arXiv subjects

Clara del Junco

Publications and source records attributed to Clara del Junco.

6 recordsLinked to original sources

arXiv2022

Front speed and pattern selection of a propagating chemical front in an active fluid

Spontaneous pattern formation in living systems is driven by reaction-diffusion chemistry and active mechanics. The feedback between chemical and mechanical forces is often essential to robust pattern formation, yet it remains poorly understood in general. In this analytical and numerical paper, we study an experimentally-motivated minimal model of coupling between reaction-diffusion and active matter: a propagating front of an autocatalytic and stress-generating species. In the absence of activity, the front is described by the the well-studied KPP equation. We find that front propagation is maintained even in active systems, with crucial differences: an extensile stress increases the front speed beyond a critical magnitude of the stress, while a contractile stress has no effect on the front speed but can generate a periodic instability in the high-concentration region behind the front. We expect our results to be useful in interpreting pattern formation in active systems with mechano-chemical coupling in vivo and in vitro.

cond-mat.soft↗

arXiv2021

A mechanism for the generation of robust circadian oscillations through ultransensitivity and differential binding affinity

Biochemical circadian rhythm oscillations play an important role in many signalling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but analytically tractable model of the circadian oscillations in the KaiABC protein system found in the cyanobacteria $S. \ elongatus$. In particular, our minimal model explicitly accounts for two experimentally characterized biophysical features of the KaiABC protein system, namely, a differential binding affinity and an ultrasensitive response. Our analytical work shows how these mechanisms might be crucial for promoting robust oscillations even in sub optimal nutrient conditions. Our analytical and numerical work also identifies mechanisms by which biological clocks can stably maintain a constant time period under a variety of nutrient conditions. Finally, our work also explores the thermodynamic costs associated with the generation of robust sustained oscillations and shows that the net rate of entropy production alone might not be a good figure of merit to asses the quality of oscillations.

physics.bio-ph↗

arXiv2020

Robust oscillations in multi-cyclic models of biochemical clocks

Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic. Understanding the physical basis for robust biochemical oscillations in the presence of fluctuations has thus emerged as an important problem. In a previous paper [C. del Junco and S. Vaikuntanathan, Phys. Rev. E 101, 012410 (2020)], we explored this question using the non-equilibrium statistical mechanics of single-ring Markov state models of biochemical networks that support oscillations. Our finding was that they can exploit non-equilibrium driving to robustly maintain the period and coherence of oscillations in the presence of randomness in the rates. Here, we extend our work to Markov state models consisting of a large cycle decorated with multiple small cycles. These additional cycles are intended to represent alternate pathways that the oscillator may take as it fluctuates about its average path. Combining a mapping to single-cycle networks based on first passage time distributions with our previously developed theory, we are able to make analytical predictions for the period and coherence of oscillations in these networks. One implication of our predictions is that a high energy budget can make different network topologies and arrangements of rates degenerate as far as the period and coherence of oscillations is concerned. Excellent agreement between analytical and numerical results confirms that this is the case. Our results suggest that biochemical oscillators can be more robust to fluctuations in the path of the oscillator when they have a high energy budget.

cond-mat.stat-mech↗

arXiv2020

High chemical affinity increases the robustness of biochemical oscillations

Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We obtain analytical expressions for the coherence and period of oscillations in these networks. These quantities are expected to depend on all details of the transition rates in the Markov state model. However, our analytical calculations reveal that driving the system out of equilibrium makes many of these details - specifically, the location and arrangement of the transition rates - irrelevant to the coherence and period of oscillations. This theoretical prediction is confirmed by excellent agreement with numerical results. As a consequence, the coherence and period of oscillations can be robustly maintained in the presence of fluctuations in the irrelevant variables. While recent work has established that increasing energy consumption improves the coherence of oscillations, our findings suggest that it plays the additional role of making the coherence and the average period of oscillations robust to fluctuations in rates that can result from the noisy environment of the cell.

cond-mat.stat-mech↗

arXiv2019

Interface height fluctuations and surface tension of driven liquids with time-dependent dynamics

Interfaces in phase-separated driven liquids are one example of how energy input at the single-particle level changes the long-length-scale material properties of nonequilibrium systems. Here, we measure interfacial fluctuations in simulations of two liquids driven by time-dependent forces, one with repulsive interactions and one with attractive interactions. The time-dependent forces lead to currents along the interface, which can modify the scaling of interface height fluctuations with respect to predictions from capillary wave theory (CWT). We therefore characterize the whole spectrum of fluctuations to determine whether CWT applies. In the system with repulsive interactions, we find that the interface fluctuations are well-described by CWT at one amplitude of the driving forces but not at others. In the system with attractive interactions, they obey CWT for all amplitudes of driving, allowing us to extract an effective surface tension. The surface tension increases linearly over two orders of magnitude of the driving forces, more than doubling its equilibrium value. Our results show how the interfaces of nonequilibrium liquids with time-dependent forces are modified by energy input.

cond-mat.stat-mech↗

arXiv2017

Energy dissipation and fluctuations in a driven liquid

Minimal models of active and driven particles have recently been used to elucidate many properties non-equilibrium systems. However, the relation between energy consumption and changes in the structure and transport properties of these non-equilibrium materials remains to be explored. We explore this relation in a minimal model of a driven liquid that settles into a time periodic steady state. Using concepts from stochastic thermodynamics and liquid state theories, we show how the work performed on the system by the various non-conservative, time dependent forces - this quantifies a violation of time reversal symmetry - modifies the structural, transport, and phase transition properties of the driven liquid

cond-mat.soft↗