Nonequilibrium Physics in Biology

Xiaona Fang, Karsten Kruse, Ting Lu, Jin Wang
Life is characterized by a myriad of complex dynamic processes allowing organisms to grow, reproduce, and evolve. Physical approaches for describing systems out of thermodynamic equilibrium have been increasingly applied to living systems, which often exhibit phenomena unknown from those traditionally studied in physics. Spectacular advances in experimentation during the last decade or two, for example, in microscopy, single cell dynamics, in the reconstruction of sub- and multicellular systems outside of living organisms, or in high throughput data acquisition have yielded an unprecedented wealth of data about cell dynamics, genetic regulation, and organismal development. These data have motivated the development and refinement of concepts and tools to dissect the physical mechanisms underlying biological processes. Notably, the landscape and flux theory as well as active hydrodynamic gel theory have proven very useful in this endeavour. Together with concepts and tools developed in other areas of nonequilibrium physics, significant progresses have been made in unraveling the principles underlying efficient energy transport in photosynthesis, cellular regulatory networks, cellular movements and organization, embryonic development and cancer, neural network dynamics, population dynamics and ecology, as well as ageing, immune responses and evolution. Here, we review recent advances in nonequilibrium physics and survey their application to biological systems. We expect many of these results to be important cornerstones as the field continues to build our understanding of life.

Click to access 2012.05067.pdf

The thermodynamics of clocks

G J Milburn
All clocks, classical or quantum, are open non equilibrium irreversible systems subject to the constraints of thermodynamics. Using examples I show that these constraints necessarily limit the performance of clocks and that good clocks require large energy dissipation. For periodic clocks, operating on a limit cycle, this is a consequence of phase diffusion. It is also true for non periodic clocks (for example, radio carbon dating) but due to telegraph noise not to phase diffusion. In this case a key role is played by accurate measurements that decrease entropy, thereby raising the free energy of the clock, and requires access to a low entropy reservoir. In the quantum case, for which thermal noise is replaced by quantum noise (spontaneous emission or tunnelling), measurement plays an essential role for both periodic and non periodic clocks. The paper concludes with a discussion of the Tolman relations and Rovelli’s thermal time hypothesis in terms of clock thermodynamics.

Click to access 2007.02217.pdf

Maxwell’s Demon and Its Fallacies Demystified

Milivoje M. Kostic
A demonic being, introduced by Maxwell, to miraculously create thermal non-equilibrium and violate the Second law of thermodynamics, has been among the most intriguing and elusive wishful concepts for over 150 years. Maxwell and his followers focused on ‘effortless gating’ a molecule at a time, but overlooked simultaneous interference of other chaotic molecules, while the demon exorcists tried to justify impossible processes with misplaced ‘compensations’ by work of measurements and gate operation, and information storage and memory erasure with entropy generation. The illusive and persistent Maxwell’s demon fallacies by its advocates, as well as its exorcists, are scrutinized and resolved here. Based on holistic, phenomenological reasoning, it is deduced here that a Maxwell’s demon operation, against natural forces and without due work effort to suppress interference of competing thermal particles while one is selectively gated, is not possible at any scale, since it would be against the physics of the chaotic thermal motion, the latter without consistent molecular directional preference for selective timing to be possible. Maxwell’s demon would have miraculous useful effects, but also some catastrophic consequences.


Analogy between thermal emission of nano objects and Hawking’s radiation

Karl Joulain
We analyze in this work some analogies between thermal emission of nano objects and Hawking’s radiation. We first focus on the famous expression of the black hole radiating temperature derived by Hawking in 1974 and consider the case of thermal emission of a small aperture made into a cavity (Ideal Blackbody). We show that an expression very similar to Hawking’s temperature determines a temperature below which an aperture in a cavity cannot be considered as standard blackbody radiating like T^4. Hawking’s radiation therefore appear as a radiation at a typical wavelength which is of the size of the horizon radius. In a second part, we make the analogy between the emission of particle-anti particle pairs near the black hole horizon and the scattering and coupling of thermally populated evanescent waves by a nano objects. We show here again that a temperature similar to the Hawking temperature determines the regimes where the scattering occur or where it is negligible.