Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes. Drawbacks of our design include the following. If input is provided non-ideally (small positive concentration of unwanted species), then energy must be continually expended to maintain correct output concentrations even at steady-state. In addition, our fuel species - those species that are permanently consumed in irreversible reactions - are not "generic"; each gate in the circuit is powered by its own specific type of fuel species. Hence different circuits must be powered by different types of fuel. Finally, we require input to be given according to the dual-rail convention, so that an input of 0 is specified not only by the absence of a certain species, but by the presence of another. That is, we do not construct a "true NOT gate" that sets its output to high concentration if and only if its input's concentration is low. It remains an open problem to design scalable, time-responsive, digital, energy-efficient molecular circuits that additionally solve one of these problems, or to prove that some subset of their resolutions are mutually incompatible.Comment: version 2: the paper itself is unchanged from version 1, but the arXiv software stripped some asterisk characters out of the abstract whose purpose was to highlight words. These characters have been replaced with underscores in version 2. The arXiv software also removed the second paragraph of the abstract, which has been (attempted to be) re-inserted. Also, although the secondary subject is "Soft Condensed Matter", this classification was chosen by the arXiv moderators after submission, not chosen by the authors. The authors consider this submission to be a theoretical computer science paper

A reassessment of Antarctic plateau reactive nitrogen based on ANTCI 2003 airborne and ground based measurements

The first airborne measurements of nitric oxide (NO) on the Antarctic plateau have demonstrated that the previously reported elevated levels of this species extend well beyond the immediate vicinity of South Pole. Although the current database is still relatively weak and critical laboratory experiments are still needed, the findings here suggest that the chemical uniqueness of the plateau may be substantially greater than first reported. For example, South Pole ground-based findings have provided new evidence showing that the dominant process driving the release of nitrogen from the snowpack during the spring/summer season (post-depositional loss) is photochemical in nature with evaporative processes playing a lesser role. There is also new evidence suggesting that nitrogen, in the form of nitrate, may undergo multiple recycling within a given photochemical season. Speculation here is that this may be a unique property of the plateau and much related to its having persistent cold temperatures even during summer. These conditions promote the efficient adsorption of molecules like HNO3 (and very likely HO2NO2) onto snow-pack surface ice where we have hypothesized enhanced photochemical processing can occur, leading to the efficient release of NOx to the atmosphere. In addition, to these process-oriented tentative conclusions, the findings from the airborne studies, in conjunction with modeling exercises suggest a new paradigm for the plateau atmosphere. The near-surface atmosphere over this massive region can be viewed as serving as much more than a temporary reservoir or holding tank for imported chemical species. It defines an immense atmospheric chemical reactor which is capable of modifying the chemical characteristics of select atmospheric constituents. This reactor has most likely been in place over geological time, and may have led to the chemical modulation of some trace species now found in ice cores. Reactive nitrogen has played a critical role in both establishing and in maintaining this reactor. © 2007 Elsevier Ltd. All rights reserved

Electron-phonon scattering in quantum point contacts

We study the negative correction to the quantized value $2e^2/h$ of the conductance of a quantum point contact due to the backscattering of electrons by acoustic phonons. The correction shows activated temperature dependence and also gives rise to a zero-bias anomaly in conductance. Our results are in qualitative agreement with recent experiments studying the 0.7 feature in the conductance of quantum point contacts.Comment: 4 pages, no figure

Flow cytometric characterization and clinical outcome of CD4+ T-cell lymphoma in dogs: 67 cases.

BackgroundCanine T-cell lymphoma (TCL) is conventionally considered an aggressive disease, but some forms are histologically and clinically indolent. CD4 TCL is reported to be the most common subtype of TCL. We assessed flow cytometric characteristics, histologic features when available, and clinical outcomes of CD4+ TCL to determine if flow cytometry can be used to subclassify this group of lymphomas.ObjectiveTo test the hypothesis that canine CD4+ T-cell lymphoma (TCL) is a homogeneous group of lymphomas with an aggressive clinical course.AnimalsSixty-seven dogs diagnosed with CD4+ TCL by flow cytometry and treated at 1 of 3 oncology referral clinics.MethodsRetrospective multivariable analysis of outcome in canine CD4+ TCL including patient characteristics, treatment, and flow cytometric features.ResultsThe majority of CD4+ TCL were CD45+, expressed low class II MHC, and exhibited an aggressive clinical course independent of treatment regimen (median survival, 159 days). Histologically, CD4+ TCL were classified as lymphoblastic or peripheral T cell. Size of the neoplastic lymphocytes had a modest effect on both PFI and survival in this group. A small number of CD4+ TCL were CD45- and class II MHC high, and exhibited an apparently more indolent clinical course (median survival not yet reached).Conclusions and clinical importanceAlthough the majority of CD4+ TCL in dogs had uniform clinical and flow cytometric features and an aggressive clinical course, a subset had a unique immunophenotype that predicts significantly longer survival. This finding strengthens the utility of flow cytometry to aid in the stratification of canine lymphoma

