Segregation in aqueous methanol enhanced by cooling and compression

Molecular segregation in methanol-water mixtures is studied across a wide concentration range as a function of temperature and pressure. Cluster distributions obtained from both neutron diffraction and molecular dynamics simulations point to significantly enhanced segregation as the mixtures are cooled or compressed. This evolution toward greater molecular heterogenity in the mixture accounts for the observed changes in the water-water radial distribution function and there are indications also of a change in the topology of the water clusters. The observed behavior is consistent with an approach to an upper critical solution point. Such a point would appear to be "hidden" below the freezing line, thereby precluding observation of the two-fluid region.     

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.     

Phase diagram and universality of the Lennard-Jones gas-liquid system

The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class.     

Is there a relation between excess volume and miscibility in binary liquid mixtures?

Molecular dynamics computer simulations of various symmetrical Lennard-Jones (LJ) models are used to elucidate how the excess volume in dense binary liquids is related to the microscopic interactions between the particles. Both fully miscible systems and systems with a liquid-liquid phase separation are considered by varying systematically the parameters of the LJ potentials. The phase diagrams with the critical points of the demixing systems are determined by means of Monte Carlo simulations in the semigrandcanonical ensemble. The different LJ models are investigated by computing Bhatia-Thornton structure factors, enthalpy of mixing, and excess volume. For the demixing systems, the LJ models show a positive enthalpy of mixing while it is negative for the systems without miscibility gap. In contrast to that, the excess volume can be negative and positive for both demixing and fully miscible systems. This behavior is explained in terms of the interplay between the repulsive and attractive terms in the LJ potential. Whereas repulsions dominate the packing of particles as reflected by the number-density structure factor, the chemical ordering and thus the concentration structure factor are strongly affected by attractive interactions, leading to the "anomalies" of the excess volume.     

A comparison of implicit- and explicit-solvent simulations of self-assembly in block copolymer and solute systems

We have developed explicit- and implicit-solvent models for the flash nanoprecipitation process, which involves rapid coprecipitation of block copolymers and solutes by changing solvent quality. The explicit-solvent model uses the dissipative particle dynamics (DPD) method and the implicit-solvent model uses the Brownian dynamics (BD) method. Each of the two models was parameterized to match key properties of the diblock copolymer (specifically, critical micelle concentration, diffusion coefficient, polystyrene melt density, and polyethylene glycol radius of gyration) and the hydrophobic solute (aqueous solubility, diffusion coefficient, and solid density). The models were simulated in the limit of instantaneous mixing of solvent with antisolvent. Despite the significant differences in the potentials employed in the implicit- and explicit-solvent models, the polymer-stabilized nanoparticles formed in both sets of simulations are similar in size and structure; however, the dynamic evolution of the two simulations is quite different. Nanoparticles in the BD simulations have diffusion coefficients that follow Rouse behavior (D ∝ M(-1)), whereas those in the DPD simulations have diffusion coefficients that are close to the values predicted by the Stokes-Einstein relation (D ∝ R(-1)). As the nanoparticles become larger, the discrepancy between diffusion coefficients grows. As a consequence, BD simulations produce increasingly slower aggregation dynamics with respect to real time and result in an unphysical evolution of the nanoparticle size distribution. Surface area per polymer of the stable explicit-solvent nanoparticles agrees well with experimental values, whereas the implicit-solvent nanoparticles are stable when the surface area per particle is roughly two to four times larger. We conclude that implicit-solvent models may produce questionable results when simulating nonequilibrium processes in which hydrodynamics play a critical role.     

Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena

An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.     

Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the "inherent structure entropy." The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.     

Effect of electric field on liquid infiltration into hydrophobic nanopores

Understanding the variation of nanofluidic behavior in the presence of an external electric field is critical for controlling and designing nanofluidic devices. By studying the critical infiltration pressure of liquids into hydrophobic nanopores using molecular dynamics (MD) simulations and experiments, important insights can be gained on the variation of the effective liquid-solid interfacial tension with the magnitude and sign of electric field, as well as its coupling with the pore size and the solid and liquid species. It is found that the effective hydrophobicity reduces with the increase of electric intensity and/or pore size, and the behavior is asymmetric with respect to the direction of the electric field. The underlying molecular mechanisms are revealed via the study of the density profile, contact angle, and surface tension of confined liquid molecules.     

Theoretical Study on the Structures and Thermal Properties of Ag–Pt–Ni Trimetallic Clusters

The structures and thermal properties of Ag–Pt–Ni ternary nanoclusters varying with different compositions and sizes are studied by Monte Carlo and molecular dynamics simulations. It can be found that silver atoms tend to occupy the surface and platinum atoms favor the subsurface occupation, whereas the inner is occupied by nickel atoms due to the different surface energies and lattice parameters. In addition, there is a non-monotonous relationship between the melting points and compositions of Ag–Pt–Ni ternary nanoclusters according to molecular dynamics simulations. In addition, a linear decrease in melting point with \(N^{ - 1/3}\) is found for both monometallic and trimetallic clusters. This behavior is consistent with Pawlow’s law.     

