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Automated Robotic Liquid Handling Assembly of Modular DNA Devices
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Analog synthetic biology.

R Sarpeshkar1

  • 1Analog Circuits and Biological Systems, Research Lab of Electronics, Massachusetts Institute of Technology, , Cambridge, MA 02139, USA.

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
|February 26, 2014
PubMed
Summary
This summary is machine-generated.

Analog computation in living cells is more resource-efficient than digital computation. Synthetic biology should adopt analog approaches for efficient cellular computations, avoiding energy and molecular budget overruns.

Keywords:
analog computationbioenergeticscytomorphiclogarithmic computationprobabilistic computationsynthetic biology

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Area of Science:

  • Biophysics
  • Synthetic Biology
  • Computational Biology

Background:

  • Living cells perform computations using gene and protein expression.
  • Noise in cellular processes imposes fundamental limits on computational precision and resource usage.
  • Understanding these limits is crucial for designing effective synthetic biological systems.

Purpose of the Study:

  • To analyze the advantages and disadvantages of analog versus digital computation within living cells.
  • To determine the resource efficiency of analog computation compared to digital computation.
  • To guide the development of synthetic biology by identifying optimal computational strategies for cellular environments.

Main Methods:

  • Analysis based on fundamental laws of noise in gene and protein expression.
  • Comparison of resource requirements (energy, time, space, molecular count, part count) for analog and digital computation.
  • Review of recent advancements in analog computation within biological systems, including cytomorphic circuits and positive-feedback linearization.

Main Results:

  • Analog computation is significantly more resource-efficient than deterministic digital computation in cells, even at high precision levels.
  • Simple synthetic computations like addition can exceed cellular energy and molecular budgets if digital approaches are used.
  • Analog DNA-protein computation schematics were presented.
  • Cytomorphic circuits can bridge electronic and biochemical design domains due to thermodynamic similarities.
  • Positive-feedback linearization enabled wide-dynamic-range logarithmic analog computation in E. coli, achieving high part efficiency.

Conclusions:

  • Synthetic biology must embrace analog, collective analog, probabilistic, and hybrid analog-digital computational methods for cellular applications.
  • Failure to adopt efficient analog strategies will hinder the development of even basic synthetic computations in cells.
  • Analog computation offers a path towards more efficient and feasible synthetic biological designs within cellular constraints.