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# Regular cosmological bouncing solutions in low energy effective action from string theories.

## I Introduction

Superstring is the most promising candidate to describe a unified theory of all interactions, gravity included. There are five consistent superstring theories in 10 dimensions, which are connected among themselves through duality transformations. To each superstring theory, there is a corresponding supergravity theory in 10 dimensions. All of them can be obtained from the 11 dimensional supergravity theory. This indicates that those superstring theories are different manifestations of a unique 11 dimensional framework, that has been named $`M`$ theory . Moreover, the superstring type-IIB can be recast in a more geometrical form in a 12 dimensional model, suggesting that perhaps a yet more fundamental framework may exist in 12 dimensions, which has been called $`F`$ theory .

The physical properties of superstring theories become relevant at energy scales comparable with the Planck scale. This renders very improbable that superstring phenomenology may be tested in the near future in some laboratory experiment (see, however, Ref.  in which the Planck mass is lowered to TeV scale by accounting for large extra dimensions). According to the hot big bang scenario, however, energy scales even as high as the usual Planck scale ($`M_{_{\mathrm{Pl}}}10^{19}`$GeV) may have been reached in the very early universe. Hence, for the moment, cosmology seems to be the most natural arena where the consequences of superstring theories may be tested. The pre-big bang paradigm  was one of the first ideas to implement superstring theories in this framework. Some relics of a cosmological string phase may also be identified , opening perhaps the possibility of testing superstring models. Furthermore, superstring theories open the possibility that some typical drawbacks of the standard cosmological model, such as the existence of an initial singularity, may be solved in the context of superstring cosmological models. The goal of the present paper is to show that, under certain conditions, it is possible to obtain completely regular bouncing cosmological models in the context of effective actions constructed from superstring theories (not involving, in particular, negative energies ), for which, moreover, the dilaton is strictly positive (nonvanishing) at all times and never diverges.

String cosmology is based on the low energy limit of string or superstring theories. In the most general case of the supersymmetric string theory, there are two sectors, related with the choice of periodic or antiperiodic boundary conditions on the spinor fields, namely the Ramond and Neveu-Schwarz (NS) sectors . Since fermions can be either left or right moving, this leads to four possible combinations of these sectors. The bosonic fields arise both from the NS-NS and Ramond-Ramond (RR) sectors. The NS-NS sector provides the Einstein-Hilbert term, as well as a three-form, called the axionic field, and the dilaton. The latter is directly related with the string perturbative expansion parameter and takes the form of a Brans-Dicke-like scalar field, nonminimally coupled to both the Einstein-Hilbert and the axionic fields. In the RR sector, $`p`$ forms appear, which are minimally coupled to the dilaton field. The dimensions of the $`p`$ forms depend on the specific superstring theory which is under consideration. In cosmological applications, we are interested in scalar fields that emerge from these different $`p`$ forms. They differ by the way they couple with the dilatonic field and between themselves.

Out of the many different possibilities stemming from string theory, one can construct in general an effective action suitable for cosmological applications with two main features: scalar fields coming from the NS-NS sector and nonminimally coupled to the dilaton, and scalar fields from the RR sector which are minimally coupled to the dilaton. All the possibilities are not exhausted by these two frameworks, but they summarize the general aspects of what has been proposed in the literature as far as effective actions coming from string theory are concerned. One can also obtain phenomenological matter fields by averaging on some components of those original $`p`$ forms.

This brief description explicits the great richness of the string effective action procedure, which implies a large variety of possible cosmological models. Notice that these effective actions exhibit great similarities with those that can be obtained from multidimensional and supergravity theories. To select one cosmological model that could be a candidate to describe the physical world, two possible prescriptions are: either the cosmological model is completely regular, with no curvature or expansion parameter singularity, or it is compatible with observation; ultimately, both criteria should be satisfied. In the present work we will concentrate on the first. The second criterion, which presents some specific challenges, will be treated in the future .

The search for singularity free cosmology in string theories is not a new subject . The string action at tree level does not lead in general to singularity free cosmological solutions, at least when the strict string case ($`\omega =1`$, $`\omega `$ being the dilatonic coupling parameter) is considered. The pre-big bang model , which is an example of a string cosmology, requires the introduction of nonlinear curvature terms in order to achieve a smooth transition from a curvature growing phase to a curvature decreasing phase. If large negative values of the dilatonic coupling parameter $`\omega `$ are allowed, it is possible, in some cases, to obtain completely regular models, including in the dilatonic sector . This may be achieved mainly in models with spatial sections with negative curvature.

Here, it will be shown that regular cosmological models may also be obtained if a radiation fluid is coupled to the string action at the tree level. Such a radiation fluid can have a fundamental motivation, for example, in the case of the superstring type IIB theory, where a 5-form appears in the RR sector. Truncation and dimensional reduction of this 5-form lead to a Maxwell term in four dimensions with the desired features . Hence, the model to be studied here is totally based on superstring theories. The string motivated phenomenological term included under the form of a radiation fluid makes it possible to connect smoothly such string cosmological models to the radiation phase of the standard cosmological model before nucleosynthesis.

In Ref. , models motivated by string theory similarly including a radiation fluid have been studied, restricted to flat spatial sections and $`\omega >3/2`$. In such cases, bouncing solutions have been obtained only for $`\omega <4/3`$. Furthermore, for these solutions, the dilaton vanishes in the infinite past, raising doubts on the validity of the tree level action in such a region. In the present paper, the curvature of the spatial sections and the value of $`\omega `$ are kept arbitrary. New bouncing regular solutions are then obtained, for which, as mentioned above, the dilaton remains finite and nonvanishing at all times. When $`\omega >3/2`$, which includes the strict string case ($`\omega =1`$), the solutions can only be bouncing provided the spatial sections have negative curvature and if the dilaton is always negative, which is not consistent with the higher dimensional framework of stringlike theories, and implies a repulsive gravity. We shall henceforth disregard such solutions. When $`\omega <3/2`$, the bouncing solutions are obtained for models with flat or negative curvature, and the dilaton is strictly positive at all times.

In the following section, we derive effective string motivated actions in four dimensions. In particular, we show how to obtain an effective string action in four dimensions with $`\omega <3/2`$ in the context of the so-called $`F`$ theory in twelve dimensions. In Sec. III we derive nonsingular cosmological solutions from these effective theories, which are thoroughly discussed in Sec. IV from the point of view of violation of energy conditions. We end up with the conclusions in Sec. V.

## II The effective action

Our analysis is based on the following effective action at tree level:

$`L=\sqrt{\stackrel{~}{g}}\mathrm{e}^{\stackrel{~}{\sigma }}\left(\stackrel{~}{R}\omega \stackrel{~}{\sigma }_{;A}\stackrel{~}{\sigma }^{;A}{\displaystyle \frac{1}{12}}H_{ABC}H^{ABC}\right)`$
$`\sqrt{\stackrel{~}{g}}({\displaystyle \frac{1}{2}}\xi _{;A}\xi ^{;A}+{\displaystyle \frac{1}{240}}F_{ABCDE}F^{ABCDE})`$ (1)
where $`\stackrel{~}{\sigma }`$ is the dilatonic field, $`H_{ABC}`$ is the axionic field, and $`\omega `$ is the dilatonic coupling constant. The two last terms come from the RR sector of superstring type IIB. The tildes indicate that all quantities are considered in a $`D`$-dimensional spacetime, $`D=10`$ in the pure superstring context.

The dilatonic coupling constant is $`\omega =1`$ for usual superstring theory. However, this may not necessarily be the case for some ten dimensional theories stemming from a more fundamental one in higher dimensions. In some specific situations, the value of $`\omega `$ can be found to be even less than $`3/2`$. As an example, the superstring type IIB action may be reformulated in 12 dimensions, in the context of the so-called $`F`$ theory. A low energy limit of the $`F`$ theory has been studied by , where an action in 12 dimensions has been established, which was shown to lead to the low energy limit of the superstring type IIB in 10 dimensions through truncation and dimensional reduction. Let us consider this twelve dimensional action, given by

$`L_{12}=\sqrt{\stackrel{~}{g}}(\stackrel{~}{R}{\displaystyle \frac{1}{2}}\mathrm{\Psi }_{;A}\mathrm{\Psi }^{;A}{\displaystyle \frac{1}{48}}\mathrm{e}^{a\mathrm{\Psi }}F_{ABCD}F^{ABCD}`$
$`{\displaystyle \frac{1}{240}}\mathrm{e}^{b\mathrm{\Psi }}G_{ABCDE}G^{ABCDE}+\lambda B_4\mathrm{d}A_3\mathrm{d}A_3),`$ (2)
with $`a^2=1/5`$ and $`b^2=4/5`$, $`\lambda `$ being a coupling parameter for the Chern-Simons type term involving the potentials of the five and four-forms. Writing the metric as

$$\mathrm{d}s_{12}^2=g_{\mu \nu }\mathrm{d}x^\mu \mathrm{d}x^\nu \mathrm{e}^{2\beta }\mathrm{d}x_i\mathrm{d}x^i,$$
(3)
with Greek indices $`\mu ,\nu `$ running from 0 to 9 and Latin indices $`i[10,11]`$, and setting the five-form equal to zero, we obtain the following Lagrangian

$`L_{10}`$ $`=`$ $`\sqrt{g}\mathrm{e}^{2\beta }(R+2\beta _{;\rho }\beta ^{;\rho }{\displaystyle \frac{1}{2}}\mathrm{\Psi }_{;\rho }\mathrm{\Psi }^{;\rho }`$ (4)
$``$ $`{\displaystyle \frac{1}{12}}\mathrm{e}^{a\mathrm{\Psi }2\beta }F_{\mu \nu \lambda }F^{\mu \nu \lambda }{\displaystyle \frac{1}{8}}\mathrm{e}^{a\mathrm{\Psi }4\beta }F_{\mu \nu }F^{\mu \nu }),`$
where we have retained just the two and three-forms coming from the four-form in the original action. The term originating the three-form was made purely imaginary in 12 dimensions. Choosing $`\mathrm{\Psi }=2\beta /a`$, and defining $`\varphi =\mathrm{e}^{2\beta }`$, one ends up with the following action in 10 dimensions:

$$L_{10}=\sqrt{g}[\varphi (R+3\frac{\varphi _{;\rho }\varphi ^{;\rho }}{\varphi ^2}\frac{1}{12}F_{\mu \nu \lambda }F^{\mu \nu \lambda })\frac{1}{8}F_{\mu \nu }F^{\mu \nu }].$$
(5)
One can see that, in this case, we obtain an action with $`\omega =3`$ together with a Maxwell term (which generates the radiation fluid). This is a remarkable example of how an effective string action with $`\omega 1`$ (in this case, $`\omega =3<3/2`$) can be realized. That is why we will maintain the value of $`\omega `$ in Eq. (1) arbitrary in what follows, unless otherwise specified.

