The computational complexity of Kauffman nets and the P versus NP problem

Complexity theory as practiced by physicists and computational complexity theory as practiced by computer scientists both characterize how difficult it is to solve complex problems. Here it is shown that the parameters of a specific model can be adjusted so that the problem of finding its global energy minimum is extremely sensitive to small changes in the problem statement. This result has implications not only for studies of the physics of random systems but may also lead to new strategies for resolving the well-known P versus NP question in computational complexity theory.Comment: 4 pages, no figure

The Number of Different Binary Functions Generated by NK-Kauffman Networks and the Emergence of Genetic Robustness

We determine the average number $\vartheta (N, K)$, of \textit{NK}-Kauffman networks that give rise to the same binary function. We show that, for $N \gg 1$, there exists a connectivity critical value $K_c$ such that $\vartheta(N,K) \approx e^{\phi N}$ ($\phi > 0$) for $K < K_c$ and $\vartheta(N,K) \approx 1$ for $K > K_c$. We find that $K_c$ is not a constant, but scales very slowly with $N$, as $K_c \approx \log_2 \log_2 (2N / \ln 2)$. The problem of genetic robustness emerges as a statistical property of the ensemble of \textit{NK}-Kauffman networks and impose tight constraints in the average number of epistatic interactions that the genotype-phenotype map can have.Comment: 4 figures 18 page

An analytic Approach to Turaev's Shadow Invariant

In the present paper we extend the "torus gauge fixing approach" by Blau and Thompson (Nucl. Phys. B408(1):345--390, 1993) for Chern-Simons models with base manifolds M of the form M= \Sigma x S^1 in a suitable way. We arrive at a heuristic path integral formula for the Wilson loop observables associated to general links in M. We then show that the right-hand side of this formula can be evaluated explicitly in a non-perturbative way and that this evaluation naturally leads to the face models in terms of which Turaev's shadow invariant is defined.Comment: 44 pages, 2 figures. Changes have been made in Sec. 2.3, Sec 2.4, Sec. 3.4, and Sec. 3.5. Appendix C is ne

Quantum entanglement, unitary braid representation and Temperley-Lieb algebra

Important developments in fault-tolerant quantum computation using the braiding of anyons have placed the theory of braid groups at the very foundation of topological quantum computing. Furthermore, the realization by Kauffman and Lomonaco that a specific braiding operator from the solution of the Yang-Baxter equation, namely the Bell matrix, is universal implies that in principle all quantum gates can be constructed from braiding operators together with single qubit gates. In this paper we present a new class of braiding operators from the Temperley-Lieb algebra that generalizes the Bell matrix to multi-qubit systems, thus unifying the Hadamard and Bell matrices within the same framework. Unlike previous braiding operators, these new operators generate {\it directly}, from separable basis states, important entangled states such as the generalized Greenberger-Horne-Zeilinger states, cluster-like states, and other states with varying degrees of entanglement.Comment: 5 pages, no figur

On the Robustness of NK-Kauffman Networks Against Changes in their Connections and Boolean Functions

NK-Kauffman networks {\cal L}^N_K are a subset of the Boolean functions on N Boolean variables to themselves, \Lambda_N = {\xi: \IZ_2^N \to \IZ_2^N}. To each NK-Kauffman network it is possible to assign a unique Boolean function on N variables through the function \Psi: {\cal L}^N_K \to \Lambda_N. The probability {\cal P}_K that \Psi (f) = \Psi (f'), when f' is obtained through f by a change of one of its K-Boolean functions (b_K: \IZ_2^K \to \IZ_2), and/or connections; is calculated. The leading term of the asymptotic expansion of {\cal P}_K, for N \gg 1, turns out to depend on: the probability to extract the tautology and contradiction Boolean functions, and in the average value of the distribution of probability of the Boolean functions; the other terms decay as {\cal O} (1 / N). In order to accomplish this, a classification of the Boolean functions in terms of what I have called their irreducible degree of connectivity is established. The mathematical findings are discussed in the biological context where, \Psi is used to model the genotype-phenotype map.Comment: 17 pages, 1 figure, Accepted in Journal of Mathematical Physic

Experimental approximation of the Jones polynomial with DQC1

We present experimental results approximating the Jones polynomial using 4 qubits in a liquid state nuclear magnetic resonance quantum information processor. This is the first experimental implementation of a complete problem for the deterministic quantum computation with one quantum bit model of quantum computation, which uses a single qubit accompanied by a register of completely random states. The Jones polynomial is a knot invariant that is important not only to knot theory, but also to statistical mechanics and quantum field theory. The implemented algorithm is a modification of the algorithm developed by Shor and Jordan suitable for implementation in NMR. These experimental results show that for the restricted case of knots whose braid representations have four strands and exactly three crossings, identifying distinct knots is possible 91% of the time.Comment: 5 figures. Version 2 changes: published version, minor errors corrected, slight changes to improve readabilit

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

Survey for Galaxies Associated with z~3 Damped Lyman alpha Systems I: Spectroscopic Calibration of u'BVRI Photometric Selection

We present a survey for z~3 Lyman break galaxies (LBGs) associated with damped Lyman alpha systems (DLAs) with the primary purpose of determining the DLA-LBG cross-correlation. This paper describes the acquisition and analysis of imaging and spectroscopic data of 9 quasar fields having 11 known z~3 DLAs covering an area of 465 arcmin^2. Using deep u'BVRI images, 796 LBG candidates to an apparent R_AB magnitude of 25.5 were photometrically selected from 17,343 sources detected in the field. Spectroscopic observations of 529 LBG candidates using Keck LRIS yielded 339 redshifts. We have conservatively identified 211 z>2 objects with =3.02+/-0.32. We discuss our method of z~3 LBG identification and present a model of the u'BVRI photometric selection function. We use the 339 spectra to evaluate our u'BVRI z~3 Lyman break photometric selection technique.Comment: 26 pages, 6 tables, 11 figures, accepted for publication in Ap

First Structure Formation: A Simulation of Small Scale Structure at High Redshift

We describe the results of a simulation of collisionless cold dark matter in a LambdaCDM universe to examine the properties of objects collapsing at high redshift (z=10). We analyze the halos that form at these early times in this simulation and find that the results are similar to those of simulations of large scale structure formation at low redshift. In particular, we consider halo properties such as the mass function, density profile, halo shape, spin parameter, and angular momentum alignment with the minor axis. By understanding the properties of small scale structure formation at high redshift, we can better understand the nature of the first structures in the universe, such as Population III stars.Comment: 31 pages, 14 figures; accepted for publication in ApJ. Figure 1 can also be viewed at http://cfa-www.harvard.edu/~hjang/research

The Asymptotic Number of Attractors in the Random Map Model

The random map model is a deterministic dynamical system in a finite phase space with n points. The map that establishes the dynamics of the system is constructed by randomly choosing, for every point, another one as being its image. We derive here explicit formulas for the statistical distribution of the number of attractors in the system. As in related results, the number of operations involved by our formulas increases exponentially with n; therefore, they are not directly applicable to study the behavior of systems where n is large. However, our formulas lend themselves to derive useful asymptotic expressions, as we show.Comment: 16 pages, 1 figure. Minor changes. To be published in Journal of Physics A: Mathematical and Genera