Bulletin of the American Physical Society
77th Annual Meeting of the Division of Fluid Dynamics
Sunday–Tuesday, November 24–26, 2024; Salt Lake City, Utah
Session J01: General Biofluid Mechanics II: Cell and Subcellular |
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Chair: Jin Liu, Washington State University Room: Ballroom A |
Sunday, November 24, 2024 5:50PM - 6:03PM |
J01.00001: Mathematical modeling of cell growth in tissue engineering scaffold with complex internal morphology. Haniyeh Fattahpour, Binan Gu, Pejman Sanaei This study introduces a network model aimed at optimizing scaffold designs in tissue engineering. Utilizing a variant of the Random Geometric Graph (RGG) method for network generation, the model simulates nutrient flow, mechanical stress distribution, and cellular migration within scaffold pores. It integrates fluid dynamics and elasticity principles to capture laminar flow and scaffold deformation. The governing equations for nutrient flow, nutrient concentration, scaffold elasticity, and cell growth are outlined, and scaling and non-dimensionalization techniques are applied to analyze the scaffold's microenvironment. The physical quantities of interest throughout the network are coupled via flux conservation at network junctions. The results underscore the significant impact of nutrient concentration and scaffold elasticity on tissue growth, providing actionable insights for designing scaffolds that enhance tissue regeneration. |
Sunday, November 24, 2024 6:03PM - 6:16PM |
J01.00002: Modeling the Nucleoid and Cytoplasm Organization Inside a Minimal Synthetic Cell Gesse Arantes Roure, Vishal Sankar Sivasankar, Roseanna N Zia The spatial arrangement of genetic material within cells can affect key processes such as transcription and translation. In bacteria such as E. coli, this genetic material is unbound but condensed into a nucleoid. This compact nucleoid partitions the cell into a porous region within, where transcription takes place, and a surrounding cytoplasm of mobile biomolecules where most of mRNA translation takes place at ribosomes. In a recent work, we observed that the E. coli nucleoid expands and contracts, changing its density and thus regulating protein expression by physical and electrostatic segregation of biomolecules in or out of the nucleoid. The compaction of the nucleoid is often attributed to a combined action of nucleoid-associated proteins (NAPs) and osmotic pressure from cytoplasmic biomolecules. In contrast to E. coli, some bacteria, such as many types of Mycoplasma species, possess a cell-spanning nucleoid. A notable example is the JCVI Syn3A synthetic cell, which is a model bacterium comprising the smallest known genome capable of life. In this work, we develop a colloidal-scale, coarse-grained model of the JCVI Syn3A minimal cell that captures the essential physics of DNA, native proteins, and ribosomes. Our model consists of a spherical enclosure, implicitly modeled cytosol, thousands of explicitly resolved biomolecules, and the chromosome, which is modeled as a semi-flexible bead chain. Through Monte Carlo simulations and Brownian Dynamics, we investigate the effects of DNA stiffness, native protein concentration, and charge distribution on nucleoid and cytoplasm organization. The effect of DNA-bending HU proteins is modeled as a random distribution of bending defects across the genome. The porous structure of the nucleoid is characterized by a Voronoi analysis, which suggests that a compact nucleoid exhibits a heterogeneous pore-size distribution that results in the separation and entrapment of larger particles. We find that an increased concentration of HU proteins may compact the chromosome and push ribosomes out into the surrounding cytoplasm, and that changes in crowder concentration and charge distribution can alter this effect. We propose how this may be connected to the experimental observation of a cell-spanning Syn3A nucleoid. |
Sunday, November 24, 2024 6:16PM - 6:29PM |
J01.00003: Effect of membrane viscosity in dynamics of red blood cell in pulsatile flows Trung Bao Le, Meraj Ahmed We investigate the impact of membrane viscosity in the dynamics of Red Blood Cell (RBCs) in pulsatile flows using numerical simulations. Our computational approach employs a hybrid continuum-particle coupling. The Red Blood Cell model includes the cell membrane and cytosol fluid, which are modeled using the Dissipative Particle Dynamics (DPD) method. The blood plasma is modeled as an incompressible fluid via the Immersed Boundary Method (IBM). The hybrid continuum-particle coupling is carried out on the membrane surface by the continuity of the loading vector. Our numerical method provides an accurate description of RBC dynamics while the extracellular flow patterns around the RBCs are also captured in detail. Our coupling methodology is validated with available experimental and computational data in the literature and shows good agreement. Our simulation results show that a host of RBC morphological dynamics emerges depending on the value of membrane viscosity. Our results show that the RBC shape is strongly dependent on the membrane viscosity. Our results suggest that the controlling of membrane viscosity can be used to induce specific morphological shapes of RBCs and the surrounding fluid patterns in bio-engineering applications. |
Sunday, November 24, 2024 6:29PM - 6:42PM |
J01.00004: Stoichiometric Model for the Microtubule-mediated dynamics of centrosome and nucleus Yuan-Nan Young, Libin Lu, Alex Barnett, Reza Farhadifar, Michael J Shelley The Stoichiometric Model (S-model) for the interaction of centrosomes with cortically anchored pulling motors through their associated microtubules (MTs) has been applied to study key steps in cell division, such as spindle positioning and elongation. The S-model evolves the astral centrosome position, a probability field of cell-surface motor occupancy by centrosomal microtubules (under an assumption of stoichiometric binding), and free boundaries of unattached, growing microtubules. In this work, we apply the S-model to investigate the hydrodynamics of the centrosome/pronucleus (CP) complex inside a cell. Formulated as a fluid-structure interaction problem using the integral formulation, we use a highly accurate boundary integral code to simulate key dynamics of the centrosome/pronucleus complex, such as the separation of centrosomes around a nucleus, centering of the centrosome/pronucleus complex, and deformation of the pronucleus due to pulling forces from the centrosomes. Focusing on the enhanced permeability and reduced rigidity of a lamin-compromised pronucleus, we find that the CP complex may lose the centering stability and exhibit orbiting dynamics. In this talk, we first provide a comprehensive study of the morphology of a pronucleus in terms of membrane permeability and bending rigidity. We then quantify how deformation affects the centering stability of the CP complex. We further illustrate how the geometry of the cell affects the dynamics of CP complex. |
Sunday, November 24, 2024 6:42PM - 6:55PM |
J01.00005: Resolving Protein Conformational Changes through Machine Learning Based Enhanced Sampling Jin Liu, Ryan E Odstrcil, Prashanta Dutta The functionalities of proteins rely on protein conformational changes during many processes. Identification of the protein conformations and capturing transitions among different conformations are important but extremely challenging in both experiments and simulations. In this work, we develop a machine learning based approach to rapidly identify a reaction coordinate that accelerates the exploration of protein conformational changes in molecular simulations. Our method has foundations in local optimization, strives to predict reaction pathways before reactions completely occur, and speeds up sampling in molecular simulations. We implement our approach to study the conformational changes of human NTHL1 during the DNA repair process. Our results identified three distinct conformations: open (stable), closed (unstable), and bundle (stable). The existence of the bundle conformation can rationalize the recent experimental observations. Comparison with an NTHL1 mutant demonstrates that a closely packed cluster of positively charged residues in the linker could be a factor to search for in the genes encoding when screening for genetic abnormalities. Results will lead to better modulation of the DNA repair pathway to protect against carcinogenesis. |
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