A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> This book is a lucid, straightforward introduction to the concepts and techniques of statistical physics that students of biology, biochemistry, and biophysics must know. It provides a sound basis for understanding random motions of molecules, subcellular particles, or cells, or of processes that depend on such motion or are markedly affected by it. Readers do not need to understand thermodynamics in order to acquire a knowledge of the physics involved in diffusion, sedimentation, electrophoresis, chromatography, and cell motility--subjects that become lively and immediate when the author discusses them in terms of random walks of individual particles. <s> BIB001 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Abstract The temporal and spatial evolution of the density of populations of chemotactic bacteria have previously been modeled by phenomenological cell balance equations based on cell motion restricted to one dimension. These one-dimensional balance equations have been used to interpret the results of experiments involving three-dimensional motion of bacterial populations with symmetry in two of the three dimensions. We develop a computer simulation to rigorously model the movement of a large population of individual chemotactic bacteria in three dimensions. Results of the simulation are compared with results using a one-dimensional phenomenological model in order to verify the range of validity of this model under situations involving one-dimensional gradients of chemical attractants. <s> BIB002 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Preface - Introduction - PART I: PHYSICAL PRINCIPLES - Mechanical Forces - Mass, Stiffness, and Damping of Proteins - Thermal Forces and Diffusion - Chemical Forces - Polymer Mechanics - PART II: CYTOSKELETON - Structures of Cytoskeletal Filaments - Mechanics of the Cytoskeleton - Polymerization of Cytoskeletal Filaments - Force Generation by Cytoskeletal Filaments - Active Polymerization - PART III: MOTOR PROTEINS - Structures of Motor Proteins - Speeds of Motors - ATP Hydrolysis - Steps and Forces - Motility Models: From Crossbridges to Motion - Afterword - Appendix - Bibliography - Index <s> BIB003 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> This review provides a comparative overview of recent developments in the modelling of cellular calcium oscillations. A large variety of mathematical models have been developed for this wide-spread phenomenon in intra- and intercellular signalling. From these, a general model is extracted that involves six types of concentration variables: inositol 1,4,5-trisphosphate (IP3), cytoplasmic, endoplasmic reticulum and mitochondrial calcium, the occupied binding sites of calcium buffers, and the fraction of active IP3 receptor calcium release channels. Using this framework, the models of calcium oscillations can be classified into ‘minimal’ models containing two variables and ‘extended’ models of three and more variables. Three types of minimal models are identified that are all based on calcium-induced calcium release (CICR), but differ with respect to the mechanisms limiting CICR. Extended models include IP3–calcium cross-coupling, calcium sequestration by mitochondria, the detailed gating kinetics of the IP3 receptor, and the dynamics of G-protein activation. In addition to generating regular oscillations, such models can describe bursting and chaotic calcium dynamics. The earlier hypothesis that information in calcium oscillations is encoded mainly by their frequency is nowadays modified in that some effect is attributed to amplitude encoding or temporal encoding. This point is discussed with reference to the analysis of the local and global bifurcations by which calcium oscillations can arise. Moreover, the question of how calcium binding proteins can sense and transform oscillatory signals is addressed. Recently, potential mechanisms leading to the coordination of oscillations in coupled cells have been investigated by mathematical modelling. For this, the general modelling framework is extended to include cytoplasmic and gap-junctional diffusion of IP3 and calcium, and specific models are compared. Various suggestions concerning the physiological significance of oscillatory behaviour in intra- and intercellular signalling are discussed. The article is concluded with a discussion of obstacles and prospects. <s> BIB004 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Molecular communication is engineered biological communication (e.g., cell-to-cell signaling) that allows nanomachines (e.g., engineered organisms, artificial devices) to communicate through chemical signals in an aqueous environment. This paper describes the design of a molecular communication system based on intercellular calcium signaling networks. This paper also describes possible functionalities (e.g., signal switching and aggregation) that may be achieved in such networks. <s> BIB005 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> 1. Introduction to Neuropsychology 1.1 Introduction to Neuropsychology 1.1.1 The 10% Myth 1.1.2 What is Neuropsychology? 