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# IISc-CTS-2/00 quant-ph/0002037 Quantum Algorithms and the Genetic Code

## I Genetic Information

I am going to talk about processes that form the basis of life and evolution. The hypothesis that living organisms have adapted to their environment, and have exploited the available material resources and the physical laws governing them to the best of their capability, is the legacy of Charles Darwin—survival of the fittest. This is an optimisation problem, but it is not easy to quantify it in mathematical terms. Often we can explain various observed features of living organisms . The explanation becomes more and more believable, as more and more of its ingredients are verified experimentally . Yet even when definite predictions exist, an explanation is an explanation and not a proof; there is no way we can ask evolution to repeat itself and observe it like many common scientific experiments.

With this attitude, let us look at life. Living organisms try to perpetuate themselves . The disturbances from the environment, and the damage they cause, make it impossible for a particular structure to survive forever. So the perpetuation is carried out through the process of replication. One generation of organisms produces the next generation, which is essentially a copy of itself. The self-similarity is maintained by the hereditary information—the genetic code—that is passed on from one generation to the next. The long chains of DNA molecules residing in the nuclei of the cells form the repository of the genetic information. These DNA molecules control life in two ways: (1) their own highly faithful replication, which passes on the information to the next generation (each life begins as a single cell, and each cell in a complex living organism contains identical DNA molecules), and (2) the synthesis of proteins which govern all the processes of a living organism (haemoglobin, insulin, immunoglobulin etc. are well-known examples of proteins) .

Computation is nothing but processing of information. So we can study what DNA does from the view-point of computer science. In the process of designing and building modern computers, we have learnt the importance of various software and hardware features. Let us look at some of them.

The first is the process of digitisation. Instead of handling a single variable covering a large range, it is easier to handle several variables each spanning a smaller range. Any desired accuracy can be maintained by putting together as many as necessary of the smaller range variables, while the instruction set required to manipulate each variable is substantially simplified. This simplification means that only a limited number of processes have to be physically implemented, leading to high speed computation. Discretisation also makes it possible to correct small errors arising from local fluctuations. There are disadvantages of digitisation in terms of increase in the depth of calculation and power consumption, but the advantages are so great that digital computers have pushed away analogue computers to obscurity. Even before the discovery of DNA, Erwin Schrödinger had emphasised the fact that an aperiodic chain of building blocks carries information , just like our systems of writing numbers and sentences. The structure of DNA and protein reveals that life has indeed taken the route of digitising its information. DNA and RNA chains use an alphabet of 4 nucleotide bases, while proteins use an alphabet of 20 amino acids.

The second is the packing of the information. When there are repetitive structures or correlations amongst different sections of a message, that reduces its capacity to convey new information—part of the variables are wasted in repeating what is already conveyed. Claude Shannon showed that the information content of a fixed length message is maximised when all the correlations are eliminated and each of the variables is made as random as possible. Our languages are not that efficient; we can immediately notice that consonants and vowels roughly alternate in their structure. When we easily compress our text files on a computer, we remove such correlations without losing information. Detailed analyses of DNA sequences have found little correlation amongst the letters of its alphabet, and we have to marvel at the fact that life has achieved the close to maximum entropy structure of coding its information.

The third is the selection of the letters of the alphabet. This clearly depends on the task to be accomplished and the choices available as symbols. A practical criterion for fast error-free information processing is that various symbols should be easily distinguishable from each-other. We use the decimal system of numbers because we, at least in India, learnt to count with our fingers. There is no way to prove this, but it is a better explanation than anything else. We can offer a better justification for why the computers we have designed use the binary system of numbers. 2 is the smallest base available for a number system, and that leads to maximal simplification of the elementary instruction set. (The difference is obvious when we compare the mathematical tables we learnt in primary schools to the corresponding operations in binary arithmetic.) 2 is also the maximum number of items that can be distinguished with a single yes/no question. (Detecting on/off in an electrical circuit is much easier than identifying more values of voltages and currents.) Thus it is worth investigating what life optimised in selecting the letters of its alphabet.

The computational task involved in DNA replication is ASSEMBLY. The desired components already exist (they are floating around in a random ensemble); they are just picked up one by one and arranged in the required order. To pick up the desired component, one must be able to identify it uniquely. This is a variant of the unsorted database search problem, unsorted because prior to their selection the components are not arranged in any particular order. (It is important to note that this replication is not a COPY process. COPY means writing a specific symbol in a blank location, and unlike ASSEMBLY, it is forbidden by the linearity of quantum mechanics.) The optimisation criterion for this task is now clear—one must distinguish the maximum number of items with a minimum number of identifying questions. I have already pointed out that in a classical search, a single yes/no question can distinguish two items. The interesting point is that a quantum search can do better.

## II Unsorted Database Search

Let the database contain $`N`$ distinct objects arranged in a random order. A certain object has to be located in the database by asking a set of questions. Each query is a yes/no question based on a property of the desired object (e.g. is this the object that I want or not?). In the search process, the same query is repeated using different input states until the desired object is found. Let $`Q`$ be the number of queries required to locate the desired object in the database.

Using classical probability analysis, it can be easily seen that (a) $`Q=N`$ when all objects are available with equal probability for each query (i.e. each query has a success probability of $`1/N`$), and (b) $`Q=(N+1)/2`$ when the objects which have been rejected earlier in the search process are not picked up again for a query. Here the angular brackets represent the average expectation values. Option (b) is available only when the system possesses memory to recognise what has already been tried before. In the random cellular environment, the rejected object is thrown back into the database, and only option (a) is available to a classical ASSEMBLY operation.

Lov Grover discovered a quantum database search algorithm that locates the desired object using fewer queries . Quantum algorithms work with amplitudes, which evolve in time by unitary transformations. At any stage, the observation probability of a state is the absolute value square of the corresponding amplitude. The quantum database is represented as an $`N`$dimensional Hilbert space, with the $`N`$ distinct objects as its orthonormal basis vectors. The quantum query can be applied not only to the basis vectors, but also to their all possible superpositions (i.e. to any state in the Hilbert space). Let $`|b`$ be the desired state and $`|s`$ be the symmetric superposition state .

$$|b=(0\mathrm{}010\mathrm{}0)^T,|s=(1/\sqrt{N})(1\mathrm{}1)^T.$$
(1)
Let $`U_b=12|bb|`$ and $`U_s=12|ss|`$ be the reflection operators corresponding to these states . The operator $`U_b`$ distinguishes between the desired state and the rest. It flips the sign of the amplitude in the desired state, and is the query or the quantum oracle. The operator $`U_s`$ treats all objects on an equal footing. It implements the reflection about the average operation. Grover’s algorithm starts with the input state $`|s`$, and at each step applies the combination $`U_sU_b`$ to it. Each step just rotates the state vector by a fixed angle (determined by $`|b|s|=1/\sqrt{N}`$) in the plane formed by $`|b`$ and $`|s`$. $`Q`$ applications of $`U_sU_b`$ rotate the state vector all the way to $`|b`$, at which stage the desired state is located and the algorithm is terminated.

$$(U_sU_b)^Q|s=|b.$$
(2)
This relation is readily solved, since the state vector rotates at a constant rate, giving

$$(2Q+1)\mathrm{sin}^1(1/\sqrt{N})=\pi /2.$$
(3)
Over the last few years, this algorithm has been studied in detail. I just summarise some of the important features:

* For a given $`N`$, the solution for $`Q`$ satisfying Eq.(3) may not be an integer. This means that the algorithm will have to stop without the final state being exactly $`|b`$ on the r.h.s. of Eq.(2). There will remain a small admixture of other states in the output, implying an error in the search process. The size of this admixture is determined by how close one can gets to $`\pi /2`$ on the r.h.s. of Eq.(3). Apart from this, the algorithm is fully deterministic.
* The algorithm is known to be optimal , going from $`|s`$ to $`|b`$ along a geodesic. No other algorithm, classical or quantum, can locate the desired object in an unsorted database with a fewer number of queries.
* The iterative steps of the algorithm can be viewed as the discretised evolution of the state vector in the Hilbert space, governed by a Hamiltonian containing two terms, $`|bb|`$ and $`|ss|`$. The former represents a potential energy attracting the state towards $`|b`$, while the latter represents a kinetic energy diffusing the state throughout the Hilbert space. The alteration between $`U_b`$ and $`U_s`$ in the discretised steps is reminiscent of Trotter’s formula used in construction of the transfer matrix from a discretised Feynman’s path integral .
* Asymptotically, $`Q=\pi \sqrt{N}/4`$. The best that the classical algorithms can do is to random walk through all the possibilities, and that produces $`Q=O(N)`$ as mentioned above. With the use of superposition of all possibilities at the start, the quantum algorithm performs a directed walk to the final result and achieves the square-root speed-up.
* The result in Eq.(3) depends only on $`|b|s|`$; the phases of various components of $`|s`$ can be arbitrary, i.e. they can have the symmetry of bosons, fermions or even anyons.

To come back to the genetic code, let us look at two of the solutions of Eq.(3) for small $`Q`$. The only exact integral solution is $`Q=1`$, $`N=4`$. Base-pairing during DNA replication can be looked upon as a yes/no query, either the pairing takes place through molecular bond formations or it does not, and its task is to distinguish between 4 possibilities. The other interesting solution is $`Q=3`$, $`N=20.2`$. The well-known triplet code of DNA has 3 consecutive nucleotide bases carrying 21 signals , 20 for the amino acids plus a STOP . 3 base-pairings between t-RNA and m-RNA transfer this code to the amino acid chain .

These solutions are highly provocative. This is the first time they have come out of an algorithm that performs the actual task accomplished by DNA. It is fascinating that they are the optimal solutions . Indeed it is imperative to investigate whether DNA has the quantum hardware necessary to implement the quantum search algorithm.

## III Molecular Biology and the Structure of DNA

Over the last fifty years, molecular biologists have learnt a lot about the structure and function of DNA by careful experiments (they have also been rewarded with many Nobel prizes). Let us quickly go through some of the facts they have unravelled .

