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This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used in the sequencing pipeline in order to allow the perpetrators to gain control over the resources used in that pipeline during sequence analysis. The scenario considered in the paper is based on perpetrators submitting synthetically engineered DNA samples that contain digitally encoded IP address and port number of the perpetrators machine in the DNA. Genetic analysis of the samples DNA will decode the address that is used by the software trojan malware to activate and trigger a remote connection. This approach can open up to multiple perpetrators to create connections to hijack the DNA sequencing pipeline. As a way of hiding the data, the perpetrators can avoid detection by encoding the address to maximise similarity with genuine DNAs, which we showed previously. However, in this paper we show how Deep Learning can be used to successfully detect and identify the trigger encoded data, in order to protect a DNA sequencing pipeline from trojan attacks. The result shows nearly up to 100% accuracy in detection in such a novel Trojan attack scenario even after applying fragmentation encryption and steganography on the encoded trigger data. In addition, feasibility of designing and synthesizing encoded DNA for such Trojan payloads is validated by a wet lab experiment.

In this paper we consider the influence of intercellular communication on the development and progression of Glioblastoma Multiforme (GBM), a grade IV malignant glioma which is defined by an interplay Grow i.e. self renewal and Go i.e. invasiveness potential of multiple malignant glioma stem cells. Firstly, we performed wet lab experiments with U87 malignant glioma cells to study the node-stem growth pattern of GBM. Next we develop a model accounting for the structural influence of multiple transmitter and receiver glioma stem cells resulting in the node-stem growth structure of GBM tumour. By using information theory we study different properties associated with this communication model to show that the growth of GBM in a particular direction (node to stem) is related to an increase in mutual information. We further show that information flow between glioblastoma cells for different levels of invasiveness vary at different points between node and stem. These findings are expected to contribute significantly in the design of future therapeutic mechanisms for GBM., Comment: 7 pages, 10 Figures- Submitted for possible publication in IEEE Conference

In this paper we show how inter-cellular molecular communication may change the overall levels of photosynthesis in plants. Individual plant cells respond to external stimuli, such as illumination levels, to regulate their photosynthetic output. Here, we present a mathematical model which shows that by sharing information internally using molecular communication, plants may increase overall photosynthate production. Numerical results show that higher mutual information between cells corresponds to an increase in overall photosynthesis by as much as 25 per cent. This suggests that molecular communication plays a vital role in maximising the photosynthesis in plants and therefore suggests new routes to influence plant development in agriculture and elsewhere., Comment: 6 pages, 6 figures- Submitted for Publication in IEEE Transactions on Molecular, Biological and Multi-scale Sciences

Both action potentials and mechanosensitive signalling are an important communication mechanisms in plants. Considering an information theoretic framework, this paper explores the effective range of multiple action potentials for a long chain of cells (i.e., up to 100) in different configurations, and introduces the study of multiple mechanosensitive activation signals (generated due to a mechanical stimulus) in plants. For both these signals, we find that the mutual information per cell and information propagation speed tends to increase up to a certain number of receiver cells. However, as the number of cells increase beyond 10 to 12, the mutual information per cell starts to decrease. To validate our model and results, we include an experimental verification of the theoretical model, using a PhytlSigns biosignal amplifier, allowing us to measure the magnitude of the voltage associated with the multiple AP and mechanosensitive activation signals induced by different stimulus in plants. Experimental data is used to calculate the mutual information and information propagation speed, which is compared with corresponding numerical results. Since these signals are used for a variety of important tasks within the plant, understanding them may lead to new bioengineering methods for plants., Comment: 12 Pages, 15 Figures, Accepted for Publication in IEEE Transactions on NanoBioscience

