text:
# Maximum-entropy calculation of end-to-end distance distribution of force stretching chains

## I Introduction

Recent advances in the molecules manipulation have made it possible to measure and characterize molecular properties at a single molecule level. One of basic characteristics is the extension-force curves (EFCs)smith96 ; bensimon ; zlatanova . These curves have provided lots of interesting and useful physical information about studied molecules, going from the detailed elastic propertiessmith96  to complex structure transitionsrief ; bockelmann ; liphardt . On theoretical side, many kinds of models have been constructed to character and explain the recorded various EFCs of different molecules lubensky ; cocco ; montanari ; zhou1 ; gerland . Except computer simulations, e.g., molecular dynamic or Monte Carlo sampling, the calculation of the end-to-end distance distributions (EEDDs) of the force stretched molecules is the center problem in using statistical mechanical method. In principle, EEDDs can be obtained by partition function. But two questions must be faced firstly: one is what physical interactions should be taken into account; the other is what mathematical technique is needed to solve the EEDDs. It is not easy to describe physical interactions in complex molecules, such as polyelectrolytes or proteins. While specific mathematical technique is not always useful in different molecular systems.

In contrast to traditional mind, in this paper we try to extract EEDDs from the recorded EFCs in experiments using the maximum-entropy (or least-biased) method (MEM). Our motivations are that, first, to our knowledge, little concern about EEDDs has been given in previous force stretching models. Although EEDDs of simpler molecules may be simpler enough, it is no reason to assume that they are still simple for complex molecules, such as secondary structure RNA; second, because the EEDDs are the results of interplay between intra-molecule and force, they can be seen as primitive examining for more realistic physical models. In addition, our studies also show that the EEDD at vanishing force calculated by MEM keeps almost all characteristic of the exact distribution without force. Therefore this method may provide a possible way to directly “measure” EEDDs by force spectroscopy.

The organization of this paper is as follows. We first, in Sec. II, briefly review the maximum entropy method. In Sec. III, the basic relations between the distance moments and EFCs are demonstrated. In Sec. IV, MEM is examined by reconstructing EEDDs of three force stretching chain models: Gaussian chain, free-joined chain and self-avoiding chain on 2-dimension lattice. We also show in Sec. V that the method is capable of resolving EEDDs of complex chain molecules stretched by force. As an illustration, the model of force unzipping double-stranded chain molecules is used to provide exact EFCs and EEDDsliuf ; these results are necessary to calculate and compare EEDDs solved by MEM. Section. VI is our conclusion.

## II Maximum entropy method

Given a finite set of the moments of a distribution function, how to construct the function is an old mathematical problem. The MEM has been proved to be useful in this problemmed ; poland . From a normalized distribution function $`P(z)`$ on the interval $`(0,1)`$, the power moments are calculated as

$`\mu _n={\displaystyle z^nP(z)𝑑z}.`$ (1)
On the other hand, given a set of $`(M+1)`$ moments, from $`\mu _0`$ to $`\mu _M`$, it is not always possible to find a positive, well-behave function $`P(z)`$ that will have these moments. The necessary and sufficient conditions for the existence of a function $`P(z)`$ with a set of $`(M+1)`$ moments on interval $`(0,1)`$ are the Hausdorff relationsmed :

$`{\displaystyle \underset{m=0}{\overset{k}{}}}(1)^m\left(\begin{array}{c}k\\ m\end{array}\right)\mu _{n+m}0`$ $`,\mathrm{for}(n,k)=(0,0)\mathrm{to}n+kM.`$ (4)
The MEM offers a definite procedure for the construction of the approximate distribution $`P_M(z)`$ based on $`(M+1)`$ moments as the following formmed :

$`P_M(z)=\mathrm{exp}\left[{\displaystyle \underset{n=0}{\overset{M}{}}}\lambda _nz^n\right].`$ (5)
The $`\lambda _n`$ are a set of $`(M+1)`$ constants determined by the $`(M+1)`$ known $`\mu _n`$. This involves a straightforward nonlinear iterative procedure that usually converges rapidlymed .

In general, a real distribution is not always defined on interval $`(0,1)`$. Hence the first step in using MEM is to convert the distribution to a function on this intervalpoland . Given that the power moments of the original distribution $`f(x)`$ are $`\gamma _m`$, and the lower and upper bounds are designated as $`\alpha _1`$ and $`\alpha _2`$ respectively. Defining the extent of the distribution

$`L=\alpha _2\alpha _1.`$ (6)
First, shift the moments $`\gamma _m`$ to interval $`(0,L)`$ by

$`\overline{\mu }_n={\displaystyle \underset{m=0}{\overset{n}{}}}(\alpha _1)^{nm}\left(\begin{array}{c}n\\ m\end{array}\right)\gamma _m.`$ (9)
Then scale these moments $`\overline{\mu }_n`$ to interval $`(0,1)`$ by

$`\mu _n=\overline{\mu }_n/L^n.`$ (10)
Thus MEM can be used to calculate distribution $`P(z)`$.

Conversely, if the approximate distribution $`P(z)`$ is solved from moments $`\gamma _m`$, the distribution can be first rescaled from interval $`(0,1)`$ to $`(0,L)`$ by the change of variable y

$`g(y)={\displaystyle \frac{1}{L}}P\left({\displaystyle \frac{y}{L}}\right),y(0,L).`$ (11)
Then shift the distribution $`g(y)`$ to interval $`(\alpha _1,\alpha _2)`$ by

$`f(x)=g(x\alpha _1),w(\alpha _1,\alpha _2).`$ (12)
## III Moments from extension-force curves

Assuming that one end of a chain consisting of $`N`$-links is fixed at origin, and external force $`f𝐳_\mathrm{𝟎}`$ is exerted on the other end, where unit vector $`𝐳_\mathrm{𝟎}`$ is along $`z`$-axis. Let $`P_N(𝐑,f)`$ be the probability distribution function that the end-to-end vector of the force stretched chain is $`𝐑=(R_x,R_y,R_z)`$. Then the power moments of component $`R_z`$ distribution $`P_N(R_z,f)`$ are calculated by

$`\overline{R_z^m}(f)`$ $`=`$ $`<(𝐑𝐳_0)^m>`$
$`=`$ $`{\displaystyle 𝑑R_z(R_z)^mP_N(R_z,f)}`$
$`=`$ $`{\displaystyle d^3𝐑(𝐑𝐳_0)^mP_N(𝐑,f)}.`$
In order to illustrate expressions more seriously and explicitly, distribution function of the ideal chains is usedklei ; doi

$`P_N(𝐑,f)`$ $`=`$ $`𝒬^1[f]{\displaystyle 𝒟[𝐫(s)]\delta ^3\left(𝐑_0^L𝑑s𝐯(s)\right)}`$ (14)
$`\times \mathrm{exp}\left[{\displaystyle \frac{1}{k_BT}}{\displaystyle _0^L}𝑑s\rho _e(𝐫,s)+{\displaystyle \frac{f}{k_BT}}𝐳_0{\displaystyle _0^L}𝑑s𝐯(s)\right],`$
where $`k_B`$ is Boltzmann constant, $`T`$ is temperature, $`L`$ is arclength of the chain, “vector” $`𝐫(s)`$ describes the local state at arclength point $`s`$, e.g., in the case of a flexible Gaussian chain, $`𝐫`$ is a three-dimensional position vector; while in case of a wormlike chain, $`𝐫`$ is the unit tangent vectormak . Vector $`𝐯(s)`$ is also different according to concrete chain model, e.g., $`𝐯=d𝐫/ds`$ for Gaussian chain, and $`𝐯=𝐫(s)`$ or the tangent vector for wormlike chain. The normalization factor $`𝒬[f]`$ is

