Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session J25: Focus Session: Biopolymers: Molecules, Solutions and Networks I |
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Sponsoring Units: DPOLY DBP Chair: Paula Hammond, Massachusetts Institute of Technology Room: Morial Convention Center 217 |
Tuesday, March 11, 2008 11:15AM - 11:27AM |
J25.00001: Conformation and Trapping of DNA at a Convergent Stagnation Point Jennifer Kreft, Yeng-Long Chen, Hsueh-Chia Chang We use a lattice-Boltzmann based Brownian dynamics simulation to investigate the elongation of DNA at a convergent stagnation point trapped by a uniform attractive potential. Surprisingly, we find that the coiled state is favored over the stretched state at high Peclet number, $Pe$. The final elongation is determined by conformation changes during transport to the stagnation point, rather than hydrodynamic stretching at that point. The trapping rate of the DNA is consistent with the classical mean-field convection-diffusion theory and scales as $Pe^{1/3}$. This scaling is insensitive to the attractive potential used. [Preview Abstract] |
Tuesday, March 11, 2008 11:27AM - 11:39AM |
J25.00002: DNA Surface Hybridization Regimes Rastislav Levicky, Ping Gong Surface hybridization reactions, in which sequence-specific recognition occurs between immobilized and solution nucleic acids, are routinely carried out to quantify and to interpret genomic information. At a surface, molecular interactions are amplified by the two-dimensional nature of the immobilized layer which focuses the nucleic acid charge and concentration to levels not encountered in solution, and which impacts the hybridization behavior in unique ways. We find that, at low ionic strengths, an electrostatic balance between the concentration of immobilized oligonucleotide charge and solution ionic strength governs the onset of hybridization. As ionic strength increases, the importance of electrostatics diminishes and the hybridization behavior becomes more complex. Suppression of hybridization affinity constants relative to solution values, and their weakened dependence on the concentration of DNA counterions, indicate that the immobilized strands form complexes. Moreover, an unusual regime is observed in which the surface coverage of immobilized oligonucleotides does not significantly influence the hybridization behavior, despite physical closeness and hence compulsory interactions between sites. These results are interpreted and summarized in a diagram of hybridization regimes. [Preview Abstract] |
Tuesday, March 11, 2008 11:39AM - 11:51AM |
J25.00003: Hybridization Pathways and Mechanisms of Model DNA Oligonucleotides in Solution. Juan Araque, Athanassios Panagiotopoulos, Marc Robert We propose a coarse-grained lattice model of short DNA strands to investigate the microscopic pathways and mechanisms of oligonucleoides hybridization in solution. The extent to which hybridization in solution conforms to two-state thermodynamics is also analyzed. Monte Carlo simulations with parallel tempering are performed to estimate the equilibrium population of single- and double-stranded states and the associated free-energy landscapes. Sequence complexity is shown to largely dominate the nucleation and helix propagation pathways. The two-state nature of the transition is found to exhibit strong sequence dependence. Although the model predictions are consistent with classical cooperativity signatures, stable intermediates appear, in violation of the two-state assumption. [Preview Abstract] |
Tuesday, March 11, 2008 11:51AM - 12:03PM |
J25.00004: Structure and applications of a temperature responsive recombinant protein hydrogel based on silk- and elastin-like amino acid motifs Lawrence Drummy, Melanie Tomczak, Joseph MacAuliffe, Richard Vaia, Rajesh Naik Proteins form the main components of many natural materials, and they can be designed to offer tailored functionality and material properties. Silk elastin-like proteins (SELP)s come from a family of repeat sequence protein polymers based on \textit{Bombyx mori} silk and mammalian elastin that are recombinantly expressed in \textit{E. coli}. SELP gels are formed by heating the protein solutions in order to induce physical crosslinking of the silk $\beta $-sheet regions, they contain approximately 80-90{\%} water by weight and they can be used for encapsulation of enzymes or nanoparticles. For example, horseradish peroxidase demonstrates added resistance to drying and heat treatment when encapsulated in the gel matrix. During gel formation, small angle X-ray scattering shows intensity increases in two distinct regions of reciprocal space, one reversible with temperature and one irreversible. By fitting the scattering data to a unified power-law/Gunier model, morphological parameters are extracted. The thermally reversible intensity changes are attributed to a hydrophilic/hydrophobic transition in the elastin segments, while the irreversible intensity change is due to the crystalline regions formed by the silk blocks. [Preview Abstract] |
