Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session W09: Stochastic Thermodynamics of Biological and Artificial Information Processing IFocus Recordings Available

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Sponsoring Units: GSNP Chair: Zhiyue Lu, University of North Carolina at Chapel Hill Room: McCormick Place W180 
Thursday, March 17, 2022 3:00PM  3:36PM 
W09.00001: Stochastic logic in thermodynamically consistent circuit models Invited Speaker: David T Limmer In this talk I will describe some of our recent efforts to apply a burgeoning understanding of fluctuations in the transport of nanoscale devices to the design of noisy logical gates. Specifically, I will employ recent developments from stochastic thermodynamics, including speed limits and generalized fluctuationdissipation relations, to elucidate the behavior of a thermodynamically consistent model of a logical circuit based on a generalization of a ressonant level model. The relationship between speed, energy consuption and accuracy will be explored in modular gate architectures of simple circuits like the D Flipflop and parity checking device. Some principles of the design of low dissipation computing will be discussed. 
Thursday, March 17, 2022 3:36PM  3:48PM 
W09.00002: Entropy production given constraints on the energy functions Artemy Kolchinsky, David H Wolpert We consider the problem of driving a finitestate classical system from some initial distribution p to some final distribution p' with vanishing entropy production (EP), under the constraint that the driving protocols can only use some limited set of energy functions S. Assuming no other constraints on the driving protocol, we derive a simple condition that guarantees that such a transformation can be carried out, which is stated in terms of the smallest probabilities in {p, p'} and a graphtheoretic property defined in terms of S. Our results imply that a surprisingly small amount of control over the energy function is sufficient (in particular, any transformation p → p' can be carried out as soon as one can control some onedimensional parameter of the energy function, e.g., the energy of a single state). We also derive a lower bound on the EP under more general constraints on the transition rates, which is formulated in terms of a convex optimization problem. 
Thursday, March 17, 2022 3:48PM  4:00PM 
W09.00003: Experimental study of a noisy information engine with memory Tushar K Saha, Jannik Ehrich, Joseph N Lucero, David A Sivak, John Bechhoefer The investigation of information engines, which use observations of the fluctuating state of a system to extract work from a heat bath, has refined our understanding of the second law of thermodynamics. Inspired by the classic thought experiment of Maxwell, our engine consists of an optically trapped bead in water, with favorable thermal fluctuations rectified by shifting the trap and converted to directed motion and even controlled trajectories. But what if the information acquired is noisy? The performance of these engines deteriorates when the feedback is based on inaccurate data. Here, we report experiments on an information engine that functions well, even when the noise in each observation is roughly equal to the size of thermal fluctuations. The key innovation is to use the memory of past observations to improve the estimate of particle position. By basing feedback on improved estimates of the system state, we can extract power even when the naive use of observations leads to a net loss of power, as too many wrong feedback decisions are made. Our engine overcomes these difficulties and shows that effective information engines can be made without requiring highly accurate observations. 
Thursday, March 17, 2022 4:00PM  4:12PM 
W09.00004: Can a single ligandreceptor simultaneously sense multiple environmental information? Asawari Pagare, Sa Hoon Min, Zhiyue Lu Yes. Cell receptor sensors provide perfect examples of information transduction in the presence of nonnegligible thermal fluctuations. Previous studies on cellular sensing have focused on minimizing the noise's impact on the accuracy of concentration sensing in ligandreceptors. However, we discovered that the thermal noise is not always an adversary  it could allow a single sensor to simultaneously receive multiple channels of environmental information (e.g., simultaneously sensing concentration, temperature, and flow speed). With minimal models of a single receptor in a Langevin bath of ligands, we demonstrate that a single receptor can simultaneously measure the ligand concentration, temperature, and flow speed (if the bath has a nonzero flow speed). Furthermore, we obtained the theoretical upper bound of informational bandwidth of a single ligandreceptor (e.g., how many environmental properties can a receptor simultaneously sense). Our results provide insights on designing novel microscopic sensors that operate in realistic and complex environments. 
