Atomistic simulations have been very useful for predicting the viscoelastic properties of polymers but face great difficulties in accessing the dynamics of dense, well entangled longchain melts with relaxation times longer than μs due to the high computational cost required. A plethora of coarse-grained models have been developed to address longer time scales. In this article we present a multiscale simulation strategy that bridges detailed molecular dynamics (MD) simulations to slip-spring based Brownian dynamics/kinetic Monte Carlo (BD/kMC) simulations of long-chain polymer melts. The BD/kMC simulations are based on a mesoscopic Helmholtz energy function incorporating bonded, slip-spring, and nonbonded interaction contributions (Macromolecules 2017, 50, 3004). Bonded contributions are expressed as sums of stretching and bending potentials of mean force derived from detailed MD simulations of shorter-chain melts, while nonbonded interaction contributions in the absence of slipsprings are derived from an equation of state that is consistent with thermodynamic properties predicted by detailed MD and measured experimentally. Monodisperse linear polyethylene melts of chain lengths C 260 to C 2080 are used as a test case. Estimates of the chain self-diffusivity, the longest relaxation time, the stress relaxation modulus, and the zero-shear viscosity from ms-long equilibrium BD/kMC simulations are in excellent agreement with MD results for the shorter-chain melts and with experiment. The BD/kMC scheme is extended to simulate Couette flow using Lees−Edwards periodic boundary conditions over a range of Weissenberg numbers (Wi) from 10 −2 to 10 5 . Predictions for the shear viscosity as a function of shear rate, the first and second normal stress difference coefficients, the startup shear stress, as well as for changes in chain conformation and entangled structure with increasing Wi are in favorable agreement with experimental and atomistic simulation evidence.

A mesoscopic, mixed particle-and field-based Brownian Dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments and their motion is dictated by the Helmholtz energy of the sample, which is a sum of the entropic elasticity of chain strands between beads; slip-springs; and non-bonded interactions. Following earlier works in the field (Phys. The mesoscopic simulation methodology is implemented for the case of cis-1,4 polyisoprene, whose structure, dynamics, thermodynamics and linear rheology in the melt state are quantitatively predicted and validated without a posteriori fitting the results to experimental measurements.

The presented work aims at exploring the influence of the mobility of the sorbent framework on both the equilibrium and the kinetic properties of the sorbed phase by means of molecular dynamics computer experiments under isochoricÀisothermal and isobaricÀisothermal statistical ensembles for several host model options, combined by Widom averaging along the entire trajectory of the hostÀguest system toward rigorously obtained sorbate isotherms within a fully flexible lattice. The methodology is adapted to the study of the self-diffusivity and the collective (MaxwellÀStefan and transport) diffusivities of carbon dioxide (CO 2 ) and methane (CH 4 ) within the zeolite imidazolate framework-8 (ZIF-8). The simulation predictions are compared with measurements from pulsed-field gradient nuclear magnetic resonance (PFG NMR), as well as with recently conducted infrared microscopy (IRM) experiments elaborated on the basis of the current modeling in the flexible ZIF-8. The modeling results reveal a significant influence on sorbate transport exerted by the 2-methilimidazolate ligands surrounding the cage-to-cage entrances, whose apertures are commensurate with the guest molecular dimensions. Moreover, calculations of the singlet probability density distribution of the sorbate molecules at selected regions within the imidazolate framework provide a plausible explanation of the transport diffusivity as a function of sorbate occupancy, measured via IRM.

Statistical-mechanics-based simulation studies at the atomistic level of argon (Ar), methane (CH(4)), and hydrogen (H(2)) sorbed in the zeolite imidazolate framework-8 (ZIF-8) are reported. ZIF-8 is a product of a special kind of chemical process, recently termed as reticular synthesis, which has generated a class of materials of critical importance as molecular binders. In this work, we explore the mechanisms that govern the sorption thermodynamics and kinetics of nonpolar sorbates possessing different sizes and strength of interactions with the metal-organic framework to understand the outstanding properties of this novel class of sorbents, as revealed by experiments published elsewhere. For this purpose, we have developed an in-house modeling procedure involving calculations of sorption isotherms, partial internal energies, various probability density functions, and molecular dynamics for the simulation of the sorbed phase over a wide range of occupancies and temperatures within a digitally reconstructed unit cell of ZIF-8. The results showed that sorbates perceive a marked energetic inhomogeneity within the atomic framework of the metal-organic material under study, resulting in free energy barriers that give rise to inflections in the sorption isotherms and guide the dynamics of guest molecules.