The $`D`$-dimensional metric is written as

$$\mathrm{d}s^2=g_{\mu \nu }\mathrm{d}x^\mu \mathrm{d}x^\nu \mathrm{e}^{2\beta }\delta _{ij}\mathrm{d}x^i\mathrm{d}x^j,$$
(6)
where $`g_{\mu \nu }`$ is the four dimensional metric, $`\mathrm{e}^\beta `$ is the scale factor of the $`d=D4`$ dimensional internal space which we suppose to be homogeneous and flat. For now on, we will consider a static internal space. This is not obligatory in some of the cases to be analyzed latter, but such a restriction considerably simplifies the unified presentation of many different cases allowed by the action given by Eq. (1).

Dimensional reduction and isotropization of the Maxwellian term \[which may come from the RR sector, or as described in the passage from Eq. (2) to Eq. (5)\], lead to the following effective action in four dimensions:

$$L=\sqrt{g}\left[\varphi \left(R\omega \frac{\varphi _{;\rho }\varphi ^{;\rho }}{\varphi ^2}\frac{\mathrm{\Psi }_{;\rho }\mathrm{\Psi }^{;\rho }}{\varphi ^2}\right)\frac{1}{2}\xi _{;\rho }\xi ^{;\rho }\right]+L_\mathrm{r},$$
(7)
where from now on Greek indices run from 0 to 3. In this action, $`\varphi =\mathrm{e}^{\stackrel{~}{\sigma }}`$ is the dilaton, the field $`\mathrm{\Psi }`$ comes from the axionic term, and is thus called the axion, while $`L_\mathrm{r}`$ represents an ordinary radiation fluid term, which can be obtained from the five-form existing in the RR sector, as was stressed above. We shall also call $`\xi `$ the RR-scalar as it originates from the same sector.

The Lagrangian described by Eq. (7) may cover theories others than pure string theory. For instance, one can consider a more general coupling between the dilatonic and axionic fields, i.e. of the type $`\varphi ^n\mathrm{\Psi }_{;\rho }\mathrm{\Psi }^{;\rho }`$, with $`n`$ a new parameter. This less restrictive coupling contains the string case if one sets $`n=1`$, but general multidimensional theories and supergravity theories in higher dimensions are examples where the parameter $`n`$ may take different values. As was discussed in Refs. , the final results depend very weakly on the parameter $`n`$ and one may thus expect that this generalized effective action will give results that are essentially similar to those obtained in the pure string case. Hence, the results presented below are of a quite general nature, and should not be understood as statements restricted to string cosmology only, even though they were derived in this specific framework.

From Eq. (7), we obtain the field equations

$`R_{\mu \nu }{\displaystyle \frac{1}{2}}g_{\mu \nu }R`$ $`=`$ $`{\displaystyle \frac{8\pi }{\varphi }}T_{\mu \nu }+{\displaystyle \frac{\omega }{\varphi ^2}}(\varphi _{;\mu }\varphi _{;\nu }{\displaystyle \frac{1}{2}}g_{\mu \nu }\varphi _{;\rho }\varphi ^{;\rho })`$ (8)
$`+{\displaystyle \frac{1}{\varphi }}(\varphi _{;\mu \nu }g_{\mu \nu }\mathrm{}\varphi )`$
$`+{\displaystyle \frac{1}{\varphi ^2}}(\mathrm{\Psi }_{;\mu }\mathrm{\Psi }_{;\nu }{\displaystyle \frac{1}{2}}g_{\mu \nu }\mathrm{\Psi }_{;\rho }\mathrm{\Psi }^{;\rho })`$
$`+{\displaystyle \frac{1}{\varphi }}(\xi _{;\mu }\xi _{;\nu }{\displaystyle \frac{1}{2}}g_{\mu \nu }\xi _{;\rho }\xi ^{;\rho }),`$
for the Einstein part,

$$\mathrm{}\varphi +\frac{2}{3+2\omega }\varphi ^1\mathrm{\Psi }_{;\rho }\mathrm{\Psi }^{;\rho }+\frac{1}{3+2\omega }\xi _{;\rho }\xi ^{;\rho }=\frac{8\pi T}{3+2\omega },$$
(9)
with $`TT_\mu ^\mu `$ the trace of the stress-energy tensor, for the dilaton $`\varphi `$, while we get

$$\mathrm{}\mathrm{\Psi }\mathrm{\Psi }_{;\rho }\frac{\varphi ^{;\rho }}{\varphi }=0,$$
(10)
to describe the dynamics of the axion $`\mathrm{\Psi }`$, and finally

$`\mathrm{}\xi `$ $`=`$ $`0,`$ (11)
$`T_{}^{\mu \nu }{}_{;\mu }{}^{}`$ $`=`$ $`0,`$ (12)
for the RR-scalar $`\xi `$ and the radiation fluid respectively. These equations we now implement in a cosmological context.

## III Cosmological solutions

Introducing the Friedman-Robertson-Walker metric

$$\mathrm{d}s^2=\mathrm{d}t^2a^2(t)\left[\frac{\mathrm{d}r^2}{1kr^2}+r^2\left(\mathrm{d}\theta ^2+\mathrm{sin}^2\theta \mathrm{d}\varphi ^2\right)\right],$$
(13)
$`k`$ being the normalized curvature of the maximally symmetric spatial sections ($`k=0,\pm 1`$), and assuming the fields now depend only on time, the field equations derived above reduce to the following equations of motion:

$$3(\frac{\dot{a}}{a})^2+3\frac{k}{a^2}=8\pi \frac{\rho }{\varphi }+\frac{\omega }{2}(\frac{\dot{\varphi }}{\varphi })^23\frac{\dot{a}}{a}\frac{\dot{\varphi }}{\varphi }+\frac{\dot{\mathrm{\Psi }}^2}{2\varphi ^2}+\frac{\dot{\xi }^2}{2\varphi },$$
(14)
which is the generalization of the Friedman equation, and

$`\ddot{\varphi }+3{\displaystyle \frac{\dot{a}}{a}}\dot{\varphi }+{\displaystyle \frac{2}{(3+2\omega )}}{\displaystyle \frac{\dot{\mathrm{\Psi }}^2}{\varphi }}+{\displaystyle \frac{\dot{\xi }^2}{(3+2\omega )}}`$ $`=`$ $`{\displaystyle \frac{8\pi (\rho 3p)}{(3+2\omega )}},`$
$`\ddot{\mathrm{\Psi }}+3{\displaystyle \frac{\dot{a}}{a}}\dot{\mathrm{\Psi }}\dot{\mathrm{\Psi }}{\displaystyle \frac{\dot{\varphi }}{\varphi }}`$ $`=`$ $`0,`$ (16)
$`\ddot{\xi }+3{\displaystyle \frac{\dot{a}}{a}}\dot{\xi }`$ $`=`$ $`0,`$ (17)
$`\dot{\rho }+3{\displaystyle \frac{\dot{a}}{a}}(\rho +p)`$ $`=`$ $`0.`$ (18)
In these expressions, $`\rho `$ is the energy density and $`p`$ is the pressure of some perfect fluid which obeys, for the sake of generality, a barotropic equation of state, $`p=\lambda \rho `$, with $`\lambda `$ an arbitrary constant. In what follows, we will specialize this fluid to the case we are interested in, namely, radiation, for which $`\lambda =\lambda _\mathrm{r}=1/3`$. A dot stands for a derivative with respect to the cosmic time $`t`$.

Equations (16), (17) and (18) admit the first integrals

$$\dot{\mathrm{\Psi }}=\frac{A\varphi }{a^3},\dot{\xi }=\frac{B}{a^3},\rho =Da^{3(1+\lambda )},$$
(19)
where $`A`$, $`B`$ and $`D`$ are integration constants. According to the string motivated action discussed above, let us now specialize the equations for the radiation fluid case and accordingly set $`\lambda =1/3`$. For this specific case, Eq. (III) simplifies to

$$\ddot{\varphi }+3\frac{\dot{a}}{a}\dot{\varphi }+\frac{2}{(3+2\omega )}\frac{A^2}{a^6}\varphi +\frac{B^2}{(3+2\omega )a^6}=0,$$
(20)
which can be solved in the following way. It is convenient to define a new timelike coordinate $`\theta `$ given by the relation

$$\mathrm{d}t=a^3\mathrm{d}\theta .$$
(21)
In terms of this new coordinate, Eq. (20) reads

$$\varphi ^{\prime \prime }+\frac{2A^2}{(3+2\omega )}\varphi +\frac{B^2}{(3+2\omega )}=0,$$
(22)
where primes denote differentiations with respect to $`\theta `$. Similarly, Eq. (14), when expressed in terms of $`\theta `$, reads

$$\left(\frac{a^{}}{a^3}\right)^2+k=\frac{M}{a^2\varphi }+\frac{\omega }{6}\frac{\varphi ^2}{a^4\varphi ^2}\frac{a^{}\varphi ^{}}{a^5\varphi }+\frac{1}{6a^4}\left(A^2+\frac{B^2}{\varphi }\right),$$
(23)
in which use has been made of Eq. (19), and we have set $`M=8\pi D/3`$, which is dimensionless in the radiation case.

Equation (23) may be recast in a very convenient form through the redefinition

$$a=\varphi ^{1/2}b,$$
(24)
which implies to change to the so-called Einstein frame. This yields

$$\left(\frac{b^{}}{b}\right)^2+(kb^2M)\frac{b^2}{\varphi ^2}=\frac{1}{6}\left(A^2+\frac{B^2}{\varphi }+\frac{3+2\omega }{2}\frac{\varphi ^2}{\varphi ^2}\right),$$
(25)
whose solution we next investigate. Notice, however, that we want to keep considering the Jordan frame as the physical frame; the conformal transformation above is introduced only for technical reasons. The solutions of Eqs. (22) and (14), with the redefinition made above for the scale factor, depend on the sign of the term $`3+2\omega `$ and on the presence of the RR scalar field. We will consider each case separately. For simplicity, we will call $`3+2\omega >0`$ ($`<0`$) as the normal (anomalous) case, and $`\xi =`$ const ($`\xi `$ const) as the axionic (RR) case.

In the special case for which $`\omega `$ assumes the critical value $`\omega =3/2`$, the dilatonic field is not a physical degree of freedom since it may be eliminated by means of a conformal transformation $`g_{\mu \nu }=\mathrm{e}^\varphi \stackrel{~}{g}_{\mu \nu }`$: it is a mere artifact of a metric redefinition. For $`\omega <3/2`$, the scalar field in the Einstein frame, obtained from the Jordan frame by a conformal transformation, does not preserve energy conditions as it appears with a sign for its kinetic term which is opposite to the usual situation, leading to a negative energy contribution \[see the last term in Eq. (25)\]. Such a negative energy field can provide the necessary compensation with the usually positive energy density contributions in order to allow bouncing solutions in general relativity . For $`\omega >3/2`$, the last term in Eq. (25) appears with the ordinary sign, implying a positive energy contribution.