Stub model for dephasing in a quantum dot

As an alternative to Buttiker's dephasing lead model, we examine a dephasing stub. Both models are phenomenological ways to introduce decoherence in chaotic scattering by a quantum dot. The difference is that the dephasing lead opens up the quantum dot by connecting it to an electron reservoir, while the dephasing stub is closed at one end. Voltage fluctuations in the stub take over the dephasing role from the reservoir. Because the quantum dot with dephasing lead is an open system, only expectation values of the current can be forced to vanish at low frequencies, while the outcome of an individual measurement is not so constrained. The quantum dot with dephasing stub, in contrast, remains a closed system with a vanishing low-frequency current at each and every measurement. This difference is a crucial one in the context of quantum algorithms, which are based on the outcome of individual measurements rather than on expectation values. We demonstrate that the dephasing stub model has a parameter range in which the voltage fluctuations are sufficiently strong to suppress quantum interference effects, while still being sufficiently weak that classical current fluctuations can be neglected relative to the nonequilibrium shot noise.Comment: 8 pages with 1 figure; contribution for the special issue of J.Phys.A on "Trends in Quantum Chaotic Scattering

Phytometric intelligence sensors

Methods and apparatus for determining when plants require watering, and methods of attending to the watering of plants including signaling the grower that the plants are in need of hydration are provided. The novel methods include real-time measurement of plant metabolics and phytometric physiology changes of intrinsic physical or behavioral traits within the plant such as determining physiological flux measurement of enzyme flux due to environmental changes such as the wind and drought stress, soil and plant mineral deficiencies, or the interaction with a bio-control for organic disease control including, cell movement, signal transduction, internal chemical processes and external environmental processes including when plants require watering, and methods of attending to the watering of plants including signaling the grower that the plants are in need of hydration

Electron fractionalization induced dephasing in Luttinger liquids

Using the appropriate fractionalization mechanism, we correctly derive the temperature (T) and interaction dependence of the electron lifetime $\tau_F$ in Luttinger liquids. For strong enough interactions, we report that $(T\tau_F)\propto g$, with $g\ll 1$ being the standard Luttinger exponent; This reinforces that electrons are {\it not} good quasiparticles. We immediately emphasize that this is of importance for the detection of electronic interferences in ballistic 1D rings and carbon nanotubes, inducing ``dephasing'' (strong reduction of Aharonov-Bohm oscillations).Comment: 5 pages, 1 figure (Final version for PRB Brief Report

Binary pattern tile set synthesis is NP-hard

In the field of algorithmic self-assembly, a long-standing unproven conjecture has been that of the NP-hardness of binary pattern tile set synthesis (2-PATS). The $k$-PATS problem is that of designing a tile assembly system with the smallest number of tile types which will self-assemble an input pattern of $k$ colors. Of both theoretical and practical significance, $k$-PATS has been studied in a series of papers which have shown $k$-PATS to be NP-hard for $k = 60$, $k = 29$, and then $k = 11$. In this paper, we close the fundamental conjecture that 2-PATS is NP-hard, concluding this line of study. While most of our proof relies on standard mathematical proof techniques, one crucial lemma makes use of a computer-assisted proof, which is a relatively novel but increasingly utilized paradigm for deriving proofs for complex mathematical problems. This tool is especially powerful for attacking combinatorial problems, as exemplified by the proof of the four color theorem by Appel and Haken (simplified later by Robertson, Sanders, Seymour, and Thomas) or the recent important advance on the Erd\H{o}s discrepancy problem by Konev and Lisitsa using computer programs. We utilize a massively parallel algorithm and thus turn an otherwise intractable portion of our proof into a program which requires approximately a year of computation time, bringing the use of computer-assisted proofs to a new scale. We fully detail the algorithm employed by our code, and make the code freely available online

Laser spectroscopy of hyperfine structure in highly-charged ions: a test of QED at high fields

An overview is presented of laser spectroscopy experiments with cold, trapped, highly-charged ions, which will be performed at the HITRAP facility at GSI in Darmstadt (Germany). These high-resolution measurements of ground state hyperfine splittings will be three orders of magnitude more precise than previous measurements. Moreover, from a comparison of measurements of the hyperfine splittings in hydrogen- and lithium-like ions of the same isotope, QED effects at high electromagnetic fields can be determined within a few percent. Several candidate ions suited for these laser spectroscopy studies are presented.Comment: 5 pages, 1 figure, 1 table. accepted for Canadian Journal of Physics (2006