STOCK: Structure mapper and online coarse‐graining kit for molecular simulations

We present a web toolkit STructure mapper and Online Coarse‐graining Kit for setting up coarse‐grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, for example, all‐atom, to low, that is, coarse‐grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse‐graining packages, for example, Versatile Object‐oriented Toolkit for Coarse‐graining Applications and DL_CGMAP. Our second tool generates effective potentials for coarse‐grained simulations preserving the structural properties, for example, radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse‐grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse‐graining web toolkit is available at http://stock.cmm.ki.si . © 2014 Wiley Periodicals, Inc.     

Implicit solvent coarse‐grained model of polyamidoamine dendrimers: Role of generation and pH

Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse‐grained model, called the Dry Martini force field, to PAMAM dendrimers. The reduced number of particles and the absence of a solvent allow the capture of longer spatiotemporal scales. This study characterizes PAMAM dendrimers of generations one through seven in acidic, neutral, and basic pH environments. Comparison with existing literature, both experimental and theoretical, is done using measurements of the radius of gyration, moment of inertia, radial distributions, and scaling exponents. Additionally, ion coordination distributions are studied to provide insight into the effects of interior and exterior protonation on counter ions. This model serves as a starting point for future designs of larger functionalized dendrimers. © 2015 Wiley Periodicals, Inc.     

Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH₂r united atoms of the cyclohexane ring, and one representing three FG CH₂r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.     

Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self‐consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle‐field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD‐SCF program profiles, serial MD‐SCF and parallel MD‐SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc.     

Reconstruction of atomistic details from coarse‐grained structures

We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low‐energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed‐phase biomolecular systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Comparing normal modes across different models and scales: Hessian reduction versus coarse‐graining

Dimension reduction is often necessary when attempting to reach longer length and time scales in molecular simulations. It is realized by constraining degrees of freedom or by coarse‐graining the system. When evaluating the accuracy of a dimensional reduction, there is a practical challenge: the models yield vectors with different lengths, making a comparison by calculating their dot product impossible. This article investigates mapping procedures for normal mode analysis. We first review a horizontal mapping procedure for the reduced Hessian techniques, which projects out degrees of freedom. We then design a vertical mapping procedure for the “implosion” of the all‐atom (AA) Hessian to a coarse‐grained scale that is based upon vibrational subsystem analysis. This latter method derives both effective force constants and an effective kinetic tensor. Next, a series of metrics is presented for comparison across different scales, where special attention is given to proper mass‐weighting. The dimension‐dependent metrics, which require prior mapping for proper evaluation, are frequencies, overlap of normal mode vectors, probability similarity, Hessian similarity, collectivity of modes, and thermal fluctuations. The dimension‐independent metrics are shape derivatives, elastic modulus, vibrational free energy differences, heat capacity, and projection on a predefined basis set. The power of these metrics to distinguish between reasonable and unreasonable models is tested on a toy alpha helix system and a globular protein; both are represented at several scales: the AA scale, a Gō‐like model, a canonical elastic network model, and a network model with intentionally unphysical force constants. Published 2012 Wiley Periodicals, Inc.     

Phase Morphologies of Binary Polymer Blends Predicted by Systematically Coarse‐Grained Models

In this work, the combined iterative Boltzmann inversion/conditional reversible work scheme is extended with a little modifications to derive the systematically coarse‐grained (CG) potentials for simulating two typical atactic polymer blends composed of poly(methyl methacrylate) (PMMA) and poly(vinyl chloride) (PVC) or polystyrene (PS). Molecular dynamics simulations are extensively performed on the two blends with a wide formulation range. It is revealed by these simulations that, throughout the entire composition range, the PMMA/PVC blend is homogeneous whereas the PMMA/PS blend undergoes phase separation, which agrees well with the experimental observation that the former exhibits strong interactions that are absent in the latter. Depending upon the formulation, the immiscible PMMA/PS blend presents one single‐ or double‐continuous phase. It is further confirmed that intermolecular interactions play the key roles in forming the phase morphologies, which in turn can be inferred from only the three nonbonded CG potentials of one unlike pair and two like pairs.

