Collection Number C13037
Collection Date -
Collection Type Conference/School
Waterloo Soft Matter Theory 2013

Calculating the free energy of antimicrobial peptide (HHC-36) dimerization in bulk

shaqa vafa University of Guelph
The 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.

Ab initio insight in supercooled water

John Tatini Titantah Western University
As 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).

Budding transition of a self-avoiding polymer confined by a soft membrane adhering onto a flat wall

Yu-Cheng Su University of Waterloo
Monte 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.

Dynamical simulation of disordered micelles in a diblock copolymer melt with fluctuations

Russell Spencer University of Guelph
By 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.

Phase-field model for cellular monolayers : a cancer cell migration studyauthors : Benoit Palmieri and Martin Grant

Benoit Palmieri McGill University
Recent 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 rocky road from non-equilibrium work to free energy

Mostafa Nategh University of Guelph
Although 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.

A Study on Dynamics of Tissue Growth Using Single Cell Based Model

Anna Mkrtchyan Western University
Tissue 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.

Molecular dynamics studies of Langmuir monolayers of cationic/PC lipids

Bin Liu University of Waterloo
Our 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.

Topological defects of tetratic liquid-crystal order on a soft spherical surface

Yao Li Tsinghua University
We 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.