Thursday, March 17, 2022 4:12PM  4:24PM 
W09.00005: Breakdown of random matrix universality in Markov models Faheem Mosam, Eric De Giuli, Diego Vidaurre Biological systems need to react to stimuli over a broad spectrum of timescales. If and how this ability can emerge without external finetuning is a puzzle. We consider this problem in discrete Markovian systems, where we can leverage results from random matrix theory. Indeed, generic large transition matrices are governed by universal results, which predict the absence of long timescales unless finetuned. We consider an ensemble of transition matrices and motivate a temperaturelike variable that controls the dynamic range of matrix elements, which we show plays a crucial role in the applicability of the large matrix limit: as the dynamic range increases, a transition occurs whereby the random matrix theory result is avoided, and long relaxation times ensue, in the entire `ordered' phase. We apply our findings to fMRI data from 820 human subjects scanned at wakeful rest. We show that the data can be quantitatively understood in terms of the random model, and that brain activity lies close to the phase transition when engaged in unconstrained, taskfree cognition  supporting the brain criticality hypothesis in this context. We also discuss the effect of matrix asymmetry, which controls entropy production, on these results. 
Thursday, March 17, 2022 4:24PM  4:36PM 
W09.00006: Estimating entropy production from waiting time distributions Dominic J Skinner, Jorn Dunkel Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra, inter or multicellular processes, a key challenge is to detect nonequilibrium behavior and quantify the rate of free energy consumption. Obtaining reliable bounds on energy consumption and entropy production directly from experimental data remains difficult in practice as many degrees of freedom typically are hidden to the observer, so that the accessible coarsegrained dynamics may not obviously violate detailed balance. Here, we introduce a novel method for bounding the entropy production of physical and living systems which uses only the waiting time statistics of hidden Markov processes and hence can be directly applied to experimental data. By determining a universal limiting curve, we infer entropy production bounds from experimental data for gene regulatory networks, mammalian behavioral dynamics and numerous other biological processes. Further considering the asymptotic limit of increasingly precise biological timers, we estimate the necessary entropic cost of heartbeat regulation in humans, dogs and mice. 
Thursday, March 17, 2022 4:36PM  4:48PM 
W09.00007: Energylandscape design principle of smart molecules for temporal pattern recognition. Chase N Slowey, Zhiyue Lu In contrast to molecules that are equilibrated in stationary environments, molecules can be driven out of equilibrium by a temporally changing environment. When a molecule has a complex energy landscape and a wide spectrum of relaxation rates, the information of the temporal pattern can be recorded into its nonequilibrium kinetics and the transient probability distribution of metastable configurations. In this work, we examine the energylandscape design principle of smart molecules that can recognize and respond to different temporal patterns of a changing environment. By constructing a minimal graph model to capture the change of energy landscape at various environmental conditions, we optimize the design of a molecule capable of distinguishing environmental temporal patterns. This allows us to study the tradeoff relation between pattern recognition performance, molecule’s complexity, and the operational cost in terms of entropy production. 
Thursday, March 17, 2022 4:48PM  5:00PM 
W09.00008: A geometric bound on the efficiency of irreversible thermodynamic cycles Adam G Frim, Michael R DeWeese Differential geometry provides powerful tools for understanding finitetime thermodynamics with notable successful applications in finding optimal protocols. Here, we use this approach to study closed thermodynamic cycles. We first focus on the Brownian Carnot engine and derive optimal geometric protocols for its finitetime operation. We find improvements over the current benchmarks in dissipated work, power, and efficiency over a wide range of experimentally accessible protocols durations. We also derive the optimal engine connecting the corners (by following the geodesics of the relevant inverse diffusion tensor) of the Carnot cycle, finding further improvements on dissipated work but at the cost of reduced power and efficiency. Building on these results, we next explore the full, unconstrained space of nonequilibrium thermodynamic cycles. We derive a novel geometric bound on the efficiency of any slowlydriven irreversible thermodynamic cycle and explicitly construct efficient heat engines operating in finite time that saturate this bound. Given the bound, these optimal cycles perform more efficiently than all other thermodynamic cycles operating as heat engines in finite time, including notable cycles such as those of Carnot, Stirling, and Otto. All of our predictions can be tested using existing experimental setups. 
