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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.
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In this paper I am presenting an overview on several topics related to nonequilibrium fluctuations in small systems. I start with a general discussion about fluctuation theorems and applications to physical examples extracted from physics and biology: a bead in an optical trap and single molecule force experiments. Next I present a general discussion on path thermodynamics and consider distributions of work/heat fluctuations as large deviation functions. Then I address the topic of glassy dynamics from the perspective of nonequilibrium fluctuations due to small cooperatively rearranging regions. Finally, I conclude with a brief digression on future perspectives.
Theoretical physics is the search for simple and universal mathematical descriptions of the natural world. In contrast, much of modern biology is an exploration of the complexity and diversity of life. For many, this contrast is prima facie evidence that theory, in the sense that physicists use the word, is impossible in a biological context. For others, this contrast serves to highlight a grand challenge. Im an optimist, and believe (along with many colleagues) that the time is ripe for the emergence of a more unified theoretical physics of biological systems, building on successes in thinking about particular phenomena. In this essay I try to explain the reasons for my optimism, through a combination of historical and modern examples.
Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme -- the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.
Is there a functional role for quantum mechanics or coherent quantum effects in biological processes? While this question is as old as quantum theory, only recently have measurements on biological systems on ultra-fast time-scales shed light on a possible answer. In this review we give an overview of the two main candidates for biological systems which may harness such functional quantum effects: photosynthesis and magnetoreception. We discuss some of the latest evidence both for and against room temperature quantum coherence, and consider whether there is truly a functional role for coherence in these biological mechanisms. Finally, we give a brief overview of some more speculative examples of functional quantum biology including the sense of smell, long-range quantum tunneling in proteins, biological photoreceptors, and the flow of ions across a cell membrane.
Neutrons and x-rays are coherent probes, and their coherent properties are used in scattering experiments. Only coherent scattering probes can elucidate collective molecular motions. While phonons in crystals were studied for half a century now, the study of collective molecular motions in soft-matter and biology is a rather new but upcoming field. Collective dynamics often determine material properties and interactions, and are crucial to establish dynamics-function relations. We review properties of neutrons and x-rays and derive the origin of coherent and incoherent scattering. Taking molecular motions in membranes and proteins as example, the difference between coherent and incoherent dynamics is discussed, and how local and collective motions can be accessed in x-ray and neutron scattering experiments. Matching of coherent properties of the scattering probe may become important in soft-matter and biology because of (1) the missing long ranged order and (2) the large length scales involved. It is likely to be important in systems, where fluctuating nanoscale domains strongly determine material properties. Inelastic scattering can provide very local structural information in disordered systems. Inelastic neutron scattering experiments point to a coexistence of short-lived nanoscale gel and fluid domains in phospholipid bilayers in the range of the gel-fluid phase transition, which may be responsible for critical behavior and determine elastic properties.
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