Water ordering at membrane interfaces controls fusion dynamics

Membrane interfaces are critical to many cellular functions, yet the vast array of molecular components involved make the fundamental physics of interaction difficult to define. Water has been shown to play an important role in the dynamics of small biological systems, for example when trapped in hydrophobic regions, but the molecular details of water have generally been thought dispensable when considering large membrane interfaces. Nevertheless, spectroscopic data indicate that water has distinct, ordered behavior near membrane surfaces. While coarse-grained simulations have achieved success recently in aiding understanding the dynamics of membrane assemblies, it is natural to ask, does the missing chemical nature of water play an important role? We have therefore performed atomic-resolution simulations of vesicle fusion to understand the role of chemical detail, particularly the molecular structure of water, in membrane fusion and at membrane interfaces more generally. These membrane interfaces present a form of hydrophilic confinement, yielding surprising, non-bulk-like water behavior.     

Mesoscale modeling of electrical percolation in fiber-filled systems

The research described in this paper primarily involves mesoscale simulations: dissipative particle dynamics (DPD) of packed assemblies of oriented fibers suspended in a viscous medium. Computer simulations have been performed in order to explore how the aspect ratio and degree of fiber alignment affect the critical volume fraction (percolation threshold) required to achieve electrical conductivity. The fiber network impedance was assessed using Monte Carlo simulations after establishing the structural arrangement with DPD. The predictions are compared with the predictions of classical percolation theory and found to be in close agreement. The approach is thus validated and can be extended to systems that cannot be tackled analytically; in particular, the work is motivated by long-standing interest in materials which display a complex percolation behavior.     

Mechanical unfolding of the beet western yellow virus -1 frameshift signal

Using mechanical unfolding by optical tweezers (OT) and steered molecular dynamics (SMD) simulations, we have demonstrated the critical role of Mg(2+) ions for the resistance of the Beet Western Yellow Virus (BWYV) pseudoknot (PK) to unfolding. The two techniques were found to be complementary, providing information at different levels of molecular scale. Findings from the OT experiments indicated a critical role of stem 1 for unfolding of the PK, which was confirmed in the SMD simulations. The unfolding pathways of wild type and mutant appeared to depend upon pH and nucleotide sequence. SMD simulations support the notion that the stability of stem 1 is critical for -1 frameshifting. The all-atom scale nature of the SMD enabled clarification of the precise role of two Mg(2+) ions, Mg45 and Mg52, as identified in the BWYV X-ray crystallography structure, in -1 frameshifting. On the basis of simulations with "partially" and "fully" hydrated Mg(2+) ions, two possible mechanisms of stabilizing stem 1 are proposed. In both these cases Mg(2+) ions play a critical role in stabilizing stem 1, either by directly forming a salt bridge between the strands of stem 1 or by stabilizing parallel orientation of the strands in stem 1, respectively. These findings explain the unexpected drop in frameshifting efficiency to null levels of the C8U mutant in a manner consistent with experimental observations.     

Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement

We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation time of the chain, tau, with the chain length N and pore diameter D. An earlier scaling analysis based on the de Gennes blob picture led to tau approximately N(2)D(13). Our numerical effort that combines molecular dynamics and Monte Carlo simulations, however, consistently produces different tau results for N up to 2000. We argue that the previous scaling prediction is only asymptotically valid in the limit N"D(53)"1, which is currently inaccessible to computer simulations and, more interestingly, is also difficult to reach in experiments. Our results are thus relevant for the interpretation of recent experiments with DNA in nano- and microchannels.     

Hydration of β-cyclodextrin: A molecular dynamics simulation study

We study by molecular dynamics simulations the hydration of -cyclodextrin. Our simulations show that within these barrel-shaped molecules hydrophobicity dominates, while at the top and bottom sides of the barrel interactions with water are mostly hydrophilic in nature. These results agree with crystallographic data at 120 K and, in particular, with the spontaneous hydration process of a cyclodextrin crystal in wet atmosphere. The predicted structure of the hydration shells is discussed and compared with previous molecular mechanics calculations which report an overall hydrophobic behavior. Moreover, the temperature dependence of the hydration process is discussed.     