$`𝒬[f]`$ $`=`$ $`{\displaystyle 𝑑𝐑𝒟[𝐫(s)]\delta \left(𝐑_0^L𝑑s𝐯(s)\right)}`$ (15)
$`\times \mathrm{exp}\left[{\displaystyle \frac{1}{k_BT}}{\displaystyle _0^L}𝑑s\rho _e(𝐫,s)+{\displaystyle \frac{f}{k_BT}}𝐳_0{\displaystyle _0^L}𝑑s𝐯(s)\right]`$
$`=`$ $`{\displaystyle 𝒟[𝐫(s)]\mathrm{exp}\left[\frac{1}{k_BT}_0^L𝑑s\rho _e(𝐫,s)+\frac{f}{k_BT}𝐳_0_0^L𝑑s𝐯(s)\right]}.`$
Replacing Eq. 14 into Eq. III and performing $`𝐑`$ integral we have

$`\overline{R_z^m}(f)`$ $`=`$ $`𝒬^1[f]{\displaystyle 𝒟[𝐫(s)]\left(𝐳_\mathrm{𝟎}_0^L𝑑s𝐯(s)\right)^m}`$ (16)
$`\times \mathrm{exp}\left[{\displaystyle \frac{1}{k_BT}}{\displaystyle _0^L}𝑑s\rho _e(𝐫,s)+{\displaystyle \frac{f}{k_BT}}𝐳_0{\displaystyle _0^L}𝑑s𝐯(s)\right].`$
It is easy to prove that Eq. 16 can be rewritten as

$`\overline{R_z^m}(f)={\displaystyle \frac{(k_BT)^m}{𝒬[f]}}{\displaystyle \frac{^m}{f^m}}𝒬[f].`$ (17)
The first moment is just the average extension $`Z(f)`$ recorded in experiments as a given force $`f`$,

$`\overline{R_z^1}=Z(f)={\displaystyle \frac{k_BT}{𝒬[f]}}{\displaystyle \frac{}{f}}𝒬[f].`$ (18)
We can alternatively relate the partition function $`𝒬[f]`$ to derivatives of $`Z(f)`$ with respect to $`f`$ as follows:

$`{\displaystyle \frac{1}{k_BT}}{\displaystyle \frac{}{f}}Z(f)`$ $`=`$ $`\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)^2+{\displaystyle \frac{𝒬^{(2)}}{𝒬}},`$
$`{\displaystyle \frac{1}{k_BT}}{\displaystyle \frac{^2}{f^2}}Z(f)`$ $`=`$ $`2\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)^33\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)\left({\displaystyle \frac{𝒬^{(2)}}{𝒬}}\right)+\left({\displaystyle \frac{𝒬^{(3)}}{𝒬}}\right),`$ (19)
$`{\displaystyle \frac{1}{k_BT}}{\displaystyle \frac{^3}{f^3}}Z(f)`$ $`=`$ $`6\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)^4+12\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)^2\left({\displaystyle \frac{𝒬^{(2)}}{𝒬}}\right)`$
$`3\left({\displaystyle \frac{𝒬^{(2)}}{𝒬}}\right)^24\left({\displaystyle \frac{𝒬^{(1)}}{𝒬}}\right)\left({\displaystyle \frac{𝒬^{(3)}}{𝒬}}\right)+\left({\displaystyle \frac{𝒬^{(4)}}{𝒬}}\right),`$
and so on, where

$`𝒬^{(n)}={\displaystyle \frac{^n}{f^n}}𝒬[f].`$ (20)
According to Eq. 17, the moments $`\overline{R_z^m}(f)`$ can be solved in terms of derivatives of $`Z(f)`$ with respect to force $`f`$ as follows:

$`\overline{R_z^1}`$ $`=`$ $`Z(f),`$
$`\overline{R_z^2}`$ $`=`$ $`k_BT{\displaystyle \frac{}{f}}Z(f)+\left(\overline{R_z^1}\right)^2,`$
$`\overline{R_z^3}`$ $`=`$ $`(k_BT)^2{\displaystyle \frac{^2}{f^2}}Z(f)2\left(\overline{R_z^1}\right)^3+3\left(\overline{R_z^1}\right)\left(\overline{R_z^2}\right),`$ (21)
$`\overline{R_z^4}`$ $`=`$ $`(k_BT)^3{\displaystyle \frac{^3}{f^3}}Z(f)+6\left(\overline{R_z^1}\right)^412\left(\overline{R_z^1}\right)^2\left(\overline{R_z^2}\right)+3\left(\overline{R_z^2}\right)^2+4\left(\overline{R_z^1}\right)\left(\overline{R_z^3}\right).`$
The above relations show that if one has the first $`(n1)`$ derivatives of $`Z(f)`$, then this is enough information to calculate the first $`n`$ moments of the distribution $`P_N(R_z,f)`$. These derivatives of $`Z(f)`$ can be obtained by expanding the extension $`Z(f)`$ in a Taylor series about the reference force $`f_0`$ as

$`Z(f)=Z(f_0)+{\displaystyle \frac{}{f}}Z(f_0)\mathrm{\Delta }f+{\displaystyle \frac{1}{2}}{\displaystyle \frac{^2}{f^2}}Z(f_0)\mathrm{\Delta }f^2+{\displaystyle \frac{1}{6}}{\displaystyle \frac{^3}{f^3}}Z(f_0)\mathrm{\Delta }f^3,`$ (22)
where

$`\mathrm{\Delta }f=ff_0.`$ (23)
In general, no analytical $`Z(f)`$ is used in real situation; only the EFCs are recorded in experiments. All the derivatives have to be calculated by numerical methods.

Before beginning the next section, we clarify our procedure: first calculate different derivatives of $`Z(f)`$ from EFCs by numerical method; then use Eq. III to obtain necessary power moments of $`P_N(R_z,f)`$; and finally, apply MEM presented in Sec. II to construct approximate EEDDs.

## IV test of MEM: three force stretching chain models

In this section, the MEM is examined with three force stretching chain models which have different statistical properties: Gaussian chain, free-joined chain and excluded-volume (EV) chain on two dimension. The main reason to choice these model is that their EEDDs with forces have exact expressions. EEDDs and EFCs of the models are solved by statistical mechanical methods firstly. Then seeing the obtained EFCs as experiment data, approximate distributions is computed by MEM according to procedure mentioned in above section. Distributions solved by two methods are compared finally.

For each chain model, EEDDs at three nonzero forces are calculated respectively. In addition, distributions at zero force are also solved. Because that EEDD without force is important in polymer research, such as the calculation of root-mean-square end-to-end distance, it is interesting to see whether the distributions calculated by MEM at zero force can keep main characteristic of the exact EEDD. Though our method only solve $`P_N(R_z,0)`$, the length distribution $`P_N(𝐑,0)`$ could be obtained from the numerical relations provided by Domb et al. earlydomb .

### IV.1 Gaussian model

As the simplest $`N`$-link chain model, the energy with force $`f𝐳_\mathrm{𝟎}`$ in Gaussian modeldoi  is expressed as

$`={\displaystyle \frac{3k_BT}{2b}}{\displaystyle _0^{L=Nb}}𝑑s\left({\displaystyle \frac{𝐫}{s}}\right)^2f𝐳_0{\displaystyle _0^{Nb}}𝑑s{\displaystyle \frac{𝐫}{s}},`$ (24)
where $`b`$ is effective bond length, $`𝐫`$ is position vector. Using path integral methodklei ; doi ; zhou , the EEDD of Gaussian chain stretched by force is derived as

$`P_N(𝐑,f)=\left({\displaystyle \frac{3}{2\pi Nb^2}}\right)^{3/2}\mathrm{exp}\left\{{\displaystyle \frac{3}{2Nb^2}}\left(𝐑{\displaystyle \frac{Nb^2f𝐳_\mathrm{𝟎}}{3k_BT}}\right)^2\right\}.`$ (25)
Correspondingly, the component $`R_z`$ distribution in $`𝐳_\mathrm{𝟎}`$ direction can be integrated by

$`P_N(R_z,f)`$ $`=`$ $`{\displaystyle 𝑑R_x𝑑R_yP_N(𝐑,f)}`$ (26)
$`=`$ $`\left({\displaystyle \frac{1}{2\pi Nb^2}}\right)^{3/2}\mathrm{exp}\left\{{\displaystyle \frac{3}{2Nb^2}}\left(R_z{\displaystyle \frac{Nb^2f}{3k_BT}}\right)^2\right\}.`$
The extension versus force then is calculated as

$`Z(f)={\displaystyle 𝑑R_zR_zP_N(R_z,f)}={\displaystyle \frac{Nb^2}{3k_BT}}f.`$ (27)
As an illustration, we choice $`N=16`$ and plot the function in Fig. 1. This function will be viewed as EFCs “measured” in experiments.