In what follows, the quantities $`\varphi _0`$ and $`a_0`$ are constants of integration subject to the constraints indicated in each case.

### III.1 Normal axionic case

In this first case for which $`\xi `$ is constant \[i.e. $`B=0`$ in Eq. (19)\] and $`\omega >3/2`$, the solution of Eq. (22) is given by

$$\varphi (\theta )=\varphi _0\mathrm{sin}(\alpha \theta ),$$
(26)
where

$$\alpha =\sqrt{\frac{2A^2}{3+2\omega }}$$
(27)
and we have chosen $`\varphi (0)=0`$.

Plugging this solution into Eq. (25) yields

$$\varphi _0^2\mathrm{sin}^2(\alpha \theta )b^2=(C^2+Mb^2kb^4)b^2,$$
(28)
where

$$C^2=\frac{1}{6}A^2\varphi _0^2.$$
(29)
We are seeking regular bouncing solutions for which the scale factor is bounded from below but can grow arbitrarily large, while $`\varphi `$ is nonvanishing and finite. This means that the function $`b`$ should also grow indefinitely on both sides of the bounce. As can be seen by inspection of Eqs. (26) and (28), a necessary condition for this to happen in a finite interval in $`\theta `$ (to ensure $`\varphi `$ remains finite at all times) is that the curvature be nonpositive. This is to be contrasted with the general relativistic case for which a positive curvature is a pre-requisite to ensure that a bounce is possible , and can be understood by stating that, in the case at hand, a positive curvature implies a finite scale factor at all times.

Under the assumption that both sides are positive definite, one can integrate Eq. (28), written as

$$_{b_0}^b\frac{\mathrm{d}\stackrel{~}{b}}{\stackrel{~}{b}\sqrt{C^2+M\stackrel{~}{b}^2k\stackrel{~}{b}^4}}=\pm _{\theta _0}^\theta \frac{\mathrm{d}\stackrel{~}{\theta }}{\varphi _0\mathrm{sin}(\alpha \stackrel{~}{\theta })},$$
(30)
to provide the solution \[see, e.g., Ref. , Eq. (2.266)\]

$$\frac{g(b)}{g(b_0)}=\frac{f(\theta )}{f(\theta _0)},$$
(31)
where

$$f(\theta )=\left|\mathrm{tan}\left(\frac{\alpha \theta }{2}\right)\right|^p,$$
(32)
and

$$g(b)=\frac{M}{C}+\frac{2}{b^2}\left(C+\sqrt{C^2+Mb^2kb^4}\right),$$
(33)
$`b_0`$ and $`\theta _0`$ being constants of integration that we choose such that $`Cg(b_0)=f(\theta _0)`$ for further convenience, and

$$p=\pm \sqrt{1+\frac{2}{3}\omega }.$$
(34)
Setting $`a_0^2=4C^2/\varphi _0`$, we finally get

$$a(\theta )=\frac{a_0}{\sqrt{\mathrm{sin}\alpha \theta }}\left\{\frac{f(\theta )}{\left[Mf(\theta )\right]^2+4C^2k}\right\}^{1/2},$$
(35)
which is the desired result for the scale factor. Note that because of the trigonometric identity

$$\mathrm{tan}\left[\left(\frac{\alpha \theta +\pi /2}{2}\right)\right]=\left[\mathrm{tan}\left(\frac{\pi /2\alpha \theta }{2}\right)\right]^1,$$
(36)
the solution (35) with $`pp`$ can be straightforwardly deduced from the original one by a mirror symmetry with respect to the point $`\alpha \theta =\pi /2`$. It is thus sufficient to consider $`p>0`$ and we shall in what follows restrict our attention to this case.

These solutions have some interesting features. As we have already discussed, for $`k=1`$, there are no bouncing solutions. On the other hand, for $`k=0`$ or $`k=1`$, it is possible to choose the parameters in such a way that the extremes of the range of validity of the variable $`\theta `$ occur for $`t\pm \mathrm{}`$, where spacetime becomes flat.

The case $`k=0`$ was presented in Ref. ; let us recall it briefly for the sake of completeness. The denominator in Eq. (35) has only two roots if $`k=0`$, and the parameter $`\theta `$ varies from $`\theta _\mathrm{i}=0`$ to $`\theta _\mathrm{f}=2\alpha ^1\mathrm{arctan}(M^{1/p})`$. Bouncing nonsingular solutions are possible only when $`3/2<\omega <4/3`$. This can be seen by considering the limit for which $`\theta \theta _\mathrm{i}=0`$. There, the scale factor is $`a\theta ^{(p1)/2}`$, and, from Eq. (21), $`t\theta ^{(3p1)/3}`$, yielding $`a|t|^{(p1)/(3p1)}`$. As $`a(t)`$ is a power law (disregarding the exceptional cases $`p=1\omega =0`$, and $`p=1/3\omega =4/3`$, also discussed in Ref.), the scalar curvature for $`k=0`$ is proportional to $`t^2`$, which converges (in fact, goes to zero) only if $`t\mathrm{}`$ as $`\theta 0`$. This happens only for $`p<1/3`$, which yields $`3/2<\omega <4/3`$. Note, however, that for $`\theta =0`$ the dilaton $`\varphi `$ vanishes, independently of the value of $`\omega `$, rendering dubious the validity of the tree level action (1) in this region.

When $`k=1`$, the denominator in Eq. (35) has now three roots. One can take the parameter $`\theta `$ varying from $`\theta _\mathrm{i}=0`$ to $`\theta _\mathrm{f}=2\alpha ^1\mathrm{arctan}[(M2C)^{1/p}]`$, supposing $`2C<M`$. In this interval, the same analysis given in the precedent paragraph is valid here: one can have bouncing solutions which present an initial singularity in the curvature and in the string expansion parameter $`g_\mathrm{s}^2=\varphi ^1`$ if $`4/3<\omega <0`$, and other bouncing solutions which do not present curvature singularities initially but still have a singularity in the string expansion parameter if $`3/2<\omega <4/3`$. One can also take the parameter $`\theta `$ to vary from $`\theta _\mathrm{i}=2\alpha ^1\mathrm{arctan}[(M2C)^{1/p}]`$ to $`\theta _\mathrm{f}=2\alpha ^1\mathrm{arctan}[(M+2C)^{1/p}]`$. Provided $`2C<M`$, the dilatonic field given by Eq. (26) is finite and never vanishes, taking constant values in the asymptotic regions.

Let us now consider the limit $`\theta \theta _\mathrm{i}`$ or $`\theta \theta _\mathrm{f}`$. Setting $`\alpha \theta =\alpha \theta _\mathrm{i}+\epsilon `$ or $`\alpha \theta =\alpha \theta _\mathrm{f}\epsilon `$, and expanding the denominator around $`\epsilon =0`$, we get $`a\epsilon ^{1/2}`$, from Eq. (21) $`|t|\epsilon ^{1/2}`$, and finally $`a|t|`$, independently of the value of $`p`$ or $`\omega `$. As we are considering $`k=1`$, this limit corresponds to Milne flat spacetime. The scale factor given by Eq. (35) thus appears to represent, with this choice of range for $`\theta `$, a universe contracting from a Milne spacetime to a minimum size, bouncing to an expansion phase, and ending asymptotically also in a Milne spacetime.

However interesting this solution might be, it is unfortunately physically meaningless since it demands the dilaton to be negative. This can be seen by looking at Eqs. (25) and (35). From Eq. (35) for $`k=1`$, one can obtain the scale factor in the Einstein frame $`b(\theta )=\sqrt{\varphi (\theta )}a(\theta )`$, which is

$$b(\theta )=4C^2\left\{\frac{f(\theta )}{\left[Mf(\theta )\right]^24C^2}\right\}^{1/2}.$$
(37)
In the above range of values of $`\theta `$, there must exist a point at which $`b^{}(\theta )=0`$. However, from Eq. (25) with $`3/2<\omega `$, this could only be possible if $`b(\theta )`$ were purely imaginary. Then, for the string-frame scale factor $`a(\theta )`$ to be real, $`\sqrt{\varphi (\theta )}`$ should also be imaginary, so that $`\varphi (\theta )`$ should be negative in the corresponding range of values. Many of the characteristic features of this solution are however present also in the cosmologically more relevant anomalous situation to which we now turn.

### III.2 Anomalous axionic case

For $`3+2\omega <0`$, the previous solution for Eq. (22) must be replaced by

$$\varphi (\theta )=\varphi _0\mathrm{sinh}(\alpha \theta ),$$
(38)
where now

$$\alpha =\sqrt{\frac{2A^2}{3+2\omega }},$$
(39)
and, as before, we have imposed $`\varphi (0)=0`$.

Again, inserting this solution into Eq. (25) yields

$$\varphi _0^2\mathrm{sinh}^2(\alpha \theta )b^2=(Mb^2C^2kb^4)b^2,$$
(40)
where $`C`$ is as before \[Eq. (29)\]. The same argument concerning the existence of a bouncing solution applies, namely, that such solutions cannot exist for $`k=1`$. Manipulations similar to those of the previous case then lead to

$`f(\theta )`$ $`=`$ $`\mathrm{ln}\left[\left|\mathrm{tanh}\left({\displaystyle \frac{\alpha \theta }{2}}\right)\right|^p\right],`$ (41)
$`g(b)`$ $`=`$ $`\mathrm{arcsin}\left({\displaystyle \frac{Mb^22C^2}{b^2\sqrt{M^24kC^2}}}\right),`$ (42)
where we have assumed $`M^24kC^2>0`$ (recall we are only interested in the cases $`k=0`$ and $`k=1`$). We now choose $`f(\theta _0)=g(b_0)`$, set

$$p=\pm \sqrt{\left(1+\frac{2}{3}\omega \right)},\text{ and }a_0^2=\frac{A^2\varphi _0}{3M},$$
(43)
to obtain the scale factor as

$$a(\theta )=\frac{a_0}{\sqrt{\mathrm{sinh}\alpha \theta }}\left[1\pm \sqrt{14\frac{kC^2}{M^2}}\mathrm{sin}f(\theta )\right]^{1/2}.$$
(44)
Regular bouncing solutions may be obtained for $`k=0`$ or $`k=1`$. Differently from the previous situation, the flat case also does not exhibit any singularity in the string expansion parameter. Furthermore, it is possible to find ranges of values of $`\theta `$ for which the dilaton is strictly positive all along. This is because Eq. (25) with $`\omega <3/2`$ admits $`b^{}(\theta )=0`$ in the Einstein frame with a real scale factor $`b`$. Hence, it is not necessary to have $`\varphi <0`$ in order to have the string frame scale factor $`a`$ real. As the dilaton is finite and strictly positive, there are also no singularities in the string expansion parameter given by $`g_\mathrm{s}^2=\varphi ^1`$, and the tree level approximation can be trusted all along. Consequently, we have obtained a perfectly regular bouncing solution in the string framework, without any singularity, even in the dilatonic field, when the curvature of the spatial section is negative or vanishing.