* DNA has the structure of a double helix. It can be schematically represented as a ladder, as in Fig.1. The sides of the ladder have a periodic structure with alternating sugar and phosphate groups. The nucleotide base pairs form the rungs of the ladder, and the genetic information is encoded in the order of these base pairs.
* DNA contains 4 nucleotide bases—A, T, C, G—which are closely related to each-other in chemical structure . The bases are always paired as A-T and C-G along the rungs of the ladder by Hydrogen bonds. This base-pairing makes the two DNA strands complementary in character.
* The sugar and phosphate groups along the side of the ladder are held together by covalent bonds. Their bonding is completely insensitive to the bases attached to them, and takes place in the presence of DNA polymerase enzymes.
* During replication, the helicase enzyme separates the two strands of DNA by breaking the Hydrogen bonds, much like opening a zipper. The unpaired bases along each of the separated strands find their partners from the surrounding molecules, producing two copies of the original DNA.
* The sides of the ladder have asymmetric ends. The replication process is directed, always proceeding from the $`5^{}`$ end to the $`3^{}`$ end (these numbers label the position of the carbon atoms in the sugar rings) of the strand being constructed. The DNA polymerase enzyme slides along the intact strand, adding one base at a time to the growing strand. During this process, base-pairing and sugar-phosphate bonding alternate.
* RNA molecules carry the nucleotide bases—A, U, C, G—with U very similar in chemical structure to T. A-U pairing is as strong as A-T pairing. Messenger RNA (m-RNA) has a single strand structure. In the first step of protein synthesis, the RNA polymerase enzyme separates the paired DNA strands and constructs an m-RNA strand on the DNA template by base-pairing (the process is the same as in DNA replication). The m-RNA strand grows as the RNA polymerase enzyme slides along the DNA from the promoter to the terminator base sequence. Finally the RNA polymerase enzyme detaches itself from the DNA, the fully constructed m-RNA strand floats away to the ribosomes in the cytoplasm of the cell, and the separated DNA strands pair up again.
* Transfer RNA (t-RNA) molecules have 3 RNA bases at one end and an amino acid at the other, with a many-to-one mapping between the two. Inside cellular structures called ribosomes, 3 t-RNA bases line up against the matching bases of m-RNA, aligning the amino acids at the other end. The aligned amino acids then split off from the t-RNA molecules and bind themselves into a chain. The process again proceeds monotonically from the $`5^{}`$ end to the $`3^{}`$ end of the m-RNA. After the amino acids split off, the remnant t-RNA molecules are recycled. This completes the transfer of the genetic code from DNA to proteins.
* Enzymes play a crucial role in many of the above steps. In addition to facilitating various processes by their catalytic action, they store energy needed for various processes, ensure that DNA keeps out U and RNA keeps out T, and perform error correction by their $`3^{}5^{}`$ exonuclease action (i.e. reversing the assembly process to remove a mismatched base pair).
* Hereditary DNA is accurately assembled, with an error rate of $`10^7`$ per base pair, after the proof-reading exonuclease action. Proteins are assembled less accurately, with an error rate of $`10^4`$ per amino acid .

Let us also recollect some useful facts about various chemical bonds.

* Ionic bonds are strong, can form at any angle, and can be explained in terms of electrostatic forces. Ions often separate in solutions.
* Covalent bonds are strong, form at specific angles, and can be explained in terms of Coulomb forces between electrons and nuclei and the exclusion principle.
* Van der Waals bonds are weak, not very angle dependent, and explainable in terms of interactions between virtual electric dipoles. They play an important role in transitions between solid, liquid and gas phases, as well as in folding and linking of polymers.
* Hydrogen bonds are weak, highly angle dependent, and explainable in terms of a proton ($`H^+`$) tunneling between two attractive energy minima. The situation is a genuine illustration of a particle in a double well potential, e.g. $`OH\mathrm{}:NO^{}:\mathrm{}HN^+`$. High sensitivity of the tunneling amplitude to the shape of the energy barrier make Hydrogen bonds extremely sensitive to the distances and angles involved. They are the most quantum of all bonds; water is a well-known example.
* Delocalisation of electrons and protons over distances of the order of a few angstroms greatly helps in molecular bond formation. It is important to note that these distances are much bigger than the Compton wavelengths of the particles, yet delocalisation is common and maintains quantum coherence. In case of electrons, the phenomena are called resonance and hybridisation, e.g. the benzene ring. In case of protons, the different configurations are called tautomers, e.g. amino $``$ imino and keto $``$ enol fluctuations of the nucleotide bases.

With all this information, the quantum search algorithmic requirements from the DNA structure are clear. It is convenient to take the distinct nucleotide bases as the quantum basis states in the Hilbert space. Then (1) The quantum query transformation $`U_b`$ must be found in the base-pairing with Hydrogen bonds. (2) The symmetric transformation $`U_s`$ must be found in the base-independent processes occurring along the sides of the ladder. (3) An environment with good quantum coherence must exist. Thermal noise is inevitable at $`T300^{}K`$ inside the cells, so the transformations must be stable against such fluctuations. Figuratively, the best that can be achieved is

$$\mathrm{Actual}\mathrm{evolution}=\genfrac{}{}{0pt}{}{lim}{\mathrm{decoherence}0}[\mathrm{Quantum}\mathrm{evolution}].$$
(4)
Thus we need quantum features that smoothly cross over to the classical regime, i.e. features that are reasonably stable against small decoherent fluctuations. Examples are: (a) geometric and topological phases, and (b) projection/measurement operators.

## IV Base-pairing as the Quantum Oracle

During DNA replication, the intact strand of DNA acts as a template on which the growing strand is assembled. At each step, the base on the intact strand decides which one of the four possible bases can pair with it. This is exactly the yes/no query (also called the oracle) used in the database search algorithm. To connect this oracle to the quantum transformation $`U_b`$, we have to look at how molecular bond formations transform a quantum state.

The generic quantum evolution operator is $`\mathrm{exp}(iHt)`$, with $`H`$ being the total Hamiltonian of the system. Global conservation of energy means that the overall phase $`\mathrm{exp}(iEt)`$ will completely factor out of the evolution and will not affect the final probabilities. What matters is only the relative phase between pairing and non-pairing bases. During the pairing process, the bases come together in an initial scattering state, discover that there is a lower energy binding state available, and decay to that state releasing the extra energy as a quantum . The interaction Hamiltonian for the bond formation process can be represented as

$$H_{int}(a^{}b+b^{}a),$$
(5)
where $`a,a^{}`$ are the transition operators between the excited and ground states of the reactants, and $`b,b^{}`$ are the transition operators between zero and one quantum states of energy released. Both the terms in Eq.(5) are necessary for the Hamiltonian to be Hermitian. The phase change $`\phi `$ during the bond formation satisfies

$$\mathrm{exp}(iH_{int}t_b)|e|0=\phi |g|1.$$
(6)
With only two states involved, Eq.(6) is easily solved by diagonalising $`H_{int}`$. In the two dimensional space, let

$$H_{int}=\mathrm{\Delta }E_H\left(\begin{array}{cc}0& 1\\ 1& 0\end{array}\right),\mathrm{eigenvectors}:\frac{1}{\sqrt{2}}\left(\begin{array}{c}1\\ \pm 1\end{array}\right),$$
(7)
and eigenvalues $`\pm \mathrm{\Delta }E_H`$. Eq.(6) then reduces to

$$\mathrm{exp}(i\mathrm{\Delta }E_Ht_b)=\phi =\mathrm{exp}(i\mathrm{\Delta }E_Ht_b),$$
(8)
with the solution $`\phi =\sqrt{1}`$.

This is the geometric phase well-known in quantum optics. A complete Rabi cycle in a two-level system gives a phase change of $`1`$, and the transition process corresponds to half the cycle. The phase $`\phi `$ does not depend on specific values of $`\mathrm{\Delta }E_H`$ or $`t_b`$, but only on the fact that the transition takes place. Quantum mechanics does not specify how $`\phi `$ will be divided between the bound state and the released energy quantum. In quantum optics, this break-up is determined by the phase of the laser. Here I assume that the process of decoherence is such that the energy quantum does not carry away any phase information.

At this stage, we discover a pleasant surprise that the base-pairing takes place not with a single Hydrogen bond but with multiple Hydrogen bonds (two for A-T and A-U, and three for C-G), as shown in Fig.2 . Multiple Hydrogen bonds are necessary for the mechanical stability of the helix. But they are also of different length, making it likely that they form asynchronously. Assuming a two-step deexcitation process during base-pairing, the geometric phase change becomes $`\phi ^2=1`$, just what is needed to implement $`U_b`$.

The energy of a single Hydrogen bond is $`\mathrm{\Delta }E_H7kT`$, giving $`\mathrm{exp}(\mathrm{\Delta }E_H/kT)10^3`$. This roughly explains the observed error rate in DNA replication. The tunneling amplitude for bond formation is related to both $`\mathrm{\Delta }E_H`$ and $`t_b`$, which determines the time scale of the base-pairing,

$$\mathrm{\Delta }E_Ht_b\mathrm{}t_b4\times 10^{15}\mathrm{sec}.$$
(9)
## V A Quantum Search Scenario

The next step is to look for the transformation $`U_s`$ in the processes occurring along the sides of the DNA-ladder. During these processes, quantum evolution produces various phases as molecular bonds get formed and broken. But these bonds treat all the nucleotide bases in the same manner, so the phases completely factor out and have no effect on the final probabilities. Thus I leave the phases out.

Suppose that $`|s`$ is the equilibrium state of the physical system, favoured by the processes that occur along the sides of the DNA-ladder. This means that any other initial state will gradually relax towards $`|s`$, with the damping provided by the environment. Let $`t_r`$ be the time scale for this relaxation process. Now $`|s`$ is a superposition state of nucleotide bases, and it can be created only if the cellular environment provides transition matrix elements between its various components. (In free space, transition matrix elements between nucleotide bases of different chemical composition vanish.) The magnitude of these transition matrix elements decides how quickly $`|s`$ cycles through its various components. Let $`t_{osc}`$ be the time scale for these oscillations. Now let us look at the DNA replication process, when the above defined time scales satisfy the hierarchy

$$t_b<<t_{osc}<<t_r.$$
(10)
1. In the initial stage, the randomly floating around nucleotide bases come into contact with the growing DNA strand, and relax to the state $`|s=(1/\sqrt{N})_i|i`$.
2. When the nucleotide base finds its proper orientation, Hydrogen bond formation suddenly takes place, changing the state to $`U_b|s`$. This state is entangled between the nucleotide bases and the energy quanta, $`U_b|s=(1/\sqrt{N})[_{ib}|i|0|b|2]`$.
3. After this sudden change, the relaxation process again tries to bring the system back to the state $`|s`$. With the time scales obeying Eq.(10), this relaxation occurs as damped oscillations, much like what happens when one gives a sudden jerk to a damped pendulum.
4. The opposite end of the damped oscillation is $`(2|ss|1)U_b|s=U_sU_b|s`$. When the system evolves to this opposite end, it discovers that it is no longer entangled between the nucleotide bases and the energy quanta, $`U_sU_b|s|0=|b|2`$ for $`N=4`$. At this point, the energy quanta are free to wander off with minimal disturbance to the quantum coherence. The departure of the energy quanta confirms the base-pairing, providing a projective measurement of the system. (I take the measurement time scale to be much smaller than $`t_{osc}`$.)
5. The energy quanta that have wandered off are unlikely to return, making the process irreversible. The replication then continues to add the next base onto the growing strand.

