203 research outputs found
Active elastohydrodynamics of vesicles in narrow, blind constrictions
Fluid-resistance limited transport of vesicles through narrow constrictions
is a recurring theme in many biological and engineering applications. Inspired
by the motor-driven movement of soft membrane-bound vesicles into closed
neuronal dendritic spines, here we study this problem using a combination of
passive three-dimensional simulations and a simplified semi-analytical theory
for active transport of vesicles that are forced through such constrictions by
molecular motors. We show that the motion of these objects is characterized by
two dimensionless quantities related to the geometry and the strength of
forcing relative to the vesicle elasticity. We use numerical simulations to
characterize the transit time for a vesicle forced by fluid pressure through a
constriction in a channel, and find that relative to an open channel, transport
into a blind end leads to the formation of an effective lubrication layer that
strongly impedes motion. When the fluid pressure forcing is complemented by
forces due to molecular motors that are responsible for vesicle trafficking
into dendritic spines, we find that the competition between motor forcing and
fluid drag results in multistable dynamics reminiscent of the real system. Our
study highlights the role of non-local hydrodynamic effects in determining the
kinetics of vesicular transport in constricted geometries
Two- and three-dimensional viscous computations of a hypersonic inlet flow
The three-dimensional parabolized Navier-Stokes code has been used to investigate the flow through a Mach 7.4 inlet. A two-dimensional parametric study of grid resolution, turbulence modeling and effect of gamma has been done and compared with experimental results. The results show that mesh resolution of the shock waves, real gas effects and turbulence length scaling are very important to get accurate results for hypersonic inlet flows. In addition a three-dimensional calculation of the Mach 7.4 inlet has been done on a straight sideplate configuration. The results show that the glancing shock/boundary layer interaction phenomena causes significant three-dimensional flow in the inlet
Leaky cell model of hard spheres
We study packings of hard spheres on lattices. The partition function, and therefore the pressure, may be written solely in terms of the accessible free volume, i.e., the volume of space that a sphere can explore without touching another sphere. We compute these free volumes using a leaky cell model, in which the accessible space accounts for the possibility that spheres may escape from the local cage of lattice neighbors. We describe how elementary geometry may be used to calculate the free volume exactly for this leaky cell model in two- and three-dimensional lattice packings and compare the results to the well-known Carnahan–Starling and Percus–Yevick liquid models. We provide formulas for the free volumes of various lattices and use the common tangent construction to identify several phase transitions between them in the leaky cell regime, indicating the possibility of coexistence in crystalline materials
Modeling the Transition between Localized and Extended Deposition in Flow Networks through Packings of Glass Beads
We use a theoretical model to explore how fluid dynamics, in particular, the
pressure gradient and wall shear stress in a channel, affect the deposition of
particles flowing in a microfluidic network. Experiments on transport of
colloidal particles in pressure-driven systems of packed beads have shown that
at lower pressure drop, particles deposit locally at the inlet, while at higher
pressure drop, they deposit uniformly along the direction of flow. We develop a
mathematical model and use agent-based simulations to capture these essential
qualitative features observed in experiments. We explore the deposition profile
over a two-dimensional phase diagram defined in terms of the pressure and shear
stress threshold, and show that two distinct phases exist. We explain this
apparent phase transition by drawing an analogy to simple one-dimensional
models of aggregation in which the phase transition is calculated analytically.Comment: 9 pages, 6 figures including Supplemental Materia
Fast solver for diffusive transport times on dynamic intracellular networks
The transport of particles in cells is influenced by the properties of
intracellular networks they traverse while searching for localized target
regions or reaction partners. Moreover, given the rapid turnover in many
intracellular structures, it is crucial to understand how temporal changes in
the network structure affect diffusive transport. In this work, we use network
theory to characterize complex intracellular biological environments across
scales. We develop an efficient computational method to compute the mean first
passage times for simulating a particle diffusing along two-dimensional planar
networks extracted from fluorescence microscopy imaging. We first benchmark
this methodology in the context of synthetic networks, and subsequently apply
it to live-cell data from endoplasmic reticulum tubular networks.Comment: 14 pages, 6 figure
Quantitative biology: where modern biology meets physical sciences
Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines
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