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

Multiple-Resampling Receiver Design for OFDM Over Doppler-Distorted Underwater Acoustic Channels

Cataloged from PDF version of article.In this paper, we focus on orthogonal frequency-divisionmultiplexing (OFDM) receiver designs for underwater acoustic (UWA) channels with user- and/or path-specific Doppler scaling distortions. The scenario is motivated by the cooperative communications framework, where distributed transmitter/receiver pairs may experience significantly different Doppler distortions, as well as by the single-user scenarios, where distinct Doppler scaling factors may exist among different propagation paths. The conventional approach of front–end resampling that corrects for common Doppler scalingmay not be appropriatein such scenarios, rendering a post-fast-Fourier-transform (FFT) signal that is contaminated by user- and/or path-specific intercarrier interference. To counteract this problem, we propose a family of front–end receiver structures thatutilizemultiple-resampling (MR)branches,eachmatched to the Doppler scaling factor of a particular user and/or path. Following resampling, FFT modules transform the Doppler-compensated signals into the frequency domain for further processing through linear or nonlinear detection schemes. As part of the overall receiver structure, a gradient–descent approachis also proposed to refine the channel estimates obtained by standard sparse channel estimators. The effectiveness and robustness of the proposed receivers are demonstrated via simulations, as well as emulations based on real data collected during the 2010 Mobile Acoustic Communications Experiment (MACE10, Martha’s Vineyard, MA) and the 2008 Kauai Acomms MURI (KAM08, Kauai, HI) experiment

Supplementary Feeding of Grazing Dairy Cows

The objective of this paper was to consider the effect of supplementary feeding of grazing dairy cows on dry matter intake (DMI), milk production and milk composition. Accurate estimations of total DMI and pasture DMI are important to the management of dairy grazing systems. The intakes of dry matter (DM) and net energy-NEL are lower on the pasture-only diet compared with cows supplementary fed with concentrate. Many pasture factors affect DMI, including pregrazing pasture mass and pasture allowance. Milk production of high producing grazing dairy cows in early lactation increases linearly as the amount of concentrate increases to 10 kg DM/day with a milk response of 1 kg milk/kg concentrate. In late lactation, increases are with a lower milk response per kilogram of supplemented concentrate. With the amount of concentrate supplementation, milk fat and protein yield increase while milk fat percentage decreases. Supplementation with rumen undegradable protein (RUP) is important for meeting requirements of grazing dairy cows, because the pasture has high ruminal crude protein (CP) degradability. Corn silage supplementation to grazing cows may increase milk production if pasture offered is restricted, but if pasture is offered ad libitum milk production does not change or can decrease. Supplementation of ruminally inert fat could have positive effect on milk production with concentrate supplemented at a lower rate

Influence of the Main Filter on QRS-amplitude and Duration in Human Electrocardiogram.

Accurate measurement of electrocardiograms (ECG) is critical for effective diagnosis of patient’s cardiac functions. Detailed examination of filters’ effects on ECG accuracy, reproducibility and robustness covering a wide range of available commercial products can provide valuable information on the relationship between quality and effectiveness of filters, and assessments of patients’ cardiac functions. In this study, ECG device with 12 leads and built-in filters used for ECG measurements was assessed on human volunteers. Results showed that with respect to measuring QRS wave duration and R-amplitude variation, there was a 4 % inaccuracy when the main filter was ON and OFF, and R-amplitude variation was most pronounced in the V4 lead. Accordingly, variability of R-amplitude and length of QRS wave can be reduced by the use of appropriate lead, and filter activation during the ECG assessment

Morphological Characteristics of Breast and Thigh Muscles of Autochthonous Breeds of Chickens

Morphological characteristics of skeletal muscles of autochthonous breeds of chickens are very important for meat quality and comparison with current hybrids for intensive production. The autochthonous breeds used in the experiment were Sombor crested and Banat naked neck, both sexes. For the purposes of morphological examination, tissue samples were taken from the thigh muscle (m. biceps femoris) and muscles of the breast (m. pectoralis profundus) of 5 male and female animals of each breed. After a standard histological procedure for conventional light microscopy, samples were stained with hematoxylin - eosin. After the processing of the samples for the histochemical analysis, samples were stained with the enzyme succinate - dehydrogenase (SDH) with the aim of determining the presence of different muscle cell types (red, white and intermediate). Morphological parameters, in this study, were diameter of muscle cells, nucleocytoplasmic ratio of muscle cells, volume density of connective tissue within the muscle and the presence of red, white and intermediate muscle cell types. Comparison of diameters of muscle cells thigh and breast muscles between Sombor crested and Banat naked neck have showed that kind of muscle, race or gender have no significant effect on the differences in this parameter. There were no statistically significant differences in the nucleo-cytoplasmic ratio of the volume density of the connective tissue of muscles. Red muscle cells were, in both autochthonous breeds, significantly more represented in m. biceps femoris than m. pectoralis profundus. The results of this study indicate that no differences were observed between autochthonous breeds in morphological parameters for examined breast and thigh muscle

Entanglement dynamics of two qubits under the influence of external kicks and Gaussian pulses

We have investigated the dynamics of entanglement between two spin-1/2 qubits that are subject to independent kick and Gaussian pulse type external magnetic fields analytically as well as numerically. Dyson time ordering effect on the dynamics is found to be important for the sequence of kicks. We show that "almost-steady" high entanglement can be created between two initially unentangled qubits by using carefully designed kick or pulse sequences