The rocky road from non-equilibrium work to free energy
Mostafa Nategh University of Guelph
PIRSA:13120036
12121 - 12132 of 20114 Results
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A Study on Dynamics of Tissue Growth Using Single Cell Based Model
Anna Mkrtchyan Western University
PIRSA:13120035Molecular dynamics studies of Langmuir monolayers of cationic/PC lipids
Bin Liu University of Waterloo
PIRSA:13120034Topological 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:13120027
The rocky road from non-equilibrium work to free energy
Mostafa Nategh University of Guelph
PIRSA:13120036Although a few of very promising methods now exist for extracting free energy profiles of a many-body system from non-equilibrium work performed on it the implementation of these methods have proven to be non-trivial. These methods (most notable of all the Jarzynski equality the FR method and the Brownian dynamic FDT) typically require a proper sampling of the work performed on the system along many trajectories in the available phase space that connect the desired initial and final macrostates. One requires a transparent way of sampling the work performed on the system along each trajectory and then to assign residual work values to each 'bin' along the range under study. This becomes a seemingly arbitrary process when done along steered molecular dynamics trajectories. As a result of Brownian motions the system will repeatedly pass back and forth the boundaries of each bin along the reaction path and proper sampling of non-equilibrium work becomes challenging.A method for measuring non-equilibrium work in such cases will be presented with discussions on error analysis and how to address the issue of correlations among adjacent samplings of work for each bin. Applications of this method to a test system and also to a couple of peptide-membrane systems will be presented and discussed as well as the relative reliability of the results based on theoretical arguments and the agreement among different methods.A Study on Dynamics of Tissue Growth Using Single Cell Based Model
Anna Mkrtchyan Western University
PIRSA:13120035Tissue topology such as proliferating epithelium topology shows striking similarities for various species. Thissuggests unified mechanism for tissue formation which can be explored with the help of physical or mathematicalmodels. Indeed it has been shown that cell divisions along with local cell rearrangements can reproduce commonlyobserved epithelium topology by using topological models.Tightly packed cells in epithelium resemble polygons. This observation gave rise to models where cells aretreated as polygons in junctional network. These models were used to investigate effects of cell mechanics andcell divisions on topology.In some cases cells undergo extensive rearrangements during tissue formation which dramatically alters tissuetopology. Based on our previous work we propose single cell based mechanical model which can naturallyaccount for cell rearrangements. Importantly this model takes into account cell elasticity and adhesion. Cellgrowth is controlled by hydrostatic pressure.In this work we study the the dynamics of tissue growth and the influence of cell mechanics and various division mechanisms on tissue formation.We also consider different growth mechanisms and investigate their effects on tissue topology.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.