Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Bauler, Patricia; Huber, Gary L.; McCammon, J. Andrew

doi:10.1063/1.4704808

Cited by 10 publications

(12 citation statements)

References 32 publications

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“…The data are noisy because of the relatively small number of particles compared to the simulations in the first paper. 31 As in the 1-D example, results did not depend significantly on the size and number of finite elements, provided the limits described above were honored. …”

Section: Spherically Symmetric Example With Three Speciesmentioning

confidence: 87%

“…Note that this is a correction to the original paper, 31 in which Eq. (25) was formulated incorrectly (this did not significantly affect the results from the first paper).…”

Section: Use Of Chargesmentioning

confidence: 98%

“…As in the previous paper, 31 the goal is to couple the stochastic model of Eq. (2) and the continuum model of Eq.…”

Section: Coupling Methodsmentioning

confidence: 99%

“…The particles in the buffer region are generated using the same method as in the previous paper, 31 but with one difference. The nodes that border both the buffer region and the particle region are included, but their hat functions do not extend into the particle region.…”

Section: Coupling Methodsmentioning

confidence: 99%

“…In this study, we extend the hybrid finite element and Brownian dynamics (FE-BD) method developed earlier 31 to simulate charged particles. While the previous study was formulated for simple particles that move under the influence of an external field that depends only on particle position, the present study takes into account the dependency of the force on particle concentrations and charge density.…”

Section: Introductionmentioning

confidence: 99%

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Hybrid finite element and Brownian dynamics method for charged particles

Huber

Miao

Zhou

et al. 2016

The Journal of Chemical Physics

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Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species. Published by AIP Publishing. [http://dx

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Section: Spherically Symmetric Example With Three Speciesmentioning

confidence: 87%

“…Note that this is a correction to the original paper, 31 in which Eq. (25) was formulated incorrectly (this did not significantly affect the results from the first paper).…”

Section: Use Of Chargesmentioning

confidence: 98%

“…As in the previous paper, 31 the goal is to couple the stochastic model of Eq. (2) and the continuum model of Eq.…”

Section: Coupling Methodsmentioning

confidence: 99%

Section: Coupling Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Hybrid finite element and Brownian dynamics method for charged particles

Huber

Miao

Zhou

et al. 2016

The Journal of Chemical Physics

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An Adaptive Local Iterative Method for Fast Calculation of Electrostatic Interactions between Charged Polymers in Dielectric Inhomogeneous System

Lin

Nie

Shang

et al. 2023

Advcd Theory and Sims

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The motion of charged polymers in the 3D dielectric inhomogeneity system is investigated using a hybrid simulation approach that combines a finite difference method with a Brownian dynamics model (FD‐BD) for the polymer chain. The interface difference scheme of the two‐dielectric model is first derived to achieve a smooth extension of the electrostatic potential values and it is verified that it has a second‐order convergence order. In addition, it is displayed that the local iteration method greatly accelerates the efficiency of calculating the electrostatic interaction forces. However, it is found that the computational efficiency improvement of the traditional local iteration is less significant (about three times) for polymer simulations such as 3D diagonal type. Therefore, a new strategy, the banded local iteration method, is proposed and the simulation results demonstrate that it can better adapt the effects of the deformation of the polymer during its motion, where the computational efficiency is increased by 29 times at most, while the relative error is controlled to less than 5.15e−4. The work can be helpful for accelerating the solution of electrostatic forces under dielectric inhomogeneity, and confer new insights into the optimization of iteration for polymer chains with different geometries in large electrostatic systems.

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Computational modeling of subcellular transport and signaling

Hake¹,

Kekenes‐Huskey²,

McCulloch³

2014

Current Opinion in Structural Biology

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Numerous signaling processes in the cell are controlled in microdomains that are defined by cellular structures ranging from nm to µm in size. Recent improvements in microscopy enable the resolution and reconstruction of these micro domains, while new computational methods provide the means to elucidate their functional roles. Collectively these tools allow for a biophysical understanding of the cellular environment and its pathological progression in disease. Here we review recent advancements in microscopy, and subcellular modeling based on reconstructed geometries, with a special focus on signaling microdomains that are important for the excitation contraction coupling in cardiac myocytes.

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Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Cited by 10 publications

References 32 publications

Hybrid finite element and Brownian dynamics method for charged particles

Hybrid finite element and Brownian dynamics method for charged particles

An Adaptive Local Iterative Method for Fast Calculation of Electrostatic Interactions between Charged Polymers in Dielectric Inhomogeneous System

Computational modeling of subcellular transport and signaling

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