Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session F36: Focus Session: Biofunctionalized Nano-Materials |
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Sponsoring Units: GSOFT DBIO Chair: Ras Pandey, University of Southern Mississippi Room: 211 |
Tuesday, March 3, 2015 8:00AM - 8:12AM |
F36.00001: Multi-scale morphology in self-assembly of peptides to proteins via a coarse-grain model Ras Pandey, Barry Farmer Self-organizing structures of short peptides (6-7 residues) and proteins (136 residues) are studied by a coarse-grained Monte Carlo simulation. Peptides and proteins are described by coarse-grained chains of residues whose interactions are described by a knowledge-based residue-residue interaction potential that captures the compositional specificity. Large-scale computer simulations are performed to study the structural evolution e.g. aggregation, network, etc. at a range of temperatures and concentrations. A number of local and global physical quantities including structure factor are examined. We find that the residue interactions, concentration, and size of chains are very important in modulating the structure of emerging morphologies in the specified temperature range. Estimates are provided for the effective (fractal) dimension of the assembly over various length scales as a function of temperature. [Preview Abstract] |
Tuesday, March 3, 2015 8:12AM - 8:24AM |
F36.00002: Interaction of Biofunctionalized Nanoparticles with Receptors on Cell Surfaces: MC Simulations Elena Dormidontova, Shihu Wang One of the areas of active development of modern nanomedicine is drug/gene delivery and imaging application of nanoparticles functionalized by ligands, aptamers or antibodies capable of specific interactions with cell surface receptors. Being a complex multifunctional system different structural aspects of nanoparticles affect their interactions with cell surfaces and the surface properties of cells can be different (e.g. density, distribution and mobility of receptors). Computer simulations allow a systematic investigation of the influence of multiple factors and provide a unified platform for the comparison. Using Monte Carlo simulations we investigate the influence of the nanoparticle properties (nanoparticle size, polymer tether length, polydispersity, density, ligand energy, valence and density) on nanoparticle-cell surface interactions and make predictions regarding favorable nanoparticle design for achieving multiple ligand-receptor binding. We will also discuss the implications of nanoparticle design on the selectivity of attachment to cells with high receptor density while ``ignoring'' cells with a low density of receptors. [Preview Abstract] |
Tuesday, March 3, 2015 8:24AM - 8:36AM |
F36.00003: Prediction of Surface and pH-Specific Binding of Peptides to Metal and Oxide Nanoparticles Hendrik Heinz, Tzu-Jen Lin, Fateme Sadat Emami, Hadi Ramezani-Dakhel, Rajesh Naik, Marc Knecht, Carole C. Perry, Yu Huang The mechanism of specific peptide adsorption onto metallic and oxidic nanostructures has been elucidated in atomic resolution using novel force fields and surface models in comparison to measurements. As an example, variations in peptide adsorption on Pd and Pt nanoparticles depending on shape, size, and location of peptides on specific bounding facets are explained. Accurate computational predictions of reaction rates in C-C coupling reactions using particle models derived from HE-XRD and PDF data illustrate the utility of computational methods for the rational design of new catalysts. On oxidic nanoparticles such as silica and apatites, it is revealed how changes in pH lead to similarity scores of attracted peptides lower than 20{\%}, supported by appropriate model surfaces and data from adsorption isotherms. The results demonstrate how new computational methods can support the design of nanoparticle carriers for drug release and the understanding of calcification mechanisms in the human body. [Preview Abstract] |
Tuesday, March 3, 2015 8:36AM - 9:12AM |
F36.00004: Aqueous amino acids and proteins near solid surfaces: ZnO, ZnS, Au, and mica Invited Speaker: Marek Cieplak We calculate potentials of the mean force for 20 amino acids in the vicinity of the (111) surface of Au, four surfaces of ZnO, and the (110) surface of ZnS using molecular dynamics simulations combined with the umbrella sampling method. In the case of Au, we compare results obtained within three different force fields: one hydrophobic (for a contaminated surface) and two hydrophilic -- with and without polarization of the solid. The properties of water near the surface sensitively depend on the force field. All of these fields lead to good binding with very different specificities and to unlike patterns in the density and polarization of water. We demonstrate that binding energies of dipeptides are distinct from the combined binding energies of their amino acidic components. We show that ZnS is more more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO -- it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile. In the case of ZnS, not all amino acids can attach to the surface and when they do, the binding energies are comparable to those found for the surfaces of ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is