scholarly journals Efficient simulation of 3D reaction-diffusion in models of neurons and networks

2022 ◽  
Author(s):  
Robert A McDougal ◽  
Cameron Conte ◽  
Lia Eggleston ◽  
Adam John Hunter Newton ◽  
Hana Galijasevic

Neuronal activity is the result of both the electrophysiology and chemophysiology. A neuron can be well represented for the purposes of electrophysiological simulation as a tree composed of connected cylinders. This representation is also apt for 1D simulations of their chemophysiology, provided the spatial scale is larger than the diameter of the cylinders and there is radial symmetry. Higher dimensional simulation is necessary to accurately capture the dynamics when these criteria are not met, such as with wave curvature, spines, or diffusion near the soma. We have developed a solution to enable efficient finite volume method simulation of reaction-diffusion kinetics in intracellular 3D regions in neuron and network models and provide an implementation within the NEURON simulator. An accelerated version of the CTNG 3D reconstruction algorithm transforms morphologies suitable for ion-channel based simulations into consistent 3D voxelized regions. Kinetics are then solved using a parallel algorithm based on Douglas-Gunn that handles the irregular 3D geometry of a neuron; these kinetics are coupled to NEURON's 1D mechanisms for ion channels, synapses, etc. The 3D domain may cover the entire cell or selected regions of interest. Simulations with dendritic spines and of the soma reveal details of dynamics that would be missed in a pure 1D simulation. We describe and validate the methods and discuss their performance.

2010 ◽  
Vol 20 (05) ◽  
pp. 731-756 ◽  
Author(s):  
VERÓNICA ANAYA ◽  
MOSTAFA BENDAHMANE ◽  
MAURICIO SEPÚLVEDA

We consider a reaction–diffusion system of 2 × 2 equations modeling the spread of early tumor cells. The existence of weak solutions is ensured by a classical argument of Faedo–Galerkin method. Then, we present a numerical scheme for this model based on a finite volume method. We establish the existence of discrete solutions to this scheme, and we show that it converges to a weak solution. Finally, some numerical simulations are reported with pattern formation examples.


2020 ◽  
Vol 34 (30) ◽  
pp. 2050294
Author(s):  
Shuheng Fang ◽  
Zhengmin Kong ◽  
Ping Hu ◽  
Li Ding

In real-world scenarios, it is difficult to know about the complete topology of a huge network with different types of links. In this brief, we propose a method to identify the topology of multidimensional networks from information transmission data. We consider information propagating over edges of a two-dimensional (2D) network, where one type of links is known and the other type is unknown. Given the state of all nodes at each unit time, we can transform the topology identification problem into a compressive sensing framework. A modified reconstruction algorithm, called Sparsity Adaptive Matching Pursuit with Mixed Threshold Mechanism (SAMPMTM), is proposed to tackle the problem. Compared with the classical Sparsity Adaptive Matching Pursuit (SAMP) algorithm, the proposed SAMPMTM algorithm can reduce the conflict rate and improve the accuracy of network recovery. We further demonstrate the performance of this improved algorithm through Monte-Carlo simulations under different network models.


Author(s):  
Muhammad Naqib Nashrudin ◽  
Mohamad Aizat Abas ◽  
Mohd Z. Abdullah ◽  
M. Yusuf Tura Ali ◽  
Zambri Samsudin

Abstract The conventional capillary underfill process has been a common practice in the industry, somehow the process is costly and time consuming. Thus, no-flow underfill process is developed to increase the effective lead time production since it integrates the simultaneous reflow and cure of the solder interconnect and underfill. This paper investigates the effect of different dispense patterns of no-flow underfill process by mean of numerical and experimental method. Finite volume method (FVM) was used for the three-dimensional simulation to simulate the compression flow of the no-flow underfill. Experiments were carried out to complement the simulation validity and the results from both studies have reached a good agreement. The findings show that of all three types of dispense patterns, the combined shape dispense pattern shows better chip filling capability. The dot pattern has the highest velocity and pressure distribution with values of 0.0172 m/s and 813 Pa, respectively. The high-pressure region is concentrated at the center of the chip and decreases out towards the edge. Low in pressure and velocity flow factor somehow lead to issue associated to possibility of incomplete filling or void formation. Dot dispense pattern shows less void formation since it produces high pressure underfill flow within the BGA. This paper provides reliable insight to the industry to choose the best dispense pattern of recently favorable no-flow underfill process.


