Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies.

Trichodesmium is an important dinitrogen (N2)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N2 fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N2 fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.

A new mathematical model to explore microbial processes and their constraints in phytoplankton colonies and sinking marine aggregates.

N2-fixing colonies of cyanobacteria and aggregates of phytoplankton and detritus sinking hundreds of meters per day are instrumental for the ocean's sequestration of CO2 from the atmosphere. Understanding of small-scale microbial processes associated with phytoplankton colonies and aggregates is therefore crucial for understanding large-scale biogeochemical processes in the ocean. Phytoplankton colonies and sinking aggregates are characterized by steep concentration gradients of gases and nutrients in their interior. Here, we present a mechanistic mathematical model designed to perform modeling of small-scale fluxes and evaluate the physical, chemical, and biological constraints of processes that co-occur in phytoplankton colonies and sinking porous aggregates. The model accurately reproduced empirical measurements of O2 concentrations and fluxes measured in sinking aggregates. Common theoretical assumptions of either constant concentration or constant flux over the entire surface did not apply to sinking aggregates. Consequently, previous theoretical models overestimate O2 flux in these aggregates by as high as 15-fold.

A hydro-kinetic scheme for the dynamics of hydrogen bonds in water-like fluids.

A hydro-kinetic scheme for water-like fluids, based on a lattice version of the Boltzmann equation, is presented and applied to the popular TIP3P model of liquid water. By proceeding in much larger steps than molecular dynamics, the scheme proves to be very effective in attaining global minima of classical pair potentials with directional and radial interactions, as confirmed by further simulations using the three-dimensional Ben-Naim water potential. The scheme is shown to reproduce the propensity of water to form nearly four hydrogen bonds per molecule, as well as their statistical distribution in the presence of thermal fluctuations, at a linear cost of computational time with the system size.

Lattice Boltzmann implementation of the three-dimensional Ben-Naim potential for water-like fluids.

We develop a three-dimensional lattice Boltzmann (LB) model accounting for directional interactions between water-like molecules, based on the so-called Ben-Naim (BN) potential [A. Ben-Naim, Molecular Theory of Water and Aqueous Solutions: Part I: Understanding Water (World Scientific Publishing Company, 2010); "Statistical mechanics of 'waterlike' particles in two dimensions. I. Physical model and application of the Percus-Yevick equation," J. Chem. Phys. 54, 3682 (1971)]. The water-like molecules are represented by rigid tetrahedra, with two donors and two acceptors at the corners and interacting with neighboring tetrahedra, sitting on the nodes of a regular lattice. The tetrahedra are free to rotate about their centers under the drive of the torque arising from the interparticle potential. The orientations of the water molecules are evolved in time via an overdamped Langevin dynamics for the torque, which is solved by means of a quaternion technique. The resulting advection-diffusion-reaction equation for the quaternion components is solved by a LB method, acting as a dynamic minimizer for the global energy of the fluid. By adding thermal fluctuations to the torque equation, the model is shown to reproduce some microscopic features of real water, such as an average number of hydrogen bonds per molecules (HBs) between 3 and 4, in a qualitative agreement with microscopic water models. Albeit slower than a standard LB solver for ordinary fluids, the present scheme opens up potentially far-reaching scenarios for multiscale applications based on a coarse-grained representation of the water solvent.

Shear stress in nonideal fluid lattice Boltzmann simulations.

The viscous stress in nonideal fluid lattice Boltzmann methods is investigated theoretically and by simulations. Three representative liquid-gas models are compared in a steady-state situation, where an analytical expression for the viscous stress is available. It is shown that, in the presence of nonideal fluid interactions or strong body forces, the accuracy of the computed viscous stress depends strongly on the underlying model.