The excitation spectrum of the density collective oscillations is computed for multi-component molecular mixtures both with Coulomb and (repulsive) short-range interactions. Distinct sound-like excitations appear, governed by the short-range interaction, which differ from the ordinary hydrodynamic sound. The dielectric function and the structure factor are also calculated. The "two-sounds phenomenon" can be understood by means of the predictions of this model.
2,6-lutidine molecules mix with water at high and low temperatures but in a wide intermediate temperature range a 2,6-lutidine/water mixture exhibits a miscibility gap. We constructed and validated an atomistic model for 2,6-lutidine and performed molecular dynamics simulations of 2,6-lutidine/water mixture at different temperatures. We determined the part of demixing curve with the lower critical point. The lower critical point extracted from our data is located close to the experimental one. The estimates for critical exponents obtained from our simulations are in a good agreement with the v…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite swapping REMD in practice. Here we show that this method naturally leads to a reformulation in terms of molecular dynamics simulations over a mixture potential, which is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also opens the door to generalizatio…
The change of sign with composition in aqueous mixtures of associating fluids is analysed by means of Molecular Dynamics simulations. The results obtained are in quantitative agreement with the experimental data in water-ethanol and water-methanol solutions, which exhibit the mentioned change of sign. A subsequent theoretical analysis is addressed to establish a relationship between the dependence of the Soret coefficient with composition with the existence of large inter-species interactions. Although the change of sign of the Soret coefficient with composition is not only due to so-called ch…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in fluctuating ratchet models for interacting molecular motors is outlined. Numerical evidence indicates that the scaling properties of dynamical behavior in such models belong to the KPZ universality class. Second, the generalization of such models to include boundary injection and removal of motors is provided. In common with known results for the asymmetric exclusio…
We report a series of molecular dynamics simulations and investigate the possibility to separate a granular mixture of inelastic hard spheres by vigorously shaking it in a box made of two connected compartments. As its one-component counterpart, the system exhibits a ``left-right'' symmetry breaking entirely due to the inelasticity of grain-grain collisions, and triggered by increasing the number of particles. In the compartment where the density of grains is larger, we observe a partial segregation with a predominance of heavy particles. However, this compartment still has a higher density of…
We show in simulations that a rich variety of novel orderings such as pinwheel and star states can be realized for colloidal molecular crystal mixtures at rational ratios of the number of colloids to the number of minima from an underlying periodic substrate. These states can have multi-step melting transitions and also show coexistence in which one species disorders while the other species remains orientationally disordered. For other mixtures, only partially ordered or frustrated states form.
By means of extensive equilibrium molecular dynamics simulations we have investigated, the behavior of the interfacial tension $γ$ of two immiscible symmetrical Lennard-Jones fluids. This quantity is studied as function of reduced temperature $T^{*}={{k_{_B} T}\over ε}$ in the range $0.6 \leq T^{*} \leq 3.0$. We find that, unlike the monotonic decay obtained for the liquid-vapor interfacial tension, for the liquid-liquid interface, $γ(T)$ has a maximum at a specific temperature. We also investigate the effect that surfactant-like particles has on the thermodynamic as well as the structural pro…
The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The combined action of both forces attempts to model the interaction of the mixture with a bath or surrounding fluid. The problem is studied by means of two independent and complementary routes. First, the Enskog kinetic equation with a Fokker-Planck term describing interactions of particles with thermostat is derived. The ratio of kinetic temperatures $T_1/T_2$ an…
Molecular dynamics in binary mixtures of water and glycerol was studied by measuring the spectrum of water velocity auto-correlation in the frequency range from 0.05 to 10 kHz by using the NMR method of modulated gradient spin echo. The method shows that the diversity of diffusion signature in the short spin trajectories provides information about heterogeneity of molecular motion due to the motion in the micro-vortexes of hydrodynamic fluctuation, which is especially pronounced for the mixtures with the low glycerol content. As concentration of glycerol increases above 10vol%, a new feature o…
The rheological properties for dilute and moderately dense granular binary mixtures of smooth, inelastic hard disks/spheres under uniform shear flow in steady state conditions are reported. The results are based on the Enskog kinetic theory, numerically solved by a dense gas extension of the Direct Simulation Monte Carlo method for dilute gases. These results are confronted to the ones also obtained by performing molecular dynamics simulations with very good agreement for the lower densities and higher coefficients of restitution. It appears that the range of densities for which the Enskog equ…
We investigate numerically and analytically size-polydisperse granular mixtures immersed into a molecular gas. We show that the equipartition of granular temperatures of particles of different sizes is established; however, the granular temperatures significantly differ from the temperature of the molecular gas. This result is surprising since, generally, the energy equipartition is strongly violated in driven granular mixtures. Qualitatively, the obtained results do not depend on the collision model, being valid for a constant restitution coefficient $\varepsilon$, as well as for the $\vareps…
We calculate the response of a molecular magnet subject to a time-varying magnetic field and coupled to a heat bath. We propose that observations of calculated oscillations transverse to the field direction may be an effective way of demonstrating quantum tunneling and thus probing the details of level repulsion. The effective model of a triangle of Heisenberg spins and weak anisotropies, as has been used to model the molecular magnets V15 and Cu3, is used to illustrate this.
