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Full-Text Articles in Physical Sciences and Mathematics

Hi-Fidelity Simulation Of The Self-Assembly And Dynamics Of Colloids And Polymeric Solutions With Long Range Interactions, Mahdy Malekzadeh Moghani Dec 2014

Hi-Fidelity Simulation Of The Self-Assembly And Dynamics Of Colloids And Polymeric Solutions With Long Range Interactions, Mahdy Malekzadeh Moghani

Doctoral Dissertations

Modeling the equilibrium properties and dynamic response of the colloidal and polymeric solutions provides valuable insight into numerous biological and industrial processes and facilitates development of novel technologies. To this end, the centerpiece of this research is to incorporate the long range electrostatic or hydrodynamic interactions via computationally efficient algorithms and to investigate the effect of these interactions on the self-assembly of colloidal particles and dynamic properties of polymeric solutions. Specifically, self-assembly of a new class of materials, namely bipolar Janus nano-particles, is investigated via molecular dynamic simulation in order to establish the relationship between individual particle characteristics, such as …


Single Molecule Studies Of A Short Rna, Peker Milas Nov 2014

Single Molecule Studies Of A Short Rna, Peker Milas

Doctoral Dissertations

The material related with orientation of Cyanine dyes and their behavior at the ends of duplex RNA is also documented in [110]. Cyanine dyes are widely used to study the folding and structural transformations of nucleic acids using fluorescence resonance energy transfer (FRET). The extent to which FRET can be used to extract inter- and intra-molecular distances has been the subject of considerable debate in the literature; the contribution of dye and linker dynamics to the observed FRET signal is particularly troublesome. We used molecular dynamics (MD) simulations to study the dynamics of the indocarbocyanine dyes Cy3 and Cy5 attached …


The Impact Of Membrane Tension On Phase Separation And Solid Domain Properties In Model Multicomponent Vesicles, Dong Chen Nov 2014

The Impact Of Membrane Tension On Phase Separation And Solid Domain Properties In Model Multicomponent Vesicles, Dong Chen

Doctoral Dissertations

Multicomponent phospholipid membranes provide an ideal model to study the complex phase behavior of biological membranes. Giant unilamellar vesicles (GUV) formed by mixtures of two or more phospholipids have particular merit as model membranes because of their simplicity, operability, and ease of viewing phase separation and testing membrane mechanics. Until the research in this thesis, biochemistry and biophysical studies of phase separation in phospholipid membranes primarily addressed the influence of membrane composition on the transition temperatures and domain shapes. This thesis focuses on a commonly neglected variable - membrane tension, analogous to pressure in bulk materials, as an important parameter …