Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

Soft Matter ◽  
2009 ◽  
Vol 5 (22) ◽  
pp. 4357 ◽  
Author(s):  
Christine Peter ◽  
Kurt Kremer
Keyword(s):  
Soft Matter ◽  
Multiscale Simulation ◽  
Coarse Grained

Systematic Coarse Graining of Biomolecular and Soft-Matter Systems

MRS Bulletin ◽  
2007 ◽  
Vol 32 (11) ◽  
pp. 929-934 ◽  
Author(s):  
Gary S. Ayton ◽  
Will G. Noid ◽  
Gregory A. Voth
Keyword(s):  
High Resolution ◽  
Soft Matter ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Atomic Scale ◽  
Coarse Grained ◽  
Statistical Mechanical ◽  
Transfer Of Information ◽  
Very High

AbstractCoarse-grained modeling is a key component in the field of multiscale simulation. Many biomolecular and otherwise complex systems require the characterization of phenomena over multiple length and time scales in order to fully resolve and understand their behavior. These different scales range from atomic to near macroscopic dimensions, and they are generally not independent of one another, but instead coupled. That is, phenomena occurring at atomic length scales have an effect at macroscopic dimensions and vice versa. Systematic transfer of information between these different scales represents a core challenge in the field of multiscale simulation. Coarse-grained modeling works at an intermediate resolution that can bridge the very high resolution (atomic) scale to the very low resolution (macroscopic) scale. As such, a significant challenge is the development of a systematic methodology whereby coarse-grained models can be derived from their high-resolution atomistic-scale counterpart. Here, a systematic theoretical and computational methodology will be described for developing coarse-grained representations of biomolecular and other soft-matter systems. At the heart of the methodology is a variational statistical mechanical algorithm that uses forcematching of atomistic molecular dynamics data to a coarse-grained representation. A theoretical analysis of the coarse-graining methodology will be presented, along with illustrative applications to membranes, peptides, and carbohydrates.

Introduction to molecular simulations in soft matter

2017 ◽  
Author(s):  
J.-L. Barrat ◽  
J. J. de Pablo
Keyword(s):  
Phase Space ◽  
Numerical Methods ◽  
Theoretical Basis ◽  
Soft Matter ◽  
Relevant Literature ◽  
Coarse Grained ◽  
Soft Interfaces ◽  
Molecular Scale ◽  
Soft Matter Physics ◽  
The Continuum

We describe the main features of the coarse-grained models that are typically useful in modelling soft interfaces, from force fields to the continuum descriptions involving density fields. We explain the theoretical basis of the main numerical methods that are used to explore the phase space associated with these models. Finally, three recent examples, illustrating the spirit in which relatively simple simulations can contribute to solving pending problems in soft matter physics, are briefly described. Clearly, a short series of lectures can offer, at best, a biased and restricted view of the available approaches. Our aim here will be to provide the reader with such an overview, with a focus on methods and descriptions that ‘bridge the scale’ between the molecular scale and the continuum or quasi-continuum one. The objective to present a guide to the relevant literature—which has now to a large extent appeared in the form of textbooks.

Multiscale simulation for soft matter: Application to wormlike micellar solution

2013 ◽  
Author(s):  
Takahiro Murashima ◽  
Masatoshi Toda ◽  
Toshihiro Kawakatsu
Keyword(s):  
Micellar Solution ◽  
Soft Matter ◽  
Multiscale Simulation

Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations

2014 ◽  
Vol 42 (5) ◽  
pp. 1418-1424 ◽  
Author(s):  
Antreas C. Kalli ◽  
Mark S. P. Sansom
Keyword(s):  
Lipid Bilayers ◽  
Molecular Mechanisms ◽  
Phospholipid Composition ◽  
Md Simulations ◽  
Multiscale Simulation ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Peripheral Proteins ◽  
Dynamics Simulations ◽  
Phosphatidylinositol Phosphates

Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.

scholarly journals Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

2012 ◽  
Vol 33 (9) ◽  
pp. 937-949 ◽  
Author(s):  
Olga Bezkorovaynaya ◽  
Alexander Lukyanov ◽  
Kurt Kremer ◽  
Christine Peter
Keyword(s):  
Multiscale Simulation ◽  
Coarse Grained ◽  
Conformational Sampling ◽  
Small Peptides

scholarly journals Binding of Ca2+-Independent C2 Domains to Lipid Membranes: a Multi-Scale Molecular Dynamics Study

