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# Quantum reversibility and a new model of quantum automaton

## 1 Reversible computing: a glance

The classical theory of reversible computing has been analyzed extensively (). The main results are the following: 1. Every irreversible computation $`f:xf(x)`$ can be effectively enclosed in a reversible computation $`F:(x,0)(f(x),x)`$. $`F`$ is reversible because its input $`(x,0)`$ is uniquely determined by its output $`(f(x),x)`$. 2. The time and space required to compute $`F`$ are linearly dependent on those required to compute $`f`$. These results imply that there are no effects on the complexity hierarchy when the time and space required to compute $`f`$ are those required to compute its reversible realization $`F`$ (reversible space equal irreversible space). To investigate whether is it possible to extend the above classical results to the quantum case, we first revisit the ideas behind classical reversible computing.

### 1.1 Reversible gates

In order to transform an irreversible gate into a reversible one, not only the gate computation result is to be codified in the gate output, but also some other information necessary to reverse the computation (garbage). To store the garbage more output lines are needed and, since a reversible gate has the same numbers of input and output lines, even more input lines are required (source). Note that, since reversibility implies that the output of a reversible gate depends on the state of the source, its state has to be properly set to compute a given boolean function by a reversible gate. Figure 1 here below outlines the logical structure of a reversible gate.

Example: Reversible AND gate. The AND gate is a two-input one-output gate, whereas its reversible realization is a three-input three-output gate. The adjunctive input line ($`s`$) constitutes the source and the two adjunctive output lines ($`g_1`$ and $`g_2`$) are the garbage. The transition function of the reversible AND gate is reported in Table 1.

Table 1 could be completed by adding the three possible inputs with $`s=1`$. In this case, however, reversibility implies that the gate does not realize the AND function. As already remarked, to use a reversible gate the value of the source lines must be prepared appropriately.

### 1.2 Reversible combinatorial circuits

To build up a reversible combinatorial circuit (i.e. a circuit without loop) from an irreversible one, every gate can be replaced by its reversible realization (that is, every boolean function is computable by a reversible circuit). However, although the final circuit works, it often has too many source and garbage lines. In fact :

> Note that, in general, (in a combinatorial circuit) the number of gates increases exponentially with the number of input lines. This is so because almost all Boolean functions are “random”, i.e., cannot be realized by a circuit simpler than one containing an exhaustive look-up table. Thus, in the “wasteful” approach the amount of garbage grows exponentially with the size of the argument.

This explains why a reversible realization of a combinatorial circuit seems less efficient than the combinatorial circuit itself with regard to space consumption. Actually, in classical case there is a way to recycle the garbage that implies a linear relation between the space required to compute a boolean function by a reversible or irreversible computation. This process, outlined in Figure 2, rests on two considerations: 1. An inverse circuit exists for every reversible circuit, and 2. A copy circuit: $`(x,0)(x,x)`$ does exist.

To be honest, the above process is really useful only when applied in a nested fashion.

### 1.3 Reversible sequential circuits

If the output lines of a combinatorial circuit are used as input lines, one ends up with a sequential circuit (finite automaton), as outlined in Figure 3. A sequential circuit constantly works in (discrete) interaction with the environment, that changes the state of the input lines. Its evolution is a three-step loop starting from a given internal state:

1. The environment sets the value of the input lines. 2. The combinatorial circuit (i.e. the transition function) is computed. 3. Some output lines are used as input lines (they codify the new internal state).

By substituting the combinatorial part of a sequential circuit for its reversible realization one does not end up with a reversible sequential circuit. In fact, every time the combinatorial circuit (transition function) is computed, the garbage is modified and the information necessary to reverse the computation is lost. Therefore, in order to build up a reversible sequential circuit, every time the transition function is computed the produced garbage has to be registered. In the following section we present a scheme of sequential circuits, or finite automata, that is able to register the output and the garbage appropriately.

### 1.4 Reversible Turing machines

Bennet  has proposed an effective procedure that transforms every irreversible one-tape Turing machine into a reversible three-tape Turing machine. The computation of this machine, that recycles the garbage with the same trick used by reversible combinatorial circuits (Fig. 2), proceeds as follows:

* Initially the three tapes contain input-source-source. The reversible function is computed.
* The tapes contain garbage-result-source. The $`2^{nd}`$ tape result is copied on the $`3^{rd}`$ tape.
* The tapes contain garbage-result-result. The inverse reversible function is computed.
* The tapes contain input-source-result.

## 2 Space consumption of quantum computing

### 2.1 Space consumption of reversible computing

In the classical framework we seldom care about space consumption. In fact, since $`PTimePSpace=NPSpaceExpTime`$, we first have to trouble about time consumption. This relation stems from the fact that if a computation needs some space, then it needs also some time to use it. Therefore every consumption of space requires a consumption of time, whereas the consumption of time does not implies a consumption of space.

In the case of reversible computing, not only every consumption of space requires a consumption of time, but also every consumption of time requires a consumption of space. In fact every unit of time, that corresponds to the execution of an elementary step, as a (reversible) gate or a transition of a (reversible) Turing machine, requires its own source. Time and space seem to be strictly tied. Let $`T`$ and $`S`$ be the time and space required by an irreversible Turing machine to end its computation, supposing that the machine halts, and let $`T^{}`$ and $`S^{}`$ be the time and space that its reversible realization does need. Then exists such $`c>1`$ that $`T^{}c+cT`$ and $`S^{}c+c(S+T)`$ . From a computational complexity point of view this suggests that reversible and irreversible computation differ. In fact $`S^{}=O(S+T)`$: if an irreversible computation is space efficient but time inefficient, then its reversible simulation is both time and space inefficient.

However, as we saw in the previous section, Bennet has proposed a way to reduce the amount of space the reversible simulation requires. His scheme has been improved overtime , and today we know that reversible and irreversible computation have the same complexity, i.e. $`T^{}O(T)`$ and $`S^{}S^2`$). The consumption of space of a reversible computation does not depend on the consumption of time of the irreversible one. This result is appreciated because, although the need of space $`S^{}c+c(T+S)`$ does not generally imply that the reversible computation is space inefficient, nevertheless it can be an unacceptable amount of space for many practically computations .

### 2.2 The quantum case

The design proposed to recycle the garbage relies on the possibility of retracing the computation, once duplicated the result. In the quantum framework this design does not work because of the no cloning theorem: it is not possible to make a copy of the state of a quantum system. This is especially true for a quantum computation that is more efficient than a classical one, for it uses superposition states. On the contrary, if a quantum computation is simply a small version of a classical reversible computation, then this problem does not arise.

It could be possible to let quantum computation be less hungry of space by relaxing reversibility. A quantum computation could proceed by applying alternatively a reversible evolution operator and an irreversible reuse of garbage. This way reversibility is lost because the garbage is erased, but this is not warring because we do not want to compute backward. With this scheme a quantum system for information processing would act in a way similar to that of the current model of quantum automata  (we will review it later on).

The problem of this design of garbage recycles stems from entanglement. Because the output of a time efficient quantum computation is entangled with the garbage, as in Shor’s factoring algorithm, the latter cannot be recycled without messing the computation.

From these considerations we conclude that a quantum system that computes a function $`f`$ consumes more space than a classical system (reversible or not) that computes the same function. Moreover, these considerations suggest that a quantum computation is necessarily reversible, i.e., it must be possible to retrace the input starting from the output (before the final measurement), not only because of the unitarity of the evolution operator, but also because output and garbage are generally entangled.

## 3 Quantum automata

Since a quantum computational system is a generalization of a classical one, it follows that its computational power should be greater or equal than that of the classical system. However, the computational power of quantum automata has been shown to be smaller than that of classical automata. We argue that this paradox origins from the fact that the currently accepted definition of quantum automaton neglects the concept of quantum reversibility. Here below, we revisit the role that reversibility plays into quantum automata and propose a new model of quantum finite automaton whose computational power is at least able to recognize regular languages.

### 3.1 The currently accepted definition of quantum automata

The currently accepted definition of quantum finite automaton has been proposed by Moore and Crutchfield  and Ambanis and Freivalds . A quantum finite automaton  $`𝒬`$ consists of:

* A Hilbert space $`H`$,
* An initial state vector $`|s_{init}H`$ with $`s_{init}|s_{init}=1`$,
* A subspace $`H_{accept}H`$ and an operator $`P_{accept}`$ that projects into it,
* An input alphabet $`A`$, and
* A unitary transition matrix $`U_a`$ for each symbols $`aA`$.

Using the shorthand $`U_w=U_{w_1}U_{w_2}\mathrm{}U_{w_k}`$ the language accepted by $`𝒬`$ is the function $`f^𝒬(w)=|P_{accept}U_w|s_{init}|^2`$ from words in $`A^{}`$ to probabilities in $`[0,1]`$.

The input alphabet consists of classical elements, whereas the internal states are represented by quantum systems (by vectors of a Hilbert space): this automaton is not fully quantum. Moreover, it is neither reversible. In fact from the final state $`U_w|s_{init}`$ one cannot trace back the computation because $`w`$ is unknown. To trace back the computation one will need some information that is not encoded in the final state. As to the computational power of this kind of quantum automaton, first A. Kondacs and J. Watrous  have showed that there is a regular language that cannot be accepted by a quantum finite automaton. Then, A. Brodosky and N. Pippenger have demonstrated that there is a whole class of regular languages that cannot be accepted by quantum finite automata.

### 3.2 (Quantum) Definite events

To build up a fully reversible model of quantum automaton we begin setting up a reversible quantum system that recognizes definite events111A definite event is a subset of a regular event whose elements have fixed length.. If $`_Q`$ is the language accepted by the finite automaton $`𝒬`$, whose reversible transition function is $`f`$, then the definite event $`_Q^n`$ is: $`_Q^n=\{x|x_Qand|x|=n\}`$. $`_Q^n`$ is recognized by the reversible combinatorial circuit of Figure 4, where $`q`$ is the initial state, and $`x_i`$ and $`s_i`$ are the $`i^{th}`$ input and his associated source respectively. This circuit is set up by connecting many combinatorial circuits that compute the transition function, each with its own input and source. Of the three output lines of these circuits, the first two ($`g_i^1`$ and $`g_i^2`$) contain the garbage, while the third encodes the new internal state. Reversibility is preserved by recording the value of the output and garbage each time the transition function is computed.

