J. G. E. M. Fraaije

Morphology of symmetric block copolymer in a cylindrical pore

The influence of confinement on morphology formation in copolymer systems is an important area of interest in theoretical research. We apply dynamic density functional theory to investigate the effect of pores on the morphology formation in a symmetric diblock copolymer system. The pore is represented by a perfect cylindrical tube. Porous systems are important in biology and are gaining interest for applications in nanotechnology. We show that for the pore sizes under investigation two equilibrium morphologies are possible depending on the surface interaction: a perpendicular or slab morphology and a parallel or multiwall tube morphology. The latter is referred to in the article as dartboard morphology. In the dynamic pathway towards this morphology an intermediate metastable helical phase is found. An important observation is that, for a wide range of pore radii and variations of polymer chain length, no mixed parallel/perpendicular morphologies were found: All observed morphologies are insensitive to the pore diameter.

Method of moments for computational microemulsion analysis and prediction in tertiary oil recovery.

We discuss the application of Helfrichs surface torque density concept to microemulsion design and analysis from three different angles: (i) from the point of view of coarse-grained molecular simulations, using Dissipative Particle Dynamics, including charge interactions and added salt, (ii) using an approximate double-film model for the surface, and (iii) comparison with formulation approaches. The simulations use that the surface torque can be calculated unambiguously from the stress profile, provided the surface is tensionless. Very good agreement is found on predicting optimal salinity (or the absence of that) for a range of surfactants: dioctyl sodium sulfosuccinate, various twin-tailed sulfonates and sodium dodecyl sulfate. The simulations are very fast, on par with times for experiments, thus they could lead to a practical tool for discovery of more efficient surfactants, although much remains to be done with respect to other important variables: oil composition, surfactant mixtures, aggregation in solution, and so on. The microscopic model (second approach) is highly approximate: it is essentially based on two opposing swelling tendencies, that are both of osmotic nature. In accordance with the model, the tails are swollen by the oil and the charged head groups are confined in a salty layer in Donnan equilibrium with the salt solution. In this way, the surface interactions are purely entropic. The comparison of the film model with existing formulation approaches (third approach) covers the interfacial tension minimum, Winsor R theory, quantitative structure property relations (QSPR), hydrophilic-lipophilic deviation (HLD), HLD-net average curvature, and temperature coefficients. Using the surface torque analysis, we succeed in deriving in an ab initio way QSPR empirical coefficients that have been known for decades, but until now, have been obscure in origin.

Microphase separation of weakly charged block polyelectrolyte solutions: Donnan theory for dynamic polymer morphologies

A mean-field dynamic density functional theory for the phase behavior of concentrated weakly charged block polyelectrolyte solutions is developed, using the Donnan membrane equilibrium approach to account for electrostatic interactions. In this limit all long-range electrostatic interactions are canceled and the net charge density in any region on a coarse-grained scale is zero. The phase diagram of a model triblock polyelectrolyte in solution as a function of the charge of the solvophilic block and the solvent concentration is established. Different mesoscopic structures (lamellar, bicontinuous, hexagonal, micellar, and dispersed coexisting phases) are formed depending on the copolymer charge asymmetry. It is found that upon changing the charge of the solvophilic copolymer block the polyelectrolyte solution does not follow the lyotropic sequence of phases of this polymer. Upon increase in the charge of the solvophilic blocks, changes in copolymer morphology take place by means of change in curvature of polymeric domains.

Mesoscopic Simulations of Lamellar Orientation in Block Copolymers

Mesoscopic simulation techniques are employed to investigate lamellar orientation in block copolymers subjected to oscillatory shear Dynamic mean-field density functional theory (MesoDyn) is able to capture parallel lamellar and perpendicular lamellar states at law and higher shear rates. At higher shear rates a third orientation state is identified from cell dynamics and MesoDyn simulations, and corresponds to predominantly paralled-aligned lamellae. This is explained on the basis of partial shear-melting at higher shear rates. The results are compared to the lamellar alignment diagram obtained experimentally for polystyrene/polyisoprene block copolymers.

