Reading List

Mostly for internal reference - a list of papers we've discussed in our fortnightly literature meetings. Highlights may be featured as blog posts.

Stochastic Analysis of Retroactivity in Transcriptional Networks through Singular Perturbation
An analysis of the restroactive effect on transcription factor abundance due to its interaction (and subsequent sequestration) with a downstream transcription site.

Information theory, predictability, and the emergence of complex life
Construction and analysis of a simple model in which the cost of being complex can be compensated by an increased ability to predict the environment.

A DNA kinetics competition strategy of  hybridization chain reaction for molecular  information processing circuit construction
A molecular circuit that responds not just to the presence of multiple signals, but distinguishes between signals in different orders.

An analysis of the costs of generating periodic behaviour in simple stochastic systems.

Signal replication in a DNA nanostructure
Localised DNA strand displacement reactions for implementing logic in which a single signal can be branched into a multiple finite number of outputs.

Kinetics and thermodynamics of first-order Markov chain copolymerization
A technique for analyzing the growth of polymers with multiple different constituent monomers, in which monomer addition/removal rates depend upon the neighbouring monomers.

Online learning in a chemical perceptron
Implementing a simple neuron using molecular reactions.

Least mean squares implementation using molecules
Implementing a learning algorithm using chemical reactions.

Design of a hyperstable 60-subunit protein icosahedron
Accurate design of megadalton-scale  two-component icosahedral  protein complexes.
Icosahedral cages assembled from genetically modified proteins, with components produced and assembling in living E coli cells.

Effective dissipation: Breaking time-reversal symmetry in driven microscopic energy transmission
An analysis of when a simple device for driving a particle up a step is most dissipative.

Catalysis in reaction networks
Proof that in weakly reversible reaction networks that don't involve catalysis, it is impossible for the concentration of any subset of species to tend asymptotically to zero.

Towards a DNA Nanoprocessor: Reusable Tile-Integrated DNA Circuits

An implementation of DNA-based logic gates that can be incorporated into a small DNA tile. 

An analysis of information exchange between multiple interacting systems. 

An analysis of an experiment in which measurement and feedback allows photons  from two competing beams to charge a capacitor (no charging occurs when photons are not measured). This paper discusses the case in which fluctuations of photon numbers in both beams are correlated, allowing more work extraction.

Mutual Information between Input and Output Trajectories of Biochemical Networks
Calculating the information passed by a signalling system. This work, by considering simple gaussian fluctuations, is able to analyse the information between entire trajectories, rather than just the instantaneous information.

Message Passing Inference with Chemical Reaction Networks
Certain types of probability distribution can be marginalised through an algorithm known as message passing. This paper discusses how to implement chemical reactions that achieve such a goal.

Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA
A proposal to implement an unconventional computing architecture in which the inherent stochasticity of molecular processes is employed to simultaneously explore many possible solutions to a problem.

Thermodynamic Uncertainty Relation for Biomolecular Processes
First in a series of papers that explore the connection between the entropy generation around a cycle of molecular states and the uncertainty in the number of cycles completed in a given time.

Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold
A new mechanism for controlling of DNA strand displacement with regulator strands.

In vitro molecular machine learning algorithm via symmetric internal loops of DNA
Encoding a classification problem into DNA molecules.

Heterotic computing: past, present and future
A review of the possibilities of using computing architectures built from components that are not themselves Turing complete.

Solving Moment Hierarchies for Chemical Reaction Networks
The authors present an approach for calculating the relative values of factorial moments for stochastic Chemical Reaction Networks in the steady state.  Factorial moments are quantities related to means and variances of chemical populations.

Universal bound on the efficiency of molecular motors
By applying the recently-derived thermodynamic uncertainty relation, the authors find a bound on the efficiency of molecular motors that depends purely on observible quantities like the average velocity and diffusion constant.

Minimum energetic cost to maintain a target nonequilibrium state
The authors discuss the minimum rate at which energy must be supplied to maintain a non-equilibrium steady state in a discreet state Markov chain. It is the rate at which the system relaxes back towards equilibrium in the absence of the control.

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cell
This paper features the development of a recombinased-based framework for gene circuits design for synthethic biology. It must be remarked that this framework allows incredibly robust designs with little need for optimization, reduction of transcriptional layers as well as real time reprogrammability using CRISPR-Cas9 systems.

Universal trade-off between power, efficiency and constancy in steady-state heat engines
Recent work has suggested that heat engines operating between two temperature reservoirs can approach the limiting Carnot efficiency at finite power. This work argues that doing so is associated with a growing variance in the output power from one point in time to another.

Biological timekeeping in the presence of stochasticity
An analysis of the time taken to reach a certain threshold concentration in some biological systems. This time is less variable if the threshold is compared to an integral of concentrations over time, rather than instantaneous concentrations.

Approximating first-passage time distributions via sequential Bayesian computation.
This paper argues that the problem of finding the first passage time of a stochastic process is equivalent to a sequential Bayesian inference problem.  It then uses approximations to efficiently calculate the first passage time distribution.

A Molecular Circuit Regenerator to Implement Iterative Strand Displacement Operations
This works shows the design of a strand displacement gate that can be regenerated through the consumption of fuel molecules of DNA. The concept is extended to the implementation of two boolean gates using on this motif.  It should be noted that enthalpic and entropic components of the reactions  have different weights in each direction, and that the regeneration reactions must have different kinetic orders in order to allow proper activation.

Nanoscale rotary apparatus formed from tight-fitting 3D DNA components
Stepping operation of a rotary DNA origami device
Two papers that aim to mimic some of the most remarkable biomolecular machines - powered rotary motors. In the first paper, the construct a freely-rotating axle from DNA, but do not power its motion. In the second case, the authors are able to set the rotational angle of one piece of DNA with repect ot the other. However, the system does not possess a truly free axle and consistent motion in a specific direction is not possible.

The authors find a bound on the distribution of the infimum of entropy production in a trajectory of a stochastic process. This can be used to find a bound on the average maximum backwards detour of a molecular motor. They calculate other quantities such as the probability of a trajectory reaching a positive entropy production before reaching the same magnitude negative entropy production and the ratio of the probability distribution of the time to reach those two states.

The RNA world hypothesis suggests that early life used RNA as both an information carrier and as chemically active catalysts. In particular, an RNA-based RNAp could in principle allow for RNA-based copying of RNA. Whilst some RNA-based polymerases do exist in nature, they are not effective at polymerising long, arbitrary sequences. Here, the authors obtain an RNA-based RNAp that can do just that by several rounds of selective evolution. Note that the functioning of the RNAp is restricted to growing a copy sequence on a single-stranded template; persistent copies can only be produced by thermal cycling.

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