We have assumed that every gate has three input lines. In general you can suppose that every line represents a group of lines, so as the internal states set and the input symbols set may contain more that two elements.

Since the transition function is invertible this circuit could be thought as a quantum circuit. In the classical case it is possible to recycle the garbage either with the typical scheme, i.e., coping of the result and computing backward, or erasing the garbage and using it as new source. These solutions, as we saw in the previous section, are not generally useful in the quantum case.

### 3.3 A new model: an informal presentation

To realize a quantum finite automaton we extend the previous construction to the case of inputs of arbitrary finite length. We do not want different systems, even if constructed uniformly, to accept $`_Q^1,_Q^2,\mathrm{},_Q^n`$. We want one system that accepts all of them simultaneously.

The solution consists in storing the input in a quantum tape, that is a collection of equal quantum systems. Because of the presence of the source, actually we introduce two quantum tapes: the input and the source-garbage tape. This is exactly what Bennet did in his model of reversible Turing machine. However we know that the length of our tapes must be equal to that of the input sequence, while in the Turing machine case the determination of the maximums tape length is an undecidable problem.

Our automaton has a read/write head and an internal quantum state. The head reads one cell on the input tape and a corresponding cell on the source-garbage tape. Then, according to the internal state and to the reversible transition function, it changes the internal state and the states of the cells it read (these cells become garbage). Then, it moves to the right and read the next cell, and the loop restart. Our automaton acts like a reversible two-tape Turing machine whose head is ever moving to the right. It repeats its loop $`n`$ times, where $`n`$ is the length of the input string.

### 3.4 A new model: formal definition

A quantum finite automaton $`𝒬`$ consists of:

* A Hilbert space $`H_{in}`$. This is the space of the internal states.
* An initial vector $`|s_0H_{in}`$ with $`s_0|s_0=1`$.
* A subspace $`H_{accept}H_{in}`$ and an operator $`P_{accept}`$ that projects into it.
* A quantum tape $``$ composed by a sequence of quantum systems whose states are described in the Hilbert space $`I`$.
* A quantum tape $`𝒮𝒢`$ composed by a sequence of quantum systems whose states are described in the Hilbert space $`SG`$.
* A unitary evolution operator $`U:H_{in}ISGH_{in}ISG`$.

The input alphabet is composed by an orthonormal basis of $`I`$, a quantum system whose dimension depend on the automaton we are constructing. If we are generalizing to the quantum case a classical reversible automaton $`𝒬`$, then the dimension of $`I`$ depends on the number of input symbols of this automaton.

The dimension of $`SG`$ is related to the way the unitary evolution operator $`U`$ acts. In particular, if we want generalize to the quantum case the reversible automaton $`𝒬`$, constructed from the irreversible automaton $`𝒬_{irr}`$ following Bennet’s procedure, then the dimension of $`SG`$ is equal to the number of elements on which the transition function of $`𝒬_{irr}`$ is defined (i.e., to the number of quadruples of $`𝒬_{irr}`$). In fact, to construct the reversible version of $`𝒬_{irr}`$, following Bennet  we have to introduce a new ‘garbage-symbol’ for each transition of $`𝒬_{irr}`$.

The state of the $`k^{th}`$ ‘cell’ of $``$ is described by a vector belonging to the space $`I_k=I`$, while the state of the $`k^{th}`$ ‘cell’ of $`𝒮𝒢`$ is described by a vector belonging to $`SG_k=SG`$. If the input string is $`|w=|w_1|w_2\mathrm{}|w_n`$, with $`|w_kI_k`$, then the tape $`𝒮𝒢`$ contains $`|0_1|0_2\mathrm{}|0_n`$, with $`|0_kSG_k`$.

In order to understand how the automaton works, we first suppose that the states of the internal state, both $``$ and $`𝒮𝒢`$ tapes, are continuously factorizing. In this case, if $`P_{in}`$ projects into $`H_{in}`$, the internal state $`|s`$ evolves as in Table 2. The input string $`|w`$ is accepted with probability $`\left|P_{accept}|s(n)\right|^2`$.

In this case the automaton is similar to a classical reversible one222Note that in the literature a classical automaton with a reversible evolution and an irreversible reuse of garbage as new source (see Fig. 2) is frequently said ‘reversible’ (as in ). This is the definition of ‘reversible’ automaton that has been generalized to the quantum case . We refer to another definition of reversible classical automaton: a reversible Turing machine  whose head moves only to the right.. Indeed, we can schematize our automaton as in Figure 5.

When the automaton is not anymore restricted the states of the quantum register and those of the quantum tapes are not generally factorizing. Although the mathematical description of the system evolution is a little trickier, the automaton works in the same way.

In this case it turns useful to define:

$$\stackrel{~}{U_i}=𝕀_1𝕀_2\mathrm{}𝕀_{i1}𝕀_{i+1}\mathrm{}𝕀_nU_i,$$

where $`𝕀_k`$ is the identity of $`I_kSG_k`$, $`U_i`$ the unitary operator $`U`$ when applied to $`H_{in}I_iSG_i`$, and

$$|0^n=|0_1|0_2\mathrm{}|0_n,|0_kSG_k.$$

With this notation $`|w=|w_1|w_2\mathrm{}|w_n`$ is accepted with probability

$$P(|w)=\left|P_{accept}\stackrel{~}{U}_n\stackrel{~}{U}_{n1}\mathrm{}\stackrel{~}{U}_1|s_0|w|0^n\right|^2.$$

It is worth noting that, although when you apply $`\stackrel{~}{U}_k`$ you formally act on the space $`\left(_{i=0}^nI_iSG_i\right)H_{in}`$, actually: 1. A local operation is performed, and 2. The states of $`I_i`$ and $`SG_i`$ with $`i>k`$ do not modify. Therefore, when $`\stackrel{~}{U}_k`$ with $`k<i`$ is applied, you do not have to dispose the ‘cells’ described by $`I_i`$ or $`SG_i`$. This further implies that at the beginning of the computation the tapes length are not to be specified and that more ‘cells’ can be added as the computation moves on. This is exactly what happens in the classical case.

### 3.5 Computational power

From  we can deduce that every classical automaton can be effectively transformed into a classical reversible automaton. This reversible automaton acts on two tapes, and moves only to the right. In fact, If we apply Bennet’s procedure  to a Turing machine whose head move only to the right, we end up to a reversible two-tape Turing machine that moves only to the right (as already remarked in the quantum case we do not use the third tape). Since our model of quantum automaton can clearly simulate this classical reversible automaton, it follows that it has at least the same computational power of classical automata.

## 4 Conclusion and future developments

In this paper we have revisited the classical theory of reversible computing and studied its generalization to the quantum case.

We have showed that it is not possible to generalize to the quantum case the design that made classical reversible computation space efficient (because of the ‘no cloning theorem’), and pointed out that, because of the entanglement, it is not possible to reuse the garbage without messing the computation. Moreover we clarified that the quantum computing reversibility, namely the possibility of tracing back the computation from the final result, due to the unitarity of the quantum evolution, is not eliminable because of the presence of non-local correlation.

These consideration had led us to propose a new model of fully quantum and reversible automaton that has at least the same computational power of classical automata. This automaton is, however, ‘angry’ of space. This is a relevant result since the computational power of the currently accepted model of quantum finite automata is thought to be smaller than that of classical finite automata. The main difference between the quantum automata here proposed and the currently accepted model of quantum automata concerns reversibility.

In future the computational power of the proposed model of quantum finite automaton should be investigated. Particularly, I am interested in the role of the garbage. Dose the computational power of the proposed model vary by allowing or preventing interference between the final state and the garbage. In other words: is the garbage useful, or is it simply a by-product of quantum computing?

### 4.1 Acknowledgments

This work is for the most part based on my degree thesis. I particularly tank my supervisor, Prof. Giuseppe Trautteur, and my co-supervisor, Prof. Vincenzo R. Marigliano, both at the Dipartimento di Scienze Fisiche dell’Università di Napoli “Federico II”.
Università di Napoli “Federico II”, Dipartimento di Scienze Fisiche. Internal report $`n^{}\text{ DSF09/2001}`$.


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# From features to expression: High-density oligonucleotide array analysis revisited.

## Raw intensities and background subtraction

The starting point in our analysis of HDONAs consists of the fluorescent intensities of all the 25-base probes on the chip, including both the PM and MM cells (.CEL files). This data has already gone through one processing step by Affymetrix, namely an average of the pixel intensities (36 pixels per cell for the Mu11k mouse chip) for each probe cell. Before moving on to consider which probes belong to which gene, it is instructive to inquire about the reproducibility of the raw data in replicate experiments. The cigar shaped cloud in Fig. 1(a) shows such a typical example. In an ideal (noiseless) experiment, the scatter plot of the replicates should produce a single straight line with unit slope, so that the broadening of the line in a real experiment reflects the noise. In HDONAs, this noise has multiple sources, including intrinsic biological and sample processing variability, hybridization kinetics and thermodynamics, noise related to the incorporation and amplification of fluorescent dyes, and the measurement of the fluorescence in the scanning process. Despite all these potential sources, the experimental situation is encouraging as indicated by the high reproducibility in (a).

