DNA as a universal substrate for chemical kinetics
Molecular programming aims to systematically engineer molecular and chemical systems of
autonomous function and ever-increasing complexity. A key goal is to develop embedded …
autonomous function and ever-increasing complexity. A key goal is to develop embedded …
Markovian dynamics on complex reaction networks
J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …
reaction channels, are ubiquitous across many scientific and engineering disciplines …
Programmable chemical controllers made from DNA
Biological organisms use complex molecular networks to navigate their environment and
regulate their internal state. The development of synthetic systems with similar capabilities …
regulate their internal state. The development of synthetic systems with similar capabilities …
Thermal logic gates: computation with phonons
L Wang, B Li - Physical review letters, 2007 - APS
Logic gates are basic digital elements for computers. We build up thermal logic gates that
can perform similar operations as their electronic counterparts. The thermal logic gates are …
can perform similar operations as their electronic counterparts. The thermal logic gates are …
[PDF][PDF] The program-size complexity of self-assembled squares
Molecular self-assembly gives rise to a great diversity of complex forms, from crystals and
DNA helices to microtubules and holoenzymes. We study a formal model of …
DNA helices to microtubules and holoenzymes. We study a formal model of …
Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction
networks of elementary reactions. Their dynamics is described by deterministic rate …
networks of elementary reactions. Their dynamics is described by deterministic rate …
A simple DNA gate motif for synthesizing large-scale circuits
The prospects of programming molecular systems to perform complex autonomous tasks
have motivated research into the design of synthetic biochemical circuits. Of particular …
have motivated research into the design of synthetic biochemical circuits. Of particular …
An RNA-based theory of natural universal computation
H Akhlaghpour - Journal of Theoretical Biology, 2022 - Elsevier
Life is confronted with computation problems in a variety of domains including animal
behavior, single-cell behavior, and embryonic development. Yet we currently do not know of …
behavior, single-cell behavior, and embryonic development. Yet we currently do not know of …
Computation with finite stochastic chemical reaction networks
A highly desired part of the synthetic biology toolbox is an embedded chemical
microcontroller, capable of autonomously following a logic program specified by a set of …
microcontroller, capable of autonomously following a logic program specified by a set of …
Energetic costs of cellular computation
Cells often perform computations in order to respond to environmental cues. A simple
example is the classic problem, first considered by Berg and Purcell, of determining the …
example is the classic problem, first considered by Berg and Purcell, of determining the …