Information, Coding, and Biological Function: The Dynamics of Life.

In the mid-20th century, two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning, cross-fertilization was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids. However, today, such synergy has not taken advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges not only are of great theoretical relevance but also represent unavoidable milestones for next-generation biology: from personalized genetic therapy and diagnosis to Artificial Life to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered a long time ago, that requires combined contributions from disciplines well beyond the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. Successfully achieving these tasks requires a wide multidisciplinary approach, including Artificial Life researchers, to address such an endeavour.

Geometric mixing.

Mixing fluids often involves a periodic action, like stirring one's tea. But reciprocating motions in fluids at low Reynolds number, in Stokes flows where inertia is negligible, lead to periodic cycles of mixing and unmixing, because the physics, molecular diffusion excepted, is time reversible. So how can fluid be mixed in such circumstances? The answer involves a geometric phase. Geometric phases are found everywhere in physics as anholonomies, where after a closed circuit in the parameters, some system variables do not return to their original values. We discuss the geometric phase in fluid mixing: geometric mixing. This article is part of the theme issue 'Stokes at 200 (part 2)'.

The fluid mechanics of poohsticks.

The year 2019 marked the bicentenary of George Gabriel Stokes, who in 1851 described the drag-Stokes drag-on a body moving immersed in a fluid, and 2020 is the centenary of Christopher Robin Milne, for whom the game of poohsticks was invented; his father A. A. Milne's The House at Pooh Corner, in which it was first described in print, appeared in 1928. So this is an apt moment to review the state of the art of the fluid mechanics of a solid body in a complex fluid flow, and one floating at the interface between two fluids in motion. Poohsticks pertains to the latter category, when the two fluids are water and air. This article is part of the theme issue 'Stokes at 200 (part 2)'.

Chemosensing versus mechanosensing in nodal and Kupffer's vesicle cilia and in other left-right organizer organs.

How is sensing carried out by cilia in the mouse node, zebrafish Kupffer's vesicle and similar left-right (LR) organizer organs in other species? Two possibilities have been put forward. In the former, cilia would detect some chemical species in the fluid; in the latter, they would detect fluid flow. In either case, the hypothesis is that an imbalance would be detected between this signalling coming from cilia on the left and right sides of the organizer, which would initiate a cascade of signals leading ultimately to the breaking of LR symmetry in the developing body plan of the organism. We review the evidence for both hypotheses. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach.

Mixing fluid in a container at low Reynolds number--in an inertialess environment--is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the "belly phase," peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing.

Excitability and optical pulse generation in semiconductor lasers driven by resonant tunneling diode photo-detectors.

We demonstrate, experimentally and theoretically, excitable nanosecond optical pulses in optoelectronic integrated circuits operating at telecommunication wavelengths (1550 nm) comprising a nanoscale double barrier quantum well resonant tunneling diode (RTD) photo-detector driving a laser diode (LD). When perturbed either electrically or optically by an input signal above a certain threshold, the optoelectronic circuit generates short electrical and optical excitable pulses mimicking the spiking behavior of biological neurons. Interestingly, the asymmetric nonlinear characteristic of the RTD-LD allows for two different regimes where one obtain either single pulses or a burst of multiple pulses. The high-speed excitable response capabilities are promising for neurally inspired information applications in photonics.

Runaway electrification of friable self-replicating granular matter.

We establish that the nonlinear dynamics of collisions between particles favors the charging of an insulating, friable, self-replicating granular material that undergoes nucleation, growth, and fission processes; we demonstrate with a minimal dynamical model that secondary nucleation produces a positive feedback in an electrification mechanism that leads to runaway charging. We discuss ice as an example of such a self-replicating granular material: We confirm with laboratory experiments in which we grow ice from the vapor phase in situ within an environmental scanning electron microscope that charging causes fast-growing and easily breakable palmlike structures to form, which when broken off may form secondary nuclei. We propose that thunderstorms, both terrestrial and on other planets, and lightning in the solar nebula are instances of such runaway charging arising from this nonlinear dynamics in self-replicating granular matter.

Three-dimensional structure of the Z-ring as a random network of FtsZ filaments.

The spatial organization of the Z-ring, the central element of the bacterial division machinery, is not yet fully understood. Using optical tweezers and subpixel image analysis, we have recently shown that the radial width of the Z-ring in unconstricted Escherichia coli is about 100 nm. The relatively large width is consistent with the observations of others. Moreover, simulation of the experimental FtsZ distribution using the theoretical three-dimensional (3D) point spread function was strongly in favour of a toroidal rather than a thin cylindrical model of the Z-ring. Here, we show that the low density of FtsZ filaments in the ring coincides within experimental uncertainty with the critical density of a 3D random network of cylindrical sticks. This suggests that the Z-ring may consist of a percolating network of FtsZ filaments. Several factors that are expected to affect the polymerization state and the extent of self-interaction of FtsZ within the Z-ring, as well as the functional implications of its sparse toroidal structure, are discussed in terms of percolation theory.