2017 ◽  
Vol 141 ◽  
pp. 405-410 ◽  
Author(s):  
Wei Bengang ◽  
Huang Hua ◽  
Lou Junshang ◽  
Wu Nannan ◽  
Dai Mingqiu ◽  
...  

2020 ◽  
Vol 10 (2) ◽  
pp. 137-149 ◽  
Author(s):  
Robert Cierniak ◽  
Piotr Pluta ◽  
Andrzej Kaźmierczak

AbstractThe paper presented here describes a new practical approach to the reconstruction problem applied to 3D spiral x-ray tomography. The concept we propose is based on a continuous-to-continuous data model, and the reconstruction problem is formulated as a shift invariant system. This original reconstruction method is formulated taking into consideration the statistical properties of signals obtained by the 3D geometry of a CT scanner. It belongs to the class of nutating reconstruction methods and is based on the advanced single slice rebinning (ASSR) methodology. The concept shown here significantly improves the quality of the images obtained after reconstruction and decreases the complexity of the reconstruction problem in comparison with other approaches. Computer simulations have been performed, which prove that the reconstruction algorithm described here does indeed significantly outperforms conventional analytical methods in the quality of the images obtained.


2020 ◽  
Author(s):  
Ron Ziv ◽  
Gal Shmuel

Soft materials with engineered microstructure support nonlinear waves which can be harnessed for various applications, from signal communication to impact mitigation. Such waves are governed by nonlinear coupled differential equations whose analytical solution is seldom trackable, hence emerges the need for suitable numerical solvers. Based on a finite-volume method in one space dimension, we here develop a designated scheme for nonlinear waves with two coupled components that propagate in soft laminates. We apply our scheme to a periodic laminate made of two alternating compressible Gent layers, and consider two cases. In one case, we analyze a motion whose component along the lamination direction is coupled to a component in the layers plane, and discover vector solitary waves in a continuum medium. In the second case, we analyze a motion with two coupled components in the plane of the layers, and observe a train of linearly polarized solitary waves, followed by a single circularly polarized wave. The framework we developed offers a platform for further investigation of these waves and their extension to higher dimensional problems.


Author(s):  
Jean-Michel Hugo ◽  
Fre´de´ric Topin ◽  
Loune`s Tadrist ◽  
Emmanuel Brun

Pore scale numerical simulation of heat and mass transfer in several foams are realized. 3D geometry is reconstructed from X-Ray tomographic images and fully characterized using the iMorph software. Microscale quantities such as temperature, pressure and velocity fields are computed using commercial software (StarCCM+) based on finite volume method. Macroscale properties are then deduced from numerical data and compared to experimental ones. Impact of foam topology and material as well as fluid nature (Fluid dynamic viscosity, solid thermal conductivity …) on transfer properties are systematically studied. We discuss correlations of these results with geometrical characteristics of the samples by scaling the metal foam in order to change pore diameter.


2011 ◽  
Vol 673 ◽  
pp. 41-46
Author(s):  
Sun Hee Yoo ◽  
Scott D. Stewart ◽  
David E. Lambert

In this paper, we demonstrate that an engineering device can be carefully designed in such a way that an overdriven solid state detonation can be initiated and propagated supersonically in a highly porous mixture of aluminum and Teflon. The equation of state and kinetics for the porous mixture are phenomenological models that were developed in our previous work [1]. This demonstration can be regarded as a good verification that the models which were used mainly in 1-D simulation are practically applicable and consistent to higher dimensional simulation of a shock dynamics in practical engineering devices.


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