Improving the Martini model: coarse-graining with dynamic charges and polarization
Yuriy Khalak University of Waterloo
PIRSA:13120031
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Spatial organization of a ring copolymer confined in a cylindrical space
Chanil Jeon University of Waterloo
PIRSA:13120046 -
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Effect of wetting on micelle fragmentation in confined channels
Mona Habibi Western University
PIRSA:13120029 -
Assembly of microparticles on thin smectic films
Mohamed Amine Gharbi University of Pennsylvania
PIRSA:13120028 -
Phase behavior of long worm-like chain confined in a cavity
Jie Gao University of Waterloo
PIRSA:13120027 -
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Emergence 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 -
Double twist liquid crystal model of collagen structure
Aidan Brown Dalhousie University
PIRSA:13120023 -
Thermodynamics of pore formation in lipid bilayers
Drew Bennett University of Waterloo
PIRSA:13120022 -
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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:13120027 -
Studying 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. -
Double twist liquid crystal model of collagen structure
Aidan Brown Dalhousie University
PIRSA:13120023Collagen is the main component of connective tissue and the most abundant protein in mammals. The structure of collagen is hierarchical with the triple-helical molecules organizing into fibrils and fibrils contained in higher-order arrangements. A fibril may be considered as a liquid crystal of individual triple helices. Their chiral molecular structure can lead to a macroscopic helical arrangement known as the cholesteric phase which has been observed in fragments of collagen fibrils. The cholesteric orientation can vary with radial distance in the fibril as a double twist. We numerically minimize mean-field Frank free energy in the bulk to solve for the liquid crystal orientation as a function of radial distance (r). By also considering surface terms the overall energy per fibril area is minimized to find the optimal fibril radius R and molecule orientation on the fibril surface (R) both of which may be compared to experimental measurements. -
Thermodynamics of pore formation in lipid bilayers
Drew Bennett University of Waterloo
PIRSA:13120022Lipid bilayers form the basic structure of cellular membranes creating a semi-permeable barrier necessary for separating distinct chemical environments. Hydrophilic pores can form in bilayers that breach the barrier potentially causing cell death or enhance the uptake of hydrophilic molecules. We use molecular dynamics simulations and free energy calculations to investigate pore formation in model bilayers. The free energy barrier for pore formation is much lower in thinner phosphatidylcholine bilayers compared to thicker bilayers. The free energy barrier is due to an unfavourable change in entropy while the enthalpy of pore formation is favourable. These results have implications on a wide range of biological and biotechnological applications such as drug delivery antimicrobial peptides and transmembrane structure and stability. -
Transport in molecular scale
Behnaz Bagheri Varnousfaderani University of Waterloo
PIRSA:13120021Recently there has been a large growth of research effort for nanoelectronic devices.Investigations of quantumly coherent nano-meter scale systems whose fabrication has been made possible by recent advances in experimental and sample preparation techniques have revealed that transport properties could be non-Ohmic and G could be quantized. Understanding electron conduction in such devices is an extremely active research topic. Our theoretical goal is to predict quantum transport properties of molecular nanodevices including their I-V characteristics from first principle theoretical method.