The intensity dependence of the noise envelope is commonly referred to as the noise funnel. In Fig. 1(a), the funnel is only very weakly intensity dependent. We observe that the onset of the intensities is shifted from zero to $`500`$, indicating that cell intensities have an additive background component. Estimating this background intensity is essential when processing low intensity data points. In HDONAs, identifying background is a priori a different problem from its analogue in cDNA spotted arrays. There, one tries to measure the intensity of regions in between adjacent spots as a measure for the local background. In contrast, the inter-feature distance in Affymetrix arrays is too small for a similar measurement and one must estimate the background from the probe cells themselves. Background is by definition non-specific, and should therefore not be sensitive to the single base sequence modification in the MM cells. Consequently, we consider the subset of probe pairs whose PM and MM intensities differ by less than a given small quantity (PM-MM \< $`ϵ`$) as representative of the background. The distributions of either the PM or MM cells obtained in this manner depend only weakly on $`ϵ`$, and can be reasonably fitted to Gaussians from their low-intensity onset up to their maximum (Fig. 1(d)). We used $`ϵ=50`$ in units of the .CEL file intensities, but using $`ϵ=100`$ leads to changes of the order of only $`1\%`$ for the mean background $`b`$ and standard deviation $`\sigma `$. Fig. 1(b) shows the raw data after background subtraction. The typical broadening of the noise funnel at low intensities end reflects the residual background (the fact that $`\sigma 0`$). In contrast, the Affymetrix procedure estimates $`b`$ and variance var$`(b)`$ from the $`2\%`$ lowest intensity cells. The mean and variance obtained this way are strongly dependent on the arbitrary cutoff ($`2\%`$). Typically, we obtain a $`b`$ larger than the value reported by the Affymetrix software $`(+15\%)`$, so that we are left with $`86\%`$ of the features lying above $`b+2\sigma `$, rather that $`93\%`$. In addition, our noise funnel is slightly broader. Nevertheless, our algorithm for composite scores still leads to a significant noise reduction (cf. Results).

As a preview, we show in Fig. 1(c) which subset of PM probes are considered by our algorithm when computing ratio scores between the two samples. It turns out consistently that noisier cells are automatically discarded, however, not on the basis of an evaluation of the funnel shape (cf. Probe cell selection).

## Constructing good estimators

The previous discussion about background intensity distributions raises the following general issue: what are good estimators for data drawn from an unknown distribution? The answer involves finding the coordinates in which the distribution is most well behaved. In the best situation, a distribution is short tailed, which ensures that moments are not only well defined but are also relevant quantities for a statistical description of the data set. In a situation of long tailed distributions (e.g. driven by a large number of outliers in a dataset), the situation is more complicated. Then, one either needs to establish a model describing how one should truncate the dataset before calculating averages, or work with estimators which are more robust to outliers, like percentiles. To formulate this more precisely, we consider the following problem: suppose we have $`n`$ samples from a positive distribution $`p(x)`$, and samples from the scaled distribution $`\lambda p(x/\lambda )`$. The problem is to find the optimal estimator for $`\lambda `$. The solution clearly shall depend on $`p`$. If $`p`$ is a well behaved distribution, then $`\lambda p(x/\lambda )/p(x)`$ ($`x=\frac{1}{n}_{i=1}^nx_i`$ denotes the arithmetic average) is a fine estimator; but it miserably fails if $`p`$ is long tailed. Conversely, the median is a suboptimal estimator in the case of well behaved distributions, but it has the advantage of being more robust in the long tailed case.

Datasets from HDONAs do exhibit such long tails, as we show in Fig. 2. The histograms (Fig. 2A) show the $`\mathrm{log}_2`$ PM intensity distributions of all probe sets, each PM cell being normalized by their probe set median. Probe sets are classified into four windows according to their median magnitude; we have verified that refined windows do not change the shape of the distributions significantly. These distributions show that cell intensities vary by factors of $`2^5`$ around their median in all the intensity windows, and that the distributions are far from Gaussian. Nevertheless, log-coordinates lead to roughly symmetric distributions, at least up to the last intensity window. We think of these distributions as the sum of a well behaved component (with converging moments to which the Central Limit Theorem applies), plus a long tailed part due to outliers. These need to be identified (cf. Probe cell selection) and discarded. Then, the meaningful estimators for the truncated data sets consist of arithmetic averages in log-coordinates (geometric means).

The ordered intensity profiles of individual, randomly picked probe sets are also shown (Fig. 2B), each of them for duplicate experiments. These emphasize the reproducibility of the broad intensity profiles.

## The mysterious MM cells

Before explaining how to discard outliers and compute a ratio score, we explain why we do not utilize the MM cells for the calculation of composite intensity and ratio scores. Single mismatch cells seem not to be consistently doing what they were originally designed for, namely to serve as a control for non-specific hybridization. Instead, we find that MM cells often act as a pale PM, essentially binding the same oligonucleotide as the PM do, but on average $`1.8`$ times weaker than the PM probes (Fig. 3). Notice that (a) presents the raw cell intensities, whereas (b) reports the distributions of composite intensities obtained by considering the PM and MM probe sets as if they were two different conditions for the same gene. It is somewhat disturbing that in the high intensity region, the cloud (a) exhibits a valley around the diagonal. This means that there is a significant number of probes where the target cRNAs bind more specifically to the MM (in contrast, non-specific hybridization would result in a maximum on the diagonal). A possible scenario for this matter are polymorphisms between the mouse specie used to design the probe sequences and that used as the target. In such instances, the MM may actually act as the effective PM, however, these should be rare events since the MM sequence is always substituted exactly at the central position.

In any case, subtracting the MM from the PM intensities is likely to be misleading, and we found it favorable to not consider the MM cells any further. As a matter of fact, it is not entirely surprising that a single base change does not provide a clear cut discrimination for non-specific hybridization in a process dominate by kinetics rather that equilibrium thermodynamics.

## Probe cell selection and ratio composites

We now describe our algorithm for the selection of cells used in the calculation of ratios. We observed that comparing two identical probe sets hybridized to two different samples leads to series of pairwise PM cells ratios $`(r_1,r_2,\mathrm{},r_N)`$ behaving quite far from an ideal homogeneous situation (all $`r_i`$ being the same). Instead, the individual cell ratios often vary over a decade; it also occurs that some cells indicate an up-regulation whereas others indicate the opposite (cf. Fig. 4 (c) and (d)). In this situation, a straightforward linear regression between PM intensities of the two samples is not adequate. It further happens that high intensity cells saturate in one or both of the samples, leading to useless (even misleading) cell ratios. Such probe cells are discarded from our analysis. The saturation thresholds (most likely due to the photomultiplier) can be read off the .CEL files, by plotting the mean cell intensities versus the standard deviation of the pixel intensities. Our purpose here is not to address the question of why such broad ratio distributions may arise, but rather how to optimize scores for them. In a first step, we order the series $`(\mathrm{log}r_1,\mathrm{log}r_2,\mathrm{},\mathrm{log}r_N)`$. Next, we aim at splitting this set in an interval $`I_{med}`$ with optimally narrow range, and a subset of outliers to be omitted from the ratio score calculation. We require the median to be a member of $`I_{med}`$ and optimize for its left and right boundaries $`i_l`$ and $`i_r`$. $`l=\mathrm{log}r_{i_r}\mathrm{log}r_{i_l}`$ denotes the range of $`I_{med}`$ and $`L`$ the range of the full probe set. In the absence of knowledge about how the ratios are distributed within $`I_{med}`$, except for the range from which the ratios are drawn, the most unbiased assumption is to assume a uniform probability $`p`$ within this range. Hence, the probability of finding a log-ratio in $`I_{med}`$ is $`p=\frac{1}{l}`$ and $`p^{}=\frac{1}{L}`$ for an outlier. We then retain $`I_{med}`$ that maximizes the likelihood of the full probe set ratios given our model. We must therefore maximize $``$$`=(Nn)\mathrm{log}Ln\mathrm{log}l`$, where $`N`$ is the total number of cells and $`n`$ the cells in $`I_{med}`$. In essence, this procedure picks the optimal interval $`I_{med}`$ as a tradeoff between having too many outliers, and letting the range of $`I_{med}`$ become too wide. Prototype situations showing how our model selects $`I_{med}`$ are presented in Fig. 5 for two different conditions. After having identified $`I_{med}`$, we compute scores by taking geometric means of cell ratios and intensities from PM cells inside $`I_{med}`$.

It is now worthwhile looking back at Fig. 1(b) and (c) showing which probe cells are actually selected. As a fact, there are only few probe sets that have common low intensity cells(cf. Fig. 2A). Instead, the low intensity cells are distributed among the probe sets, which is clearly reflected in Fig. 1(c) by the low density of points at the low end.

## Results

To demonstrate the potential of our method, we analyzed a set of HDONA hybridizations evaluating the transcriptional profiles of six different mouse brain regions using the Mu11k mouse A and B chip series. The dissections and enzymatic steps (making the target cRNA) were performed in duplicate in all experiments and the two obtained samples were hybridized onto separate arrays. Fig. 5A shows the scatter plots of the replicates from four brain regions, the A and B chips being superimposed on the same plot.

Our scores exhibit a much tighter scatter, especially in the mid to low intensity range. Further, we are able to report scores for all the genes on the arrays, whereas the Affymetrix algorithm reports non-negative values (negative intensities are meaningless and not plotable on a logarithmic scale) for $`70\%`$ of the probe sets. As mentioned, the reason we obtain relatively few low intensity genes ($`2\sigma `$ of residual background $`100`$ in these units) is that low intensity cells tend to be distributed among different probe sets rather than being grouped. The histograms in Fig. 5B show the distributions of the $`\mathrm{log}_2`$ ratios from the four combined regions in intensity windows. Our distributions are well fitted by narrow Gaussians with standard deviations $`\sigma 0.2`$ for intensities $`>300`$. $`2\sigma `$ then corresponds to a fold change of $`1.25`$. In contrast, the Affymetrix scores lead to longer tails especially in the mid to low intensity range. Next, we contrast a replicate experiment Fig. 6(a) with a comparison of two different experimental conditions Fig. 6(b). As $`\sigma `$ is not strongly intensity dependant, we have tentatively indicated in red the fold changes of $`1.25`$. Consistently, $`6\%`$ of the genes lie beyond the $`2\sigma `$ lines in (a). For the comparison of two different condition (b), $`20\%`$ of the genes are differentially expressed by a factor $`1.25`$. We should further mention that the location of our points in the scatter plot is equivalent to the reported ratio, which is not the case for the Fold Change calculated by Affymetrix.

