The thermodynamic binding networks (TBN) model [Breik et al., 2021] is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition, focusing on two key determinants of a system’s energetics common to any chemical substrate: how many molecular bonds are formed, and how many separate complexes exist in the system. We formulate as an integer program the NP-hard problem of computing stable (a.k.a., minimum energy) configurations of a TBN: those configurations that maximize the number of bonds and complexes. We provide open-source software solving this integer program. We give empirical evidence that this approach enables dramatically faster computation of TBN stable configurations than previous approaches based on SAT solvers [Breik et al., 2019]. Furthermore, unlike SAT-based approaches, our integer programming formulation can reason about TBNs in which some molecules have unbounded counts. These improvements in turn allow us to efficiently automate verification of desired properties of practical TBNs. Finally, we show that the TBN has a natural representation with a unique Hilbert basis describing the "fundamental components" out of which locally minimal energy configurations are composed. This characterization helps verify correctness of not only stable configurations, but entire "kinetic pathways" in a TBN.

We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions ƒ:Nd→ N. We consider output-oblivious CRNs in which the output species is never a reactant (input) to any reaction. The class of output-oblivious CRNs is fundamental, appearing in earlier studies of CRN computation, because it is precisely the class of CRNs that can be composed by simply renaming the output of the upstream CRN to match the input of the downstream CRN.

Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers seems to require knowledge of the specific molecular substrate, we develop a novel substrate-independent approach. We extend the recently-developed model known as thermodynamic binding networks, demonstrating programmable kinetic barriers that arise solely from the thermodynamic driving forces of bond formation and the configurational entropy of forming separate complexes. Our kinetic model makes relatively weak assumptions, which implies that energy barriers predicted by our model would exist in a wide variety of systems and conditions. We demonstrate that our model is robust by showing that several variations in its definition result in equivalent energy barriers. We apply this model to design catalytic systems with an arbitrarily large energy barrier to uncatalyzed reactions. Our results could yield robust amplifiers using DNA strand displacement, a popular technology for engineering synthetic reaction pathways, and suggest design strategies for preventing undesired kinetic behavior in a variety of molecular systems.

In this paper, we propose a generalized framework for local clustering based on isoperimetric inequalities. We also demonstrate that contemporary approaches are included in its scope and that it can accommodate data sets of different types, including those with overlapping communities. We then present an efficient, greedy algorithm using the new framework and compare the output of the new algorithm with existing methods.

By exploiting superimposed signals at relays, physicallayer network coding (PNC) could significantly improve the throughput of wireless communications systems. However, it is challenging to achieve perfect synchronization between superimposed signals at the relay. In this paper, we propose an approach to resolve the issue of frame-misalignment in PNC using type-I Euclidean geometry low-density parity-check (EG-LDPC) codes with cyclic prefix or zero padding. To estimate the arrival delay between two transmitted signals at the relay, Gold sequences are adopted as pilot sequences in our transmit frames. Simulation results show that our approach can effectively resolve the frame-misalignment issue in PNC.

In this paper we investigate the interactions between antenna orientations, propagation link geometry and Faraday rotation for a line-of-sight VHF satellite communication link. A key contribution is development of a three dimensional (3D) equivalent baseband model that incorporates link geometry, antenna radiation patterns and the rotation of the polarization of the radio wave as it passes through the electron plasma of the ionosphere in the presence of Earth's magnetic field. Through simulations of an overhead pass for a low earth orbit (LEO) satellite in night and day ionospheric conditions, we characterize the combined effect of the link geometry and Faraday rotation. We show that Faraday rotation may in fact improve the channel quality. The power transferred from transmitter to receiver including Faraday rotation can be greater than that for a link with no Faraday effects. This occurs when the antenna orientation at the receiver is favourably aligned with the rotated polarization of the incoming radio wave.

To improve energy efficiency in low power short-range communication systems such as Wireless Sensor Networks (WSNs) and Wireless Body Area Networks (WBANs), adaptive techniques have been proposed to adjust the transmit waveforms according to the channel conditions. The estimation of channel quality, such as Signal-to-Noise Ratio (SNR), plays an important role in the waveform switching. Errors introduced by the estimation result in wrong decisions on transmit mode, which would further affect the overall energy efficiency. In this paper, we consider a low power system that adopts Link Adaptation (LA) switching between multiple modulation schemes. We point out that the decision of switch between different modulations only requires the knowledge of whether the SNR falls into a certain range, rather than that of an exact value. Therefore we propose a novel SNR estimation and decision making framework based on Hypothesis Testing (HT) theory. This framework provides a generic way to both evaluate and control the probabilities of different types of estimation errors. Hence approach can be adjusted for different applications to improve energy efficiency by reducing the probability of the errors associated with significant energy cost. We also highlight that the conventional estimation method is a special case of the proposed framework.

