Branching processes with resetting as a model for cell division

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 sub-processes: 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 process, and identify separate contributions due to branching and resetting. We apply our framework to well-known 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.

Information flow, Gating, and Energetics in dimeric molecular motors

Molecular motors belonging to the kinesin and myosin super family hydrolyze ATP by cycling through a sequence of chemical states. These cytoplasmic motors are dimers made up of two linked identical monomeric globular proteins. Fueled by the free energy generated by ATP hydrolysis, the motors walk on polar tracks (microtubule or filamentous actin) processively, which means that only one head detaches and executes a mechanical step while the other stays bound to the track. Thus, the one motor head must regulate chemical state of the other, referred to as "gating", a concept that is not fully understood. Inspired by experiments, showing that only a fraction of the energy from ATP hydrolysis is used to advance the kinesin motors against load, we demonstrate that additional energy is used for coordinating the chemical cycles of the two heads in the dimer - a feature that characterizes gating. To this end, we develop a general framework based on information theory and stochastic thermodynamics, and establish that gating could be quantified in terms of information flow between the motor heads. Applications of the theory to kinesin-1 and Myosin V show that information flow occurs, with positive cooperativity, at external resistive loads that are less than a critical value, Fc. When force exceeds Fc, effective information flow ceases. Interestingly, Fc, which is independent of the input energy generated through ATP hydrolysis, coincides with force at which the probability of backward steps starts to increase. Our findings suggest that transport efficiency is optimal only at forces less than Fc, which implies that these motors must operate at low loads under in vivo conditions.

Skewness and Kurtosis in Stochastic Thermodynamics

The thermodynamic uncertainty relation is a prominent result in stochastic thermodynamics that provides a bound on the fluctuations of any thermodynamic flux, also known as current, in terms of the average rate of entropy production. Such fluctuations are quantified by the second moment of the probability distribution of the current. The role of higher order standardized moments such as skewness and kurtosis remains largely unexplored. We analyze the skewness and kurtosis associated with the first passage time of thermodynamic currents within the framework of stochastic thermodynamics. We develop a method to evaluate higher order standardized moments associated with the first passage time of any current. For systems with a unicyclic network of states, we conjecture upper and lower bounds on skewness and kurtosis associated with entropy production. These bounds depend on the number of states and the thermodynamic force that drives the system out of equilibrium. We show that these bounds for skewness and kurtosis do not hold for multicyclic networks. We discuss the application of our results to infer an underlying network of states.

Irreversibility and Biased Ensembles in Active Matter: Insights from Stochastic Thermodynamics

Active systems evade the rules of equilibrium thermodynamics by constantly dissipating energy at the level of their microscopic components. This energy flux stems from the conversion of a fuel, present in the environment, into sustained individual motion. It can lead to collective effects without any equilibrium equivalent, some of which can be rationalized by using equilibrium tools to recapitulate nonequilibrium transitions. An important challenge is then to delineate systematically to what extent the character of these active transitions is genuinely distinct from equilibrium analogs. We review recent works that use stochastic thermodynamics tools to identify, for active systems, a measure of irreversibility comprising a coarse-grained or informatic entropy production. We describe how this relates to the underlying energy dissipation or thermodynamic entropy production, and how it is influenced by collective behavior. Then, we review the possibility of constructing thermodynamic ensembles out-of-equilibrium, where trajectories are biased toward atypical values of nonequilibrium observables. We show that this is a generic route to discovering unexpected phase transitions in active matter systems, which can also inform their design. Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Uncertainty-induced instantaneous speed and acceleration of a levitated particle

Levitating nanoparticles trapped in optical potentials at low pressure open the experimental investigation of nonlinear ballistic phenomena. With engineered non-linear potentials and fast optical detection, the observation of autonomous transient mechanical effects, such as instantaneous speed and acceleration stimulated purely by initial position uncertainty, are now achievable. By using parameters of current low pressure experiments, we simulate and analyse such uncertainty-induced particle ballistics in a cubic optical potential demonstrating their evolution, faster than their standard deviations, justifying the feasibility of the experimental verification. We predict, the maxima of instantaneous speed and acceleration distributions shift alongside the potential force, while the maximum of position distribution moves opposite to it. We report that cryogenic cooling is not necessary in order to observe the transient effects, while a low uncertainty in initial particle speed is required, via cooling or post-selection, to not mask the effects. These results stimulate the discussion for both attractive stochastic thermodynamics, and extension of recently explored quantum regime.

Temporal irreversibility of neural dynamics as a signature of consciousness

Even though the fundamental laws of physics are the same when the direction of time is inverted, dissipative systems evolve in the preferred temporal direction indicated by the thermodynamic arrow of time. The fundamental nature of this temporal asymmetry led us to hypothesize its presence in the neural activity evoked by conscious perception of the physical world, and thus its covariance with the level of conscious awareness. Inspired by recent developments in stochastic thermodynamics, we implemented a data-driven and model-free deep learning framework to decode the temporal inversion of electrocorticography signals acquired from non-human primates. Brain activity time series recorded during conscious wakefulness could be distinguished from their inverted counterparts with high accuracy, both using frequency and phase information. However, classification accuracy was reduced for data acquired during deep sleep and under ketamine-induced anesthesia; moreover, the predictions obtained from multiple independent neural networks were less consistent for sleep and anesthesia than for conscious wakefulness. Finally, the analysis of feature importance scores highlighted transitions between slow (≈20 Hz) and fast frequencies (> 40 Hz) as the main contributors to the temporal asymmetry observed during conscious wakefulness. Our results show that a preferred temporal direction is simultaneously manifest in the neural activity evoked by conscious mentation and in the phenomenology of the passage of time, establishing common ground to tackle the relationship between brain and subjective experience.