1.1.3 Heart, Mind, and Brain: The Early History of Neuropsychology 1.1.4 The Mind-Body problem 1.2 The Recent History of Neuropsychology 1.2.1 Cataloguing the Effects of Lesions. 1.2.2 Focus on the Neuron. 1.2.3 The Brain Mappers. 1.2.4 Functional Neurosurgery. 1.2.5 The Paradigm Shift in Neuropsychology 2. Neuroanatomy 2.1 Cells of the Nervous System. 2.1.1 Neurons & Glia: Structure and Function 2.1.2 Communication within the Neuron: The Action Potential 2.1.3 Communication between Neurons: The Synapse 2.1.4 Neurotransmitters 2.2 The Nervous System. 2.2.1 Positional Terms 2.2.2. Divisions of the Nervous System 2.2.3 Spinal Cord.2.2.4 Divisions of the Brain 2.2.5 Hindbrain 2.2.6 Midbrain 2.2.7 Forebrain 2.2.8 Connections between the two halves of the brain 2.2.9 Cranial Nerves 2.2.10 Blood Supply 2.2.11 Protection 2.2.11.1 Bone 2.2.11.2 The Meninges 2.2.11.3 The Ventricular System 2.2.11.4 The Blood-Brain Barrier. 3. Techniques in Neuropsychology 3.1 Study of the damaged nervous system. 3.1.1. The Scientific Method 3.1.2 Non-human animal models 3.1.3 Cognitive testing. 3.2 Brain Imaging. 3.2.1 Structural Imaging 3.2.2 Electrophysiological Measures 3.2.3 Functional imaging 4. Laterality 4.1 Methods. 4.1.1 Split brain 4.1.2 Sodium Amytal 4.1.3 Dichotic Listening 4.1.4 Tachistoscopic Presentations 4.1.5 Dual Task Paradigms 4.2 Neuroanatomical, Neurochemical, and Behavioral Findings. 4.2.1 Neuroanatomical asymmetries 4.2.2 Neurochemical asymmetries 4.2.3 Functional asymmetries 4.3 Why is there Hemispheric Specialization? 4.3.1 Environmental theories 4.3.2 Genetic theories 4.3.3 Developmental theories 4.3.4 Evolutionary theories. 5. The Sensorimotor System 5.1 Sensorimotor System. 5.1.1 Why sensorimotor? 5.1.2 Somatosensory receptors 5.1.3. Somatosensory pathways in the brain 5.1.4 Association Cortex 5.1.5 Secondary Motor Cortex 5.1.6 Primary Motor Cortex 5.1.7 Basal Ganglia and Cerebellum. 5.1.8 Descending and Ascending Motor Pathways 5.2 Deficits in the Sensorimotor System. 5.2.1 Cortical Sensorimotor Disorders 5.2.2 Subcortical Motor Disorders 6. Sensation and Perception: Vision 6.1 Organization of sensory systems. 6.1.1 Hierarchical Organization 6.1.2 Segregation 6.1.3 Parallel Processing 6.2 Visual System. 6.2.1 Light: Stimulus for the visual system 6.2.2 The Eye and Retina 6.2.3 Retino-geniculate-striate system 6.2.4 Dorsal and Ventral Stream of Processing 6.3 Deficits in the Visual System. 6.3.1 Agnosia. 6.3.2 Optic Aphasia 6.3.3 Blindsight 7. Memory 7.1 Types of Memories. 7.1.1 Working Memory and Short-term Memory. 7.1.2 Long-term Memory 7.2 Disorders of Memory. 7.2.1 Amnesia: Retrograde and Anterograde 7.2.2 Dementias 8. Hearing and Language Processing 8.1 Auditory System. 8.1.1 Sound 8.1.2 The Ear 8.1.3 Auditory Pathways 8.1.4 Auditory Cortices 8.2 Language systems in the brain. 8.2.1 Models of Spoken Language 8.2.2 Models of Visual Language 8.2.3 Prosody and the Role of the Right Hemisphere in Language Processing. 8.2.4 Interim Summary 8.3 Disorders of Language and Auditory Perception. 8.3.1 Aphasia 8.3.2 Subtypes of acquired alexia 8.3.2 Alexia without agraphia 8.3.3 Agraphia without alexia 8.3.4 Subtypes of acquired agraphia 8.3.5 Aprosodias 9. Emotion 9.1 Emotion. 9.1.1 What is emotion? How does it differ from motivation? 9.1.2 Theories of emotion 9.1.3 Laterality of emotion 9.1.4 Role of subcortical structures in emotion. 9.1.5 Role of cortex in emotion 9.2 Disorders of Emotion. 9.2.1 Brain Damage and Lack of Affect 9.2.2 Kluver-Bucy Syndrome 9.2.3 Mood Disorders 10. Spatial Ability 10.1 Spatial Ability. 10.1.1 What is Spatial Ability? 10.1.2 Hemispheric Representation of Space 10.1.3 Parietal Lobes 10.1.4 Frontal Lobes 10.1.5 Temporal Lobes 10.1.6 Personal Representations of Space 10.1.7 Extrapersonal Space. 10.2 Disorders of Spatial Ability. 10.2.1 Disturbances in Personal Space 10.2.2 Disturbances of Extrapersonal Space 10.2.3 Balint-Holmes Syndrome. 11. Attention and Consciousness 11.1 Studying Attention. 11.1.1 Early versus late selection 11.1.2 How does attention shift? Voluntary versus Reflexive Orienting 11.1.3 Neural system(s) subserving attention 11.2 Studying Consciousness. 11.2.1 Defining Consciousness 11.2.2 The neural basis of consciousness 11.2.3 Methods of Studying Consciousness 11.3 Disorders of Attention and Consciousness. 11.3.1 Blindsight 11.3.2 Spatial Neglect 11.3.3 Balint-Holmes syndrome. 12. Neural Development and Developmental Disorders 12.1 Neural Development 12.1.1 Early Development 12.1.2 Post Natal development 12.1.2.1 Parietal Lobe Development 12.1.2.2 Occipital Lobe Development 12.1.2.3 Temporal Lobe Development 12.1.2.4 Frontal Lobe Development 12.2 Disorders of Development 12.2.1 Potential Causes of Developmental Abnormalities 12.2.2 Developmental Dyslexia 12.2.3 Attention Deficit Disorder (ADD) 12.2.4 Autism 13. Human Brain Damage 13.1 Causes of Brain Damage. 