Molecular dynamics simulations of self-assembly and nanotube formation by amphiphilic molecules in aqueous solution: a coarse-grain approach

Srinivas, Goundla; Klein, Michael L.

doi:10.1088/0957-4484/18/20/205703

Cited by 24 publications

(24 citation statements)

References 71 publications

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“…49 The cation-induced narrowing of the minor groove was studied. Such structural changes were estimated from the average interphosphate distance between opposite strands measured for the following pairs: {(5, 24), (6, 23), (7,22), (8,21), (9,20), (10,19), (11,18), (12,17)} (italics indicate the residue numbers at the AT track). Cations were considered to be bound to the minor groove if their distance to the phosphate groups of both opposite strands was below 0.5 nm.…”

Section: Methodsmentioning

confidence: 99%

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Darré

Machado

Dans

et al. 2010

J. Chem. Theory Comput.

124

199

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Biological processes occur on space and time scales that are often unreachable for fully atomistic simulations. Therefore, simplified or coarse grain (CG) models for the theoretical study of these systems are frequently used. In this context, the accurate description of solvation properties remains an important and challenging field. In the present work, we report a new CG model based on the transient tetrahedral structures observed in pure water. Our representation lumps approximately 11 WATer molecules into FOUR tetrahedrally interconnected beads, hence the name WAT FOUR (WT4). Each bead carries a partial charge allowing the model to explicitly consider long-range electrostatics, generating its own dielectric permittivity and obviating the shortcomings of a uniform dielectric constant. We obtained a good representation of the aqueous environment for most biologically relevant temperature conditions in the range from 278 to 328 K. The model is applied to solvate simple CG electrolytes developed in this work (Na + , K + , and Cl -) and a recently published simplified representation of nucleic acids. In both cases, we obtained a good resemblance of experimental data and atomistic simulations. In particular, the solvation structure around DNA, partial charge neutralization by counterions, preference for sodium over potassium, and ion mediated minor groove narrowing as reported from X-ray crystallography are well reproduced by the present scheme. The set of parameters presented here opens the possibility of reaching the multimicroseconds time scale, including explicit solvation, ionic specificity, and long-range electrostatics, keeping nearly atomistic resolution with significantly reduced computational cost.

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Section: Methodsmentioning

confidence: 99%

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Darré

Machado

Dans

et al. 2010

J. Chem. Theory Comput.

124

199

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“…In particular, the CG parametrization of polycyclic aromatic hydrocarbons (PAHs), which constitute the aromatic regions in asphaltenic structures, connote some further challenges [63][64][65][66][67] . In a contribution which is very relevant to this study, von Lilienfeld and Andrienko 44 coarse-grain polycyclic aromatic hydrocarbons by fitting effective Lennard-Jones potentials to density-functional theory calculations, showing that the potential parameters of the CG units are specific to the aromatic molecule in the study.…”

Section: Introductionmentioning

confidence: 99%

Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations

et al. 2019

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Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena and the understanding of the role that molecular structure plays therein. However, the detail included at this scale of molecular modeling is at odds with the required spatial and temporal resolution needed to fully understand the asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterised by effective interactions. In this work CG force fields developed via the SAFT-γ [Müller, E.A., Jackson, G. (2014) Annu. Rev. Chem. Biomolec. Eng., 5, 405-427] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [Müller, E.A. and Mejía, A. (2017) Langmuir, 33, 11518-11529], that allows parametrizing homonuclear rings, is selected as the starting point to propose CG models for polycyclic aromatic hydrocarbons (PAHs). The new aromatic-core parameters, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform Molecular Dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in explicit solvent investigating the effect of asphaltene concentration, solvent composition, and temperature on aggregation. Upon employing large systems facilitated by the CG models, we observe stable continuous distributions of molecular aggregates at conditions away from the two-phase precipitation point. As a further example application, a widely accepted interpretation of cluster-size distributions in asphaltenic systems is challenged by performing system-size tests, reversibility proofs and time-dependence analysis. The coarse-graining procedure proposed is seen to be general and predictive, hence, can be applied to other asphaltenic molecular structures.

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“…Though initially developed with a fully atomistic perspective, with secondary efforts pursuing more “coarse‐grained” potentials,[17, 18] development and application of coarse‐grained models continues at a rigorous pace today. [19–24] Nevertheless, under the current paradigmatic approach to force field development, such models are generally referenced to results from fully atomistic simulations. Thus, the need for accurate all‐atom potentials still persists.…”

Section: Introductionmentioning

confidence: 99%

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

et al. 2011

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We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the Particle Mesh Ewald method (PME) for solution of Poisson’s Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17004, 68484 and 273936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (SCD), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.

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Molecular dynamics simulations of self-assembly and nanotube formation by amphiphilic molecules in aqueous solution: a coarse-grain approach

Cited by 24 publications

References 71 publications

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

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