Before applying MEM, firstly expand Eq. 27 in Taylor series about force $`f_0`$ as

$`Z(f)=Z(f_0)+{\displaystyle \frac{Nb^2}{3k_BT}}(ff_0),`$ (28)
or $`Z(f_0)=Nb^2f_0/3k_BT`$ and $`Z/f_0=Nb^2/3k_BT`$. Three moments can be obtained at any given force $`f_0`$ through Eq. III directly. Then approximate distributions are solved by MEM. Three distributions calculated by MEM and their comparing with exact Eq. 26 at forces $`0.0,1.0,2.0,3.0k_BT/b`$ are shown in Fig .2. Considering that the extension is linear with force, three moments approximation is used in this model. Obviously, MEM can precisely reconstruct distributions of the Gaussian chain. In fact, because the approximation function $`P_2(R_z,f)`$ is just the Gaussian distribution, it is not unexpected that MEM reconstruct EEDDs of Gaussian chain perfectly. In addition, EEDD at $`f=0.0k_BT/b`$ is the same with distributions at nonzero forces, since the first-order derivate of $`Z(f)`$ is constant at any force,

### IV.2 Free-joined chain model

Free-joined chain model has been used to fit the observed EFCs of force stretching single-stranded DNA experimentssmith96 . The model is defined as a chain with N-link of length $`b`$ in which all rotational angles occur with equal probabilityklei ; doi . When exerted external force $`f𝐳_\mathrm{𝟎}`$ on one end of the chain, the force potential energy is written as

$`_f=f𝐳_\mathrm{𝟎}{\displaystyle \underset{n=1}{\overset{N}{}}}𝐫_𝐧,`$ (29)
where $`r_n`$ are bond vectors with constant length $`|r_n|=b`$. According to Eq. 14, the distribution function $`P_N(𝐑,f)`$ of the end-to-end vector $`𝐑`$ is

$`P_N(𝐑,f)`$ $`=`$ $`{\displaystyle \frac{\mathrm{exp}\left[\beta f𝐳_\mathrm{𝟎}𝐑\right]P_N(𝐑,0)}{𝑑𝐑\mathrm{exp}\left[\beta f𝐳_\mathrm{𝟎}𝐑\right]P_N(𝐑,0)}},`$
where $`\beta =1/k_BT`$, and $`P_N(𝐑,0)`$ is the EEDD without applied force, which has been given in literatureklei

$`P_N(𝐑,0)`$ $`=`$ $`{\displaystyle \frac{1}{2^{N+1}(N2)!\pi b^2R}}{\displaystyle \underset{n=0}{\overset{[(NR/b)/2]}{}}}(1)^n\left(\begin{array}{c}n\\ N\end{array}\right)(N2nR/b)^{N2},`$ (33)
where $`R`$ is the length of vector $`𝐑`$. The normalization factor or the partition function $`𝒬[f,T]`$ can be calculated exactly as

$`𝒬[f,T]`$ $`=`$ $`{\displaystyle 𝑑𝐑P_N(𝐑,f)}`$ (34)
$`=`$ $`\left({\displaystyle \frac{4\pi }{\beta fb}}\mathrm{sinh}\left(\beta fb\right)\right)^N.`$
Then EEDD of component $`R_z`$ can be obtained by integral of Eq. IV.2 with respect to components $`R_x`$ and $`R_y`$ as

$`P_N(R_z,f)={\displaystyle \frac{\mathrm{exp}\left(\beta fR_z\right)}{\left[4\pi \mathrm{sinh}\left(\beta fb\right)/\beta fb\right]^N}}P_N(R_Z,0),`$ (35)
where

$`P_N(R_z,0)={\displaystyle \frac{1}{2^N(N2)!b}}{\displaystyle _{R_z/b}^N}𝑑x{\displaystyle \underset{0}{\overset{[(Nx)/2]}{}}}(1)^n\left(\begin{array}{c}n\\ N\end{array}\right)(N2nx)^{N2},\mathrm{R}_\mathrm{z}0.`$ (38)
The average extension $`Z(f)`$ is then given as

$`Z(f)`$ $`=`$ $`bN\left[{\displaystyle \frac{1}{\beta fb}}+\mathrm{coth}\left(\beta fb\right)\right].`$ (39)
Eq. 39 is served as experiment data to check our MEM. As an example, take N=$`16`$, and its EFC is shown in Fig. 3.

We expand Eq. 39 in Taylor series at different forces, $`0.0,0.5,1.7`$, and $`4.0k_BT/b`$. EFC at these forces has different asymptotic formula; see dash curves in Fig. 3. Similarly to the case of of Gaussian model, EEDDs calculated by MEM and their comparing with exact distribution are shown in Fig. 4. At $`f=0.0k_BT/b`$, because the third-order derivative of $`Z(f)`$ is not zero, EEDDs of three and five moments are solved by MEM respectively; see Fig. 4(a). The distributions of three and five moments are slightly different at origin: EEDD of three moments is the same with the distribution of Gaussian model; while distribution value at origin calculated by five moments is smaller, which is the same with prediction of exact EEDD. Our results show that MEM is sensitive enough to detect the fine difference of EEDDs from simple EFCs. When force is nonzero, EEDDs solved by MEM are the same with exact EEDDs.

### IV.3 Self-avoiding chain model

As a more realistic model, the self-avoiding chain which accounts for EV interactions plays very important role in polymer theorydoi ; flore . But in force stretching problem, almost all theoretical models implicated that EV interaction can be negligible. This assumption is doubted at small force region. In this section, We try to simulate the force stretched EV chain of $`N`$-link as $`N`$-step self-avoiding walks (SAW) on two dimensional (2D) quadratic lattice. The early work of Domb et al. has demonstrated that EEDD of self-avoiding chain differ appreciably from Gaussian distributiondomb . It is interesting to see weather MEM can recover the EV properties exactly when the force tends to zero.

First we formulate the force stretching partition function $`𝒬[f,T]`$ and EEDD $`P_N(n,f)`$ as follows

$`𝒬[f,T]={\displaystyle \underset{n=N}{\overset{n=+N}{}}}C_N^x\left(n\right)\mathrm{exp}\left(f\beta n\right),`$ (40)
and

$`P_N(n,f)={\displaystyle \frac{C_N^x\left(n\right)\mathrm{exp}\left(f\beta n\right)}{𝒬[f,T]}},`$ (41)
where $`C_N^x\left(n\right)`$ is the number of walks whose final $`x`$ coordinates are $`n`$. Extension function $`Z(f)`$ then can be calculated from EEDD accurately.

As an illustration, we exactly enumerate all $`20`$-step SAWs on 2D lattice. According to Eq. 40, we calculate EFC and plot it in Fig. 5.

