Thermodynamic Effects Are Essential for Surface Entrapment of Bacteria.

The entrapment of bacteria near boundary surfaces is of biological and practical importance, yet the underlying physics is not well understood. We demonstrate that it is crucial to include a commonly neglected thermodynamic effect related to the spatial variation of hydrodynamic interactions, through a model that provides analytic explanation of bacterial entrapment in two dimensionless parameters: α_{1} the ratio of thermal energy to self-propulsion, and α_{2} an intrinsic shape factor. For α_{1} and α_{2} that match an Escherichia coli at room temperature, our model quantitatively reproduces existing experimental observations, including two key features that have not been previously resolved: The bacterial "nose-down" configuration, and the anticorrelation between the pitch angle and the wobbling angle.

The colloidal nature of complex fluids enhances bacterial motility.

The natural habitats of microorganisms in the human microbiome, ocean and soil ecosystems are full of colloids and macromolecules. Such environments exhibit non-Newtonian flow properties, drastically affecting the locomotion of microorganisms. Although the low-Reynolds-number hydrodynamics of swimming flagellated bacteria in simple Newtonian fluids has been well developed, our understanding of bacterial motility in complex non-Newtonian fluids is less mature.

Localization, Disorder, and Entropy in a Coarse-Grained Model of the Amorphous Solid.

We study the role of disorder in producing the metastable states in which the extent of mass localization is intermediate between that of a liquid and a crystal with long-range order. We estimate the corresponding entropy with the coarse-grained description of a many-particle system used in the classical density functional model. We demonstrate that intermediate localization of the particles results in a change of the entropy from what is obtained from a microscopic approach using for sharply localized vibrational modes following a Debye distribution.

An effective and efficient model of the near-field hydrodynamic interactions for active suspensions of bacteria.

Near-field hydrodynamic interactions in active fluids are essential to determine many important emergent behaviors observed, but have not been successfully modeled so far. In this work, we propose an effective model capturing the essence of the near-field hydrodynamic interactions through a tensorial coefficient of resistance, validated numerically by a pedagogic model system consisting of an bacterium and a passive sphere. In a critical test case that studies the scattering angle of the bacterium-sphere pair dynamics, we prove that the near-field hydrodynamics can make a qualitative difference even for this simple two-body system: Calculations based on the proposed model reveal a region in parameter space where the bacterium is trapped by the passive sphere, a phenomenon that is regularly observed in experiments but cannot be explained by any existing model.

Dependence of the configurational entropy on amorphous structures of a hard-sphere fluid.

The free energy of a hard-sphere fluid for which the average energy is trivial signifies how its entropy changes with packing. The packing η_{f} at which the free energy of the crystalline state becomes lower than that of the disordered fluid state marks the freezing point. For packing fractions η>η_{f} of the hard-sphere fluid, we use the modified weighted density functional approximation to identify metastable free energy minima intermediate between uniform fluid and crystalline states.

The yielding transition in amorphous solids under oscillatory shear deformation.

Amorphous solids are ubiquitous among natural and man-made materials. Often used as structural materials for their attractive mechanical properties, their utility depends critically on their response to applied stresses. Processes underlying such mechanical response, and in particular the yielding behaviour of amorphous solids, are not satisfactorily understood.

Linking density functional and mode coupling models for supercooled liquids.

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ].

Metastable-state dynamics of a liquid: a free-energy landscape study.

Using the time dependence of density fluctuations in a supercooled liquid obtained from the solutions of the equations of nonlinear fluctuating hydrodynamics (NFH), the evolution of the system in the free energy landscape is studied. A crossover from a continuous fluid type dynamics to that of hopping between different free energy minima is observed as the liquid is increasingly supercooled. We demonstrate that our results are also in agreement with equilibrium density functional analysis of the same system.