Introducing Quadrupole Interactions into the Peptide Design Toolkit

Proteins and peptides are often described as the machinery of life. Even the simplest bacteria have hundreds of proteins, and these proteins work in concert with each other to conduct thousands of distinct functions. The fidelity of these functions relies on the specificity of interactions between the units of the machinery, between the proteins. By studying the forms and functions of proteins, and tracing these back to amino acid sequences the “rules” for their self-assembly can be obtained, thus allowing de novo peptide design and yielding novel forms and functions. The design of linear amino acid sequences that fold into defined secondary structures, or motifs, such as a-helices or b-sheets is relatively well understood. The greater challenge is to engineer specific interactions between these motifs, that is between precisely positioned side chains. An improved ability to direct intermolecular interactions will increase the functionality of the peptide assemblies that we are able to construct, and correspondingly, increase their potential applications. Until recently, the chemical toolkit for introducing peptide–peptide molecular recognition has consisted of four tools, or noncovalent interactions between amino acid side chains. These are ionic interactions, hydrogen bonding, hydrophobic interactions, and p stacking. Zheng and Gao have recently described a new tool, the quadrupole interaction (Figure 1), which is a refinement of p stacking. The ways in which these tools are utilized to impart specificity to peptide interactions are touched upon in the following paragraphs, with particular reference to coiled coils, which are the best understood peptide machinery. 5] 1. Hydrophobic interactions. The hydrophobic effect is generally the strongest component in protein and peptide quaternary interactions, and the degree of steric matching between hydrophobic side chains is important for increasing the stability of the complexes. However the interactions are not as specific as those between hydrophilic side chains. With regards to coiled coils, hydrophobic design principles have been used to greatest effect in determining the oligomerization state or relative orientation of ahelices in complexes rather than specifying binding partners. This strong but non-exclusive form of molecular recognition is complemented with other binding mechanisms in de novo peptides. 2. Ionic interactions. Amino acids with charged side chains are important determinants of specificity in peptide complexes, and this is the most frequently used strategy. Specificity is often achieved by negative design, whereby a unique structure is achieved by destabilizing the other possible complexes. Many heterodimeric coiled coils have charged residues bordering the hydrophobic core such that one helix is positively charged and the other negatively charged, hence preventing homodimeric coiledcoils from forming. Controlling intermolecular electrostatic interactions by using changes in pH values or salt concentrations can also be used to switch peptide binding specificity. This concept has been demonstrated with iterative pH cycles, specifically replacing one, two, or all three initial helices of a coiled-coil trimer. 3. Hydrogen bonds. Hydrogen bonds are also used to impart specificity to coiled coils by the placement of hydrogenFigure 1. Space-filling model of the aromatic side chains of phenylalanine and perfluorophenylalanine stacked face-to-face. The distribution of electrostatic potential is indicated, with blue being positive, and red negative. Phenyl and perfluorophenyl have opposite quadrupole moments, allowing a net electrostatic attraction between the p faces to occur.

Coarse-grained hybrid simulation of liposomes

We developed a new hybrid model for efficient modeling of complete vesicles with molecular detail. Combining elements of Brownian dynamics (BD) and dynamic density functional theory (DDFT), we reduce the computational load of an existing coarse grained particle-based dissipative particle dynamics (DPD) model by representing the solvent as a continuum variable or a field, in a consistent manner. Both particle and field representations are spatially unrestricted and there is no need to treat boundaries explicitly. We focus on developing a general framework for deriving the parameters in this hybrid approach from existing DPD representations, and validate this new method via a comparison to DPD results. In addition, we consider a few proof of principle calculations for large systems, including a vesicle of realistic dimensions (∼45 nm radius) containing (104) lipids simulated for (106) time steps, to illustrate the performance of the new method.

Shear-induced transitions in a ternary polymeric system

The first three-dimensional simulation of shear-induced phase transitions in a polymeric system has been performed. The method is based on dynamic density-functional theory. The pathways between a bicontinuous phase with developing gyroid mesostructure and a lamellar/cylinder phase coexistence are investigated for a mixture of flexible triblock ABA copolymer and solvent under simple steady shear.

Microstructure of nematic amorphous block copolymers: Dependence on the nematic volume fraction

We present a model for the structure formation in nematic amorphous copolymers and simulation results for a two-dimensional (2D) implementation. The model is based on a dynamic mean-field method, which allows one to specify the polymer system on two different levels of detail. On the detailed level the nematic amorphous block copolymer molecules are represented by a wormlike chain, characterized by three profiles defining its architecture. The first profile sets the sequence of different monomer types along the chain. The second distinguishes whether individual segments do or do not contribute to the nematic order. The third profile defines how the stiffness varies along the chain. On the coarsened level the system is described in terms of density distributions representing the different monomer species and an orientation distribution for the local alignment of the nematic segments. The simulations investigate how the volume fraction of the nematic component effects the resulting mesostructure. With incre...

Efficient solvent-free dissipative particle dynamics for lipid bilayers

We rigorously derived effective potentials for solvent-free DPD simulation of lipid bilayers. The derivation relies on an earlier developed hybrid particle/field method and is based on the idea that the solvent is always in local equilibrium on a coarse-grained time scale, given the instantaneous templates set by the self-assembly structure. By relating the parameters in the effective implicit-solvent potentials directly to the lipid-solvent interactions and membrane properties for the explicit solvent DPD model, we constitute an efficient and general procedure for reformulating any DPD membrane model in an implicit-solvent form. Here, we determined these membrane properties for two existing DPD models, via an analysis of membrane fluctuation spectra. Equivalent single-processor implicit- and explicit-solvent calculations show the trade-mark of implicit solvent simulation: a 20-fold reduction of the total simulation time for a system containing 92% solvent. This increased efficiency enabled us to realistically simulate the spontaneous formation of a ∼20 nm diameter vesicle on a single processor overnight. We believe that this work will contribute to an enhanced computational study of large vesicles and thus a better understanding of experimental liposome dynamics.

Orientations of the lamellar phase of block copolymer melts under oscillatory shear flow

We develop a theory to describe the reorientation phenomena in the lamellar phase of block copolymer melts under reciprocating shear flow. We show that, similar to the steady shear, the oscillating flow anisotropically suppresses fluctuations and gives rise to the [parallel]--> [perpendicular] transition. The experimentally observed high-frequency reverse transition is explained in terms of interaction between the melt and the shear-cell walls.