These steps are schematically shown in Fig.3. They provide a highly tuned yet a robust algorithm. There are no fine-tuned parameters; the hierarchy of Eq.(10) has enough room to take care of substantial variation in individual time scales. Life couldn’t be simpler!

To illustrate the possibility that processes with time scales obeying the hierarchy of Eq.(10) do physically occur, let us look at a quantum example. Consider the processes involved in the functioning of the $`NH_3`$ maser. $`NH_3`$ is a molecule with two equivalent configurations, corresponding to the Nitrogen atom being above or below the triangle of Hydrogen atoms. These two configurations can be distinguished by the direction of their electric dipole moments. Quantum tunneling of the Nitrogen atom through the triangle of Hydrogen atoms mixes these two configurations, and the ground state is the symmetric superposition of the two. In $`NH_3`$ gas, any initial state decays towards this equilibrium ground state (molecular collisions help in this relaxation). If a electric field is applied to the gas for a short duration, it favours one of the two configurations and kicks the molecules out of their equilibrium state. After the removal of the electric field, the kicked molecules oscillate from one configuration to the other, till the oscillations are damped out by the decay process. Shining the molecules with a radio-frequency pulse resonant with $`t_{osc}`$ removes the extra energy quickly by stimulated emission and produces a coherent maser.

The relaxation time scale $`t_r`$ depends on temperature as well as on various molecular concentrations, and governs the overall replication rate. Under normal circumstances, DNA replication is observed to occur at the rate of 1000 base-pairings/sec, constraining $`t_r`$ to be smaller than $`O(10^3)`$ sec. Without any knowledge of the transition matrix elements, I do not have any estimate of $`t_{osc}`$.

Strictly speaking, I should not talk about quantum states in processes that involve damping; the proper mathematical formulation must be in the language of density matrices. But when the damping is small, as is the case here, it is easier to talk about states. The steps above can be easily transcribed in the language of density matrices, without changing their outcomes.

Now we can proceed to the remaining pieces needed to complete the scenario: a mechanism that favours the state $`|s`$ as the equilibrium state, and an environment that permits an almost coherent quantum evolution. For that I have to appeal to the ingredients ignored so far—the enzymes.

## VI The Role of the Enzymes

Enzymes play a very important role in many biochemical reactions, and some of the things they do were mentioned in section III. The rates of various biochemical reactions, when estimated with the standard thermodynamical analysis (probability distributions, diffusion processes, kinetic theory, etc.), fall too short of the observed rates, often by orders of magnitudes. One is left with no choice but to admit that these reactions are catalysed.

Enzymes are the objects which catalyse biochemical reactions. They are large complicated molecules, much larger than the reactants they help, made of several peptide chains. Their shapes play an important part in catalysis, and often they completely surround the reaction region. They do not bind to either the reactants or the products, just help them along the way. The standard explanation is that enzymes lower reaction barriers. Just how this lowering of reaction barriers occurs is not clearly understood, and is an active area of research (for example, enzymes can form weak bonds with the transition state or suck out solvent molecules from in between the reactants). Ultimately it must be explained in terms of some underlying physical laws.

I put forward two specific hypotheses about what enzymes accomplish in the processing of genetic information.

* Enzymes provide a shielded environment where quantum coherence of the reactants is maintained. This is a rather passive task, consistent with the properties of enzymes mentioned above, and it is also plausible. For instance, diamagnetic electrons do an extraordinarily good job of shielding the nuclear spins from the environment—the coherence time observed in NMR is $`O(10)`$ sec, much longer than the thermal environment relaxation time ($`\mathrm{}/kTO(10^{14})`$ sec) and the molecular collision time ($`O(10^{11})`$ sec), and still neighbouring nuclear spins couple through the electron cloud. A few orders of magnitude increase in coherence time is sufficient in many reactions for faster quantum algorithms to take over from their classical counterparts, and provide the catalytic speed-up.
* Enzymes are able to create superposed states of chemically distinct molecules. This is an active task. Various nucleotide bases differ from each other only in terms of small chemical groups, containing less than 10 atoms, at their Hydrogen bonding end. To convert one base into another, enzymes have to be repositories of these chemical groups which differentiate between various nucleotide bases. Enzymes are known to do cut-and-paste jobs with such chemical groups (e.g. one of the simplest substitution processes is methylation, replacing $`H`$ by $`CH_3`$, which converts U to T). Given such transition matrix elements, quantum dynamics automatically produces a superposition state as the lowest energy equilibrium state. (Note that the cut-and-paste job in a classical environment would produce a mixture, but in a quantum environment it produces superposition.) It is mandatory that the enzymes do the cut-and-paste job only on the growing strand and not on the intact strand. Perhaps this is ensured by other molecular bonds.

These hypotheses are powerful enough to explain many observed properties of enzymes from a new perspective. For example,

* It is obvious why DNA replication always takes place in the presence of enzymes. If base-pairing were to occur by chance collisions, it would occur anywhere along the exposed unpaired strand.
* Since enzymes control the transition matrix elements, they can keep U out of DNA and T out of RNA.
* Quantum processes can tunnel through the reaction barriers, instead of climbing over them.
* As long as quantum coherence is maintained, the replication process is reversible. This can easily explain the error-correcting exonuclease action of the polymerase enzymes.

More importantly, these hypotheses are experimentally testable, provided one can observe the replication process at its intermediate stages. That is within the grasp of modern techniques such as X-ray diffraction analysis, electron microscopy, NMR spectroscopy, radioactive tagging of atoms in chemical reactions, and femtosecond photography.

## VII Summary and Future

I have proposed a quantum algorithmic mechanism for DNA replication and protein synthesis. This genetic information processing takes place at the molecular level, where quantum physics is indeed the dominant dynamics (classical physics effects appear as decoherence and are subdominant). It is reasonable to expect that if there was something to be gained from quantum computation, life would have taken advantage of that at this physical scale . For DNA replication, the quantum search algorithm provides a factor of two speed-up over classical search, but it is still an advantage. Quantum algorithms can provide a bigger advantage for more complicated processes involving many steps.

Implementation of quantum database search does not require a general purpose quantum computer. A system that can implement the quantum oracle and quantum state reflections is sufficient. I have described the physical analogues of these operations in genetic information processing, and it is not unusual for living organisms to find the correct ingredients without bothering about generalities. In fact various pieces of the scenario have fitted together so nicely (database search paradigm, optimal $`(Q,N)`$ values—$`(1,4)`$ and $`(3,20.2)`$, quantum transformations implementing $`U_b`$ and $`U_s`$), that with the courage of conviction, I have made bold hypotheses to fill the remaining gaps. The role that enzymes play, as described in section VI, is both plausible and experimentally verifiable. The other assumptions I have made (i.e. two-step cascade deexcitation in base-pairing, energy quanta not carrying away any phase information, energy quanta departing only when they cause minimal decoherence to the system) concern how decoherence modifies pure quantum evolution, and are also experimentally testable. Such experimental tests would decide the future of this proposal.

It is clear that if experiments verify the quantum scenario for genetic information processing presented here, there will be a significant overhaul of conventional molecular biology. There is nothing inappropriate in that—the subject of molecular biology was born out of quantum physics, and quantum physics has not yet had its last word on it.

I also want to acknowledge that molecular biology is a far more complicated subject than the simplest features I have explored in this work. If quantum physics provides better explanations for other more complex phenomena of life, it would be a wonderful development.

## Appendix: Some Questions and Answers

I am grateful to the audience for their many comments and questions. I summarise below some of the important concepts they brought out.

Q: Are there any examples of genetic codes which use other values of $`Q`$, say $`Q=2`$?

A: I do not know of any such examples. May be some day we shall become clever enough to synthesise such instances in the laboratory.

Q: Parallel processing can also speed-up algorithms. Why is that not used in the case of genetic code?

A: In case of DNA replication, enzymes separate only a limited region of paired strands as they slide along replicating the information. Complete separation of the strands would break too many Hydrogen bonds and cost too much in energy. Thus the replication remains a local process. In case of protein synthesis, random pairing of t-RNA and m-RNA at several different locations would lead to a lot of mismatches and errors, since the triplet code needs precise starting and ending points. Parallel processing does take place though: several ribosomes work simultaneously on a single m-RNA strand, each one traversing the full length of m-RNA from one end to the other and constructing identical amino acid chains.

Q: Three nucleotide bases can form 64 distinct codes. Why do you still say that 20 is the optimal number for the triplet code?

A: When the DNA assembly takes place, with each base as a separate unit, the number of possibilities explored is indeed $`4^Q`$. But this is not what happens in the matching between t-RNA and m-RNA. The three bases come as a single group, without any possibility of their rearrangement. The whole group has to be accepted or rejected as a single entity. In such a situation, the number of objects that can be distinguished is smaller, as given by Eq.(3).

Q: Do you have any understanding of degeneracy of the triplet code?

A: With only 21 signals embedded amongst 64 possibilities, the amino acid code is indeed degenerate. Moreover, all the amino acids are not present in living organisms with equal frequency, quite unlike the nucleotide bases. Ribosomes are also much bigger and more complicated molecules than the polymerase enzymes, and so capable of carrying out more complex tasks. All this makes protein synthesis a more difficult process to study than DNA replication. I have not analysed it in detail, and I am unable to provide any understanding of the degeneracy of the triplet code.

Q: The energy quanta do not have to be released exactly at the opposite end of the oscillation. Oscillations spend more time near their extrema anyway, and so even random emission will give high probability for correct base-pairing.

A: I agree. But a smaller success probability means that more trials will be necessary to achieve the correct base-pairing. That would diminish the advantage of the quantum algorithm.

Q: Enzymes are also proteins which have to be synthesised by the DNA. How are they synthesised in the first place?

A: Classical algorithms can do everything that quantum algorithms do, albeit slower. In the absence of enzymes, various steps will take place only by random chance, and so the start-up will be slow. But once processes get going, as in a living cell, enzymes will be manufactured along the way and there will be no turning back to slower algorithms.

Q: If polymerase enzymes have to keep on supplying various chemical groups to nucleotide bases, they would run out of their stock at some stage. What happens then?

A: In my proposal, the polymerase enzymes substitute one chemical group for another. With the DNA base sequence being random, the chemical groups are recycled with high probability. So with a reasonable initial stock an enzyme can perform its task for a long time. Of course if an enzyme runs out of its stock, it has no choice but to quit and replenish its stock.

Q: How essential is the environment of a living cell in DNA replication? Are there any other molecules besides enzymes involved?

A: DNA replication can take place without cellular environment. With proper enzymes in the solution, the polymerase chain reaction can rapidly multiply DNA. This is used in DNA fingerprinting from dead cells.

