scholarly journals Modern Stochastic Thermodynamics

10.5772/13847 ◽  
2011 ◽  
Author(s):  
A. D. ◽  
O. N.
Keyword(s):  
Stochastic Thermodynamics

scholarly journals Close to Optimal Cell Sensing Ensures the Robustness of Tissue Differentiation Process: The Avian Photoreceptor Mosaic Case

Entropy ◽  
2021 ◽  
Vol 23 (7) ◽  
pp. 867
Author(s):  
Arnab Barua ◽  
Alireza Beygi ◽  
Haralampos Hatzikirou
Keyword(s):  
Cell Fate ◽  
Cell Metabolism ◽  
Explanatory Power ◽  
Spatial Order ◽  
Cell Level ◽  
Stochastic Thermodynamics ◽  
Cell Fate Decisions ◽  
Model Predictions ◽  
Sensing Radius ◽  
Photoreceptor Mosaic

The way that progenitor cell fate decisions and the associated environmental sensing are regulated to ensure the robustness of the spatial and temporal order in which cells are generated towards a fully differentiating tissue still remains elusive. Here, we investigate how cells regulate their sensing intensity and radius to guarantee the required thermodynamic robustness of a differentiated tissue. In particular, we are interested in finding the conditions where dedifferentiation at cell level is possible (microscopic reversibility), but tissue maintains its spatial order and differentiation integrity (macroscopic irreversibility). In order to tackle this, we exploit the recently postulated Least microEnvironmental Uncertainty Principle (LEUP) to develop a theory of stochastic thermodynamics for cell differentiation. To assess the predictive and explanatory power of our theory, we challenge it against the avian photoreceptor mosaic data. By calibrating a single parameter, the LEUP can predict the cone color spatial distribution in the avian retina and, at the same time, suggest that such a spatial pattern is associated with quasi-optimal cell sensing. By means of the stochastic thermodynamics formalism, we find out that thermodynamic robustness of differentiated tissues depends on cell metabolism and cell sensing properties. In turn, we calculate the limits of the cell sensing radius that ensure the robustness of differentiated tissue spatial order. Finally, we further constrain our model predictions to the avian photoreceptor mosaic.

scholarly journals Skewness and Kurtosis in Stochastic Thermodynamics

2021 ◽  
Author(s):  
Andre Cardoso Barato ◽  
Taylor Wampler
Keyword(s):  
Entropy Production ◽  
Average Rate ◽  
First Passage Time ◽  
Passage Time ◽  
Higher Order ◽  
Upper And Lower Bounds ◽  
Thermodynamic Force ◽  
First Passage ◽  
Stochastic Thermodynamics ◽  
Skewness And Kurtosis

Abstract 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.

scholarly journals Energy dissipation and fluctuations in a driven liquid

2018 ◽  
Vol 115 (14) ◽  
pp. 3569-3574 ◽  
Author(s):  
Clara del Junco ◽  
Laura Tociu ◽  
Suriyanarayanan Vaikuntanathan
Keyword(s):  
Phase Transition ◽  
Steady State ◽  
Time Reversal ◽  
Time Dependent ◽  
Time Reversal Symmetry ◽  
Nonequilibrium Systems ◽  
Minimal Models ◽  
Stochastic Thermodynamics ◽  
Periodic Steady State ◽  
Time Periodic

Minimal models of active and driven particles have recently been used to elucidate many properties of nonequilibrium systems. However, the relation between energy consumption and changes in the structure and transport properties of these nonequilibrium 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 various nonconservative, time-dependent forces—this quantifies a violation of time reversal symmetry—modifies the structural, transport, and phase transition properties of the driven liquid.

scholarly journals Stochastically pumped adaptation and directional motion of molecular machines

2018 ◽  
Vol 115 (38) ◽  
pp. 9405-9413 ◽  
Author(s):  
R. Dean Astumian
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
High Efficiency ◽  
Probability Distributions ◽  
Molecular Machines ◽  
High Energy ◽  
Stochastic Thermodynamics ◽  
Recent Developments ◽  
Directional Motion ◽  
External Fluctuations

Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium.

Organization and Self-Assembly Away from Equilibrium: Toward Thermodynamic Design Principles

2021 ◽  
Vol 12 (1) ◽  
pp. 273-290
Author(s):  
Michael Nguyen ◽  
Yuqing Qiu ◽  
Suriyanarayanan Vaikuntanathan
Keyword(s):  
Energy Dissipation ◽  
Self Assembly ◽  
Biological Systems ◽  
Design Principles ◽  
Nonequilibrium Process ◽  
Nanoscale Materials ◽  
Stochastic Thermodynamics ◽  
Synthetic Materials ◽  
Starting Point

Studies of biological systems and materials, together with recent experimental and theoretical advances in colloidal and nanoscale materials, have shown how nonequilibrium forcing can be used to modulate organization in many novel ways. In this review, we focus on how an accounting of energy dissipation, using the tools of stochastic thermodynamics, can constrain and provide intuition for the correlations and configurations that emerge in a nonequilibrium process. We anticipate that the frameworks reviewed here can provide a starting point to address some of the unique phenomenology seen in biophysical systems and potentially replicate them in synthetic materials.

Stochastic Thermodynamics

2021 ◽  
pp. 87-118
Author(s):  
Sarah A. M. Loos
Keyword(s):  
Stochastic Thermodynamics

scholarly journals Energy dissipation bounds for autonomous thermodynamic cycles

2020 ◽  
Vol 117 (7) ◽  
pp. 3478-3483 ◽  
Author(s):  
Samuel J. Bryant ◽  
Benjamin B. Machta
Keyword(s):  
Energy Dissipation ◽  
Energy Cost ◽  
Control Parameter ◽  
Thermodynamic Process ◽  
Stochastic Thermodynamics ◽  
Controlled System ◽  
Single Degree Of Freedom ◽  
Thermodynamic Cycles ◽  
Single Degree ◽  
The Cost

How much free energy is irreversibly lost during a thermodynamic process? For deterministic protocols, lower bounds on energy dissipation arise from the thermodynamic friction associated with pushing a system out of equilibrium in finite time. Recent work has also bounded the cost of precisely moving a single degree of freedom. Using stochastic thermodynamics, we compute the total energy cost of an autonomously controlled system by considering both thermodynamic friction and the entropic cost of precisely directing a single control parameter. Our result suggests a challenge to the usual understanding of the adiabatic limit: Here, even infinitely slow protocols are energetically irreversible.

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