Ice polyamorphism in the minimal Mercedes-Benz model of water.

We investigate ice polyamorphism in the context of the two-dimensional Mercedes-Benz model of water. We find a first-order phase transition between a crystalline phase and a high-density amorphous phase. Furthermore, we find a reversible transformation between two amorphous structures of high and low density; however, we find this to be a continuous and not an abrupt transition, as the low-density amorphous phase does not show structural stability. We discuss the origin of this behavior and its implications with regard to the minimal generic modeling of polyamorphism.

Interactions between hair cells shape spontaneous otoacoustic emissions in a model of the tokay gecko's cochlea.

BACKGROUND: The hearing of tetrapods including humans is enhanced by an active process that amplifies the mechanical inputs associated with sound, sharpens frequency selectivity, and compresses the range of responsiveness. The most striking manifestation of the active process is spontaneous otoacoustic emission, the unprovoked emergence of sound from an ear. Hair cells, the sensory receptors of the inner ear, are known to provide the energy for such emissions; it is unclear, though, how ensembles of such cells collude to power observable emissions. METHODOLOGY AND PRINCIPAL FINDINGS: We have measured and modeled spontaneous otoacoustic emissions from the ear of the tokay gecko, a convenient experimental subject that produces robust emissions. Using a van der Pol formulation to represent each cluster of hair cells within a tonotopic array, we have examined the factors that influence the cooperative interaction between oscillators. CONCLUSIONS AND SIGNIFICANCE: A model that includes viscous interactions between adjacent hair cells fails to produce emissions similar to those observed experimentally. In contrast, elastic coupling yields realistic results, especially if the oscillators near the ends of the array are weakened so as to minimize boundary effects. Introducing stochastic irregularity in the strength of oscillators stabilizes peaks in the spectrum of modeled emissions, further increasing the similarity to the responses of actual ears. Finally, and again in agreement with experimental findings, the inclusion of a pure-tone external stimulus repels the spectral peaks of spontaneous emissions. Our results suggest that elastic coupling between oscillators of slightly differing strength explains several properties of the spontaneous otoacoustic emissions in the gecko.

Influence of microstructure on the transitions between mesoscopic thin-film morphologies in ballistic-diffusive models.

We study the influence of the symmetries of competing microstructures on the emergence of different mesoscopic morphologies in the growth by vapor deposition of thin solid films. We show the results of numerical simulations in (1+1) - and (2+1) -dimensional systems including different microstructures, as well as thermally activated surface diffusion in combination with a ballistic algorithm to model the deposition process. We focus on the characterization of the transitional structures that appear in the empirical structure zone model (SZM) through the evaluation of the mean packing density and the mean coordination number. We show that the maximum coordination number of the underlying microstructure classifies the statistics of the transitional morphologies at the border between zone I in the SZM, characterized by the formation of fractal-like patterns, and zone II, where pronounced faceting develops. We analyze the appearance of lattice frustration and texture competition effects in complex microstructures having mutually exclusive symmetries.

Modeling the resonant release of synaptic transmitter by hair cells as an example of biological oscillators with cooperative steps.

The initial synapses of the auditory system, which connect hair cells to afferent nerve fibers, display two unusual features. First, synaptic transmission occurs in a multiquantal fashion: the contents of multiple synaptic vesicles are discharged simultaneously. Second, synaptic transmission may be tuned to specific frequencies of stimulation. We developed a minimal theoretical model to explore the possibility that hair-cell synapses achieve both multiquantal release and frequency selectivity through a cooperative mechanism for the exocytotic release of neurotransmitter. We first characterized vesicle release as a four-step cycle at each release site, then generalized the result to an arbitrary number of steps. The cyclic process itself induces some degree of resonance, and may display a stable, underdamped fixed point of the release dynamics associated with a pair of complex eigenvalues. Cooperativity greatly enhances the frequency selectivity by moving the eigenvalues toward the imaginary axis; spontaneously oscillatory release can arise beyond a Hopf bifurcation. These phenomena occur both in the macroscopic limit, when the number of release sites involved is very large, and in the more realistic stochastic regime, when only a limited number of release sites participate at each synapse. It is thus possible to connect multiquantal release with frequency selectivity through the mechanism of cooperativity.

Fluid dynamics in developmental biology: moving fluids that shape ontogeny.

Human conception, indeed fertilization in general, takes place in a fluid, but what role does fluid dynamics have during the subsequent development of an organism? It is becoming increasingly clear that the number of genes in the genome of a typical organism is not sufficient to specify the minutiae of all features of its ontogeny. Instead, genetics often acts as a choreographer, guiding development but leaving some aspects to be controlled by physical and chemical means. Fluids are ubiquitous in biological systems, so it is not surprising that fluid dynamics should play an important role in the physical and chemical processes shaping ontogeny. However, only in a few cases have the strands been teased apart to see exactly how fluid forces operate to guide development. Here, we review instances in which the hand of fluid dynamics in developmental biology is acknowledged, both in human development and within a wider biological context, together with some in which fluid dynamics is notable but whose workings have yet to be understood, and we provide a fluid dynamicist's perspective on possible avenues for future research.

