Local ordering of polymer-tethered nanospheres and nanorods and the stabilization of the double gyroid phase

We present results of Brownian dynamics simulations of tethered nanospheres and tethered nanorods. Immiscibility between tether and nanoparticle facilitates microphase separation into the bicontinuous, double gyroid structure (first reported by Iacovella et al. [Phys. Rev. E 75, 040801(R) (2007)] and Horsch et al. [J. Chem. Phys. 125, 184903 (2006)], respectively). We demonstrate the ability of these nanoparticles to adopt distinct, minimal energy local packings, in which nanospheres form icosahedral-like clusters and nanorods form splayed hexagonal bundles. These local structures reduce packing frustration within the nodes of the double gyroid. We argue that the ability to locally order into stable structures is key to the formation of the double gyroid phase in these systems.     

Molecular simulation study of cavity-generated instabilities in the superheated Lennard-Jones liquid

Previous equilibrium-based density-functional theory (DFT) analyses of cavity formation in the pure component superheated Lennard-Jones (LJ) liquid [S. Punnathanam and D. S. Corti, J. Chem. Phys. 119, 10224 (2003); M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007)] revealed that a thermodynamic limit of stability appears in which no liquidlike density profile can develop for cavity radii greater than some critical size (being a function of temperature and bulk density). The existence of these stability limits was also verified using isothermal-isobaric Monte Carlo (MC) simulations. To test the possible relevance of these limits of stability to a dynamically evolving system, one that may be important for homogeneous bubble nucleation, we perform isothermal-isobaric molecular dynamics (MD) simulations in which cavities of different sizes are placed within the superheated LJ liquid. When the impermeable boundary utilized to generate a cavity is removed, the MD simulations show that the cavity collapses and the overall density of the system remains liquidlike, i.e., the system is stable, when the initial cavity radius is below some certain value. On the other hand, when the initial radius is large enough, the cavity expands and the overall density of the system rapidly decreases toward vaporlike densities, i.e., the system is unstable. Unlike the DFT predictions, however, the transition between stability and instability is not infinitely sharp. The fraction of initial configurations that generate an instability (or a phase separation) increases from zero to unity as the initial cavity radius increases over a relatively narrow range of values, which spans the predicted stability limit obtained from equilibrium MC simulations. The simulation results presented here provide initial evidence that the equilibrium-based stability limits predicted in the previous DFT and MC simulation studies may play some role, yet to be fully determined, in the homogeneous nucleation and growth of embryos within metastable fluids.     

Microphase separation induced by interfacial segregation of isotropic, spherical nanoparticles

In a recent experiment by Chung et al. [Nano Lett. 5, 1878 (2005)] and simulation by Stratford et al. [Science 309, 2198 (2005)] on immiscible blends containing nanoscale particles, it was shown that the phase separation of the two polymers can be prevented as a result of the aggregation of the nanoparticles at the interfaces between the two polymers. Motivated by these studies, we performed large scale systematic simulations, based on the dissipative particle dynamics approach, on immiscible binary (A-B) fluids containing moderate volume fractions of isotropic nanoscale spherical particles N. The nanoparticles preferentially segregate at the interfaces between the two fluids if the pairwise interactions between the three components are such that chi(AB)>/chi(AN)-chi(BN)/. We find that at later times, the average domain size saturates to a value, L approximately R(N)/phi(N), where R(N) and phi(N) are the radius and volume fraction of the nanoparticles, respectively. For small nanoparticles, however, full phase separation is observed.     

Binary hairy nanoparticles: Recent progress in theory and simulations

Binary polymer brushes, including mixed homopolymer brushes and diblock copolymer brushes, are an attractive class of environmentally responsive nanostructured materials. Owing to microphase separation of the two chemically distinct components in the brush, multifaceted nanomaterials with functionalized and patterned surfaces can be obtained. This review summarizes recent progress on the theory and simulations related to binary polymer brushes grafted to flat, spherical, and cylindrical substrates, with a focus on patterned morphologies of multifaceted hairy nanoparticles, an intriguing class of hybrid nanostructured particles (e.g., nanospheres and nanorods). In particular, powerful field theory and particle-based simulations suitable for revealing novel structures on these patterned surfaces, including self-consistent field theory and dissipative particle dynamics simulations, are emphasized. The unsolved yet critical issues in this research field, such as dynamic response of binary polymer brushes to environmental stimuli and the hierarchical self-assembly of binary hairy nanoparticles, are briefly discussed. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 1583–1599     

