DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

Hard limits on the postselectability of optical graph states

Coherent control of large entangled graph states enables a wide variety of quantum information processing tasks, including error-corrected quantum computation. The linear optical approach offers excellent control and coherence, but today most photon sources and entangling gates---required for the construction of large graph states---are probabilistic and rely on postselection. In this work, we provide proofs and heuristics to aid experimental design using postselection. We derive a fundamental limitation on the generation of photonic qubit states using postselected entangling gates: experiments which contain a cycle of postselected gates cannot be postselected. Further, we analyse experiments that use photons from postselected photon pair sources, and lower bound the number of classes of graph state entanglement that are accessible in the non-degenerate case---graph state entanglement classes that contain a tree are are always accessible. Numerical investigation up to 9-qubits shows that the proportion of graph states that are accessible using postselection diminishes rapidly. We provide tables showing which classes are accessible for a variety of up to nine qubit resource states and sources. We also use our methods to evaluate near-term multi-photon experiments, and provide our algorithms for doing so.Comment: Our manuscript comprises 4843 words, 6 figures, 1 table, 47 references, and a supplementary material of 1741 words, 2 figures, 1 table, and a Mathematica code listin

Auralization of Air Vehicle Noise for Community Noise Assessment

This paper serves as an introduction to air vehicle noise auralization and documents the current state-of-the-art. Auralization of flyover noise considers the source, path, and receiver as part of a time marching simulation. Two approaches are offered; a time domain approach performs synthesis followed by propagation, while a frequency domain approach performs propagation followed by synthesis. Source noise description methods are offered for isolated and installed propulsion system and airframe noise sources for a wide range of air vehicles. Methods for synthesis of broadband, discrete tones, steady and unsteady periodic, and a periodic sources are presented, and propagation methods and receiver considerations are discussed. Auralizations applied to vehicles ranging from large transport aircraft to small unmanned aerial systems demonstrate current capabilities

Is it the boundaries or disorder that dominates electron transport in semiconductor `billiards'?

Semiconductor billiards are often considered as ideal systems for studying dynamical chaos in the quantum mechanical limit. In the traditional picture, once the electron's mean free path, as determined by the mobility, becomes larger than the device, disorder is negligible and electron trajectories are shaped by specular reflection from the billiard walls alone. Experimental insight into the electron dynamics is normally obtained by magnetoconductance measurements. A number of recent experimental studies have shown these measurements to be largely independent of the billiards exact shape, and highly dependent on sample-to-sample variations in disorder. In this paper, we discuss these more recent findings within the full historical context of work on semiconductor billiards, and offer strong evidence that small-angle scattering at the sub-100 nm length-scale dominates transport in these devices, with important implications for the role these devices can play for experimental tests of ideas in quantum chaos.Comment: Submitted to Fortschritte der Physik for special issue on Quantum Physics with Non-Hermitian Operator

Non-linear effects in knowledge production

The generation of technological knowledge is paramount to our present development. Economic science concentrates on representing the functions of production applied to all sectors, e.g., the well known Cobb-Douglas model, associated with parameters such as capital and labor. Based on the paradigm, demonstrated in another paper, that the production of technological knowledge is governed by the same Cobb-Douglas type model, by the means of research and the intelligence level replacing capital, respectively labor, we are exploring the basic behavior of present days economies that are producing technological knowledge, along with the 'usual' industrial production. Considering the intercorrelations of technology and industrial production we determine a basic behavior that turns out to be a 'Henon attractor', well known as one of the first analyzed systems that present chaotic behavior confined to strange attractors. The behavior inside the basin of the attractor's dynamic shows some interesting features such as the fact that too little effort in technological knowledge production is associated to low industrial production, while too much resource allocation to technological production is also reaching an area of low industrial production. This effect clearly shows that too little allocation of resources to research is equivalent to a disproportionate allocation of resources to research, namely that both hamper the industrial production. Moreover, there is an area of large industrial production that corresponds to a certain rate of technology production that, in some way, optimizes development. Measures are introduced for the gain of technological knowledge and the information of technological sequences that are based on the underlying multi-valued logic of the technological research and on nonlinear thermodynamic considerations. We have witnessed in the last decades several cases of economies, e.g., Ireland and Finland, in Europe, the Asian tigers and China in Asia, which had had a moment in their history when research (both means and intelligence) was a main priority. Luckily, the globalization acted as a stabilizer that kept them close to the optimum of 'As High As Reasonably Acceptable' technological production. By contrast to ALARA (as low as reasonably acceptable) principle, that applies in risk analysis, here we may introduce the AHARA principle resulting from the nonlinear behavior of technological production vs. industrial production.knowledge management, strange attractors, experimental state of knowledge

Entropy involved in fidelity of DNA replication

Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.Comment: 25 pages, 5 figure