Q: Many inorganic reactions can be speeded up by appropriate catalysts. Are they quantum reactions too?

A: In my view, catalysts convert random walk processes into directed walks, providing a $`\sqrt{N}`$ speed-up in the number of steps. Quantum superposition is one way to achieve this, but it does not have to be the only way. There may be even classical mechanisms which can do the same job.

Q: Living organisms are known to emit radiation, which is coherent and not thermal (black-body). Is there any connection between these biophotons and your proposal?

A: This is the first time I have heard about biophotons. If they are related to some quantum processes going on inside living cells, that would be great.

Q: Are there any applications of your proposal?

A: Understanding the basic processes of life will always lead to new applications. For example, molecular biologists have been working on accelerating synthesis of desired proteins and inhibiting growth of cancer and harmful viruses. I am not inclined to speculate more on this issue right now.


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# First results of the air shower experiment KASCADE

## 1 INTRODUCTION

The air shower experiment KASCADE  aims at the investigation of the knee region of the charged cosmic rays. It is built up as a multidetector setup for measuring simultaneously a large number of observables in the different particle (electromagnetic, muonic and hadronic) components of the extended air shower (EAS). This enables to perform a multivariate multiparameter analysis for the registered EAS on an event-by-event basis to account for the non parametric, stochastic processes of the EAS development in the atmosphere. In parallel the KASCADE collaboration tries to improve the tools for the Monte Carlo simulations with the relevant physics. The code CORSIKA  allows not only the detailed three dimensional simulation of the shower development in all particle components (including neutrinos) down to the observation level, but it has been implemented several high-energy interaction models. As the basic physics of these models in the relevant energy region and in the extreme forward direction cannot be tested at present days’ accelerators, the test of these models emerged as one of the goals of the KASCADE experiment. The following overview is based on results presented at the 26th International Cosmic Ray Conference in Salt Lake City, Utah 1999 .

## 2 THE KASCADE EXPERIMENT

The KASCADE array consists of 252 detector stations in a $`200\times 200`$m2 rectangular grid containing unshielded liquid scintillation detectors ($`e/\gamma `$-detectors) and below 10 cm lead and 4 cm steel plastic scintillators as muon-detectors. The total sensitive areas are $`490`$m2 for the $`e/\gamma `$\- and $`622`$m2 for the muon-detectors. In the center of the array a hadron calorimeter ($`16\times 20`$m2) is built up, consisting of more than 40,000 liquid ionisation chambers in 8 layers with a trigger layer consisting of 456 scintillation detectors in between. Below the calorimeter a setup of position sensitive multiwire proportional chambers (MWPC) in two layers measures high-energy muons ($`E_\mu >2`$GeV) of the EAS.
For each single shower a large number of observables are reconstructed with small uncertainties. For example, the errors for the so-called shower sizes, i.e. total numbers of electrons $`N_e`$ and number of muons in the range of the core distance $`40200`$m $`N_\mu ^{tr}`$, are smaller than 10$`\%`$.
The resulting frequency spectra of the sizes (inclusive the spectra of the hadron number and muon density spectra at different core distances) show kinks at same integral fluxes. This is a strong hint for an astrophysical source of the knee phenomenon based on pure experimental data, since same intensity of the flux corresponds to equal primary energy.
But for the reconstruction of the primary energy spectrum and the chemical composition detailed Monte Carlo simulations are indispensable due to the unknown initial parameters and the large intrinsic fluctuations of the stochastic process of the shower development in the atmosphere. The usage of a larger number of less correlated observables in a multivariate analysis parallel to independent tests of the simulation models tries to find the solution of this dilemma.

## 3 ANALYSES AND RESULTS

In the air shower simulation program CORSIKA several high-energy interaction models are embedded including VENUS, QGSJET and SIBYLL (Refs. see in ). The models are based on the Gribov-Regge-theory and QCD in accordance with accelerator data. Extrapolations for the EAS physics in the knee region are necessary due to the high interaction energy and for

the extreme forward direction. To compare KASCADE data with Monte Carlo expectations a detector simulation by GEANT is performed for each CORSIKA simulated shower.
One test is the comparison of simulated integral muon trigger and hadron rates with the measurements. This test is sensitive to the energy spectrum of the hadrons which are produced in the forward direction at primary energies around 10 TeV, where the chemical composition is roughly known (Fig.1). For higher primary energies the hadronic part of the interaction models are tested by comparisons of different hadronic observables in ranges of shower sizes . In general it is seen that the high-energy interaction models predict a too large number of hadrons at sea level compared with the measurements.
Nonparametric multivariate methods like “Neural Networks” or analyses based on the “Bayesian decision rules” are applied to the KASCADE data for the estimation of the energy and mass of the cosmic rays on an event-by-event basis. The necessary “a-priori” information in form of probability density distributions are won by detailed Monte Carlo simulations with large statistics.
For the energy reconstruction the shower sizes $`N_e`$ and $`N_\mu ^{tr}`$ as parameters are used in a neural network analyses (Fig.2). A parametric approach to the same data leads to compatible results (Fig.2):

here a simultaneous fit to the $`N_e`$ and $`N_\mu ^{tr}`$ size spectra is performed. The kernel function of this fit contains the size-energy correlations for two primary masses (proton and iron) obtained by Monte Carlo simulations.
An analysis of the size-ratio $`\mathrm{lg}(N_\mu ^{tr})/\mathrm{lg}(N_e)`$ calculated for each single event leads to results of the elemental composition for different energy ranges (Fig.3). The measured distribution of these ratios is assumed to be a superposition of simulated distributions for different primary masses. The large iron sampling calorimeter of KASCADE allows to investigate the hadronic part of EAS in terms of the chemical composition. For six different hadronic observables (won by spatial and energy distributions of the hadrons) the deviations of the mean values to expectations of pure proton and iron primaries in certain energy ranges are calculated.
Besides the use of global parameters like the shower sizes, sets of different parameters are used for neural network and Bayesian decision analyses. Examples of such observables are the number of reconstructed hadrons in the calorimeter, their reconstructed energy sum, number of muons in the shower center, or parameters obtained by a fractal analysis of the hit pattern of muons and secondaries at the MWPC.

The latter ones are sensitive to the structure of the shower core which is mass sensitive due to different shower developments of light and heavy particles in the atmosphere. In Figure 3 results of a Bayesian analyses and of a separate neural net analysis using the fractal parameters are shown.
As the tendency of the results of each described method is consistent with a heavier primary mass after the knee region, but the absolute scale strongly depends on the particle component of which the observables are constructed from, the syllogism is that the balance of the energy and number of particles between the muonic, electromagnetic and hadronic part in the EAS differs for simulations and the real shower development.

## 4 CONCLUSIONS

First results of the KASCADE experiment can be summarized by following statements: All secondary particle components of the showers display a kink in the size spectra. This strongly supports an astrophysical origin of the “knee”, rather than effects of the interaction of the primaries in the atmosphere. The knee is sharper for the light primary component than for the heavy one. This result follows from the measurement as an increasing average mass of the primary cosmic rays above the observed kink, together with the energy dependent mass classification of single air showers. But none of the high-energy interaction models en vogue is able to fit the data of all observables consistently.


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# Fundamental parameters of Galactic luminous OB stars

## 1 Introduction

Although microturbulence is a fundamental parameter when deriving abundances from stellar spectra, it has been systematically ignored when deriving He abundances from quantitative spectroscopical NLTE analyses of OB stars (Herrero et al. Herrero92 (1992), Smith & Howarth Smith&Howarth94 (1994)), being the first exceptions to this the works by McErlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)).

One of the main reasons to ignore it is that the use of NLTE techniques reduced the need of microturbulence for the reproduction of the observed metallic line strengths and they even made abundances less sensitive to the value adopted for microturbulence than in LTE analyses (Becker & Butler Becker&Butler89 (1989)).

In quantitative NLTE analyses of OB stars, the lines of H and He are used to determine stellar parameters (namely, effective temperature, $`T_{\mathrm{eff}}`$, logarithmic surface gravity, $`\mathrm{log}g`$, and He abundance). Their line profiles are dominated by the Stark broadening, and microturbulence, included in the standard way, only adds an extra Doppler width to the thermal broadening. First values for microturbulence found in LTE for main sequence B stars, of the order of 5 kms-1 (Hardorp & Scholz Hardorp&Scholz70 (1970)), showed to be small enough to be of no importance when compared to H and He thermal velocities, that in such hot atmospheres are well above 5 kms-1. This together with the use of NLTE made the influence of microturbulence in the overall profile seem negligible.

When measuring microturbulence in OB supergiants the situation is quite different, as its value has always showed to be comparable or well above the thermal velocities of H and He, and even, in some cases, above the speed of sound in these atmospheres (Lamers Lamers72 (1972), Lennon & Dufton Lennon&Dufton86 (1986)). This was not changed by later NLTE analyses (Lennon et al. Lennon91 (1991), Hubeny et al. Hubeny91 (1991), Gies & Lambert Gies&Lambert92 (1992), Smartt et al. Smartt97 (1997)), in which the values of microturbulence obtained are usually reduced but never to values clearly without contradiction. Kudritzki (Kudritzki92 (1992)) and Lamers & Achmad (Lamers&Achmad94 (1994)) explained that this could be due to the presence of wind outflow in these stars, that can mimic the effect of microturbulence in the line profiles.

Most of the previously referred works are on early B and late O supergiants. Little work has been done on early O stars (see Hubeny et al. Hubeny91 (1991)), mainly because for them, with scarce metallic lines, it is very difficult to measure the value of microturbulence. And it is in the whole range of O stars that we are interested.

One problem that is systematically found in all analyses of OB spectra is the imposibility of finding a consistent fit of all He i lines with a unique set of parameters. This difficulty appears worse in supergiants than in main sequence stars, and it is bigger between results from singlet and from triplet lines, but also appears within different lines in one system. We call this the *He i lines problem*.

This discrepancy between singlet and triplet lines of He i was investigated by Voels et al. (Voels89 (1989)), who considered that atmospheric extension was responsible and so they called this effect “generalized dilution effect”. But recent works with spherical, mass losing models show that this can not be the only reason (Herrero et al., Herrero95 (1995), Herrero00 (2000)). Furthermore, McErlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)) find that the inclusion of microturbulence in the line formation calculations reduces, although not to all its extent, the discrepancy between the fits of singlet and triplet lines. They also find better and more consistent fits for the whole set of He i lines when microturbulence is considered.

One more reason that encourages us to study the effect of microturbulence is that a careful inspection of several works shows that even for main sequence stars,values of microturbulence comparable to the thermal velocities of at least He are obtained in NLTE (Gies & Lambert Gies&Lambert92 (1992), Kilian et al. Kilian91 (1991)), which can invalidate the hypothesis of negligible influence of microturbulence in the profiles.

