Models and information-theoretic bounds for nanopore sequencing

Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore sequencers can acquire long reads, the high error rates (20%-30%) pose a technical challenge. In a nanopore sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the "channel" from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore sequencer. This model incorporates impairments like (non-linear) inter-symbol interference, deletions, as well as random response. These information bounds have two-fold application: (1) The decoding rate with a uniform input distribution can be used to calculate the average size of the plausible list of DNA sequences given an observed current trace. This bound can be used to benchmark existing base-calling algorithms, as well as serving a performance objective to design better nanopores. (2) When the nanopore sequencer is used as a reader in a DNA storage system, the storage capacity is quantified by our bounds

Spectral Efficiency Optimization in Flexi-Grid Long-Haul Optical Systems

Flexible grid optical networks allow a better exploitation of fiber capacity, by enabling a denser frequency allocation. A tighter channel spacing, however, requires narrower filters, which increase linear intersymbol interference (ISI), and may dramatically reduce system reach. Commercial coherent receivers are based on symbol by symbol detectors, which are quite sensitive to ISI. In this context, Nyquist spacing is considered as the ultimate limit to wavelength-division multiplexing (WDM) packing. In this paper, we show that by introducing a limited-complexity trellis processing at the receiver, either the reach of Nyquist WDM flexi-grid networks can be significantly extended, or a denser-than-Nyquist channel packing (i.e., a higher spectral efficiency (SE)) is possible at equal reach. By adopting well-known information-theoretic techniques, we design a limited-complexity trellis processing and quantify its SE gain in flexi-grid architectures where wavelength selective switches over a frequency grid of 12.5GHz are employed.Comment: 7 pages, 9 figure

Adaptive Molecule Transmission Rate for Diffusion Based Molecular Communication

In this paper, a simple memory limited transmitter for molecular communication is proposed, in which information is encoded in the diffusion rate of the molecules. Taking advantage of memory, the proposed transmitter reduces the ISI problem by properly adjusting its diffusion rate. The error probability of the proposed scheme is derived and the result is compared with the lower bound on error probability of the optimum transmitter. It is shown that the performance of introduced transmitter is near optimal (under certain simplifications). Simplicity is the key feature of the presented communication system: the transmitter follows a simple rule, the receiver is a simple threshold decoder and only one type of molecule is used to convey the information

Application of Expurgated PPM to Indoor Visible Light Communications - Part I: Single-User Systems

Visible light communications (VLC) in indoor environments suffer from the limited bandwidth of LEDs as well as from the inter-symbol interference (ISI) imposed by multipath. In this work, transmission schemes to improve the performance of indoor optical wireless communication (OWC) systems are introduced. Expurgated pulse-position modulation (EPPM) is proposed for this application since it can provide a wide range of peak to average power ratios (PAPR) needed for dimming of the indoor illumination. A correlation decoder used at the receiver is shown to be optimal for indoor VLC systems, which are shot noise and background-light limited. Interleaving applied on EPPM in order to decrease the ISI effect in dispersive VLC channels can significantly decrease the error probability. The proposed interleaving technique makes EPPM a better modulation option compared to PPM for VLC systems or any other dispersive OWC system. An overlapped EPPM pulse technique is proposed to increase the transmission rate when bandwidth-limited white LEDs are used as sources.Comment: Journal of Lightwave Technolog

Nonlinearity Mitigation in WDM Systems: Models, Strategies, and Achievable Rates

After reviewing models and mitigation strategies for interchannel nonlinear interference (NLI), we focus on the frequency-resolved logarithmic perturbation model to study the coherence properties of NLI. Based on this study, we devise an NLI mitigation strategy which exploits the synergic effect of phase and polarization noise compensation (PPN) and subcarrier multiplexing with symbol-rate optimization. This synergy persists even for high-order modulation alphabets and Gaussian symbols. A particle method for the computation of the resulting achievable information rate and spectral efficiency (SE) is presented and employed to lower-bound the channel capacity. The dependence of the SE on the link length, amplifier spacing, and presence or absence of inline dispersion compensation is studied. Single-polarization and dual-polarization scenarios with either independent or joint processing of the two polarizations are considered. Numerical results show that, in links with ideal distributed amplification, an SE gain of about 1 bit/s/Hz/polarization can be obtained (or, in alternative, the system reach can be doubled at a given SE) with respect to single-carrier systems without PPN mitigation. The gain is lower with lumped amplification, increases with the number of spans, decreases with the span length, and is further reduced by in-line dispersion compensation. For instance, considering a dispersion-unmanaged link with lumped amplification and an amplifier spacing of 60 km, the SE after 80 spans can be be increased from 4.5 to 4.8 bit/s/Hz/polarization, or the reach raised up to 100 spans (+25%) for a fixed SE.Comment: Submitted to Journal of Lightwave Technolog

Molecular communication in fluid media: The additive inverse Gaussian noise channel

We consider molecular communication, with information conveyed in the time of release of molecules. The main contribution of this paper is the development of a theoretical foundation for such a communication system. Specifically, we develop the additive inverse Gaussian (IG) noise channel model: a channel in which the information is corrupted by noise with an inverse Gaussian distribution. We show that such a channel model is appropriate for molecular communication in fluid media - when propagation between transmitter and receiver is governed by Brownian motion and when there is positive drift from transmitter to receiver. Taking advantage of the available literature on the IG distribution, upper and lower bounds on channel capacity are developed, and a maximum likelihood receiver is derived. Theory and simulation results are presented which show that such a channel does not have a single quality measure analogous to signal-to-noise ratio in the AWGN channel. It is also shown that the use of multiple molecules leads to reduced error rate in a manner akin to diversity order in wireless communications. Finally, we discuss some open problems in molecular communications that arise from the IG system model.Comment: 28 pages, 8 figures. Submitted to IEEE Transactions on Information Theory. Corrects minor typos in the first versio