Self-tuned critical anti-Hebbian networks.

It is widely recognized that balancing excitation and inhibition is important in the nervous system. When such a balance is sought by global strategies, few modes remain poised close to instability, and all other modes are strongly stable. Here we present a simple abstract model in which this balance is sought locally by units following "anti-Hebbian" evolution: all degrees of freedom achieve a close balance of excitation and inhibition and become "critical" in the dynamical sense. At long time scales, a complex "breakout" dynamics ensues in which different modes of the system oscillate between prominence and extinction; the model develops various long-tailed statistical behaviors and may become self-organized critical.

Impact and permanence of LASIK-induced structural changes in the cornea on pneumotonometric measurements: contributions of flap cutting and stromal ablation.

PURPOSE: To determine the factors that lead to changes in intraocular pressure (IOP) measurements after laser-assisted in situ keratomileusis (LASIK) and their long-term stability. PATIENTS AND METHODS: Five hundred twenty-two myopic eyes and 296 hyperopic eyes were enrolled in the study. Pneumotonometry was used to measure IOP once in the preoperative stage and twice in the postoperative stage-1 month after the operation and 1 year later. Ultrasonic pachymetry was used to determine preoperative and intraoperative corneal thicknesses and axial length of the eye, whereas optical pachymetry was used in the preoperative stage and 1 month after surgery. Corneal topography was used to determine the preoperative and postoperative mean curvature of the anterior surface of the cornea over 3 and 5-mm diameter regions. Comparative statistical analysis of the retrospective data series was performed. RESULTS: A highly significant reduction of IOP readings is found after LASIK for both myopic and hyperopic eyes. The reduction is stable 1 year after LASIK. In the case of myopic eyes, the reduction has a highly significant linear correlation with the amount of tissue ablated in the central region of the cornea. CONCLUSIONS: Pneumotonometric IOP readings after LASIK are reduced, without recovering preoperative values even 1 year after surgery, because of flap cutting and tissue removal in the central region of the cornea. The contribution of flap cutting is estimated to be (1.6+/-0.8) mm Hg, whereas ablation contributes an additional (0.029+/-0.003) mm Hg/microm of removed tissue. This effect should be considered when evaluating the accuracy of IOP measurements in LASIK patients who are at risk for developing glaucoma.

Dynamics of tidal synchronization and orbit circularization of celestial bodies.

We take a dynamical-systems approach to study the qualitative dynamical aspects of the tidal locking of the rotation of secondary celestial bodies with their orbital motion around the primary. We introduce a minimal model including the essential features of gravitationally induced elastic deformation and tidal dissipation that demonstrates the details of the energy transfer between the orbital and rotovibrational degrees of freedom. Despite its simplicity, our model can account for both synchronization into the 1:1 spin-orbit resonance and the circularization of the orbit as the only true asymptotic attractors, together with the existence of relatively long-lived metastable orbits with the secondary in p:q synchronous rotation.

Fluid dynamics of nodal flow and left-right patterning in development.

The manner in which the nodal flow determines the breaking of left-right symmetry during development is a beautiful example of the application of fluid dynamics to developmental biology. Detailed understanding of this crucial developmental process has greatly advanced by the transfer of ideas between these two disciplines. In this article, we review our and others' work on applying fluid dynamics and dynamical systems to the problem of left-right symmetry breaking in vertebrates.

Fluid dynamics of establishing left-right patterning in development.

How does the clockwise motion of tens of monocilia drive a leftward flow in the node? And, as the observed flow is leftward, how is the fluid recirculating within the node, as it must, because the node is a closed structure? How does the nodal flow lead to left-right symmetry breaking in the embryo? These questions are within the realm of fluid physics, whose application to the problem of left-right symmetry breaking in vertebrates has led to important advances in the field.

Fronts between rhythms: spatiotemporal dynamics of extended polyrhythmic media.

We study the propagation of fronts in extended oscillatory reaction-diffusion systems that contain several coexisting limit cycles. In contrast with the variational behavior, fronts between regions oscillating in two different limit cycles are found to propagate not necessarily towards the region of the less stable limit cycle, but towards the regions of the largest amplitudes, provided that the frequency mismatch between the cycles is sufficiently large. In other words, the smaller oscillations can always be made to control the whole system.

Ostwald ripening, chiral crystallization, and the common-ancestor effect.

We introduce an agent-based model for advection-mediated chiral autocatalysis in which we take into account dissolution-crystallization processes through Ostwald ripening. We demonstrate that the latter phenomenon is the key to explaining previously puzzling experimental results whereby complete chiral symmetry breaking is attained from an initially unbiased mixture of seed crystals. We show that this homochirality is achieved by what has been termed the common-ancestor effect: Ostwald ripening removes competing lineages, leaving only one common ancestor for the entire system.