The numerical expansions of extension of the chain at forces $`0.0,0.10,0.25`$, and $`0.70k_BT/b`$ are calculated respectively. Then using MEM, EEDDs at these forces are solved; see Fig. 6. At force $`0.0k_BT/b`$, distributions of three and five moments are different apparently. Domb et al. have pointed out that instead of Gaussian distribution, the distributions considering EV effect on 2D lattice can be well fitted by a function form of $`\mathrm{exp}(\left|x\right|^4)`$, which will be seen that the portion of the EEDD near to the origin is more “flat-topped”, and the decay of distribution for

larger values of x is sharperdomb . EEDD calculated by five moments at zero force precisely recovers these major aspects. However, it is unexpected that even a slight dip in the value of distribution can be recovered by the MEM; see Fig. 6(a). Because the origin of the dip arises from the restriction of no returns to the origindomb , the result demonstrates again that the MEM is very sensitive to detect the fine structure restrictions from the simple EFC. This characteristic in distribution is still preserved at small forces, such as at force $`0.10k_BT/b`$ in Fig. 6(b).

From the analysis of self-avoid chain, we conclude that EV may play important role even in force stretching problem. Especially, EV effect can be reflected more explicitly from EEDD, instead of simple EFCs.

## V EEDDs of force stretching complex molecules: hairpin and secondary structure conformations

From the deduction of Eq. III, the relations are independent of interactions between the units in a chain. On the other hand, units of any real polymer always interact with each other, e.g., the simple electrostatic repulsion of the phosphodiester backbone of DNA, and complex hydrophobic interaction in proteins. Hence it is valuable to see what MEM can tell us about the interactions in molecule. Because recent mechanical single molecular experiments have turn their attentions to molecular structure transitions induced by force, such as dsDNA or ssDNA (RNA) force unzippingbockelmann ; liphardt , it is natural to apply MEM to these experiment data firstly. In particular, the EEDDs at critical force is of interestliphardt . However, considering that the MEM is very sensitive to the shapes of EFCs, and current experiment data are not fine enough, in this paper we do not ready to apply our method in experiment data directly. In this section we will make use of EFCs solved by an theoretical model of force stretching hairpin and secondary structures conformations in 2D planeliuf  as “experiment” data. Because our model also provide the exact EEDDs, comparing with EEDDs derived by MEM will ensure the availability of MEM when our method is applied to real scenario in future. In following section, we first give a brief overview about the statistical model of force stretching chain molecules of hairpin and secondary structure conformations. The details of the model are given elsewhereliuf .

### V.1 A statistical mechanical model of force stretching chains of hairpin and secondary structure conformations

Hairpin and secondary structure conformations are the basic models for antiparallel $`\beta `$-sheet in protein and RNA moleculeschen1 ; chen2 . The partition function $`𝒬_N(T;f)`$ of a $`(N+1)`$ monomer ((N+1)-mer) chain molecules stretched by force $`f`$ is formulated as

$`𝒬_N(T;f)={\displaystyle \underset{E}{}}{\displaystyle \underset{\mathrm{\Delta }}{}}g_N(E;\mathrm{\Delta })e^{\beta (Ef\mathrm{\Delta })},`$ (42)
where $`\mathrm{\Delta }`$ is end-to-end distance (EED) of the chain along force direction, and $`g_N(E;\mathrm{\Delta })`$ is the number of conformations having energy $`E`$ and EED $`\mathrm{\Delta }`$. Because the energy contributed by force is only related with EEDs, we divide any conformation of the chain into two parts: one is main chain (MC), in which does not involve any contacts; the other is nested regions (NRs), which form hairpins, loops and turns. If only one NR is allowed in conformations, they are named hairpin, otherwise secondary structure conformations. On 2D lattice, the nested regions contribute $`\pm 1`$ or $`0`$ to whole EED value according their outmost contacts directionsliuf . The $`g_N(E;\mathrm{\Delta })`$ is simplified as a multiplication of the number of conformations of MC and NRs, i.e., Eq. 42 can be rewritten as

$`𝒬_N(T;f)={\displaystyle \underset{n}{}}{\displaystyle \underset{E}{}}{\displaystyle \underset{\mathrm{\Delta }}{}}C^{MC}(n,\mathrm{\Delta })C^{NRs}(n,E)e^{\beta (Ef\mathrm{\Delta })},`$ (43)
where $`n`$ is the number of unrelated NRs in conformations, $`C^{MC}(n,\mathrm{\Delta })`$ and $`C^{NRs}(n,E)`$ are the number of conformations of MC and NRs respectively. For hairpin conformations $`n=1`$.

Because our model is restricted on 2D lattice, the values of $`C^{MC}(n,\mathrm{\Delta })`$ at given $`n`$ can be counted exactly by enumeration and extrapolation methodliuf . Whereas calculation of $`C^{NRs}(n,E)`$ is modified and extended from nested polymer graph theory (NPGT) developed by Chen and Dill recentlychen1 ; chen2 . The idea behind the NPGT is that the number of conformations of any arrangement of NRs is a product of each number of conformations of each NR restricted by EV requirement. In NPGT, different arrangement of NRs is represented by polymer graph, the diagrammatic representations of intrachain contacts, and each unrelated NR can be independently seen as a polymer graph or subpolymer graph. So the calculation of the number of conformations for any given subpolymer graph is the centra of NPGT. According to the NPGT, the number of conformations of any subpolymer graph having $`m`$ subunits is a product of matrices:

$`𝐔𝐒_{t_m}𝐘_{𝐭_𝐦𝐭_{𝐦\mathrm{𝟏}}}𝐒_{t_{m1}}\mathrm{}𝐒_{t_1}𝐔^t,`$ (44)
where $`𝐔=\{1,1,1,1\}`$, $`𝐔^t`$ is the transpose of $`𝐔`$, $`𝐒_i`$ is structure matrix of $`i`$th subunit, and $`Y_{ij}`$ is viability matrixchen1 ; chen2 .

We obtain EEDD from the partition function $`𝒬(T;f)`$,

$`P_N(\mathrm{\Delta },f)=e^{\beta f\mathrm{\Delta }}\times {\displaystyle \underset{n}{}}{\displaystyle \underset{E}{}}C^{MC}(n,\mathrm{\Delta })C^{NRs}(n,E)e^{\beta E}/𝒬_N(T;f),`$ (45)
and the average extension function $`Z(f)`$ is calculated exactly from above EEDDs. For comparing, we calculate EFCs of 70-mer homogeneous chains of hairpin and secondary structure conformations; see Fig. 7. Here the homogeneous chain means that any contact of two monomers in chain contributes energy $`\epsilon `$ ($`\epsilon >0`$). Considering to the importance of sequence in secondary structure molecules, we also give EFC of a 70-mer specific sequence, A$`\mathrm{}`$ACCCCCU$`\mathrm{}`$UC$`\mathrm{}`$CAAAAAG$`\mathrm{}`$G, where the dots represent 15-mer A, U, C and G respectively; see Fig. 9(a). In contrast to homogeneous chain, only A-U or C-G pair contributes energy $`\epsilon `$.

### V.2 Single- and multipeak distributions

To be the same with previously section, we compute all EEDDs by numerical expansion of EFCs at different forces for different chain molecules; see Figs. 8 and 9(b).

The shapes of the EEDDs of the complex molecules are very different from those of simple molecules observed in Sec. IV. The most obvious feature is that the distribution regions of the complex chains expand in middle force whereas shrinking at smaller and larger forces. It is results of attracted interaction between monomers. Secondly, it seems that EFCs of homogeneous chains of hairpin and secondary structure conformations are similar except that extensions increase slowly or fast, however, the EEDDs calculated by MEM are completely different: only one peak is observed in the distribution at any force in secondary structure conformations; see Fig. 8 (a); while in hairpin conformations, two peaks located at shorter and longer EEDs present during narrow force range (between 0.42 to 0.49$`\epsilon /b`$), but no conformations with other EEDs in between; see Fig. 8 (b). In addition, EEDDs of specific sequence show more complex shapes. At $`f=0.39\epsilon /b`$ the distribution has two peaks, then they quickly fuse into one peak with a small force increasing 0.03$`\epsilon /b`$, and finally the peak separates into two peaks at $`f=0.45\epsilon /b`$. To explore the phenomena of single- or multipeak, comparing with the exact EEDD is essential. These results are plotted in corresponding figures. We find that the two peaks in distributions predicted by MEM are consistent with exact EEDDs of specific sequence and homogeneous hairpin chain. At force $`0.42\epsilon /b`$, however the exact distribution of specific sequence appears three peaks, whereas MEM predicts one peak only.

