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# Observation of a Chiral State in a Microwave Cavity

## Abstract

A microwave experiment has been realized to measure the phase difference of the oscillating electric field at two points inside the cavity. The technique has been applied to a dissipative resonator which exhibits a singularity – called exceptional point – in its eigenvalue and eigenvector spectrum. At the singularity, two modes coalesce with a phase difference of $`\pi /2.`$ We conclude that the state excited at the singularity has a definitiv chirality.

Recently a surprising phenomenon occurring in systems described by non-hermitian Hamiltonians has received considerable attention: the coalescence of two eigenmodes. If the system depends on some interaction parameter $`\lambda ,`$ the value $`\lambda _{\mathrm{EP}}`$ at which the coalescence occurs is called an exceptional point (EP) Kato . At an EP, the eigenvalues *and* eigenvectors show branch point singularities Kato ; Hesa ; BerryEP ; Mondragon ; Rotter  as functions of $`\lambda .`$ This stands in sharp contrast to two-fold degeneracies, where no singularity but rather a diabolic point BerryDP  occurs. EPs have been observed in laser induced ionization of atoms Latinne , acoustical systems Shuva , microwave cavities BrentanoEP ; DemboEP , certain absorptive media Pancha , and in “crystals of light” Oberthaler . The broad variety of systems showing EPs indicates that their occurrence is *generic* which is discussed further in BerryEP ; BerryPancha . So far EPs have been observed in decaying systems described by a complex symmetric effective Hamiltonian WW . While the theoretical and experimental articles cited above discuss the properties of systems in the vicinity of an EP, a recent theoretical work PhaseTheo  investigates the complex symmetric Hamiltonian of a two-level system *at* the EP. The eigenfunction at the EP turns out to be

$$|\psi _{\mathrm{EP}}|1\pm i|2$$
(1)
for *any* choice of the basis states $`|1`$ and $`|2.`$ This is a chiral state: in quantum, acoustical and electromagnetic systems the two orthogonal basis states oscillate in time; if they are superimposed according to Eq. (1) – where they follow each other with a time lag of a quarter period – the result is rotating either clockwise or counter-clockwise. This is in analogy with the generation of circularly polarized light being a superposition of two orthogonal linearly polarized waves phase shifted by $`\pi /2`$. The sign of the chirality is defined via the direction of time and in the experiment the positive direction of time is given by the decay of the eigenstates. The first observation of such a chiral state in a microwave cavity experiment is the gist of the present paper.

The high precision of such an experiment makes it a prime choice to observe the chirality of $`|\psi _{\mathrm{EP}}`$, yet measuring a phase difference of $`\pm \pi /2`$ between two superimposed modes is an unusual and demanding experimental task. A setup had to be designed that allows to excite the two modes with an adjustable frequency difference $`f_1f_2,`$ and in the case of $`f_1=f_2`$ with an adjustable *phase difference* between them. The cavity is composed of two almost identical semi-circular parts, see Fig. 1. They are coupled by a slit of variable width $`s.`$ In order to reach $`f_1=f_2`$ one needs a second tunable parameter, namely the position $`\delta `$ of a teflon semi-circular stub in part $`1`$ of the cavity on Fig. 1.

These two parameters make up the interaction parameter $`\lambda (s,\delta ).`$ The two eigenmodes coalesce at a critical value $`\lambda _{\mathrm{EP}}=(s^{\mathrm{EP}},\delta ^{\mathrm{EP}})`$. In the sequel we chose $`\lambda `$ to be close enough to $`\lambda _{\mathrm{EP}}`$ so as to consider the cavity a two-state-system. This is possible when the distance between the two coalescing eigenvalues is much smaller than the distance to any third one. As in DemboEP , the EP has been found by looking at the behavior of the real and imaginary parts of the eigenvalues, i.e. the resonance frequencies $`f_1,f_2`$ and widths $`\mathrm{\Gamma }_1,\mathrm{\Gamma }_2.`$ For weak coupling, i.e. $`s<s^{\mathrm{EP}}`$, one observes a crossing of $`f_1,f_2`$ and an avoided crossing of $`\mathrm{\Gamma }_1,\mathrm{\Gamma }_2`$ when one sweeps $`\delta .`$ For strong coupling, i.e. $`s>s^{\mathrm{EP}},`$ an avoided crossing of $`f_1,f_2`$ and a crossing of $`\mathrm{\Gamma }_1,\mathrm{\Gamma }_2`$ takes place Hesa ; DemboEP ; he99 . It is only *at* the EP that one expects the real *and* imaginary parts of the eigenvalues to be equal. In addition to the eigenvalues, the eigenfunctions were studied by mapping the distributions of the electric field. When the EP is encircled in the space of $`\lambda ,`$ *one* of the eigenvectors undergoes a change of sign DemboEP , i.e. it picks up a so-called ”geometric phase” BerryBuch . Which eigenvector changes its sign is defined by the only freedom left: the orientation of the closed loop around the EP. This is a first fingerprint of the definite chirality of the EP.

For $`s<s^{\mathrm{EP}}`$ the two modes discussed in the following are each *localized* in one of the semi-circular parts of the cavity – as the measured field distributions show (cf. insets of Fig. 2). We consider these localized modes as the basis configurations $`|1`$ and $`|2`$ of the two-state system.

They can be excited separately even if $`f_1=f_2`$ by appropriately positioned dipole antennas RichterBuch  which are located at mirror positions in the cavity. The coupling between the antennas and the resonator is proportional to the square of the electric field at the locations of the antennas RichterBuch ; StoeckmannPhase . If the electric field is approximately zero at the location of a given antenna the mode cannot be excited. In Fig. 2 the reflection spectra for two different antennas are shown for $`s=38`$mm. The parameter $`\delta `$ is tuned so that that $`f_1`$ is slightly different from $`f_2.`$ Still each spectrum shows only a single resonance – not a doublet. It follows that each antenna indeed excites only one basis configuration.

In the two-state-regime, the eigenstates $`|\psi _k`$ of the cavity are expanded according to

$$|\psi _k=a_{k1}|1+a_{k2}|2,$$
(2)
however, for sufficiently small $`s`$, the eigenmodes $`|\psi _k`$ approach the localized modes $`|1,`$ and $`|2`$ as can be seen in Fig. 2. The relative phase of the amplitudes $`a_{k1}`$ and $`a_{k2}`$ of $`|\psi _1`$ and $`|\psi _2`$ has been measured by the following technique, applied – to the best of our knowledge – for the first time in microwave cavities. A microwave source, an HP8510C vectorial network analyzer is emitting continuous rf-radiation with a fixed frequency, split by a power divider (Narda 4313-2) and fed into the cavity via two paths labeled (a) and (b) in Fig. 1. The phase of the signal travelling through (b) can be shifted by $`\mathrm{\Delta }\varphi `$ using a Narda 3752 phaseshifter. Several circulators Circulator  are used to suppress reflections along path (b). The amplitude $`S`$ of the signal outcoupled by antenna 2 is a superposition of two coherent waves with different phases, i.e.

$$St+re^{i\mathrm{\Delta }\varphi }.$$
(3)
Here, $`t`$ and $`r`$ denote the transmission and reflection coefficients of the cavity. For further analysis, two cases have to be distinguished: First, for $`s<s^{\mathrm{EP}}`$, $`\delta `$ is tuned in such a way that the frequencies of the two eigenstates $`|\psi _1`$ and $`|\psi _2`$ are the same and both are excited in resonance by the two signals coupled to the cavity. Second, for $`s=s^{\mathrm{EP}},`$ the *only* state present, $`|\psi _{\mathrm{EP}}`$, is excited by both signals.

In both cases, $`t`$ and $`r`$ are known from scattering theory (see e.g. SMatrix1 ; SMatrix2 ; SMatrix3 ) and the dependence of the signal received by the network analyzer from $`\mathrm{\Delta }\varphi `$ is given by

$$|S(\mathrm{\Delta }\varphi )|^2C+\mathrm{cos}^2\left(\frac{\mathrm{\Delta }\varphi \varphi _0\stackrel{~}{\varphi }}{2}\right).$$
(4)
Here, the constant $`C0`$ determines the contrast of the pattern. When $`C`$ is large, the contrast is small, which occurs whenever the basis states contribute very unevenly to the eigenmodes. The angle $`\varphi _0`$, i.e. the phase difference between the oscillating fields at the position of the antennas, is given by the relative phases of the expansion coefficients in (2), i.e.

$$\varphi _0=\mathrm{arg}(a_{12}/a_{11})$$
(5)
for an isolated eigenmode and

$$\varphi _0=\mathrm{arg}\left(\frac{a_{12}+a_{22}}{a_{21}}\right)$$
(6)
for the superposition of two eigenmodes. If Eq. (1) holds true we expect $`\varphi _0=\pm \pi /2`$ for $`|\psi _{\mathrm{EP}}`$, proving the chirality of $`|\psi _{\mathrm{EP}}`$.

