arXiv subjects

Davide Chiuchiù

Publications and source records attributed to Davide Chiuchiù.

3 recordsLinked to original sources

arXiv2019

Assembly of heteropolymers via a network of reaction coordinates

In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a sequence of discrete chemical reactions between intermediate meta-stable states. In this paper, we use ideas from reaction rate theory and describe non-equilibrium assembly of a heteropolymer via a continuous reaction coordinate. Our approach allows to estimate the copy error and incorporation speed from the Gibbs free energy landscape of the process. We apply our theory to several examples, from a simple reaction characterized by a free energy barrier to more complex cases incorporating error correction mechanisms such as kinetic proofreading.

cond-mat.stat-mech↗

arXiv2018

Cost of remembering a bit of information

In 1961, Rolf Landauer pointed out that resetting a binary memory requires a minimum energy of $k_BT \ln(2)$. However, once written, any memory is doomed to loose its content if no action is taken. To avoid memory losses, a refresh procedure is periodically performed. In this paper we present a theoretical model and an experiment on a micro-electro-mechanical system to evaluate the minimum energy required to preserve one bit of information over time. Two main conclusions are drawn: i) in principle the energetic cost to preserve information for a fixed time duration with a given error probability can be arbitrarily reduced if the refresh procedure is performed often enough; ii) the Heisenberg uncertainty principle sets an upper bound on the memory lifetime.

cond-mat.stat-mech↗

arXiv2018

Mapping of uncertainty relations between continuous and discrete time

Lower bounds on fluctuations of thermodynamic currents depend on the nature of time: discrete or continuous. To understand the physical reason, we compare current fluctuations in discrete-time Markov chains and continuous-time master equations. We prove that current fluctuations in the master equations are always more likely, due to random timings of transitions. This comparison leads to a mapping of the moments of a current between discrete and continuous time. We exploit this mapping to obtain new uncertainty bounds. Our results reduce the quests for uncertainty bounds in discrete and continuous time to a single problem.

cond-mat.stat-mech↗