According to Eq. III, the first-order derivative of the average extension $`\overline{R_z^1}(f)`$ with respect of force $`f`$ can also be written as $`d\overline{R_z^1}/df=(\overline{R_z^2}\overline{R_z^1}^2)/k_BT`$. The formula is the same with the definition of heat capacity $`C(T)`$ except that the energy and temperature are replaced by EED and force, respectively. We believe that the EED plays important roles in force stretching chains problem, which is very similar with the roles played by energy in thermal melting biomolecules, at least in nucleic acidsliuf . Many useful insights can be given through this analogy. Since the energy distribution can reveal molecular structure transitions induced by heatingpoland , the EEDD might discover structure transitions driven by force. E.g., the EEDDs in Fig. 8 show that the transitions in secondary structure and hairpin conformations are “one-state” and “two-state”, respectively. These terms are borrowed from thermal melting casepoland ; tostesen . The transition difference exhibited in two conformations warns us that the simpler EFCs may cover critical physical information; the investigation of EEDDs is necessary to determine physical properties in force “melting” chain molecules.

In traditional theory, physical properties of polymers only relate with the number of monomers, such as cooperativity or melting transition typedoi ; flore . But in biomolecules, the monomer sequence may affect physical results dramatically. The apparent case in EEDDs is the number of peaks of the specific sequence in Fig. 9, though its EFC is simpler. The case of specific sequence warns us again that EFCs may be too simple to obtain real and useful information about the studied molecules. Because five moments cannot reconstruct three peaks in distributionpoland , we only solved a quick expansion in the distribution region. To explore three or more peaks in EEDDs, higher moments are necessary. Although our MEM fails to predict three peaks, the abnormal expansion of the distribution observed by MEM between two forces arising two peaks still can be seen as a sign of appearing of multipeak.

## VI Conclusions

In this paper, contrary to the traditional mind, we calculate end-to-end distance distribution of force stretching chain molecules from the measured EFCs by using MEM. Because the method is independent of polymer energy formula or structure details, it provide a useful and simple way to detect the real physical information about complex molecules. Many results, such as the important role played by EV interactions, single- or multipeak in EEDDs can be obtained from the simple EFCs. It is interesting to see whether these results can be found in real stretching experiments.

###### Acknowledgements.

It is a pleasure to acknowledge Dr. H.-J. Zhou, Y. Zhang and Prof. H.-W. Peng for many helpful discussions in this work.


format: text

text:
# Remarks on type IIB pp waves with Ramond-Ramond fluxes and massive two dimensional nonlinear sigma models

## I Introduction

Recently Maldacena and Maoz malmao  have constructed an interesting class of supersymmetric pp-wave solutions in ten dimensional type IIB supergravity, which includes the maximally supersymmetric plane-wave solution blau  as a special case. The nontrivial curvature is supported by null Ramond-Ramond (RR) five-forms which are non-constant, and it is argued that the light cone string actions in Green-Schwarz formalism are nonlinear sigma models with potential terms. When the target space is curved the spacetime supersymmetry requires it to have special holonomy. For solutions with $`(2,2)`$ worldsheet supersymmetry the target spaces are Calabi-Yau four-folds in general, and RR five-forms give holomorphic superpotential and Killing vector terms, whereas when one demands only $`(1,1)`$ supersymmetry the target geometry has reduced Spin(7) holonomy most generally and non-constant five-forms are translated into real harmonic superpotentials on the worldsheet. These solutions are shown to be exact string backgrounds using the U(4) formalism bermal  and also by considering possible higher order correction terms to the string effective actions russo . Thus a large class of interacting two dimensional field theories, including integrable models, are added to the list of quantizable RR backgrounds. For subsequent works on these pp-wave string theories see cvetic ; berkovits ; bonelli ; hubeny ; hikida ; gomez ; sonn .

Although the solutions in malmao  comprise quite general class of massive nonlinear sigma models, certainly they do not have the most general potential terms. The supersymmetry requirements of potential terms in two dimensional nonlinear sigma models are summarised in alvarez . With $`𝒩=(2,2)`$ the target spaces are Kähler and two commuting holomorphic Killing vector terms and one holomorphic superpotential term can be present. And for $`𝒩=(1,1)`$ the target space can be any real manifold and the potential terms include one real superpotential and one Killing vector term. Supersymmetry also requires that the Lie derivative of the superpotential should be constant along the Killing vectors. Compared to this, first of all the field theories from pp-waves are special in the sense that the target space is always eight dimensional with special holonomy, and secondly we see that one Killing vector contribution is missing both in $`𝒩=(2,2)`$ and $`𝒩=(1,1)`$ solutions. It is conceivable that RR three-forms can provide the missing potential terms on the worldsheet. It is the aim of this paper to show it is indeed the case.

In sec. II we closely follow and repeat the analysis of malmao  with nontrivial RR three-forms as well as five-forms. We identify the spacetime supersymmetry requirements on the Killing vectors from RR three-forms and find they are consistent with the results in alvarez  as quoted above. For the analysis of $`𝒩=(1,1)`$ solutions we find it more illuminating to assume that the transverse space has Spin(7) holonomy, and find supersymmetry requires the Killing vector to preserve the Spin(7) structure. In sec. III we conclude with a few comments.

## II IIB PP-wave solutions with Ramond-Ramond backgrounds

For IIB supergravity in ten dimensions we follow the conventions of schw , and take the ansatz

$`ds^2`$ $`=`$ $`2dx^+dx^{}+H(x^i)(dx^+)^2+ds_8^2,`$
$`F^{(5)}`$ $`=`$ $`dx^+\xi (x^i),`$ (1)
$`F^{(3)}`$ $`=`$ $`dx^+\theta (x^i),`$
where $`i=1,2\mathrm{}8`$ denote the transverse eight dimensional space with Euclidean signature, $`F^{(5)},F^{(3)}`$ are the RR fields and all other fields are set to zero. The Einstein’s equation has only one nontrivial component

$$^2H=\frac{2}{3}\xi _{ijkl}\xi ^{ijkl}\frac{1}{2}\theta _{ij}\theta ^{ij},$$
(2)
and from other field equations and the Bianchi identities $`\xi `$ is anti-self-dual, closed and co-closed, and $`\theta `$ is a closed two-form in eight dimensions.

The supersymmetry transformations for the dilatino $`\lambda `$ and the gravitino $`\psi _a`$ are given in terms of a Weyl spinor $`ϵ`$,

$`\delta \lambda `$ $`=`$ $`{\displaystyle \frac{1}{24}}G_{abc}\mathrm{\Gamma }^{abc}ϵ,`$ (3)
$`\delta \psi _a`$ $`=`$ $`D_aϵ\mathrm{\Omega }_aϵ\mathrm{\Lambda }_aϵ^{},`$ (4)
with

$`\mathrm{\Omega }_a`$ $`=`$ $`{\displaystyle \frac{i}{480}}F_{bcdef}^{(5)}\mathrm{\Gamma }^{bcdef}\mathrm{\Gamma }_a,`$
$`\mathrm{\Lambda }_a`$ $`=`$ $`{\displaystyle \frac{1}{96}}(\mathrm{\Gamma }_aG_{bcd}\mathrm{\Gamma }^{bcd}+2G_{bcd}\mathrm{\Gamma }^{bcd}\mathrm{\Gamma }_a).`$
$`a,b,c\mathrm{}`$ are used to denote the ten dimensional frame indices and the gamma matrices are constants subsequently. $`G_{abc}`$ is the complexified three-form, and since we have set Neveu-Schwarz (NS) fields to zero $`G`$ is pure imaginary, i.e. $`G=iF^{(3)}`$.