Finally, we demonstrate that our procedure leads to a greatly enhanced consistence between the scores obtained from probe sets for identical genes. There are $`700`$ genes represented twice or more on the combined A and B Mu11k mouse chips. The sequences for two such sets may probe different locations on the same gene, or one probe set may represent a subsequence of the other. Nevertheless, they correspond to the same physical gene and should ideally lead to identical scores. Let $`p_1`$ and $`p_2`$ be two such probe sets for a common gene, and $`r_i`$ ($`i=1,2`$) the ratio of the $`p_i`$ intensities probed in two different brain regions. In Fig. 7, we show the distributions of $`\mathrm{log}_2(\frac{r_1}{r_2})`$ for two comparisons C1 and C2 (C2 corresponds to Fig. 1(b)). The figure is separated into left and right according to whether the Affymetrix fold change was reported with a “$``$” in at least one of the two representations $`p_1`$ or $`p_2`$ (the “$``$” indicates that the baseline intensity was within the residual background, suggesting that the reported value is unreliable). It is evident that our ratios are far more consistent than the Affymetrix scores, especially in the right panels. Our standard deviations $`\sigma `$ are similar throughout all plots, the $`\sigma `$ on the right panels being barely larger. Taking $`2\sigma 0.4`$ implies that $`95\%`$ of the pairs ($`r_1,r_2)`$ differ in ratios by a factor less than $`1.3`$, which is a significant narrowing in comparison to the distributions produced by the current Affymetrix algorithm.

## Summary

We presented an improved approach for computing composite ratio scores for high-density oligonucleotide arrays. Our new method differs significantly from the current Affymetrix algorithm in the following manner: (i) MM cells are not included because their information content is unclear; (ii) ratios between two different samples are derived from comparing the PM cell intensities pairwise, and then identifying a subset of probe cells leading to optimally consistent scores; (iii) geometric averages are used because the intensity and ratios of probe sets are distributed on a exponential scale. We showed that our method acts as a noise reducing filter in the sense that (i) replicate experiments show an increased reproducibility; (ii) ratio scores for probe sets probing the same gene show a much greater correlation. We emphasized that because the distribution of intensities within a probe set is often much broader than the distribution of cell ratios taken from a pairwise comparison, the most reliable information lies in ratio and not in absolute intensity composites. Therefore, we designed our algorithm to primarily compute ratios, and reported intensities (e.g. in scatterplots) always dependent upon a comparison.

Our method should be considered as a the simplest way to extract the most information from just two hybridization arrays, therefore allowing benefits from working with small data sets of very homogeneous quality. In contrast, the more involved model-based approach requires large data sets for calibration, and is therefore more sensitive to the variability introduced by slight changes in the experimental protocol. Further, knowledge of the probe sequences would enable one to develop more elaborate approaches based on the kinetic and thermodynamic properties of the probes.

We have applied our method to a large microarray data set studying the neurogenesis in adult mice brains, which lead to highly significant biological results. The generated data sets could be clustered robustly using standard hierarchical techniques. Finally, the fact that MM cells are not explicitely needed opens the possibility of screening twice as many genes on a given microarray. Considering that the current estimates about the number of genes in the human genome predict fewer than $`40,000`$ genes, it is not unrealistic to expect single arrays for all human genes in the near future.

We thank E. van Nimwegen for suggesting many interesting ideas. We benefitted from inspiring discussions with J. Luban, M. Asmal and A. Alvarez-Buylla. Help from C. Hacker has been invaluable for generating the extremely high quality data. F. N. acknowledges the the Swiss National Science Foundation for financial support. D. A. L. was supported by the NIH grant GM07739.


text:
# 𝑓(𝑅) gravity theory and CMBR constraints

## I Introduction

The inflation scenario in the early universe provides a consistent and successful mechanism for generating the seed fluctuations of the observed large-scale cosmic structures as well as the gravitational wave background . As a natural consequence, the observed large-scale structures, in particular, the observed anisotropies of the cosmic microwave background radiation (CMBR) in the large-angular-scale in return, can provide constraints on the physics during the inflation era which is usually based on model scalar fields or generalized versions of gravity theories. Recent spectacular developments in the CMBR anisotropy observations  are transforming this branch of cosmology into a quantitative science.

In the theoretical side, the multipole moments of the CMBR anisotropies are basically governed by the seed fluctuations of the scalar- and tensor-type structures which provide the initial spectra, and the transfer function which incorporates the evolution of the initial spectra through recombination till the present epoch. The transfer function is known to depend rather sensitively on many cosmological parameters: present day Hubble constant, spatial curvature, cosmological constant, density parameters of variety of constituents of the universe, possible reionization, etc. However, with the observational perspective at present epoch alone we cannot distinguish the transfer function from the initial condition. In choosing the initial conditions one needs prior assumptions on the favored seed generating mechanism. Although it is a common practice in the literature to assume a simple scale-invariant power-spectrum based on the single inflaton fluctuation without tensor-type contribution, the initial conditions can be convoluted with the transfer functions in a rather intricated manner: both encouraging  and discouraging  conclusions can be drawn from reasonable variations of the initial conditions. Since different theoretical inflation models provide different seed generating mechanism it can affect only the initial conditions.

In the present work we investigate another theoretical aspect of the study showing that the inflationary seed generating mechanism based on the completely different gravity theory can in fact give similar viable initial conditions. Here, we will consider a gravity theory which is a general function of the scalar curvature. Historically, the original proposal of a modern version of accelerated expansion in the early universe was, in fact, based on the gravity with quantum one-loop correction . The curvature-square terms naturally appear in many theories: gravity with quantum corrections, Kaluza-Klein models, string/M-theory program, etc. The $`R^2`$ gravity, in particular, has a natural reheating mechanism  thus providing a self-contained inflation model without introducing a field or a phase transition.

In this paper, using the large-angular-scale CMBR data we will derive constraints on an inflation scenario based on $`f(R)`$ gravity theory. We will take a phenomenological approach by trying to reconstruct the successful inflation based on $`f(R)`$ gravity from observational results. We consider general $`f(R)`$ term in the Lagrangian, and show that the ordinary slow-roll assumption during inflation together with Zel’dovich spectral conditions for the scalar- and tensor-type structures chooses $`R^2`$ gravity as the unique candidate, eq. (25). The considered models naturally lead to specific near scale-invariant Zel’dovich spectra both for the scalar- and tensor-type perturbations, eqs. (26,34). From the COBE-DMR data we derive a strong constraint on the coupling constant of the $`R^2`$ term and the energy scale during inflation epoch, eq. (33). It also predicts the the gravitional wave contribution should be negligible, eq. (33). We show that parallel analyses made in the conformally transformed Einstein frame give the observationally identical results.

Before presenting our main results in §V-VII, in §II-IV we summarize recent developments of the classical evolution and the quantum generation processes for the scalar- and tensor-type perturbations, and their observational consequences; these are presented in a general context and in a unified manner. We set $`c1`$.

## II Classical evolution

We consider a gravity

$`L={\displaystyle \frac{1}{2}}f(\varphi ,R){\displaystyle \frac{1}{2}}\omega (\varphi )\varphi ^{;c}\varphi _{,c}V(\varphi ),`$ (1)
where $`f(\varphi ,R)`$ is a general algebraic function of the scalar field $`\varphi `$ and the scalar curvature $`R`$; $`\omega (\varphi )`$ and $`V(\varphi )`$ are general algebraic functions of $`\varphi `$. We introduce $`Ff/R`$.

We consider a spatially flat homogeneous and isotropic FLRW metric together with the most general scalar- and tensor-type spacetime dependent perturbations

$`ds^2`$ $`=`$ $`a^2\left(1+2\alpha \right)d\eta ^2a^2\beta _{,\alpha }d\eta dx^\alpha `$ (3)
$`+a^2\left(\delta _{\alpha \beta }+2\phi \delta _{\alpha \beta }+2\gamma _{,\alpha \beta }+2C_{\alpha \beta }\right)dx^\alpha dx^\beta ,`$
where $`C_{\alpha \beta }`$ is a transverse-tracefree tensor-type perturbation corresponding to the gravitational wave. We also decompose $`\varphi =\overline{\varphi }+\delta \varphi `$, $`F=\overline{F}+\delta F`$, etc.

In  we analysed the classical evolution and the quantum generation processes of the scalar- and tensor-type structures. Perturbed action can be written in a unified form as

$`\delta ^2S={\displaystyle \frac{1}{2}}{\displaystyle a^3Q\left(\dot{\mathrm{\Phi }}^2\frac{1}{a^2}\mathrm{\Phi }^{|\gamma }\mathrm{\Phi }_{,\gamma }\right)𝑑td^3x}.`$ (4)
This is valid for the second-order gravity system such as either $`f=F(\varphi )R`$ in the presence of a field $`\varphi `$ or $`f=f(R)`$ without the field; an overdot indicates the time derivative based on $`t`$ with $`dtad\eta `$. For the scalar- and tensor-type perturbations we have :

$`\mathrm{\Phi }=\phi _{\delta \varphi },Q={\displaystyle \frac{\omega \dot{\varphi }^2+3\dot{F}^2/2F}{(H+\dot{F}/2F)^2}},`$ (5)
$`\mathrm{\Phi }=C_\beta ^\alpha ,Q=F,`$ (6)
where $`H\dot{a}/a`$. $`\phi _{\delta \varphi }\phi H\delta \varphi /\dot{\varphi }`$ is a gauge-invariant combination introduced in . The equation of motion and the solution in the large-scale limit become

$`{\displaystyle \frac{1}{a^3Q}}(a^3Q\dot{\mathrm{\Phi }})^{}{\displaystyle \frac{\mathrm{\Delta }}{a^2}}\mathrm{\Phi }=0,`$ (7)
$`\mathrm{\Phi }=C(𝐱)D(𝐱){\displaystyle _0^t}{\displaystyle \frac{dt}{a^3Q}}.`$ (8)
Thus, ignoring the transient solution we have a temporally conserved behavior

$`\mathrm{\Phi }(𝐱,t)=C(𝐱).`$ (9)
Using $`za\sqrt{Q}`$ and $`vz\mathrm{\Phi }`$ eq. (7) becomes $`v^{\prime \prime }+\left(k^2z^{\prime \prime }/z\right)v=0`$, where a prime denotes the time derivative based on $`\eta `$. Thus, the large-scale assumption used in eq. (8) is $`z^{\prime \prime }/zk^2`$.