Role of the first coordination shell in determining the equilibrium structure and dynamics of simple liquids

The traditional view that the physical properties of a simple liquid are determined primarily by its repulsive forces was recently challenged by Berthier and Tarjus, who showed that in some cases ignoring the attractions leads to large errors in the dynamics [L. Berthier and G. Tarjus, Phys. Rev. Lett. 103, 170601 (2009); J. Chem. Phys. 134, 214503 (2011)]. We present simulations of the standard Lennard-Jones liquid at several condensed-fluid state points, including a fairly low density state and a very high density state, as well as simulations of the Kob-Andersen binary Lennard-Jones mixture. By varying the range of the forces via a shifted-forces cutoff, results for the thermodynamics, dynamics, and structure show that the determining factor for getting the correct statics and dynamics is not whether or not the attractive forces per se are included in the simulations. What matters is whether or not interactions are included from all particles within the first coordination shell - the attractive forces can thus be ignored, but only at extremely high densities. The recognition of the importance of a local shell in condensed fluids goes back to van der Waals; our results confirm this idea and thereby the basic picture of the old hole and cell theories for simple condensed fluids.     

Transport properties of Mie(14,7) fluids: molecular dynamics simulation and theory

An extensive computer simulation study is presented for the self-diffusion coefficient, the shear viscosity, and the thermal conductivity of Mie(14,7) fluids. The time-correlation function formalism of Green-Kubo is utilized in conjunction with molecular dynamics (MD) simulations. In addition to molecular simulations, the results of a recent study [A. Eskandari Nasrabad, J. Chem. Phys. 128, 154514 (2008)] for the mean free volume are applied to calculate the self-diffusion coefficients within a free volume theory framework. A detailed comparison between the MD simulation and free volume theory results for the diffusion coefficient is given. The density fluctuation theory of shear viscosity is used to compute the shear viscosity and the results are compared to those from MD simulations. The density and temperature dependences of different time-correlation functions and transport coefficients are studied and discussed.     

A molecular dynamics study of water nucleation using the TIP4P/2005 model

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nose?-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.     

A quantum-classical treatment of non-adiabatic transitions

We have carried out molecular dynamics simulations of non-adiabatic processes with the help of a newly formulated potentially exact quantum-classical approach derived from a method proposed earlier [J. Chem. Phys. 118 (2003) 5302]. In this method, time-dependent Schroedinger equation is solved by representing Ψ on a moving Gauss–Hermite DVR grid, the motion of grid-centre being handled classically, but self consistently with the quantum evolution of the wavefunction. Electronic transitions are allowed anywhere in the configuration space among any number of coupled states. We have tested the method on three model problems proposed by J.C. Tully [J. Chem. Phys. 93 (1990) 1061]. These models are relevant to a wide range of gas-phase and condensed-phase phenomena occurring even at low energies. Excellent agreement of computed transition probabilities with corresponding quantum mechanical (DVR/FFT) results even in the deep quantum regime and its cost-efficiency (computational) are encouraging.     

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].     

Nonlinear elasticity and yielding of nanoparticle glasses

We employ experiment and theory to explore the nonlinear elasticity and yielding of concentrated suspensions of nanoparticles which interact via purely repulsive forces. These glassy suspensions are found to exhibit high exponent power law or simple exponential dependences of the shear elastic modulus and perturbative yield stress on nanoparticle volume fraction, as well as a monotonic decrease of the perturbative yield strain with increasing concentration. Our experimental observations are in good agreement with the predictions of a recently developed microscopic statistical mechanical theory, which describes glassy dynamics based on a nonequilibrium free energy that incorporates local cage correlations and activated barrier hopping processes [(1) Schweizer, K. S.; Saltzman, E. J. J. Chem. Phys. 2003, 119, 1181. (2) Saltzman, E. J.; Schweizer, K. S. J. Chem. Phys. 2003, 119, 1197. (3) Kobelev, V.; Schweizer, K. S. Phy. Rev. E 2005, 71, 021401].     