Given the ansatz Eq.(1), it is natural to employ the following decomposition of $`ϵ`$,

$`ϵ`$ $`=`$ $`{\displaystyle \frac{1}{2}}\mathrm{\Gamma }_+\mathrm{\Gamma }_{}ϵ{\displaystyle \frac{1}{2}}\mathrm{\Gamma }_{}\mathrm{\Gamma }_+ϵϵ_++ϵ_{}.`$
It is important to note that $`ϵ_+,ϵ_{}`$ have opposite chiralities in SO(8). Now we write down the Killing spinor equations in terms of $`ϵ_\pm `$. First by setting the variation of the dilatino to zero,

$$\theta /ϵ_+=0,$$
(5)
and from $`\delta \psi _a=0`$ we get

$`_{}ϵ_+=_{}ϵ_{}=0,`$ (6)
$`_+ϵ_++{\displaystyle \frac{i}{8}}\theta /ϵ_+^{}=0,`$ (7)
$`_iϵ_+=0,`$ (8)
$`_+ϵ_{}+{\displaystyle \frac{i}{2}}\xi /ϵ_{}+{\displaystyle \frac{i}{4}}\theta /ϵ_{}^{}{\displaystyle \frac{1}{4}}\mathrm{\Gamma }_{}/Hϵ_+=0,`$ (9)
$`_iϵ_{}{\displaystyle \frac{i}{4}}\mathrm{\Gamma }_{}\xi /\mathrm{\Gamma }_\mu ϵ_++{\displaystyle \frac{i}{16}}\mathrm{\Gamma }_{}(\mathrm{\Gamma }_\mu \theta /2\theta /\mathrm{\Gamma }_\mu )ϵ_+^{}=0,`$ (10)
where $`\xi /=\frac{1}{4!}\xi _{ijkl}\mathrm{\Gamma }^{ijkl},\theta /=\frac{1}{2}\theta _{ij}\mathrm{\Gamma }^{ij}`$. First from Eq.(6) we see that the Killing spinors are independent of $`x^{}`$.

We find it useful to recall here the interpretation of different Killing spinor solutions given in malmao . The Killing spinor solutions with nonvanishing $`ϵ_+`$ are related to dynamical supersymmetries in the light cone worldsheet action when it is rearranged to give a nonlinear sigma model. On the other hand for the other half of Killing spinor components $`ϵ_+`$ can be set to zero and we can try to solve the remaining equations of $`ϵ_{}`$ . These Killing spinors are related to the kinematic part of the supersymmetries in the light cone gauge, and in the nonlinear sigma models they are related to the number of free fields. Note that these Killing spinors in general depend on $`x^+`$, and the $`x^+`$ dependence of $`ϵ_+`$-nonvanishing Killing spinors can be ignored by exploiting that we are free to superpose two different types of Killing spinor solutions. Since our aim here is to show that RR three-forms give potentials involving Killing vector terms to the string worldsheet action, and in flat spaces the isometries are trivial, we concern ourselves particularly with nontrivial target geometry. We thus look for Killing spinors with nonzero $`ϵ_+`$ only.

### II.1 Solutions with four supercharges

In order to have two linearly independent complex spinors with nonvanishing $`ϵ_+`$, we see first from Eq.(8) that the transverse eight-dimensional space should most generally be a Calabi-Yau four-fold. It is thus useful to consider how $`\xi ,\theta `$, originally in $`\mathrm{𝟑𝟓},\mathrm{𝟐𝟖}`$ of SO(8) are decomposed into SU(4).

$`\mathrm{𝟑𝟓}`$ $``$ $`\mathrm{𝟏𝟓}+\mathrm{𝟏𝟎}+\overline{\mathrm{𝟏𝟎}},`$ (11)
$`\mathrm{𝟐𝟖}`$ $``$ $`\mathrm{𝟏𝟓}+\mathrm{𝟔}+\overline{\mathrm{𝟔}}+\mathrm{𝟏}.`$ (12)
When we choose the basis where the Killing spinors satisfy

$$\mathrm{\Gamma }_{12}ϵ_+=\mathrm{\Gamma }_{34}ϵ_+=\mathrm{\Gamma }_{56}ϵ_+=\mathrm{\Gamma }_{78}ϵ_+,$$
(13)
it becomes natural to choose the Fock space notations with $`\gamma _\mu =\mathrm{\Gamma }_{2\mu 1}+i\mathrm{\Gamma }_{2\mu },\mu =1,2,3,4`$ and states $`|0,|\stackrel{~}{0}`$ satisfying $`\gamma ^\mu |0=\gamma ^{\overline{\mu }}|\stackrel{~}{0}=0`$.

Now $`ϵ_+`$ can be written as

$$ϵ_+=\alpha |0+\zeta |\stackrel{~}{0},$$
(14)
where $`\alpha ,\zeta `$ are complex constants, and we used the fact that in Calabi-Yau spaces a gauge choice for the spin connections can be made such that the Killing spinors are constants. Using this basis, it is easy to see from Eq.(5) that only $`\mathrm{𝟏𝟓}`$, a traceless $`(1,1)`$-form, can be nonzero since they annihilate the Killing spinor $`ϵ_+`$ in Eq.(14) for arbitrary $`\alpha ,\zeta `$. When $`\mathrm{𝟔}`$ and $`\overline{\mathrm{𝟔}}`$, holomorphic and anti-holomorphic two-forms of SU(4) respectively, are dual to each other with respect to the holomorphic four-form $`ϵ_{\mu \nu \lambda \rho }`$, Eq.(14) can be satisfied with a relation between $`\alpha ,\zeta `$, making the number of worldsheet supercharges reduced to two, i.e. $`𝒩=(1,1)`$. Together with $`\mathrm{𝟏𝟓}`$, there are 21 components of $`\theta `$ which now satisfy Eq.(14) and it is better described as $`\mathrm{𝟐𝟏}`$ of Spin(7) in SO(8). This will be studied in more detail in the next subsection and here we consider the solutions with arbitrary $`\alpha ,\zeta `$.

Using the fact that $`ϵ_+,ϵ_{}`$ have opposite SO(8) chiralities we can write

$`ϵ_{}`$ $`=`$ $`\mathrm{\Gamma }_{}(\beta _{\overline{\mu }}\gamma ^{\overline{\mu }}|0+\delta _\mu \gamma ^\mu |\stackrel{~}{0}).`$ (15)
Now it is straightforward to find equations for $`\alpha ,\zeta ,\beta _{\overline{\mu }},\delta _\mu `$ from the Killing spinor equations. Following malmao  we introduce a holomorphic tensor $`\xi _{\mu \nu }\frac{1}{3!}\xi _{\mu \overline{\lambda \rho \sigma }}ϵ^{\overline{\lambda \rho \sigma \nu }}g_{\overline{\nu }\nu }`$ and a hermitian tensor, $`\xi _{\mu \overline{\nu }}\frac{1}{2}g^{\lambda \overline{\lambda }}\xi _{\mu \overline{\nu }\lambda \overline{\lambda }}`$.

