Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session F5: Physics at Bio-Nano Interface IIFocus
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Sponsoring Units: DBIO DPOLY Chair: Binquan Luan, IBM T. J. Watson Research Center Room: 264 |
Tuesday, March 14, 2017 11:15AM - 11:51AM |
F5.00001: Large Scale Molecular Simulation of Nanoparticle-Biomolecule Interactions and their Implications in Nanomedicine Invited Speaker: Ruhong Zhou Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects and related molecular mechanism/physics as well. In this talk, I will discuss some of our recent works, mostly molecular modelling, on nanotoxicity and their implications in de novo design of nanomedicine. We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins. The hydrophobic interactions between the carbon nanotubes and hydrophobic residues, particularly aromatic residues through the so-called $\pi $-$\pi $ stacking interactions, are found to play key roles. Meanwhile, metallofullerenol Gd@C82(OH)22 is found to inhibit tumour growth and metastases with both experimental and theoretical approaches. Graphene and graphene oxide (GO) nanosheets show strong destructive interactions to E. coli cell membranes (antibacterial activity) and A$\beta $ amyloid fibrils (anti-AD, Alzheimer's disease, capability) with unique molecular mechanisms, while on the other hand, they also show a strong supportive role in enzyme immobilisation such as lipases through lid opening. In particular, the lid opening is assisted by lipase's sophisticated interaction with GO, which allows the adsorbed lipase to enhance its enzyme activity. The lipase enzymatic activity can be further optimized through fine tuning of the GO surface hydrophobicity. These findings might provide a better understanding of ``nanotoxicity'' at the molecular level with implications in de novo nanomedicine design. [Preview Abstract] |
Tuesday, March 14, 2017 11:51AM - 12:03PM |
F5.00002: Heat generation and nanoscale thermal transport in thermo-magnetic genetic cellular stimulation Rahul Munshi, Idoia Castellanos-Rubio, Arnd Pralle Magnetic nanoparticles act as heat sources, when exposed to alternating magnetic fields, creating steep temperature gradients around them. We studied the capabilities of various geometrical distribution of such particles to be efficient transducers for stimulating cellular signaling, upon magnetic field application. We tagged synthesized core-shell nanoparticles with fluorescent dye molecules and attached them via membrane proteins, effectively creating a sheet of particles, wrapped around the cellular membrane. Exploiting the thermo-sensitivity of fluorescent proteins, we systematically studied temporal evolution of temperature gradients with magnetic fields, by monitoring fluorescence intensity changes on the particles confined to particular geometrical arrangements, on cells as well as in fabricated polymer matrices. We also studied the impact of magnetic dipolar interactions on heat generation in tightly packed self-assemblies, like particle chains in magnetotactic bacteria. Lastly, we show how nanoparticles can be targeted with specificity to deep brain neurons to evoke remotely stimulated behavioral changes in awake mice. [Preview Abstract] |
Tuesday, March 14, 2017 12:03PM - 12:15PM |
F5.00003: Nano-plumbing with two-dimensional metamaterials Saroj Dangi, Robert Riehn It is well known that if a DNA molecule is confined to a nanochannel of size less than the radius of gyration of the molecule, the entropy of the molecule is lowered and it is forced to stretch at equilibrium. Here we present the transport of DNA molecules in two dimensional metamaterials which are made up of symmetric lattices formed by intersecting arrays of nanochannels. In this study, we introduce a hexagonal unit cell with asymmetries in channel widths, where some channels are flow free. We demonstrate a DNA concentrator and a structure for buffer exchange of a single molecule. The mechanism will be explained as a combination of flow forces and confinement energies, that can be independently set within the device. [Preview Abstract] |
Tuesday, March 14, 2017 12:15PM - 12:27PM |
F5.00004: Theory of Passive Polymer Translocation Through Amphiphilic Membranes Marco Werner, Jasper Bathmann, Vladimir Baulin, Jens-Uwe Sommer We propose a theoretical framework for examining the translocation of flexible polymers through amphiphilic membranes: A generic model for monomer-membrane interactions is formulated and the Edwards equation is employed for calculating the free energy landscape of a polymer in a membrane environment. By the example of homopolymers it is demonstrated that polymer adsorption and the symmetry of conformations with respect to the membrane's mid-plane trigger passive polymer translocation in a narrow window of polymer hydrophobicity. We demonstrate that globular conformations can be taken into account by means of a screening of the external potential, which leads to excellent agreement of predicted translocation times with dynamic lattice Monte Carlo (MC) simulations. The work opens a theoretical road-map on how to design translocating flexible polymers by referring to universal phenomena only: adsorption and conformational symmetry. As confirmed by MC simulations on amphiphilic polymers, promising candidates of translocating polymers in practice are short-block amphiphilic copolymers, which in the limit of small block sizes resemble homopolymers on a coarse grained level. [Preview Abstract] |
Tuesday, March 14, 2017 12:27PM - 12:39PM |
