Molecular communication via diffusion (MCvD) is a molecular communication method that utilizes the free diffusion of carrier molecules to transfer information at the nano-scale. Due to the random propagation of carrier molecules, inter-symbol interference (ISI) is a major issue in an MCvD system. Alongside ISI, inter-link interference (ILI) is also an issue that increases the total interference for MCvD-based multiple-input-multipleoutput (MIMO) approaches. Inspired by the antenna index modulation (IM) concept in traditional communication systems, this paper introduces novel IM-based transmission schemes for MCvD systems. In the paper, molecular space shift keying (MSSK) is proposed as a novel modulation for molecular MIMO systems, and it is found that this method combats ISI and ILI considerably better than existing MIMO approaches. For nanomachines that have access to two different molecules, the direct extension of MSSK, quadrature molecular space shift keying (QMSSK) is also proposed. QMSSK is found to combat ISI considerably well whilst not performing well against ILI-caused errors. In order to combat ILI more effectively, another dualmolecule-based novel modulation scheme called the molecular spatial modulation (MSM) is proposed. Combined with the Gray mapping imposed on the antenna indices, MSM is observed to yield reliable error rates for molecular MIMO systems.

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