Calculating the free energy of antimicrobial peptide (HHC-36) dimerization in bulk
shaqa vafa University of Guelph
PIRSA:13120043
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Budding transition of a self-avoiding polymer confined by a soft membrane adhering onto a flat wall
Yu-Cheng Su University of Waterloo
PIRSA:13120041 -
Dynamical simulation of disordered micelles in a diblock copolymer melt with fluctuations
Russell Spencer University of Guelph
PIRSA:13120040 -
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Phase-field model for cellular monolayers : a cancer cell migration studyauthors : Benoit Palmieri and Martin Grant
Benoit Palmieri McGill University
PIRSA:13120037 -
The rocky road from non-equilibrium work to free energy
Mostafa Nategh University of Guelph
PIRSA:13120036 -
A Study on Dynamics of Tissue Growth Using Single Cell Based Model
Anna Mkrtchyan Western University
PIRSA:13120035 -
Molecular dynamics studies of Langmuir monolayers of cationic/PC lipids
Bin Liu University of Waterloo
PIRSA:13120034 -
Topological defects of tetratic liquid-crystal order on a soft spherical surface
Yao Li Tsinghua University
PIRSA:13120033 -
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Improving the Martini model: coarse-graining with dynamic charges and polarization
Yuriy Khalak University of Waterloo
PIRSA:13120031
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Calculating the free energy of antimicrobial peptide (HHC-36) dimerization in bulk
shaqa vafa University of Guelph
PIRSA:13120043The increasing demand for antibiotics has contributed to the investigation of possible novel antibiotics by many researchers. For this purpose experimental and theoretical studies have been carried out to draw scientists' attention to antimicrobial peptides and their interaction with the surface of bacterial membranes. Their ability to disrupt the functioning of bacterial membranes has been probed from different perspectives. The most desirable antimicrobial peptides are those which do not harm plant or animals' membranes but which disrupt bacterial membranes. It has been found that some cationic antimicrobial peptides (CAPs) satisfy these requirements. CAPs interacting with the outer membrane of gram-negative bacteria and the membrane of gram-positive bacteria have been studied recently.We conduct a Molecular Dynamics simulation study of peptide-peptide interactions in physiological solutions and investigate the mechanism of CAPs aggregation since aggregation of the peptides could precede their interaction with the membrane. Different algorithms are applied to calculate the potential mean force of the aggregation process of peptides to select the most efficient one. Also we have run CD spectroscopy and calorimetry experiments to predict the structure of the peptide and measure the peptide-peptide binding enthalpy and compared these results with our simulation data. The particular CAP studied is HHC-36 a peptide selected by high throughput screening (A. Cherkasov et al ACS Chem. Biol. 2009 4 (1) pp 6574) (M. Kazemzadeh-Narbat et al Biomed. Mater. Res. Part B 2012 5 pp1344-1352) (M. Ma et al Biomed. Mater. Res. Part A 2012 2 pp278-185) which has nine amino acid residues and charge +5. -
Ab initio insight in supercooled water
John Tatini Titantah Western University
PIRSA:13120042As an extension to previous ab initio studies on water [12] we present 400 psBorn-Oppenheimer ab initio Molecular dynamics study on water at deep supercooled temperatures (down to 220 K) and confirm a crossover from a fragile to strongliquid around the Widom line. This crossover is accompanied by the passage from relatively weaker hydrogen bonds in the dominantly high density liquid (HDL) at high temperatures to strong hydrogen bond in dominantly low density liquid (LDL). This crossover is accompanied by a maximum in the excess specific heat at constant volume and may lend further support to the existence of a liquid-liquid critical point (LLCP) in supercooled water as was predicted by Peter Poole and collaborators using ST2 water model[3].References[1] J. T. Titantah and M. Karttunen Long-Time Correlations and Hydrophobe-Modified Hydrogen-Bonding Dynamics in Hydrophobic Hydration. J. Am. Chem. Soc. 134 9362 (2012)[2] J. T. Titantah and M. Karttunen Water dynamics: Relation between hydrogen bond bifurcations molecular jumps local density & hydrophobicity. Sci. Rep. 3 2991 (2013)[3] Poole P. H. Sciortino F. Essmann U. & Stanley H. E. Phase behaviour of metastable water. Nature 360 324328 (1992) -
Budding transition of a self-avoiding polymer confined by a soft membrane adhering onto a flat wall
Yu-Cheng Su University of Waterloo
PIRSA:13120041Monte Carlo simulation is used to study the structural properties of the system consisting of a self-avoiding polymer chain confined between a fluid membrane and a flat hard surface. As the adhesion between the soft membrane and the hard-wall surface increases the polymer is subject to a strong confinement; a pancake-shaped polymer conformation state eventually yields to a bud state through an abrupt first-order phase transition. We explore the scaling behavior of the physical properties of the system as functions of the polymers size the membranes surface tension and the adhesion energy for both pancake and bud states in terms of Monte Carlo data and analytic scaling theories. -
Dynamical simulation of disordered micelles in a diblock copolymer melt with fluctuations
Russell Spencer University of Guelph
PIRSA:13120040By including composition fluctuations in our dynamical simulation of the time-dependent Landau-Brazovskii model for a diblock copolymer melt we find that disordered micelles form above the order-disorder transition to a BCC phase. At high-temperatures the micelle number density and volume fraction are effectively zero and the melt is disordered at the molecular level. As we lower the temperature the micelle number density increases gradually and approaches the number density in the BCC phase. If we increase the strength of the fluctuations the temperature range over which disordered micelles exist broadens and the onset of BCC order is suppressed. By tracking trajectories we also investigate the dynamical behaviour of individual micelles in an environment of disordered micelles We find diffusive behaviour which we investigate as a function of temperature and micelle volume fraction. -
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Phase-field model for cellular monolayers : a cancer cell migration studyauthors : Benoit Palmieri and Martin Grant
Benoit Palmieri McGill University
PIRSA:13120037Recent experimental work [1] suggests that the increased motility of cancer cells observed in a confluent monolayer of normal cells is due to the mechanical mismatch between the two cell types. The soft cancer cell undergoes large deformations and can squeeze between small channels defined by the space between the normal cells. We developed a phase-field model description of cellular monolayers to study such a process. The system is setup as a free-boundary problem where each cell is a highly deformable soft body [2]. The motion of each cell is described by a persistent random walk where the velocities and persistent times can be obtained from experimental observations. Our model is used to test the hypothesis that the mechanical mismatch alone increases the motility of softer cells when all other parameters are the same.[1] Lee et al. Biophys. J. vol. 102 p. 2731 (2012).[2] Najem et al. Europhys. Lett. vol. 102 p. 16001 (2013). -
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.