F5.00005: Nanopore detection of DNA molecules in crowded neutral polymer solutions Rajesh Kumar Sharma, Liang Dai, Patrick Doyle, Slaven Garaj Nanopore sensing is a precise technique for analysis of the structure and dynamics of individual biomolecules in different environments, and has even become a prominent technique for next-gen DNA sequencing. In the nanopore sensor, an individual DNA molecule is electrophoretically translocated through a single, nanometer-scaled pore in a solid-state membrane separating two chambers filled with electrolyte. The conformation of the molecule is deduced from modulations in the ionic current through the pore during the translocation event. Using nanopores, we investigated the dynamics of the DNA molecules in a crowded solution of neutral polymers of different sizes and concentrations. The translocation dynamics depends significantly on the size and concentration of the polymers, as different contributions to the electrophoretic and entropic forces on the DNA molecules come into play. This setup offers an excellent, tuneable model-system for probing biologically relevant questions regarding the behaviour of DNA molecules in highly confined and crowded environments. [Preview Abstract] |
Tuesday, March 14, 2017 12:39PM - 12:51PM |
F5.00006: Confinement Effect on Structure and Elasticity of Proteins Interfacing Polymers Haoyu Wang, Pinar Akcora E-beam patterned nanoporous PMMA thin films are used as templates for protein functionalization to study the confinement effect on structural and mechanical properties of the globular lysozyme and the rod-shaped fibrinogen. We characterize the structure and elasticity of these proteins tethered inside the pores, and discuss the relations between the concentration of attached proteins, protein orientation and conformation in different pore sizes. Adhesion force mapping measured in atomic force microscopy reveals that the end-on attached fibrinogens induce higher concentration than the side-on attached proteins. Fourier-transform infrared spectroscopic analysis of protein secondary structures and nanoindentation results show that fibrinogen undergoes less structural changes and behaves less stiff when pore size is close to the protein size, which is due to less protein-surface interactions and higher concentration of end-on attached fibrinogen in 50nm pores than other pore sizes. Lysozyme, on the other hand, retains its native-like structure and exhibits the highest modulus in 15nm pores due to the lower macromolecular crowding effect the protein faces compared to lysozyme within larger pores. [Preview Abstract] |
Tuesday, March 14, 2017 12:51PM - 1:03PM |
F5.00007: Dehydration as a Universal Mechanism for Ion Selectivity in Graphene and Other Atomically Thin Pores Subin Sahu, Massimiliano Di Ventra, Michael Zwolak Ion channels play a critical role in regulating cell behavior and in electrical signaling. In these settings, polar and charged functional groups -- as well as protein response -- give rise to ion selective transport, allowing the channels to perform specific tasks in the operation of cells. According to recent experiments, graphene nanopores can have both weak to strong selectivity, the origin of which is unclear. Here, we establish that graphene displays an alternative, novel mechanism for selectivity: Dehydration -- the most fundamental physical process in ion transport -- yields selective pores without the presence of charges or structural changes of the pore. This fundamental mechanism -- one that depends only on the geometry and hydration -- is the starting point for selectivity for all channels and pores. Its likely detection in graphene pores resolves the conflicting selectivity results, as well as opens up a new paradigm for engineering molecular/ionic selectivity in filtration and other applications. [Preview Abstract] |
Tuesday, March 14, 2017 1:03PM - 1:15PM |
F5.00008: Mesophase Assembly of Nanoscale Prisms Ziwei Wang, Zihao Ou, Qian Chen, Erik Luijten Predicting structures self-assembled from basic building blocks remains a central problem in materials design and engineering. Entropy-driven packing behavior has been studied extensively via simulations of hard objects. However, in many experimental systems intrinsic, highly anisotropic interactions play an important role as well, and can overwhelm the entropic effects of shape, especially on the nanoscale. As a result, omission of enthalpic effects in large-scale simulations leaves many essential mesophases unexplored. We perform Monte Carlo simulations of nanoscale prisms with properly modeled interactions, and demonstrate that these give rise to a novel plastic-crystal mesophase of prisms stacked with random in-plane orientations, organized on a 2D hexagonal lattice. These simulations explain direct experimental observations performed with liquid-phase transmission electron microscopy. [Preview Abstract] |
Tuesday, March 14, 2017 1:15PM - 1:27PM |
F5.00009: Nano-assays for the detection of circulating biomarkers and their interaction dynamics Loredana Casalis, Pietro Parisse, Elena Ambrosetti The availability of devices for cancer biomarker detection at early stages of the disease is one of the most critical issues in biomedicine. Towards this goal, to increase the assay sensitivity, device miniaturization strategies empowered by the employment of high affinity protein binders constitute a valuable approach. We propose here two different surface-based miniaturized platforms for biomarker detection in body fluids: the first platform is an atomic force microscopy (AFM)-based nanoarray, where AFM is used to generate functional nanoscale areas and to detect biorecognition through careful topographic measurements; the second platform consists of a miniaturized electrochemical cell to detect biomarkers through electrochemical impedance spectroscopy (EIS) analysis. Both devices rely on robust and highly-specific protein binders as aptamers or nanobodies and were tested for the detection of thrombin as well as relevant cancer biomarkers as the circulating portion of Her2. We succeeded in capturing antigens in concentrations as low as tens of pM, in conditions of real matrix (serum) and low biosample volumes ($\mu $L range). [Preview Abstract] |
