498 citations · 3.5k across the 66 of their papers we have counts for
7 papers · 1 filter
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
Pedro Fonseca, Flavio Romano, John S. Schreck +3
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculat…
Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions
Ruslan L. Davidchack, Thomas E. Ouldridge, Michael V. Tretyakov
We introduce new Langevin-type equations describing the rotational and translational motion of rigid bodies interacting through conservative and non-conservative forces, and hydrod…
High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits
Abhishek Deshpande, Thomas E. Ouldridge
Retroactivity arises when the coupling of a molecular network to a downstream network results in signal propagation back from to $\mathcal…
Chemical Boltzmann Machines
William Poole, Andrés Ortiz-Muñoz, Abhishek Behera +4
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemic…
What we learn from the learning rate
Rory A. Brittain, Nick S. Jones, Thomas E. Ouldridge
The learning rate is an information-theoretical quantity for bipartite Markov chains describing two coupled subsystems. It is defined as the rate at which transitions in the downst…
Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability
Abhishek Deshpande, Manoj Gopalkrishnan, Thomas E. Ouldridge +1
We consider the technologically relevant costs of operating a reliable bit that can be erased rapidly. We find that both erasing and reliability times are non-monotonic in the unde…