13.1.1 Tumors 13.1.1.1 Tumors arising from glial cells. 13.1.1.2 Tumors arising from the meninges 13.1.1.3 Metastatic tumors 13.1.2 Cerebrovascular Disorders 13.1.3 Head Injuries 13.1.3.1 Traumatic Brain Injury 13.1.3.2 Closed versus Open head Injury 13.1.4 Infections 13.1.5 Neurotoxins 13.2 Neurological and Psychiatric Diseases. 13.2.1 The Epilepsies. 13.2.2 Multiple Sclerosis and Amyotrophic Lateralizing Sclerosis 13.2.3 Schizophrenia 13.2.4 Mood Disorders <s> BIB006 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Several lines of evidence indicate that the elaborated calcium signals and the occurrence of calcium waves in astrocytes provide these cells with a specific form of excitability. The identification of the cellular and molecular steps involved in the triggering and transmission of Ca(2+) waves between astrocytes resulted in the identification of two pathways mediating this form of intercellular communication. One of them involves the direct communication between the cytosols of two adjoining cells through gap junction channels, while the other depends upon the release of "gliotransmitters" that activates membrane receptors on neighboring cells. In this review we summarize evidence in favor of these two mechanisms of Ca(2+) wave transmission and we discuss that they may not be mutually exclusive, but are likely to work in conjunction to coordinate the activity of a group of cells. To address a key question regarding the functional consequences following the passage of a Ca(2+) wave, we list, in this review, some of the potential intracellular targets of these Ca(2+) transients in astrocytes, and discuss the functional consequences of the activation of these targets for the interactions that astrocytes maintain with themselves and with other cellular partners, including those at the glial/vasculature interface and at perisynaptic sites where astrocytic processes tightly interact with neurons. <s> BIB007 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> We aimed to create autonomous on-chip systems that perform targeted translocations of nano- or microscale particles in parallel using machinery that mimics biological systems. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA-labeled microtubules gliding on kinesin-coated surfaces acted as cargo translocators and that single-stranded DNA-labeled cargoes were loaded/unloaded onto/from gliding microtubules at micropatterned loading/unloading sites specified by DNA base sequences. Our results will help to create autonomous molecular sorters and sensors. <s> BIB008 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Although Ca(i)(2+) waves in networks of astrocytes in vivo are well documented, propagation in vivo is much more complex than in culture, and there is no consensus concerning the dominant roles of intercellular and extracellular messengers [inositol 1,4,5-trisphosphate (IP(3)) and adenosine-5'-triphosphate (ATP)] that mediate Ca(i)(2+) waves. Moreover, to date only simplified models that take very little account of the geometrical struture of the networks have been studied. Our aim in this paper is to develop a mathematical model based on realistic cellular morphology and network connectivity, and a computational framework for simulating the model, in order to address these issues. In the model, Ca(i) (2+) wave propagation through a network of astrocytes is driven by IP(3) diffusion between cells and ATP transport in the extracellular space. Numerical simulations of the model show that different kinetic and geometric assumptions give rise to differences in Ca(i)(2+) wave propagation patterns, as characterized by the velocity, propagation distance, time delay in propagation from one cell to another, and the evolution of Ca(2+) response patterns. The temporal Ca(i)(2+) response patterns in cells are different from one cell to another, and the Ca(i)(2+) response patterns evolve from one type to another as a Ca(i)(2+) wave propagates. In addition, the spatial patterns of Ca(i)(2+) wave propagation depend on whether IP(3), ATP, or both are mediating messengers. Finally, two different geometries that reflect the in vivo and in vitro configuration of astrocytic networks also yield distinct intracellular and extracellular kinetic patterns. The simulation results as well as the linear stability analysis of the model lead to the conclusion that Ca(i)(2+) waves in astrocyte networks are probably mediated by both intercellular IP(3) transport and nonregenerative (only the glutamate-stimulated cell releases ATP) or partially regenerative extracellular ATP signaling. <s> BIB009 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> We aimed to create an autonomous on-chip system that performs targeted delivery of lipid vesicles (liposomes) as nano- or microscale reactors using machinery from biological systems. Reactor-liposomes would be ideal model cargoes to realize biomolecular-motor-based biochemical analysis chips; however, there are no existing systems that enable targeted delivery of cargo-liposomes in an autonomous manner. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA (ssDNA)-labeled microtubules (MTs), gliding on kinesin-coated surfaces, acted as cargo transporters and that ssDNA-labeled cargo-liposomes were loaded/unloaded onto/from gliding MTs without bursting at loading reservoirs/micropatterned unloading sites specified by DNA base sequences. Our results contribute to the development of an alternative strategy to pressure-driven or electrokinetic flow-based microfluidic devices. <s> BIB010 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> We present an extended computer simulation method which allows in silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors. The simulation reproduced molecular shuttle movements under external forces and dissociation of shuttles from guiding track surfaces. The simulation was validated by comparing the simulation results with the corresponding experimental ones. Using the simulation, track designers can change guiding track designs, choose guiding methods, tune the strength of external forces, and test the module performance. This simulation would significantly reduce the effort expended in designing guiding tracks for molecular shuttles powered by kinesin motors. <s> BIB011 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Molecular communication has been recently proposed for interconnected nano-scale devices as an alternative to classical communication paradigms such as electromagnetic waves, acoustic or optical communication. In this novel approach, the information is encoded as molecules that are transported between nano-scale devices within different distances. For short distances (nm-mm ranges) there exist molecular motors and calcium signaling techniques to realize the communication. For long distances (mm-m ranges), pheromones are used to transport information. In this work, the medium-range is explored to cover distances from ?m to mm and a molecular network architecture is proposed to realize the communication between nano-machines that can be deployed over different (short, medium and long) distances. In addition, two new communication techniques, flagellated bacteria and catalytic nanomotors, are proposed to cover the medium-range. Both techniques are based on the transport of DNA encoded information between emitters and receivers by means of a physical carrier. Finally, a qualitative comparison of both communication techniques is carried out and some future research topics are pointed out. <s> BIB012 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> a b s t r a c t This paper describes a Bacteria-based Nanonetwork for communication between eukaryotic cell sized nano devices. The communication is achieved by the exchange of DNA molecules which are transported by bacteria guided by chemotaxis. First, the modules of the network are described and all the biological phenomena that support the basic communication steps are explained in detail. Then an analytical model is developed to assess the communication range and the network performance in terms of capacity and end-to-end delay by considering the available information about the biological mechanisms used. As there are no appropriate estimates of the propagation delay introduced by bacterial chemotaxis, our newly developed simulator is introduced which helps us to obtain the statistics on bacteria propagation. Finally, by combining the analytical model with the simulation results, a network performance in terms of end-to-end delay, capacity and end-to-end throughput is obtained which is 4 orders of magnitude higher than the other molecular communication approaches. <s> BIB013 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Nanonetworks are the interconnection of nanomachines and as such expand the limited capabilities of a single nanomachine. Several techniques have been proposed so far to interconnect nanomachines. For short distances (nm-mm ranges), researchers are proposing to use molecular motors and calcium signaling. For long distances (mm-m), pheromones are envisioned to transport information. In this work we propose a new mechanism for medium-range communications (nm-µm): flagellated bacteria. This technique is based on the transport of DNA-encoded information between emitters and receivers by means of a bacterium. We present a physical channel characterization and a simulator that, based on the previous characterization, simulates the transmission of a DNA packet between two nanomachines. <s> BIB014 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Preface 1. Structural organization of the nervous system 2. Resting and action potentials 3. The ionic permeability of the nerve