Bulletin of the American Physical Society
Spring 2017 Meeting of the APS New England Section, held jointly with NanoWorcester
Volume 62, Number 5
Friday–Saturday, April 14–15, 2017; Worcester, Massachusetts
Session D3: Computational Methods |
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Chair: Nima Rahbar, Worcester Polytechnic Institute Room: Olin Hall 109 |
Saturday, April 15, 2017 10:15AM - 10:27AM |
D3.00001: Opening Remarks |
Saturday, April 15, 2017 10:27AM - 10:47AM |
D3.00002: Chain Exchange Kinetics in Tadpole, Linear {\&} Mixed Linear/Tadpole Diblock Copolymer Micelles Prhashanna Ammu, Elena Dormidontova With advancements in polymerization techniques, a variety of new chain architectures have become available. Chain architecture is known to control macro-molecular self-assembly and furthermore affect in a complex way nanostructure stability. In the present study, using dissipative particle dynamics simulations the equilibrium properties and chain exchange kinetics of tadpole-shaped core-forming block copolymer micelles are evaluated and compared with that for the linear block copolymers of similar block length. Tadpole block copolymer micelles are found to have smaller aggregation number and exhibit faster chain exchange kinetics at equilibrium compared to linear block copolymers of similar chemical nature and block length. We also studied mixed micelles of tadpole/linear block copolymers. In mixed micelles, the tadpole chains are found to be located near the periphery of the micelle core. The chain exchange between mixed micelles is determined to be slower than in tadpole micelles, but quicker than in linear diblock copolymer micelles. Furthermore, the chain exchange kinetics of individual components in mixed micelles is influenced by the presence of other component, as will be discussed. [Preview Abstract] |
Saturday, April 15, 2017 10:47AM - 11:07AM |
D3.00003: Self-assembly of Gold Nanoparticles Directed by Lipid Nanodiscs: Molecular Dynamics Study. Hari Sharma, Elena E. Dormidontova Metal nanoparticles with their unique physical properties have attracted growing attention for a variety of technological applications. Gold nanoparticles (AuNPs) in combination with lipid nanocarriers are an attractive platform for biomedical applications. Using molecular dynamics simulation with the MARTINI force field, we show that, self-assembled lipid nanodiscs can be used to direct aggregation of AuNPs into ring- or string-like structures. We found that equilibrium encapsulation of hydrophobically modified 1 nm AuNPs into mixed lipid nanodisc composed of dipalmitoylphosphatidylcholine (DPPC) and dihexanoylphosphatidylcholine (DHPC) occurs at the rim of the nanodisc leading to the formation of ring-like structures along the nanodisc circumference. Upon temperature increase, the order parameter of lipid tails decreases resulting in a spontaneous transition of nanodiscs into vesicles with embedded AuNP string or into an open ``round vase'' structure with a ring of AuNPs along the rim. The effect of the length of hydrophobic alkane tether (C$_{\mathrm{8}}$, C$_{\mathrm{12}}$ and C$_{\mathrm{16}})$ grafted to the gold surface on the stability of lipid nanodisc and clustering of AuNPs will be discussed and compared with experimental and computer simulation data. [Preview Abstract] |
Saturday, April 15, 2017 11:07AM - 11:27AM |
D3.00004: Boundary effects in FRAP recovery in the confined geometries of animal, plant and fungal cells J. Kingsley WPI—Fluorescence Recovery After Photobleaching (FRAP) has been an important tool for cell biologists to study diffusion and binding kinetics of proteins, vesicles and other molecules. In FRAP, a laser is used to photobleach a target area, and the transport of fluorescent molecules into the bleached area is used determine their diffusion coefficient and bound fraction. While many FRAP models have been developed to assist in analysis, the influence of complex boundaries and optical effects has been largely neglected. Here, we developed a three-dimensional computational model of the FRAP process, incorporating particle diffusion, cell boundary effects, and the optical properties of the microscope, and validated this model using the tip- growing cells of Physcomitrella patens. We show that these effects confound FRAP analysis, affecting the apparent bound fraction and number of dynamic states of a fluorescent protein. Finally, we illustrate how existing theoretical and computational models perform in each of these scenarios, and provide guidelines on how to use FRAP quantitatively in prohibitive geometries. [Preview Abstract] |
Saturday, April 15, 2017 11:27AM - 11:47AM |
D3.00005: Molecular dynamics simulations of coil-helix transition of polyethylene oxide in solution and in presence of carbon nanotube. Udaya Dahal, Elena Dormidontova Hydrogen bonding between polymer and solvent determines macromolecular properties, e.g. conformation, in solution as well as under nanoconfinement. Using atomistic molecular dynamics simulations, we investigate the dynamics and conformation of polyethylene oxide (PEO) in water, isobutyric acid and in presence of a carbon nanotube (CNT). We found that, isobutyric acid hydrogen bonded to PEO has longer residence lifetime than hydrogen bonded water in aqueous solution. We show that this higher stability of hydrogen bonded solvent is responsible for helix-like PEO conformation in isobutyric acid solution compared to coil-like conformation of PEO in aqueous solution. Under the presence of a CNT, we find that PEO spontaneously enters the CNT from aqueous solution and forms rod-like, helix and wrapped chain conformation depending on CNT diameter. The helix formation under nanoconfinement is attributed to the stable water arrangement around PEO inside the CNT. We further discuss the implication of hydrogen bond stability and solvent arrangement for PEO chain conformation and mobility. [Preview Abstract] |
Saturday, April 15, 2017 11:47AM - 12:07PM |
D3.00006: Thin film deposition using rarefied gas jet Dr. Sahadev Pradhan The rarefied gas jet of aluminium is studied at Mach number \textit{Ma }$=$\textit{ (U\textunderscore j / }$\backslash $\textit{sqrt\textbraceleft kb T\textunderscore j / m\textbraceright )}in the range \textit{.01 \textless Ma \textless 2}, and Knudsen number \textit{Kn }$=$\textit{ (1 / (}$\backslash $\textit{sqrt\textbraceleft 2\textbraceright }$\backslash $\textit{pi d\textasciicircum 2 n\textunderscore d H)} in the range \textit{.01 \textless Kn \textless 15}, using two-dimensional (2D) direct simulation Monte Carlo (DSMC) simulations, to understand the flow phenomena and deposition mechanisms in a physical vapor deposition (PVD) process for the development of the highly oriented pure metallic aluminum thin film with uniform thickness and strong adhesion on the surface of the substrate in the form of ionic plasma, so that the substrate can be protected from corrosion and oxidation and thereby enhance the lifetime and safety, and to introduce the desired surface properties for a given application. Here, $H$is the characteristic dimension, \textit{U\textunderscore j}and \textit{T\textunderscore j}are the jet velocity and temperature, \textit{n\textunderscore d}is the number density of the jet, $m$and $d$ are the molecular mass and diameter, and \textit{kb}is the Boltzmann constant. An important finding is that the capture width (cross-section of the gas jet deposited on the substrate) is symmetric around the centerline of the substrate, and decreases with increased Mach number due to an increase in the momentum of the gas molecules. DSMC simulation results reveals that at low Knudsen number \textit{((Kn }$=$\textit{ 0.01);}shorter mean free paths), the atoms experience more collisions, which direct them toward the substrate. However, the atoms also move with lower momentum at low Mach number$,$which allows scattering collisions to rapidly direct the atoms to the substrate. [Preview Abstract] |
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