So in this paper we want to study microturbulence in the range of parameters typical for O stars of any luminosity class, specifically pointing to its effect on the determination of stellar parameters and also on the *He i lines problem*. We are specially interested in investigating whether the inclusion of microturbulence can solve the He discrepancy (Herrero et al. Herrero92 (1992)), as Vrancken (Vrancken97 (1997)), McErlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)) suggest. This now well known problem has induced a lot of theoretical improvements in both evolutionary and model atmosphere theories in order to explain it. Recent works including sphericity and mass loss in the spectral analysis (Herrero et al. Herrero95 (1995), Herrero00 (2000), Israelian et al. Israelian99 (2000)) show that with these new models, more suitable for these stars than the plane–parallel hydrostatic ones, the discrepancy is not solved. Evolutionary models including additional mixing inside the star can explain enhanced He photospheric abundances during the H-burning phase, this mixing being induced by different physical mechanisms like rotation and turbulent diffusion (Dennisenkov, denn94 (1994), Meynet & Maeder, Meynet&Maeder97 (1997), Maeder & Zahn, Maeder&Zahn98 (1998)), or turbulent diffusion and semiconvection (Langer Langer92 (1992)). Sometimes angular rotational velocity changes during evolution are included (Langer & Heger, LH98 (1998), Heger, Heger98 (1998)). For a recent review, see Maeder & Meynet (maemey00 (2000)). Therefore it becomes of great importance to see whether microturbulence can be responsible for the He discrepancy.

In Sect. 2 we present line formation calculations of H and He lines and their behaviour with microturbulence in the O stars domain. In Sect. 3 we determine the effect of including microturbulence in the determination of stellar parameters, and in Sect. 4 we analyze some stars with and without considering microturbulence. Sections 5 and 6 are then dedicated to our discussion and conclusions, respectively .

## 2 Microturbulence in H and He line formation calculations

In order to study the behaviour of H and He lines with microturbulence, we perform line formation calculations in the parameter range typical for O to early B stars of any luminosity class:

–between 30 000 and 45 000 K in $`T_{\mathrm{eff}}`$

–between 3.05 and 4.00 in $`\mathrm{log}g`$ (in c.g.s. units)

–for $`ϵ`$= 0.10 and 0.20, with $`ϵ=\frac{N(He)}{N(He)+N(H)}`$

where N(x) is the number density of atom X. We follow the classical technique of calculating a NLTE model atmosphere of H and He, in radiative and hydrostatic equilibrium and with plane–parallel geometry (calculated with ALI, see Kunze, Kunze95 (1995)), and then solve the statistical equilibrium and transfer equations and perform the formal solution for the lines of H and He chosen using DETAIL & SURFACE (Butler & Giddings Butler&Giddings85 (1985)). In this final step we have included UV metal line opacities in the calculations, in order to obtain more realistic profiles (see Herrero, Herrero94 (1994), and Herrero et al., Herrero00 (2000), for details). As shown in the last reference, plane–parallel models are unable to reproduce properly spectra of massive OB stars around 50 000 K and hotter, that is why we stop our study at 45 000K.

Microturbulence is introduced in the standard way, by adding an extra Doppler width to the thermal broadening of the line, which is then convolved with the rest of the broadening mechanisms. We have considered it in both the equations of statistical equilibrium and radiative transfer. As we don’t consider other motions (turbulent or not) in the determination of the stellar structure, we prefer to restrict the introduction of microturbulence to the absorption coefficient. Therefore, we do not include it in the calculation of the structure of the atmosphere via turbulent pressure. For similar reasons also we do not even bother about its dependence on depth. We don’t treat separately the effect on the populations and line profiles, as this has been recently studied by McErlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)) (whose results we support).

We make line formation calculations for the lines we usually consider to perform our analyses: Hγ and Hβ for H i; He i $`\lambda `$$`\lambda `$ 4387, 4922, 4471 Å for He i; and He ii $`\lambda `$$`\lambda `$ 4200, 4541, 4686 Å for He ii.

In order to study the behaviour of these lines with microturbulence, we perform line formation calculations for microturbulence velocity values from 0 to 20 kms-1, for different sets of parameters, representing the spectral types and luminosity classes we are interested in:

$`T_{\mathrm{eff}}`$= 30 000, $`\mathrm{log}g`$= 3.05, $`ϵ`$= 0.10 for late O and early B supergiants. The same with $`\mathrm{log}g`$= 4.00 for dwarfs.

$`T_{\mathrm{eff}}`$= 35 000, $`\mathrm{log}g`$= 3.20, $`ϵ`$= 0.10 for “middle” O supergiants. The same with $`\mathrm{log}g`$= 4.00 for dwarfs.

$`T_{\mathrm{eff}}`$= 40 000, $`\mathrm{log}g`$= 3.40, $`ϵ`$= 0.10 for early O supergiants. The same with $`\mathrm{log}g`$= 4.00 for dwarfs.

$`T_{\mathrm{eff}}`$= 45 000, $`\mathrm{log}g`$= 3.60, $`ϵ`$= 0.10 for very early O supergiants. The same with $`\mathrm{log}g`$= 4.00 for dwarfs.

The values of $`\mathrm{log}g`$ for supergiants are close to the lowest that could be converged for every $`T_{\mathrm{eff}}`$. For dwarfs of increasing $`T_{\mathrm{eff}}`$, $`\mathrm{log}g`$ becomes a little below 4.00, but this value still represents well this luminosity class. Finally, these calculations were repeated for $`ϵ`$= 0.20, to look for differential effects with He abundance.

Figs. 1, 2 and 3 display the behaviour of H and He line profiles with microturbulence, for three different models, adequate respectively for late O supergiants, late O dwarfs and early O supergiants. In Table 1 equivalent widths are given for all these lines. The first two Figs. will allow us to compare the effects of microturbulence when varying $`\mathrm{log}g`$, whereas the first and last Figs. will be used to compare the effects when varying $`T_{\mathrm{eff}}`$ . The other calculated models behave consistently with what it is shown in Figs. 13 and will not be further discussed.

Looking first at Fig. 1 we see that there are two different line groups. The first one is composed by the strong H lines and the relatively weak lines He ii $`\lambda \lambda `$ 4200, 4541. All these lines are not affected by microturbulence, although our highest values are comparable to the thermal velocity of H atoms and well above that of He atoms. The reason is that the Stark broadening dominates the profiles, and therefore masks the changes that microturbulence produce.

The second group is composed by He i lines and the strong He ii$`\lambda `$4686 line. He i lines show sensitivity to microturbulence in both core and wings, while the core of He ii $`\lambda `$4686 is desaturated by microturbulence, but its effect is masked in the wings by the Stark broadening, because, as it has been explained by Smith & Howarth (Smith&Howarth98 (1998)), the effect of microturbulence will depend on the stepness of the line wings.

When we then compare Figs. 1 and 2 we see that the increased pressure broadening (directly related to the increased density) simply reduces the effect of microturbulence in the line profiles. Thus, as gravity increases, the effect of microturbulence decreases for all considered lines. In the case of He ii lines this effect is reinforced by the displacement introduced in the He ionization equilibrium, that makes He ii lines weaker.

More interesting is the comparison with higher temperatures. Looking to Fig. 1 and Fig. 3 we can see the behaviour of the lines of supergiants with increasing $`T_{\mathrm{eff}}`$. For higher values of $`T_{\mathrm{eff}}`$ marginal effects on H i and He ii line cores are seen (Fig. 3), but only He i lines and He ii $`\lambda `$4686 are again really sensitive to microturbulence. He ii line profiles are still insensitive, although they are now much stronger and even have a larger equivalent width than He i lines, because they are dominated by the Stark broadening. The reason why He i line profiles are still sensitive to microturbulence, although they are much weaker, has to be found in the influence of microturbulence on the shape of the absorption profile of weak lines. Thus, we see that He i $`\lambda \lambda `$ 4387, 4922 are not saturated in the whole temperature range. Their equivalent widths increase with increasing microturbulence, until, as $`T_{\mathrm{eff}}`$ increases, they become weak enough to have equivalent widths, but not line profiles, independent of microturbulence. This happens at 40 000 K for He i $`\lambda `$ 4387 (see Table 1) and at 45 000 K for He i $`\lambda `$ 4922. For them, Doppler broadening is important enough to let microturbulence shape the profiles appreciably in the whole temperature range. He i $`\lambda `$ 4471 is saturated at $`T_{\mathrm{eff}}`$ 30 000 K, but it desaturates at $`T_{\mathrm{eff}}`$= 35 000, and starts behaving like the other He i lines.

Finally, we point out that all these results also apply for models with $`ϵ=0.20`$, and that they are a natural extension to O stars of the results of Mc Erlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)).

## 3 The influence of microturbulence in the determination of parameters of O-stars

In this work we are interested in estimating the changes introduced in the derived stellar parameters by the inclusion of microturbulence in the analysis of O stars, with special attention to its influence in the derived He abundance. As we saw in the previous section, models of low gravity, corresponding to supergiants, are more sensitive to microturbulence, and so we expect supergiants to show the largest changes.

Values of microturbulence of 10, 12 kms-1 are found for late O and early B stars (see references in the introduction), therefore we decided to choose a fixed value for microturbulence of 15 kms-1 to perform a test of the influence of microturbulence in the determination of $`T_{\mathrm{eff}}`$ , $`\mathrm{log}g`$ and He abundance.

As a first approach to the problem, we take a model spectrum at $`\xi `$=15 kms-1 as the *observed* spectrum, to which we fit model profiles in a grid around it at $`\xi `$=0 kms-1, with parameters differing in 500 to 1000 K in $`T_{\mathrm{eff}}`$, 0.05 to 0.10 in $`\mathrm{log}g`$ and 0.02 to 0.04 in $`ϵ`$ (these small values are suggested by previous inspection of a larger, coarser grid). To maximize the effect of microturbulence, we consider neither rotational broadening nor instrumental broadening. Taking advantage of the fact that we are using only theoretical profiles (although the one with $`\xi `$= 15 kms-1 has been adopted as *the observation*) we use a least–squares fit procedure to determine the best fit.