In systems with parallel analogue-to-digital converters (ADC), diversity combining can improve the signal to noise ratio (SNR) of the digitised signal. We consider a novel architecture, where the parallel ADCs operate on differently attenuated signals, in conjunction with maximal ratio combining and gain weighted combining. Both schemes reduce the effective quantization noise and provide significant SNR improvements over a single ADC and signal averaging, which takes the unweighted average of the ADC output signals. The key to achieving these SNR gains is to carefully select branch attenuations that lead to negative correlation of the quantization noise across branches.

The mobile outdoor radio environment is challenging for vehicular communications. Although multipath propagation offers diversity and benefits in non-line-of-sight (NLOS) conditions, simultaneous multipath and mobility results in a doubly-selective fading channel. In practice, this means that the channel parameters vary significantly in both time and frequency within the bandwidth and typical packet durations used in 802.11p/WAVE standards for short-range vehicular communications. This paper presents the results of extensive field trial campaigns conducted in several countries, totaling over 1100 km. These field trials are scenario based, focusing on challenging low-latency, high-reliability vehicle-to-vehicle (V2V) safety applications including intersection collision warning, turn across path, emergency electronic brake light, do not pass warning, and precrash sensing. Vehicle-to-infrastructure (V2I) applications are also considered. The field trials compared the performance of off-the-shelf WiFi-based radio equipment with a more advanced 802.11p compliant radio employing more sophisticated channel estimation and tracking. Field trial results demonstrate significantly improved performance using the advanced radio, translating into greatly increased driver warning times and stopping distances. In fact the results show that off-the-shelf WiFi equipment fails to provide sufficient stopping distance to avert accidents in some cases. During the field trials, channel sounding data were also captured. Analysis of these channel measurements reveals the critical importance of accurate channel estimation, tracking the channel in both time and frequency within each packet. Delay spread and Doppler spread statistics computed from the channel measurements validate previously reported results in the literature. The results in this paper, however, provide the first instance of channel measurements performed simultaneously to application performance evaluation. The objective is to firmly establish the link between radio channel characteristics and the performance of critical V2V safety applications.

Low-density parity-check (LDPC) codes may be decoded using a circuit implementation of the sum-product algorithm which maps the factor graph of the code. By reusing the decoder for encoding, both tasks can be performed using the same circuit, thus reducing area and verification requirements. Motivated by this, iterative encoding techniques based upon the graphical representation of the code are proposed. Code design constraints which ensure encoder convergence are presented, and then used to design iteratively encodable codes, while also preventing 4-cycle creation. We show how the Jacobi method for iterative matrix inversion can be applied to finite field matrices, viewed as message passing, and employed as the core of an iterative encoder. We present an algebraic construction of4-cycle free iteratively encodable codes using circulant matrices. Analysis of these codes identifies a weakness in their structure, due to a repetitive pattern in the factor graph. The graph supports pseudo-codewords of low pseudo-weight. In order to remove the repetitive pattern in the graph, we propose a recursive technique for generating iteratively encodable codes. The new codes offer flexibility in the choice of code length and rate, and performance that compares well to randomly generated, quasi-cyclic and extended Euclidean-geometry codes.

We provide a thorough analysis for a class of iteratively encodable low-density parity-check codes. The iterative encoding technique is based upon the graphical representation of the code and allows the decoder circuit to also be used for encoding, thus saving circuit area. The analysis identifies a weakness in the structure of the code, which arises due to a repetitive pattern in its factor graph. We show that the graph supports pseudo-codewords of low pseudo-weight, and relate this to the empirical observation of some near-codewords. We then propose a new recursive technique for constructing iteratively encodable codes which have improved expansion. The new codes offer a large amount of flexibility in the choice of code length and rate, and performance that compares well to both randomly generated and extended Euclidean-geometry codes

Motivated by the potential to reuse the decoder architecture, and thus reduce circuit space, we explore the use of iterative encoding techniques which are based upon the graphical representation of the code. We design codes by identifying associated encoder convergence constraints and also eliminating some well known undesirable properties for sum-product decoding such as 4-cycles. In particular we show how the Jacobi method for iterative matrix inversion can be viewed as message passing and employed as the core of an iterative encoder. Example constructions of both regular and irregular LDPC codes that are encodable using this method are investigated.