A mesoscopic simulation approach is developed for liquid–gas interfaces of weakly and strongly entangled polymer melts and implemented for linear polyethylene at 450 K. A combined particle and field-theoretic treatment is adopted based on aggressive coarse-graining, each polymer bead representing ∼50 carbon atoms, with effective bonded interactions extracted from atomistic simulations. Nonbonded interactions in the mesoscopic model are dictated by an equation of state (here the Sanchez–Lacombe) in conjunction with a variant of gradient theorythe discrete square gradient theory. The dynamics of free films is examined in the presence and in the absence of topological constraints (modeled by slip-springs) to unveil the impact of the latter on chain self-diffusion, to assess their contribution to the interfacial free energy, and to explore how this contribution can be removed by invoking a compensating potential. The molar mass dependence of surface tensionwhich arises from bonded contributions among beads in the mesoscopic chainsis extracted over a broad range of molar masses (103–106 g/mol), in excellent agreement with experiment. Two approaches for computing the surface tension are adopted, based on stress profiles and based on changes in free energy with interfacial area, leading to consistent results. The predicted density profiles, conformations, and orientational tendencies of the mesoscopic chains are retrieved from the simulations and shown to reproduce very well the corresponding results from atomistic simulations. An annealing scheme is developed with the purpose of accelerating transitions of metastable states into more stable biphasic states such as spherical and cylindrical droplets, free films, and spherical and cylindrical bubbles, which minimize the free energy of the periodic model system. Results for the phase diagram as a function of polymer volume fraction conform to the predictions of atomistic simulations of simpler systems.

In previous work by the authors, a new methodology was developed for Brownian dynamics/kinetic Monte Carlo (BD/kMC) simulations of polymer melts. In this study, this methodology is extended for dynamical simulations of crosslinked polymer networks in a coarse-grained representation, wherein chains are modeled as sequences of beads, each bead encompassing a few Kuhn segments. In addition, the C++ code embodying these simulations, entitled Engine for Mesoscopic Simulations for Polymer Networks (EMSIPON) is described in detail. A crosslinked network of cis-1,4-polyisoprene is chosen as a test system. From the thermodynamic point of view, the system is fully described by a Helmholtz energy consisting of three explicit contributions: entropic springs, slip springs and non-bonded interactions. Entanglements between subchains in the network are represented by slip springs. The ends of the slip springs undergo thermally activated hops between adjacent beads along the chain backbones, which are tracked by kinetic Monte Carlo simulation. In addition, creation/destruction processes are included for the slip springs at dangling subchain ends. The Helmholtz energy of non-bonded interactions is derived from the Sanchez–Lacombe equation of state. The isothermal compressibility of the polymer network is predicted from equilibrium density fluctuations in very good agreement with the underlying equation of state and with experiment. Moreover, the methodology and the corresponding C++ code are applied to simulate elongational deformations of polymer rubbers. The shear stress relaxation modulus is predicted from equilibrium simulations of several microseconds of physical time in the undeformed state, as well as from stress-strain curves of the crosslinked polymer networks under deformation.

Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.

A coarse-grained model is derived for a liquid-crystal-forming molecule, 4-cyano-4′-pentylbiphenyl (5CB), from a detailed atomistic model using the iterative Boltzmann inversion (IBI) method in the isotropic phase at 315 K and 1 bar. The coarse-grained model consists of five "superatoms" (one for the cyano group, two for the aromatic rings in the biphenyl moiety, and two for the alkyl tail), which are categorized as three types. A modification of IBI, wherein only one of the effective intermolecular potentials (the one corresponding to the superatom pair whose intermolecular correlation function exhibits the highest deviation from the atomistic one) is updated at each iteration, proves to be necessary to achieve convergence. The coarse-grained model, which enables a savings of a factor of 35 in computational cost relative to atomistic simulation, is used to explore ordering into liquid-crystalline phases at lower temperatures. It is found to yield a first-order ordering transition at 288 K with small hysteresis and negligible system size effects. A detailed investigation in terms of various structural and dynamical measurements indicates that the ordered phase is of the smectic type rather than nematic, as observed experimentally. The ordering temperature can be brought close to the experimental value of 308.5 K through the simple rescaling of the intermolecular effective interaction potentials employed in the coarse-grained model. A nematic ordered phase can be obtained from the coarse-grained model by scaling up the head-head and tail-tail effective interaction potentials obtained by IBI.