The angle $`\stackrel{~}{\varphi }`$ in Eq. (4) is due to the remaining length difference of the paths (a) and (b) and the fact that the antennas (1) and (2) may cause additional and different phase shifts. It has to be determined by analyzing an eigenstate with known $`\varphi _0.`$ One easily finds StoeckmannPhase  modes with $`\varphi _0=0`$ or $`\pi .`$ Figure 3a shows $`|S(\mathrm{\Delta }\varphi )|^2`$ for a mode with $`\varphi _0=0`$, i.e. the electric field at the position of the two antennas oscillates *in phase*, cf. Fig. 3a, where the antennas are sketched as crosses with attached lines.

By fitting Eq. (4) to the measured $`|S(\mathrm{\Delta }\varphi )|^2`$ we find $`\stackrel{~}{\varphi }\pi `$, which is expected from measurements of the reflection coefficients padamsee  of the antennas which shift the phase of an emitted wave by $`\pi `$. In Fig. 3b we show $`|S(\mathrm{\Delta }\varphi )|^2`$ for a mode with $`\varphi _0=\pi `$, as can be seen from the measured field distribution. The data agrees again well with Eq. (4).

Having verified that this setup allows to measure the phase shift between different points of a field distribution, we turn to the investigation of $`|\psi _{\mathrm{EP}}`$. To reach the EP the slit is at first set to $`s=3\mathrm{mm}`$, i.e. $`s<s^{\mathrm{EP}}.`$ The teflon semi-circle can be moved from the outside, i.e. *while* microwave power is coupled into the cavity and therefore $`\delta `$ can be tuned such that $`f_1=f_2.`$ Then the pattern $`|S(\mathrm{\Delta }\varphi )|^2`$ exhibits only a weak contrast (see the upper part of Fig. 4).

This occurs because $`|a_{12}|`$ is very small compared to $`|a_{11}|`$ and $`|a_{22}|`$ is large compared to $`|a_{21}|`$ for such a weak coupling. Nevertheless, $`\varphi _0`$ can be obtained by fitting Eq. (4) to the measured data. It is close to $`\pi `$ for $`s<28\mathrm{mm}`$, cf. Fig. 5, which agrees with general arguments given below.

Secondly we set $`\lambda \lambda _{\mathrm{EP}}`$ so that $`|\psi _{\mathrm{EP}}`$ is the only mode present (lower part of Fig. 4). The contrast of the pattern $`|S(\mathrm{\Delta }\varphi )|^2`$ is high because the expansion coefficients of $`|\psi _{\mathrm{EP}}`$ have the same absolute value. For $`s=46\mathrm{mm}`$ one obtains $`\varphi _0=\pi /2\pm 0.05,`$ cf. Fig. 5. This is the phase predicted in Eq. (1) – constituting the first experimental observation of a mode, were the electric field between two points oscillates with a phase difference of $`\pi /2`$. As pointed out, this is a chiral mode rotating clockwise in the basis frame spanned by $`|1`$ and $`|2`$.

Figure 5 shows the behavior of $`\varphi _0`$ from small to large slit openings. For each value of $`s,`$ $`|S(\mathrm{\Delta }\varphi )|^2`$ has been taken as displayed on Fig. 4 by sweeping $`\mathrm{\Delta }\varphi `$ over $`400^{}.`$ The error of $`\varphi _0`$ is a systematic error caused by varying bending radii of the coaxial microwave cables and the corresponding variation of the length of the wave paths during the measurement. The surface properties of the connections between the cables and the antennas – which cannot be exactly controlled – are another source of error.

For $`43\mathrm{mm}<s<48\mathrm{mm}`$ a crossing of the resonance frequencies *and* widths is observed and we conclude that this is the precision with which the present experiment yields $`s^{\mathrm{EP}}.`$ This does not contradict the theory Hesa  – the experiment simply cannot resolve the tiny avoided frequency or widths crossings that occur for $`s`$ very near to $`s^{\mathrm{EP}}.`$

For better understanding of the results of Figs. 4 and 5 let us recapitulate the two-state model of PhaseTheo . The Hamiltonian

$$H=\left(\begin{array}{cc}E_1i\gamma _1& H_{12}\\ H_{12}& E_2i\gamma _2\end{array}\right)$$
(7)
is complex symmetric. All its entries are functions of the geometric parameters $`\lambda .`$ An EP occurs whenever the eigenvalues of $`H`$ coincide and $`H_{12}0.`$ The sum of the relative amplitudes occurring in Eq. (6) is

$$\frac{a_{12}}{a_{11}}+\frac{a_{22}}{a_{21}}=\frac{\mathrm{\Delta }Ei\mathrm{\Delta }\gamma }{H_{12}},$$
(8)
where $`\mathrm{\Delta }E=E_1E_2`$ and $`\mathrm{\Delta }\gamma =\gamma _1\gamma _2.`$ At the EP, Eq. (8) becomes

$$\frac{a_{12}}{a_{11}}+\frac{a_{22}}{a_{21}}=\pm 2i.$$
(9)
The argument of the l.h.s of Eq. (9) coincides with the r.h.s of Eq. (6) if $`a_{11}=a_{21}`$ as is the case in the experiment. For a weak coupling the r.h.s. of Eq. (8) is large because $`H_{12}`$ approaches zero linearly with $`s.`$ As we enforce equality of the real parts of the eigenvalues of $`H`$, a particular weak coupling limit is specified. It implies $`\mathrm{\Delta }E=0.`$ The finding $`\varphi _0\pi `$ in Fig. 5 means that $`H_{12}`$ tends towards zero along the imaginary axis. This describes just the coupling within a purely absorptive system.

In summary, we have performed a microwave cavity experiment to measure the phase difference $`\varphi _0`$ between two points of a field distribution inside the resonator. The technique has been applied to the superposition of two eigenmodes on a path to an EP. At the EP, the modes coalesce into the single, non-localized mode $`|\psi _{\mathrm{EP}}=|1+i|2,`$ i.e. $`\varphi _0=\pi /2.`$ The phase $`\varphi _0`$ is determined from the pattern $`|S(\mathrm{\Delta }\varphi )|^2`$ of interference between the amplitude for transmission through the cavity and a wave with the arbitrary phase shift $`\mathrm{\Delta }\varphi .`$ To our knowledge, it represents the first experimental observation of a mode in a microwave resonator, where the electric field oscillates with a phase difference of $`90^{}`$ at two different points.

The decay of the eigenmodes is essential for the EP to occur. Therefore the experiment has been performed at room temperature rather than under conditions of superconductivity RichterBuch . The irreversibility of the decay causes $`|\psi _{\mathrm{EP}}`$ to change under the operation of time reversal. This should not be confused with fundamental time reversal symmetry breaking observed e.g. in the system of the neutral Kaons CPLEAR . There the Hamiltonian of the decaying two-state system is not complex symmetric. Similarly, the chirality of $`|\psi _{\mathrm{EP}}`$, i.e. the fact that $`|1+i|2`$ is rotating clockwise, is not due to a parity violating interaction as in $`\beta `$-decay Wu . It rather is a property of the EP that we have investigated. The set of EPs that one can find in the resonator is expected to exhibit both chiralities Hesa . In this sense the present chirality closely resembles the chirality of molecules Pasteur , underlining the importance and the generic aspects of EPs even further.

We are particularly grateful to T.H. Seligman for discussing the results with us. C.D., B.D., and A.H. thank CONACyT for financial support during the workshop on Chaos in few and many body problems at CIC. This work has been supported by the DFG under contract number Ri 242/16-3.


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# Reparametrizing the loop entropy weights: effect on DNA melting curves

## I Introduction

A standard method to unbind the two strands of a double-stranded DNA (dsDNA) in solution is that of increasing the temperature of the system. This process, known as DNA thermal denaturation or DNA melting, has been studied since the sixties as it provides important information about the interaction between base pairs, the stability of the double helix, the effect of the solvent and of the salt concentration (for a review see Ref. wart85 ).