Investigation of the asymptotic behaviors reveals that, for $`k=0`$, the universe displays a radiation dominated phase in both extremities of the range ($`a1/|\theta |`$, i.e. $`a|t|^{1/2}`$ for $`t\pm \mathrm{}`$), while for $`k=1`$, the curvature dominates in the asymptotic regions, leading to a Milne universe ($`a|\theta |^{1/2}|t|`$). Hence, in the $`k=0`$ case, we have a bounce between two asymptotic radiation dominated standard cosmological models, one contracting and the other expanding, while for $`k=1`$ the bounce connects two Milne asymptotic regions.

Recovering the units and connecting the parameters with the real Universe in order to evaluate the value of $`M`$, we consider $`G_{\mathrm{eff}}=G__\mathrm{N}/\varphi `$, where $`G__\mathrm{N}`$ is the value of the gravitational coupling today, and make the replacements $`\varphi \varphi /G__\mathrm{N}`$, $`\mathrm{\Psi }\mathrm{\Psi }/G__\mathrm{N}`$, $`ta_0t`$, $`a_01/H_0`$ ($`H_0`$ being the present Hubble parameter, which we choose to be our inverse unit of time). Assuming the present amount of radiation ($`\rho _{0\mathrm{r}}=\mathrm{\Omega }_{0\mathrm{r}}\rho _\mathrm{c}10^4\rho _\mathrm{c}10^{33}\mathrm{g}/\mathrm{cm}^3`$, with $`\rho _\mathrm{c}`$ the critical density today), we obtain from Eq. (14), assuming the radiation term to dominate at the time under consideration, that $`M8\pi G__\mathrm{N}\rho _{0\mathrm{r}}H_0^2/3=\mathrm{\Omega }_{0\mathrm{r}}10^4`$.

It is interesting to note that these models can provide a quite effective way of enhancing the gravitational coupling. To illustrate this point with a numerical example, let us choose $`p=1`$ (i.e. the case derived in Sec. II with $`\omega =3`$, our prototypical example), $`k=0`$, $`f(\theta _\mathrm{i})=7\pi /2`$ and $`f(\theta _\mathrm{f})=3\pi /2`$. One then obtains $`\varphi _\mathrm{i}10^3`$ and $`\varphi _\mathrm{f}1`$, where the constant $`\varphi _0`$ is chosen $`\varphi _010^2`$ in order to obtain the effective gravitational “constant” today equal to Newton constant $`G__\mathrm{N}`$. With this choice of parameters, the enhancement of the effective gravitational “constant” in the past was therefore of three orders of magnitude. Note that the dilaton is strictly positive and finite in this range.

### III.3 Normal RR case

Integrating the equations of motion (22) after inclusion of $`\xi `$, i.e., with a nonvanishing $`B`$ and still for $`\omega >3/2`$, simply turns the solution given by Eq. (26) into

$$\varphi (\theta )=\varphi _0\left(\mathrm{sin}\alpha \theta s\right),$$
(45)
where

$$s=\frac{B^2}{2A^2\varphi _0},$$
(46)
provides the particular solution of the inhomogeneous equation, and we have assumed the same initial condition for the homogeneous part. The constant $`\alpha `$ is defined as in the normal axionic case.

After some straightforward calculations, we get that Eq. (30) is modified into

$$_{b_0}^b\frac{\mathrm{d}\stackrel{~}{b}}{\stackrel{~}{b}\sqrt{\pm C^2+M\stackrel{~}{b}^2k\stackrel{~}{b}^4}}=\pm \frac{1}{\varphi _0}_{\theta _0}^\theta \frac{\mathrm{d}\stackrel{~}{\theta }}{\mathrm{sin}(\alpha \stackrel{~}{\theta })s},$$
(47)
where now

$$C^2=\frac{1}{6}A^2\varphi _0^2|1s^2|$$
(48)
takes into account the inhomogeneous part. In Eq. (47), the sign in front of the factor $`C^2`$ in the denominator of the right-hand side integrand is positive or negative depending on whether $`s^2<1`$ or $`s^2>1`$ respectively. We shall treat both cases separately.

#### III.3.1 Small RR-scalar

We assume from now on that even though we allow variations for $`\xi `$, those are limited in such a way that $`s^2<1`$. Equation (47), being in a form similar to Eq. (30), yields the same result that bounces cannot be realized unless $`k0`$.

Integrating both sides of Eq. (47), we obtain the function $`b`$, thanks to which we can write the scale factor as

$$a(\theta )=\frac{a_0}{\sqrt{\mathrm{sin}\alpha \theta s}}\left\{\frac{f(\theta )}{\left[Mf(\theta )\right]^2+4C^2k}\right\}^{1/2},$$
(49)
with \[see again Ref. , Eq. (2.551/3)\]

$$f(\theta )=\left|\frac{2}{s}\left[\frac{s\mathrm{tan}\left(\alpha \theta /2\right)1+\sqrt{1s^2}}{1+\sqrt{1s^2}s\mathrm{tan}\left(\alpha \theta /2\right)}\right]\right|^p,$$
(50)
where $`a_0`$, $`p`$ and the choice for the relationship between $`f(\theta _0)`$ and $`g(b_0)`$ are the same as in the normal axionic case, except for the new definition (48) of the constant $`C`$. The normalization in Eq. (50) has been chosen in such a way that the limit $`s0`$ gets indeed back to the normal axionic case (32).

The properties of these solutions are qualitatively the same as in the normal axionic case.

#### III.3.2 Large RR-scalar

In the opposite situation for which $`s^2>1`$, one can normalize the solution in such a way that \[see Ref. , Eq. (2.551/3)\]

$$f(\theta )=2p\mathrm{arctan}\left[\frac{1s\mathrm{tan}\left(\alpha \theta /2\right)}{\sqrt{s^21}}\right],$$
(51)
and, provided $`a_0^2=2C/(M\varphi _0)`$, the solution can be written as

$$a(\theta )=\frac{a_0}{\sqrt{s\mathrm{sin}(\alpha \theta )}}\left[1\pm \sqrt{14\frac{kC^2}{M^2}}\mathrm{sin}f(\theta )\right]^{1/2}.$$
(52)
These solutions, both in the large and small RR-scalar sectors, share with the normal axionic case the feature of requiring a meaningless negative dilaton field. They were derived here for the sake of completeness.

### III.4 Anomalous RR case

Finally, the last situation, for which Eq. (22) is solved by

$$\varphi =\varphi _0\left[\mathrm{sinh}\left(\alpha \theta \right)s\right],$$
(53)
is very similar to the anomalous axionic case except that the hyperbolic sine squared in Eq. (40) is replaced by $`[\mathrm{sinh}(\alpha \theta )s]^2`$, with the same definition for the constant $`s`$ and $`C`$ as in the anomalous axionic situation. This case is essentially similar to the normal RR one, except that we obtain a different function \[see Ref. , Eq. (2.441/3)\]

$$f(\theta )=p\mathrm{ln}\left|\frac{2}{s}\left[\frac{s\mathrm{tanh}\left(\alpha \theta /2\right)+1\sqrt{1+s^2}}{1+\sqrt{1+s^2}+s\mathrm{tanh}\left(\alpha \theta /2\right)}\right]\right|,$$
(54)
where the normalization again ensures that the limit $`s0`$ is equivalent to the anomalous axionic case. With the new scale factor normalization

$$a_0^2=\frac{A^2\varphi _0}{3M}(1+s^2),$$
(55)
the new solution is expressed as

$$a(\theta )=\frac{a_0}{\sqrt{\mathrm{sinh}\alpha \theta s}}\left[1\pm \sqrt{14\frac{kC^2}{M^2}}\mathrm{sin}f(\theta )\right]^{1/2}.$$
(56)
Again, as in the anomalous axionic case, completely nonsingular solutions, also with respect to the dilatonic field, which is strictly positive, are obtained for $`k=0`$ or $`k=1`$. The properties of both anomalous (axionic and RR) cases are very similar, even in the asymptotic regions. The significant feature of this case is that, for $`k=0`$, it is not difficult to choose the free parameters in order to allow huge increases of the dilaton along the evolution of such universes.

The anomalous cases are the ones that present bouncing eras connecting asymptotically contracting and (standard) expanding cosmological models which can represent the real Universe (with attractive gravitation). The key requirement to obtain these solutions is that $`\omega <3/2`$, a property that can be obtained from $`F`$ theory in twelve dimensions.

The presence of the axion and/or the RR scalar field is not important qualitatively. They just change the functions $`f(\theta )`$ which appear in the scale factor given by Eqs. (35), (44), (49), (52) and (56). In fact, one can find solutions without the axion, or with neither the axion nor the RR scalar field, which are also given by the very same equations but with different (and actually simpler) $`f(\theta )`$. For instance, in the case where neither the axion nor the RR scalar field are present, we have $`[f(\theta )]^{1/p}=|\varphi (\theta )||\theta |`$ and $`[f(\theta )]^{1/p}=\mathrm{ln}(|\varphi (\theta )|)=\mathrm{ln}(|\theta |)`$ in Eqs. (35) and (44), respectively. Those solutions can also be obtained as limiting cases of Eqs. (32) and (41) as $`A0`$. The qualitative behavior of these solutions is the same as in the case with the axion (normal and anomalous axionic cases).

## IV The null energy condition

For a nonpositive curvature universe described by general relativity, the null energy condition (NEC) $`\rho __\mathrm{T}+p__\mathrm{T}0`$, where the subscript “T” denotes the total contribution of all the fields and type of matter, must be violated in order for a bounce to occur (see Ref.  and references therein for a discussion of the relevant singularity theorems in general relativity ). In the context under consideration here, this result cannot be straightforwardly applied since the nonminimal coupling involved prevents an easy identification of the energy density and pressure sourcing the Einstein geometry (many results can however be applied to a theory with nonminimal coupling; this is discussed in, e.g. Ref. ).