Tuesday, March 14, 2017 1:27PM - 1:39PM |
F5.00010: Hierarchical organization of butterfly gyroid nanostructures provide a time-frozen glimpse of intracellular membrane development Bodo Wilts, Benjamin Winter, Michael Klatt, Benjamin Butz, Michael Fischer, Stephen Kelly, Erdmann Spieker, Ullrich Steiner, Gerd Schroeder-Turk The formation of the biophotonic gyroid material in butterfly wing scales is an exceptional feat of evolutionary engineering of functional nanostructures. Previous work hypothesized that this nanostructure forms by chitin polymerization inside a convoluted membrane of corresponding shape in the endoplasmic reticulum. In vivo imaging however cannot yet elucidate this dynamic formation process, including whether membrane folding and chitin expression are simultaneous or subsequent processes. Here we show an unusual hierarchical ultrastructure in a Hairstreak butterfly that allows high-resolution 3D microscopy. Rather than the conventional polycrystalline space-filling arrangement, the gyroid occurs in isolated facetted crystallites with a pronounced size-gradient. This arrangement is interpreted as a sequence of time-frozen snapshots of the morphogenesis. This provides insight into the formation mechanisms of the nanoporous gyroid material, especially when compared among other butterflies with different arrangements. [Preview Abstract] |
Tuesday, March 14, 2017 1:39PM - 1:51PM |
F5.00011: Unexpected Pinhole-shaped-defects in an Ultra-low-noise Solid-state Nanopore: Generation Mechanism and Prevention Methods Kazuma Matsui, Yusuke Goto, Itaru Yanagi, Yoshimitsu Yanagawa, Yu Ishige, Ken-ichi Takeda To achieve DNA sequencing with a solid-state nanopore, it is necessary to reduce the electric noise current by lowering the device capacitance. However, we found that pinhole-shaped defects are unexpectedly generated with ultralow capacitance devices. These defects surprisingly attributes to uncontrolled dielectric breakdown in an ultrathin membrane, induced by electric charge imbalance between chambers. Furthermore, theoretical analysis reveals that the charge imbalance mainly originates from the static charge on the surface of a flow cell outside the chambers. We also demonstrated that the generation of defects could be prevented by two methods: to remove static charge using an anti-static agent and to cancel the electric charge imbalance by connecting bypass wiring between the chambers. [Preview Abstract] |
Tuesday, March 14, 2017 1:51PM - 2:03PM |
F5.00012: Modeling Adsorption Based Filters (Bio-remediation of Heavy Metal Contaminated Water) Chris McCarthy I will discuss kinetic models of adsorption, as well as models of filters based on those mechanisms. These mathematical models have been developed in support of our interdisciplinary lab group, which is centered at BMCC/CUNY (City University of New York). Our group conducts research into bio-remediation of heavy metal contaminated water via filtration. The filters are constructed out of biomass, such as spent tea leaves. The spent tea leaves are available in large quantities as a result of the industrial production of tea beverages. The heavy metals bond with the surfaces of the tea leaves (adsorption). The models involve differential equations, stochastic methods, and recursive functions. I will compare the models' predictions to data obtained from computer simulations and experimentally by our lab group. [Preview Abstract] |
Tuesday, March 14, 2017 2:03PM - 2:15PM |
F5.00013: Kinetically controlled transition from disordered aggregates to ordered lattices of a computationally designed peptide sequence. Yu Tian, Huixi Zhang, Kristi Kiick, Jeffrey Saven, Darrin Pochan Peptides with well-defined secondary-structures have the ability to exhibit specific, local shapes, which enables the design of complex nanostructures through intermolecular assembly. Our computationally designed coiled-coil homotetrameric peptide building block can self-assemble into 2-D nanomaterial lattices with predetermined symmetries by control of the coiled-coil bundle exterior amino acid residues. And the assemblies can be controlled kinetically. Firstly, the solution pH influences the assembly by affecting the external charged state of peptide bundles which can lead the bundles to be either repulsive or attractive to each other. At room temperature when peptides are under the least charged pH conditions, disordered aggregates are formed that slowly transformed into the desired 2-D lattice structures over long periods of time (weeks). Around neutral pH, even subtle charge differences that come from small pH changes can have an influence on the thickness of afterwards formed plates. Secondly, the solution temperature can largely eliminate the formation of disordered aggregates and accelerate the assembling of matured, desired nanomaterial plates by providing extra energy for the organization process of assembly building blocks. The ability to control the assembly process kinetically makes our peptide plate assemblies very promising templates for further applications to develop inorganic-organic hybrid materials. [Preview Abstract] |
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