     

Solvent‐Responsive Behavior of Polymer‐Brush‐Modified Amphiphilic Gold Nanoparticles

Amphiphilic polymer brushes grafted onto gold nanoparticles impart distinct solvent‐responsive behavior via the change to particle size and surface chemistry and, therefore, wide application prospects can be expected. Coarse‐grained simulations are performed for block and/or mixed polystyrene (PS)/poly(ethylene oxide) (PEO)‐modified amphiphilic gold nanoparticles (AuNP) to investigate their responsive behavior in five different solvents by analyzing their morphology, distribution density profiles, and gyration radii. Typical core–shell, Janus‐type, buckle‐like, ring‐like, jellyfish‐like, and octopus‐like morphologies are formed. Influence of block sequence, mixing mode, and several other effects are discussed. Responsive particle size and surface hydrophilicity can be successfully reproduced by altering solvents.

     

Coarse‐Grained Simulations of Model Polymer Nanofibres

We describe the development of a coarse‐grained (CG) force field for nylon‐6 (polycaprolactam) and its application to the simulation of the structure and macromolecular dynamics within cylindrical fibres formed by this polymer, having diameters in the 14–28 nm range. Our CG model is based on the MARTINI force field for the non‐bonded interactions and on Boltzmann‐inverted gas‐phase atomistic simulations for intramolecular stretching and bending energies. The simulations are carried out on infinite, isolated nanofibres at temperatures of 300, 400 and 500 K, with different starting configurations. Starting from ordered chain‐extended configurations, we simulate the melting of the polymer in the nanofibres and, after cooling back to room temperature, its re‐crystallization in a chain‐folded lamellar configuration. This agrees with experimental observations on electrospun nylon‐6 nanofibres and demonstrated the suitability of the approach for the simulation of these systems. The effect of nanoscale confinement on the structure and dynamics of the polymer chains is extensively discussed.

     

A coarse‐grained MARTINI‐like force field for DNA unzipping in nanopores

In nanopore force spectroscopy (NFS) a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. We present a new model that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all‐atom simulations. The scaled conductivities in bulk solution are consistent with experimental results for NaCl for a wide range of electrolyte concentrations and temperatures. The dependence of the ionic current through a nanopore on the applied voltage is symmetric and, in the voltage range used in experiments (up to 2 V), linear and in good agreement with experimental data. The thermal stability and geometry of DNA is well represented. The model was applied to simulations of DNA hairpin unzipping in nanopores. The results are in good agreement with all‐atom simulations: the scaled translocation times and unzipping sequence are similar. © 2015 Wiley Periodicals, Inc.     

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

We have used systematic structure‐based coarse graining to derive effective site–site potentials for a 10‐site coarse‐grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse‐grained model the same site–site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid–water molar ratios. It was shown that there is a non‐negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid‐like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse‐grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self‐aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles. © 2014 Wiley Periodicals, Inc.     

Prediction of viscoelastic properties with coarse‐grained molecular dynamics and experimental validation for a benchmark polyurea system

To explore the relationship between microscopic structure and viscoelastic properties of polyurea, a coarse‐grained (CG) model is developed by a structure matching method and validated against experiments conducted on a controlled, benchmark material. Using the Green‐Kubo method, the relaxation function is computed from the autocorrelation of the stress tensor, sampled over equilibrium MD simulations, and mapped to a real time scale established by matching self‐diffusion rates of atomistic and CG models. Master curves computed from the predicted stress relaxation function are then compared with dynamic mechanical analysis experiments mapped to a wide frequency range by time–temperature superposition, as well as measurements of ultrasonic shear wave propagation. Computational simulations from monodisperse and polydisperse configurations, representative of the benchmark polyurea, show excellent agreement with the experimental measurements over a multidecade range of loading frequency. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 797–810     

Simulation of the self‐assembly of poly(α‐glutamate) and dodecyltrimethylammonium: Diffusive role of the surfactant cations

The self‐assembly process of stoichiometric complexes formed by poly(α‐glutamate) and dodecyltrimethylammonium molecular cations has been studied at the atomistic by molecular dynamics simulations. The results presented in this work depict a time‐dependent succession of events. Among them, the formation of the assembled complex is an extraordinarily fast event. On the other side, the surfactant units do not influence the kinetics of the polypeptide folding process, showing that the characteristic independent organization experimentally detected for the charged groups and aliphatic tails has its reflection during the assembly process. Through these results, it is possible to infer new strategies to engineer the final nano‐organization that these stoichiometric complexes can adopt. The instantaneous assembly of the oppositely charged components allows a further kinetic control over the polypeptide folding process, which is expected to take place in time scales that are between 10 and 100 times larger than those explored in this work. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 917–924, 2008     