## III Quantum generation

We introduce parameters

$`ϵ_1{\displaystyle \frac{\dot{H}}{H^2}},ϵ_2{\displaystyle \frac{\ddot{\varphi }}{H\dot{\varphi }}},ϵ_3{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{F}}{HF}},ϵ_4{\displaystyle \frac{1}{2}}{\displaystyle \frac{\dot{E}}{HE}},`$ (10)
where $`EF[\omega +3\dot{F}^2/(2\dot{\varphi }^2F)]`$. For $`\dot{ϵ}_1=0`$ we have $`\eta =1/[(1+ϵ_1)aH]`$, thus, $`a|\eta |^{1/(1+ϵ_1)}t^{1/ϵ_1}`$. For $`\dot{ϵ}_i=0`$ we have $`z^{\prime \prime }/z=n/\eta ^2`$ where for the scalar- ($`n=n_s`$) and tensor-type ($`n=n_t`$) perturbations

$`n_s={\displaystyle \frac{(1ϵ_1+ϵ_2ϵ_3+ϵ_4)(2+ϵ_2ϵ_3+ϵ_4)}{(1+ϵ_1)^2}},`$ (11)
$`n_t={\displaystyle \frac{(1+ϵ_3)(2+ϵ_1+ϵ_3)}{(1+ϵ_1)^2}}.`$ (12)
With constant $`n`$ eq. (7) becomes a Bessel’s equation. After a canonical quantization we can derive the vacuum expectation value of the quantum field $`\widehat{\mathrm{\Phi }}`$. In the quantization process of the gravitational wave we need to take into account of the two polarization states properly . In the large scale limit, $`k|\eta |1`$, the power-spectra based on vacuum expectation value become

$`𝒫_{\widehat{\phi }_{\delta \varphi }}^{1/2}(k,\eta )={\displaystyle \frac{1}{\sqrt{Q}}}{\displaystyle \frac{H}{2\pi }}{\displaystyle \frac{1}{aH|\eta |}}{\displaystyle \frac{\mathrm{\Gamma }(\nu _s)}{\mathrm{\Gamma }(3/2)}}\left({\displaystyle \frac{k|\eta |}{2}}\right)^{3/2\nu _s},`$ (13)
$`𝒫_{\widehat{C}_{\alpha \beta }}^{1/2}(k,\eta )=\sqrt{{\displaystyle \frac{2}{Q}}}{\displaystyle \frac{H}{2\pi }}{\displaystyle \frac{1}{aH|\eta |}}{\displaystyle \frac{\mathrm{\Gamma }(\nu _t)}{\mathrm{\Gamma }(3/2)}}\left({\displaystyle \frac{k|\eta |}{2}}\right)^{3/2\nu _t},`$ (14)
where $`\nu _s\sqrt{n_s+1/4}`$ and $`\nu _t\sqrt{n_t+1/4}`$, and we have ignored dependences on the vacuum choices; for $`\nu _s=0=\nu _t`$ we have additional $`\mathrm{ln}(k|\eta |)`$ factors.

## IV Observational consequences

The observationally relevant scales exit Hubble horizon within about $`60`$ $`e`$-folds before the end of the latest inflation. Far outside the horizon the quantum fluctuations classicalize and we can identify $`𝒫_\mathrm{\Phi }=𝒫_{\widehat{\mathrm{\Phi }}}`$ where the l.h.s. is the power-spectrum based on spatial averaging. Since $`\mathrm{\Phi }`$ is conserved while in the large-scale limit, the power-spectra in eqs. (13,14) can be identified as the classical power-spectra at later epoch. Later, we will consider a scenario with the inflation based on $`f(R)`$ gravity followed by ordinary radiation and matter dominated eras based on Einstein gravity. We have shown in  that as long as the scale remains in the super-horizon scale $`\mathrm{\Phi }`$ is conserved independently of the changing gravity theory from one type to the other. Thus, since eqs. (13,14) are now valid for the classical power-spectra the spectral indices of the scalar and tensor-type perturbations are

$`n_S1=3\sqrt{4n_s+1},n_T=3\sqrt{4n_t+1}.`$ (15)
For the scale independent Zel’dovich ($`n_S1=0=n_T`$) spectra the quadrupole anisotropy becomes

$`a_2^2=a_2^2_S+a_2^2_T={\displaystyle \frac{\pi }{75}}𝒫_{\phi _{\delta \varphi }}+7.74{\displaystyle \frac{1}{5}}{\displaystyle \frac{3}{32}}𝒫_{C_{\alpha \beta }}.`$ (16)
The ratio between two types of perturbations is

$`r_2{\displaystyle \frac{a_2^2_T}{a_2^2_S}}=3.46{\displaystyle \frac{𝒫_{C_{\alpha \beta }}}{𝒫_{\phi _{\delta F}}}}.`$ (17)
The four-year COBE-DMR data give :

$`a_2^21.1\times 10^{10}.`$ (18)
## V Spectral constraints

We consider a gravity

$`L={\displaystyle \frac{1}{2}}f(R),`$ (19)
which is a special case of eq. (1). Results in §II-IV remain valid by setting $`\omega \dot{\varphi }^2`$ term in eq. (6) equal to zero, and replacing $`\phi _{\delta \varphi }`$ to $`\phi _{\delta F}\phi H\delta F/\dot{F}`$. Consequently, the slow-roll parameter $`ϵ_4`$ in eq. (10) changes to $`ϵ_4\ddot{F}/(H\dot{F})`$ and we have $`ϵ_2=0`$ .

Equations for the background are

$`H^2={\displaystyle \frac{1}{3F}}\left({\displaystyle \frac{RFf}{2}}3H\dot{F}\right),`$ (20)
$`\dot{H}={\displaystyle \frac{1}{2F}}\left(\ddot{F}H\dot{F}\right),`$ (21)
with $`R=6(2H^2+\dot{H})`$. Equation (21) gives

$`ϵ_1=ϵ_3(1ϵ_4).`$ (22)
Since we have $`R=6(2+ϵ_1)H^2`$, eq. (20) gives $`f=RF(1+ϵ_12ϵ_3)/(2+ϵ_1)`$.

As the slow-roll conditions, as in the MSF (minimally coupled scalar field) , we consider

$`|ϵ_1|1.`$ (23)
We have $`ϵ_2=0`$. Equations (13,14) are available for $`\dot{ϵ}_i=0`$; since the large-scale structures are generated from a short duration (about 60 $`e`$-folds) of the inflation we expect time variation of $`ϵ_i`$ during that period is negligible. The spectral indices in eqs. (12,15) are valid for arbitrary but constant $`ϵ_i`$s. For constant $`ϵ_i`$ we have $`fR^{(2+ϵ_1)/(1+ϵ_12ϵ_3)}`$. From eqs. (22,23) we have $`ϵ_30`$ or $`ϵ_41`$. If $`ϵ_41`$, the spectral constraint $`n_S10`$ thus $`n_s2`$ in eq. (12) implies $`ϵ_31`$ or $`4`$ both of which are excluded if we impose $`n_T0`$ thus $`n_t2`$ in eq. (12). Thus we have $`ϵ_31`$ and

$`fR^{2ϵ_1+4ϵ_3}.`$ (24)
Imposing $`ϵ_30`$ in eq. (12) with $`n_s2`$ leads to $`ϵ_40`$ or $`3`$; correspondingly we have $`ϵ_1ϵ_3`$ or $`4ϵ_3`$. In the case with $`ϵ_43`$ we have exactly $`f=R^2`$ to the linear order in $`ϵ_i`$! In the case with $`ϵ_40`$ we have $`ϵ_3=ϵ_1`$, thus

$`fR^{2+3ϵ_1}.`$ (25)
In this case we have $`|ϵ_i|1`$.

Therefore, the requirement of near scale-invariant Zel’dovich spectra for both structures generated from inflation based on $`f(R)`$ gravity chooses $`fR^2`$ gravity. The current observations of CMBR, however, provide a constraint on only the sum of the two types of structures. It is often believed that the observations provide constraint on the scalar-type perturbation, thus its amplitude and the spectral index. In such a case, our use of the Zel’dovich type spectral index for the tensor-type structure as well to sort out the $`R^2`$ can be regarded as having a loop-hole in the argument. However, notice that we have used the $`n_T`$ constraint to exclude the cases of $`ϵ_41`$, thus $`ϵ_31`$ or $`4`$ just above eq. (24). If we accept these cases, we have $`fR^2`$ or $`R^{2/7}`$, respectively, and eqs. (12,15) give $`n_T2`$ or $`8`$, respectively, which look like not very promising cases.

In the case of $`|ϵ_i|1`$ the spectral indices in eq. (15) become

$`n_S12(3ϵ_1ϵ_4),n_T0,`$ (26)
to $`ϵ_i`$-order. We can estimate $`ϵ_4=3ϵ_1+\dot{ϵ}_1/(Hϵ_1)`$, and because we have $`\dot{ϵ}_1𝒪(ϵ_i^2)`$ we cannot ignore the second term. In the MSF case eqs. (12,15) remain valid with $`ϵ_3=0=ϵ_4`$, thus we have $`n_S14ϵ_12ϵ_2`$ and $`n_T2ϵ_1`$.

## VI COBE-DMR constraints

Now, we consider the following gravity during inflation

$`f={\displaystyle \frac{m_{pl}^2}{8\pi }}\left(R+{\displaystyle \frac{R^2}{6M^2}}\right).`$ (27)
We can show that the trace of gravitational field equation gives $`\mathrm{}RM^2R=0`$ . Thus, $`R`$ behaves like a MSF with mass $`M`$. There have been many studies of the $`R^2`$ inflation model . During inflation we assume the second term dominates over the Einstein action which requires $`H_{\mathrm{infl}}^2M^2`$; this is a slow-roll regime and we have $`|ϵ_i|1`$. For the model in eq. (25), the pure $`R^2`$ gravity implies $`ϵ_1=0`$ and exponential inflation. However, in our case of eq. (27) we do not have vanishing $`ϵ_1`$. In the slow-roll regime we have $`ϵ_3=ϵ_1`$, thus eq. (26) remains valid.

From eqs. (13,14) we have

$`𝒫_{\phi _{\delta F}}^{1/2}={\displaystyle \frac{H}{2\pi }}{\displaystyle \frac{1}{\sqrt{Q}}},𝒫_{C_{\alpha \beta }}^{1/2}={\displaystyle \frac{H}{2\pi }}\sqrt{{\displaystyle \frac{2}{Q}}}.`$ (28)
Assuming $`H^2M^2`$ we have

$`𝒫_{\phi _{\delta F}}^{1/2}={\displaystyle \frac{1}{2\sqrt{3\pi }}}{\displaystyle \frac{1}{|ϵ_1|}}{\displaystyle \frac{M}{m_{pl}}},𝒫_{C_{\alpha \beta }}^{1/2}={\displaystyle \frac{1}{\sqrt{\pi }}}{\displaystyle \frac{M}{m_{pl}}},`$ (29)
where we ignored $`[1+𝒪(ϵ_i)]`$ factors. Thus, $`𝒫_{C_{\alpha \beta }}^{1/2}/𝒫_{\phi _{\delta F}}^{1/2}=2\sqrt{3}|ϵ_1|`$, and from eq. (17) we have

$`r_2=41.6ϵ_1^2.`$ (30)
These results can be compared with the MSF case where the power-spectra ratio becomes $`2\sqrt{ϵ_1}`$ and the quadrupole ratio $`r_2=6.93n_T`$ which is the well known consistency relation; for a consistency relation with general $`\mathrm{\Lambda }`$, see . Since $`r_2`$ in eq. (30) is quadratic order in $`ϵ_1`$, and $`n_T`$ in eq. (26) vanishes to the linear order in $`ϵ_i`$, in order to check whether the consistency relation holds in the $`R^2`$ gravity we need to investigate the second-order effects of the slow-roll parameters.

From eqs. (16,29) using eq. (18) we have

$`{\displaystyle \frac{M}{m_{pl}}}=3.1\times 10^4|ϵ_1|.`$ (31)
Similar constraint has been known in the literature . Compared with previous works which are based on an asymptotic solution of the background $`R^2`$-gravity inflation model (see below), our approach is based on exact solutions available when $`\dot{ϵ}_i=0`$, where instead we can handle the perturbations analytically; also, our results are derived without using the conformal transformation.

In fact, based on the known inflation solution we can make the constraints more concrete. From eqs. (20,21) we can derive $`\dot{H}^26H^2\dot{H}H^2M^22H\ddot{H}=0`$. In the limit $`H^2M^2`$, and in the regime of vanishing $`\ddot{H}`$ term, we have a solution during the inflation as $`H=H_iM^2(tt_i)/6`$ . Assuming that the inflation ends near $`(t_et_i)6H_i/M^2`$, we can estimate the number of $`e`$-folds from $`t_k`$ (when the relevant scale $`k`$ exits the Hubble horizon and reaches the large-scale limit) till the end of inflation as

$`N_k{\displaystyle _{t_k}^{t_e}}H𝑑t={\displaystyle \frac{H^2}{2\dot{H}}}(t_k)={\displaystyle \frac{1}{2ϵ_1(t_k)}}.`$ (32)
\[In this case we are considering piecewise constancy of $`ϵ_1`$. Since $`\dot{ϵ}_1𝒪(ϵ_i^2)`$, eqs. (13,14) are not affected to the linear order in slow-roll parameters.\] Thus $`H(t_k)/M=\sqrt{N_k/3}`$. Since the large-angular CMBR scales exit horizon about $`5060`$ $`e`$-folds before the end of the latest inflation, $`N_k60`$ requires $`|ϵ_1|=\frac{1}{2N_k}0.0083`$. Consequently from eqs. (30,31) we have

$`r_20.0029,{\displaystyle \frac{M}{m_{pl}}}2.6\times 10^6,{\displaystyle \frac{H(t_k)}{M}}4.5.`$ (33)
Thus we have negligible gravitational wave contribution to CMBR anisotropies. In addition, we can show that $`\dot{ϵ}_1=2ϵ_1^2`$ and $`\ddot{H}𝒪(ϵ_1^3)`$, thus $`ϵ_4=ϵ_1`$ and eq. (26) becomes $`n_S14ϵ_12/N_k`$, thus

$`n_S10.033,n_T0.00.`$ (34)
## VII Conformal transformation method

It is well known that by a conformal transformation the $`f(R)`$ gravity in eq. (19) can be transformed to Einstein gravity plus a minimally coupled scalar field with a special potential . For $`R^2`$ gravity in eq. (27) under the conformal transformation $`\widehat{g}_{ab}\mathrm{\Omega }^2g_{ab}`$ with $`\mathrm{\Omega }\sqrt{8\pi F}/m_{pl}e^{\frac{1}{2}\sqrt{\frac{16\pi }{3}}\varphi /m_{pl}}`$, thus $`\varphi \sqrt{\frac{3}{16\pi }}m_{pl}\mathrm{ln}(1+\frac{1}{3M^2}R)`$, the potential becomes

$`V(\varphi )={\displaystyle \frac{3M^2m_{pl}^2}{32\pi }}\left(1e^{\sqrt{16\pi /3}\varphi /m_{pl}}\right)^2.`$ (35)
In the limit $`\varphi /m_{pl}1`$ (corresponding to $`RM^2`$) we have a soll-roll inflation, whereas in the other limit $`\varphi m_{pl}`$ we have $`V=\frac{1}{2}M^2\varphi ^2`$ which provides a reheating; $`R^2`$ gravity has both features simultaneously as well . The two gravity theories conformally related are not necessarily the same physically. The equations for background are:

$`H^2={\displaystyle \frac{8\pi }{3m_{pl}^2}}\left({\displaystyle \frac{1}{2}}\dot{\varphi }^2+V\right),\ddot{\varphi }+3H\dot{\varphi }+V_{,\varphi }=0.`$ (36)
Now, we derive the spectra generated during the slow-roll inflation regime. The number of $`e`$-folds in eq. (32) gives

$`N_k={\displaystyle \frac{8\pi }{m_{pl}^2}}{\displaystyle _{\varphi _e}^{\varphi _k}}{\displaystyle \frac{Vd\varphi }{V_{,\varphi }}}={\displaystyle \frac{3}{4}}\sqrt{{\displaystyle \frac{3}{\pi }}}{\displaystyle \frac{H^2m_{pl}}{V_{,\varphi }}}(t_k).`$ (37)
We can estimate $`ϵ_i`$’s in eq. (10) as

$`ϵ_1={\displaystyle \frac{3}{4N_k^2}},ϵ_2={\displaystyle \frac{1}{N_k}}+{\displaystyle \frac{3}{4N_k^2}}.`$ (38)
The spectral indices are given by eqs. (15) as

$`n_S1={\displaystyle \frac{2}{N_k}}{\displaystyle \frac{9}{2N_k^2}},n_T={\displaystyle \frac{3}{2N_k^2}}.`$ (39)
The power-spectra follow from eqs. (13,14) as

$`𝒫_{\phi _{\delta \varphi }}^{1/2}={\displaystyle \frac{1}{\sqrt{3\pi }}}{\displaystyle \frac{M}{m_{pl}}}N_k,𝒫_{C_{\alpha \beta }}^{1/2}={\displaystyle \frac{1}{\sqrt{\pi }}}{\displaystyle \frac{M}{m_{pl}}},`$ (40)
where we ignored $`[1+𝒪(ϵ_i)]`$ factors. These results coincide exactly with the expressions in eq. (29): this is understandable because both $`\phi _{\delta \varphi }`$ and $`C_{\alpha \beta }^{(t)}`$ are invariant under the conformal transformation . We can show

$`r_2=3.46{\displaystyle \frac{3}{N_k^2}}=6.92n_T,`$ (41)
where the first step coincides with eqs. (30,32); the second step is the well known consistency relation. From eqs. (16,18,40) we have

$`{\displaystyle \frac{M}{m_{pl}}}={\displaystyle \frac{1.6\times 10^4}{N_k}}2.6\times 10^6,`$ (42)
which coincides exactly with eq. (31). Therefore, using $`N_k60`$ the observationally verifiable results of $`n_S`$, $`n_T`$ and $`r_2`$ in eqs. (39,41) coincide precisely with the ones based on the original $`R^2`$ gravity: these are predictions on the gravitational wave contribution and the spectral index in eqs. (33,34).

We can show that using the conformal transformation in  the results in the original frame can be recovered from the ones derived in Einstein frame; this is understandable because the two gravity theories are related to each other through conformal transformation in the action level. In comparison, what we have shown above is that the observationally verifiable results in the two frames coincide exactly which, we believe, are not necessarily obvious.

## VIII Discussions

The main results of this paper are eqs. (25,33,34). We have two testable predictions of the inflation model based on successful $`f(R)`$ gravity theory, thus $`R^2`$ gravity. Firstly, we should have the specific nearly scale-invariant Zel’dovich spectra in eq. (34) which are valid considering the linear order in slow-roll parameters, i.e., $`𝒪(ϵ_i)`$. The recent high precision measurements of the CMBR by Boomerang and Maxima-1 in small angular scale  together with COBE-DMR data  suggest the scalar spectral index $`n_S10.01_{0.14}^{+0.17}`$ at the $`95\%`$ confidence level . Thus, the inflation model considered in this paper can provide viable seeds for the large-scale cosmic structures which pass the current observational limits. Secondly, in order to have a successful inflation we should have negligible contribution of the gravitational wave to the CMBR anisotropies as in eq. (33). The results in the conformally transformed Einstein frame provide observationally identical results with precise predictions on the gravitational wave contribution and the spectral index: compare eqs. (39,41) with eqs. (33,34). Therefore, future observations of the spectral indices and/or the contribution of the gravitational wave to CMBR temperature/polarization anisotropies will provide strong tests for the considered inflation model. Other inflation models based on different gravity theories with similar scale-invariant Zel’dovich spectra and suppressed gravitational wave contribition are known in the literature .