distinct. The covalent bond with the sulfur atom on cysteine is modeled by the Morse potential. For the hydrophobic Au, adsorption events of a small protein (the tryptophan cage) are driven by attraction to the strongest binding amino acids. This is not so for ZnO, ZnS and for the hydrophilic models of Au -- a result of smaller specificities combined with the difficulty for proteins, but sometimes not for single amino acids, to penetrate the first layer of water. Molecular dynamics studies of several proteins near mica with a net charge on its surface indicate existence of two types of states: deformed and unfolded. Using a coarse-grained model, we also study a glassy behavior of protein layers at air-water interfaces. REFERENCES: [1] A. Starzyk and M. Cieplak, Denaturation of proteins near polar surfaces, J. Chem. Phys. 135, 235103 (2011); [2] G. Nawrocki and M. Cieplak, Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations, Phys. Chem. Chem. Phys. 15, 13628-13636 (2013); [3] G. Nawrocki and M. Cieplak, Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations, J. Chem. Phys. 140, 095101 (2014); [4] G. Nawrocki and M. Cieplak, Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields, J. Phys. Chem. C 118, 12929-12943 (2014); [5] M. Cieplak, D. B. Allen, R. L. Leheny, and D. H. Reich, Proteins at air-water interfaces: a coarse-grained approach, Langmuir (in press). [Preview Abstract] |
Tuesday, March 3, 2015 9:12AM - 9:24AM |
F36.00005: Aptamer functionalized lipid multilayer gratings for label free detection of specific analytes Plengchart Prommapan, Troy W. Lowry, David Van Winkle, Steven Lenhert Lipid multilayer gratings have been formed on surfaces with a period of 700 nm. When illuminated with white light incident at about 50$^{\circ}$, these gratings diffract green light perpendicular to their surface. We demonstrate the potential of these gratings as sensors for analytes by monitoring changes in the diffracted light due to the changes in the size and shape of the grating in response to analyte binding. To demonstrate this potential application, a lipid multilayer grating was functionalized with a thrombin binding aptamer. The selectivity of our aptamer functionalized lipid gratings was confirmed both by monitoring the diffracted light intensity and by fluorescence microscopy. Furthermore, the results show that the binding activity between the aptamer and thrombin depends on the relative composition of a zwitterionic lipid (DOPC) and a cationic lipid (DOTAP). This work shows that nanostructured lipid multilayers on surfaces are a promising nanomaterial for label-free bio-sensing applications. [Preview Abstract] |
Tuesday, March 3, 2015 9:24AM - 9:36AM |
F36.00006: Materials Integration by Nanointaglio Troy Lowry, Aubrey Kusi-Appiah, Jingjiao Guan, David Van Winkle, Michael Davidson, Steven Lenhert Nanointaglio\footnote{Lowry, T. W. Kusi-Appiah, A., Guan, J., Van Winkle, D.H., Davidson, M.W., Lenhert, S. Materials Integration by Nanointaglio. Advanced Materials Interfaces 1, doi:10.1002/admi.201300127 (2014).} is a printing process from a microstructured intaglio stamp that in combination with established microarray technology is suitable for heterogeneous materials integration of lipid multilayer micro- and nanostructures. Nanointaglio offers both size dependent functionality and massively parallel materials integration capabilities. The scalable, multi-integrative characteristics of nanointaglio have potential applications in high throughput screening and biosensor arrays. [Preview Abstract] |
Tuesday, March 3, 2015 9:36AM - 9:48AM |
F36.00007: Protein-Polymer Functionalized Nanopatterned Surfaces Haoyu Wang, Pinar Akcora Understanding and controlling the protein interactions with surfaces for biosensors and biomedical implants is a fundamental problem for biocompatible nanomaterial design. Proteins attached in ordered nanopores can exhibit superior biological activities compared to smooth microstructured surfaces. We developed heterogeneous and nanopatterned surfaces decorated with polymer brushes and proteins to control protein fates through elasticity. The heterogeneity of surfaces is controlled with well-defined chemistry, pattern size and geometry, stiffness of polymers and protein types. We will present our recent nanoindentation results on nanopatterned and biofunctionalized flat surfaces and discuss the pattern size effect on protein activity, hence conformation. [Preview Abstract] |
Tuesday, March 3, 2015 9:48AM - 10:00AM |
F36.00008: Air-stable droplet interface bilayers Charles Collier Droplet interface bilayers are versatile model membranes useful for synthetic biology and biosensing; however, to date they have been for the most part confined to fluid reservoirs. Here, we demonstrate that when two or more water droplets meet on an oil-infused substrate, they exhibit noncoalescence due to the formation of a thin oil film that gets squeezed between the droplets from the bottom up. We show that when phospholipids are included in the water droplets, a stable droplet interface bilayer forms between the noncoalescing water droplets. As with traditional oil-submerged droplet interface bilayers, we were able to characterize ion channel transport by incorporating peptides into each droplet. We demonstrate the ability of these air-stable droplet interface bilayers (airDIBs) to incorporate ligand-gated ion channels via fusion of microsomes, which enables the biosensing of airborne matter. [Preview Abstract] |
