Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining

Izvekov, Sergei; Voth, Gregory A.

doi:10.1021/jp810440c

Cited by 84 publications

(99 citation statements)

References 73 publications

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“…Izvekov and Voth 59 adapted their variational coarse graining ͑which creates a many-body potential for a coarse-grained unit by fitting forces from a finer grained model͒ to the case of implicit solvent lipid models. As well, Boltzmann-inversion procedures may also be employed systematically to create a coarse-grained from a finer grained model.…”

Section: Discussionmentioning

confidence: 99%

An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

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Section: Discussionmentioning

confidence: 99%

An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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“…However, the membrane also contains cyto- and nucleoskeletal elements that can transmit shear, which must be accounted for by incorporating a solid component. Parameters were based on results found by atomistic simulations (Izvekov and Voth 2009; Ovalle-García et al 2011; Patra et al 2003). …”

Section: Mathematical Modelingmentioning

confidence: 99%

Mechanotransduction of Ultrasound is Frequency Dependent Below the Cavitation Threshold

Louw

Budhiraja

Viljoen

et al. 2013

Ultrasound in Medicine & Biology

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This study provides evidence that low-intensity ultrasound directly affects nuclear processes, and the magnitude of the effect varies with frequency. In particular, we show that the transcriptional induction of first load-inducible genes, which is independent of new protein synthesis, is frequency dependent. Bovine chondrocytes were exposed to low-intensity below the cavitational threshold) ultrasound at 2,5 and 8 MHz. Ultrasound elevated the expression of early response genes c-Fos, c-Jun and c-Myc, maximized at 5 MHz. The phosphorylated ERK inhibitor PD98059 abrogated any increase in c-series gene expression, suggesting that signaling occurs via the MAPPK/ERK pathway. However, phosphorylated ERK levels did not change with ultrasound frequency, indicating that processes downstream of ERK phosphorylation (such as nuclear transport and chromatin reorganization) respond to ultrasound with frequency dependence. A quantitative, biphasic mathematical model based on Biot theory predicted that cytoplasmic and nuclear stress is maximized at 5.2 ± 0.8 MHz for a chondrocyte, confirming experimental measurements.

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“…In the second category, called direct parameterization, the coarse-grained potentials are determined from all-atom molecular dynamics simulations. One example is the force matching method [49,[83][84][85].…”

Section: Coarse-grained Simulationsmentioning

confidence: 99%

“…The solvent-free coarse-graining approach [84] does not work well for flexible macromolecules in solution because of the significant configurational entropy loss from the absence of explicit solvent molecules. To overcome this problem, the configurational entropy was restored by reintroducing coarse-grained solvent molecules to the system.…”

Section: The Physical Properties Of Complex Systems Of Dendrimers Witmentioning

confidence: 99%

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim

Lamm

2012

Polymers

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Dendrimers have been widely used as nanostructured carriers for guest species in a variety of applications in medicine, catalysis, and environmental remediation. Theory and simulation methods are an important complement to experimental approaches that are designed to develop a fundamental understanding about how dendrimers interact with guest molecules. This review focuses on computational studies aimed at providing a better understanding of the relevant physicochemical parameters at play in the binding and release mechanisms between polyamidoamine (PAMAM) dendrimers and guest species. We highlight recent contributions that model supramolecular dendrimer-guest complexes over the temporal and spatial scales spanned by simulation methods ranging from all-atom molecular dynamics to statistical field theory. The role of solvent effects on dendrimer-guest interactions and the importance of relating model parameters across multiple scales is discussed.

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Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining

Cited by 84 publications

References 73 publications

An implicit solvent coarse-grained lipid model with correct stress profile

An implicit solvent coarse-grained lipid model with correct stress profile

Mechanotransduction of Ultrasound is Frequency Dependent Below the Cavitation Threshold

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

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