From Eq.(9), we have

$`2i(\beta _{\overline{\mu }}\xi _{\overline{\nu }}^{\overline{\mu }}+\delta _\mu \xi _{\overline{\nu }}^\mu ){\displaystyle \frac{i}{2}}\theta _{\overline{\nu }}^{\overline{\mu }}\delta _{\overline{\mu }}`$ $`=`$ $`{\displaystyle \frac{\alpha }{4}}_{\overline{\nu }}H,`$ (16)
$`2i(+\beta _{\overline{\mu }}\xi _\nu ^{\overline{\mu }}\delta _\mu \xi _\nu ^\mu )+{\displaystyle \frac{i}{2}}\theta _\nu ^\mu \beta _\mu `$ $`=`$ $`{\displaystyle \frac{\zeta }{4}}_\nu H,`$ (17)
with $`\beta _\mu \beta _{\overline{\mu }}^{},\delta _{\overline{\mu }}\delta _\mu ^{}`$. Eq.(10) gives

$`_{\overline{\mu }}\beta _{\overline{\nu }}i\zeta \xi _{\overline{\mu }\overline{\nu }}`$ $`=`$ $`0,`$ (18)
$`_\mu \delta _\nu i\alpha \xi _{\mu \nu }`$ $`=`$ $`0,`$ (19)
$`_\mu \beta _{\overline{\nu }}+i\alpha \xi _{\mu \overline{\nu }}+{\displaystyle \frac{i}{4}}\zeta ^{}\theta _{\mu \overline{\nu }}`$ $`=`$ $`0,`$ (20)
$`_{\overline{\mu }}\delta _\nu +i\zeta \xi _{\overline{\mu }\nu }{\displaystyle \frac{i}{4}}\alpha ^{}\theta _{\mu \overline{\nu }}`$ $`=`$ $`0.`$ (21)
Of course apart from the terms involving $`\theta `$’s the above equations are the same as the ones found in malmao , and we can proceed in the same spirit to find the solutions for $`\beta _{\overline{\mu }},\delta _\mu `$ in terms of arbitrary $`\alpha ,\zeta `$ and identify the requirements on $`\xi ,\theta `$ from consistency.

By exploiting the properties like closure and anti-self-duality of $`\xi ,\theta `$ and considering the integrability conditions we find we can write

$`\xi _{\mu \nu }`$ $`=`$ $`2_\mu _\nu W,`$ (22)
$`\xi _{\mu \overline{\nu }}`$ $`=`$ $`2_\mu _{\overline{\nu }}G_1,`$ (23)
$`\theta _{\mu \overline{\nu }}`$ $`=`$ $`8_\mu _{\overline{\nu }}G_2,`$ (24)
with the coefficients chosen for later convenience. $`W`$ is a holomorphic function and $`G_1,G_2`$ are real harmonic functions which serve as the potentials for holomorphic Killing vectors $`V_\mu ^1=i_\mu G_1`$ and $`V_\mu ^2=i_\mu G_2`$. The fact that $`G_1,G_2`$ are harmonic is obvious from the group theory consideration that they are $`\mathrm{𝟏𝟓}`$, i.e. $`(1,1)`$-form which is traceless.

The solution for $`ϵ_{}`$ is given by

$`\beta _{\overline{\mu }}`$ $`=`$ $`2i(\alpha _{\overline{\mu }}G_1+\zeta _{\overline{\mu }}\overline{W}+\zeta ^{}_{\overline{\mu }}G_2),`$ (25)
$`\delta _\mu `$ $`=`$ $`2i(\zeta _\mu G_1+\alpha _\mu W+\alpha ^{}_\mu G_2).`$ (26)
When they are substituted into Eqs.(16) and (17) we find from consistency

$`_\nu G_2^\nu _\mu G_1_\nu G_1^\nu _\mu G_2`$ $`=`$ $`0,`$
$`_\nu (^\nu G_1_\mu W)`$ $`=`$ $`0,`$
$`_\nu (^\nu G_2_\mu W)`$ $`=`$ $`0,`$
and the complex conjugates. It is obvious what they mean. As promised, the spacetime supersymmetry requires that the two Killing vectors should commute with each other and the Lie derivative of the holomorphic superpotential along the Killing vectors should vanish. This precisely matches the field theory supersymmetry conditions in alvarez .

Finally the metric is given in terms of

$$H=32g^{\mu \overline{\nu }}(_\mu G_1_{\overline{\nu }}G_1+_\mu G_2_{\overline{\nu }}G_2+_\mu W_{\overline{\nu }}\overline{W}).$$

### II.2 Solutions with two supercharges

The existence of one Killing spinor solution to $`_iϵ_+=0`$ implies that the transverse eight-dimensional space has a reduced holonomy Spin(7) in general. The Killing spinor which is left invariant under Spin(7) subgroup of SO(8) will be denoted as $`\eta `$ and is chosen to be real. As it is well-known Spin(7) holonomy is characterised by the Cayley four-form $`\mathrm{\Psi }`$ which can be constructed from the Killing spinor

$$\mathrm{\Psi }_{ijkl}=\eta ^T\mathrm{\Gamma }_{ijkl}\eta ,$$
(27)
which is covariantly constant by construction and self-dual in SO(8) when we take the convention that $`\xi `$ is anti-self-dual. We assume that $`\eta `$ is normalised appropriately and $`\mathrm{\Psi }`$ can take values $`0,\pm 1`$. In the standard basis the non-zero components of $`\mathrm{\Psi }`$ are given as

$`1`$ $`=`$ $`\mathrm{\Psi }_{1234}=\mathrm{\Psi }_{5678}=\mathrm{\Psi }_{3478}=\mathrm{\Psi }_{2468}=\mathrm{\Psi }_{2367}`$
$`=`$ $`\mathrm{\Psi }_{1368}=\mathrm{\Psi }_{1256}=\mathrm{\Psi }_{1357}=\mathrm{\Psi }_{1458}=\mathrm{\Psi }_{2457}`$
$`=`$ $`\mathrm{\Psi }_{1287}=\mathrm{\Psi }_{1476}=\mathrm{\Psi }_{3465}=\mathrm{\Psi }_{2385}.`$
The basic identity involving $`\mathrm{\Psi }`$ is

$$\mathrm{\Psi }_{ijkp}\mathrm{\Psi }^{lmnp}=\frac{1}{6}\delta _{[i}^{[l}\delta _j^m\delta _{k]}^{n]}\frac{1}{4}\mathrm{\Psi }_{[ij}^{[lm}\delta _{k]}^{n]},$$
(28)
which will prove useful in verifying the statements in the following discussions.

Now in order to solve the Killing spinor equations involving $`\xi ,\theta `$, we first recall that

$`\mathrm{𝟑𝟓}_{asd}`$ $``$ $`\mathrm{𝟑𝟓},`$ (29)
$`\mathrm{𝟐𝟖}`$ $``$ $`\mathrm{𝟐𝟏}+\mathrm{𝟕}.`$ (30)
It turns out that $`\mathrm{𝟑𝟓}`$ of Spin(7) can be alternatively described as a traceless symmetric rank-two tensor when we make use of $`\mathrm{\Psi }`$. It is straightforward to show that

$$(\mathrm{\Psi }\xi )_{ij}\mathrm{\Psi }_{iklm}\xi _j^{klm}$$
(31)
is symmetric and traceless.

The decomposition of the adjoint representation Eq.(30) and its implication on the solution of Eq.(5) is rather famous. Projection operators for two-forms in eight dimensions can be explicitly constructed using $`\mathrm{\Psi }`$, so that

$$\theta _{ij}^\pm =\lambda _\pm \mathrm{\Psi }_{ij}^{kl}\theta _{kl}^\pm ,$$
(32)
where $`\theta ^+`$ is $`\mathrm{𝟐𝟏}`$ with $`\lambda ^+=\frac{1}{2}`$, while $`\theta ^{}`$ is $`\mathrm{𝟕}`$ with $`\lambda ^{}=\frac{1}{6}`$. This was first considered in corrigan  as a generalization of the four-dimensional self-dual gauge fields, and extended to nontrivial special holonomy manifolds in acharya . It is customary to call 21 self-dual and 7 anti-self-dual. Since $`ϵ_+`$ is proportional to $`\eta `$, the invariance of the dilatino means that we should keep $`\mathrm{𝟐𝟏}`$ while $`\mathrm{𝟕}`$ should be set to zero. This is consistent with what we observed in the previous subsection with transverse Calabi-Yaus. When we demand two complex $`ϵ_+`$ spinors we keep only $`\mathrm{𝟏𝟓}`$ of SU(4), but when $`\mathrm{𝟔}`$ and $`\overline{\mathrm{𝟔}}`$ are nonzero and dual to each other we still have one spinor solution to Eq.(5) $`\eta =|0+|\stackrel{~}{0}`$.

