Hossein Ali Karimi-Varzaneh

IBIsCO: A molecular dynamics simulation package for coarse‐grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse‐grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe–Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse‐graining. The reverse nonequilibrium molecular dynamics simulation method (Müller‐Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.

Coarse-Grained Modeling for Macromolecular Chemistry

The physical phenomena and properties of macromolecules such as polymers or biological materials cover a wide range of length and time scales: from Ångströms and subpicoseconds to millimeters and minutes. Multiscale simulation methods link different computer simulation approaches, which cover these scales and the respective levels of resolution. Different simulation methods that bridge the atomistic description of the system to a coarser level have been developed in order to reach the mesoscopic time and length scales important for many material properties. Here, we give a short introduction to multiscale simulation approaches in macromolecular chemistry. Then, we review the coarse-grained simulation models developed to drive a simple model from a more detailed one. Some different methodological aspects such as time scale and dynamics in coarse-grained simulations and several typical problems are briefly addressed, finishing with a look at future challenges.

Studying long-time dynamics of imidazolium-based ionic liquids with a systematically coarse-grained model

A coarse-grained ionic liquid model has been developed to investigate the structure and dynamic properties of 1-n-alkyl-3-methylimidazolium hexafluorophosphate [C(n)mim][PF(6)] ionic liquids with alkyl chains up to ten carbon atoms. Two mapping schemes are compared, showing that different ways of grouping the atoms into coarse-grained beads affect differently the structure and dynamics of the liquid. The simulations predict that upon increasing the length of the alkyl tail the diffusion coefficients of the cations expectedly decrease while the anion diffusion becomes slightly faster. Moreover, the reduced dynamic heterogeneity of the liquids at low temperature is due to a decrease in the number of the slow particles only. At the timescale where the models show their highest dynamic heterogeneity, the cross-over displacement, after which part of the anions show fast dynamics, is consistently higher in C(10) than in C(4) and it is higher than the one found for the cations. This suggests that the cages in which the anions are trapped (at this time scale) are larger in [C(10)mim][PF(6)] than in [C(4)mim][PF(6)]. For the cations, the cross-over displacement has almost the same value for [C(4)mim][PF(6)] and [C(10)mim][PF(6)].

Reactive Molecular Dynamics with Material-Specific Coarse-Grained Potentials: Growth of Polystyrene Chains from Styrene Monomers

We have developed a reactive molecular dynamics (RMD) scheme to simulate irreversible polymerization of realistic polymer systems in a coarse-grained resolution. We have studied the chain propagation of styrene to polystyrene. For monodisperse polystyrene samples, we reproduce the results of equilibrium MD simulations: density, end-to-end distance, radius of gyration, and different geometrical distribution functions. The RMD simulations on polydisperse systems should be considered as case studies intended to understand the influence of different tuning parameters of the RMD approach on calculated polymer quantities. The parameters for the irreversible polymerization include the number and position of the initiator units (I*) as well as capture radii r(I) (r(P)) defining the geometrical conditions for chain initiation (propagation) and a characteristic delay time τ(r) separating two reactive MD time steps. As a function of the r(I) (r(P)) and τ(r), it is possible to model polymerization processes both in the limit of almost unrelaxed and fully relaxed samples. The strong influence of the spatial localization of the I* on the polymer size distribution is discussed in detail. The RMD results are used to formulate optimized computational conditions for the simulation of irreversible polymerizations, to explain observed trends in the polydispersity index, and to suggest experiments that might lead to an unexpected polymer size distribution.

Fast dynamics in coarse-grained polymer models: The effect of the hydrogen bonds

Based on a mesoscale model developed recently for polyamide-66, here we present a simple algorithm for reinserting the atomistic details neglected in the coarse-grained (CG) description. The resulting CG and detailed models are tested successfully against several structural properties including the number of hydrogen bonds (HBs). From a quantitative analysis of the HB dynamics and thermodynamics it turns out that the CG model is characterized by a weaker HB network than the corresponding atomic model. We show that the relaxation of the HB network and the diffusion of the polymer chains are coupled. Moreover, we find that the temperature-dependent scaling factor accounting for the fast dynamics of the CG model is strongly linked to the relaxation time of the HB at each temperature.

