arXiv subjects

Andre C. Barato

Publications and source records attributed to Andre C. Barato.

27 records · Page 2Linked to original sources

arXiv2015

A formal view on 2.5 large deviations and fluctuation relations

We obtain the rate function for the level 2.5 of large deviations for pure jump and diffusion processes. This result is proved by two methods: tilting, for which a tilted process with an appropriate typical behavior is considered, and a spectral method, for which the scaled cumulant generating function is used. We also briefly discuss fluctuation relations, pointing out their connection with large deviations at the level 2.5.

cond-mat.stat-mech↗

arXiv2015

Nonequilibrium sensing and its analogy to kinetic proofreading

For a paradigmatic model of chemotaxis, we analyze the effect how a nonzero affinity driving receptors out of equilibrium affects sensitivity. This affinity arises whenever changes in receptor activity involve ATP hydrolysis. The sensitivity integrated over a ligand concentration range is shown to be enhanced by the affinity, providing a measure of how much energy consumption improves sensing. With this integrated sensitivity we can establish an intriguing analogy between sensing with nonequilibrium receptors and kinetic proofreading: the increase in integrated sensitivity is equivalent to the decrease of the error in kinetic proofreading. The influence of the occupancy of the receptor on the phosphorylation and dephosphorylation reaction rates is shown to be crucial for the relation between integrated sensitivity and affinity. This influence can even lead to a regime where a nonzero affinity decreases the integrated sensitivity, which corresponds to anti-proofreading.

physics.bio-ph↗

arXiv2015

Universal Bound on the Fano Factor in Enzyme Kinetics

The Fano factor, an observable quantifying fluctuations of product generation by a single enzyme, can reveal information about the underlying reaction scheme. A lower bound on this Fano factor that depends on the thermodynamic affinity driving the transformation from substrate to product constrains the number of intermediate states of an enzymatic cycle. So far, this bound has been proven only for a unicyclic network of states. We show that the bound can be extended to arbitrary multicyclic networks, with the Fano factor constraining the largest value of the effective length, which is the ratio between the number of states and the number of products, among all cycles.

physics.chem-ph↗

arXiv2015

Thermodynamic uncertainty relation for biomolecular processes

Biomolecular systems like molecular motors or pumps, transcription and translation machinery, and other enzymatic reactions can be described as Markov processes on a suitable network. We show quite generally that in a steady state the dispersion of observables like the number of consumed/produced molecules or the number of steps of a motor is constrained by the thermodynamic cost of generating it. An uncertainty $ε$ requires at least a cost of $2k_BT/ε^2$ independent of the time required to generate the output.

cond-mat.stat-mech↗

arXiv2014

Stochastic thermodynamics with information reservoirs

We generalize stochastic thermodynamics to include information reservoirs. Such information reservoirs, which can be modeled as a sequence of bits, modify the second law. For example, work extraction from a system in contact with a single heat bath becomes possible if the system also interacts with an information reservoir. We obtain an inequality, and the corresponding fluctuation theorem, generalizing the standard entropy production of stochastic thermodynamics. From this inequality we can derive an information processing entropy production, which gives the second law in the presence of information reservoirs. We also develop a systematic linear response theory for information processing machines. For a unicyclic machine powered by an information reservoir, the efficiency at maximum power can deviate from the standard value of 1/2. For the case where energy is consumed to erase the tape, the efficiency at maximum erasure rate is found to be 1/2.

cond-mat.stat-mech↗

arXiv2014

Efficiency of cellular information processing

We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an informational efficiency that can be used to study cellular information processing. We analyze three models of increasing complexity inspired by the E. coli sensory network, where the external process is an external ligand concentration jumping between two values. We start with a simple model for which ATP must be consumed so that a protein inside the cell can learn about the external concentration. With a second model for a single receptor we show that the rate at which the receptor learns about the external environment can be nonzero even without any dissipation inside the cell since chemical work done by the external process compensates for this learning rate. The third model is more complete, also containing adaptation. For this model we show inter alia that a bacterium in an environment that changes at a very slow time-scale is quite inefficient, dissipating much more than it learns. Using the concept of a coarse-grained learning rate, we show for the model with adaptation that while the activity learns about the external signal the option of changing the methylation level increases the concentration range for which the learning rate is substantial.

physics.bio-ph↗

arXiv2014

Optimized finite-time information machine

We analyze a periodic optimal finite-time two-state information-driven machine that extracts work from a single heat bath exploring imperfect measurements. Two models are considered, a memory-less one that ignores past measurements and an optimized model for which the feedback scheme consists of a protocol depending on the whole history of measurements. Depending on the precision of the measurement and on the period length the optimized model displays a phase transition to a phase where measurements are judged as non-reliable. We obtain the critical line exactly and show that the optimized model leads to more work extraction in comparison to the memory-less model, with the gain parameter being larger in the region where the frequency of non-reliable measurements is higher. We also demonstrate that the model has two second law inequalities, with the extracted work being bounded by the change of the entropy of the system and by the mutual information.

cond-mat.stat-mech↗

arXiv2014

Stochastic thermodynamics of bipartite systems: transfer entropy inequalities and a Maxwell's demon interpretation

We consider the stationary state of a Markov process on a bipartite system from the perspective of stochastic thermodynamics. One subsystem is used to extract work from a heat bath while being affected by the second subsystem. We show that the latter allows for a transparent and thermodynamically consistent interpretation of a Maxwell's demon. Moreover, we obtain an integral fluctuation theorem involving the transfer entropy from one subsystem to the other. Comparing three different inequalities, we show that the entropy decrease of the first subsystem provides a tighter bound on the rate of extracted work than both the rate of transfer entropy from this subsystem to the demon and the heat dissipated through the dynamics of the demon. The latter two rates cannot be ordered by an inequality as shown with the illustrative example of a four state system.

cond-mat.stat-mech↗

arXiv2008

Nonequilibrium phase transition in a spreading process on a timeline

We consider a nonequilibrium process on a timeline with discrete sites which evolves by a non-Markovian update rule in such a way that an active site at time t activates one or several sites in the future at time t+dt. The time intervals dt are distributed algebraically as dt^(-1-kappa), where 0<kappa<1 is a control paramter. Depending on the activation rate, the system display a nonequilibrium phase transition which may be interpreted as directed percolation transition driven by temporal Levy flights in the limit of zero space dimensions. The critical properties are investigated by extensive numerical simulations and compared with field-theoretic predictions.

cond-mat.stat-mech↗