Several techniques are currently available for the investigation of DNA thermal denaturation such as UV absorption, differential scanning calorimetry, circular dichroism, NMR, fluorescence emission and temperature gradient gel electrophoresis bloo00 . Perhaps the most established of these is the UV absorption method which consists in irradiating the sample with UV light at $`270`$ nm, a wavelength which is preferentially absorbed by single stranded DNA (ssDNA). The total fraction of absorbed light, $`\stackrel{~}{A}`$, is therefore simply proportional to the fraction of dissociated base pairs of the sequence and provides a direct measurement of the order parameter of the problem. In experimental studies, rather than analyzing directly $`\stackrel{~}{A}`$, it is customary to consider its temperature derivative: the plot of $`d\stackrel{~}{A}/dT`$ vs. $`T`$ is known as the differential melting curve wart85 , but we will simply refer to it, in the rest of the paper, as the melting curve.

Melting curves can show a single or several peaks (typical examples, as observed in experiments, are shown in Fig. 1) whose positions and heights depend on the sequence length and composition as well as on external parameters as the salt concentration. For very short sequences, i.e. of about $`10^210^3`$ base pairs (bps), the melting curve shows a single peak indicating a sudden unbinding of the two strands (see Fig. 1(a)). The peak is rounded by finite size effects and thus can become quite broad for very short chains. Somewhat longer sequences ($`10^310^4`$ bps) are instead characterized by several peaks of typical width of about $`0.5^{}C`$ or less (Fig. 1(b)). These peaks are the signatures of sharp transitions of cooperatively melting regions, as for instance inner loop openings or the unbinding of double stranded regions at the edges of the chain. Finally, in very long chains ($`10^6`$ bps) there is again only a single broad peak covering about $`1520^{}C`$, which is actually the superposition of many distinct peaks associated with the denaturation of single domains \[Fig. 1(c)\]. These single peaks cannot be resolved anymore for such long sequences and the melting curve becomes again rather featureless.

The computational prediction of DNA melting curves is a basic bioinformatics task which is needed for a large variety of applications such as primer design, DNA control during Polymerase Chain Reaction or mutation analysis lyon01 . Also the denaturation behavior of DNA sequences of genomic size is of interest for studies of sequence complexity and evolution and for gene identification and mutation yera00 ; yera00b ; bizz98 ; gare03 . Consequently, specialized tools, such as Meltsim blak99 , were developed for this purpose.

The first attempts to model the DNA denaturation dates back from the sixties (for a recent review see Ref. theo03 ). The simplest model employed for this purpose was the one-dimensional Ising model where the two spin states $`s_i=0,1`$ represent the open ($`s_i=0`$) or closed ($`s_i=1`$) configuration for complementary base pairs zimm59 ; zimm60 . This model obviously does not provide a real thermodynamical phase transition but only a smooth crossover between the closed (dsDNA) and open (ssDNA) regimes. The inclusion of an entropic term, which takes into account the number of possible configurations of the denaturated loops, induces an effective long range interaction in the system and thus a genuine phase transition may occur, as shown long ago by Poland and Sheraga pola66 .

On rather short DNA sequences ($`10^2`$ bps) the loop entropy contribution is not very important as loops are rare and rather short and the DNA denaturates mainly trough unbinding from the edges. A description based on the 1d Ising model with appropriate experimentally determined energy parameters is therefore sufficient (see, e.g., Ref. owcz97 ). A calculation aimed at reproducing experimental melting curves with several peaks of different heights and widths \[as that shown in Fig. 1(b)\] however needs, besides accurate energy parameters, also a good estimate of the entropy of the denaturated loops.

A broadly known method to calculate DNA melting curves for a given input sequence is the Poland algorithm pola74  in which the probability for each base pair to be in an open or closed state can be calculated from a set of recursive relations. The entropy of the denaturated loops is given by counting the number of configurations for a closed self-avoiding walk fish66 . This approach overestimates the actual entropy as it does not take into account that the number of configurations available to the loop is limited by the presence of the rest of the chain. Recent advances in the statistical mechanics of polymers provided new insight on how to calculate entropies for loops which are embedded in chains kafr00 ; carl02 .

The aim of this paper is to discuss whether DNA thermal denaturation experiments are able to fix unequivocally the form of the parameters involved in the entropy of denaturated loops. We analyze the effect of the improved loop entropy estimate on the melting curves for DNA sequences of various lengths (up to $`5\times 10^6`$ base pairs) and compositions. We show that the modification of the entropic parameters associated with the loops may have quite a strong effect on the melting curves, especially for sequences of intermediate lengths where several peaks are present \[as in the example of Fig. 1(b)\]. We also discuss how the effects described here can be best measured experimentally.

This paper is organized as follows: In Sec. II we review some recent results on the entropy of loops embedded into a chain. In Sec. III we present some melting curves for sequences of various lengths and investigate the effect of a modification of the parameters associated with the loop entropy on these curves. In Sec. IV we discuss how the double helix rigidity could influence the results for the entropy, while Sec. V concludes the paper.

## II Entropy of a loop embedded in a chain

In the Poland algorithm the partition function of a loop of total length $`l`$ is given by the number of configurations of a self-avoiding walk returning for the first time to the origin fish66  after $`l`$ steps (Fig. 2(a)), which in the limit $`l\mathrm{}`$ assumes the following form vand98 :

$$L_l\sigma \frac{\mu ^l}{l^c}$$
(1)
where $`\mu `$ is a nonuniversal geometric factor, while $`c`$, the so called loop closure exponent, is a universal quantity. In Eq. (1) we also included a prefactor $`\sigma `$, which only makes sense when comparing the loop partition function with that of a double stranded helix, and measure the absolute probability of interrupting a double helix to open a loop. This quantity is known as the cooperativity parameter.

A small value of $`\sigma `$ suppresses loop formation so that loops proliferate only at temperatures very close to the melting point and are typically large in order to minimize the effect of a small $`\sigma `$. The transition becomes highly cooperative, in the sense that large portions of the chain will tend to unbind simultaneously. On the contrary, for a $`\sigma 1`$, there is no extra big penalty for loop openings and many small loops may form already well below the melting point. The transition is less cooperative, and peaks in the melting curves appear more rounded-off.

For self-avoiding walks embedded in a three dimensional space the exponent $`c`$ has been estimated numerically to be $`c1.75`$ vand98 . Other loop parameters have to be fixed by fitting to the available experimental data. In particular, a lot of effort has been devoted to the measurement of the cooperativity parameter $`\sigma `$. Its most accurate determination was performed by Blake and Delcourt blak98  who analyzed the melting of several tandemly repeated inserts on a linearized plasmid DNA and found that the value $`\sigma =1.26\times 10^5`$ fits best the experimental melting curves. This value is consistent with previous estimates wart85 ; oliv77 ; amir81 ; blak87 .

Recent developments in the field of polymer physics allow us to calculate the total number of configurations for a loop embedded in a chain, as for those shown in Fig. 2(b). Analytical estimates, relying on the general theory of polymer networks dupl86 , indicate that the form given in Eq. (1) is still valid, however with a higher value for the exponent $`c`$ kafr00 . The reason for the higher value of $`c`$ is the lower number of configurations available for the loop due to the presence of the rest of the chain, compared to the number of configurations available for an isolated loop. Monte Carlo simulations on suitable three dimensional lattice models yield $`c2.15`$ carl02 ; baie02 , a value which is also in agreement with analytical estimates, which place this exponent in the range $`2.10c2.20`$ kafr00 . It is also well-known pola66 ; fish66  that increasing the value of $`c`$ has an effect of sharpening the transition. A value $`c>2`$ implies a first order transition in the case that the energy difference between different base pairs is neglected pola66 ; fish66 ; first order melting was indeed found numerically caus00 .

It is clear that accepting $`c=2.15`$ as the most appropriate estimate of the loop exponent entering in the partition function (1) implies that the existing estimate of the cooperativity parameter $`\sigma `$ has to be revisited as its experimental determinations relied on the choice $`c=1.75`$. The aim of this paper is to investigate this issue in detail. To this purpose we analyze the melting curves for DNA sequences of a wide range of lengths up to the full genome of the E. coli which amounts to $`5\times 10^6`$ bps.