For each line of each model in the grid, we calculate the quadratic difference with the *observed* line, and then we add the results for all lines of a given ion. For example for H we calculate:

$$\chi _\mathrm{i}^2(\mathrm{H})=\underset{Hlines}{}\frac{1}{\mathrm{\Delta }\lambda }\underset{\lambda }{}w_\lambda (f_{\lambda ,grid}f_{\lambda ,obs})^2$$

as the result for H for model i of the grid, where $`w_\lambda `$ is the spectral sampling and $`\mathrm{\Delta }\lambda `$ is the wavelength interval containing the whole line. We perform these calculations for all the models in the grid and then normalize these values to their minimum, so that a 1.00 gives us the model that best fits the lines of the ion at all temperatures, gravities and He abundances. The calculation is performed in the same way for He lines, taking He i and He ii lines separately. Finally we define for model i:

$`\chi _\mathrm{i}^2`$= $`\chi _\mathrm{i}^2(\mathrm{H})`$+$`\chi _\mathrm{i}^2`$(He i)+$`\chi _\mathrm{i}^2`$(He ii)

so that the best fit is adopted to be that of the model with the minimum value of $`\chi _\mathrm{i}^2`$.

We have carried on the exercise for a model with $`T_{\mathrm{eff}}`$=40 000 K, $`\mathrm{log}g`$=3.40, $`ϵ`$=0.10 and $`\xi `$=15 kms-1 as the *observed* spectrum. In Fig. 4 we have plotted contour levels of $`\chi ^2`$ in the $`T_{\mathrm{eff}}`$$`\mathrm{log}g`$ plane for $`ϵ`$ = 0.10. We see that, at this He abundance, there are two models that fit well the *observation*, with parameters $`T_{\mathrm{eff}}`$= 40 000K, $`\mathrm{log}g`$= 3.40 and $`T_{\mathrm{eff}}`$= 42 000K, $`\mathrm{log}g`$= 3.45. Although the last model has a slightly lower value of $`\chi _\mathrm{i}^2`$ (5.190), the dispersion in the individual $`\chi _\mathrm{i}^2`$ values is larger, reflecting the fact that looking at the line fits we would choose the other as the best compromise. This is a indication of the differences between both criteria, we should improve our $`\chi ^2`$ fitting criterium in order to match the fitting by eye.

In Table 2 we list the results for the best fits at other He abundances. We see inmediately that for $`ϵ`$ = 0.06 and 0.14 we find large values of $`\chi ^2`$, indicating a relatively poor fit. On the contrary, the models for $`ϵ`$= 0.12, 0.10, 0.08 fit with approximately the same quality (without a more detailed study we cannot say whether the difference in $`\chi ^2`$ is significant). In a fit by eye we would choose the model at $`ϵ`$ 0.08 as the best fit. Actually, this is the model with the lowest value of $`\chi ^2`$ and has a *lower* He abundance than the *observed* spectrum. The reason is that the larger gravity rather than the He abundance mimics the microturbulence effect. In principle, it would be also possible to choose the model with $`ϵ`$= 0.12, in which the higher He abundance corresponds with a lower gravity. Fig. 5 shows the fit of the “best model” to the *observed* spectrum. The lack of rotation and instrumental broadening makes the differences in He i lines appear evident.

Thus, the conclusion of our exercise is that neglection of microturbulence will change slightly the derived stellar parameters, but keeping them within our standard error box (see next Sect.). The direction in which parameters are moved will depend on the criteria used for defining a model as “the best model fit”, such as the relative weight given to different lines, or to the core and wings of a line. Thus the definition of these criteria for the “best model” will be a critical point of any future automatic fitting procedure, which will soon be demanded by new observing capabilities.

## 4 Spectral analysis including microturbulence

Now we want to see the difference we obtain in the derived parameters of real observed O stars spectra when we include microturbulence in the calculations. We selected two late-O supergiants to see how our results match with previous works, as well as one intermediate and two early ones, in order to cover the whole O spectral type. We chose HD 5 689 in particular, an O6 V fast rotator with a high He-overabundance derived in previous works without microturbulence (see Herrero et al., Herrero00 (2000)), to check how it can modify this strong overabundance.

The description of the observations and data reduction can be found in Herrero et al. (Herrero92 (1992), Herrero00 (2000)).

To analyse stellar spectra we first determine the projected rotational velocity of the star (see Herrero et al. Herrero92 (1992) for details). This is an additional parameter that, in fact, reduces the effect of microturbulence in the derivation of stellar parameters. The results of the analyses are listed in Table 3.

The fitting procedure and adopted errors of $`\pm `$ 1 500 K in $`T_{\mathrm{eff}}`$, $`\pm `$ 0.1 in $`\mathrm{log}g`$ and $`\pm `$ 0.03 in $`ϵ`$ are explained in Herrero et al. (Herrero99 (1999)).

To make the new analyses with microturbulence we construct a model with the same parameters but for $`\xi `$= 15 kms-1, and also a small grid around it with changes in $`T_{\mathrm{eff}}`$ of $`\pm `$ 500 to 2000 K, in $`\mathrm{log}g`$ of $`\pm `$ 0.05 to 0.15 dex and in $`ϵ`$ of $`\pm `$ 0.02 to 0.04. These small changes are suggested by the results of the preceeding section, and are in fact confirmed by the small differences in the fit we see between the two models at 0 and 15 kms-1. The new best fit is found as explained above, and it gives the new parameters for the star at $`\xi `$=15 kms-1.

All the stars except HDE 338 926 have been previously analyzed by our group without microturbulence (Herrero et al., Herrero92 (1992), Herrero00 (2000)). In the present analysis, small differences for the stars in common, specially with respect to the first reference, can be found due to the larger weight given here to He i $`\lambda `$4387, rather than to He i $`\lambda `$4922, and to the inclusion of line–blocking in the calculations (the temperatures of the late type supergiants are slightly hotter in the present analysis). All this also helps to solve the small difference between He i $`\lambda `$ 4387 and He i $`\lambda `$ 4922 found in Herrero et al. (Herrero92 (1992)) for these late O supergiants.

In Table 3 we see the results for the five stars. Changes in the parameters induced by microturbulence are not beyond the standard error box of the analysis , and in particular, we see that He abundance is reduced for four of the stars, but only slightly. In Table 4 we see the values obtained for the radius, mass and luminosity, following the same procedures outlined in Herrero et al. (Herrero92 (1992)). We see that changes are not significant. (We point out that the values for mass, radius and luminosity given in Table 4 for HD 210 809 and HD 18 409 differ slightly from those given in Herrero et al. (Herrero92 (1992)). These differences are not due to the new parameters, but to a change in the distance moduli. Herrero et al. used the values from Humphreys (hum78 (1978)), while we use the values from Garmany & Stencel (GarS (1992))).

In Figs. 6 to 10 we can see the fits with microturbulence 0 and 15 kms-1. The quality of the fits to individual lines is the same at both values, although the triplet line He i $`\lambda `$ 4471 becomes stronger at 15 kms-1, which produces an improved fit, but not to the extent as to completely resolve the so–called dilution effect. Sometimes, a compromise between He i $`\lambda `$4387 and He i $`\lambda `$4922 is adopted, like in HD 5 689 and HD 210 809 (realize that for 15 km$`s^1`$ the first one is slightly weak and the second one slightly strong).

With respect to HDE 338 926, that has been analyzed here for the first time, we have to point out that the analysis has been very difficult. The final parameters are extrapolated beyond the models we could converge. However, we are confident that these parameters do characterize the star appropriately (or as appropriately as those of other stars), because the fits with already converged models are reasonably good, and because we are able to fit the star with converged models when we do not consider line–blocking. Thus, it is only the small temperature increase introduced by line–blocking that moves the star beyond the convergence region. The value we obtain for the evolutionary mass, derived from the tracks by Schaller et al., (Schall92 (1992)), is 57.6 $`M_{\mathrm{}}`$ without microturbulence, and 56.8 $`M_{\mathrm{}}`$ with 15 kms-1. Comparing with the values in Table 4, it is clear that HDE 338 926 also shows a mass discrepancy, as usual. Of course, we will have to reanalyze HDE 338 926 in the future with spherical, mass lossing models.

## 5 Discussion

We will not go here into the discussion of the real physical entity of microturbulence, neither on the validity of the aproximation of small scale turbulent movements assumed to introduce it just as an extra Doppler width, which may be not suitable for the big values we deal with. This is beyond the scope of this work. As explained in Sect. 2 we do not introduce microturbulence in the structure calculations because we think that, having neglected other motions, it is actually not more physically consistent to introduce a turbulent pressure term. We just accept the necessity of using microturbulence in the analysis of stellar spectra, specially in the determination of metal abundances, that is our final interest.

We find that contrary to our previous considerations, He i lines and He ii $`\lambda `$ 4686 do have profiles sensitive to the usual values of microturbulence found in OB stars. We confirm this for the whole range of parameters describing O and early B spectra, in agreement with McErlean et al. (McErlean98 (1998)) and Smith & Howarth (Smith&Howarth98 (1998)) for early B and late O supergiants respectively. This sensitivity is first due to the fact that the Stark broadening is not dominating completely these profiles and second to the high values of microturbulence involved, that are comparable to the thermal velocity of He ions. Taking (0.84 $`T_{\mathrm{eff}}`$) as representative of the temperature in the zone of formation of the lines, we find that for $`T_{\mathrm{eff}}`$= 30 000 K $`v_{\mathrm{th}}`$ of He ions is 10 kms-1, and for $`T_{\mathrm{eff}}`$= 45 000 K it is 12 kms-1. For H ions, with a fourth of the He atomic weigth, thermal velocities are two times larger, so thermal broadening and Stark broadening dominate the profile. For all other He ii lines Stark broadening is hiding the effect of microturbulence.

Quantifying the effect of microturbulence on the determination of stellar parameters we find that they are not changed beyond the standard error box of our analyses. This implies that for stars with high He overabundances, such as HD 5 689 analysed here, the He discrepancy will not be solved by considering microturbulence. This result is also supported by what we obtained in Sect. 3.

This seems to be in contradiction with Smith & Howarth (Smith&Howarth98 (1998)) and McErlean et al. (McErlean98 (1998)), who affirm that solar He abundances are found for the supergiants they analyse, when microturbulence is considered. However, the situation is still unclear, as an analysis of published results can show.

Let us begin with the He overabundances obtained by Herrero et al. (Herrero92 (1992)). Following the argument by Smith & Howarth (Smith&Howarth98 (1998)) and McErlean et al. (McErlean98 (1998)), the preferred use of the strong line He i $`\lambda `$ 4922 in the analyses (slightly more sensitive to microturbulence than He i $`\lambda `$ 4387) would be responsible for the high He abundances found in that work. As a conclusion, the derived He overabundances would be an artifact introduced by the neglection of microturbulence.

This argument applies in the cases in which Herrero et al. (Herrero92 (1992)) found a discrepancy between He i $`\lambda `$ 4922 and He i $`\lambda `$ 4387, but not in the rest of the cases.

In Fig. 11 we have plotted He abundance versus $`T_{\mathrm{eff}}`$, as derived by Herrero et al. (Herrero92 (1992)), using different symbols for stars for which a discrepancy between these two lines was reported. We can see that the priority given to He i $`\lambda `$ 4922 can affect some of the abundances derived, specially at lower temperatures.