## Acknowledgments

We thank Dominik Schwarz for useful discussions during CAPP2000 conference in Verbier which initiated this work. We also wish to thank Ewan Stewart for useful comments. This work was supported by Korea Research Foundation Grant (KRF-99-015-DP0443).


text:
# Renormalisation in Quantum Mechanics, Quantum Instantons and Quantum Chaos

## 1 INTRODUCTION

Quantum mechanics, which describes physics at atomic length scales can not be understood by the laws of classical physics valid at macroscopic length scales. Examples are: Heisenberg’s uncertainty principle, quantum tunneling, Schrödinger’s cat paradox, entangled states, Einstein-Rosen-Podolski paradox, quantum cryptology, quantum computing etc. On the other hand, in modern physics there are notions which have proven to be quite useful and which have their origin in classical physics. Examples are instantons and chaos. Instantons play a role in quantum chromodynamics (QCD), the standard model of strong interactions. They may be important for the mecanism of confinement of quarks. Presumably they play an important role in nuclear matter at high temperature and density, where a phase transition from the hadronic phase to the quark-gluon plasma has been predicted. Even a richer phase structure may exist . Furthermore, in the inflationary scenario of the early universe, instantons are important. For a review see Ref.. During inflation, quantum fluctuations of the primordial field expand exponentially and eventually end up as a classical field. The fluctuations are of the size of the horizon . The classical fluctuations eventually lead to galaxy formation . Chaos has been observed by a huge number of phenomena in macroscopic i.e. classical physics. But chaotic phenomena were also found in systems ruled by quantum mechanics. For an overview see Ref. . Examples are: The hydrogen atom in a strong magnetic field, showing strong irregularities in its spectrum . Irregular patterns have been found in the wave functions of the quantum mechanical model of the stadium billard . Billard like boundary conditions have been realized experimentally in mesoscopic quantum systems, like quantum dots and quantum corrals, formed by atoms in semi-conductors . So what is the problem with instantons and chaos in quantum physics? It has to do with its proper definition. The underlying reason is due to the dynamical group of time evolution. In classical mechanics time evolution of a system can be viewed as an infinite sequence of infinitesimal canonical transformations. The corresponding dynamical group is the symplectic group. In quantum mechanics, a system governed by a time independent Hamiltonian, follows the time evolution of the unitary group. This difference has simple but drastic consequences: In classical physics, chaos is characterized, e.g. by Lyapunov exponents or Poincaré sections. This is based on identifying trajectories in phase space (position and conjugate momentum). In quantum mechanics, Heisenberg’s uncertainty relation $`\mathrm{\Delta }x\mathrm{\Delta }p\mathrm{}/2`$ does not allow to specify a point in phase space with zero error! Consequently, the apparatus of classical chaos theory can not be simply taken over to quantum physics. The same problem occurs also with instantons. Let us consider a 1-D system in quantum mechanics with a particle of mass $`m`$ moving in a potential $`V(x)=A(x^2a^2)^2`$. This potential has two minima at $`x=\pm a`$. The instanton $`x_{inst}(t)`$ is the solution of the classical equation of motion in imaginary time, with boundary conditions such that the particle starts at $`x(t=\mathrm{})=a`$, $`\dot{x}(t=\mathrm{})=0`$ and arrives at $`x(t=+\mathrm{})=+a`$, $`\dot{x}(t=+\mathrm{})=0`$. The problem again is that quantum mechanics does not allow to specify both, position and momentum with zero uncertainty. Due to this problem, workers in quantum chaos have tried to characterize such systems in different ways, alternative to those of classical chaos. One successful route has been to characterize the spectral density of quantum system with chaotic classical counterpart by Poisson versus Wigner distributions. There is a conjecture by Bohigas et al. , which says that the signature of a classical chaotic system is a the spectral density following a Wigner distribution.

### 1.1 Bridge between classical and quantum physics

A different way to look at the problem of quantum chaos is the following. Quantum mechanics is a branch of physics which can be looked upon from many view points. There is the historic duality between the particle and wave interpretation (de Broglie). But there is a more modern view point: Renormalisation and the effective action. In short terms it means that the action of a system in quantum physics can be written as the action of the classical system, however, with modified parameters (mass, potential parameters).

Renormalisation and the effective action is useful to describe an equivalent low-energy theory, starting from a high-energy theory. The construction of a low-energy theory in nuclear physics has been discussed by Lepage . The effective action in connection with the linear sigma model is presented in Ref.. In a more narrow sense the effective action $`\mathrm{\Gamma }`$ has been introduced in quantum field theory in such a way gives an expectation value $`<\varphi >`$ which minimizes the potential energy, giving the ground state energy .

An effective action has been also considered at finite temperature . Because the effective action has a mathematical structure similar to the classical action, and the quantum effects are taken into account by parameters different from their classical counter parts, the effective action looks like the ideal way to bridge the gap from quantum to classical physics and eventually solve the quantum chaos and quantum instanton problem. However, there is a catch. The effective potential and the effective action in quantum mechanics has been computed using perturbation theory by Cametti et al. . Consider the Lagrangian

$`L(q,\dot{q},t)`$ $`=`$ $`{\displaystyle \frac{m}{2}}\dot{q}^2V(q),V(q)={\displaystyle \frac{m}{2}}\omega ^2q^2+U(q),`$ (1)
and $`U(q)`$ is, say, a quartic potential $`U(q)q^4`$. Then the effective action is obtained in doing a loop $`(\mathrm{})`$ expansion

$`\mathrm{\Gamma }[q]`$ $`=`$ $`{\displaystyle }dt(V^{eff}(q(t))`$
$`+`$ $`{\displaystyle \frac{Z(q(t))}{2}}\dot{q}^2(t)+A(q(t))\dot{q}^4(t)+B(q(t))(d^2q/dt^2)^2(t)+\mathrm{})`$
$`V^{eff}`$ $`=`$ $`{\displaystyle \frac{1}{2}}m\omega ^2q^2+U(q)+\mathrm{}V_1^{eff}(q)+O(\mathrm{}^2)`$
$`Z(q)`$ $`=`$ $`m+\mathrm{}Z_1(q)+O(\mathrm{}^2)`$
$`A(q)`$ $`=`$ $`\mathrm{}A_1(q)+O(\mathrm{}^2)`$
$`B(q)`$ $`=`$ $`\mathrm{}B_1(q)+O(\mathrm{}^2).`$ (2)
There are higher loop corrections to the effective potential $`V^{eff}`$ as well as to the mass renormalisation $`Z`$. The most important property is the occurrence of higher time derivative terms. Actually, there is an infinite series of increasing order. Here comes the problem. When we want to interpret $`\mathrm{\Gamma }`$ as effective action, the higher time derivatives require more intial/boundary conditions than the classical action. This is a catastrophy. In the following we will present an alternative way to construct an action taking into acount quantum corrections.

## 2 THE QUANTUM ACTION

We suggest to construct a renormalized or quantum action from transition matrix elements, which involve the time evolution . In Q.M. the transition amplitude from $`x_{in}`$, $`t_{in}`$ to $`x_{fi}`$, $`t_{fi}`$ is given by

$$G(x_{fi},t_{fi};x_{in},t_{in})=[dx]\mathrm{exp}[\frac{i}{\mathrm{}}S[x]]|_{x_{in},t_{in}}^{x_{fi},t_{fi}},$$
(3)
where

$$S=𝑑t\frac{m}{2}\dot{x}^2V(x).$$
(4)
denotes the classical action. In some cases, this path integral can be expressed as a sum over classical paths only.

$$G(x_{fi},t_{fi};x_{in},t_{in})=\underset{\{x_{cl}\}}{}Z\mathrm{exp}\left[\frac{i}{\mathrm{}}S[x_{cl}]|_{x_{in},t_{in}}^{x_{fi},t_{fi}}\right].$$
(5)
An example is the harmonic oscillator ($`V(x)=\frac{m}{2}\omega ^2x^2`$), where

$`S[x_{cl}]|_{x_{in},t_{in}}^{x_{fi},t_{fi}}`$ $`=`$ $`{\displaystyle \frac{m\omega }{2\mathrm{sin}(\omega T)}}\left[(x_{fi}^2+x_{in}^2)\mathrm{cos}(\omega T)2x_{in}x_{fi}\right],`$
$`Z`$ $`=`$ $`\sqrt{{\displaystyle \frac{m\omega }{2\pi i\mathrm{}\mathrm{sin}(\omega T)}}},T=t_{fi}t_{in},`$ (6)
where $`S[x_{cl}]`$ denotes the classical action evaluated along the classical trajectory from $`x_{in}`$, $`t_{in}`$ to $`x_{fi}`$, $`t_{fi}`$. In the following we suggest to introduce the quantum action defined by a generalisation of Eq.(5) where the action has mathematically a structure like the classical action, and where quantum effects are taken into account by modified action parameters (renormalisation).

Conjecture: For a given classical action $`S=𝑑t\frac{m}{2}\dot{x}^2V(x)`$ there is a quantum action $`\stackrel{~}{S}=𝑑t\frac{\stackrel{~}{m}}{2}\dot{x}^2\stackrel{~}{V}(x)`$, which allows to express the transition amplitude by

$$G(x_{fi},t_{fi};x_{in},t_{in})=\stackrel{~}{Z}\mathrm{exp}[\frac{i}{\mathrm{}}\stackrel{~}{S}[\stackrel{~}{x}_{cl}]|_{x_{in},t_{in}}^{x_{fi},t_{fi}}].$$
(7)
Here $`\stackrel{~}{x}_{cl}`$ denotes the classical path, such that the action $`\stackrel{~}{S}(\stackrel{~}{x}_{cl})`$ is minimal (we exclude the occurrence of conjugate points or caustics). $`\stackrel{~}{Z}`$ denotes the normalisation factor corresponding to $`\stackrel{~}{S}`$. Eq.(7) is valid with the same action $`\stackrel{~}{S}`$ for all sets of boundary positions $`x_{fi}`$, $`x_{in}`$ for a given time interval $`T=t_{fi}t_{in}`$. The parameters of the quantum action depend on the time $`T`$. The quantum action converges to a non-trivial limit when $`T\mathrm{}`$. Any dependence on $`x_{fi},x_{in}`$ enters via the trajectory $`\stackrel{~}{x}_{cl}`$. $`\stackrel{~}{Z}`$ depends on the action parameters and $`T`$, but not on $`x_{fi},x_{in}`$.