## III Calculation of melting curves

The calculations of DNA melting curves are obtained from our own C-version of the Meltsim package (for details concerning this program, see Ref. blak99 ), which is a program based on the Poland recursive algorithm for the calculation of the probabilities $`A(i)`$ that the $`i`$-th base pair is in a open state. The program uses the Fixman-Friere fixm77  method, which consists of approximating the loop partition function of Eq. (1) as a sum of $`I`$ exponentials:

$$L_l\sigma \underset{k=1}{\overset{I}{}}a_ke^{b_kl}$$
(2)
where $`a_k`$ and $`b_k`$ are fitting coefficients. As for a sequence of total length $`N`$ the longest possible loop corresponds to $`l=2N`$, the fitting is done in a limited interval of lengths. Therefore, the shorter the sequence, the smaller is the number of coefficient $`I`$ necessary to obtain a very good fit of Eq. (1) for the relevant loop lengths for the problem. Typically a sum with $`I10`$ coefficients is sufficient for our needs. The advantage of the exponential approximation is that it reduces the computational time for a sequence of $`N`$ base pairs from $`O(N^2)`$ to $`O(N\times I)`$ without any significant loss in accuracy fixm77 .

For various temperatures we calculated $`A(i)`$, the probability that the $`i`$-th base pair is in an open state. From numerical differentiation of the average:

$$A=\frac{1}{N}\underset{i=1}{\overset{N}{}}A(i)$$
(3)
for a sequence of $`N`$ base pairs, we obtained the melting curves $`dA/dT`$ vs. $`T`$.

In this work we have chosen the ten stacking energy parameters given in Ref. blak99 . Another parameter that needs to be specified in the calculation is the concentration of the monovalent salt in solution, which in our calculation varies between $`0.05`$ M and $`0.1`$ M.

### III.1 Melting of short sequences

We first analyzed a series of existing experimental data blak98  for short sequences consisting of oligomeric repeat patterns shown in Table 1. These sequences were inserted in a linearized recombinant pN/MCS$`x`$ plasmid ($`x`$ abbreviates a specific sequence). The insertions are AT-rich and melt at lower temperatures than the rest of the plasmid chain, which plays the role of an energetic barrier to prevent further melting. The insertions were placed at one end, and in the middle of the linearized plasmid, thus their melting occurs through end or loop openings, respectively (see Fig. 3).

The experimental results, tabulated in Ref. blak98 , are re-analyzed here using the exponent $`c=2.15`$, appropriate for a loop inserted in a chain. To induce both loop and end openings we embedded the sequences of Table 1 in the middle and at one end of a pure CGCGCG chain. Due to the higher stability of the CG-domains, their melting will occur at much higher temperatures than those of the inserted sequences.

Figure 4 shows a plot of the differential melting curves for the Seq. 11 of Table 1, embedded in the middle of a CG matrix, as calculated by our program. We first fixed $`\sigma =1.26\times 10^5`$, the value reported in blak98 . The change of $`c`$ from $`1.75`$ to $`2.15`$ causes a shift of the position of the melting curves peak of about $`0.2^{}`$ C and a slight increase of height (the peak position defines the loop melting temperature $`T_\mathrm{M}^{\mathrm{loop}}`$). By choosing $`c=2.15`$, $`\sigma =1.75\times 10^4`$ one recovers a melting curve which almost perfectly overlaps the original one obtained with $`c=1.75`$, $`\sigma =1.25\times 10^5`$ (solid and dashed lines of Fig. 4). This curve fits well the experimental data (see Ref. blak98 ), thus we conclude that for the choice $`c=2.15`$ and $`\sigma =1.75\times 10^4`$ yields a melting curve consistent with the experimental values.

In order to provide an estimate of $`\sigma `$ from several independent measurements we reanalyzed the procedure followed in Ref. blak98 . Figure 5 shows experimental data (empty circles) for the temperature difference of the sequences of Table 1, $`\mathrm{\Delta }T_MT_M^{\mathrm{loop}}T_M^{\mathrm{end}}`$, plotted as functions of the inverse domain length $`1/N`$ (data taken from Table I of Ref. blak98 ). Here $`T_M^{\mathrm{loop}}`$ and $`T_M^{\mathrm{end}}`$ denote the location of the maxima of $`dA/dT`$ for sequences inserted in the interior and at the end of the plasmid chain, The dashed line shows the calculated $`\mathrm{\Delta }T_M`$ in the case of $`c=1.75`$ $`\sigma =1.26\times 10^5`$, where the latter value was determined using a regression analysis to fit the experimental data. We have repeated this procedure here fixing $`c=2.15`$ for which we find an equally good fit of the data with the choice $`\sigma =1.25\times 10^4`$. Given the precision of the experimental data which we could not assess or analyze further, we find that our calculated curve matches the data very well. Deviations between both theoretical curves clearly appear for shorter chains (loops) where the application of the asymptotic form of the loop partition function of Eq. (1) may not be appropriate.

### III.2 Melting of sequences of intermediate length

We next consider the melting of two sequences of intermediate length. We used two protein-coding cancer-related genes, eIF-4G ($`2900`$ bps) and LAMC1 ($`7900`$ bps), selected from a series of other sequences analyzed for their predominant loop melting effects.

Figure 6(a) shows the melting curves for three different values of $`c`$ and $`\sigma `$ for a fragment of DNA of eIF-4G as calculated from our program. Four major distinct peaks, labeled from $`1`$ to $`4`$ are visible. The denaturation maps, i.e. plots of $`1A(i)`$ as function of $`i`$, the base position along the chain, which are shown in Fig. 6(b), provide further insight on the type of transitions associated with each peak. We recall that $`1A(i)`$ is the average probability that the $`i`$-th base pair is in a closed state. The six plots of Fig. 6(b), labeled as $`\alpha `$, $`\beta `$$`\varphi `$, correspond to the six temperatures marked by the vertical arrows in Fig. 6(a).

Comparing the configurations at the temperatures just below and above the peak $`3`$ ($`\gamma `$ and $`\delta `$) we notice that this peak corresponds to the opening of a big loop extending roughly from base pair $`1300`$ to $`2300`$. The melting curves were calculated for three different sets of parameters, starting from the standard choice $`c=1.75`$, the value associated with isolated loops, together with $`\sigma =1.26\times 10^5`$, which is the most recent estimate for the cooperativity parameter blak98 . While keeping $`\sigma `$ fixed we first consider the exponent for a loop embedded in the chain $`c=2.15`$. For such a combination of parameters the melting peaks $`1`$ and $`2`$ are shifted from their positions, while peak $`4`$ vanishes in the signal background. The main influence of a change in $`c`$ is on peak $`3`$, which for $`c=2.15`$ becomes roughly twice as high ($`dA/dT|_{\mathrm{max}}1.1`$ compared to $`dA/dT|_{\mathrm{max}}0.6`$ in the case $`c=1.75`$). The reason for this is that, as shown from the study of the denaturation maps, the peak $`3`$ corresponds to the opening of a long loop of about $`1000`$ bps, thus any modification of the parameters entering in the loop entropy will have a particularly strong effect on it. Increasing $`c`$, while keeping $`\sigma `$ fixed makes the transition sharper, as expected pola66 ; fish66 .

The third melting curve we plotted is obtained again with $`c=2.15`$, but with a cooperativity parameter which is one order of magnitude larger: $`\sigma =1.26\times 10^4`$. This curve overlaps quite well with the original one. The region where the first and third curves differ the most is around peaks $`3`$ and $`4`$, where the chain contains a $`1000`$ bps long loop, and is shown in the inset of Fig. 6(a). Even in this region the differences are not very big: e.g., the shift of the maximum for peak $`3`$ is $`\mathrm{\Delta }T_{\mathrm{max}}0.1^{}`$, while both peaks keep the same heights.

We repeated similar calculations for other sequences in the same range of lengths. Figure 7(a) shows the melting curves for a fragment of LAMC1 about $`7900`$ bps long, for the same choice of parameters as in Fig. 6. Compared to the previous example there is a larger number of peaks, as the sequence is more than twice as long as the previous one and more subtransitions take place. The most relevant difference between the melting curves calculated for different values of $`c`$ and $`\sigma `$ is within the region around $`81^{}C`$, where a melting peak doubles its height going from the original choice of $`c=1.75`$ to $`c=2.15`$, while keeping the cooperativity parameter fixed at $`\sigma =1.26\times 10^5`$. As in the eIF-4G sequence, when $`\sigma `$ is rescaled by a factor $`10`$ we obtain a melting curve running extremely close to the original one in the whole range of temperatures.