Tuesday, March 11, 2008 12:03PM - 12:15PM |
J25.00005: Fractal Nature of Semiflexible Networks in beta-Hairpin Peptide Hydrogels Rohan Hule, Darrin Pochan De novo designed beta hairpin peptides with asymmetric beta strands, capable of self-assembly and hydrogel formation, were investigated. The stimuli responsive self-assembly occurs via a strand interdigitation mechanism, resulting in physically crosslinked fibrillar networks. Fibrils with distinct nanostructures varying from non-twisted, twisted to laminated morphologies were rationally designed by modulating the peptide strand registry. The fractal dimension and correlation lengths of these networks, both, at the network as well as individual fibril length scales varies significantly with concentration and is directly related to the fibril morphology, as evidenced by SANS and cryogenic TEM. In case of the laminated fibrils, an increase in the peptide concentration induces a change from surface to mass fractal behavior at high q due to the disruption of fibril lamination as a result of faster assembly kinetics from higher peptide concentration. Non-twisting peptide fibril morphologies exhibit an increase the network density with higher peptide concentration and, therefore, an increase in mass fractal dimension. Oscillatory rheology of hydrogels reveals enhanced moduli for laminating networks over non-twisting or twisting networks. These interdigitating peptides constitute a model system to study structure-property relations in other semiflexible networks. [Preview Abstract] |
Tuesday, March 11, 2008 12:15PM - 12:27PM |
J25.00006: A molecular model for toughening in double-network hydrogels Wen-li Wu, Vijay Tirumala, Taiki Tominaga, Sanghun Lee, Paul Butler, Eric Lin, Jian Ping Gong, Hidemitsu Furukawa A molecular mechanism is proposed for the toughness enhancement in double network (DN) hydrogels prepared from poly (2{\-}acrylamido, 2-methyl,1-propanesulfonicacid) (PAMPS) polyelectrolyte network and polyacrylamide (PAAm) linear polymer. It is an extension of the phenomenological model set forth recently by Gong \textit{et al}. This mechanism takes into consideration all the observed changes in molecular structure of the constituents via \textit{in-situ} small angle neutron scattering (SANS) measurements, the composition dependence of the solution viscosity and the thermodynamic interaction parameters of PAMPS and PAAm molecules from our previous neutron scattering studies. More specifically, this proposed mechanism provides an explanation of the observed periodic compositional fluctuation in the micrometer range induced by large strain deformation. [Preview Abstract] |
Tuesday, March 11, 2008 12:27PM - 1:03PM |
J25.00007: De novo designed peptide and peptide-polymer conjugate for biomolecular materials Invited Speaker: Peptides, nature's ``own'' building blocks, provide control of functional groups over nanometer distances with sub-Angstrom resolution and can be de novo designed to self-assemble into multidimensional molecular constructs that mimic natural proteins or perform functions not found in nature. Conjugating synthetic polymers to peptides, forming peptide-polymer conjugates, takes advantages of both the stability and processibility of synthetic polymers and the built-in peptide functions. Helical bundles, a ubiquitous folding motif, underpin many structural and catalytic functions of natural proteins. By attaching a polymer chain to a helical bundle-forming peptide, the polymer chain will mediate the interactions between the helical bundle and its external environment, enable the macroscopic self-assembly and, potentially, allow the helical bundle to function in non-biological environments. A new design of peptide-polymer conjugates will be presented where the polymer chain is covalently linked to the side chain of the peptide. Upon attaching poly(ethylene glycol) (PEG) to the exterior of the helix bundle, the peptide secondary structure and also the tertiary structure, i.e. coiled-coil helix bundle formation, are stabilized. More importantly, using a photoactive heme-binding 4-helix bundle peptide as an example, this new design preserves the built-in functionalities in the interior of the helix bundle. [Preview Abstract] |
Tuesday, March 11, 2008 1:03PM - 1:15PM |
J25.00008: Single polymer stretching in elastic turbulence of polymer solution Yonggang Liu, Victor Steinberg Coil-stretch transition of single T4 DNA molecule in an elastic turbulence is studied in a polymer solution with the same molecules. Two mechanisms of saturation of polymer stretching in elastic turbulence, the nonlinearity of polymer stretching and the back reaction of stretched polymer chains to the flow, are demonstrated based on experiments of single polymer dynamics at different polymer concentrations. The elastic stress calculated from single polymer stretching agrees with the PIV measurement of the flow properties, indicating that polymer stretching can be used as an elastic stress probe of the flow properties. [Preview Abstract] |
Tuesday, March 11, 2008 1:15PM - 1:27PM |