Micromechanical modeling of the elastic properties of semicrystalline polymers: A three‐phase approach

The mechanical performance of semicrystalline polymers is strongly dependent on their underlying microstructure, consisting of crystallographic lamellae and amorphous layers. In line with that, semicrystalline polymers have previously been modeled as two and three‐phase composites, consisting of a crystalline and an amorphous phase and, in case of the three‐phase composite, a rigid‐amorphous phase between the other two, having a somewhat ordered structure and a constant thickness. In this work, the ability of two‐phase and three‐phase composite models to predict the elastic modulus of semicrystalline polymers is investigated. The three‐phase model incorporates an internal length scale through crystalline lamellar and interphase thicknesses, whereas no length scales are included in the two‐phase model. Using linear elastic behavior for the constituent phases, a closed form solution for the average stiffness of the inclusion is obtained. A hybrid inclusion interaction model has been used to compute the effective elastic properties of polyethylene. The model results are compared with experimental data to assess the capabilities of the two‐ or three‐phase composite inclusion model. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010     

Coarse‐grained A‐graft‐B model of poly(lactic acid) for molecular dynamics simulations

A mesoscopic model of poly(lactic acid) is developed where the polymer is represented as an A‐graft‐B chain with monomer units consisting of two covalently connected beads. A coarse‐graining algorithm is proposed to convert an atomistic model of PLA into a coarse‐grained one. The developed model is based on atomistic simulations of oligolactides to take into account terminal groups correctly. It was used for coarse‐grained simulations of polylactide. Gyration radii and end to end distances of polymer chains as well as the density of the polymer melt are shown to be in a good agreement with those obtained from atomistic simulations. The thermal expansion coefficients of the OLA melts calculated using the coarse‐grained model are in reasonable agreement with those obtained from all‐atom molecular dynamics. The model provides a 17‐fold speedup compared with atomistic calculations. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 604–612     

Hyperelastic characterization of the interlamellar domain and interphase layer in semicrystalline polyethylene

The interphase layer in semicrystalline polyethylene (PE) serves as the transition between the crystalline lamellae and the amorphous domains and is recognized as the third constituent of PE. When PE undergoes large deformations, this interphase layer together with the amorphous phase behaves hyperelastically. Because of the metastable nature and nanometric size of the interphase and its intimate mechanical coupling to the neighboring crystal and amorphous domains, detailed characterization of its hyperelastic properties have eluded detailed experimental evaluation. To extract these properties, a combined algorithm is proposed based on applying the constitutive relations of an isotropic, compressible, hyperelastic continuum to the molecular dynamics simulation results of a PE stack from Lee and Rutledge (Macromolecules 2011, 3096–3108). The simulation element is incrementally deformed to a large strain, during which the stress–strain information is recorded. Assuming a neo‐Hookean model, the tensorial constitutive equation is derived. The hyperelastic parameters for the central amorphous phase, the interphase layer, and the interlamellar domain are identified with the help of the optimization notion and a set of nonnegative objective functions. The identified hyperelastic parameters for the interlamellar domain are in good agreement with the ones estimated experimentally and frequently used in the literature for the noncrystalline phase. The specifically developed sensitivity analysis indicates that the shear modulus is identified with a higher degree of certainty, in contrast to the bulk modulus. It is also revealed that the presented continuum mechanics analysis is able to capture the melting/recrystallization and rotation of crystalline chains that take place during the deformation. The evolutions of the boundaries of the hyperelastic elements are also identified concurrently with the hyperelastic parameters as the by‐product of the presented methodology. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013 , 51, 1692–1704     

Needs and Opportunities – Molecular Modeling Meets Polymer Process Modeling

Summary: A non-exhaustive and somehow arbitrary review on actual trends and remaining challenges for a model based process development is given. An example how state of the art molecular modeling methods help to provide kinetic information is explained in some detail. A brief sketch of various methods providing thermodynamic information for engineering is given, and finally, recent concurrent coupling schemes of particle based simulation and computational fluid dynamics are highlighted.