It is interesting to take a closer look at the average configurations around the peak at $`T=80.5^{}C`$. The inset of Fig. 7(b) shows a blow up of the denaturation maps $`\beta `$ and $`\gamma `$ in a region around base pairs $`i=35004000`$, where a loop opening occurs. While keeping $`c=2.15`$ we plot in the inset the maps both for $`\sigma =1.26\times 10^5`$ (thin lines) and $`\sigma =1.26\times 10^4`$ (thick lines). It is remarkable how little thick and thin lines differ, compared to the big effect of a change of $`\sigma `$ in the differential melting curves of Fig. 7(a). The ”robustness” of the denaturation maps with respect to a change of the thermodynamic parameters has also been observed recently by Yeramian yera00 . The curves in the inset clearly demonstrate the increase of cooperativity when $`\sigma `$ is decreased: Either loops are suppressed (case $`\beta `$) or two neighboring loops tend to merge (case $`\gamma `$) in order to minimize the effect of a small value of $`\sigma `$. Although the peak at $`83^{}`$ C corresponds to the formation of a loop of about $`2000`$ bps, as can be seen from the denaturation maps $`\delta `$ and $`\epsilon `$, a change in the loop parameters $`c`$ and $`\sigma `$ does not seem to modify much this peak, as the transition considered is not an opening of a double helical segment, but rather a merging of two loops with a corresponding enlargement. We conclude that loops merging transitions are less affected by a change in $`c`$ and $`\sigma `$ as compared to a genuine loop opening.

We notice also that changing the loop parameters do not affect at all the small peak at $`T89^{}C`$, because this corresponds to a transition not involving inner loops, but rather the melting of the region $`0<i<900`$ through opening from the edges (see $`\varphi `$ in Fig. 7(b)).

### III.3 Melting of long sequences (E-Coli)

In order to further asses the validity of the previous analysis we calculated melting curves for much longer DNA sequences ($`10^6`$ bps). Longer sequences have the advantage that they develop loops of a broad range of length scales, thus one may test the influence in a change of loop parameters simultaneously for very short and very long loops. Unfortunately a limiting factor in this case is that, as pointed out in the introduction, the melting curves are rather featureless (as for Fig. 1(c)).

Figure 8 show the calculated melting curves for the full DNA of E. coli which is of about $`4.6\times 10^6`$ bps with a known sequence (taken from ecoli ). The curves are almost continuous, although some irregular structure is still visible, indicating that the discrete sharp peaks of the underlying sequence have not been completely averaged out. The melting curves extend now over about $`15^{}C`$ and have a typical asymmetric shape, with a gentle growth in the low temperature region, and a steeper descent above $`T_{\mathrm{max}}`$, the temperature for which $`dA/dT`$ is maximal.

As before we calculate the melting curves for three different combinations of the parameters $`c`$ and $`\sigma `$. Again we find that by changing the loop closure exponent from $`c=1.75`$ to $`c=2.15`$ while rescaling of $`\sigma `$ by one order of magnitude brings the curve back to the original one. The two curves obtained in this way are perfectly overlapping. A change of $`c`$ only, while leaving $`\sigma =1.26\times 10^5`$ makes the melting curve somewhat sharper as observed previously for shorter sequences. However the increase of the peak height is limited to about $`10\%`$, a rather small effect compared to the doubling of the height found for some peaks of Figs. 6 and 7.

It is interesting to notice that by changing the loop parameters $`c`$ and $`\sigma `$ the part of the melting curves for $`TT_{\mathrm{max}}`$ apparently is not modified much as all three curves plotted in Fig. 8 run with good accuracy on top of each other, in this temperature interval. It is only at at $`TT_{\mathrm{max}}`$ and above that the curves start separating, as shown in the inset. We also point out that the comparison of experimental and calculated melting curves for E. coli of Ref. blak99  show some differences in the high temperature region $`TT_{\mathrm{max}}`$. These differences could be due to some non-equilibrium effects, which are known to be more severe for very long sequences wart85 .

## IV Effect of the double helix stiffness

There has been some discussion recently about the influence of the stiffness of the double helix on the exponent $`c`$ hank03 ; kafr03 . In the very ideal limit of a loop attached to two infinitely rigid rods, the appropriate value of the loop exponent is the same of that of an isolated loop $`c=1.75`$, as the loop does not interact with the rest of the chain. The dsDNA has a persistence length which is typically much larger than that of the ssDNA ($`\xi _{\mathrm{ds}}\xi _{\mathrm{ss}}`$), therefore it is legitimate to question the applicability of the polymer network theory dupl86 , from which a higher loop exponent $`c2.1`$ was derived kafr00 , to real DNA sequences.

A different persistence length between dsDNA and ssDNA was incorporated in lattice Monte Carlo simulations carl02 . In these calculations the exponent $`c`$, estimated from an analysis of the distributions of the loop lengths using realistic values for $`\xi _{\mathrm{ds}}`$ and $`\xi _{\mathrm{ss}}`$, was found to be consistent with that of the case in which the difference between persistence lengths is neglected. However these lattice models did not incorporate a cooperativity parameter.

In Ref. hank03  it was estimated that sequences up to $`5000`$ bps are still too short to show any interaction effects between a loop with the rest of the chain, so that the appropriate value of the loop exponent should be that of an isolated loop $`c1.75`$. There is however still disagreement about this conclusion kafr03 .

Here we would like to point out some effects which have been overlooked in the present literature. The main interest in the exponent $`c`$ is that of modeling the DNA melting curves and the melting process typically takes place at around $`80^{}90^{}`$ C (see Figs. 6, 7 and 8). Therefore, in order to discuss the applicability of the higher loop exponent $`c2.1`$ to real DNA sequence, it is the difference in persistence length of dsDNA and ssDNA in this range of temperatures which should be investigated. At room temperatures the persistence lengths are $`\xi _{\mathrm{ds}}(T=20^{}\mathrm{C})500`$ Å, while $`\xi _{\mathrm{ss}}(T=20^{}\mathrm{C})40`$ Å corresponding to roughly $`100`$ bps and $`8`$ bps, respectively mark95 . Both conformational fluctuations and electrostatic interactions contribute to the persistence length of dsDNA in solution odij77 . In the limit of high salt concentrations electrostatic interactions are totally screened and the persistence length is expected to scale as function of the temperature as in the classical wormlike chain model doi87 , i.e. $`\xi =\kappa /T`$, with $`\kappa `$ temperature independent. This formula implies a reduction of about $`20\%`$ of the dsDNA persistence length in the melting region compared to the room temperature value. However the assumption that the electrostatic interactions are totally screened may not be fully justified for the range of salt concentrations used here ($`[Na]=0.1`$M or lower). Thus the $`20\%`$ should be rather considered as an upper bound.

A more relevant effect for the reduction of the dsDNA persistence length is the proliferation of small denaturated bubbles within a dsDNA segment. Within the model considered here the characteristic lengths close to melting, as the loop and double helix segment lengths, scale as $`1/\sigma `$. As pointed out before, a large cooperativity (small $`\sigma `$), would imply typically long loops and long double helical segments. However, the conclusion that short (i.e. $`10`$ bps) loops would be totaly suppressed due to the small $`\sigma `$, is too simplistic. Several studies showed that the nearest neighbor model largely underestimates the opening probability for small loops (see the discussion in wart85  and references therein), so it cannot be a quantitatively reliable tool at too short length scales. Such short loops are present in real DNA samples.

We can demonstrate this effect explicitly by analyzing the experimental melting curves recently obtained alta03  in a study of dsDNA bubble dynamics. This study was performed on short sequences (of about $`30`$ bps) containing an internal AT region surrounded on both sides by short CG clamps. Experiments show that the inner AT region melts at temperatures in which the CG edges are still bound alta03 .

In Fig. 9 we present the calculated melting curves for the probabilities of having the base pair $`i=1`$ and $`i=17`$ in an open state for the sequence $`M_{18}`$ of Ref. alta03 , which can be directly compared with the experimental results as both quantities $`A(1)`$ and $`A(17)`$ have been measured experimentally through fluorescence measurements alta03  (the base pair $`i=17`$ is in the middle of the AT-region). As the sequence is very short the calculated melting curves are not sensitive to a change in $`c`$. For $`\sigma =1.26\times 10^4`$ (Fig. 9(a)) the typical value for the cooperativity parameter used previously in the paper, our calculations show that $`A(1)`$ and $`A(17)`$ are at all temperatures very close to each other, which implies that no loops are formed and that the sequence rather melts from edge openings, although the CG edges are energetically more stable than the inner AT region. This is an effect of the small value of $`\sigma `$ used in the calculation. In order to verify this we have plotted in Fig. 9(b), just as an illustration, the same quantities with $`\sigma =5\times 10^2`$. The reduced cooperativity allows for the formation of loops and now produces results closer to what is observed in experiments (see Fig. 2 of Ref. alta03 ). Thus, despite that the small cooperativity parameter ($`\sigma 10^4`$) correctly describes long loop ($`>100`$ bps) formations in DNA melting, small loops ($`10`$ bps) openings in AT-rich domains are still possible. The importance of small bubbles formation in DNA oligomers melting has been recently emphasized in an analysis of the melting of DNA oligomers zocc03 .

