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Abstract Impact of ice coverage is significant in controlling the depth-averaged velocity profile and influencing morphological processes in alluvial channels. However, this impact is largely unknown under field conditions. In this work, a numerical method is introduced to compute the depth-averaged velocity profile in irregular cross-sections of ice-covered flows, based on the Shiono-Knight approach. The momentum equation is modified to account for the presence of secondary flows and the ice coverage. The equations are discretized and solved with velocity boundary conditions at the bank and at one vertical. Our approach only requires the cross-section geometry and a single velocity measurement near the high-velocity region, offering a significant advantage in inaccessible locations by avoiding the need to measure the velocity profile in the entire cross-section. The proposed model is then validated using depth-averaged velocity profile and secondary flow patterns from laboratory observations, analytical solution, and Large-Eddy Simulation. Finally, the method is applied to infer depth-averaged velocity profiles in the Red River of the North, United States, to test its performance in meandering sections. The proposed method demonstrates its robustness in reconstructing flow profiles in ice-covered conditions with a minimal amount of available data, which is crucial for assessing erosion risks and managing spring floods in cold regions. 

Abstract This work presents the development of a novel approach to model cancer cell dynamics in microcirculation. The proposed numerical model is based on a hybrid continuum-particle approach. The cancer cell model includes the cell membrane, nucleus, cytoplasm and the cytoskeleton. The Dissipative Particle Dynamics method was employed to simulate the mechanical components. The blood plasma is modeled as a Newtonian incompressible fluid. A Fluid-Structure Interaction coupling, leveraging the Immersed Boundary Method is developed to simulate the cell's response to flow dynamics. The model is applied to resolve the transport of cancer cells with realistic morphologies in microcirculatory flows. Our results suggest that the controlling of oscillatory flows can be utilized to induce specific morphological shapes and the surrounding fluid patterns, allowing full manipulation and control of the cell. Furthermore, the intracellular and extracellular dynamics response of the cancer cell is intrinsically linked to their shape, in which certain morphologies displayed strong resistance to the fluid-induced forces and the ability to migrate in various directions. Our computational framework provides new capabilities for designing bioengineering devices for cell manipulation and separation. 

Abstract The objective of this study is to investigate the rolling dynamics of leukocytes in microchannel flows using a hybrid continuum-particle approach. Leukocytes play an essential role in the immune system, and their margination behavior has been extensively studied both experimentally and numerically. In this study, we have developed a series of numerical experiments using a hybrid DPD-CFD solver with the membrane stiffness of the modeled leukocytes as the primary investigation subject. Our results show that increasing the stiffness of the cell's membrane influences its deformability and trajectory in microchannel flows. The results obtained from this study could be valuable in designing next-generation micro-carriers for targeted drug delivery systems, which mimic the margination behavior of leukocytes. 

Abstract We performed the transport of a breast cancer cell (MB231-TGFb) in a microvessel using high-resolution simulations. Using open-source imaging software Slicer3D and Meshmixer, the 3D surface mesh forming the cell membrane was reconstructed from confocal microscopic images. The Dissipative Particle Dynamics method is used to model the cell membrane. The extracellular fluid flow is modeled with the Immersed Boundary Method to solve the governing equations of the blood plasma. The unsteady flow is applied at the inlet of the microchannel with an oscillatory pattern. Our results showed that the extracellular flow patterns are highly dependent on the waveform profile. The oscillatory flow showed the creation of vortices that influence the cellular deformations in the microchannel. These results could have implications on the destination of the cancer cells during transport in physiological flows. 

Our study aims to identify the role of fluid flow in the growth of human bone cancer cells during metastasis. In our experiments, the cancer cells are seeded on the surface of cylindrical scaffolds in a bioreactor. The flow is laminar flow, which mimics the physiological conditions of the human body. A full-scale 3D high-resolution computational mesh of scaffold was created based on the physical scaffold's Micro-CT scans using open-source imaging software Slicer3D and Meshmixer. To investigate the influences of the flow on the seeded cells, we performed Computational Fluid Dynamics (CFD) simulations with the immersed boundary method (Gilmanov, Le, Sotiropoulos, JCP 300, 1, 2015). The computational domain was generated using the commercial software Gridgen. Our results show that the fluid flow velocity is highly dependent on the shape and pore sizes. In addition, the magnitude of the velocity on the surface where the cells are seeded is in between [0-0.05] μm/sallowing the cells to grow without being detached from the surface of the scaffold. Our future work will focus on (i) investigating the role of the shear stress on the distribution and orientation of the cancer cells. (ii) Simulating multiple scaffolds within the bioreactor to further quantify the impact of the gap on the flow velocity and shear. 

Transport of cells in fluid flow plays a critical role in many physiological processes of the human body. Recent developments of in vitro techniques have enabled the understanding of cellular dynamics in laboratory conditions. However, it is challenging to obtain precise characteristics of cellular dynamics using experimental method alone, especially under in vivo conditions. This challenge motivates new developments of computational methods to provide complementary data that experimental techniques are not able to provide. Since there exists a large disparity in spatial and temporal scales in this problem, which requires a large number of cells to be simulated, it is highly desirable to develop an efficient numerical method for the interaction of cells and fluid flows. In this work, a new Fluid-Structure Interaction formulation is proposed based on the use of hybrid continuum-particle approach, which can resolve local dynamics of cells while providing large-scale flow patterns in the vascular vessel. Here, the Dissipative Particle Dynamics (DPD) model for the cellular membrane is used in conjunction with the Immersed Boundary Method (IBM) for the fluid plasma. Our results show that the new formulation is highly efficient in computing the deformation of cells within fluid flow while satisfying the incompressibility constraints of the fluid. We demonstrate that it is possible to couple the DPD with the IBM to simulate the complex dynamics of Red Blood Cells (RBC) such as parachuting. Our key observation is that the proposed coupling enables the simulation of RBC dynamics in realistic arterioles while ensuring the incompressibility constraint for fluid plasma. Therefore, the proposed method allows an accurate estimation of fluid shear stresses on the surface of simulated RBC. Our results suggest that this hybrid methodology can be extended for a variety of cells in physiological conditions. 

Abstract Metastatic cancer in bones is incurable, which causes significant mobility and mortality to the patients. In this work, we investigate the role of interstitial fluid flow on cancer cells' growth within the interconnected pores of human bone. In-vitro experiments were carried out in a bio-reactor which includes bone-like scaffold specimens. A pump is used to maintain a laminar flow condition inside the bioreactor to resemble fluid flow in bones. The scaffold specimens are harvested after 23 days in the bioreactor. The scaffold specimen is scanned with Micro-CT under the resolution of 70 micrometers. We created a full-scale 3D computational model of the scaffold based on the micro-CT data using the open-source software Seg3D and Meshmixer. Based on the geometrical models, we generated the computational grids using the commercial software Gridgen. We performed Computational Fluid Dynamics (CFD) simulations with the immersed boundary method (Gilmanov, Le, Sotiropoulos, JCP 300, 1, 2015) to investigate the flow patterns inside the pores of the scaffolds. The results reveal a non-uniform flow distribution in the vicinity of the scaffold. The flow velocity and the shear stress distributions inside the scaffold are shown to be convoluted and very sensitive to the pore sizes. Our future work will further quantify these distributions and correlate them to cancer cells' growth observed in the experiments.