J25.00009: Shape and conformation of confined biopolymers. Ya Liu, Bulbul Chakraborty Biological macromolecules living in cells are confined on length scales comparable to their intrinsic persistence length. In these environments, the bending rigidity plays a decisive role in determining shape and conformations. We have used numerical simulations to investigate the statistical properties of a semiflexible polymer confined in a square box. Simulations exhibit a shape transition when the bare persistence length becomes comparable to the box size. An order parameter is introduced to quantify and analyze the nature of this transition. The shape change is accompanied by a qualitative change in the effective persistence length, which starts differing significantly from the intrinsic persistence length. A mean-field model, including Gaussian fluctuations around the saddle point solution, provides a quantitative description of the evolution of the tangent-tangent correlation function with increasing confinement. [Preview Abstract] |
Tuesday, March 11, 2008 1:27PM - 1:39PM |
J25.00010: Raft Formation of Rod-like Polyelectrolytes Daniel W. Sinkovits, Erik Luijten We investigate the formation of raft-like aggregates by charged rod-like polyelectrolytes, as reported from experiments employing F-actin as well as from theoretical analyses. Through extensive molecular-dynamics simulations of pairs of rods at different salt concentrations we construct free-energy landscapes, which in turn elucidate the most likely kinetic pathways to aggregation. Additional simulations of layers of rods at varying skew orientations and lateral spacings demonstrate to what extent the lessons learned from pair simulations apply to large aggregates. [Preview Abstract] |
Tuesday, March 11, 2008 1:39PM - 1:51PM |
J25.00011: Vapor-liquid coexistence of patchy attractive fluids: Wertheim theory study Hongjun Liu, Sanat Kumar, Glenn Evans Our system consists of spherical particles whose pair potential contains hard core repulsion, short-ranged square well attraction and several distributed attractive patches on its surface. The simplicity of the model makes it possible to compare simulations and theoretical predictions based on Wertheim's thermodynamic perturbation theory (TPT). Wertheim's TPT is in good agreement with simulation data. In the broader parameter ranges, we show the patchy hard sphere fluids obey a generalized law of corresponding states (GLCS) and GLCS seems to hold for all patchy square well fluids with four to six interaction sites. [Preview Abstract] |
Tuesday, March 11, 2008 1:51PM - 2:03PM |
J25.00012: Strong Keratin-like Nanofibers Made of Globular Protein Yael Dror, Vadim Makarov, Arie Admon, Eyal Zussman Protein fibers as elementary structural and functional elements in nature inspire the engineering of protein-based products for versatile bio-medical applications. We have recently used the electrospinning process to fabricate strong sub-micron fibers made solely of serum albumin (SA). This raises the challenges of turning a globular non-viscous protein solution into a polymer--like spinnable solution and producing keratin-like fibers enriched in inter S-S bridges. A stable spinning process was achieved by using SA solution in a rich trifluoroethanol-water mixture with $\beta $-mercaptoethanol. The breakage of the intra disulfide bridges, as identified by mass spectrometry, together with the denaturing alcohol, enabled a pronounced expansion of the protein. This in turn, affects the rheological properties of the solution. X-ray diffraction pattern of the fibers revealed equatorial orientation, indicating the alignment of structures along the fiber axis. The mechanical properties reached remarkable average values (Young's modulus of 1.6GPa, and max stress of 36MPa) as compared to other fibrous protein nanofibers. These significant results are attributed to both the alignment and inter disulfide bonds (cross linking) that were formed by spontaneous post-spinning oxidation. [Preview Abstract] |
Tuesday, March 11, 2008 2:03PM - 2:15PM |
J25.00013: Electrospinning of Natural Polymers Aihua He, Shanshan Xu, Huarong Nie, Junxing Li, Charles C. Han Electrospinning is an effective and simple method to fabricate polymer fibers in the range of nano scale. However, electrospinning of natural polymers is a challenge. The key reason for this problem is that natural polymers have very different chain conformation and hydrodynamic responses in solution, especially in aqueous solution, when compared with synthesized polymers. The objective of our study is to find the key parameters in order to have a good control in the electrospinning process. We studied the electrospinnings of gelatin from its aqueous solution, of hyluronic acid without airblowing, and of pure alginate. It was found that electrospinning of those natural-polymer solutions could be successfully carried out when key parameters were properly adjusted, such as viscosity, elasticity (chain entanglement) and sufrace tension. [Preview Abstract] |
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