As the ssDNA has, at $`90^{}`$ C, an estimated persistence length corresponding to roughly $`5`$ bps, we expect that the opening of a small loop of about $`15`$ bps would be sufficient to decorrelate completely the two dsDNA segments at its two sides. To provide an estimate of the persistence length of the dsDNA one would need to know the average density of small loops and their probabilities, which depends on the sequence composition. It is however conceivable that this effect would make the dsDNA at $`8090^{}`$C much more flexible, compared to its room temperature behavior, so that the use of the loop embedded exponent for $`c`$ is justified.

## V Conclusion

In this paper we have analyzed the effect of reparametrizing the loop weight contribution, in the calculation of DNA melting curves for sequences of a broad range of lengths, up to the full genome of the E-coli ($`5.6\times 10^6`$ bps). Using the closure exponent for a loop embedded in a chain ($`c=2.15`$) we found that in order to reproduce correctly the existing experimental data and melting curves one needs to increase the cooperativity parameter $`\sigma `$ by about one order of magnitude. An increase of the cooperativity parameter, which is the weight associated with the interruption of an helix to form a loop, implies that loops are more probable within the chain.

It is clear that a simultaneous change of the loop exponent $`c`$ and of $`\sigma `$ cannot reproduce two perfectly overlapping melting curves. We found that rescaling $`\sigma `$ by about one order of magnitude together with a change in $`c`$ from $`1.75`$ to $`2.15`$ produces typically very small shifts in peak positions ($`0.1^{}`$) and heights. Accurate melting experiments would be able to distinguish between the two choices and fix unequivocally both $`c`$ and $`\sigma `$. In any case our analysis indicates that the best samples where to test the above effects are sequences of intermediate lengths ($`10^310^4`$ bps). We showed that in these sequences rather large loops may be formed and that the associated melting peaks are extremely sensitive to a change in loop parameters $`c`$ and $`\sigma `$. The disadvantage of shorter sequences is that they predominantly melt through end openings (unless they are designed to do otherwise, as in the example of the preceding section). The melting curves of very long sequences, as we showed for E. Coli, are only weakly affected by a change in the parameters $`c`$ and $`\sigma `$.

Acknowledgment. We thank I. Diesinger and E. Meese for their help in finding suitable sequences for melting analysis. Discussions with A. Hanke, R. Metzler and D. Mukamel are gratefully acknowledged.


text:
# Rejection of the Light Quantum: The Dark Side of Niels Bohr 22footnote 2 Open Lecture presented at the 4th Workshop on Rigged Hilbert Space and Resonances. Jaca,HU, Spain, June 2.001

## 1 BOHR AND THE LIGHT QUANTUM.

In the Trilogy , the famous $`1.913`$ paper ”On the Constitution of Atoms and Molecules” in three parts by Niels BOHR ($`1.8851.962`$), there are quite a few mentions to the Light Quantum Hypothesis . For instance , p. 6

”…the energy radiation from an atomic system does not take place in the continuous way assumed in the ordinary electrodynamics but…, on the contrary, takes place in distinctly separated emissions…”

Later in the same Trilogy Bohr describes the radiation emitted by the atom as \[ I, p. 172\]

”…emission of one of several quanta ”

which later turned to be mainly only one. Bohr, however does not use Einstein s word *Lichquanten* but Planck s *energy* quanta.

So at the very begining Bohr embraced both the failure of classical electrodynamics to acount for the atom s stability, and also the emission by discrete quanta. But very soon he changed the perspective: classical electrodynamics was to be mantained, indeed used as a guide, quantization limited to matter, and all references to discrete emission of (energy) quanta discarded. What brought about this change? We can trace back precisely the moment: when Bohr discovers, and tells Rutherford at once in a letter , that for large quantum numbers the frequency of the emitted radiation coincides with the frequency of the revolution electron, as the clasical theory would predict; Bohr had discovered (letter to Rutherford, $`21III1.913`$)

”…the most beautiful analogi \[sic\] between the old electrodynamics and the considerations used in my paper”

This was crucial for Bohr future view of quantum physics, and through Bohr s overwhelming influence to the whole of the physics community: the *Correspondence Principle* had germinated; indeed, it was criptically expresed already in p. $`1314`$ of the Trilogy. Henceforth Bohr takes it as the guiding principle to discoveries in the old quantum theory. Indeed, the original quantum conditions of Planck on oscillators, in which Bohr’s first atom paper is based, are *rejected*. Heilbron and Kuhn  already realized the contradictions between the July, $`1.913`$ trilogy, and the December-$`1.913`$ Copenhagen communication . In the latter, Bohr considers *misleading* the original derivation of the quantum rules (kinetic energy $`T=\nu h/2`$, the original quantum rule that Bohr borrows from Planck): the *correspondence criterion* is elevated to the correspondence *principle*.

In his writings $`1.9131.920`$ Bohr steadily gets farther and farther away from the photon concept, and relying more and more on the classical radiation theory. A few quotations will suffice :

”…the theory of spectra must be considered in a certain sense as the rational generalization of the ideas of the usual radiation theory” \[$`1.918`$\]

”…On the other hand radiation had to be described by the classical electromagnetic theory” \[$`1.921`$\]

”\[interference phenomena\] cannot possibly be understood on the basis of a theory such as Newton s. In fact, the picture provided by Einstein cannot more than give any sort of explanation of the interference phenomenon \[$`1.918`$\]

There is no point in keeping quoting Bohr: all the authors agree on that Bohr rejected the corpuscular nature of light. Particularly detailed studies are in Pais  and Murdoch . Timidly, Pais points out the true reason: the correspondence principle clashes head-on with the light quantum concept!

There is some irony in Bohr’s writings of the epoch; let us look at two cases. Sommerfeld in München was developing a quasi-consistent quantization system of rules for atomic systems, and was not happy with the correspondence principle, as *”…etwas Fremdartigen”* to the theory, a ”magic wand, which operates only in Kobenhavm” . Bohr, of course, disliked Sommerfeld approach:

”…in every fine point that came up Sommerfeld was wrong” .

The irony was, of course, that the difficult Sommerfeld *Feinstruckturformel* was one of big successes of the Old Quantum Theory, an issue in which him, Bohr, failed (he did apply relativity to the *circular* orbits only). Sommerfeld never got the Nobel prize, to the surprise of many (including A. Pais, an admirer of Bohr). Actually, Bohr never recommended Sommerfeld to the Swedish Academy, whereas most of his recommendees did get the Prize (for a full list see ; ).

In a comment on Einstein s *Lichquantum*, Bohr ($`1.920`$) had this to say

”…the Light Quantum hypothesis is so formal, that even Einstein himself shrouded it of mysticism, talking about the *Gespensterfeld* to guide the ”photons”

The irony here is double: first, Bohr himself, in the ill-fated BKS paper (which we shall comment later) introduced the ”guiding field” in terms of virtual oscillators, altough he borrows the idea from Slater; and secondly, Einstein s $`1.920`$ (unpublished, see , p. $`287`$) idea was later, in the hands of Schrödinger, instrumental in founding the wave mechanics, which Bohr embraced! (see also later) because after all it came to the rescue of his beloved classical e.m. theory. The *Gespensterfeld*, in the hands of Max Born, became the basis for the probability interpretation, today universally accepted, also by Bohr, as part of *his* complementarity point of view. Of course, complementarity and the Born interpretation are at odds which each other. It had to be a philosopher (Karl Popper, ), coming from outside, who pointed out the contradiction.

