there are actually only two independent asymmetries since $`A_2=A_3`$. Thus, as in case I, data from other final states will need to be included and a large simultaneous fit performed. It is clear from this discussion that it will be somewhat easier to isolate the positions of the various SM fermions in the extra dimensions by using off-resonance measurements than via on-peak data.

## 4 Summary and Conclusions

In this paper we have investigated the capability of future lepton colliders to probe the locations of the SM fermions when they are ‘stuck’ at specific points in extra dimensions as suggested by the Arkani-Hamed-Schmaltz model. There were several major steps necessary to perform this analysis which we now summarize.

* We consider two classes of models: I and II; they differ by whether or not the $`Z_2`$ odd components of the gauge KK towers are allowed to propagate and couple to the SM fermions. These two classes of models are identical when the fermions live at the fixed points put differ significantly if the fermions can live at arbitrary locations.
* In order to investigate the fermion locations at an accelerator the first requirement is to determine the scale of the the compactification which determines the mass of the KK gauge boson spectrum. Direct searches for such states at the Tevatron only provide limits on the $`0.8`$ TeV range while those from indirect searches, i.e., the use of precision electroweak data, can provide limits in the several TeV range. For the case at hand, allowing for the left-handed electron and $`\mu `$ to occupy different locations within the thick wall, we found KK mass constraints that are fairly sensitive to the separation of these two fields as well as the SM Higgs mass. Scanning over the parameter space a typical bound we obtained by this procedure is $`4`$ TeV. In some cases it may be possible to obtain a higher average bound by considering various FCNC processes but these are much more model dependent. Clearly, to reach and probe the $`4`$ TeV scale with sufficient statistics will require CLIC or a Muon Collider with very high integrated luminosities $`1ab^1`$.
* Since this center of mass energy is quite high it is important that we first ascertain what can be learned from data taken below the resonance. In this energy range, for any given process such as $`e^+e^{}f\overline{f}`$, the cross section and various asymmetries depend only upon the locations of these specific fermions, i.e., $`e_{L,R}`$ and $`f_{L,R}`$. The simplest process to consider is thus Bhabha scattering. Dividing the mass range up into bins of equal integrated luminosity and making use of the cross section and asymmetry observables we were able to obtain the allowed regions for the locations of $`e_{L,R}`$ which differed significantly for cases I and II. In case I we found, consistent with theoretical expectations, that only the quantity $`|x_Lx_e|`$ could be precisely determined, with the allowed parameter space thus appearing as striped-shaped regions in the $`x_Lx_e`$ plane, whereas in case II both $`x_{L,e}`$ can be well-determined separately. Adding information from another process, such as $`e^+e^{}b\overline{b}`$, led to a four parameter fit; for case I the size and locations of the allowed regions in location space were shown to be rather sensitive to the assumed values of the input parameters. On the otherhand, in case II the fermion location sensitivity was observed not to be sensitive to the choice of input. If case II holds, it is clear that from a generalization of our procedure to other fermion final states that locating the SM fermions will be rather straightforward using data obtained below the first KK pole. For case I such a situation is more problematic since the allowed regions, projected in two dimensions, are stripe-shaped. It may be, however, that if enough final states are accessible, a large simultaneous fit can lead to rather small allowed regions for the various fermion locations.
* We demonstrated that on-resonance measurements will be much harder to use in determining fermion locations. The reason for this is that for any particular fermion decay mode, the locations of all the SM fermions are involved in determining the value of the associated observables. Fortunately, we demonstrated that the these additional dependencies can be isolated into a only one(for case II) or three(for case I) additional unknowns when conducting the appropriate fits. Even with this simplification, however, we argued that large simultaneous fits involving many observables will be necessary to extract location information for either case I or II in order to obtain a sufficient number of independent quantities to fit the rather large number of unknowns. Given the huge on-resonance statistics, the errors in such fits will certainly be systematics dominated. In addition, we speculated on the possibility of distinguishing a KK resonance from a single Breit-Wigner through its’ shape; such an analysis will require a detailed study including initial state radiation, beamstrahlung and finite energy resolution effects and is beyond the scope of this paper.

From our analysis it is clear that future lepton colliders will provide a means to map out the positions of SM fermions if they are localized in extra dimensions.

Acknowledgements

The author would like to thank N. Arkani-Hamed, Y. Grossman and M. Schmaltz for discussions on localized fermion models during the early stages of this work. The author would also like to thank H. Davoudiasl and J.L. Hewett for general discussions on models with extra dimensions.