The Biological Microprocessor, or How to Build a Computer With Biological Parts

Abstract

Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.

Molecular Governor: DNA Feedback Regulator for Molecular Robotics

“…Let the concentrations of S 1 , I (1) 1 , I (2) 1 , W (1) 1 , I (3) 1 , F 1 , I (4) 1 , I (5) 1 , W (2) 1 , OB 1 , S 2 , I (1) 2 , I (2) 2 , W (1) 2 , I (3) 2 , F 2 , I (4) 2 , I (5) 2 , W (2) 2 , OB 2 , W 12 , C 1 , and C 2 be defined by x i (i = 1, . .…”

“…Recent significant progress in nanotechnology has enabled the creation of a variety of computing circuits embedded in a series of deoxyribonucleic acid (DNA) reactions in a test tube [1]. In particular, the developed circuit design incorporating toehold-mediated strand displacement (TMSD) reactions dramatically expands the design possibilities of both DNA logic gates, such as AND, OR, and NOT gates [2], and DNA analog circuits, such as adder, multiplier, and divider circuits [3].…”

Recent advances and opportunities in synthetic logic gates engineering in living cells

“…Synthetic Biology arose out of a desire to implement engineering-level precision in constructing a biological circuit. This gave rise to the concept of parts standardization, composition standards, logic gates, reprogramming pathways and Computer Aided Design of biological networks (Endy 2005;Moe-Behrens 2013). A number of promoters (Lutz and Bujard 1997;Alper et al 2005), proteins and RNAs (Basu et al 2005;Pfleger et al 2006;Win and Smolke 2008) and scaffolds (Park et al 2003;Dueber et al 2009) have been designed and characterized.…”

Selective inactivation of enzymes conjugated to nanoparticles using tuned laser illumination

“…Another important characteristic of gold nanoparticles is their surface plasmon resonance: under optical illumination, gold nanoparticles efficiently create heat, which is especially significant when the energy (wavelength) of incident photons is close to the plasmon frequency of the nanoparticles. The method can be utilized for advanced biomedical applications as well as cell-free synthetic biology applications (30,31). The heat generated by the illuminated gold nanoparticles is proportional to the duration and energy of the illumination, and can reach temperatures of hundreds of degrees Celsius (26).…”

“…By using different shapes of gold nanoparticles conjugated to different enzymes, selective inactivation can be achieved. The method can be utilized for advanced biomedical applications as well as cell-free synthetic biology applications (30,31). Turning on (for example "hot-start" enzyme) and turning off enzymatic activity in a quantitative manner by illumination presents a potential method for biochemical computations (32).…”