Theoretical analysis and computer simulation of fluorescence lifetime measurements. I. Kinetic regimes and experimental time scales

The configuration-controlled regime and the diffusion-controlled regime of conformation-modulated fluorescence emission are systematically studied for Markovian and non-Markovian dynamics of the reaction coordinate. A path integral simulation is used to model fluorescence quenching processes on a semiflexible chain. First-order inhomogeneous cumulant expansion in the configuration-controlled regime defines a lower bound for the survival probability, while the Wilemski-Fixman approximation in the diffusion-controlled regime defines an upper bound. Inclusion of the experimental time window of the fluorescence measurement adds another dimension to the two kinetic regimes and provides a unified perspective for theoretical analysis and experimental investigation. We derive a rigorous generalization of the Wilemski-Fixman approximation [G. Wilemski and M. Fixman, J. Chem. Phys. 60, 866 (1974)] and recover the 1/D expansion of the average lifetime derived by Weiss [G. H. Weiss, J. Chem. Phys. 80, 2880 (1984)].     

Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries

A numerical method to simulate the dynamics of polymer solutions in confined geometries has been implemented and tested. The method combines a fluctuating lattice-Boltzmann model of the solvent [Ladd, Phys. Rev. Lett. 70, 1339 (1993)] with a point-particle model of the polymer chains. A friction term couples the monomers to the fluid [Ahlrichs and Dunweg, J. Chem. Phys. 111, 8225 (1999)], providing both the hydrodynamic interactions between the monomers and the correlated random forces. The coupled equations for particles and fluid are solved on an inertial time scale, which proves to be surprisingly simple and efficient, avoiding the costly linear algebra associated with Brownian dynamics. Complex confined geometries can be represented by a straightforward mapping of the boundary surfaces onto a regular three-dimensional grid. The hydrodynamic interactions between monomers are shown to compare well with solutions of the Stokes equations down to distances of the order of the grid spacing. Numerical results are presented for the radius of gyration, end-to-end distance, and diffusion coefficient of an isolated polymer chain, ranging from 16 to 1024 monomers in length. The simulations are in excellent agreement with renormalization group calculations for an excluded volume chain. We show that hydrodynamic interactions in large polymers can be systematically coarse-grained to substantially reduce the computational cost of the simulation. Finally, we examine the effects of confinement and flow on the polymer distribution and diffusion constant in a narrow channel. Our results support the qualitative conclusions of recent Brownian dynamics simulations of confined polymers [Jendrejack et al., J. Chem. Phys. 119, 1165 (2003) and Jendrejack et al., J. Chem. Phys. 120, 2513 (2004)].     

Simulating critical dynamics in liquid mixtures: short-range and long-range contributions

Recently, Das et al. [J. Chem. Phys. 125, 024506 (2006)] established that computer simulations of critical dynamics in a binary Lennard-Jones mixture are consistent with the predicted Stokes-Einstein behavior of the asymptotic decay rate of the order-parameter fluctuations near criticality. Here, we show that the noncritical or "background" contributions to the computed diffusion coefficient are also in agreement with both theory and experiment, thus further validating the feasibility of molecular dynamics simulations for studying dynamic critical behavior.     

Theory for an order-driven disruption of the liquid state in water

Water is known to exhibit a number of peculiar physical properties because of the strong orientational dependence of the intermolecular hydrogen bonding interactions that dominate its liquid state. Recent full-atom simulations of water in a nanolayer between graphite plates submersed in an aqueous medium have raised the possibility of a new addition to this list of peculiarities: they show that application of a strong, uniform electric field normal to and between the plates can cause a pronounced decrease in particle density, rather than the increase expected from electrostriction theory for polarizable fluids [Vaitheeswaran et al., J. Phys. Chem. B 70, 6629 (2005)]. However, in seeming contradiction to this result, another study that simulated a range of similar systems has reported a less surprising electrostrictive increase in particle density upon application of the field [Bratko et al., J. Am. Chem. Soc. 129, 2504 (2007)]. In this work, we attempt to reconcile these conflicting simulation phenomena using a statistical mechanical lattice liquid model of water in an applied field. By solving the model using mean-field theory, we show that a field-induced transition to a markedly lower-density phase such as that observed in recent simulations is possible within a certain parameter regime, but that outside of this regime, the more conventional electrostrictive result should be obtained. Upon modifying the model to treat the case of bulk water under constant pressure in an applied field, we predict a density drop with rising field, and subsequently observe the predicted behavior in our own molecular dynamics simulations of liquid water. Our findings lead us to propose that the model considered here may be useful in a variety of contexts for describing the trade-off between orientational ordering of water molecules and their participation in the liquid phase.     

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.     