In what follows, we sketch an analysis of the problem of violation of the energy conditions, adapting the expressions for the nonminimal coupling with the dilatonic field. The effective energy density $`\rho _{\mathrm{eff}}`$ and pressure $`p_{\mathrm{eff}}`$ are derived from the field equations (8), whose right-hand side we take to be the effective stress-energy tensor $`T_{\mathrm{eff}}^{\mu \nu }`$ we are looking for, assuming an Einstein-like form for Eq. (8) as

$$R_{\mu \nu }\frac{1}{2}g_{\mu \nu }R=8\pi G__\mathrm{N}T_{\mu \nu }^{\mathrm{eff}}.$$
(57)
The corresponding cosmological equations are then seen as projections of Eq. (57) by means of a normalized timelike vector $`u_\mu `$ (with $`u_\mu u^\mu =1`$): defining $`\rho _{\mathrm{eff}}=T_{\mathrm{eff}}^{\mu \nu }u_\mu u_\nu `$ and $`p_{\mathrm{eff}}=\frac{1}{3}T_{\mathrm{eff}}^{\mu \nu }\left(g_{\mu \nu }u_\mu u_\nu \right)`$, Eqs. (8) are then nothing but the usual system describing a cosmological background with a fluid.

Starting with the field equations derived above, one obtains the following expressions:

$`8\pi G__\mathrm{N}\rho _{\mathrm{eff}}`$ $`=`$ $`{\displaystyle \frac{8\pi }{\varphi }}\rho +{\displaystyle \frac{\omega }{2}}{\displaystyle \frac{\dot{\varphi }^2}{\varphi ^2}}+{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{\mathrm{\Psi }}^2}{\varphi ^2}}+{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{\xi }^2}{\varphi }}`$ (58)
$`3{\displaystyle \frac{\dot{a}}{a}}{\displaystyle \frac{\dot{\varphi }}{\varphi }},`$
$`8\pi G__\mathrm{N}p_{\mathrm{eff}}`$ $`=`$ $`{\displaystyle \frac{8\pi }{3\varphi }}\rho +{\displaystyle \frac{\omega }{2}}{\displaystyle \frac{\dot{\varphi }^2}{\varphi ^2}}+{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{\mathrm{\Psi }}^2}{\varphi ^2}}+{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{\xi }^2}{\varphi }}`$ (59)
$`+{\displaystyle \frac{\ddot{\varphi }}{\varphi }}+2{\displaystyle \frac{\dot{a}}{a}}{\displaystyle \frac{\dot{\varphi }}{\varphi }},`$
which, contrary to the standard cosmological situation, are both not positive definite. The energy conditions may therefore be violated, due to the terms arising from the nonminimal coupling and if either $`\omega `$ or $`\varphi `$ is negative.

To understand the causes for the bounces in our solutions, it is also useful to use Eq. (25). In the normal cases (from the purely mathematical point of view) with nonvanishing dilaton, we have seen that one must have $`\varphi <0`$ (repulsive gravity) in order to have a bounce. In this case, the negative dilaton is sufficient to make the bounce, and there is no need to have $`\omega <0`$. In the normal cases with the dilaton vanishing at some point, $`b`$ does not actually bounce. Hence the dilaton $`\varphi `$ can be positive. The bounce then comes from the requirement $`\omega <0`$.

In the anomalous cases, where the dilaton is strictly positive and finite, it is the negative value of $`\omega `$, more precisely the fact that $`\omega <3/2`$, which causes the bounces. Figure 1 illustrates two cases of bounces for which the scale factors are shown, taken in the anomalous axionic case, i.e. using the solution (44). In terms of the scale factor, the expression for the null energy condition reads

$$8\pi G__\mathrm{N}\left(\rho _{\mathrm{eff}}+p_{\mathrm{eff}}\right)=\frac{2}{a^6}\left[4\left(\frac{a^{}}{a}\right)^2\frac{a^{\prime \prime }}{a}+ka^4\right],$$
(60)
which coincides, on shell, with what is obtained by summing Eqs. (58) and (59). Plotting the right hand side of this expression as in Fig. 2 for the cases of Fig. 1, we verify that the null energy condition can be violated in large domains around the bounce, depending on the choice of parameters. One should notice that the timelike coordinate $`\theta `$ has been chosen to emphasize the bounce itself. In terms of the cosmic time, the domain where the NEC is violated is in fact reduced to just a small fraction of the whole interval, since the latter is actually infinite. Moreover, no violation is observed in the large positive time limit, where the models tend to Milne or radiation dominated universes.

## V Conclusions

We have constructed fully regular cosmological solutions in the framework of effective actions derived from string theory principles. These solutions present bouncing behaviors for a wide range of parameters ($`\omega <3/2`$), and are singularity free; furthermore, the spacetimes they lead to are geodesically complete, thereby improving the so-called horizon problem of standard cosmology. Stemming from string theory in the context of the so-called $`F`$ theory in twelve dimensions, where it is possible to have $`\omega <3/2`$, they have a reasonably sound basis as long as the dilaton is strictly positive and finite in such a case. As a consequence, it is not necessary to go beyond the tree level approximation in any part of their histories: the analytic solutions exhibited above can describe the whole history of the cosmological models they represent. Their consequences may, in turn, be used as cosmological tests.

Remembering that the radiation fluid included here also has a motivation in the superstring type IIB action, this turns out to be, to our knowledge, the first case where a complete regular bouncing cosmological solution is obtained in the string framework and related theories, which moreover is smoothly connected with the standard cosmological model radiation dominated phase. This solution may have flat or negative curvature spatial sections.

In the axionic and RR cases with $`k=0`$ or $`k=1`$, there are nonsingular bouncing solutions for $`3/2<\omega <4/3`$ but with vanishing dilaton in the beginning, where the tree level action cannot be trusted, and bouncing solutions with an initial curvature singularity if $`4/3<\omega <0`$. If $`k=1`$ and $`3/2<\omega <0`$ (normal, including the pure string case), one can have singularity free bouncing solutions with, however, a negative definite dilaton field.

As all the models with $`\omega <3/2`$ have the interesting feature to approach flat spacetime in the infinite past (either in Milne coordinates for $`k=1`$, or the infinitely large radiation dominated standard model with $`k=0`$), there is the possibility to implement a quantum spectrum of perturbations in the initial asymptotics without any trans-Planckian problem , and, at the same time, to accomplish a smooth transition to the standard cosmological model when, after the bounce, a standard radiation dominated phase is recovered (asymptotically in the $`k=0`$ case), preserving some of its main achievements like, e.g. primordial nucleosynthesis. The bouncing solutions with $`\omega >3/2`$ and positive dilaton still present some sort of trans-Planckian problem as long as the string expansion parameter diverges initially and one must go beyond the tree level action in such cases.

Notice that, in the cases where the dilaton is strictly positive, the initial value of the dilatonic field can be made smaller than its final value. Hence, the gravitational coupling can be initially given a much greater value than it would have today. This opens the possibility to solve the hierarchical problem of the gravitational coupling, in a spirit similar to the so-called brane cosmology .

###### Acknowledgements.

We thank CNPq (Brazil) for financial support.


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# Opening of DNA double strands by helicases. Active versus passive opening

## 1 Introduction

A helicase is a molecular-motor protein which opens double-stranded nucleic acid (NA) molecules. The strand separation is fueled by nucleoside triphosphate (NTP) hydrolysis, typically of ATP. Since the discovery of the first helicase in 1976 , more than 60 distinct helicase proteins have been found , including 12 apparent helicases solely in the bacterium E. coli. Helicases play a role in nearly every cellular process which involves NA, including replication, transcription, translation, repair, and RNA processing . All helicases share the ability to move along NA strands, and to couple that motion to strand separation. For this reason, helicases are often referred to as DNA translocases . Certain helicases, because of their role in repair of DNA damage, are crucial to maintain a stable (undamaged) genome. For example, helicase mutations play a role in the human diseases Xeroderma Pigmentosum, Bloom syndrome and Werner syndrome, all of which are associated with a predisposition to cancer .

Given the ubiquity of helicases in cellular processes which access nucleic acids and the large number of different types of helicase, it is not surprising that a variety of different helicase structures exist. We note that the many different examples of helicases are not all similar, and their unwinding mechanisms are not necessarily the same. The earliest known helicases were ring-shaped hexamers; other helicases have been shown to function as dimers. In the last 5 years, the helicase superfamilies I and II (SF1 and SF2, based on sequence comparison) have been discovered; this work led to a revision of the view that helicase function requires a multimeric protein. For a review of the SF1 and SF2 helicases see .

This paper was inspired by experiments on the SF1 and SF2 helicases. The monomeric proteins are known to bind to single-stranded (ss) NA and translocate directionally along it. Upon reaching the ss-double strand (ds) junction, the helicase continues and moves the junction foward, creating additional ssNA “track” as it goes. In this paper, we describe the physical principles of this process and show how to optimize performance of the enzyme. The coupling between the helicase translocation and NA opening is loosely classified in the literature  as “passive” or “active.” Passive unwinding means that the helicase unwinds indirectly, by binding ssNA available due to a fluctuation which opens part of the dsNA. We also call this “hard” unwinding for reasons discussed below, and to avoid confusion with other meanings of passive/active. In active unwinding (which we refer to as “soft” unwinding) the helicase directly destabilizes the dsNA, presumably by binding to the dsNA and changing the free energy of the ds state.

Experiments on the SF1 protein PcrA support a soft mechanism. Velankar et al.  solved crystal structures of the enzyme bound to a forked (part ss and part ds) DNA substrate. In one of these structures, the protein binds the non-hydrolyzable ATP analog ADPNP and represents the helicase prior to ATP hydrolysis. A second structure contains a sulfur ion and represents the conformation after ATP hydrolysis. These structures showed that the helicase binds ssDNA and tracks along the single strand as it moves. However, in one crystal, a portion of the PcrA also binds to the duplex DNA ahead of the ss-ds junction, causing a distortion of the helical structure. The authors suggested that this distortion promotes melting of the helix, thereby facilitating strand separation. The crystal structures and footprinting studies  showed that the contact between the protein and the double helix occurs 4-5 base pairs (bp) from the junction and again 12-13 bp from the junction. Soultanas et al. mutated the residues of PcrA which interact with the duplex portion of the DNA . The mutant proteins unwound dsDNA 10-30 fold more slowly than the wild-type protein, depending on which residue is mutated. These experiments provide evidence that PcrA unwinds softly and suggest that hard unwinding may be slower and less effective than soft.

In this paper, we use a simple model to explore the theoretical consequences of soft and hard opening. We suppose that the helicase and the NA ss-ds junction interact. Physically, the interaction corresponds to an interaction potential which describes how the presence of the helicase modifies the free-energy change of the NA opening. In our formulation, passive opening corresponds to a hard-wall potential: the helicase cannot advance beyond the ss-ds junction, but the presence of the helicase does not affect the energetics of dsNA opening. Softer potentials correspond to active opening, because the helicase changes the local energetics at the junction.

