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A suitably programmed quantum computer should act on a number x to produce another number f(x) for some specified function f. Appropriately interpreted, with an accuracy that increases with increasing k, we can treat such numbers as non-negative integers less than 2k. Each integer is represented in the quantum computer by the corresponding computational-basis state of k Qbits.
If we specify the numbers x as n-bit integers and the numbers f(x) as m-bit integers, then we shall need at least n + m Qbits: a set of n-Qbits, called the input register, to represent x, and another set of m-Qbits, called the output register, to represent f(x). Qbits being a scarce commodity, you might wonder why we need separate registers for input and output. One important reason is that if f(x) assigns the same value to different values of x, as many interesting functions do, then the computation cannot be inverted if its only effect is to transform the contents of a single register from x to f(x). Having separate registers for input and output is standard practice in the classical theory of reversible computation. Since quantum computers must operate reversibly to perform their magic (except for measurement gates), they are generally designed to operate with both input and output registers. We shall find that this dual-register architecture can also be usefully exploited by a quantum computer in some strikingly nonclassical ways.
Simon's problem (Section 2.5) starts with a subroutine that calculates a function f(x), which satisfies f(x) = f(y) for distinct x and y if and only if y = x ⊕ a, where ⊕ denotes the bitwise modulo-2 sum of the n-bit integers a and x. The number of times a classical computer must invoke the subroutine to determine a grows exponentially with n, but with a quantum computer it grows only linearly.
This is a rather artificial example, of interest primarily because it gives a simple demonstration of the remarkable computational power a quantum computer can possess. It amounts to finding the unknown period a of a function on n-bit integers that is “periodic” under bitwise modulo-2 addition. A more difficult, but much more natural problem is to find the period r of a function f on the integers that is periodic under ordinary addition, satisfying f(x) = f(y) for distinct x and y if and only if x and y differ by an integral multiple of r. Finding the period of such a periodic function turns out to be the key to factoring products of large prime numbers, a mathematically natural problem with quite practical applications.
We illustrate here the mathematics of the final (post-quantum-computational) stage of Shor's period-finding procedure. The final measurement produces (with high probability) an integer y that is within ½ of an integral multiple of 2n/r, where n is the number of Qbits in the input register, satisfying 2n > N2 > r2. Deducing the period r of the function f from such an integer y makes use of the theorem that if x is an estimate for the fraction j/r that differs from it by less than ½r2, then j/r will appear as one of the partial sums in the continued-fraction expansion of x. In the case of Shor's period finding algorithm x = y/2n. If j and r happen to have no factors in common, r is given by the denominator of the partial sum with the largest denominator less than N. Otherwise the continued-fraction expansion of x gives r0: r divided by whatever factor it has in common with the random integer j. If several small multiples of r0 fail to be a period of f, one repeats the whole procedure, getting a different submultiple r1 of r. There is a good chance that r will be the least common multiple of r0 and r1, or a not terribly large multiple of it. If not, one repeats the whole procedure a few more times until one succeeds in finding a period of f.
The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model.
We consider the defect theorem in the context of labelledpolyominoes, i.e., two-dimensional figures. The classical version ofthis property states that if a set of n words is not a code thenthe words can be expressed as a product of at most n - 1 words, thesmaller set being a code. We survey several two-dimensionalextensions exhibiting the boundaries where the theorem fails. Inparticular, we establish the defect property in the case of threedominoes (n × 1 or 1 × n rectangles).
For finitary set functors preserving inverse images, recursive coalgebras A of Paul Taylor are proved to be precisely those for which the system described by A always halts in finitely many steps.
Duplication is the replacement of a factor w within a word by ww. This operation can be used iteratively to generate languages starting from words or sets of words. By undoing duplications, one can eventually reach a square-free word, the original word's duplication root. The duplication root is unique, if the length of duplications is fixed.Based on these unique roots we define the concept of duplication code. Elementary properties are stated, then the conditions under which infinite duplication codes exist are fully characterized; the relevant parameters are the duplication length and alphabet size. Finally, some properties of the languages generated by duplication codes are investigated.
We investigate the density and distribution behaviors of the chinese remainder representationpseudorank. We give a very strong approximation to density, and derive two efficientalgorithms to carry out an exact count (census) of the bad pseudorank integers. One ofthese algorithms has been implemented, giving results in excellent agreement withour density analysis out to 5189-bit integers.
We know from Section 2.2.2 that configuration spaces of general linkages that are permitted to self-intersect, even in ℝ2, can have exponentially many connected components. On the other hand, we know from Section 5.1.1.1 (p. 59) and Section 5.1.2 (p. 66) that configuration spaces of open and closed 3D chains that are permitted to self-intersect have just one connected component. We also know from Section 5.3 (p. 70) that configuration spaces of planar chains have just one connected component when permitted to move into ℝ3 but forbidden to self-cross. We have until now avoided the most natural questions, which concern chains embedded in ℝd, with motion confined to the same space ℝd, without self-crossings. These questions avoid the generality of linkages on the one hand, and the special assumptions of planar embeddings or projections on the other hand.
The main question addressed in this context is which types of linkages always have connected configuration spaces. A linkage with a connected configuration space is unlocked: no two configurations are prevented from reaching each other. If a linkage in 3D or higher dimensions has a disconnected configuration space, it is locked. But for connectivity of the configuration space to be possible in 2D, we need to place an additional constraint, because planar closed chains cannot be turned “inside-out” as they could in Section 5.1.2 when we permitted the chain to self-intersect.