2020 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Mark S.P. Sansom
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Md Simulations ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Type I ◽  
Type Ii ◽  
Binding Modes ◽  
C2 Domains ◽  
Anionic Lipids

AbstractC2 domains facilitate protein-lipid interaction in cellular recognition and signalling processes. They possess a β-sandwich structure, with either type I or type II topology. C2 domains can interact with anionic lipid bilayers in either a Ca2+-dependent or a Ca2+-independent manner. The mechanism of recognition of anionic lipids by Ca2+-independent C2 domains is incompletely understood. We have used molecular dynamics (MD) simulations to explore the membrane interactions of six Ca2+– independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse grained MD simulations these C2 domains bound to lipid bilayers, forming transient interactions with zwitterionic (phosphatidylcholine, PC) bilayers compared to long lived interactions with anionic bilayers also containing either phosphatidylserine (PS) or PS and phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops (as is typically the case for Ca2+-dependent C2 domains). C2 domains interacted strongly (up to 120 kJ/mol) with membranes containing PIP2 causing the bound anionic lipids to clustered around the protein. The C2 domains bound less strongly to anionic membranes without PIP2 (<50 kJ/mol), and most weakly to neutral membranes (<33 kJ/mol). Productive binding modes were identified and further analysed in atomistic simulations. For PTEN and SHIP2, CG simulations were also performed of the intact enzymes (i.e. phosphatase domain plus C2 domain) with PIP2-contating bilayers and the roles of the two domains in membrane localization were compared. From a methodological perspective, these studies establish a multiscale simulation protocol for studying membrane binding/recognition proteins, capable of revealing binding modes alongside details of lipid binding affinity and specificity.

Transport Mechanisms Underlying Ionic Conductivity in Nanoparticle-Based Single-Ion Electrolytes

2020 ◽  
Author(s):  
Sanket Kadulkar ◽  
Delia Milliron ◽  
Thomas Truskett ◽  
Venkat Ganesan
Keyword(s):  
Ionic Conductivities ◽  
Solvent Polarity ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Design Parameters ◽  
Transport Pathways ◽  
Surface Transport ◽  
High Particle ◽  
Conductivity Increase ◽  
Ion Conducting

<div>Recent studies have demonstrated the potential of nanoparticle-based single-ion conductors as battery electrolytes. In this work, we introduce a coarse-grained multiscale simulation approach to identify the mechanisms underlying the ion mobilities in such systems and to clarify the influence of key design parameters on conductivity. Our results suggest that for the experimentally studied electrolyte systems, the dominant pathway for cation transport is along the surface of nanoparticles, in the vicinity of nanoparticle-tethered anions. At low nanoparticle concentrations, connectivity of cationic surface transport pathways and conductivity increase with nanoparticle loading. However, cation mobilities are reduced when nanoparticles are in close vicinity, causing conductivity to decrease for suffciently high particle loadings. We discuss the impacts of cation and anion choice as well as solvent polarity within this picture and suggest means to enhance ionic conductivities in single-ion conducting electrolytes based on nanoparticle salts.</div>

Transport Mechanisms Underlying Ionic Conductivity in Nanoparticle-Based Single-Ion Electrolytes

2020 ◽  
Author(s):  
Sanket Kadulkar ◽  
Delia Milliron ◽  
Thomas Truskett ◽  
Venkat Ganesan
Keyword(s):  
Ionic Conductivities ◽  
Solvent Polarity ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Design Parameters ◽  
Transport Pathways ◽  
Surface Transport ◽  
High Particle ◽  
Conductivity Increase ◽  
Ion Conducting

<div>Recent studies have demonstrated the potential of nanoparticle-based single-ion conductors as battery electrolytes. In this work, we introduce a coarse-grained multiscale simulation approach to identify the mechanisms underlying the ion mobilities in such systems and to clarify the influence of key design parameters on conductivity. Our results suggest that for the experimentally studied electrolyte systems, the dominant pathway for cation transport is along the surface of nanoparticles, in the vicinity of nanoparticle-tethered anions. At low nanoparticle concentrations, connectivity of cationic surface transport pathways and conductivity increase with nanoparticle loading. However, cation mobilities are reduced when nanoparticles are in close vicinity, causing conductivity to decrease for suffciently high particle loadings. We discuss the impacts of cation and anion choice as well as solvent polarity within this picture and suggest means to enhance ionic conductivities in single-ion conducting electrolytes based on nanoparticle salts.</div>

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