Now we take the following ansatz for Killing spinors,

$`ϵ_+=\alpha \eta ,ϵ_{}=i\mathrm{\Gamma }_{}v_i\mathrm{\Gamma }^i\eta ,`$ (33)
where $`\alpha `$ is a constant and $`v_i`$ is an unknown nonconstant vector to be determined. From Eq.(10) we have

$$_iv_j=\frac{\alpha }{4!}(\mathrm{\Psi }\xi )_{ij}+\frac{1}{8}\theta _{ij}\alpha ^{}.$$
(34)
In deriving this and other equations we have chosen the gauge for spin connections which makes $`\eta `$ constant, like the discussions about Calabi-Yau four-folds in the last subsection. A proof that it is possible also with exceptional holonomy manifolds can be found for instance in bilal .

Since $`\mathrm{\Psi },\xi `$ are closed, $`(\mathrm{\Psi }\xi )_{ij}`$ is curl-free. Therefore we can write locally

$$\frac{1}{4!}(\mathrm{\Psi }\xi )_{ij}=_i_jU,$$
(35)
where $`U`$ is a real harmonic function since $`(\mathrm{\Psi }\xi )_{ij}`$ is traceless, and $`U`$ becomes the real superpotential of $`𝒩=(1,1)`$ nonlinear sigma models in the light cone lagrangian. Then Eq.(34) implies that the gauge potential for $`\theta `$ can be chosen to be a Killing vector, i.e.

$$\frac{1}{8}\theta _{ij}=D_iG_j,D_{(i}G_{j)}=0.$$
(36)
When we substitute

$$v_i=\alpha _iU+\alpha ^{}G_i,$$
(37)
into Eq.(9) we get a consistency condition on the Killing vector $`G`$,

$$D_i(G^j_jU)=0\mathrm{or}_GU=\mathrm{const}$$
(38)
which matches with the condition for potential terms of $`𝒩=(1,1)`$ supersymmetric nonlinear sigma models. When we integrate what remains we obtain

$$H=4(G_iG^i+_iU^iU),$$
(39)
which serves as the scalar potential of the light cone worldsheet lagrangian.

Before we finish let us point out that an alternative interpretation can be given to the requirement that the Killing vector should be in the adjoint representation $`\mathrm{𝟐𝟏}`$ of Spin(7). We note that for any Killing vector $`K`$,

$`_K\mathrm{\Psi }`$ $``$ $`(di_K+i_Kd)\mathrm{\Psi }`$
$`=`$ $`_jK^n\mathrm{\Psi }_{nklm}dx^jdx^kdx^ldx^m`$
$`=`$ $`(_jK^n)^{}\mathrm{\Psi }_{nklm}dx^jdx^kdx^ldx^m.`$
In order to get the third line Eq.(28) and Eq.(32) are used. We thus see that the Killing vector $`G`$’s being $`\mathrm{𝟐𝟏}`$ means it preserves the Spin(7) structure, in the sense that the Lie derivative of $`\mathrm{\Psi }`$ vanishes along $`G`$.

## III Discussions

In this paper we have presented a general class of IIB pp-wave solutions with Ramond-Ramond backgrounds. In the light cone gauge the bosonic string action can be simply read off from the metric and it is obvious we have nonlinear sigma models with eight dimensional special holonomy manifold target spaces followed by potential terms given by $`H`$. Then the worldsheet supersymmetries inherited by the Killing spinors found above dictates how the terms with fermions should be written. In particular the non-vanishing RR fields give fermionic mass terms or Yukawa couplings more generally.

The potential terms of supersymmetric nonlinear sigma models are studied in alvarez . The analysis does not make use of the superfield formalism; it started with the most general lagrangian and supersymmetry transformation rules allowed by Lorentz invariance and found the consistency conditions. The potential is given in terms of one holomorphic superpotential and two commuting holomorphic Killing vectors for $`𝒩=(2,2)`$ models and one real superpotential and one Killing vector for $`𝒩=(1,1)`$ solutions. The Lie derivatives of the superpotentials along the Killing vectors are required to be constants. The supergravity analysis presented in malmao  and here is found to be consistent with the field theory results, but in general the spacetime supersymmetry is more restrictive. It is particularly distinctive with $`𝒩=(1,1)`$ solutions; the superpotential is a harmonic function and the Killing vector should be self-dual with respect to Spin(7). For $`𝒩=(2,2)`$ solutions the Killing potentials are required to be harmonic.

Perhaps it is useful to consider an example of the pp-wave with nonzero three-form. In flat transverse space mass terms can be given to the worldsheet fields by a holomorphic Killing vector, for instance one can consider a pure RR three-form background such as

$`F_{+12}^{(3)}=F_{+34}^{(3)}=F_{+56}^{(3)}=F_{+78}^{(3)}=m.`$ (40)
This solution is already considered in bena  where generic supersymmetric plane-wave solutions with nonvanishing RR fields are studied. This solution in fact preserves 28 spacetime supersymmetries. What is special with this solution is that the worldsheet fields all have the same mass. With bosons it is obvious from the metric and the worldsheet supersymmetry guarantees that fermion masses are the same. In other words, the light cone string spectrum of this background is the same as that of the maximally supersymmetric solution with nontrivial five-form metsaev . This of course is a natural consequence of our claim that for $`𝒩=(2,2)`$ solutions the same Killing vector terms on the worldsheet can come from either RR five-forms or three-forms. Our result is also consistent with the observation made in bena  that the plane-wave solutions can be superposed. In this paper we have extended it to nontrivial target geometries and non-constant form fields, i.e. general pp-waves. Although we expect the degeneracy will be lifted once string interactions are taken into account, it will be interesting if we can find a field theory dual of this solution using the Penrose limit as in bmn ; bfp . It is not immediately obvious how or whether the solution Eq.(40) can be obtained from an AdS solution as the Penrose limit bena . It might be also worth mentioning that our results can be used to regularize the orbifolds of solutions found in bena  by replacing the orbifolded part of the target spaces with, e.g., Eguchi-Hanson space.

In russo  pp-wave solutions with nonvanishing NS and RR three-forms are considered and the authors concluded that three-forms cannot induce worldsheet interactions without breaking supersymmetry. Our result does not contradict theirs, since in flat target spaces the Killing vectors can give mass terms at most. It is essentially the target space curvature and the superpotential which make the worldsheet action interacting, but the message of our analysis is that the RR three-forms can be succinctly incorporated into interacting models.

Finally we reckon it is an important enterprise to study the field theoretical properties of the massive nonlinear sigma models found in this paper. They are special in the sense that although manifestly non-conformal they can be embedded into exact superconformal theories. By working out the quantum corrections one might be able to identify the hidden conformal covariance of these massive two dimensional field theories. It should also help rectifying the definition of supersymmetric D-branes in the class of nonlinear sigma models considered in this paper.

###### Acknowledgements.

We wish to thank S. Fredenhagen, V. Schomerus, and S. Theisen for helpful discussions at various stages of this work, B. Acharya for correspondences, and especially P. Kaste for drawing our attention to bilal . The conversation with P. Kaste took place during the 35th International Symposium Ahrenshoop held at Berlin, 26-30 August 2002. We thank the organisers for hospitality. This work was supported by the DFG - German Science Foundation.