## 2 KRAMERS vs. KRAMERS.

It will be prophilactic to describe now the episodes in which Bohr clashed with people on the ”photon” issue. The *first victim* was (Hans) A. Kramers ($`1.8941.952`$), Bohr’s first collaborator, and a ”yes man” for Bohr, as Slater later put it. Now the historian-physicists A.Pais and M. Dresden talk ( I resume from  and ):

In Spring, $`1.921`$ ”The indications are that Kramers had obtained the conservation law description of the Compton effect, using the photon description explicitely… Bohr would object violently to the publication of these results. He and Kramers engaged inmediately in a series of daily ”no holds barred” 333The spanish sentence *a calzón quitado* is more vivid. arguments about the photon…In these discussions…Kramers…was simply grounded down by Bohr… After these discussions, which left Kramers exhausted, depressed, and let down, \[he\] got sick and spent some time in the hospital. During his stay in the hospital, Kramers gave up the photon notion…altogether. Instead, he soon became violently opposed to the photon notions, and never let an opportunity pass by to criticize or even ridicule the concept. He disposed of most of his early calculations, but inadvertedly left a few, early rough notes \[which are extant, fortunately, in Kramers’s family’s hands. LJB\]

The Bohr-Kramers discussions are in spring, $`1.921`$. That year Bohr was overworked with the building a new institute, and had to renounce to participate in the Solvay meeting. But a glance of the spiritual turmoil is felt, I think, in the following revealing letter to Ehrenfest

”You have no idea how much your friendship means to me. Especially at a time when I almost feel as a criminal in relation to all kinds of people here and elsewhere”

As the incident with Kramers is an important one, let us recall that already in his $`1.967`$ book, ter Haar said

”Debye ($`1.923`$) developed the theory of the Compton effect as did Kramers, who was persuaded by Bohr not to publish…”

Further evidence comes from Jost, Pauli, O. Klein, Hugenholtz, Casimir, and others. It is interesting to read Kramers *abjuration*, which reminds me very much of the self-indicted declarations of the comunists, in Russia or China:

”The theory of Light Quanta might be compared with a medicine which will cause the disease to vanish, but kills the patient. The fact must be emphasized that this theory in no way has sprung from Bohr theory, to say nothing of its being a necessary consequence of it”444 Kramers-Holst book, ($`1.923`$)

Were it not because that title belongs to Leon Rosenfeld, one would call Kramers

*”Plus royalist que le Roi”* 555 Again, the spanish expression *Más papista que el Papa* is better. with respect to Bohr. One should also feel sorry for Kramers; the fact that he was a man with poor health alleviates the burden. His argument to reject the photon was, it seems, that it was not invented by God (*alias* Niels Bohr). The irony is that precisely it is in the Bohr atom that the photon concepts enters in the most natural way. Many modern books describing the Bohr atom mention expressly the emission of a photon, when a valence electron makes a transition, as if it was part of the original hypothesis of Bohr!

Kramers left Bohr in $`1.926`$ to a distinguished career in his native Holland.

## 3 J. C. SLATER.

The *next victim* is the brilliant american physicist John Clark Slater ($`1.9001976`$). I show here some evidence gathered from , Pais again , and Slater Recollections . Slater conceived around November $`1.923`$ in England a theory to reconcile the apparent wavelike properties of light (interference and diffraction) with the corpuscular photon of Einstein. Slater had the excited atom to ”communicate” with other atoms by virtue of some ”virtual field” before emitting a photon:

”As soon as the atom reaches a stationary state the \[virtual\] field is set up… containing all the frecuencies the atom can radiate. These fields determine the probabily of emission of a quantum…Finally a quantum of someone of the frequencies will be emitted, \[and\] the radiation will cease. Meanwhile the quantum is travelling…until it is absorbed…

As soon as I discussed \[this\] with Bohr and Kramers \[Dec-$`1.923`$\] I found…to my consternation that they completely refused to admit the real existence of the photons 666Slater wrote this much later, when already the *Lichtquantum* of Einstein was universally called the photon, name due to G.N. Lewis, ($`1.926`$).. It had never ocurred to me that they would object to what seemed like so obvious a deduction from many types of experiments…They grudgingly allowed me to send a Note to *Nature* indicating that my original idea had included the real existence of the photons, but that I had given that up at their instigation” \[Slater s abjuration, see soon below. LJB\]

In a letter to van der Wärden  Slater has this to say ($`1.964`$)

”…Bohr and Kramers opposed this view \[of the photon\] so vigorously that I saw the only way to keep peace and get the main part of the suggestion \[the virtual oscillators\] published was to go along with them…”

Before relating Slater s abjuration, let us comment briefly the ill-fated $`1.924`$ Bohr-Kramers-Slater paper. It was written entirely by Bohr and Kramers, while Slater was kept locked up in another room. The paper has $`18`$ pages with a single formula, $`E=h\nu `$. Bohr gave up conservation of energy lest the photon survive. Einstein, Heisenberg and Pauli opposed strongly; of course, energy conservation was vindicated in both sides of the Atlantic pretty soon . Did then Bohr accepted the photon ? No! But let us first listen to Slater confession:

”…it seems possible to build up a more adequate picture of optical phenomena than has previously existed, by associating the *essentially continuous* radiation field with the continuous existence of stationary states, and the discontinuous changes of energy and momentum with the discontinuous transitions from one state to another” \[my italics. LJB\] 777Letter sent to Nature, $`28I1.924`$

In other words, Slater renounces to the photon…Some scattered comments convey more the spirit of the abdication:

”I have finally become convinced that the way they \[Bohr and Kramers\] want things, without the little lump carried along the waves…is better…I am going to have a chance at least to suggest changes”

Eventually Slater received an apology from Bohr: ”I had bad conscience about you when in Copenhagen…” J. C. Slater went on to another distinguished career in physics in the East Cost, being instrumental in buiding the theoretical physics in the U.S., as the *transition* person from the meteoric start of W. Gibbs to the preeminence with J. R. Oppenheimer, etc.

After the Compton-Simon and Bothe-Geiger experiments  (spring $`1.925`$), Bohr renounced to statistical-only conservation of energy and momentum, but he does *not* embrace the photon. Heisenberg says he believed around early $`1.925`$ Bohr was the only notorious physicist unbeliever about photons. Bohr’s conclusion instead was: one should renounce to a spacetime description of physical atomic phenomena; he took cold confort in another enigma at the time, the discovery of the (Townsend-) Ramsauer effect (anomalous low energy scattering of electrons by noble gases), to delve in (meta-)physical thoughts about non space-time descriptibility of microscopic phenomena; the irrationality so apparent in many of Bohr’s statements in $`1.92730`$, somewhat attenuated afterwards, take their roots here.

## 4 SCHRÖDINGER and HEISENBERG.

In September, $`1.926`$ E. Schrödinger ($`1.8871.96`$1) joined W. Heisenberg ($`1.9011.976`$) and N. Bohr in Copenhagen. We shall learn more of the way Bohr dealt with opponents. The report is by Heisenberg :

”The discussions between Bohr and Schrödinger began already at the train station and were continued each day from early morning til late at night…And Bohr…now appeared to me almost as an unrelentic fanatic, who was not prepared to make a single concession to his discussion partner…So the discussion continued for many hours throughout day and night without a consensus being reached. After a couple of days, Schrödinger fell ill …He had to stay in bed with a feverish cold. Mrs. Bohr nursed him and brought tea and cakes, but Niels Bohr sat on the bedside and spoke earnestly to Schrödinger…”

At issue was the wave-like interpretation of the wave mechanics, no so much the photon; but I bring this incident to sharpen the reader s ideas on Bohr. Schrödinger later reported to a friend how was he \[S.\] astonished by Bohr s happy coexistence with contradictions bordering the irrational; also

”…There will hardly again be a man who…in his sphere of work is honored almost like a demigod by the whole world and who yet remains…rather shy and diffident like a theology student…

\[Bohr\] talks often for minutes almost in a dreamlike, visionary and really quite unclear manner…”

We are approaching the climax now. When Schrödinger left, the two men, Bohr and Heisenberg, embarked, through a socratic dialogue, to set up the conceptual foundations of quantum mechanics, what soon will become the Copenhagen interpretation; but the starting points of them were very different: Bohr took the correspondence principle as a guide, and had already extracted the (unwarranted ?) conclusion that

”Every description of natural processes must be based on ideas which have been introduced and defined by the classical theory” ($`1.923`$; , p. $`300`$)

Bohr would take this phrase almost literally to *hold also in the new interpretation* (see later, Como conference report). As for Heisenberg,

”I dislike this \[Bohr s\] approach. I want to start from the fact that quantum mechanics \[H. here means the Göttingen matrix theory as started by him, elaborated by Dirac and in the *Dreimännerarbeit*, and sharpened in the transformation theory of Jordan and Dirac; he is more explicit in \]…already imposed a unique physical interpretation…so…we no longer had any freedom with…interpretation” , p. $`303`$).