This work builds on our earlier work on designing demodulators for diffusion-based molecular communications using a Markovian approach. The demodulation filters take the form of an ordinary differential equation (ODE) which computes the log-posteriori probability of observing a transmission symbol given the continuous history of receptor activities. A limitation of our earlier work is that the receiver is assumed to be a small cubic volume called a voxel. In this work, we extend the maximum a-posteriori demodulation to the case where the receiver may consist of multiple voxels and derive the ODE for log-posteriori probability calculation. This extension allows us to study receiver behaviour of different volumes and shapes. In particular, it also allows us to consider spatially partitioned receivers where the chemicals in the receiver are not allowed to mix. The key result of this paper is that spatial partitioning can be used to reduce bit-error rate in diffusion-based molecular communications., Comment: 39 pages, 20 figures, submitted for possible publication in IEEE

Many plants, such as Mimosa pudica (the sensitive plant), employ electrochemical signals known as action potentials (APs) for rapid intercellular communication. In this paper, we consider a reaction diffusion model of individual AP signals to analyze APs from a communication and information theoretic perspective. We use concepts from molecular communication to explain the underlying process of information transfer in a plant for a single AP pulse that is shared with one or more receiver cells. We also use the chemical Langevin equation to accommodate the deterministic as well as stochastic component of the system. Finally we present an information theoretic analysis of single action potentials, obtaining achievable information rates for these signals. We show that, in general, the presence of an AP signal can increase the mutual information and information propagation speed among neighboring cells with receivers in different settings., Comment: 13 Pages, 15 Figures, Accepted for Publication in IEEE Transactions on NanoBioscience

This paper considers an electro-chemical based communication model for intercellular communication in plants. Many plants, such as Mimosa pudica (the "sensitive plant"), employ electrochemical signals known as action potentials (APs) for communication purposes. In this paper we present a simple model for action potential generation. We make use of the concepts from molecular communication to explain the underlying process of information transfer in a plant. Using the information-theoretic analysis, we compute the mutual information between the input and output in this work. The key aim is to study the variations in the information propagation speed for varying number of plant cells for one simple case. Furthermore we study the impact of the AP signal on the mutual information and information propagation speed. We aim to explore further that how the growth rate in plants can impact the information transfer rate and vice versa., Comment: 6 pages, 5 Figures, Submitted to IEEE Conference, 2018

This paper considers the capacity of a diffusion-based molecular communication link assuming the receiver uses chemical reactions. The key contribution is we show that enzymatic reaction cycles, which is a class of chemical reactions commonly found in cells consisting of a forward and a backward enzymatic reaction, can improve the capacity of the communication link. The technical difficulty in analysing enzymatic reaction cycles is that their reaction rates are nonlinear. We deal with this by assuming that the amount of certain chemicals in the enzymatic reaction cycle is large. In order to simplify the problem further, we use singular perturbation to study a particular operating regime of the enzymatic reaction cycles. This allows us to derive a closed-form expression of the channel gain. This expression suggests that we can improve the channel gain by increasing the total amount of substrate in the enzymatic reaction cycle. By using numerical calculations, we show that the effect of the enzymatic reaction cycle is to increase the channel gain and to reduce the noise, which results in a better signalto- noise ratio and in turn a higher communication capacity. Furthermore, we show that we can increase the capacity by increasing the total amount of substrate in the enzymatic reaction cycle., Comment: 38 Pages, 10 Figures

This paper considers a diffusion-based molecular communication system where the transmitter uses Reaction Shift Keying (RSK) as the modulation scheme. We focus on the demodulation of RSK signal at the receiver. The receiver consists of a front-end molecular circuit and a back-end demodulator. The front-end molecular circuit is a set of chemical reactions consisting of multiple chemical species. The optimal demodulator computes the posteriori probability of the transmitted symbols given the history of the observation. The derivation of the optimal demodulator requires the solution to a specific Bayesian filtering problem. The solution to this Bayesian filtering problem had been derived for a few specific molecular circuits and specific choice(s) of observed chemical species. The derivation of such solution is also lengthy. The key contribution of this paper is to present a general solution to this Bayesian filtering problem which can be applied to any molecular circuit and any choice of observed species., Comment: 34 Pages , 9 Figures