Thursday, March 17, 2022 5:00PM  5:12PM 
W09.00009: Bounds on fluctuations of continuous machines in stochastic thermodynamics Matthew Gerry Thermal machines, such as heat engines and refrigerators, may be described at the nanoscale, with stochastic processes underlying the exchange of heat with thermal baths, and the input or output of work. As a result, heat and work are represented by stochastic variables, exhibiting fluctuations, which often play a significant role in evaluating device performance at this scale. In this talk, I will focus on continuous stochastic thermal machines: those whose operation is characterized by steadystate energy currents through an open system away from equilibrium. I will introduce basic models of such machines, and discuss a set of novel bounds on the ratio of fluctuations in their output currents to those in their input currents. Namely, for a given machine, this ratio is bounded from below by the square of the machine's efficiency, and from above by the square of the relevant Carnot bound. This leads to a tighterthanCarnot bound on the efficiency itself. These results have been proven universally for continuous thermal machines operating near equilibrium, in the regime of linear response. Various analytic and computational approaches have been taken towards extending them to the farfromequilibrium regime. 
Thursday, March 17, 2022 5:12PM  5:24PM 
W09.00010: Inferring entropy production rate from partially observed Langevin dynamics systems under coarsegraining Aishani Ghosal, Gili Bisker The entropy production rate (EPR) is a measure of irreversibility in systems operating far from equilibrium. The challenge in quantifying the EPR for a system obeying Langevin dynamics lies in the finite spatiotemporal resolution and the limited accessibility to all of the nonequilibrium degrees of freedom. In this talk, I will present an estimation of a lower bound on the EPR in an observed system variable following Langevin dynamics, coarsegrained into a few discrete states. In the observed variable space, the underlying driven process follows semiMarkov statistics, and thus the probability density functions of the waiting times associated with the transitions are distancetime dependent. By invoking the underlying broken timereversal symmetry, we calculate the EPR from the KullbackLeibler divergence of the density functions. We show that with finer spatial resolution, the mean dwelltime asymmetry factor increases, and that the lower bound on the EPR is highly correlated with the mean dwelltime asymmetry factor. 
Thursday, March 17, 2022 5:24PM  5:36PM 
W09.00011: Spontaneous fluctuationsymmetry breaking and the Landauer principle Lorenzo Buffoni, Michele Campisi We will present a novel approach to the problem of the energetic cost of information erasure by looking at it through the lens of the Jarzynski equality. We will point out in what sense the Landauer principle can be distinguished from the second law of thermodynamics. The Landauer bound, $\langle W \rangle \geq kT \ln 2$, on average dissipated work $\langle W \rangle$ associated to an erasure process, literally emerges from the underlying second law bound as formulated by Kelvin, $\langle W \rangle \geq 0$, as consequence of a spontaneous breaking of the CrooksTasaki fluctuationsymmetry, that accompanies logical irreversibility. The latter does not generally hold true when absolute irreversibility is present, just like the Gibbs distribution becomes inappropriate for describing, e.g., ferromagnets below the critical temperature. While the second law is a direct consequence of the fluctuation relation, the Landauer principle is a direct consequence of its breakdown. We illustrate and corroborate this insight with numerical simulations of the process of information erasure performed on a 2D Ising ferromagnet. 
Thursday, March 17, 2022 5:36PM  5:48PM 
W09.00012: Insights from an information thermodynamics analysis of a synthetic molecular motor Emanuele Penocchio, Massimiliano Esposito, Shuntaro Amano, Elisabeth Kreidt, David A Leigh, Benjamin Roberts

Thursday, March 17, 2022 5:48PM  6:00PM 
W09.00013: Thermodynamics of branching processes with resetting constrains models of cell division Arthur Genthon, Reinaldo Garcı́aGarcı́a, David Lacoste We study the Stochastic Thermodynamics of cell growth and division using a theoretical framework based on branching processes with resetting. Cell division may be split into two subprocesses: branching, by which a given cell gives birth to an identical copy of itself, and resetting, by which some properties of the daughter cells (such as their size or age) are reset to new values following division. We derive the first and second laws of Stochastic Thermodynamics for this system, and identify separate contributions due to branching and resetting. We assume a Brownian dynamics for cell variables of interest, with or without thermal noise. The athermal case is particularly important for variables like the age or the size, which often undergo a deterministic dynamics between divisions. We apply our framework to wellknown models of cell size control, such as the sizer, the timer, and the adder. We show that the entropy production of resetting is negative and that of branching is positive for these models in the regime of exponential growth of the colony. This property suggests an analogy between our model for cell growth and division and heat engines, and the introduction of a thermodynamic efficiency, which quantifies the conversion of one form of entropy production to another. 
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