A Many-Body Hamiltonian for Nanoparticles Immersed in a Polymer Solution

We developed an analytical theory for the many-body potential of mean force (POMF) between N spheres immersed in a continuum chain fluid. The theory is almost exact for a T polymer solution in the protein limit (small particles, long polymers), where N-body effects are important. Polydispersity in polymer length according to a SchulzFlory distribution emerges naturally from our analysis, as does the transition to the monodisperse limit. The analytical expression for the POMF allows for computer simulations employing the complete N-body potential (i.e., without n-body truncation; n < N). These are compared with simulations of an explicit particle/polymer mixture. We show that the theory produces fluid structure in excellent agreement with the explicit model simulations even when the system is strongly fluctuating, e.g., at or near the spinodal region. We also demonstrate that other commonly used theoretical approaches, such as truncation of the POMF at the pair level or the Asakura Oosawa model, are extremely inaccurate for these systems

Fluid-Fluid Transitions at Bulk Supercritical Conditions

We use three different polymer solvent mixture models to theoretically determine the existence of capillary-induced phase separation in simple pores under supercritical bulk conditions. These models undergo bulk demixing, due to quite different mechanisms, yet readily display supercritical transitions without the use of esoteric interactions in the capillary. The theoretical method used to analyze these systems is density functional theory. We find that capillary demixing is not reliant on the presence of a pure surface transition but may occur in the absence of the latter. This is shown by considering cases where the surface enhancement factor is too weak to cause demixing at a single surface or else the bulk conditions are supercritical to both bulk and surface transitions. This phenomenon may prove useful in applications involving adsorption from mixtures into porous particles

Influence of ion pairing in ionic liquids on electrical double layer structures and surface force using classical density functional approach.

We explore the influence of ion pairing in room temperature ionic liquids confined by planar electrode surfaces. Using a coarse-grained model for the aromatic ionic liquid [C4MIM(+)][BF4 (-)], we account for an ion pairing component as an equilibrium associating species within a classical density functional theory. We investigated the resulting structure of the electrical double layer as well as the ensuing surface forces and differential capacitance, as a function of the degree of ion association. We found that the short-range structure adjacent to surfaces was remarkably unaffected by the degree of ion pairing, up to several molecular diameters. This was even the case for 100% of ions being paired. The physical implications of ion pairing only become apparent in equilibrium properties that depend upon the long-range screening of charges, such as the asymptotic behaviour of surface forces and the differential capacitance, especially at low surface potential. The effect of ion pairing on capacitance is consistent with their invocation as a source of the anomalous temperature dependence of the latter. This work shows that ion pairing effects on equilibrium properties are subtle and may be difficult to extract directly from simulations

Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol

Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the WimleyWhite interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was similar to 25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol

Classical density functional theory &amp; simulations on a coarse-grained model of aromatic ionic liquids.

A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF4(-), respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented

Fused coarse-grained model of aromatic ionic liquids and their behaviour at electrodes.

A fused coarse-grained model of aromatic ionic liquids 1-alkyl-3-methylimidazoliums tetrafluoroborate ([CnMIM(+)][BF4(-)]) has been constructed. Structural and dynamical properties calculated from our model are compared with experimental data as well as with corresponding results from simulations of other suggested models. Specifically, we adopt a fused-sphere coarse-grained model for cations and anions. This model is utilized to study structure and differential capacitance in models of flat and porous carbon electrodes. We find that the capacitance varies with pore size, in a manner that is related to the packing of ions inside the pore. For very narrow pores, diffusion is slow and the establishment of thermodynamic equilibrium may exceed the practical limits for our molecular dynamics simulations

Theoretical predictions of structures in dispersions containing charged colloidal particles and non-adsorbing polymers

We develop a theoretical model to describe structural effects on a specific system of charged colloidal polystyrene particles, upon the addition of non-adsorbing PEG polymers. This system has previously been investigated experimentally, by scattering methods, so we are able to quantitatively compare predicted structure factors with corresponding experimental data. Our aim is to construct a model that is coarse-grained enough to be computationally manageable, yet detailed enough to capture the important physics. To this end, we utilize classical polymer density functional theory, wherein all possible polymer configurations are accounted for, subject to a mean-field Boltzmann weight. We make efforts to counteract drawbacks with this mean-field approach, resulting in structural predictions that agree very well with computationally more demanding simulations. Electrostatic interactions are handled at the fully non-linear Poisson-Boltzmann level, and we demonstrate that a linearization leads to less accurate predictions. The particle charge is an experimentally unknown parameter. We define the surface charge such that the experimental and theoretical gel point at equal polymer concentration coincide. Assuming a fixed surface charge for a certain salt concentration, we find very good agreements between measured and predicted structure factors across a wide range of polymer concentrations. We also present predictions for other structural quantities, such as radial distribution functions, and cluster size distributions. Finally, we demonstrate that our model predicts the occurrence of equilibrium clusters at high polymer concentrations, but low particle volume fractions and salt levels

DNA condensation in live E. coli provides evidence for transertion

Condensation studies of chromosomal DNA in E. coli with a tetra nuclear ruthenium complex are carried out and images obtained with wide-field fluorescence microscopy. Remarkably different condensate morphologies resulted, depending upon the treatment protocol. The occurrence of condensed nucleoid spirals in live bacteria provides evidence for the transertion hypothesis