To illustrate the situation, let us briefly discuss one of these objects for which Herrero et al. report a difference between He i $`\lambda `$ 4922 and He i $`\lambda `$ 4387: HD 210 809. This star has been analyzed here again, where we have given more weight to He i $`\lambda `$ 4387 (contrary to Herrero et al.). The final difference between the He abundance obtained here with a microturbulence of 15 kms-1 and that obtained by Herrero et al. is 0.04 (our new He abundance being lower). This, however, has to be adscribed to different effects. First, giving more weight to He i $`\lambda `$ 4387 in absence of microturbulence results in a higher temperature (as already stated by Herrero et al.), which leads to a lower He abundance to keep the fit of He ii lines. The effect of line blocking, not included in Herrero et al., goes in the same direction. This accounts for a difference of 0.02 and the additional difference of 0.02 is purely due to microturbulence (see Table 3). Comparing our Fig. 9 with Fig. 5 of Herrero et al. (Herrero92 (1992)) we see that the effects considered here help to reduce the discrepancy between the two He i lines.

The discrepancy between He i $`\lambda `$ 4387 and He i $`\lambda `$ 4922 found by Herrero et al. (Herrero92 (1992)) is larger at lower temperatures, and thus, around 30 000 K it cannot be solved by varying $`T_{\mathrm{eff}}`$ or introducing line blocking. Therefore, around or below this temperature microturbulence is at present the only considered effect that could bring them into agreement.

In the literature we can find analyses of early B and late O supegiants including microturbulence (Gies & Lambert, Gies&Lambert92 (1992), Smith & Howarth, Smith&Howarth94 (1994), Smith&Howarth98 (1998), Smith et al., Smithetal98 (1998), McErlean et al., McErlean98 (1998)). In Table 5 we list stars for which parameters have been derived with and without microturbulence.

Comparisons in Table 5 have to be done with care. It mixes results from different authors and different criteria. We see however that it indicates that the changes found here are consistent with those of other authors, i.e., stellar parameters are changed within the uncertainties adopted here. These changes do not follow a clear, systematic pattern (i.e., going always in the same direction when introducing microturbulence) and thus we conclude that the effect of microturbulence is indeed not larger than present–day uncertainties. An exception to this might be $κ$ Ori, which shows a large change in He abundance. However, this large reduction of the He abundance found by McErlean et al. (McErlean98 (1998)) as compared to Lennon et al. (Lennon91 (1991)) is accompanied by a large change in the stellar parameters. Even if we attribute the whole change to the effect of microturbulence (and not to a new analysis with new data and more refined calculations) we see that $κ$ Ori is by far the coolest of the stars in Tables 3 and 5 and thus we expect a larger influence of microturbulence for it. In addition, we note that McErlean et al. (McErlean98 (1998)) do not exclude a larger He abundance for this star. We conclude that data in the literature do not lead to the conclusion that the He discrepancy in O and early B supergiants is completely due to microturbulence, although microturbulence helps to reduce it.

Except for the discussed reduction of the He abundance, we do not see a clear pattern in the parameter changes in Tables 3 and 5. $`T_{\mathrm{eff}}`$ and $`\mathrm{log}g`$ can both increase or decrease when microturbulence is introduced, and thus we are tempted to conclude that these changes are still dominated by internal inconsistencies in the analyses that appear when we compare values that cannot be distinguished within the adopted uncertainties.

About the problem of the consistency of the fits to He i lines, we find that the dilution of He i $`\lambda `$ 4471 is only partially solved, even when line–blocking is considered as here. The fits to the rest of He i lines do not improve much either in the stars we analyze here. So the consideration of both microturbulence and line–blocking in the analysis cannot completely make an agreement between the results from triplet and singlet He i lines, though they help to improve it.

## 6 Conclusions

We study for the first time the effect of microturbulence in the whole O spectral range, from late to early O types. Introducing microturbulence in the solution of the statistical equilibrium and transfer equations, and then in the formal solution (i.e., in the absorption coefficient), we conclude that for higher gravities the effect in the lines is negligible. This together with the low values of microturbulence usually found for high luminosity class stars, lead us to conclude that only O supergiants have sensitivity to microturbulence effects at a given $`T_{\mathrm{eff}}`$.

In examining the behaviour with microturbulence of the lines we use in our analysis, we show that only He i lines and the core of He ii $`\lambda `$ 4686 Å are sensitive to microturbulence. For He i lines we show that, as should be expected, there is not a constant pattern for each line, but it depends on the parameters considered, that determine the strength of the line and its degree of saturation. This invalidates generalizations to the whole O spectral range made upon results obtained just for a certain spectral type.

In order to quantify the sensitivity of stellar parameters to microturbulence we find that changes in the parameters induced by a value of microturbulence of 15 kms-1 are enclosed within the standard error box of our analyses. We think that the lack of a clear pattern in the changes induced in $`T_{\mathrm{eff}}`$ and $`\mathrm{log}g`$ is just due to the fact that we are varying the parameters within this error box. We do however find a systematic change in $`ϵ`$ towards lower He abundances when microturbulence is introduced. In particular we find that late O supergiants show a decrease of 0.02–0.04 in $`ϵ`$ (this last value when including other effects that add to microturbulence), which is in agreement with previous results pointing to the inverse relation between the microturbulence assumed and the He abundance obtained (Smith & Howarth Smith&Howarth98 (1998)). Early types are less sensitive to microturbulence, and might not show a difference in the derived He abundance.

Thus microturbulence is not capable of explaining the He discrepancy at all for early O stars, and neither it is for late O types with high overabundances.

Looking to individual lines we find that the fits to He i $`\lambda `$ 4471 Å are improved when considering microturbulence, but not to the extent of completely explaining its dilution. On the other hand He i $`\lambda `$$`\lambda `$ 4922, 4387 Å are sometimes slightly better and sometimes slightly worse fitted, in the last case with model cores a bit too strong or a bit too weak, respectively. The rest of the lines keep the same quality in the fit. The *He i lines problem* is therefore only partially solved by simply considering microturbulence, even with line–blocking included in the model profiles.

Therefore our conclusion is that microturbulence is affecting the derivation of stellar parameters, but its effect is comparable to the adopted uncertainties. Thus it can reduce moderate He overabundances and solve line fit quality differences, but it cannot explain by itself large He overabundances in O stars, and we are forced to conclude that these are due to other effects, whether real or caused by artifacts in our analyses. This last point will probably not find a definitive answer until we are able to derive reliable abundances of C, N and O in the atmospheres of O stars that we can correlate with the He abundances.

###### Acknowledgements.

We want to thank Neil McErlean and Danny Lennon for their help, suggestions and many clarifying discussions. AH wants to acknowledge support for this work by the spanish DGES under project PB97-1438-C02-01


text:
# Interfering with Interference: a Pancharatnam Phase Polarimeter

## I Introduction

Pancharatnam  explored how the phase of polarized light changes as the light passes through cycle of polarizations. He found that the phase increases by $`\mathrm{\Omega }/2`$, where $`\mathrm{\Omega }`$ is the solid angle that the geodesic path of polarizations subtends on the Poincaré sphere. If the path does not consist of great circles, an additional dynamical phase will develop. Berry  developed corresponding theory for general quantum systems and re-derived Pancharatnam’s result .

A series of experiments have been performed which demonstrate the Pancharatnam phase  and the related geometric phase . De Vito and Levrero  have criticized many of these experiments because they use retarders which introduce a dynamical component to the phase. Berry & Klein  and Hariharan et al.  have performed a series of experiments using only polarizers and beam splitters to introduce and measure the geometric phase.

In this paper, I describe a simple experiment using polarizers and a double slit to demonstrate the Pancharatnam phase and use this phase to determine the polarization state of the incoming light. If the incoming light is linearly polarized and the polarizers are also linear, the resulting phase is limited to 0 or $`\pi `$. However, elliptically polarized light will result in intermediate values of the phase. This experiment uses a double slit rather than a half silvered mirror to split the beam, eliminating a possible source of dynamic phase; furthermore, with fewer and less complex optical elements this experiment may be performed over a wide range of photon energies. Furthermore, since the optics are simple, one can analyze the experiment in terms of Maxwell’s equations, illustrating the connection between these equations and the Pancharatnam phase.

## II Experimental Apparatus

Fig. 1 illustrates the experiment setup (c.f. ). RP and FP denote rotatable and fixed linear polarizers respectively. Each fixed linear polarizer covers one of the two slits and is oriented perpendicular to the other. Each rotatable polarizer is oriented at forty-five degrees to the polarizers to maximize throughput. Incidentally, if the final polarizer is removed, the interference pattern disappears according to the Frensel-Arago law .

The arrangement is similar to that used by Schmitzer, Klein & Dultz . Instead of using a Babinet-Soleil compensator to vary the geometric phase. The phase depends on the input and output polarizations of interferometer. If the two polarizers are aligned, the Pancharatnam phase between the two paths vanishes; and if they are orthogonal, the phase is $`\pi `$.

The setup is identical to the standard physics demonstration of Young’s double-slit experiment with the exception that each slit is covered with a polarizing filter; consequently, both the construction and analysis of the experiment are amenable as a demonstration or student laboratory experiment. Furthermore, the light follows the same spatial trajectory, independent of the position of the polarizers and the geometric phase observed.

## III The Poincaré Sphere

Understanding how the apparatus works for a general polarization is most simply achieved by tracing the polarization of the light through the system along the Poincaré sphere. The initial polarization from the laser is unknown but it is depicted in the figures as left circular. The left panel of Fig. 2 depicts the configuration for zero geometric phase. As the laser passes through the first polarizer, its polarization is projected onto the horizontal direction. After passing through the two slits, the polarization is projected onto two orthogonal polarizations oriented at forty-five degrees to the horizontal. Finally, the last polarizer projects the polarization back onto the horizontal. One can form a closed loop by following the path along one leg and returning along the other leg (c.f.  ). This closed loop does not enclose any solid angle on the sphere.

The right panel of Fig. 2 illustrates the path of the polarization when the two rotatable polarizers are orthogonal. The polarization is now projected onto the vertical first, followed by the two diagonal polarizations and the final horizontal projection. Constructing the closed loop as described earlier yields an area of $`2\pi `$ and a Pancharatnam phase of $`\pi `$ between the two slits.