We study how NA strand separation depends on the interaction. In particular, we show that passive opening is always slower than a simple form of active opening. We calculate the rate of hard opening for the helicase PcrA, and discuss how the rate increases for soft opening. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that soft opening can increase the unwinding rate by 7 fold compared to hard opening. This result is consistent with the mutation studies of PcrA discussed above.

Although extensive biochemical and structural studies of helicases have been performed, relatively little has been done to characterize the function of helicases theoretically. An important review of helicase mechanism by von Hippel and Delagoutte  synthesizes the thermodynamic and kinetic properties of helicases into a general framework and emphasizes the importance of considering helicase-NA binding, translocation, and strand-separation independently. Doering et al.  developed a “flashing field” model specific to hexameric ring helicases. Recently Bhattacharjee and Seno  considered the coexistence of ss and dsDNA in the presence of a helicase. Chen et al.  described a helicase as a biased random walk, and considered how the density of histones affects the random walk. However, we know of no theoretical work which addresses how the interaction between helicase and NA affects the unwinding in general, or the difference between active and passive unwinding in particular. Helicases offer a particularly appealing choice for a simplified physical description because they are an important class of enzyme which interacts with NA, yet they have many relatively simple features. For example, many helicases have unwinding rates which are independent of the NA sequence unwound. Thus, the information content of the NA does not play an essential role in helicase operation—a large simplification compared to RNA polymerases, for example. Monomeric helicases are a relatively simple system that may serve as a building block for future theoretical studies of helicases. However, the principles discussed here are quite general and could also apply to multimeric helicases.

### 1.1 Helicase properties

Extensive experiments in the last thirty years have characterized several important properties of helicases. A helicase may bind a ss tail of NA adjoining a duplex, a forked NA containing both a ds region and two ss arms, or the blunt end of dsNA. Most helicases bind and translocate with polarity: they move—either on a single strand, or on one of the two strands of a duplex—in a preferred direction. A 3’-5’ helicase moves toward the 5’ end of the NA strand to which it is bound. The monomeric SF1 helicases we consider here bind to a ssNA tail. Thus after binding, the helicase moves along the ss tail to the ss-ds junction, then continue moving to unwind.

Once a helicase has bound to a strand and begins moving, it unwinds at a measurable average rate, ranging from a few (for PcrA) to thousands (for RecBCD) of bp/sec. The average number of base pairs unwound before the helicase falls off the NA is known as the processivity; measured values for different types of helicases vary from 40 to 30,000 bases unwound . Both the rate and the processivity of a helicase are strongly affected by the presence of accessory proteins as well as solution conditions. For example, E. coli single-strand binding protein (SSB) decreases the average free energy cost of unwinding a segment of dsDNA, and has also been observed to increase the processivity of helicases. High values of processivity, such as the 30,000 bp measured for RecBCD, are usually observed in the presence of SSB. Hexameric ring helicases also tend to have higher processivities than dimeric or monomeric helicases. In the absence of any accessory proteins, the monomeric helicase PcrA translocates on ssDNA at a rate of about 80 bases/s  and has a low processivity of about 50 bp unwound .

A helicase is able to unwind dsNA because it uses the energy released by nucleotide hydrolysis (usually by ATP) for its motion. The average number of bp unwound per ATP molecule hydrolyzed is called the efficiency of unwinding (this quantity is often called the “efficiency” of the helicase in the literature; we prefer to call it the efficiency of unwinding to distinguish it from the efficiency of energy transduction, which is related but not exactly the same). Again, the presence of SSB changes the free energy balance and increases helicase efficiency of unwinding. Under E. coli conditions at room temperature, ATP hydrolysis releases about 23 kT, and the average free-energy change from melting one base pair is approximately 1.7–2.5 kT . The theoretical limit on efficiency of unwinding is thus 9–12 bp unwound per ATP hydrolysis. Experimentally measured values are typically smaller, usually 0.33–1 bp unwound/ATP hydrolyzed. For PcrA, the measured efficiency of unwinding is approximately 1 bp unwound/ATP .

## 2 Hopping Model

We formulate a discrete model for helicase motion and strand separation (Fig. 1). We consider two degrees of freedom: the helicase position $`n`$ along the NA strand and the position $`m`$ of the NA ss-ds junction. Since we are considering only single-base hops, both $`n`$ and $`m`$ are integers. (In our units the length of a ss base is 1.) The helicase hops one base forwards towards the dsNA with rate $`k^+`$, and backwards with rate $`k^{}`$. Since the helicase hydrolyzes ATP, it is out of equilibrium111The rates $`k^+`$, and $`k^{}`$ can be derived from a more complicated model which explicitly treats the nonequilibrium nature of the enzyme. A forthcoming article will address this issue. and has $`k^+>k^{}`$. Similarly, the NA opens by one base222We consider only the breathing modes of the NA in which it opens or closes by one base pair. Modes in which larger number of bases open are present, but they are much less probable than the single-base opening or closing. with rate $`\alpha `$ and closes with rate $`\beta `$. Because the NA tends to close (in the absence of melting agents ) we have $`\beta >\alpha `$. Thus the motion of the helicase and the junction tend to drive their positions closer together.

Our simple picture neglects several effects. We ignore binding and unbinding of the helicase, and thus consider the motion of the helicase along the NA strand only. The NA strand we treat as a rigid, one-dimensional track (twist relaxation is fast compared to the unwinding rate). We neglect effects of the NA sequence; each NA base is identical. We ignore the different biochemical states of the helicase and describe it only by forward and backward rates.

For a helicase to unwind a NA duplex, it must interact with (and move) the ss-ds junction. The form of this interaction determines whether the unwinding is soft or hard. We describe this interaction by an potential $`U(mn)`$ between the helicase and the NA ss-ds junction which depends only on the difference between $`m`$ and $`n`$. For large separations $`mn1`$ we assume that the junction and the helicase have no effect on each other, so the coupling potential tends to zero. However, when $`mn`$ is small the coupling potential $`U`$ changes both the helicase motion and the junction motion: $`U>0`$ inhibits the forward motion of the helicase and increases the relative opening rate of the junction.

We use detailed balance (the law of mass action) to write how this coupling potential changes the rates. If the NA closes (so $`mm1`$), the change in interaction energy is $`U(mn)U(mn1)`$. The opening and closing of the NA happens without an external energy source, so detailed balance applies. The ratio of the opening and closing rates is

$$\frac{\beta _m}{\alpha _{m1}}=\frac{\beta }{\alpha }e^{\frac{U(mn1)U(mn)}{kT}},$$
(1)
where $`\alpha `$ and $`\beta `$ are the sequence-averaged rates when the helicase and ss-ds junction are far apart. (See Section 4 for a discussion of the values of the different rates.)

We now apply the same argument to the helicase motion. The change in energy $`U(mn1)U(mn)`$ represents the effective force acting on the helicase. We describe the force dependence of helicase motion by writing the ratio of forward and backward rates as

$$\frac{k_n^+}{k_{n+1}^{}}=\frac{k^+}{k^{}}e^{\frac{U(mn1)U(mn)}{kT}}$$
(2)
Eq. (2) is not valid in general, because the helicase is driven by ATP hydrolysis and detailed balance cannot be used. However, it holds for certain cases in a model for motion generation by ATP hydrolysis333 A forthcoming article will address this issue. and is very useful for a discussion of the principles.

The essence of passive opening is to suppose that the helicase provides a steric inhibition of NA closing when it is near the junction. If the junction is at position $`m=n+1`$, then the helicase covers the ss base adjacent to the junction and prevents base-pairing with the complementary NA strand. Thus hard opening requires $`\beta _m`$ to equal 0 when $`m=n+1`$. By equation (1), we see that $`\beta _m=0`$ if $`U(0)`$ is infinite. This is the hard-wall potential sketched in Fig. 2a.

The effect of this potential on the helicase motion makes intuitive sense, as seen in Eq. (2). If $`U(0)`$ is infinite then $`k_n^+=0`$ when $`m=n+1`$. In other words, the helicase is unable to advance into the double-stranded NA region and must wait until a thermal fluctuation opens the NA before advancing. This example shows how we describe hard opening: when the helicase and dsNA cannot overlap, the interaction energy $`U`$ is infinite for $`nm`$.

The interaction potential $`U(mn)`$ can be “softer” than the hard wall form. Such a potential (as in Fig. 2b) leads to active opening, because the interaction with the helicase increases the opening rate of the dsNA. Recall Eq. (1) for the position dependence of the rates. Whenever the NA closing increases the interaction energy ($`U(mn1)>U(mn)`$), the ratio of NA closing to opening rate decreases, relative to $`\beta /\alpha `$. Thus the interaction with the helicase can increase the rate of opening or decrease the rate of closing (or both). The crystal structure of PcrA discussed above, which shows that the enzyme can bind to the dsDNA and distort it suggests active opening. In addition, point mutations of the region of PcrA which binds the duplex DNA decrease the unwinding rate . In our picture, the mutations could alter the potential so it approaches a hard-wall form (which corresponds to hard opening).

For a real helicase such as PcrA we do not know the exact form of the potential. We explore different forms of $`U(mn)`$ subject to the requirements (i) $`U0`$ for $`mn`$ (when the helicase and the junction are far apart, there is no interaction) and (ii) $`U\mathrm{}`$ for $`nm`$. The second requirement means that the helicase cannot bind solely to dsNA and always retains some “footing” on the ssNA. An increase in the energy for $`n>m`$ is necessary to confine the helicase near the ss-ds junction and prevent it from wandering off into the ds region.

In the analysis of this model, we address several questions. How does changing the potential affect the unwinding rate? We showed above that an increasing interaction potential has two effects: it leads to relatively faster NA opening and relatively slower helicase forward motion. We wish to understand how this trade-off can be resolved. In particular, is there a choice of interaction potential which leads to the fastest possible rate of opening? We address these questions below for certain simplified forms of the potential $`U`$.

### 2.1 Solving for the opening rates

We wish to determine the rate of dsNA unwinding for the hopping model, given the rates $`k^+`$, $`k^{}`$, $`\alpha `$, $`\beta `$, and the potential $`U(mn)`$. We consider the probability $`P(n,m,t)`$ that the helicase is at base $`n`$ and the ss-ds junction at base $`m`$ at time $`t`$. We give the details of this calculation in App. A and outline the main features here. Our approach is similar to the polymerization ratchet of Peskin, Odell, and Oster, who examined how a polymerizing filament is able to produce a force . In their work, the two fluctuating degrees of freedom are the tip of a filament and a wall, which are analogous to our helicase and ss-ds junction. However, they considered a hard-wall interaction; thus our work may be considered a generalization of their approach. The probability distribution satisfies the Eq. (17), which describes the changes to $`P(n,m,t)`$ due to opening/closing of the NA (which changes $`m`$) and helicase hopping (which changes $`n`$).

