Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.

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Physics of microswimmers--single particle motion and collective behavior: a review.

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Physics of Microswimmers - Single Particle Motion and Collective Behavior

Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior among the simplest forms of life and is important for fluid mixing and molecular transport on the microscale. The mathematical characterization of turbulence phenomena in active nonequilibrium fluids proves even more difficult than for conventional liquids or gases. It is not known which features of turbulent phases in living matter are universal or system-specific or which generalizations of the Navier–Stokes equations are able to describe them adequately. Here, we combine experiments, particle simulations, and continuum theory to identify the statistical properties of self-sustained meso-scale turbulence in active systems. To study how dimensionality and boundary conditions affect collective bacterial dynamics, we measured energy spectra and structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D geometries. Our experimental results for the bacterial flow statistics agree well with predictions from a minimal model for self-propelled rods, suggesting that at high concentrations the collective motion of the bacteria is dominated by short-range interactions. To provide a basis for future theoretical studies, we propose a minimal continuum model for incompressible bacterial flow. A detailed numerical analysis of the 2D case shows that this theory can reproduce many of the experimentally observed features of self-sustained active turbulence.

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Meso-scale turbulence in living fluids

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function The unifying theme in this review is energetics The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides We provide an overview of the principles of stability and where available the experimental data that report on these principles Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence

Stability and kinetics of G-quadruplex structures

Dynamic light scattering (DLS) techniques for studying sizes and shapes of nanoparticles in liquids are reviewed. In photon correlation spectroscopy (PCS), the time fluctuations in the intensity of light scattered by the particle dispersion are monitored. For dilute dispersions of spherical nanoparticles, the decay rate of the time autocorrelation function of these intensity fluctuations is used to directly measure the particle translational diffusion coefficient, which is in turn related to the particle hydrodynamic radius. For a spherical particle, the hydrodynamic radius is essentially the same as the geometric particle radius (including any possible solvation layers). PCS is one of the most commonly used methods for measuring radii of submicron size particles in liquid dispersions. Depolarized Fabry-Perot interferometry (FPI) is a less common dynamic light scattering technique that is applicable to optically anisotropic nanoparticles. In FPI the frequency broadening of laser light scattered by the particles is analyzed. This broadening is proportional to the particle rotational diffusion coefficient, which is in turn related to the particle dimensions. The translational diffusion coefficient measured by PCS and the rotational diffusion coefficient measured by depolarized FPI may be combined to obtain the dimensions of non-spherical particles. DLS studies of liquid dispersions of nanometer-sized oligonucleotides in a water-based buffer are used as examples.

Dynamic Light Scattering Measurement of Nanometer Particles in Liquids

Two theories relating the translational and rotational diffusion coefficients Dt and Dr of a rod‐like macromolecule to its length and diameter, proposed by Broersma [J. Chem. Phys. 74, 6989 (1981)], and Tirado and Garcia de la Torre [J. Chem. Phys. 71, 2581 (1979); 73, 1986 (1980)] are shown to predict different values of the coefficients for a particle of given dimensions. Next, we use the two theories to analyze existing experimental data of sedimentation coefficients s and translational and rotational diffusion coefficients of short DNA fragments, and obtain values of the hydrated diameter of DNA d which is treated as an adjustable parameter. The results are compared with the expected value, d≂26A. This comparison favors clearly the Tirado–Garcia de la Torre theory in the case of Dt and s. For Dr, and using a rise per base pair r=3.4 A, this theory gives best agreement for all the data examined, while when r=3.3 A, the agreement depends on the source of data.

Comparison of theories for the translational and rotational diffusion coefficients of rod‐like macromolecules. Application to short DNA fragments

Using rigid-body Monte Carlo simulation coupled with rigorous treatment of hydrodynamic interaction, translational coefficients and intrinsic viscosities of linear and cyclic polymers with excluded volume interactions are calculated using two models: freely jointed chains with hard-sphere interactions and Gaussian chains with Lennard-Jones potential. The results are compared with literature experimental data

http://leonardo.inf.um.es/macromol/publications/070MAC91.pdf

Monte carlo calculation of hydrodynamic properties of linear and cyclic polymers in good solvents

https://onlinelibrary.wiley.com/doi/pdf/10.1002/bip.360230402

Dimensions of short, rodlike macromolecules from translational and rotational diffusion coefficients. Study of the gramicidin dimer

Monte Carlo simulation and the rigid-body treatment have been used to calculate the radius of gyration, (s*), friction coefficient, f , and intrinsic viscosity, [TI , of cyclic polymers a t nearly ideal conditions. Three chain models, one with fixed bond lengths, another with Gaussian bonds, and another including balanced, attractive, and repulsive interactions, have been studied. They all yield the expected chainlength dependence of ( s z ) , f , and [?] at ideal conditions. The results are finally expressed in terms of the Flory parameters 9 and P , combining (9) with, respectively, [ v ] and f , and the ratios qs, qf, and q1 of the properties of the cyclic polymer to those of the linear polymer of the same length. We have analyzed experimental data for polystyrene and poly(dimethylsi1oxane). The conditions at which cyclic polymers behave ideally are different from those for linear polymer, and therefore the use of the q ratios is somewhat ambiguous or even misleading. On the other hand, our simulation results indicate that the q's may be model dependent. We thus conclude that the Flory parameters are more significant. Our results for 9 and P of cyclic polymers are in much better agreement with the experimental ones than those calculated by Bloomfield and Zimm through a treatment in which hydrodynamic interaction was preaveraged. This conclusion complements a similar one obtained for linear polymer, stressing the need of a rigorous treatment of hydrodynamic interactions.

M. Mercedes Tirado

Papers

Comparison of theories for the translational and rotational diffusion coefficients of rod‐like macromolecules. Application to short DNA fragments

Monte carlo calculation of hydrodynamic properties of linear and cyclic polymers in good solvents

Dimensions of short, rodlike macromolecules from translational and rotational diffusion coefficients. Study of the gramicidin dimer

Monte Carlo calculation of hydrodynamic properties of cyclic polymers in ideal solution