Since a constant phase difference of $`\pi `$ is equivalent to $`\pi `$, this implementation hides the fact that the area on the sphere is oriented and consequently the geometric phase may be positive or negative. A third configuration when the input polarizer is followed by a quarter-wave plate yielding right-hand circular polarized input to the interferometer illustrates this point. The direction that the loop is traversed determines which slit is designated by $`\varphi _1`$ such that $`\varphi _1\varphi _2=\mathrm{\Omega }/2`$. The phase difference is given by $`\pi /2`$ if the final polarizer lies clockwise relative to polarizer behind the first slit, and $`\pi /2`$ if the final polarizer lies counterclockwise. The converse result holds for left-hand polarized light.

If the axis of polarizer behind left-hand slit (as one looks toward the screen) lies clockwise of that of the final polarizer, one obtains the result that the fringes will shift to the left (relative to their position for the input and output polarizations being identical) if the light is left elliptically polarized and to the right if it is right elliptically polarized. This configuration automatically includes the minus sign present in Pancharatnam’s definition of the geometric phase. The upper and lower panels of Fig. 3 show the fringe pattern produced by the apparatus in the configuration described above for the input and output polarizations being linear and identical and linear and orthogonal. The middle panel shows the fringes for left-hand circularly polarized input light at the input with the input polarizer removed.

## IV Measuring the Input Polarization

If the input polarizer is removed, the apparatus can be used to measure the polarization of the light source. The procedure requires four measurements of the fringe positions: two for calibration and two to determine the geometric phases.

1. Locate the positions of the fringes with the input and output polarizers parallel and midway between the polarizers at the slits.
2. Remove the input polarizer and compare the position of the fringes relative to the two previous measurements. Let $`\alpha /(2\pi )`$ be the ratio of the offset of the fringes in step (2) relative to step (1) to the distance between the fringes in step (1). Also, note the direction that fringes shift – left for left-circular polarization and right for right-circular polarization.
3. Rotate either all of the polarizers by forty-five degrees or rotate the light source by forty-five degrees and repeat steps (1) and (2) and denote the resulting ratio by $`\beta /(2\pi )`$.

The left panel of Fig. 4 depicts how the polarization evolves on the Poincaré sphere for the two configurations. It is straightforward to calculate the input polarization using spherical trigonometry by following the right panel of Fig. 4. $`\mathrm{sin}d`$ gives the fraction of circular polarization and $`e`$ is the angle between the long axis of the polarization ellipse and the vertical axis. Napier’s analogies yield

$$a=\left\{\mathrm{tan}^1\left[\frac{\mathrm{sin}\frac{1}{2}(\alpha \beta )}{\mathrm{sin}\frac{1}{2}(\alpha +\beta )}\right]+\mathrm{tan}^1\left[\frac{\mathrm{cos}\frac{1}{2}(\alpha \beta )}{\mathrm{cos}\frac{1}{2}(\alpha +\beta )}\right]\right\}$$
(1)
and the law of sines gives

$$\mathrm{sin}d=\mathrm{sin}a\mathrm{sin}\beta .$$
(2)
Combining these two results yields

$$\mathrm{tan}\frac{e}{2}=\mathrm{tan}\frac{1}{2}(ad)\frac{\mathrm{sin}\left(\frac{\pi }{4}+\frac{\beta }{2}\right)}{\mathrm{sin}\left(\frac{\pi }{4}\frac{\beta }{2}\right)}$$
(3)
If the input polarization is linear, one finds that measurements of the fringes can only locate the polarization vector to within forty-five degrees. However, the contrast of the interference pattern constrains the linear polarization further, as well as the fractional polarization of the input light.

## V Conclusions

A variation of Young’s double-slit experiment provides a excellent and simple demonstration of the Pancharatnam phase for polarized light. Furthermore, the observed phase difference between the two slits is simply related to the polarization of the incoming light. The phase difference determines upon which great circle of the Poincaré sphere the polarization lies, and by performing the measurement after rotating the apparatus the input polarization can be determined precisely.

The distinct advantage of the experiment is the simplicity of the optics. Only linear polarizers and a double slit are required. Since the Pancharatnam phase is achromatic, the procedure may be performed for the wide range of photon energies where suitable materials are available. A companion paper discusses the implementation of the experiment in X-rays and possible applications.

## ACKNOWLEDGMENTS

I would like to thank Jackie Hewitt, Lior Burko and Eugene Chiang for useful discussions and to acknowledge a Lee A. DuBridge Postdoctoral Scholarship.


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# SELEXTalk given at the Session honoring Leon Lederman at the VII Mexican Workshop on Particles and Fields, Mérida, México, November 10-17, 1999. Proceedings to be published by AIP.

## The history: E761

Experiment E761, “An Electroweak Enigma: Hyperon Radiative Decays” proposal:761  was my first encounter with experimental high energy physics.

I got experience on silicon micro strip and wire chamber detectors, magnet spectrometers for momentum precision measurements, data acquisition and trigger systems based on NIM and CAMAC, reconstruction and analysis packages, and performed high precision physics measurements of the $`\mathrm{\Sigma }^+`$ magnetic moment and of the $`\mathrm{\Sigma }^+`$ and $`\overline{\mathrm{\Sigma }}^{}`$ production polarization am:ptxfspol ; am:mmssb ; am:ssbpol .

This experiment now represents the starting push for the particle physics group at San Luis Potosí.

## The present: SELEX

There are several aspects to talk about SELEX, recent hyperon and charm physics results, I only highlight a few of them.

Also prior to talk about physics I should mention that E781 or SELEX is the first experiment where San Luis Potosí is a formal collaborating institution. Two students have gotten their master degree thesis related to SELEX, Ricardo López Fernández working in the RICH group and analyzing the beam composition using the RICH, and Galileo Domínguez Zacarías working with the $`K_s^0`$ sample looking into $`\pi `$ asymmetry uaslp:trlf ; uaslp:tgdz . Personally I worked in the smart crate controller in the CAMAC setup and trigger installation. An impact at San Luis Potosí also happen in relation to this collaboration: Jürgen Engelfried, member of SELEX and previously WA89 at CERN, accepted to work as professor at San Luis Potosí, his expertise brings more life and conforms the local group and opens more physics opportunities as I’ll discuss in the section “The near future”.

SELEX is a new fixed target experiment designed to enhance charm - strange baryon over meson data. The data taking lasted from summer 1996 to fall 1997. It includes a tagged hadron beam on $`\pi `$, $`\mathrm{\Sigma }`$ and proton using a TRD detector; a micro-vertex detector, and particle id using TRD, lead glass, and RICH detectors; all these detectors distributed among three magnet spectrometers proposal:781 .

SELEX was designed to be a high $`x_F`$ charm baryon spectrometer, and in fact this can be appreciated by the high acceptance at $`x_F`$ $`>`$ 0.5. In the three modes, $`\mathrm{\Lambda }_c^+\text{ }pK^{}\text{ }\pi ^+\text{ }`$ , $`D^0\text{ }K^{}\text{ }\pi ^+\text{ }`$ , and $`D^+\text{ }K^{}\text{ }\pi ^{}\text{ }\pi ^+\text{ }`$, the acceptance is grater than 6 %, and identical for particle and antiparticle decays. The control on the acceptance gives the opportunity to study charm baryon production as a function of $`x_F`$ with very good precision for challenging theoretical models and other experiments talk:fernanda ; fg:ucla ; jr:vancuver .

Charm baryon and meson lifetime measurements are also under control in the experiment. SELEX was designed with a trigger to enhance all charm baryon production and decay modes, as a result it has the ability to look for unseen decay modes, right now SELEX is reporting the first observation of Cabibbo suppressed $`\mathrm{\Xi }_c^+\text{ }pK^{}\text{ }\pi ^+\text{ }`$ decay selex:cabibbo .

The fact of having a $`\mathrm{\Sigma }^{}`$ beam to study charm production also provides by its own nature the tool to study properties of the hyperon itself. At present there are preliminary reports on $`\mathrm{\Sigma }^{}`$ radius and total cross section of $`\mathrm{\Sigma }^{}`$ beam on different target material uwe:total ; mam:inelastic ; vk:ados ; ivo:hyperon .

## The near future: CKM & Instrumentation

On April 26 1996, Fermilab invited physicists for a workshop towards the use of a 120 GeV/c proton beam on collider and fixed target mode. All mexican groups had the opportunity for joining this activity. The event really represented a great opportunity for young mexican groups since the enterprises are small in size and with a lot of opportunities to start at the zero point of the design and construction for leading a project or subproject. Of all the mexican existing groups only San Luis Potosí, so far, has taken the challenge to participate actively in one of these experiments.

CKM “Charged Kaons at the Main Injector”, a proposal for a Precision Measurement of the Decay $`K^+\text{ }\pi ^+\text{ }\nu \text{ }\overline{\nu }\text{ }`$ and Other Rare $`K^+`$ Processes at Fermilab Using the Main Injector, is one of the experiments which were born after the April 96 workshop proposal:ckm .

The experiment will measure the branching ratio of the ultra-rare charged kaon decay $`K^+\text{ }\pi ^+\text{ }\nu \text{ }\overline{\nu }\text{ }`$ by observing a large sample of those decays with small background. The physics goal is to measure the magnitude of the Cabibbo, Kobayashi, Maskawa matrix element $`V_{td}`$ with a statistical precision of about 5% based upon a $``$ 100 event sample with total backgrounds of less than 10 events. This decay mode is known to be theoretically clean. The only significant theoretical uncertainty in the calculation of this branching ratio is due to the charm contribution. A 10% measurement of the branching ratio will yield a 10% total uncertainty on the magnitude of $`V_{td}`$.

In this experiment IF-UASLP is in charge for testing parts and the whole design of two Ring Imaging Cherenkov Counters, RICH’s plan:erik . Experience on this technology came from the participation of Jürgen Engelfried on the design, construction, operation, and analysis of two previous RICH’s, one in WA89 and another in SELEX. Also, in SELEX, Ricardo López Fernández, graduate student from IF-UASLP, worked on and used the RICH as part of his M.Sc. thesis.

CKM marks the near future experimental enterprise we are working on at IF-UASLP. We are initiating high energy physics instrumentation at IF-UASLP, aimed right now at the RICH technology applied to the CKM experiment.

## HEP: a group at IF-UASLP

Experimental high energy physics evolves with projects and this aspect is also reflected on the IF-UASLP group which has seen the pass of experiments E761, WA89, E781 and now CKM. Presently, the group is creating a high energy instrumentation laboratory towards detector research and development. The basic idea of the laboratory is to target user defined detectors at world wide experiments, right now we have the RICH design and testing for CKM. In 1999, IF-UASLP just hired Ruben Flores Mendieta to strength particle physics theory and phenomenology research. Looking backwards from the beginning of the 80’s to the end of the 90’s a spawn of close to 20 years has happened for initiating an experimental group at San Luis Potosí, that is a positive result from an initial kick.

## Acknowledgement

This work was partly financed by IF-UASLP and CONACyT.