IEEE Transactions on Molecular, Biological, and Multi-Scale Communications 

About: IEEE Transactions on Molecular, Biological, and Multi-Scale Communications is an academic journal published by Institute of Electrical and Electronics Engineers. The journal publishes majorly in the area(s): Molecular communication & Computer science. It has an ISSN identifier of 2332-7804. Over the lifetime, 205 publications have been published receiving 3236 citations. The journal is also known as: Transactions on molecular, biological, and multi-scale communications & IEEE Trans Mol Biol Multiscale Commun.

Inferring Biological Networks by Sparse Identification of Nonlinear Dynamics

Abstract: Inferring the structure and dynamics of network models is critical to understanding the functionality and control of complex systems, such as metabolic and regulatory biological networks. The increasing quality and quantity of experimental data enable statistical approaches based on information theory for model selection and goodness-of-fit metrics. We propose an alternative data-driven method to infer networked nonlinear dynamical systems by using sparsity-promoting optimization to select a subset of nonlinear interactions representing dynamics on a network. In contrast to standard model selection methods-based upon information content for a finite number of heuristic models (order 10 or less), our model selection procedure discovers a parsimonious model from a combinatorially large set of models, without an exhaustive search. Our particular innovation is appropriate for many biological networks, where the governing dynamical systems have rational function nonlinearities with cross terms, thus requiring an implicit formulation and the equations to be identified in the null-space of a library of mixed nonlinearities, including the state and derivative terms. This method, implicit-SINDy, succeeds in inferring three canonical biological models: 1) Michaelis-Menten enzyme kinetics; 2) the regulatory network for competence in bacteria; and 3) the metabolic network for yeast glycolysis.

DNA-Based Storage: Trends and Methods

Abstract: We provide an overview of current approaches to DNA-based storage system design and of accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage channels. The analytic contribution of our work is the construction and design of sequences over discrete alphabets that avoid pre-specified address patterns, have balanced base content, and exhibit other relevant substring constraints. These schemes adapt the stored signals to the DNA medium and thereby reduce the inherent error-rate of the system.

ISI Mitigation Techniques in Molecular Communication

Abstract: Molecular communication via diffusion (MCvD) is a new field of communication where molecules are used to transfer information. One of the main challenges in MCvD is the intersymbol interference (ISI), which inhibits communication at high data rates. Furthermore, at nanoscale, energy efficiency becomes an essential problem. Before addressing these problems, a pre-determined threshold for the received signal must be calculated to make a decision. In this paper, an analytical technique is proposed to determine the optimum threshold, whereas in the literature, these thresholds are calculated empirically. Since the main goal of this paper is to build an MCvD system suitable for operating at high data rates without sacrificing quality, new modulation and filtering techniques are proposed to decrease the effects of ISI and enhance energy efficiency. As a transmitter-based solution, a modulation technique, molecular transition shift keying (MTSK), is proposed in order to increase the data rate by suppressing ISI. Furthermore, for energy efficiency, a power adjustment technique that utilizes the residual molecules is proposed. Finally, as a receiver-based solution, a new energy efficient decision feedback filter (DFF) is proposed as a substitute for the conventional decoders in the literature. The error performance of DFF and MMSE equalizers are compared in terms of bit error rates, and it is concluded that DFF may be more advantageous when energy efficiency is concerned, due to its lower computational complexity.

Information Theory of Molecular Communication: Directions and Challenges

Abstract: Molecular communication (MC) is a communication strategy that uses molecules as carriers of information, and is widely used by biological cells. As an interdisciplinary topic, it has been studied by biologists, communication theorists and a growing number of information theorists. This paper aims to specifically bring MC to the attention of information theorists. To do this, we first highlight the unique mathematical challenges of studying the capacity of molecular channels. Addressing these problems requires use of known, or development of new mathematical tools. Toward this goal, we review a subjective selection of the existing literature on information theoretic aspect of MC The emphasis here is on the mathematical techniques used, rather than on the setup or modeling of a specific paper. Finally, as an example, we propose a concrete information theoretic problem that was motivated by our study of MC.

Molecular Versus Electromagnetic Wave Propagation Loss in Macro-Scale Environments

Abstract: Molecular communications (MC) has been studied as a bio-inspired information carrier for micro-scale and nano-scale environments. On the macro-scale, it can also be considered as an alternative to electromagnetic (EM) wave based systems, especially in environments where there is significant attenuation to EM wave power. This paper goes beyond the unbounded free space propagation to examine three macro-scale environments: the pipe, the knife edge, and the mesh channel. Approximate analytical expressions shown in this paper demonstrate that MC has an advantage over EM wave communications when: 1) the EM frequency is below the cut-off frequency for the pipe channel, 2) the EM wavelength is considerably larger than the mesh period, and 3) when the receiver is in the high diffraction loss region of an obstacle.