A study of the static yield stress in a binary Lennard-Jones glass

The stress-strain relations and the yield behavior of a model glass (a 80:20 binary Lennard-Jones mixture) is studied by means of molecular dynamics simulations. In a previous paper it was shown that, at temperatures below the glass transition temperature, Tg, the model exhibits shear banding under imposed shear. It was also suggested that this behavior is closely related to the existence of a (static) yield stress (under applied stress, the system does not flow until the stress sigma exceeds a threshold value sigmay). A thorough analysis of the static yield stress is presented via simulations under imposed stress. Furthermore, using steady shear simulations, the effect of physical aging, shear rate and temperature on the stress-strain relation is investigated. In particular, we find that the stress at the yield point (the "peak"-value of the stress-strain curve) exhibits a logarithmic dependence both on the imposed shear rate and on the "age" of the system in qualitative agreement with experiments on amorphous polymers, and on metallic glasses. In addition to the very observation of the yield stress which is an important feature seen in experiments on complex systems like pastes, dense colloidal suspensions and foams, further links between our model and soft glassy materials are found. An example is the existence of hysteresis loops in the system response to a varying imposed stress. Finally, we measure the static yield stress for our model and study its dependence on temperature. We find that for temperatures far below the mode coupling critical temperature of the model (Tc = 0.435 in Lennard-Jones units), sigmay decreases slowly upon heating followed by a stronger decrease as Tc is approached. We discuss the reliability of results on the static yield stress and give a criterion for its validity in terms of the time scales relevant to the problem.     

Modeling of droplet traffic in interconnected microfluidic ladder devices

The problem of controlling the droplet motion in multiphase flows on the microscale has gained increasing attention because the droplet-based microfluidic devices provide great potentials for chemical and biological applications. It is critical to understand the relevant physics on droplet hydrodynamics and thus control the generation, motion, splitting, and coalescence of droplets in complex microfluidic networks. Numerical simulations using the volume of fluid algorithm are conducted to investigate the time-dependent dynamics of droplets in gas-liquid multiphase devices. An analytical model based on the electronic-hydraulic analogy is developed to describe the hydrodynamic behavior of the droplets in interconnected microfluidic ladder devices. It is found that the pressure drop caused by the droplets plays a critical role in the droplet synchronization. A fitted formula for pressure drops in the presence of surfactant is achieved by using numerical simulations. Both the numerical and the theoretical results agree well with the corresponding experimental results.     

Parametric studies of interaction strengths in polymer/CO2 systems: discontinuous molecular dynamics simulations

Discontinuous molecular dynamics simulations are performed on homopolymer/solvent and surfactant/solvent systems. The homopolymer and surfactant molecules are modeled as freely jointed square-well chains. Solvent molecules are modeled as both hard spheres and square-well spheres. We explore how the various interaction parameters affect the types of phase behavior and micellization observed in the homopolymer/solvent and surfactant/solvent systems. Increasing the packing fraction of homopolymers in both hard-sphere solvents and square-well solvents increases the solvent's ability to dissolve homopolymers only when the segment-solvent interaction strength exceeds a critical value. Although only upper critical solution temperature (UCST) behavior is observed for homopolymers in hard-sphere solvents, both UCST and lower critical solution temperature (LCST) behavior are observed for homopolymers in square-well solvents, depending upon the interaction strengths and chain length. This indicates that it is necessary to account for the solvent-solvent attraction to model LCST behavior in supercritical CO2. Our simulation results on surfactants in hard-sphere solvents show that it is necessary to account for the interactions experienced by both the head and tail blocks in order to capture the essential features of surfactant/supercritical CO2 systems.     

Anomalous mixing behavior of polyisobutylene/polypropylene blends: molecular dynamics simulation study

The unusual mixing behavior of polyisobutylene (PIB) with head-to-head (hhPP) and head-to-tail polypropylene (PP) is studied using large-scale molecular dynamics (MD). The heats of mixing and Flory chi parameters were computed from MD simulations of both blends using a united atom model. The chi parameters from the simulations were estimated from the structure factors using the random phase approximation in analogy with neutron scattering (SANS) experiments. MD simulations for syndiotactic hhPP/PIB predicted a lower critical solution temperature with a chi parameter in very good agreement with SANS experiments on the atactic hhPP/PIB blend. MD simulations also predicted that the isotactic PP/PIB blend was immiscible at high molecular weight in qualitative agreement with cloud point measurements on atactic PP/PIB.     

Nucleation of self-associating fluids: free versus activated association

We use the density functional theory of statistical mechanics in a square gradient approximation to analyze the structure, size, and work of formation of critical nuclei in self-associating fluids where association reduces the strength of the interactions between bonded particles. This effect is expected in systems of strongly dipolar particles that associate into chains. In this work we analyze the nucleation behavior of two types of self-associating fluids: a system comprised of particles that can freely associate, and a system in which the association process involves a thermally activated initiation step. For the first case, we explore the properties of critical nuclei in fluids that exhibit a metastable critical point between a vapor phase and a highly associated liquid phase. In fluids where the association dynamics involves an initiation step, we investigate the nucleation behavior in the vicinity of the polymerization transition. In both cases critical nuclei undergo a structural transition that shares many of the features of the coil-globule transition reported in Monte Carlo simulations of strongly dipolar Stockmayer fluids. Our results suggest that the sharp structural transition observed in these simulations is evidence of the existence of a second-order or nearly second-order association transition in these model fluids.