In correspondence of H. with Pauli, which I shall not reproduce here, it is clear the main fighting point: Bohr wanted to include waves, and to make a blend of Schrödinger wave mechanics, but of course not his \[S.\] interpretation, whereas H. insisted in the particle point of view, with Max Born s probability interpretation for the matrix elements, in particular, for the wave function itself; (von Neumann ($`1.929`$) would definitely clarify this, showing that Heisenberg was using a *energy* representation, Schrödinger a *coordinate* representation, equally valid, and equivalent mathematically). That much is perfectly clear in Heisenberg s original writing of the *Umbestimmheit* paper (March, $`1.927`$). When Bohr came back of his skiing holiday in Norway, he corrected rightly a small mistake in the paper of Heisenberg (he had made a similar error in his oral examination for the Ph. D., which nearly costed him the degree: Wien was reluctant, but Sommerfeld came to his rescue); then the fight between the two men was very acute, as witnessed by Oscar Klein; as described by Heisenberg,

”Bohr tried to explain \[my paper\] was not right and I shouldn’t publish the paper. I…ended by my breaking out in tears because I just couldn’t stand this pressure from Bohr …So it was very disagreable \[for\] a short period of perhaps ten days or so in which we really disagreed rather strongly…\[but after\] we agreed that the paper could be published if it was improved on these points…” \[ A. Pais, , p. $`308`$\]

The published version of the uncertainty paper contains, as a *Nachtrag*, Heisenberg s abdication:

”After submission of this work,…Bohr has pointed out that I have overlooked essential features…The uncertainty in an observation depends not only on the ocurrrence of discontinuities, but also directly on the requirement that…measurements are to be made…as in particle theory or…as in *wave theory*…For permission to mention his new research…I was privileged to learn…at his genesis, I owe my heartfelt thanks to Professor Bohr ” (my italics. LJB)

The abdication of Heisenberg was a full *volte face*, same as Kramers had experienced six years before. The phrase ”Kopenhagener Geist der Quantentheorie” is Heisenberg’s own .

To fully analyze how Bohr passed from *Correspondence* to *Complementarity* is beyond our purpose. In a nutshell, Bohr kept from the old principle about the survival of classical radiation theory (instead of, as I think it should be, deduce the classical wave behaviour as statistical averaging of the individual quantum particles; but I shall not argue on this), the coexistence of particles and waves. Of course, an element of irrationality creeps in, but Bohr was happy with it , as already Schrödinger noticed; see this other testimony, by Bohr:

”…our endeavor is, by means of a suitably limited use of mechanical and electromagnetic concepts, to obtain a statistical description of the atomic phenomena that appears as a rational generalization of the classical physical theories, in spite of the fact that the quantum of action from their point of view must be considered as an irrationality” ($`1.933`$ .

Interpretation: Bohr invites us to study the quanta as a *rational* generalization of the classical theory, inspite of the fact that the quantum, from the very clasical point of view, is seen as an *irrationality*. If this is intelligible, *que venga Dios y lo vea*.

I find this hard to swallow, to say the least, and I think Einstein, Schrödinger, Planck, and others, who opposed to the Copenhagen interpretation, did that because they were unable to digest this. Einstein is very explicit: ”I never understood what Bohr means by the complementarity principle, inspite of a careful study of it”. If the first intelligence of the XX Century is unable to grasp the meaning of complementarity, the odds are…is un-understable; and perhaps this is what Bohr really had in mind. ”We must understand, that there is nothing to be understood”. Einstein did not *accept* the probability interpretation, but did not *understand* complementarity; there is a world of difference…

There some other episodes of rudeness of Bohr, with Landau and with Brioullin, for example, which would end to delineate the dark side of Bohr I’m showing; I just refer to the cartoon by G. Gamow with respect to Bohr s reaction to a paper by Landau and Peierls ($`1.931`$)

## 5 CONCLUSIONS.

1. Bohr started using Planck’s and Einstein’s hypothesis to explain the atom and its radiation.
2. Very soon, before the first part of the Trilogy is published, he discovers that for large quantum number $`n`$ the radiation and the rotation frequencies coincide; it acts like a *revelation* for him.
3. He next substitutes the quantum conditions by the ”correspondence principle”, if dressed with the *adiabatic principle* of Ehrenfest (this is very clear in the ”Tetralogy” )
4. As a consequence, the *classical radiation* theory is set up as a *referent* for the new discoveries; the little original love for the energy quantum dissapears completely. Later Bohr was the staunchest enemy of Einstein s photon concept, to the point of ridicule.
5. Part of the classical heritage is the necessity of speaking of all the concepts, *even the quantum ones*, with a classical lenguage; at some point Bohr even said. ”There is NO quantum world”.
6. There is strong competition between the München school of Sommerfeld and Bohr’s in Copenhagen; *each spurns the other*.
7. After the Compton effect, he still is antiphoton, but starts to develop an irrational attitude towards the quantum, because coexistence of classical pictures, which he wants to mantain at any cost, and the hard reality of genuine quantum processes.
8. The advent of quantum mechanics (in matrix form; Heisenberg, July $`1.925`$) caught Bohr *off* guard; he always tought of making himself a contribution to its discovery.
9. He became a great fan of Heisenberg, to whom he considered as a kind of Messiah.
10. There is no evidence Bohr ever went through the intricacies of matrix mechanics; but he salutates the wave mechanics of Schrödinger (January, $`1.926`$), and after the fall-$`26`$ discussions with Schr. and Hei., embarks himself in a crusade for THE right interpretation of Quantum Mechanics. He thinks he achieves this in the snow in Norway (February, $`1.927`$).
11. He brainswashed Heisenberg, as had done with Kramers and Slater, forcing him to modify his paper; H. became thoroughly convinced.
12. His climax occurs at the time of the Como conference (Volta Death Centenary, $`16`$ September $`1.927`$). I cannot refrain repeating some phrases, which reflect Bohr’s fidelity to his concepts:  ”…nuestra interpretación de los datos experimentales se apoya de manera fundamental en los conceptos clásicos ”(p. $`98`$).

”Este postulado \[the postulate Bohr calls quantum \] atribuye una…individualidad a todo proceso atómico e implica la renuncia a una coordinación causal de los procesos atómicos en el espacio y en tiempo” (p.$`99`$).

”Por lo que se refiere a la luz, su propagación en el espacio y en el tiempo queda descrita de manera satisfactoria por la teoría electromagnética \[read: Bohr does still not accept in the fall 1.927! the propagation of photons\]…para llegar a una expresión exacta de la conservación de la energía…es preciso recurrir a la idea del fotón de Einstein \[ notice how reluctantly introduces Bohr the photon\]…Esta situación muestra con claridad la imposibilidad de mantener una descripción causal y espacio-temporal de los fenómenos luminosos….” ( p. $`101`$).
13. The overwhelming personality of Bohr’s wins everybody in the young generation (Pauli, Dirac, Landau, even Max Born) to his point of view. Heisenberg will be the new prophet:

”Since the conclusive studies of Bohr in $`1.927`$ there have been no essential changes in these \[fundamental quantum\] principles” \[26, Pref.\]
14. Nevertheless, practitioners of Q. M. just *ignore* complementarity. Wigner was not impressed at all in Como; the books by Dirac and Landau do not mention it.

The degree of brainwashing by Bohr in all of us is remarkable (I learned the expression from Murray Gell-Mann). For example, in the ”Welches Weg?” experiments, either the two slit screens or Mach-Zehnder interferometer, people say (excuse me for not quoting!) that there is *complementarity* between waves or particles bzw. according the photon runs through both paths (that is, we mantain coherence) or only by one (incoherence, meaning we know which path). But this is as saying that interferences are ondulatory, but diffraction is corpuscular!! The photon, a particle, is quantic, so his path does not exist if it is not observed. The Feynman s path integral formalism is just perfect to explain the ”propension” of the particle (photon or Mach truck !) to explore *all* paths.

## Acknowledgements

I thanks listeners in several places for patience and questions.


text:
# Meson model for 𝑓₀(980) production in peripheral pion-nucleon reactions

## I Acknowledgment

The support of this work by the Deutsche Forschungsgemeinschaft (DFG 447AUS 113/14/0) is gratefully acknowledged.