The meeting of worlds: theoretical and physical understanding of biological processes

Locked nucleic acid-based DNA circuits with ultra-low leakage

This work aims to reduce leak in DNA-based strand displacement circuits by incorporating LNAs into strands. LNAs are modified nucleotides that retain base-pairing properties but bind DNA (or RNA/other LNAs) with increased stability. Here, LNAs are placed at extremities of gate complexes in strand displacement circuits, and the authors report significant leak reduction in all circuits tested, with a signal loss of ~10% compared to control DNA-only circuits. 

Locked nucleic acids based DNA circuits with ultra-low leakage | SpringerLink

Detailed Balance = Complex Balance + Cycle Balance: A Graph-Theoretic Proof for Reaction Networks and Markov Chains

This work introduces the idea of cycle balance as an easier condition to check than formal balance. A system is detailed balanced if the net flux along any edge of a process is zero. A process is complex balanced if the total flux out of any node is equal to the total flux into that node. A process if complex balanced if the net flux around any cycle is zero. Previous work showed that if a process was both formally balanced and complex balanced, then it was detailed balanced. This work now defines a process to be cycle balanced if for any cycle, there is both an edges faster in the anti-clockwise direction and an edges faster in the clockwise direction. They then show that a system which is complex balanced and cycle balanced is detailed balanced.

https://link.springer.com/article/10.1007/s11538-020-00792-1

Physical constraints in intracellular signaling: the cost of sending a bit

Bryant and Machta analyse a number of distinct communication channels used by biological systems. They consider the scaling of the energy cost with the separation of transmitter and receiver and the size of both transmitter and receiver, for a given frequency. In general, communication beyond a certain characteristic lengthscale is prohibitively hard. This effect is particularly true for chemical signals that rely on diffusion, since it is impossible to send coherent waves via this mechanism. However, the low cost of chemical signalling makes it ideal over short distances. Neuron-like ion channels work well over longer distances, but also suffer from the inability to transmit coherent waves. Acoustic communication, which exploits coherent wave propagation, is best over large distances. Before the characteristic cut-off in distance, each mechanism has its own particular scaling of cost depending on the system parameters.

[2205.15356] Physical constraints in intracellular signaling: the cost of sending a bit (arxiv.org)

Branching processes with resetting as a model for cell division

The paper describes modelling cell division as a process involving branching and resetting. Their model is based on 1-dimensional Brownian motion in a potential V, with the additional possibility for particles to branch and give birth to more particles, whose positions are reset relative to the position of the original particles. The model is applied to three different cell division schemes:

1. Sizer: Cells size determines branching probability (cell size is used as the Brownian space dimension).
2. Timer: Cell age determines branching probability (cell age is used as the Brownian space dimension).
3. Adder: Branching probability is dependent on the added volume since birth.

For all three processes, branching reduces entropy (as it tends to make more probable states even more probable), and resetting increases entropy. They then claim that an efficiency can be measured by considering the ratio of branching entropy to resetting entropy, and explicitly calculate this value to be 0.41 for the timer cell division scheme in the infinite limit of a branching rate parameter.

https://iopscience.iop.org/article/10.1088/1751-8121/ac491a/meta

An autonomously oscillating supramolecular self-replicator

This work describes the design of a network of sulphides and disulphides which autonomously forms and destroys a supramolecular assembly under the constant flow of peroxide as fuel. Disulphides with aromatic head and long aliphatic tail forms micellar structures with can encapsulate free thiols inside it. After a certain point, the micelle ruptures releasing the thiols back into the reaction medium. The combination of such molecular and supramolecular events produces sustained oscillations in the concentration of the components.

An autonomously oscillating supramolecular self-replicator | Nature Chemistry