Sorption and diffusion of carbon dioxide and nitrogen in poly(methyl methacrylate)

Molecular dynamics simulations are performed to determine the solubility and diffusion coefficient of carbon dioxide and nitrogen in poly(methyl methacrylate) (PMMA). The solubilities of CO2 in the polymer are calculated employing our grand canonical ensemble simulation method, fixing the target excess chemical potential of CO2 in the polymer and varying the number of CO2 molecules in the polymer matrix till establishing equilibrium. It is shown that the calculated sorption isotherms of CO2 in PMMA, employing this method well agrees with experiment. Our results on the diffusion coefficients of CO2 and N2 in PMMA are shown to obey a common hopping mechanism. It is shown that the higher solubility of CO2 than that of N2 is a consequence of more attractive interactions between the carbonyl group of polymer and the sorbent. While the residence time of CO2 beside the carbonyl group of polymer is about three times higher than that of N2, the diffusion coefficient of CO2 in PMMA is higher than that of N2. The higher diffusion coefficient of CO2, compared to N2, in PMMA is shown to be due to the higher (≈3 times) swelling of polymer upon CO2 uptake.

Nonperiodic stochastic boundary conditions for molecular dynamics simulations of materials embedded into a continuum mechanics domain

A scheme is described for performing molecular dynamics simulations on polymers under nonperiodic, stochastic boundary conditions. It has been designed to allow later the embedding of a particle domain treated by molecular dynamics into a continuum environment treated by finite elements. It combines, in the boundary region, harmonically restrained particles to confine the system with dissipative particle dynamics to dissipate energy and to thermostat the simulation. The equilibrium position of the tethered particles, the so-called anchor points, are well suited for transmitting deformations, forces and force derivatives between the particle and continuum domains. In the present work the particle scheme is tested by comparing results for coarse-grained polystyrene melts under nonperiodic and regular periodic boundary conditions. Excellent agreement is found for thermodynamic, structural, and dynamic properties.

Validation of Force Fields of Rubber through Glass-Transition Temperature Calculation by Microsecond Atomic-Scale Molecular Dynamics Simulation

Microsecond atomic-scale molecular dynamics simulation has been employed to calculate the glass-transition temperature (Tg) of cis- and trans-1,4-polybutadiene (PB) and 1,4-polyisoprene (PI). Both all-atomistic and united-atom models have been simulated using force fields, already available in literature. The accuracy of these decade old force fields has been tested by comparing calculated glass-transition temperatures to the corresponding experimental values. Tg depicts the phase transition in elastomers and substantially affects various physical properties of polymers, and hence the reproducibility of Tg becomes very crucial from a thermodynamic point of view. Such validation using Tg also evaluates the ability of these force fields to be used for advanced materials like rubber nanocomposites, where Tg is greatly affected by the presence of fillers. We have calculated Tg for a total of eight systems, featuring all-atom and united-atom models of cis- and trans-PI and -PB, which are the major constituents of natural and synthetic rubber. Tuning and refinement of the force fields has also been done using quantum-chemical calculations to obtain desirable density and Tg. Thus, a set of properly validated force fields, capable of reproducing various macroscopic properties of rubber, has been provided. A novel polymer equilibration protocol, involving potential energy convergence as the equilibration criterion, has been proposed. We demonstrate that not only macroscopic polymer properties like density, thermal expansion coefficient, and Tg but also local structural characteristics like end-to-end distance (R) and radius of gyration (Rg) and mechanical properties like bulk modulus have also been equilibrated using our strategy. Complete decay of end-to-end vector autocorrelation function with time also supports proper equilibration using our strategy.

A nano-mechanical instability as primary contribution to rolling resistance

Rolling resistance ranks among the top ten automobile megatrends, because it is directly linked to fuel efficiency and emissions reduction. The mechanisms controlling this phenomenon are hidden deeply inside the complexity of tire tread materials and do elude direct experimental observation. Here we use atomistic molecular modelling to identify a novel nano-mechanical mechanism for dissipative loss in silica filled elastomers when the latter are subjected to dynamic strain. The force-vs-particle separation curve of a single silica particle-to-silica particle contact, embedded inside a polyisoprene rubber matrix, is obtained, while the contact is opened and closed by a cyclic force. We confirm the occurrence of spontaneous relative displacements (‘jolts’) of the filler particles. These jolts give rise to energy dissipation in addition to the usual viscous loss in the polymer matrix. As the temperature is increased the new loss mechanism becomes dominant. This has important technical implications for the control and reduction of tire rolling resistance as well as for many other elastomer composite applications involving dynamic loading.

Ab initio simulations of bond breaking in sulfur crosslinked isoprene oligomer units

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In this work, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car-Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber.