Molecular dynamics studies of Langmuir monolayers of cationic/PC lipids
Bin Liu University of Waterloo
PIRSA:13120034
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Topological defects of tetratic liquid-crystal order on a soft spherical surface
Yao Li Tsinghua University
PIRSA:13120033Improving the Martini model: coarse-graining with dynamic charges and polarization
Yuriy Khalak University of Waterloo
PIRSA:13120031Spatial organization of a ring copolymer confined in a cylindrical space
Chanil Jeon University of Waterloo
PIRSA:13120046Effect of wetting on micelle fragmentation in confined channels
Mona Habibi Western University
PIRSA:13120029Assembly of microparticles on thin smectic films
Mohamed Amine Gharbi University of Pennsylvania
PIRSA:13120028Phase behavior of long worm-like chain confined in a cavity
Jie Gao University of Waterloo
PIRSA:13120027Emergence of Hierarchical Morphologies in Binary Blends of Diblock Copolymers
Ashkan Dehghan McMaster University
PIRSA:13120025"Diffusing diffusivity": A model of "anomalous yet Brownian" diffusion
Mykyta Chubynsky University of Ottawa
PIRSA:13120024
Molecular dynamics studies of Langmuir monolayers of cationic/PC lipids
Bin Liu University of Waterloo
PIRSA:13120034Our research focuses on computer simulations of cationic and Phosphatidylcholine (PC) containing lipid monolayers and their potential applications in drug and gene delivery. The ultimate motivation is to unravel how cationic compounds such as CTAB function for encapsulating novel DNA based drugs and other drugs e.g. protein based drugs into a delivery system. The major advantage of these drugs over traditional chemical agents is their specificity and selectivity.We employed the Berger lipid model to model lipid molecules. The Berger lipid model is based on GROMOS96 53a6 force field which has strength for describing proteins but has weakness for describing the long alkane chains of lipid molecules. The Berger lipid model did the improvement by using the Rychaert-Bellemans proper dihedral potential. Knowledge about partial charges distribution of cationic lipid molecules was retrieved from HF/MP2 level quantum chemistry calculation with the Natural Population Analysis partial charge scheme. The most important properties and behaviors of Langmuir monolayers can be obtained from the surface tension-area isotherm of the system at a given temperature. Thus a series of NVT simulations of monolayer systems of systematically varied box sizes with various cationic lipids: PC lipids ratio were done to evaluate the surface tension-area isotherms from the simulated trajectory averages. Our current results show that the cationic lipids have a tendency to stabilize the monolayers especially when the systems are more densely packed. Further investigations are on the way to fully explore other properties and behaviors of Langmuir monolayers of cationic/PC lipids.Topological defects of tetratic liquid-crystal order on a soft spherical surface
Yao Li Tsinghua University
PIRSA:13120033We model the orientational and positional order of tetratically shaped molecules each having four-fold structural symmetryconfined on a spherical surface. Our Monte Carlo simulation shows that at a high molecular density a tetratic orientational orderdevelops in the system accompanied by eight disclinations arranged in an anticube form on the hard spherical surface. We alsoconsider an elastic-energy model which consists of both Helfrich and Frank energies for a soft surface; the solution confirms theMonte Carlo study and further predicts the tetratic morphology that can be realized on the surface of a soft vesicle. Assumingthat the induced interaction between these disclinations are repulsive we demonstrate that the anticube structure has a lower freeenergy than for example the cubic structure.Electrostatics
Norman Lam University of Toronto
PIRSA:13120032Electrostatic phenomena in soft matter systems are often intriguing or even counterintuitive. DNA condensation by polyvalent counterions is now a classic example by which highly-negatively charged DNA strands attract each other in the presence of poly-cations. Also Mg2+ can stabilize inverted hexagonal phases of lipid aggregates that would otherwise form lamellar phases. Here we discuss another intriguing electrostatic phenomenon: electrostatic modification of lipid membranes by poly-cations. In particular we examine how the poly-anionic nature of LPS (lipopolysaccharide) molecules is implicated in the permeability properties of LPS membranes.Improving the Martini model: coarse-graining with dynamic charges and polarization
Yuriy Khalak University of Waterloo
PIRSA:13120031While successfully reproducing hydrophobic and hydrophilic interactions the Martini model is insufficient to keep a protein folded as it lacks electrostatic interactions. Using split charge equilibration at each time step can yield realistic dynamic bead charges. Combining this with a Drude oscillator based polarization model for all beads will permit modeling of hydrogen bonds to maintain secondary protein structure and will enable more accurate coarse-grained simulations of protein-protein and protein-membrane interactions.Spatial organization of a ring copolymer confined in a cylindrical space
Chanil Jeon University of Waterloo
PIRSA:13120046Confinement can influence qualitatively the spatial organization of polymer chains. Cylindrical confinement is of particular interest since it not only stiffens individual chains but also enhances their segregation. Here we discuss a ring copolymer confined in a closed cylindrical space as a model nucleoid (an intracellular space where the bacterial chromosome is confined). When the cylinder and polymer parameters are chosen properly our model explains quantitatively recent experimental results for the spatial organization of the E. coli chromosome.Quantized contact angles in the dewetting of a structured liquid
PIRSA:13120030A thin partially wetting layer of liquid will dewet from an unfavourable substrate resulting in spherical cap shaped droplets next to a microscopically thin residual wetting layer of the liquid. We have measured a discrete spectrum of contact angles for dewetted droplets of a lamellar diblock copolymer in its disordered phase instead of the single unique contact angle that is usually observed. The different contact angles coexist with various thicknesses of wetting layer and the spectrum of measured contact angles shifts as the temperature is raised. The contact angle at the base of the droplets is a direct probe of the energy minimum of the film-thickness dependent effective interface potential. Self-consistent field theory was used to calculate the effective interface potential as a function of film thickness for a lamellar diblock copolymer. The results of the calculation show multiple minimums in the potential energy caused by substrate induced ordering within the liquid. The locations and depths of these minimums in the effective interface potential correspond to the wetting layer thicknesses and contact angles of the dewetted droplets respectively. The qualitative behaviour of the calculated contact angles at higher temperature agrees well with the experimental results. Since the contact angles wetting layer thickness are such a sensitive probe of the free energy of the film over a wide range of film thickness this system provides an excellent testing ground for quantitative theoretical predictions as well.Effect of wetting on micelle fragmentation in confined channels
Mona Habibi Western University
PIRSA:13120029We use coarse-grained molecular-dynamics (MD) simulations to study the fragmentation of sodium dodecyl sulfate micelles under Poiseuille-like flow in a die-extruder geometry. The effect of flow confinement and wetting on spherical micelles is explored. We demonstrate that the interplay between flow and the wettability of the channel determines the size of daughter micelles inside the channel.Assembly of microparticles on thin smectic films
Mohamed Amine Gharbi University of Pennsylvania
PIRSA:13120028Colloidal particles organize spontaneously at fluid interfaces owing to a variety of interactions to form well organized structures that can be exploited to synthesize advanced materials. While the physics of colloidal assembly at isotropic interfaces is well understood the mechanisms that govern interactions between particles at liquid crystal interfaces are not yet clearly established. In particular smectic liquid crystal films offer important degrees of freedom that can be used to direct particles into new structures. In this work we report on the behavior of micrometric silica spheres with homeotropic anchoring confined within or at interfaces of smectic films. We study the interactions and self-assembly of these particles as a function of film thickness in both supported and in free standing films. When particles are captured in thin membranes they induce distortions of the smectic interface to satisfy wetting properties at particle boundaries leading to capillary interactions between the particles. These capillary interactions compete with elastic interactions owing to particle-induced distortions in the smectic layers. The resulting potential drives assembly of the spheres into different structures ranging from 1D chains to 2D aggregates. By increasing the thickness of the smectic we control the formation of focal conic domains (FCDs) and their organization. The FCDs interact with particles at the interface and can be used to direct the formation of complex particle structures. Recent progress in understanding the process of particle self-organization is presented.Phase behavior of long worm-like chain confined in a cavity
Jie Gao University of Waterloo
PIRSA:13120027Studying protein adsorption on bone surfaces using molecular simulations
PIRSA:13120026Mineral-associated proteins have been proposed to play a central role not only in assisting the growth of biomineral crystals in hard tissues but also in preventing or limiting mineral formation in soft tissues. The elucidation of protein-biomineral interactions may lead to the design of mineralized tissues with novel properties and most importantly the development of therapies for common diseases such as kidney stones calcification in blood vessels osteoporosis etc. However the mechanism of the interaction at this unique organic-inorganic interface is still poorly understood. X-ray crystallography techniques have provided important information on the adsorbed states. Unfortunately these methods have limitations in determining the driving forces of the adsorption and the underlying roles played by the lattice ions and ionic solutions. We employ all-atom enhanced-sampling simulations and free-energy calculation techniques to characterize these interactions with the final goal of designing proteins with improved adsorption properties and capacity to prevent or enhance crystal growth.Emergence of Hierarchical Morphologies in Binary Blends of Diblock Copolymers
Ashkan Dehghan McMaster University
PIRSA:13120025The self-assembled structures formed in binary blends of AB/CD diblock copolymers are studied using self-consistent field theory focusing on cases with attractive A/C and repulsive B/D interactions. The attractive A/C interaction prevents macroscopic phase separation whereas the repulsive B/D interaction promotes B/D separation leading to the formation of complex hierarchical structures. The combination of these features makes the AB/CD blend an ideal model system for the study of hierarchical self-assembly. Our results demonstrate that the B/D separation leads to the emergence of modulated and alternate morphologies from the classical lamellar hexagonal spherical and gyroid structures. A common phase transition sequence from the mixed to modulated to alternate B/D structures is observed as a function of B/D interaction strength. The theoretical predictions of our model are consistent with available experiments and more importantly provide an interesting route for the engineering of hierarchically ordered structures using block copolymer blends."Diffusing diffusivity": A model of "anomalous yet Brownian" diffusion
Mykyta Chubynsky University of Ottawa
PIRSA:13120024Wang et al. [PNAS 106 (2009) 15160] have found that in several systems, the linear time dependence of mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian displacement distribution (DD), with roughly exponential tails at short times, a situation termed “anomalous yet Brownian” diffusion. We point out that lack of “direction memory” in the particle trajectory (a jump in a particular direction does not change the probability of subsequent jumps in that direction) is sufficient for a strictly linear MSD (assuming that the system is pre-equilibrated), but if at the same time there is “diffusivity memory” (a particle diffusing faster than average is likely to keep diffusing faster for some time), the DD will be non-Gaussian at short times. A gradual change in diffusivity can be due to the environment of the particle changing slowly on its own, the particle moving between different environments, or both. In our model, this is represented by the particle diffusivity itself undergoing a (perhaps biased) random walk (“diffusing diffusivity”). Roughly exponential tails of the DD, as in experiment, are observed in several variants of the model.