DNA
as a universal substrate for chemical kinetics
This paper
discusses development of control circuitry within a chemical system to direct
molecular events using strand displacement reactions. The authors show basic
methods to construct unimolecular and bimolecular reactions (along with a short
kinetic analysis associated with each reaction system). these 2 reaction types
can then be used to construct any complex CRN (chemical reaction network). They
show this by developing DNA reactions that recreate a Lotka-Volterra chemical
oscillator, a limit cycle oscillator, a chaotic system, and a 2-bit pulse
counter.
https://www.pnas.org/content/pnas/107/12/5393.full.pdf
Undesired
usage and the robust self-assembly of heterogeneous structures
This work
introduces a formal description of the “principle of undesired usage”. This
principle states that the yield of assembling a structure is not determined by
ensuring a perfect stoichiometry between its components but by tuning the
reagents chemical potentials, e.g. concentrations, to avoid undesired
structures. They demonstrate this principle across several types of assembly
processes, with several different modelling techniques.
https://www.nature.com/articles/ncomms7203
SAT-assembly: A new approach for designing self-assembling systems
This paper presents a method of identifying patchy particle assembly components for a given structure. The foundation of the method is based on SAT, a well-known problem in computer science. The SAT problem consists of finding boolean values that solve a given set of boolean equations with a fixed number of variables. The paper goes into great detail on the variables and clauses that characterize patchy particle assembly as SAT problems. The method is performed on a cubic diamond lattice, and the resulting assembly kit is tested using an OxDNA simulation, which found that the correct structure was indeed formed.
https://arxiv.org/pdf/2111.04355.pdf
Local
time of random walks on graphs
This paper
looks at finding expressions for averages of functions of the local time to
be in a given state in a discrete state discrete time Markov
process. The local time for a state is the number of times that state is
visited in a given time window. The approach taken by the
authors here is inspired by path integration techniques from quantum
physics. The paper provides a method for finding the z-transform for the
average of a given function of the local time. The z-transform is similar
to a generating function for the averages of the function of local time in
a time window n. Specifically, the average of the function of local time
up to time n will be the coefficient of z^-n of the z transform expanded
in powers of 1/z. This then does have the limitation, that finding
the desired average given the z-transform can be a lot of work.
However, overall it was nice to see a more interesting way for
finding these functions of local time.
https://journals.aps.org/pre/pdf/10.1103/PhysRevE.104.044302
Imaging
RNA polymerase III transcription using a photostable RNA-fluorophore complex.
Quantitative
measurement of transcription rates in live cells is important for revealing
mechanisms of transcriptional regulation. RNA Pol III is particulary
challenging as this RNAP transcribes RNA molecules so it is not possible to use
protein reporters. To address this issue, this group developed Corn RNA
fluorescent aptamer that resembles the fluorophore found in red fluorescent
protein. With this new tool, the authors were able to study and imaging the
corn-tagged Pol III transcript levels.
https://www.nature.com/articles/nchembio.2477.pdf
Dissipation bounds the amplification of transition rates far from equilibrium
Kuznets-Speck and Limmer seek to demonstrate an idea
that has long been gnawing at people working on the physics of computation. A
system with two metastable states is capable of acting a bit. The lifetime of
those metastable states determines how long the bit can reliably store
information. Another related timescale is the time it takes to switch the bit,
when such a switch is required. There is a general feeling that if you want
both a long reliability time, and a short switching time, this should be costly
(in terms of the energy you have to put in). However, such a tradeoff has not
been found, in general, using the tools of modern stochastic thermodynamics.
The title of this manuscript suggests that they have been able to identify a
hard tradeoff; however, this tradeoff only appears when certain conditions are
met. The authors argue that these conditions are quite general, but it is still
unclear whether there is a limit on designing a reliable bit that can be
switched quickly at low thermodynamic cost.
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