membrane 4. Membrane permeability changes during excitation 5. The molecular structure and functioning of voltage-gated ionic channels 6. Cable theory and saltatory conduction 7. Neuromuscular transmission 8. Synaptic transmission in the nervous system 9. Skeletal muscles 10. The mechanism of contraction in skeletal muscle 11. Non-skeletal muscles Further reading References Index. <s> BIB015 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Intracellular cargo is transported by multiple motor proteins. Because of the force balance of motors with mixed polarities, cargo moves bidirectionally to achieve biological functions. Here, we propose a microtubule gliding assay for a tug-of-war study of kinesin and dynein. A boundary of the two motor groups is created by photolithographically patterning gold to selectively attach kinesin to the glass and dynein to the gold surface using a self-assembled monolayer. The relationship between the ratio of two antagonistic motor numbers and the velocity is derived from a force-velocity relationship for each motor to calculate the detachment force and motor backward velocity. Although the tug-of-war involves .100 motors, values are calculated for a single molecule and reflect the collective dynein and non-collective kinesin functions when they work as a team. This assay would be useful for detailed in vitro analysis of intracellular motility, e.g., mitosis, where a large number of motors with mixed polarities are involved. <s> BIB016 </s> A Comprehensive Survey of Recent Advancements in Molecular Communication <s> 5) Microtubule Filament Motility Over Stationary Kinesin: <s> Nanoshuttles powered by the molecular motor kinesin have the potential to capture and concentrate rare molecules from solution as well as to transport, sort and assemble them in a high-throughput manner. One long-thought-of goal has been the realisation of a molecular assembly line with nanoshuttles as workhorses. To harness them for this purpose might allow the community to engineer novel materials and nanodevices. The central milestone towards this goal is to expose nanoshuttles to a series of different molecules or building blocks and load them sequentially to build hierarchical structures, macromolecules or materials. Here, we addressed this challenge by exploiting the synergy of two so far mostly complementary techniques, nanoshuttle-mediated active transport and pressure-driven passive transport, integrated into a single microfluidic device to demonstrate the realisation of a molecular assembly line. Multiple step protocols can thus be miniaturised to a highly parallelised and autonomous working lab-on-a-chip: in each reaction chamber, analytes or building blocks are captured from solution and are then transported by nanoshuttles across fluid flow boundaries in the next chamber. Cargo can thus be assembled, modified, analysed and eventually unloaded in a procedure that requires only one step by its operator. <s> BIB017
Although in biological cells kinesin moves over microtubule tracks, in  it was shown that stationary kinesin attached to a substrate can mobilize microtubule filaments. This scheme is very suitable for molecular communication in on-chip applications BIB008 , where the transmitter and receiver are located in a lab-on-a-chip device. For example, recently it was shown that electrical currents can be used to control the speed and direction of the microtubules [51]-  . However, unlike kinesin which can naturally carry cargoes, a technique for carrying information particles by microtubule filaments is necessary. In BIB010 , BIB008 , DNA hybridization bonds are proposed for carrying cargoes such as vesicles. A single strand of DNA is made up of many nucleotides. Each nucleotide is made up of one of the four possible nucleobase compounds: guanine (G), adenine (A), thymine (T), or cytosine (C). A DNA strand is made up of two single stranded DNAs (ssDNA)s connected together using hybridization bounds, with adenine bonding only to thymine in two hydrogen bonds, and cytosine bonding only to guanine in three hydrogen bonds. This is called complementary base pairing. The bonding occurs when two ssDNAs with complementary base pairs come close together. Figure 6 shows an example of two ssDNAs hybridizing. In BIB010 , BIB008 , both cargo vesicles, transmission area, receiver area, and microtubules are covered with ssDNAs. Microtubules moving over a kinesin covered glass substrate are covered with 15 base ssDNAs, and the information particles or the vesicles are also covered with 23 base ssDNAs which is complementary to that of the microtubules' ssDNAs. When the microtubule glides close to an information particle or a vesicle, the two ssDNA sequences hybridize and the microtubule carries the cargo until it gets close to the receiver. The receptor module at the receiver is covered with 23 base ssDNAs, which are complementary to that of the cargo. When a loaded