Tuesday, March 3, 2015 10:00AM - 10:12AM |
F36.00009: Interactions of Lysozyme and Azobenzene Derivatives in the Solution and on a Surface Tao Wei, Katherine Shing The reversible isomerization of the azobenzene and its derivatives can control protein structure in an aqueous environment with the alternation of visible and UV lights for very promising applications in drug delivery. However, an atomistic description of Azo-molecules and protein amino acid residues is still lacking. In this study we performed atomistic molecular dynamics simulation to study the interactions between a lysozyme molecule and the Azobenzene derivative (in the bulk solution and grafted on the Silica surfaces). Protein structural arrangements (i.e., the shape and secondary structures) and its mobility, as a function of tran/cis ratio in the bulk solution and on the self-assembling monolayer surface's density and morphology, are systematically investigated. [Preview Abstract] |
Tuesday, March 3, 2015 10:12AM - 10:24AM |
F36.00010: Computational investigation of CNT-based DNA polymerase nanocircuits Yan Li, Miroslav Hodak, Wenchang Lu, Jerry Bernholc, Philip Collins DNA polymerases are important enzymes that replicate DNA molecules with very low error rates -- about one error in 10$^{5}$ bases. Recently, it was found that the replication process can be electrically monitored by attaching a Klenow fragment of polymerase I to the surface of a carbon nanotube and monitoring the current along the tube [1]. In this talk, we report results from computational studies on DNA polymerase nanocircuits. We have first performed classical molecular dynamics (MD) calculations to get snapshots of different enzymatic stages, particularly the open state (no DNA binding) and the closed state (DNA double helix binding). We then used density functional theory (DFT) and Keldysh non-equilibrium Green's function (NEGF) formalism to calculate transmission coefficients and currents for each enzymatic state. Our results show that the transmission spectrum and the currents change significantly when the enzyme moves from the open to the closed state. While the initial experiments did not show signal differences between dissimilar bases, the theoretical work in progress is investigating conditions where bases might have distinct signatures, which would allow for DNA sequencing. [Preview Abstract] |
Tuesday, March 3, 2015 10:24AM - 10:36AM |
F36.00011: Graphene under one-dimensional periodic potentials using DNA-assembled parallel nanotubes as a periodic gate array Yong Wu, Si-ping Han, William Goddard, Marc Bockrath Graphene under an applied one-dimensional (1D) periodic potential is predicted to show many interesting and unique phenomena such as electron supercollimation and additional Dirac points [1], and some progress has been made in observing graphene in this regime [2]. Here, we use parallel nanotubes assembled using DNA linkers [3] as a back gate to apply periodic or quasi-periodic 1D potentials to graphene layers. The pitch of the nanotube array can be controlled by the linker length which we can vary from 8nm-20nm. We can independently control the periodic potentials using the nanotube array and the carrier density using a top gate to study the transport properties of the system. Our latest results will be discussed. \\[4pt] [1] Anisotropic behaviours of massless Dirac fermions in graphene under periodic potentials, Nature Physics, C-H Park, Steven Louie \\[0pt] [2] Tunable Superlattice in Graphene To Control the Number of Dirac Points, Mandar M. Deshmukh\\[0pt] [3] DNA-Linker-Induced Surface Assembly of Ultra Dense Parallel Single Walled Carbon Nanotube Arrays, Nanoletter, Si-ping Han, William Goddard [Preview Abstract] |
Tuesday, March 3, 2015 10:36AM - 10:48AM |
F36.00012: Graphene decorated with mu-opioid receptor: the ionic screening effect and detection of enkephalin Jinglei Ping, A.T. Charlie Johnson, Renyu Liu We investigated the properties of graphene field effect transistors (GFETs) decorated with a computaionally redesigned, water-soluble variant of the human mu-opioid receptor (wsMOR) in physiological buffer solution. The shift of the Fermi level in the GFETs is quantitatively described by chemical-gating effect of charges on the wsMOR that are screened by the ionic solution. Our results suggest that sensitivity to the molecular target is lost when the Debye screening length of the solution is shorter than the distance from the graphene to the wsMOR; thus de-salting may be necessary when wsMOR decorated GFETs are used as biosensors in solution. We used this insight to detect DAMGO, a synthetic analog to the endogenous opioid peptide encephalin, at a concentration of 10 pM (5.1 pg/mL) in artificial cerebrospinal fluid (aCSF) diluted to 5{\%} of its normal salt concentration. When the sensors were measured in a dry state, the limit of detection for DAGMO was 1 pM (0.5 pg/mL), one-third of the baseline in human body.Funding for this work was provided by DARPA. [Preview Abstract] |
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