We rewrite this equation using difference and midpoint variables $`j=mn`$ and $`l=m+n`$ (Eq. (18)). This allows an important simplification since the coefficients in Eq. (18) are independent of $`l`$. By summing Eq. (18) over $`l`$, we obtain Eq. (19) for the difference-variable distribution $`𝒫_j=_lP(j,l)`$. This equation describes the relaxation of the difference-variable distribution to a stationary one, which corresponds to a constant current in the difference variable $`j`$. The potential diverges as $`j\mathrm{}`$, which implies that the helicase cannot pass the junction. Therefore, the $`j`$-current must vanish, which leads to a simple recursion relation for $`𝒫_j`$ that depends on the interaction potential.

The strand separation velocity can be calculated assuming that the distribution $`𝒫_j`$ is stationary. The distribution $`𝒫_j`$ reaches its steady state after a relaxation time related to the rates $`\alpha `$, $`\beta `$, $`k^+`$, and $`k^{}`$. Summing Eq. (18) over $`j`$ leads to a discrete drift-diffusion equation for $`\mathrm{\Pi }_l=_jP(j,l)`$ (Eq. (24)). The corresponding current in $`l`$ does not vanish and determines the mean strand separation velocity

$$v=\frac{1}{2}\underset{j}{}(k_j^++\alpha _jk_j^{}\beta _j)𝒫_j.$$
(3)
The expression for $`v`$ has a simple physical interpretation. The quantity in parentheses is the unwinding rate at separation $`j`$—either a forward hop of the helicase ($`k_j^+`$) or NA opening ($`\alpha _j`$) move the helicase/junction complex forward. Similarly, a backward hope of the helicase ($`k_j^{}`$) or NA closing ($`\beta _j`$) move the complex backwards. We then take the unwinding velocity at separation $`j`$ and multiply it by the probability $`𝒫_j`$ of finding the complex at separation $`j`$. Repeating this addition for all possible $`j`$, we arrive at the total unwinding rate. Thus we see that, under our assumptions, solving Eq. (21) for the stationary probability distribution $`𝒫_j`$ is suffient to calculate the mean helicase opening velocity. The diffusive part of the equation for $`\mathrm{\Pi }_l`$ allows us to determine the effective diffusion coefficient which characterizes velocity fluctuations

$$D=\frac{1}{4}\underset{j}{}(k_j^++\alpha _j+k_j^{}+\beta _j)𝒫_j$$
(4)
## 3 Hard versus soft opening

Consider the hard wall model for passive opening, with the wall at $`j=0`$. As described above, this means $`k^+`$, $`k^{}`$, $`\alpha `$ and $`\beta `$ are constant in the region $`j>0`$ except at $`j=1`$, where $`k_1^+=\beta _1=0`$. Since the rates are constant, we have

$$𝒫_j=A\left(\frac{\alpha +k^{}}{\beta +k^+}\right)^j=Ac^j,$$
(5)
where we have defined $`c=\frac{\alpha +k^{}}{\beta +k^+}`$ and the constant $`A`$ is determined from normalization: $`A=(\beta +k^{}\alpha k^{})/(\alpha +k^+)`$. Evaluating Eq.(3) for the helicase opening velocity, we find

$$v_{HW}=\frac{\alpha k^+\beta k^{}}{\beta +k^+}$$
(6)
The opening velocity is positive whenever $`k^+/k^{}>\beta /\alpha `$, that is, the free energy change which drives DNA closing must be smaller than the effective free energy change of the helicase. This requirement intuitively makes sense: the helicase must have a sufficiently high forward rate to overcome the energetically favorable DNA closing. The sequence-averaged value of $`\beta /\alpha `$ for DNA is 7 (corresponding to an average free energy change per base closed of 2 kT). Thus, even by this simple calculation we see that for passive opening to be possible we must have $`k^+>7k^{}`$. The backward rate $`k^{}`$ must be considerably smaller than the forward rate, as observed in experiments.

### 3.1 Soft opening: the staircase

Next we consider a simple example of soft opening shown in Fig. 2b. Instead of a hard-wall potential, we insert a step of height $`U_o`$ at $`j=0`$ and a hard wall at $`j=1`$. Thus the DNA junction and the helicase can overlap by one base if the energetic cost is paid. The ratios of the forward and backward rates at the step must satisfy the relations

$`{\displaystyle \frac{k_0^{}}{k_1^+}}`$ $`=`$ $`{\displaystyle \frac{k^{}}{k^+}}e^{U_0},`$ (7)
$`{\displaystyle \frac{\alpha _0}{\beta _1}}`$ $`=`$ $`{\displaystyle \frac{\alpha }{\beta }}e^{U_0},`$ (8)
$`k_0^+=\beta _0`$ $`=`$ $`0.`$ (9)
These relations affect only the ratios of the rates. We also have to specify how the rates themselves change. This is determined by the position of the barrier which must be crossed for the helicase to move or for the NA to open/close. We describe this by a weighting factor $`0<f<1`$. (Note that $`f`$ is the same for the helicase motion and the NA breathing since both phenomena involve the same barrier.) Smaller values of $`f`$ imply that the barrier influences mainly backward rates, while for large $`f`$ the barrier affects forward rates. We have

$`k_1^+`$ $`=`$ $`k^+e^{fU_o},`$ (10)
$`k_0^{}`$ $`=`$ $`k^{}e^{(f1)U_o},`$ (11)
$`\beta _1`$ $`=`$ $`\beta e^{fU_o},`$ (12)
$`\alpha _0`$ $`=`$ $`\alpha e^{(f1)U_o}.`$ (13)
With these values, we can calculate the opening velocity $`v_1`$ for one step. For comparison, we present the opening velocity relative to $`v_{HW}`$ of Eq. (6):

$$\frac{v_1}{v_{HW}}=\frac{c+(1c)e^{fU_o}}{c+(1c)e^{U_o}}.$$
(14)
where $`c=\frac{\alpha +k^{}}{\beta +k^+}`$. Since $`0<f<1`$, the opening velocity $`v_1`$ for a single step is always larger than $`v_{HW}`$. However, the size of $`v/v_{HW}`$ depends strongly on the choice of $`f`$ (Fig. 3a). Smaller values of $`f`$ increase the opening velocity. The maximal opening rate occurs when $`f=0`$. From Eq.(14), we see that for $`f=0`$ and large $`U_o`$, $`v_1v_{HW}/c7v_{HW}`$. For small values of $`f`$ the helicase forward rate $`k^+`$ and the DNA closing rate $`\beta `$ do not change much due to the step, whereas the helicase backward rate $`k^{}`$ and the DNA opening rate $`\alpha `$ increase significantly. The main advantage of active opening is that it increases the opening rate of the DNA. It is more advantageous to increase the opening rate than to decrease the closing rate, because with an increased opening rate the strand-separation timescale is faster.

The unwinding rate also depends on the step height $`U_o`$. For small $`U_o`$, the velocity is little changed from the hard-wall velocity. As the step height increases, so does the opening velocity, as a result of the increase in DNA opening rate caused by the presence of the step. For a height of 1 kT and $`f=0.05`$, the opening velocity is approximately twice the hard-wall velocity. We draw particular attention to the barrier height of 2 kT. This means that the helicase at $`j=0`$ causes the base-pair nearest the junction to be indifferent to opening. A 2 kT step height with $`f=0.05`$ increases the opening velocity by approximately a factor of 3 relative to the hard-wall velocity. For a further comparison of our calculation to experimental data, please see the Discussion below.

### 3.2 Multi-step staircase

Evidence from the crystal structures of PcrA bound to a forked DNA substrate discussed above suggests that we consider more than one “step” in the potential. The structures indicate that the helicase and dsDNA interact 4-5 bp from the junction, and again 12-13 bp from the junction. Thus we should consider an interaction potential with a variable number of steps. For a multi-step staircase (with $`n`$ identical steps, each of height $`U_o`$, see Fig. 2c) the unwinding velocity is

$$\frac{v_n}{v_{HW}}=\frac{c^n+(1c)e^{(f1)U_o}_{j=1}^nc^{nj}e^{jU_o}}{c^n+(1c)_{j=1}^nc^{nj}e^{jU_o}}.$$
(15)
This expression can be simplified by performing the summation, but as written one can see the similarity between this expression and Eq. (14) for the one-step unwinding velocity. In particular, note that for $`n=1`$ the expression here reduces to Eq. (14). Fig. 3b shows how the velocity changes with step number (for $`f=0.1`$). Adding additional steps allows the opening velocity to increase faster, and the maximum opening speed increases with the number of steps. We note that as the number of steps becomes large, the step size $`U_o`$ corresponding the the maximum opening velocity approaches $`U_{max}\mathrm{ln}c`$. In other words, in the limit of a large number of steps, the optimal step height approaches the free energy change of melting one base of NA: the fastest opening occurs when the interaction between helicase and NA causes the melting of one NA base pair to be energetically neutral.

For a step height of 2 kT, adding one step increase the opening velocity by a factor of 3.5, whereas for 5 steps of height 2 kT the opening velocity is 5 times the hard-wall velocity. This is a significant increase over the hard-wall velocity. The PcrA mutation studies  found that mutating the residues which interact with the dsDNA decreased the unwinding rate by a factor of 10-30. While our model shows a decrease in the opening velocity (when opening changes from soft to hard) of at most a factor of $`1/c7`$, we find it striking that such a simple model can demonstrate such a large change in the velocity. We emphasize that because our result looks at the ratio of active to passive unwinding rates, it is independent of particular helicase properties such as $`k^+`$ and $`k^{}`$. Our result depends only on the sequence-averaged ratio of DNA opening and closing rates $`c`$ as well as the number of steps $`n`$ and the step size $`U_o`$.

Indeed, while hard opening is significantly slower than the PcrA single-strand translocation rate, the helicase that chooses (or evolves) an appropriate interaction potential can open NA nearly as fast as the rate it moves on ssNA.

## 4 Discussion

In this paper, we have described the opening of NA by a helicase in terms of two hopping degrees of freedom: the position of the helicase, which hops along ssNA driven by ATP hydrolysis, and the position of the ss-ds NA junction, which fluctuates passively. This simplified model allows us to focus on how the motion is affected by the interaction between these two degrees of freedom. We demonstrate that active opening in general leads to a faster overall unwinding rate that can approach the velocity of motion of helicase along the ssNA.

We show that the interaction between helicase and dsNA determines the speed of unwinding. If rapid unwinding is advantageous, helicases will evolve towards interaction potentials which optimize this speed. In our calculations we can make quantitative predictions of how different potentials change the unwinding rate.

