Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

Fu, Szu-Pei; Peng, Zhangli; Yuan, Hongyan; Kfoury, Ralph; Young, Yuan-Nan

doi:10.1016/j.cpc.2016.09.018

Cited by 40 publications

(43 citation statements)

References 18 publications

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“…It is also worth noting that Fu et al recently published an implementation of a related RBC model in LAMMPS [32], which can simulate 1.15×10 6 particles for 10 5 time steps on 864 CPU cores in 2761 seconds. However, the use of explicit solvent particles in their model generates difficulty to establish a fair performance comparison between their implementation and OpenRBC.…”

Section: Validation and Benchmarkmentioning

confidence: 99%

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Tang

et al. 2017

Biophysical Journal

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We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment-simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles-using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells.

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Section: Validation and Benchmarkmentioning

confidence: 99%

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Tang

et al. 2017

Biophysical Journal

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“…This work adopts the lipid-lipid interaction potential of Yuan et al (24), hereafter referred to as the Yuan potential. The Yuan potential has been shown to represent well the mechanical properties of a RBC bilayer membrane, including a diffusive fluid phase, due to the separation of attractive and repulsive branches (14). It has an orientational dependence which allows the complex lipid hydrophobicity to be represented, being essential for the self-assembly of the bilayer in an aqueous environment (8,26).…”

Section: Methodsmentioning

confidence: 99%

“…To date, the most popular have been continuum methods such as the finite element method (FEM), and the particle-based dissipative-particle-dynamics (DPD) approach (2,3,11). However, recently coarse-grained molecular dynamics (CGMD) has seen increasing popularity (8,(12)(13)(14)(15). In CGMD, an atomic system is coarse-grained (CG) into a more computationally efficient representation, with CG particle interactions managed by inter-particle potentials.…”

Section: Introductionmentioning

confidence: 99%

“…Despite being an implicit-fluid model with notable care taken to ensure computational efficiency, simulating the full-scale cell (consisting of 3.2 million particles) for 100, 000 time-steps on 20 CPU cores still took on the order of a day. An alternative speed-up approach has been to simulate "miniature" cells, consisting of far fewer particles, but whilst adopting the same length scaling (14,18). These cells thus have a significantly reduced physical diameter, but assume elastic properties equivalently representative to those of a full-scale cell.…”

Section: Introductionmentioning

confidence: 99%

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Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

Appshaw

Seddon

Hanna

2020

Preprint

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Due to the high computational cost of full-cell coarse-grained molecular dynamics modelling, being able to simulate "miniature" cells that effectively represent their full-sized counterparts would be highly advantageous. To accurately represent the morphological and elastic properties of a human red blood cell in silico, such a model is employed utilising the molecular dynamics package LAMMPS. The scale invariance of the model is first tested qualitatively by following the shape evolution of red blood cells of various diameters, then quantitatively by evaluating the membrane shear modulus from simulations of optical tweezer-style stretching. Cells of physical diameter of at least 0.5μm were able to form the characteristic biconcave shape of human red blood cells, though smaller cells instead equilibrated to bowl-shaped stomatocytes. A positive correlation was found between the cell size and both magnitude of deformation from optical tweezer stretching and scaled shear modulus, indicating a lack of scale invariance in the models elastic response. However, the stable morphology and measured shear modulus of the 0.5 – 1.0μm diameter cells are deemed close enough to past in vitro studies on human red blood cells for them to still offer valuable use in making simplified predictions of whole-cell mechanics.

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“…CGMD simulations take into account both repulsive and attractive interactions between beads to describe molecular behavior. These systems generally employ a Lennard-Jones (LJ) potential, such as a MARTINI force field [16,17]. Interaction parameters of CG models are determined by comparing the results of all-atom MD or experiment.…”

Section: Introductionmentioning

confidence: 99%

Parametric Study of Lennard–Jones Potentials to Predict Physical Behavior via Coarse-Grained Molecular Dynamics Simulations of Water and Ethylene Glycol Over Wide Temporal and Spatial Scales

Cha

Lee

Shin

et al. 2020

Multiscale Sci. Eng.

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To develop advanced and elaborate nanotechnologies, the behavior of materials must be understood at the nanoscale. Since direct observation is not generally possible experimentally, molecular dynamics simulations have been used to estimate nanoscale behavior, although simulations still have spatio-temporal limitations. Thus, coarse-grained molecular dynamics (CGMD) simulations have been suggested to study the physical properties and molecular behavior of mesoscale systems. A 'bead' composed of several atoms or molecules can represent the physical properties of a materials. In this study, we performed CGMD simulations of water and ethylene glycol, represented by Lennard-Jones parameters with various numbers of molecules within a single bead, to determine interaction parameters by comparing our results against empirically determined physical properties. Our results show the possible range of the number of molecules per bead satisfying a particular physical property such as density and self-diffusion coefficient. These data yielded the most suitable number of molecules to be included in a bead for CGMD simulations containing water and ethylene glycol. Moreover, we identified and discussed the effects of time scale factor, of which the empirically applicable range of 4-10, on self-diffusivity coefficients.

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Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

Cited by 40 publications

References 18 publications

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

Optical Tweezer Stretching of Miniature Coarse-Grained Red Blood Cells

Parametric Study of Lennard–Jones Potentials to Predict Physical Behavior via Coarse-Grained Molecular Dynamics Simulations of Water and Ethylene Glycol Over Wide Temporal and Spatial Scales

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