One may ask: what is the difference between effective and quantum action? Conceptually, effective action and quantum action are quite similar. However, its technical definition is different and also its physical content. While the effective action corresponds to infinite time and allows to obtain the ground state energy, the quantum action is defined for arbitrary finite time $`T`$. In Euclidean formulation, the inverse time corresponds to temperature. Thus the quantum action allows to describe quantum physics at finite temperature (including excited states). However, the effective action can be defined also at finite temperature . The effective action can be computed analytically by perturbation theory (loop expansion). However, this series is not convergent. Practically, it can be used only for some small number of loops and small values of the perturbation parameter. The quantum action can be computed non-perturbatively for all values of the coupling parameter. The effective action has the defect of generating higher order time derivatives. The quantum action is postulated to be free of higher time derivative terms. To construct the quantum action being sensitive to excited states, one needs transition matrix elements beyond the vacuum sector. We have chosen to use position states in Q.M. In Q.F.T. this corresponds to Bargman states. The definition of the quantum action is related to the Schrödinger functional method in Q.F.T. .

### 2.1 Quantum action at finite temperature

First we make a Wick rotation to imaginary time. The purpose is, first to make the path integral well defined (Wiener measure) allowing to apply Monte Carlo methods for its numerical computation. Secondly, the instanton is defined in imaginary time. One effect of this transformation is that it changes a relative sign between the kinetic term and the potential term of the action. Thus in the following we work with imaginary time (Euclidean) actions and Green’s functions. Let us see how the quantum action is related to finite temperature physics. According to the laws of quantum mechanics and thermodymical equilibrium, the expectation value of some observable $`O`$, like e.g. average energy is given by

$`<O>`$ $`=`$ $`{\displaystyle \frac{Tr\left[O\mathrm{exp}[\beta H]\right]}{Tr\left[\mathrm{exp}[\beta H]\right]}}`$ (8)
$`=`$ $`{\displaystyle \frac{_{\mathrm{}}^+\mathrm{}𝑑x_{\mathrm{}}^+\mathrm{}𝑑y<x|O|y><y|\mathrm{exp}[\beta H]|x>}{_{\mathrm{}}^+\mathrm{}𝑑x<x|\mathrm{exp}[\beta H]|x>}},`$
where $`\beta `$ is related to the temperature $`\tau `$ by $`\beta =1/(k_B\tau )`$. On the other hand the (Euclidean) transition amplitude is given by

$$G(x_{fi},T;x_{in},0)=<x_{fi}|\mathrm{exp}[HT/\mathrm{}]|x_{in}>$$
(9)
Thus from the definition of the quantum action, Eq.(7), one obtains

$$<O>=\frac{_{\mathrm{}}^+\mathrm{}𝑑x_{\mathrm{}}^+\mathrm{}𝑑y<x|O|y>\mathrm{exp}[\stackrel{~}{S}_\beta |_{x,0}^{y,\beta }]}{_{\mathrm{}}^+\mathrm{}𝑑x\mathrm{exp}[\stackrel{~}{S}_\beta |_{x,0}^{x,\beta }]},$$
(10)
if we identify $`\beta =\frac{1}{k_B\tau }=T/\mathrm{}`$. As a result, the quantum action $`\stackrel{~}{S}_\beta `$ computed from transition time $`T`$, describes equilibrium thermodynamics at $`\beta =T/\mathrm{}`$, i.e. temperature $`\tau =1/(k_B\beta )`$. As an important consequence, once having determined the quantum action for some finite time, one can use it for the study of quantum instantons and quantum chaos at finite temperature (see below).

### 2.2 Construction of quantum action

Suppose the classical action is given by

$$S=_0^T𝑑t\frac{m}{2}\dot{x}^2+v_4x^4(t).$$
(11)
Then we make an ansatz for the quantum action

$$\stackrel{~}{S}=_0^T𝑑t\frac{\stackrel{~}{m}}{2}\dot{x}^2+\stackrel{~}{v}_0+\stackrel{~}{v}_1x(t)+\mathrm{}+v_Nx^N(t).$$
(12)
Then $`\stackrel{~}{m}`$, $`\stackrel{~}{v}_0`$, …, $`\stackrel{~}{v}_N`$ are the renormalized parameters which take into account the quantum corrections. Their values have been determined by making a global best fit to a number of transition amplitudes $`G(x_j,T;x_i,0)`$ (which satisfies Eq.7), where $`x_i`$, $`x_j`$ haven been taken from a set of points $`\{x_1,\mathrm{},x_J\}`$ and those points have been chosen to cover some interval $`[a,+a]`$. More details are given in Ref..

## 3 RESULTS

(i) Firstly we have considered a harmonic oscillator with a weak anharmonic perturbation,

$$S=𝑑t\frac{m}{2}\dot{x}^2+v_2x^2+\lambda v_4x^4,\mathrm{}=m=v_2=\frac{1}{2}m\omega ^2=v_4=1.$$
(13)
In the ansatz of the quantum action, we have (for sake of numerical effort) restricted the parameter space of the potential to 4th order polynomials. We have varied the parameter $`\lambda `$ in the range $`0\lambda 0.1`$ (weak perturbation). We have computed numerically the quantum action (at transition time $`T=4`$) and compared it with the predictions of low order perturbation theory of the effective action. The latter predicts to one loop order and up to 2nd order of the coupling parameter $`\lambda `$

$`v_2^{eff}`$ $`=`$ $`v_2+\delta v_2,\delta v_2={\displaystyle \frac{3}{m\omega }}\lambda `$
$`v_4^{eff}`$ $`=`$ $`v_4+\delta v_4,\delta v_4={\displaystyle \frac{9}{m\omega ^2}}\lambda ^2.`$ (14)
The results are shown in Fig.1.1. One observes that the effective potential and the potential of the quantum action are close for small $`\lambda `$. The discrepancy for $`\lambda 1`$ is due to neglect of of higher order perturbative corrections, i.e. the onset of non perturbative effects. Moreover, one observes that for $`T=0`$, the quantum action agrees with the classical action. Odd terms $`\stackrel{~}{v}_1`$ and $`\stackrel{~}{v}_3`$ are compatible with zero, due to parity conservation. (ii) Secondly, we have considered the quartic potential ($`m=\mathrm{}=1`$) given by $`V(x)=v_4x^4`$, $`v_4=1`$. The parameters of the renormalized action are shown in Tab.1 and in Fig.2. In Tab.1 the parameters are shown for transition time $`T=0.5`$ corresponding to temperature $`\tau =2`$ ($`\mathrm{}=k_B=1`$). The table also shows the estimated error of the parameters from the fit and the value of $`\chi ^2`$ of the fit. Also variation of parameters under variation of the boundary points (i.e. the interval $`[a,+a]`$) is shown. The magnitude of variance is comparable to the magnitude of errors. Fig.2 shows the behavior of renormalized parameters as function of the transition time $`T`$ (inverse temperature). The error bars represent the error estimates of the fit. One observes that for $`T0`$, the renormalized action parameters tend to their classical counter part (except for the $`\stackrel{~}{v}_4`$ term, which is presumably due to a numerical shortcoming). For $`T\mathrm{}`$, the renormalized parameters tend to some asymptotic values. The asymptotic regime is reached at about $`T4.5`$. (iii) Finally, we have considered a double well potential, of the form $`V(x)=A(x^2a^2)^2`$, with $`a=1`$, $`A=1/2`$. The parameters are equivalent to $`v_0=v_4=1/2`$, $`v_2=1`$. Tab.2 shows the renormalized parameters for $`T=0.5`$ under variation of the interval of initial and end points. Like in Tab.1 one observes the magnitude of the estimated errors compatible with the variance under variation of the size of the interval. The quantum action parameters as a function of $`T`$ are displayed in Fig.3. Like in Fig.2 one observes for $`T0`$ that the renormalized parameters tend to their classical counterparts and for large $`T`$ ($`T9`$) there is a regime of asymptotic convergence. The error bars in the figure are composed of two parts. The upper part represents the error estimated from the fit, while the lower part represents the $`\sigma `$ value of the estimator of the parameters under variation of the interval size. From both tables and Fig.3 we can see that the parameters of the quantum action is reasonnably independent of the initial and final points. This was postulated in the conjecture. Hence the numerical results support the conjecture. For further discussion and more details see Ref..

## 4 IMPLICATIONS ON INSTANTONS AND CHAOS

As can be seen from Fig.3, for all $`T`$ in the range $`0T9`$ one observes that the quantum potential has also a double well structure like the classical potential ($`\stackrel{~}{v}_0>0`$, $`\stackrel{~}{v}_4>0`$, but $`\stackrel{~}{v}_2<0`$). Thus in all of this range it has an instanton solution. According to the Feynman-Kac formula, for $`T\mathrm{}`$ (corresponding to temperature $`\tau 0`$) the propagator is dominated by the ground state wave function and energy. Thus the quantum instanton corresponding to temperature zero is approximately given by the instanton solution of the quantum potential with $`T`$ large ($`T9`$). Quantum instantons of larger temperature are those solutions corresponding to smaller values of $`T`$. Such quantum instanton solutions have been computed in Ref.. As far as quantum chaos is concerned, 1-dimensional conservative systems with time-independent Hamiltonian do not generate classical chaos. Thus they are not appropriate to search for quantum chaos. However, the quantum action can be constructed for 2-dim Hamiltonian systems, which are known to display classical chaos, like the Henon Heiles system, Paul-trap, etc. Thus we suggest to apply the tools of classical chaos theory (like Lyapunov exponents, Poincaré sections) to the quantum action of those systems.

Acknowledgements
H.K. and K.M. are grateful for support by NSERC Canada. X.Q.L. has been supported by NSF for Distinguished Young Scientists of China, by Guangdong Provincial NSF and by the Ministry of Education of China.