MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

Bernaschi, Massimo; Melchionna, Simone; Succi, Sauro; Fyta, Maria; Kaxiras, Efthimios; Sircar, Joy

doi:10.1016/j.cpc.2009.04.001

Cited by 121 publications

(101 citation statements)

References 26 publications

(30 reference statements)

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“…Particle-based numerical methods, such as the Lattice-Boltzmann method [20], dissipative particle dynamics (DPD) [21,22] and multiparticle collision (MPC) dynamics [8,9,16], have more recently led to numerical solutions for flow through a local constriction. The Lattice-Boltzmann method has also recently been used for blood flow studies in complex flow geometries for realistic cardiovascular flow domains [23][24][25]. The method has been reviewed recently in [26], and its use for complex flows has been reviewed in [27].…”

Section: Introductionmentioning

confidence: 99%

Quantifying Compressibility and Slip in Multiparticle Collision (MPC) Flow Through a Local Constriction

Akhter

Rohlf

2014

Entropy

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The flow of a compressible fluid with slip through a cylinder with an asymmetric local constriction has been considered both numerically, as well as analytically. For the numerical work, a particle-based method whose dynamics is governed by the multiparticle collision (MPC) rule has been used together with a generalized boundary condition that allows for slip at the wall. Since it is well known that an MPC system corresponds to an ideal gas and behaves like a compressible, viscous flow on average, an approximate analytical solution has been derived from the compressible Navier-Stokes equations of motion coupled to an ideal gas equation of state using the Karman-Pohlhausen method. The constriction is assumed to have a polynomial form, and the location of maximum constriction is varied throughout the constricted portion of the cylinder. Results for centerline densities and centerline velocities have been compared for various Reynolds numbers, Mach numbers, wall slip values and flow geometries.

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Section: Introductionmentioning

confidence: 99%

Quantifying Compressibility and Slip in Multiparticle Collision (MPC) Flow Through a Local Constriction

Akhter

Rohlf

2014

Entropy

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“…These examples show the capabilities of the method in typical operating conditions, whereas much more non-conventional settings can be built to look at inhomogeneous or compartmentalized conditions. All simulations in this section were performed by using the MUlti-PHYsics (MUPHY) software package, developed over the years to enable the simulation of biological and non-biological composite systems [35].…”

Section: Resultsmentioning

confidence: 99%

Multiscale simulation of molecular processes in cellular environments

Chiricotto

Sterpone

Derreumaux

et al. 2016

Phil. Trans. R. Soc. A.

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One contribution of 17 to a theme issue 'Multiscale modelling at the physics-chemistry-biology interface' . We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

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“…We simulate the airflow in nasal cavities using the Lattice Boltzmann method (LBM) implemented by Muphy (Bernaschi et al 2009). The LBM utilizes a uniform Cartesian grid, which we obtain by determining which cells of a regular grid lie inside the surface mesh.…”

Section: Computational Fluid Dynamicsmentioning

confidence: 99%

Validated reconstructions of geometries of nasal cavities from CT scans

Zwicker

Yang

Melchionna

et al. 2018

Biomed. Phys. Eng. Express

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Developing validated objective measures of nasal airflow is paramount for improving the management of nasal obstruction. Nasal airflow can be studied objectively by simulating the flow in the computer. This requires a faithful reconstruction of the nasal geometry since the simulated airflow is sensitive to small variations of the complex shape of the nasal cavity. We here show that altering the geometry by less than 1 mm can change the airflow two-fold. We also show that a faithful reconstruction of the nasal geometry is possible with a threshold-based segmentation. Utilizing the known geometry of a CT phantom, we determine an optimal segmentation threshold of −450 HU. Changing this threshold by 100 HU alters the geometry by only about 0.1 mm. We use this verified segmentation to extract nasal geometries of three patients and simulate the respective airflows using the Lattice Boltzmann method. Using a simple model, we can predict how the reconstruction threshold affects the resistance to airflow. Since the segmentation and the simulation can be automated completely, this is an important step toward an objective analysis of nasal airflow based on CT scans.

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MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

Cited by 121 publications

References 26 publications

Quantifying Compressibility and Slip in Multiparticle Collision (MPC) Flow Through a Local Constriction

Quantifying Compressibility and Slip in Multiparticle Collision (MPC) Flow Through a Local Constriction

Multiscale simulation of molecular processes in cellular environments

Validated reconstructions of geometries of nasal cavities from CT scans

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