Because the helicase moves primarily forward, the backward rate $`k^{}`$ is small compared to $`k^+`$. Dillingham, Wigley, and Webb used two different techniques to measure the rate of PcrA motion on ssDNA. In our notation, this is $`k^+k^{}=80`$ bases/sec. They found that their data were well-fit by a model with no backward steps ($`k^{}=0`$), although our analysis of their results found a comparably good fit with values of $`k^{}`$ up to 10% of $`k^+`$. The free-energy change $`\mathrm{\Delta }F`$ of opening one base determines the ratio $`\alpha /\beta =e^{\mathrm{\Delta }F/kT}`$. This ratio is approximately $`\mathrm{\Delta }F2kT`$ for a base-pair near a junction. This value is consistent with bulk melting-curve results  and is the origin of our number $`\alpha /\beta =e^21/7`$. For the actual values of $`\alpha `$ and $`\beta `$, we deduce a number using the experimental results of Bonnet, Krichevsky, and Libchaber  who found that the opening rate of a 5-bp hairpin loop at 300 K and at 0.1 M NaCl was $`k3000/`$sec. Using a simple kinetic model444We assume that each of the 5 bases has an opening rate $`\alpha `$ and a closing rate $`\beta `$ and the ratio $`\alpha /\beta =c`$. With $`P_n`$ denoting the relative probability of having $`n`$ base pairs open, the opening rate is given by $`k=J/P_n=\alpha c^3/(1+2c+3c^2+4c^3+c^4(1+c+c^2+c^3+c^4))`$, where $`J=\alpha P_0\beta P_1=\alpha P_4`$ is the current. With this expression we estimate $`\alpha `$, given $`k`$ and $`c`$. we estimate from this value of $`k`$ that $`\alpha 1.4\times 10^6`$/sec. We use this value of $`\alpha `$ in our calculations below. This estimate can be compared with theoretical estimates of the base-pair opening rate $`\alpha `$, which range from $`10^5`$/sec to $`10^6`$/sec .

Here we compare the results of our model to experimental data, using the experimental values of $`k^+`$, $`k^{}`$, $`\alpha `$, and $`\beta `$ discussed above The maximum possible hard-wall opening velocity occurs in the case where $`k^{}=0`$. Then

$$v_{HW}=\frac{\alpha }{\beta }\left(\frac{k^+}{1+k^+/\beta }\right)11\text{bases/sec}.$$
(16)
Note that this is an upper bound on the velocity: any non-zero value of $`k^{}`$ decreases the hard-wall velocity. Unfortunately, to our knowledge the unwinding rate has not been directly measured for SF1 helicases such as PcrA. Existing unwinding assays  use gel electrophoresis to determine the fraction of dsDNA molecules completely unwound at a given time. Therefore we cannot make a direct comparison between our calculation and measured unwinding velocities.

Adding a single-step-staircase potential allows the velocity to increase by up to a factor of 7. We choose a modest step height of 2 kT, which gives a maximum increase over the hard-wall velocity of a factor of 3 (for $`f=0.1`$). Thus the DNA opening velocity could be up to 33 bases/sec for a single-step-staircase potential. For a multi-step staircase, 5 steps of height 2 kT increase the opening rate by a factor of 5. Thus the helicase unwinding rate can increase to 55 bases/sec from the hard rate of 11 bases/sec. This velocity is nearly as large as the single-strand translocation speed itself. Thus we demonstrate that soft opening—despite the extemely simplified form of the interaction potential we have chosen—can significantly increase the strand-separation rate.

We emphasize that changes to the helicase hopping rates $`k^+`$ and $`k^{}`$, for example due to changes in the ATP concentration, lead to changes in the unwinding rate which our model predicts quantitatively. Similarly, the free energy change of melting one NA base pair can by changed by altering solution conditions or by applying a force to the NA molecule. Such a change directly alters the parameter $`c\alpha /\beta `$ in our model, and we quantitatively predict the resulting change in the unwinding rate. Here, we have neglected the effects of the base sequence on NA opening which are believed to be weak for helicases. However, work by Lubensky and Nelson  suggest that interesting effects can arise if a random DNA sequence is opened.

The simplified structure of this model means it may be useful in other situations where two degrees of freedom interact. For example, two motor proteins which walk on a microtubule may affect each other’s motion. As mentioned above, our work may be viewed as a generalization of the work of Peskin et al.  to include an arbitrary type of interaction potential. This generalization may also be relevant to the problem originally addressed in Ref. : the production of a force by a polymerizing filament. Introducing a potential (which describes the interaction between the growing filament tip and the obstacle against which the polymer pushes) affects the polymerization speed and the force-velocity relation of the filament.

We thank David Lubensky, Thomas Perkins, and Jacques Prost for helpful discussions. MDB acknowledges the support of a Chateaubriand Fellowship and funding from the VIGRE program of the NSF.

## Appendix A Calculation of the Unwinding Velocity

Here we determine the rate of dsNA opening for the hopping model, given the rates $`k^+`$, $`k^{}`$, $`\alpha `$, $`\beta `$, and the coupling potential $`U(mn)`$. Consider the probability $`P(n,m,t)`$ that the helicase is at position $`n`$ and the ss-ds junction at position $`m`$ at time $`t`$. The probability satisfies

$$\begin{array}{c}\frac{P(n,m)}{t}=(k_{mn}^++k_{mn}^{}+\alpha _{mn}+\beta _{mn})P(n,m)+\alpha _{mn1}P(n,m1)\hfill \\ \hfill +\beta _{mn+1}P(n,m+1)+k_{mn+1}^+P(n1,m)+k_{mn1}^{}P(n+1,m).\end{array}$$
(17)
Note that the subscript $`mn`$ means the hop starts at $`mn`$ and moves either right or left. After rewriting using the difference and midpoint variables $`j=mn`$ and $`l=m+n`$, we have

$$\begin{array}{c}\frac{P(j,l)}{t}=(\alpha _j+\beta _j+k_j^++k_j^{})P(j,l)+\alpha _{j1}P(j1,l1)+\beta _{j+1}P(j+1,l+1)\hfill \\ \hfill +k_{j+1}^+P(j+1,l1)+k_{j1}^{}P(j1,l+1).\end{array}$$
(18)
Since the coefficients in Eq. (18) do not depend on $`l`$, we can obtain an equation for the difference variable distribution $`𝒫_j=_jP(j,l)`$ by summing over $`l`$

$$\frac{𝒫_j}{t}=(k_j^++k_j^{}+\alpha _j+\beta _j)𝒫_j+\alpha _{j1}𝒫_{j1}+\beta _{j+1}𝒫_{j+1}+k_{j+1}^+𝒫_{j+1}+k_{j1}^{}𝒫_{j1}.$$
(19)
This is the equation for a position-dependent hopping model with forward rate $`k_j^{}+\alpha _j`$ and backward rate $`k_j^++\beta _j`$. The stationary probability distribution for $`j`$ satisfies the recursion relation $`I(j)=I(j1)`$, where we have defined the current

$$I(j)=(k_{j+1}^++\beta _{j+1})𝒫_{j+1}(k_j^{}+\alpha _j)𝒫_j.$$
(20)
The stationary probability distribution corresponds to a constant current solution. In the case of a potential $`U(j)\mathrm{}`$ as $`j\mathrm{}`$, the current must be zero (no helicases can escape to $`j\mathrm{}`$). This gives the zero-current relation

$$𝒫_{j+1}=\frac{k_j^{}+\alpha _j}{k_{j+1}^++\beta _{j+1}}𝒫_j$$
(21)
In the zero-current case, and if the rates are are constant (independent of $`j`$), $`𝒫_j`$ has a power law form with a constant determined by normalization. For the general case where the rates $`k_j^+`$, $`k_j^{}`$, $`\alpha _j`$, and $`\beta _j`$ vary with $`j`$, we can solve Eq. 21 iteratively, using the conditions (i) $`𝒫0`$ as $`j\mathrm{}`$, and (ii) $`_j𝒫_j=1`$.

The difference variable distribution relaxes to a steady state in a finite time while the midpoint variable $`l`$ undergoes a drift with diffusion. We can find a simple equation for the midpoint motion if we focus on times longer than the relaxation time of $`P_j`$. (Since the DNA opening/closing times are of order of microseconds, we expect the relaxation time to be at most hundreds of microseconds. This time is short compared to the overall rate of unwinding). In this limit, the probability $`P(j,l)`$ becomes of the form $`P(j,l)=𝒫_j\mathrm{\Pi }_l`$. If we define

$`p`$ $`=`$ $`{\displaystyle \underset{j}{}}(\alpha _j+k_j^+)𝒫_j,`$ (22)
$`q`$ $`=`$ $`{\displaystyle \underset{j}{}}(\beta _j+k_j^{})𝒫_j.`$ (23)
then the equation for $`\mathrm{\Pi }_l`$ reduces to a hopping model with effective forward and backward rates $`p`$ and $`q`$:

$$\frac{\mathrm{\Pi }_l}{t}=(p+q)\mathrm{\Pi }_l+p\mathrm{\Pi }_{l1}+q\mathrm{\Pi }_{l+1}.$$
(24)
The rates $`p`$ and $`q`$ are independent of $`l`$, because of our assumption that all rates depend only on the difference variable $`j`$. As above, defining the current $`\mathrm{{\rm Y}}(l)=p\mathrm{\Pi }_lq\mathrm{\Pi }_l`$ the equation for the stationary distribution $`\mathrm{\Pi }`$ becomes $`\mathrm{{\rm Y}}(l)=\mathrm{{\rm Y}}(l1).`$ For the midpoint motion, there is no confining potential which localizes the probability distribution. Thus we expect a solution with non-zero current. The solution is $`\mathrm{\Pi }_o=\frac{1}{N}`$ and $`\mathrm{{\rm Y}}=(pq)\mathrm{\Pi }_o`$, where $`N`$ is the total number of NA bases. The mean opening velocity of a single helicase is

$$v=\frac{1}{2}(pq)=\frac{1}{2}\underset{j}{}(k_j^++\alpha _jk_j^{}\beta _j)𝒫_j.$$
(25)
As discussed in the text, $`v`$ is the unwinding rate at separation $`j`$ multiplied by the probability $`𝒫_j`$ of finding the complex at separation $`j`$. Repeating this addition for all possible $`j`$, we arrive at the total unwinding rate. The factor of 1/2 appears because we use $`l=m+n`$ for convenience, while the true midpoint location is $`l/2`$. Thus we see that, under our assumptions, solving Eq. 21 for the stationary probability distribution $`𝒫_j`$ immediately gives the exact mean helicase opening velocity.

We can also determine the effective diffusion coefficient which characterizes velocity fluctuations

$$D=\frac{1}{4}\underset{j}{}(k_j^++\alpha _j+k_j^{}+\beta _j)𝒫_j$$
(26)