The Art of Molecular Dynamics Simulation

Rapaport, D. C.; Blumberg, R.; McKay, Susan R.; Christian, Wolfgang

doi:10.1063/1.4822471

Cited by 1,172 publications

(1,652 citation statements)

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“…Lipid Lateral Diffusion. We have calculated the lipid lateral diffusion coefficient using the Einstein expression, 72 as is standard practice in membrane simulations. [21][22][23] Figure 11 shows the lipid lateral diffusion coefficient D lat computed for two different measurement times.…”

Section: Resultsmentioning

confidence: 99%

A Quantitative Coarse-Grain Model for Lipid Bilayers

et al. 2007

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A simplified particle-based computer model for hydrated phospholipid bilayers has been developed and applied to quantitatively predict the major physical features of fluid-phase biomembranes. Compared with available coarse-grain methods, three novel aspects are introduced. First, the main electrostatic features of the system are incorporated explicitly via charges and dipoles. Second, water is accurately (yet efficiently) described, on an individual level, by the soft sticky dipole model. Third, hydrocarbon tails are modeled using the anisotropic Gay-Berne potential. Simulations are conducted by rigid-body molecular dynamics. Our technique proves 2 orders of magnitude less demanding of computational resources than traditional atomic-level methodology. Self-assembled bilayers quantitatively reproduce experimental observables such as electron density, compressibility moduli, dipole potential, lipid diffusion, and water permeability. The lateral pressure profile has been calculated, along with the elastic curvature constants of the Helfrich expression for the membrane bending energy; results are consistent with experimental estimates and atomic-level simulation data. Several of the results presented have been obtained for the first time using a coarse-grain method. Our model is also directly compatible with atomic-level force fields, allowing mixed systems to be simulated in a multiscale fashion.

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Section: Resultsmentioning

confidence: 99%

A Quantitative Coarse-Grain Model for Lipid Bilayers

et al. 2007

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“…A periodic boundary condition was applied in the axial direction of a tubule of length l containing 180 water molecules (182 when R = 17). The temperature T and the internal axial-pressure P zz (the pressure tensor parallel to the axis) were maintained using a modified Nosé-Andersen's method 25 . The axial dimension l fluctuates to keep P zz constant during a simulation; continuous change in l is possible because the force field of the model SWCN is smooth and structureless, and thus is independent of l. The simulation time at each state point (given T, P zz , and R) was 10-40 ns, and at certain states was over 200 ns, which is one or two orders of magnitude longer than a typical simulation time for bulk water.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Formation of ordered ice nanotubes inside carbon nanotubes

Koga

Gao

Tanaka

et al. 2001

Nature

1,062

914

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“…37 Depending on the parameters, simulations are carried over 10 to 20 million time steps with a step size ⌬ ϭ 0.005 ( ϭ ͌(m 2 / ) being the unit of dimensionless time). Snapshots of the simulation are recorded every 10 4 time steps starting after the 5 millionth time step, which is well beyond a typical eq Ϸ 2 ϫ 10 6 time steps it took to equilibrate even the largest system sizes at highest concentrations.…”

Section: Model and Simulation Detailsmentioning

confidence: 99%

Nanoparticle Ordering via Functionalized Block Copolymers in Solution

Sknepnek¹,

Anderson²,

Lamm

et al. 2008

ACS Nano

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We consider nanoparticles and functionalized copolymers, block copolymers with attached end groups possessing a specific affinity for nanoparticles, in solution. Using molecular dynamics, we show that nanoparticles are able to direct the self-assembly of the polymer/ nanoparticle composite. We perform a detailed study for a wide range of nanoparticle sizes and concentrations. We show that the nanoparticles order in a number of distinct phases: simple cubic, layered hexagonal, hexagonal columnar, gyroid, and a novel square columnar. Our results show that nanoparticles ordered with functionalized block copolymers can provide a simple and efficient tool for assembling novel materials with nanometer scale resolution. B lock copolymers in solutions or melts are known to self-assemble into mesophases with one-, two-, or threedimensional periodic order with typical repeating distances in the 10Ϫ200 nm range. 1,2 In solutions, the self-assembly of the different phases can be controlled by tuning external conditions such as pH or temperature. The wide availability and relatively inexpensive synthesis of block copolymers as well as the ability to exquisitely control so many diverse phases with periodic order make them compelling candidates for the building blocks of novel materials. Thin films of block copolymers can provide "bottom-up" templates for fabrication of devices on sub-30-nm length scales that are inaccessible to standard lithography techniques, opening the door for molecular size electronic components and ultrahigh density magnetic storage media. Applications include growth of nanowires 3,4 and nanocrystals used in devices such as flash memory, 5 metal-oxidesemiconductor capacitors, 6,7 arrays of quantum dots, 8,9 and photonic crystals. 10 For most applications, the proposed fabrication process consists of forming a thin copolymer film on a substrate, which is then chemically treated to remove one of the copolymer components. The remaining component is used as a mask for growing the active component. It would be even more desirable to include the active component (e.g., metallic or silica nanoparticles) from the outset and form the desired structure in a single pass. Direct application of this method is limited mainly due to nanoparticle aggregation and incompatibility of nanoparticle surface and ionic solutions with the polymers. 11 These problems can be circumvented by the use of self-assembling functionalized block copolymers, that is, polymers with covalently attached end groups that show specific affinity for nanoparticles, as agents for assembling ordered nanoparticle structures. 12,13 The theoretical understanding of the factors that lead to a successful self-assembly of nanocomposites is relatively limited. Recent studies include investigations of the influence of nanoparticles on the selfassembly and nanostructure formation of diblock copolymer melts based on solving cell dynamical system equations, 14 Monte Carlo simulations, 15 and self-consistent mean field/density functional theory. 16,17 ...

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The Art of Molecular Dynamics Simulation

Cited by 1,172 publications

References 0 publications

A Quantitative Coarse-Grain Model for Lipid Bilayers

A Quantitative Coarse-Grain Model for Lipid Bilayers

Formation of ordered ice nanotubes inside carbon nanotubes

Nanoparticle Ordering via Functionalized Block Copolymers in Solution

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