https://doi.org/10.1088/1751-8121/aa672f
When systems are coupled to thermodynamic baths, the irreversibility of transitions in the system are constrained by dissipation in the baths. Lower bounds on the magnitude of fluctuations in certain integrated currents can be used to infer the dissipation within the system. By considering a driven diffusion process on a lattice near the continuum limit, the authors apply results usually reserved for discrete state systems to a continuum process. It is demonstrated that the dissipation can still be constrained by fluctuations in macroscopic, rather than mesoscopic currents.
Homogeneous and universal detection of various targets based on dual‐step transduced toehold switch sensor
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201900749
The toehold switch system can be used to translate the nucleic acid based signals to protein level response. However, engineering and optimizing input sequence of the riboswitch system is a non-trivial task. This paper adds an additional layer of strand-displacement reactions involving an arbitrary input strand to generate a complex with a pre-existing strand to open the riboswitch. They have used in-vitro translation system to confirm the activity of their system using various targets including aptamers.
Dynamic DNA material with emergent locomotion behaviour powered by artificial metabolism
https://robotics.sciencemag.org/content/4/29/eaaw3512
The present work by Hamada and collaborators displays the construction of an artificial DNA-based system capable of growing a pattern following a template pattern on a microfluidic chip. The material is powered by an artificial metabolism consisting of the synthesis of DNA precursors by a phage DNA polymerase and the subsequent diffusion of the molecules, dissipative assembly and degradation. With this set up and in laminar flow, the material can autonomously grow similarly to how slime molds do (according to the authors). However, there are some limitations to this system since the emergent spatial patterns come from interactions with elements of the microfluidic chip rather than being encoded in the possible interactions within the DNA species.
The business of DNA nanotechnology: Commercialization of origami and other technologies
In this paper, Dunn analyzes the trends on both DNA nanotechnology publications and patent filings up until 2018. She describes growth trends in both sides of the field. The main conclusionis that until as recently as 2017 there was a gap between the scientific literature available - which seems to grow steady year by year - and derived applications that were commercially available - which did not seem to get the same momentum until the last year. However, in 2018 there was a noticeable surge in the number of patents filled. The paper also gives some details on the profile of some start ups on the field and they commercialized products: mainly research solutions and diagnosis applications.
Mathematical Models of Protease-Based Enzymatic Biosensors
In this paper, the authors presented a rapid detection system to chosen chemical and optical inputs using protease-based logic circuits. In the presence of a specific input, the protease activity will be restored and will cleave a specific substrate to produce a read-out signal. Enzymatic-based circuits operate at much faster time scales than the transcription-based circuits. In this work, the authors modeled and optimized experimentally the reactions to build a biosensor based on Boolean OR and XOR Boolean logic gates. In conclusion, enzymatic reactions can be used to develop biosensors capable of rapidly detecting multiple inputs.
An RNA polymerase ribozyme that synthesizes its own ancestor
By directed mutagenesis, a ligase I RNAzyme is transformed into a polymerase that can produce long RNA copies from an RNA template. The mutated RNAzyme is composed of three different RNA strands that can hybridize to form the final RNAzyme. With the correct template, the mutated RNAzyme is capable of polymerising the RNA sequences that produce the original ligase I.
However, the precision of the mutated RNAzyme is far from perfect. The average fidelity for the addition of NTPs is below 90%, thus adding several mutations to the copies, which end up losing their function in the majority of the cases. These results emphasize that one of the main challenges of polymerisation is the fidelity of the produced copies.
Thermodynamic costs of Turing Machines
Kolchinsky and Wolpert present an analysis that seeks to combine statistical thermodynamics with the algorithmic information theory of Turing Machines. Their central results come in three parts.
(a) They identify conditions under which a function G(x) can be interpreted as the heat function of a physically realizable construction of a Turing machine. Here, the heat function Q_T(x) is the heat generated by running Turing machine T on input x.
(b) Using these rules, the authors argue that a UTM that is thermodynamically reversible for the coin flip distribution of inputs is physically realizable. They go on to show that the heat cost of running this coin flip realization on an input x is bounded by the sum of the length of x, -1* the Kolmogorov
complexity of x calculated via that UTM, and a constant. As a result, the authors argue that such computations generate more heat if the input program is chosen inefficiently (it is too long), and that if we happened to have the shortest program needed to calculate y, there is a finite upper bound on the
heat cost involved. However, finding the shortest algorithm is not a computable problem, and if random inputs are used, the expected heat generated is infinite.
(c) Returning to the rules, the authors show that the conditional Kolmogorov complexity of an input given its output for a TM T, K(x|T(x)), can be a heat function (ie., there is a physical realization that generates heat Q(x)=K(x|T(x)) for input x). They call this the dominating realization, and argue that for any other realization of T, Q(x) can only be lower than Q_dom if the Kolmogorov complexity K(Q) is large. Thus K(x|T(x)) is some kind of cost that is either paid for during the operation of the device, or in its design (a complex K(Q) being taken as costly to build).
Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003669
The paper develops mathematical and computational methods for studying stability and long-time dynamics of stochastic biochemical reaction networks, mirroring analogous methods from the deterministic setting. The framework is applied to a number of examples, including a feedback loop, stochastic switch and a circadian clock.
Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003669
The paper develops mathematical and computational methods for studying stability and long-time dynamics of stochastic biochemical reaction networks, mirroring analogous methods from the deterministic setting. The framework is applied to a number of examples, including a feedback loop, stochastic switch and a circadian clock.