Pathways of cluster growth and kinetic slowing down in a model of short-range attractive colloids

We present the results of an extensive 3D Brownian dynamics simulation of the self-assembly of colloidal particles for a short-range attractive model that is quenched below its metastable critical point. In particular, results are obtained in the small-volume-fraction, low-temperature region in which we find so-called sticky beads that diffuse around the system, without reaching a final large cluster on the timescale of our simulation. For larger volume fractions in this low-temperature regime, a gel forms as the result of kinetically slowed down spinodal decomposition, as shown earlier for other short-range attractive models (Foffi, G.; De Michele, C.; Sciortino, F.; Tartaglia, P. Phys. Rev. Lett. 2005, 94, 078301. Zaccarelli, E. J. Phys.: Condens. Matter 2007, 19, 323101). We also show that for quenches below the critical point but above the intersection of the binodal with the glass line, two-step crystallization takes place. For sufficiently small volume fractions, the first step is the nucleation of dense fluid drops, followed by the second step of crystallization within these drops, as first proposed for a model of protein crystallization for quenches just above the metastable critical point (ten Wolde, P. R.; Frenkel, D. Science 1997, 277, 1975). For larger values of the volume fraction, the initial step is spinodal decomposition that leads to the formation of an interconnected network of low- and high-density fluids. The second step is crystallization that takes place within the dense fluid phase.     

Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cis-1,4-polybutadiene

The dynamics of cis-1,4-polybutadiene (cis-1,4-PB) over a wide range of temperature and pressure conditions is explored by conducting atomistic molecular dynamics (MD) simulations with a united atom model on a 32-chain C128 cis-1,4-PB system. The local or segmental dynamics is analyzed in terms of the dipole moment time autocorrelation function (DACF) of the simulated polymer and its temperature and pressure variations, for temperatures as low as 195 K and pressures as high as 3 kbars. By Fourier transforming the DACF, the dielectric spectrum, epsilon* = epsilon' + i epsilon" = epsilon*omega, is computed and the normalized epsilon"/epsilon(max)" vs omega/omega(max) plot is analyzed on the basis of the time-temperature and time-pressure superposition principles. The relative contribution of thermal energy and volume to the segmental and chain relaxation processes are also calculated and evaluated in terms of the ratio of the activation energy at constant volume to the activation energy at constant pressure, Q(V)/Q(P). Additional results for the temperature and pressure dependences of the Rouse times describing terminal relaxation in the two polymers show that, in the regime of the temperature and pressure conditions covered here, segmental and chain relaxations are influenced similarly by the pressure and temperature variations. This is in contrast to what is measured experimentally [see, e.g., G. Floudas and T. Reisinger, J. Chem. Phys. 111, 5201 (1999); C. M. Roland et al.,J. Polym. Sci. Part B, 41, 3047 (2003)] for other, chemically more complex polymers that pressure has a stronger influence on the dynamics of segmental mode than on the dynamics of the longest normal mode, at least for the regime of temperature and pressure conditions covered in the present MD simulations.     

Molecular dynamics simulations of surface-initiated melting of nitromethane

The melting of nitromethane initiated at solid-vacuum interfaces has been investigated using molecular dynamics nvt simulations with a realistic force field [D. C. Sorescu et al., J. Phys. Chem. B 104, 8406 (2000)]. The calculated melting point (251+/-5 K) is in good agreement with experiment (244.73 K) and values obtained previously (approximately 255.5 and 266.5+/-8 K) using other simulation methods [P. M. Agrawal et al., J. Chem. Phys. 119, 9617 (2003)]. Analyses of the molecular orientations and diffusion during the simulations as functions of the distance from the exposed surfaces show that the melting is a direct crystal-to-liquid transition, in which the molecules first gain rotational freedom, then mobility. There is a slight dependence of the melting temperature on the exposed crystallographic face.     

The Vliegenthart-Lekkerkerker relation: the case of the Mie-fluids

The Vliegenthart-Lekkerkerker relation for the second virial coefficient value at the critical temperature found in the work of Vliegenthart and Lekkerkerker [J. Chem. Phys. 112, 5364 (2000)] is discussed in connection with the scale invariant mean-field approach proposed by Kulinskii and Bulavin [J. Chem. Phys. 133, 134101 (2010)]. We study the case of the Mie-class potentials, which is widely used in simulations of the phase equilibrium of the fluids. It is shown that due to the homogeneity property of the Mie-class potentials it is possible to connect the loci of the fluids with these model potentials in different dimensions.