microtubule filament glides close to the receptor module, it will unload the information particle or the vesicle through hybridization bound with the complementary 23 base ssDNA at the receptor module. Since 23 base hybridization bound is stronger than the 15 base hybridization bonds between the cargo and the microtubules, the particles or the vesicles are unloaded at the receiver. Figure 7 depicts the microtubule motility mechanism on a DNA micro array. In  , BIB011 it was shown that the motion of the microtubule Fig. 7 . Cargo transport mechanism for microtubule filaments gliding over stationary kinesin substrate using DNA hybridization bonds. filaments over stationary kinesin can be simulated using Monte Carlo simulations. The motion of the microtubules is largely regular, with Brownian motion effects causing random fluctuations. Moreover, the microtubules move only in the x and y directions, and do not move in the z direction (along the height of the channel) because they move right on top of kinesins. In simulations, a two-dimensional motion of a microtubule can be simulated over discrete time intervals of ∆t seconds. Given some initial position (x 0 , y 0 ) at time t = 0, for any integer k > 0, the motion of the microtubule is given by the sequence of coordinates (x i , y i ) for i = 1, 2, . . . , k. Each coordinate (x i , y i ) represents the position of the microtubule's head at the end of the time t = i∆t, where This is similar to the equations for Brownian motion, because the motion of the microtubules are effected by the same physical processes. In this case, the step size ∆r at each step is an iid Gaussian random variable with mean and variance where v avg is the average velocity of the microtubule, and D is the microtubule's diffusion coefficient. The angle θ i is no longer independent from step to step: instead, for some stepto-step angular change ∆θ, we have that Now, for each step, ∆θ is an iid Gaussian-distributed random variable with mean and variance where L p is the persistence length of the microtubule's trajectory. In  , these values were given as v avg = 0.85 µm/s, D = 2.0·10 −3 µm 2 /s, and L p = 111 µm. In case of a collision with a boundary, we assume that the microtubule does not reflect off the boundary, as in an elastic collision, but instead sets θ i so as to follow the boundary  . It may also be possible to use actin filaments and myosin in place of microtubule filaments and kinesin BIB003 . Myosin are motor proteins that are used for muscle contraction and actin filaments are rod-like proteins. Although they are not exactly similar to kinesin and microtubules, the motion is generated using a very similar manner by employing ATP hydrolysis. In  it was shown that silicon nanowires covered with myosin can be used as tracks for actin filaments. Dynein molecular motor and microtubule filaments is another example of motor protein-filament motility BIB016 . It is also possible to use active transport in conjunction with flow based propagation in microfluidic lab-on-chip devices as was shown in BIB017 . 6) Bacteria Assisted Propagation: In BIB012 , BIB013 , bacteria were proposed for transferring information particles from a transmitter to a receiver. In this scheme, the information particles are placed inside bacteria at the transmitter and the loaded bacteria are released into the channel. The bacteria then propagate in the channel until they reach the receiver and deliver the information particles. In order to assist this propagation, flagellated bacteria, which are self propelling organisms could be used. Figure 8 depicts a flagellated bacteria and the structure of flagella. A Flagellum consists of a filament and a motor section. The motor section rotates the filament which in turn propels the bacteria in a certain direction. To guide the bacteria towards the receiver, attractant molecules can be released by the receiver. The bacteria are then attracted towards the receiver by following the concentration gradient and moving towards the increasing concentration of attractant molecules. It is possible to simulate the motion of bacteria as shown in BIB001 , BIB002 , BIB014 . 7) Propagation Through Gap Junction: Gap junctions are intercellular connections between neighboring cells located at the cell membrane. They are literally gaps that are formed out of two aligned connexon structures which connect the cytoplasm of two adjacent cells. These gap junctions allow the free diffusion of selected small molecules between these two neighboring cells. Their permeability can vary from time to time, allowing different molecules to pass between the cells. Also, they can be closed and reopened by the cell during the lifetime of a cell. Intercellular calcium wawe (ICW) is one of the main intercellular communication systems observed among biological cells [5] . In this system, after a cell is stimulated, it generates a response to this stimulus with an increased