Collective oscillation period of inter-coupled biological negative cyclic feedback oscillators

A number of biological rhythms originate from networks comprised of multiple cellular oscillators. But analytical results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has been reported, may be different from that of an autonomous oscillator. Based on cyclic feedback oscillators, we analyze the collective oscillation pattern of coupled cellular oscillators. First we give a condition under which the oscillator network exhibits oscillatory and synchronized behavior. Then we estimate the collective oscillation period based on a novel multivariable harmonic balance technique. Analytical results are derived in terms of biochemical parameters, thus giving insight into the basic mechanism of biological oscillation and providing guidance in synthetic biology design.Comment: arXiv admin note: substantial text overlap with arXiv:1203.125

Advanced Algorithms for Satellite Communication Signal Processing

Dizertační práce je zaměřena na softwarově definované přijímače určené k úzkopásmové družicové komunikaci. Komunikační kanály družicových spojů zahrnujících komunikaci s hlubokým vesmírem jsou zatíženy vysokými úrovněmi šumu, typicky modelovaného AWGN, a silným Dopplerovým posuvem signálu způsobeným mimořádnou rychlostí pohybu objektu. Dizertační práce představuje možné postupy řešení výpočetně efektivní digitální downkonverze úzkopásmových signálů a systému odhadu kmitočtu nosné úzkopásmových signálů zatížených Dopplerovým posuvem v řádu násobků šířky pásma signálu. Popis navrhovaných algoritmů zahrnuje analytický postup jejich vývoje a tam, kde je to možné, i analytické hodnocení jejich chování. Algoritmy jsou modelovány v prostředí MATLAB Simulink a tyto modely jsou využity pro ověření vlastností simulacemi. Modely byly také využity k experimentálním testům na reálném signálu přijatém z družice PSAT v laboratoři experimentálních družic na ústavu radioelektroniky.The dissertation is focused on software defined receivers intended for narrowband satellite communication. The satellite communication channel including deep space communication suffers from a high level of noise, typically modeled by AWGN, and from a strong Doppler shift of a signal caused by the unprecedented speed of an object in motion. The dissertation shows possible approaches to the issues of computationally efficient digital downconversion of narrowband signals and the carrier frequency estimation of narrowband signals distorted by the Doppler shift in the order of multiples of the signal bandwidth. The description of the proposed algorithms includes an analytical approach of its development and, if possible, the analytical performance assessment. The algorithms are modeled in MATLAB Simulink and the models are used for validating the performance by the simulation. The models were also used for experimental tests on the real signal received from the PSAT satellite at the laboratory of experimental satellites at the department of radio electronics.

Data optimizations for constraint automata

Constraint automata (CA) constitute a coordination model based on finite automata on infinite words. Originally introduced for modeling of coordinators, an interesting new application of CAs is implementing coordinators (i.e., compiling CAs into executable code). Such an approach guarantees correctness-by-construction and can even yield code that outperforms hand-crafted code. The extent to which these two potential advantages materialize depends on the smartness of CA-compilers and the existence of proofs of their correctness. Every transition in a CA is labeled by a "data constraint" that specifies an atomic data-flow between coordinated processes as a first-order formula. At run-time, compiler-generated code must handle data constraints as efficiently as possible. In this paper, we present, and prove the correctness of two optimization techniques for CA-compilers related to handling of data constraints: a reduction to eliminate redundant variables and a translation from (declarative) data constraints to (imperative) data commands expressed in a small sequential language. Through experiments, we show that these optimization techniques can have a positive impact on performance of generated executable code

GPUVerify: A Verifier for GPU Kernels

We present a technique for verifying race- and divergence-freedom of GPU kernels that are written in mainstream ker-nel programming languages such as OpenCL and CUDA. Our approach is founded on a novel formal operational se-mantics for GPU programming termed synchronous, delayed visibility (SDV) semantics. The SDV semantics provides a precise definition of barrier divergence in GPU kernels and allows kernel verification to be reduced to analysis of a sequential program, thereby completely avoiding the need to reason about thread interleavings, and allowing existing modular techniques for program verification to be leveraged. We describe an efficient encoding for data race detection and propose a method for automatically inferring loop invari-ants required for verification. We have implemented these techniques as a practical verification tool, GPUVerify, which can be applied directly to OpenCL and CUDA source code. We evaluate GPUVerify with respect to a set of 163 kernels drawn from public and commercial sources. Our evaluation demonstrates that GPUVerify is capable of efficient, auto-matic verification of a large number of real-world kernels

Programmable rate modem utilizing digital signal processing techniques

The engineering development study to follow was written to address the need for a Programmable Rate Digital Satellite Modem capable of supporting both burst and continuous transmission modes with either binary phase shift keying (BPSK) or quadrature phase shift keying (QPSK) modulation. The preferred implementation technique is an all digital one which utilizes as much digital signal processing (DSP) as possible. Here design tradeoffs in each portion of the modulator and demodulator subsystem are outlined, and viable circuit approaches which are easily repeatable, have low implementation losses and have low production costs are identified. The research involved for this study was divided into nine technical papers, each addressing a significant region of concern in a variable rate modem design. Trivial portions and basic support logic designs surrounding the nine major modem blocks were omitted. In brief, the nine topic areas were: (1) Transmit Data Filtering; (2) Transmit Clock Generation; (3) Carrier Synthesizer; (4) Receive AGC; (5) Receive Data Filtering; (6) RF Oscillator Phase Noise; (7) Receive Carrier Selectivity; (8) Carrier Recovery; and (9) Timing Recovery