Theoretical frameworks for multiscale modeling and simulation

Zhou, Huan‐Xiang

doi:10.1016/j.sbi.2014.01.004

Cited by 32 publications

(26 citation statements)

References 91 publications

(92 reference statements)

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“…[16,18 • ,51,96]). Yet there is no general framework as for hybrid classical/quantum mechanics methods, and the best techniques are inherently tailored.…”

Section: Perspectivementioning

confidence: 99%

“…Multiscale modeling has also earned the 2013 Nobel Prize in Chemistry for Karplus, Levitt, and Warshel for their pioneering work in linking classical and quantum-mechanical levels for enzymatic reactions [17]. General multiscale computations remain a challenge, though much progress has been made [18 • ]. There is, however, no general approach for linking chromatin's many scales of spatial as well as temporal scales in analogy to the quantum and classical degrees of freedom for protein catalysis.…”

Section: Introductionmentioning

confidence: 99%

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The chromatin fiber: multiscale problems and approaches

Ozer

Luque

Schlick

2015

Current Opinion in Structural Biology

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The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails of the nucleosomes to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modeling techniques at the atomic, mesoscopic, and chromosomal scales with a view toward developing multiscale computational strategies to integrate such findings. Innovative modeling methods that connect molecular to chromosomal scales are crucial for interpreting experiments and eventually deciphering the complex dynamic organization and function of chromatin in the cell.

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“…[16,18 • ,51,96]). Yet there is no general framework as for hybrid classical/quantum mechanics methods, and the best techniques are inherently tailored.…”

Section: Perspectivementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The chromatin fiber: multiscale problems and approaches

Ozer

Luque

Schlick

2015

Current Opinion in Structural Biology

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“…As illustrated in Figure 1, the rise of scientific supercomputing has allowed for the study of the living cell in unparalleled detail, from the scale of the atom [1, 2] to a whole organism [3, 4, 5] and at all levels in between [6]. In particular, the past three decades have witnessed the evolution of molecular dynamics (MD) simulations as a “computational microscope” [7], which has provided a unique framework for the study of the phenomena of cell biology in atomic (or near-atomic) detail.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations of large macromolecular complexes

Perilla

Goh

Cassidy

et al. 2015

Current Opinion in Structural Biology

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300

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Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.

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“…The emerging multiscale simulation methods 12,[15][16][17][18][19][20] are the optimal way to tackle such situations as they bypass the trade-off between accuracy and efficiency of a model. The adaptive resolution scheme (AdResS) is such a method and allows one to simulate a system at multiple resolutions.…”

Section: Introductionmentioning

confidence: 99%

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Zavadlav

Melo

Marrink

et al. 2015

The Journal of Chemical Physics

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Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study The Journal of Chemical Physics 138, 234901 (2013) Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License. [http://dx

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Theoretical frameworks for multiscale modeling and simulation

Cited by 32 publications

References 91 publications

The chromatin fiber: multiscale problems and approaches

The chromatin fiber: multiscale problems and approaches

Molecular dynamics simulations of large macromolecular complexes

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

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