Bulletin of the American Physical Society
2015 Annual Spring Meeting of the APS Ohio-Region Section
Volume 60, Number 3
Friday–Saturday, March 27–28, 2015; Kent, Ohio
Session E4: Biophysics/Soft Matter II |
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Chair: John Portman, Kent State University Room: KSU Student Center 316 |
Saturday, March 28, 2015 10:10AM - 10:25AM |
E4.00001: Coarse-Grained Molecular Simulations of Allosteric Cooperativity Prithviraj Nandigrami, John Portman We develop a mixed Monte Carlo-Molecular Dynamics scheme to simulate the classic Monod-Wyman-Changeux (MWC) model of allostery at the molecular level. Ligand binding in this model is cooperative due to the coupling between the binding sites provided by the conformational transition of the protein. We present results for calcium binding to the two binding loops within each domain of Calmodulin (CaM). We find that relative binding free energies of an individual loop is determined by the conformational compatibility of the binding site in the bound conformation, as well as the conformational flexibility of the binding site in the unbound conformation. This simple coarse-grained model captures the qualitative differences for calcium binding to the isolated domains of CaM such as overall affinity and the relative binding cooperativity. A simple two state MWC model provides an accurate description of the simulated population for the ligation states of each domain as a function of concentration. [Preview Abstract] |
Saturday, March 28, 2015 10:25AM - 10:40AM |
E4.00002: Ambient STM Study of 1-Dodecanethiol SAMs on Au Thin Film Capped HOPG Mackenzie Maurer, Alexis Bowers, Indrajith Senevirathne Thiol-based self-assembled monolayers (SAM) surfaces are ubiquitous in many device applications including sensor engineering. The conductivity characteristics and surface molecular structure and orientation of these SAMs are important as physiochemical properties are dependent on the surface arrangement. This study attempts to quantify and model long chain --R terminated (hydrophobic) 1-dodecanethiol on thermally annealed Au thin films capped on Highly Oriented Pyrolytic Graphite (HOPG) substrates. Specifically, this study uses Scanning Tunneling Microscopy (STM) and contact angle measurements to assess the HOPG surface, the Au thin film capped HOPG surface, and the SAM layered surface exclusively. 5mM concentrated solutions of 1-dodecanethiol dissolved in 200 proof ethanol were prepared for the self-assembly process. These solutions were used in developing SAMs on HOPG, in which Au thin layers were sputter deposited and subsequently annealed. Data indicated Au deposition and thermally annealing changes the surface consistency. Uniqueness of this study is the ambient conditions under which data was obtained. Surface structure, consistency and possible thiol molecular arrangement of the SAM layer will be discussed. [Preview Abstract] |
Saturday, March 28, 2015 10:40AM - 10:55AM |
E4.00003: Fly-casting in a reaction limited binding of pKID-KIX Talant Ruzmetov, John Portman Flexible and robust nature of encounter complex is an advantage for Natively Unstructured Proteins(IDPs) to facilitate fast molecular recognition associated with coupled folding and binding. Several factors involving the weak non-specific interactions between the IDP and its binding partner can lead to enhanced binding rates such as Fly-casting and reduced orientational constraints of flexible binding partners. Here we investigate how overcoming desolvation barriers between the binding partners influences coupled folding and binding kinetics of an IDP (pKID) to its taget (KIX). We compare the free energy binding surface and kinetics for models with and without desolvation barriers between pKID and KIX for a range of flexibilities. We find that compared to a more structured unbound protein, the simulated binding rate of flexible binding partners is an order of magnitude faster. This difference in binding rate, which is much larger than the range without desolvation barriers, can be understood by the ability of a flexible binding partner to overcome desolvation barriers sequentially while rigid proteins must overcome them more collectively. In addition,carefully choosing reaction coordinate, we witness Fly-casting in the reaction limited binding regime. [Preview Abstract] |
Saturday, March 28, 2015 10:55AM - 11:10AM |
E4.00004: Partition function zeros for the polymer adsorption transition Mark Taylor, Samip Basnet, Jutta Luettmer-Strathmann Modern computer simulation techniques, such as the Wang-Landau (WL) algorithm, allow for direct computation of the density of states, and thus the partition function, of a many-body system. The partition function encodes all thermodynamic information including details of phase behavior. Here we describe the application of the WL approach to the adsorption transition for both lattice [1] and continuum chains tethered to an attractive surface. We compute the canonical partition function for chains up to length N=1536 and analyze the zeros of these function in the complex inverse-temperature plane. These zeros define a nearly closed circular region, centered on the origin, intersected near the positive real axis by two flaring tails. With increasing chain length the intersection point pinches down towards the positive real axis, dividing the real axis into two distinct regions or phases in accord with Yang-Lee theory. We apply finite size scaling theory (including corrections to scaling) for the leading partition function zeros to locate the adsorption transition in the thermodynamic limit and obtain values for the polymer crossover, order parameter, and specific heat exponents. \\[4pt] [1] M.P. Taylor and J. Luettmer-Strathmann, J. Chem. Phys. 141, 204906 (2014). [Preview Abstract] |
Saturday, March 28, 2015 11:10AM - 11:25AM |
E4.00005: Smart Nanoscale Hydrogels Based on Natural Polymers Sahil Sandesh Gandhi, Huan Yan, Chanjoong Kim Smart polymeric nanoscale hydrogels have gained considerable attention due to their unique properties tailored from the combination of stimuli-responsiveness and nanoscale size in a single material system. Such nanogel systems hold great potential for use in biomedical applications such as controlled drug release, tissue engineering, biosensors, etc. We present a novel tunable thermoresponsive gelatin nanogel that exhibits a volume reduction of more than $30\times$ at $32^{\circ}$C due to the helix to random coil transition of gelatin chains confined in the nanogels. This novel helix-melting mechanism is markedly different from the reversible random coil to globule transition that occurs at the lower critical solution temperature (LCST) in popular thermosensitive polymers like pNIPAM. Using dynamic light scattering, transmission electron microscopy, and polarimetry, we study how temperature changes affect the particle size and the molecular configuration of smart gelatin nanogels and determine key factors influencing the thermoresponsive properties. The thermosensitive properties of these nanogels can be exploited in the development of new types of stimuli-responsive, biomedically relevant materials based on natural polymers. [Preview Abstract] |
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