Method for measurement of collagen monomer orientation in fluorescence microscopy.

SIGNIFICANCE: Collagen is the most abundant protein in vertebrates and is found in tissues that regularly experience tension, compression, and shear forces. However, the underlying mechanism of collagen fibril formation and remodeling is poorly understood. AIM: We explore how a collagen monomer is visualized using fluorescence microscopy and how its spatial orientation is determined. Defining the orientation of collagen monomers is not a trivial problem, as the monomer has a weak contrast and is relatively small. It is possible to attach fluorescence tags for contrast, but the size is still a problem for detecting orientation using fluorescence microscopy. APPROACH: We present two methods for detecting a monomer and classifying its orientation. A modified Gabor filter set and an automatic classifier trained by convolutional neural network based on a synthetic dataset were used. RESULTS: By evaluating the performance of these two approaches with synthetic and experimental data, our results show that it is possible to determine the location and orientation with an error of ∼37 deg of a single monomer with fluorescence microscopy. CONCLUSIONS: These findings can contribute to our understanding of collagen monomers interaction with collagen fibrils surface during fibril formation and remodeling.

Mechanistic Description of Convective Gas-Liquid Mass Transfer in Biotrickling Filters Using CFD Modeling.

The gas-liquid mass transfer coefficient is a key parameter to the design and operation of biotrickling filters that governs the transport rate of contaminants and oxygen from the gas phase to the liquid phase, where pollutant biodegradation occurs. Mass transfer coefficients are typically estimated via experimental procedures to produce empirical correlations, which are only valid for the bioreactor configuration and range of operational conditions under investigation. In this work, a new method for the estimation of the gas-liquid mass transfer coefficient in biotrickling filters is presented. This novel methodology couples a realistic description of the packing media (polyurethane foam without a biofilm) obtained using microtomography with computational fluid dynamics. The two-dimensional analysis reported in this study allowed capturing the mechanisms of the complex processes involved in the creeping porous air and water flow in the presence of capillary effects in biotrickling filters. Model predictions matched the experimental mass transfer coefficients (±30%) under a wide range of operational conditions.

Computational tomography and CFD simulation of a biofilter treating a toluene, formaldehyde and benzo[α]pyrene vapor mixture.

In this work, a 3D computational tomography (CT) of the packing material of a laboratory column biofilter is used to model airflow containing three contaminants. The degradation equations for toluene, formaldehyde and benzo[α]pyrene (BaP), were one-way coupled to the CFD model. Physical validation of the model was attained by comparing pressure drops with experimental measurement, while experimental elimination capacities for the pollutants were used to validate the biodegradation kinetics. The validated model was used to assess the existence of channeling and to predict the impact of the three-dimensional porous geometry on the mass transfer of the contaminants in the gas phase. Our results indicate that a physically meaningful simulation can be obtained using the techniques and approach presented in this work, without the need of performing experiments to obtain macroscopic parameters such as gas-phase axial and radial dispersion coefficients and porosities.