We report molecular dynamics results for the contact values of the radial distribution functions of binary additive mixtures of hard disks. The simulation data are compared with theoretical predictions from expressions proposed by Jenkins and Mancini [J. Appl. Mech. \textbf{54}, 27 (1987)] and Santos et al. [J. Chem. Phys. \textbf{117}, 5785 (2002)]. Both theories agree quantitatively within a very small margin, which renders the former still a very useful and simple tool to work with. The latter (higher-order and self-consistent) theory provides a small qualitative correction for low densitie…
Spatially correlated noise (SCN), i.e. the thermal noise that affects neighbouring particles in a similar manner, is ubiquitous in soft matter systems. In this work, we apply the over-damped SCN-driven Langevin equations as an effective, one-component model of the dynamics in dense binary mixtures. We derive the thermodynamically consistent fluctuation-dissipation relation for SCN to show that it predicts the molecular arrest resembling the glass transition, i.e. the critical slow-down of dynamics in the disordered phases. We show that the mechanism of singular dissipation is embedded in the d…
We study bosonic atoms near a Feshbach resonance, and predict that in addition to a standard normal and atomic superfluid phases, this system generically exhibits a distinct phase of matter: a molecular superfluid, where molecules are superfluid while atoms are not. We explore zero- and finite-temperature properties of the molecular superfluid (a bosonic, strong-coupling analog of a BCS superconductor), and study quantum and classical phase transitions between the normal, molecular superfluid and atomic superfluid states.
We combine molecular dynamics simulations with experiments to estimate solubilities of organic salts in complex growth environments. We predict the solubility by simulations of the growth and dissolution of ions at the crystal surface kink sites at different solution concentrations. Thereby, the solubility is identified as the solution's salt concentration, where the energy of the ion pair dissolved in solution equals the energy of the ion pair crystallized at the kink sites. The simulation methodology is demonstrated for the case of anhydrous sodium acetate crystallized from various solvent-a…
We present a combined experimental and theoretical study on the role of copolymer architecture in the self-assembly of binary PEO-PCL mixtures in water-THF, and show that altering the chain geometry and composition of the copolymers can control the form of the self-assembled structures and lead to the formation of novel aggregates. First, using transmission electron microscopy and turbidity measurements, we study a mixture of sphere-forming and lamella-forming PEO-PCL copolymers, and show that increasing the molecular weight of the lamella-former at a constant ratio of its hydrophilic and hydr…
Thermophysical properties of hydrogen, helium, and hydrogen-helium mixtures have been investigated in the warm dense matter regime at electron number densities ranging from $6.02\times10^{29}\sim2.41\times10^{30}$/m$^{3}$ and temperatures from 4000 to 20000 K via quantum molecular dynamics simulations. We focus on the dynamical properties such as the equation of states, diffusion coefficients, and viscosity. Mixing rules (density matching, pressure matching, and binary ionic mixing rules) have been validated by checking composite properties of pure species against that of the fully interacting…
We consider the stochastic gene expression process with inter-state flip-flops. An exact steady-state solution to the master equation is calculated. One of the main goals in this paper is to investigate whether the probability distribution of gene copies contains even-odd number oscillations. A master equation previously derived in the adiabatic limit of fast switching by Kepler and Elston \cite{kepler} suggests that the oscillations should be present. However our analysis demonstrates that the oscillations do not happen not only in the adiabatic case but they are entirely absent. We discuss t…
We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] for the dielectric constant of neutral site-site molecular models to mixtures of both charged and uncharged molecules. This provides a unified derivation connecting the Stillinger-Lovett moment conditions for ions to standard results for the dielectric constant for polar species and yields exact expressions for the small-k expansion of the two-point intermolecular charge-density function used to determine the total Coulomb energy. The latter is useful in determining corrections to the thermodynamics of uniform site-site m…
We report here the observation of a surprising phenomenon consisting in a oscillating phase transition which appears in a binary mixture, PMMA/3-octanone, when this is enlightened by a strongly focused infrared laser beam. PMMA/3-octanone has a UCST (Upper Critical Solution Temperature) which presents a critical point at temperature Tc = 306.6 K and volume fraction $ϕ$c = 12.8 % [Crauste et al., ArXiv 1310.6720, 2012]. This oscillatory phenomenon appears because of thermophoretic and electrostriction effects and non-linear diffusion. We analyze these oscillations and we propose a simple model …
We study the structure and interfacial properties of model athermal mixtures of colloids and excluded volume polymers. The colloid particles are modeled as hard spheres whereas the polymer coils are modeled as chains formed from tangentially bonded hard spheres. Within the framework of the nonlocal density functional theory we study the influence of the chain length on the surface tension and the interfacial width. We find that the interfacial tension of the colloid-interacting polymer mixtures increases with the chain length and is significantly smaller than that of the ideal polymers. For ce…
Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following a temperature quench. We compute equilibrium and time varying migrant density profiles and wetting layer thickness using coarse grained molecular dynamics and mesoscale hydrodynamics simulations to demonstrate that surface migration in oligomer-gel systems is significantly reduced due to network elasticity. Further, phase separation proces…
Demixing of binary fluids subjected to slow temperature ramps shows repeated waves of nucleation which arise as a consequence of the competition between generation of supersaturation by the temperature ramp and relaxation of supersaturation by diffusive transport and flow. Here, we use an advection-reaction-diffusion model to study the oscillations in the weak- and strong-diffusion regime. There is a sharp transition between the two regimes, which can only be understood based on the probability distribution function of the composition rather than in terms of the average composition. We argue t…
