I. INTRODUCTION  
A. Motivation and Scope  
C. Signaling Particles  
D. Biological Components of Transmitter and Receiver  
E. Organization of the Paper  

II. PROTONS AS SIGNALING PARTICLES  
A. Transmitters  
B. Receivers  

III. CALCIUM IONS AS SIGNALING PARTICLES  
A. Transmitters  
B. Receivers  

IV. NEUROTRANSMITTERS AS SIGNALING PARTICLES  
A. Transmitters  
B. Receivers  

V. PHOSPHOPEPTIDES AS SIGNALING PARTICLES  
A. Transmitter  
B. Receiver  

VI. COMPARISON, APPLICATIONS, AND PRACTICAL CONSIDERATIONS  
A. Comparison of the Considered Signaling Particles  
B. Potential Medical Applications  

VII. FUTURE RESEARCH DIRECTIONS  
A. Directions and Challenges for Theoretical Research  
B. Implementation Challenges  

VIII. CONCLUSIONS