cytosolic Ca 2+ concentration through the usage of the secondary messenger molecule inositol 1,4,5-triphosphate (IP 3 ). Then Ca 2+ concentration wave passes to the neighboring cells via usage of IP 3 or ATP. There are two main pathways: the internal pathway and the external pathway. In the internal pathway case, IP3 molecules diffuse through gap junctions, while in the latter, ATP molecules are released to the extracellular space and diffuse freely to trigger nearby cells. According to experimental studies, it has been shown that these pathways complement each other rather than being alternative approaches BIB009 . The frequency and effective range of ICW heavily depends on which pathway is used. Using internal pathway enables frequent fast communication between nearby cells, however reaching distant cells requires the usage of external pathway BIB009 . ICW can reach to 200−350 µm in one dimension at a speed of 15−27 µm/s and oscillate in the 10 −3 − 1 Hz range BIB007 , BIB004 . It has been shown experimentally that cells encode the information on the frequency and amplitude components of ICWs BIB004 . Based on the ICW system, Nakano et al. have proposed a molecular communication system called calcium signaling BIB005 . The system is composed of two types of devices, the transmitting pair (i.e., source and destination devices) and the ICW-capable intermediary cells. Similar to other communication systems, calcium signaling is composed of three main steps: modulation, propagation, and demodulation. The source device modulates the information onto an ICW wave by generating a stimulus to the closest intermediary cell in the ICW channel. Then the calcium signal propagates through the intermediary cells via the internal and external pathways until the destination device is reached. In  , authors present the capabilities, limitations, and deployment scenarios of calcium signaling system. 8) Neurochemical Propagation : Neurotransmitters are endogenous chemicals that transmit signals across a synapse from one neuron to another target cell. Target cell can be another neuron or another junction cell as in the case of neuro mascular junctions (NMJ). Neurotransmitters are packaged into synaptic vesicles on the presynaptic side of a synapse and then they are released into and diffuse across the synaptic cleft, where they bind to specific receptors in the membrane on target cell BIB006 . NMJ is one of the many occurrences in biological systems where two cell communicate with each other using an intermediary molecule that diffuse in the extracellular environment. It is a semi-closed environment between a pair of nerve and muscle cell, with a typical length of 10 to 100 nm  , BIB015 . When muscles in a specific part of the body need to be contracted, the nerve cells in that region send a signal via neurotransmitters to the muscle tissue through these junctions to trigger the contraction [5] . As an action potential reaches the end of a motor neuron, neurotransmitters are released into the synaptic cleft. In vertebrates, motor neurons release acetylcholine (ACh), a small molecule neurotransmitter, which diffuses through the synapse and binds ACh receptors (AChRs) on the plasma membrane of the muscle fiber. This allows the opening up of ion channels at the cell membrane which in turn allows the passage of Na + and K + ions. The increased cytosolic concentration of these ions causes the muscle cell to be contracted. The neurotransmitters stay in the bounded state for some time after which the bond degrades and the ACh molecule are again set free to the NMJ. The degradation of this bond is crucial to the muscle contraction procedure, allowing the muscle to relax and gradually revert back to its original resting position, awaiting further contraction signals. After the degradation of the bonds between ACh and AChR, the neurotransmitter molecules are highly likely to re-bond with the receptors. Such an occurrence causes further unwanted muscle contractions, and after a few muscle contraction signals the NMJ will be filled with ACh molecules. This causes the ion channels linked to the AChRs to become inactive, which in turn blocks all further contraction signals. To keep the communication between the nerve and muscle cell, the ACh molecules in the environment should be removed from the NMJ after the muscle cell is successfully contracted. This cleaning process is achieved through the use of a secondary type of molecule, called acetylcholinesterase (AChE), which reside in the muscle cell part of the NMJ environment. AChE is a special kind of enzyme that is capable of attracting and hydrolyzing the ACh molecules into their two building blocks, Acetate and Choline. Since both of these substructures are incapable of forming bonds with AChR, we can say that in practice AChE molecules remove (or destroy) the ACh molecules from the NMJ and almost all the molecules contribute to the signal only once.