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Workshop "Nanostructures in biology and physics"

Location: WPI, Seminarroom C 714 Mon, 21. Jul - Fri, 25. Jul 08
Remark: Click HERE for the programme.

Talks in the framework of this event

Blick, Robert WPI, Seminarroom C 714 Tue, 22. Jul 08, 9:30
"Radio-Frequency Rectification and Transmission on Bilipid Membrane bound Pores"
We present measurements on direct radio-frequency pumping of ion channels and pores bound in bilipid membranes. We make use of newly developed microcoaxes, which allow delivering the high frequency signal in close proximity to the membrane bound proteins and ion channels. We find rectification of the radio-frequency signal, which is used to pump ions through the channels and pores.
  • Event: Workshop "Nanostructures in biology and physics" (2008)

Prada, Marta WPI Seminarroom C 207 Tue, 22. Jul 08, 10:45
"Long- lived states in Si- based quantum computing nanoarchitecutres"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Poghossian, Arshak WPI Seminarroom C 207 Tue, 22. Jul 08, 13:30
"Label-free detection of charged macromolecules with field-effect devices: Possible mechanisms of signal generation"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Ertl, Peter WPI, Seminarroom C 714 Wed, 23. Jul 08, 9:30
"Monitoring cytotoxicities of nanoparticles using a lab-on-a-chip"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Heitzinger, Clemens WPI, Seminarroom C 714 Wed, 23. Jul 08, 10:45
"Multi- scale modeling and simulation of field- effect biosensors"
BioFEDs (biologically sensitive field-effect devices) are field-effect biosensors with semiconductor transducers. Their device structure is similar to an ISFET (ion-selective field-effect transistor), but the surface of the transducer is functionalized with receptor molecules. Conductance modulations of the transducer after binding of the analyte to the surface receptors provide the detection mechanism. The main advantage of BioFEDs is label-free operation.

In recent experiments, DNA strands and tumor markers were detected by silicon-nanowire devices. Despite the experimental successes, a quantitative theory to explain the functioning of the biosensors and to understand the experiments has been missing. The modeling of the biosensors is complicated by the fact that they consist of a biomolecular and a nanoelectronic part with different length scales, yet both parts have to be considered self-consistently.

We present the first self-consistent model for the quantitative analysis of BioFEDs. It is centered around a multi-scale model involving homogenized interface conditions for the Poisson equation for cylindrical and planar geometries (i.e., for nanowires and nanoplates). The mathematical analysis shows that not only the surface charge density, but also the dipole moment density of the biofunctionalized surface layer influences the conductance of the transducers. These simulation results are the first quantitative explanation of the functioning of BioFEDs.
  • Event: Workshop "Nanostructures in biology and physics" (2008)

Rempe, Susan WPI Seminarroom C 207 Wed, 23. Jul 08, 13:30
"Ion Discrimination by Nanoscale Design"
Natural systems excel at discriminating between molecules on the basis of subtle differences. Membrane-spanning protein channels, for example,are exquisitely designed to differentiate between Na+ (sodium) and K+(potassium) ions despite their identical charges and only sub-Angstrom differences in size. Consequently nearly all cells can selectively transport these ions across their membranes, a process that underlies such diverse physiological tasks as nerve cell signaling, heart rhythm control, and kidney function.
While scientists have long known that ion selectivity lies in the ability of the channel to satisfy or frustrate ion solvation requirements, the persistent question revolves around how channels and other biological structures give rise to such a subtle effect between Na+ and K+. By understanding ion discrimination in natural systems, we can potentially learn how to harness nature’s design principles in nano-scale devices that mimic biological function for varied applications, including fast, efficient water desalination. Here we present a novel explanation for ion discrimination in the celebrated potassium-selective protein channels, we contrast this explanation of natural ion discrimination with the unexpectedly antithetical mechanism found in a natural potassium-selective ion carrier, and finally we describe current work toward implementing ion selectivity in synthetic channels.

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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Deszo, Boda WPI Seminarroom C 207 Wed, 23. Jul 08, 14:45
"Double layers are everywhere"
lectrical double layers (DL) are formed in a phase containing mobile charge carriers near a charged surface. Depending on the material carrying the mobile charges, DLs appear in electrolytes, molten salts, ionic liquids, plasmas, and even fast ion conductors (solid electrolytes). DLs in solutions of dissolved ions have special importance in electrochemistry, biology, and colloid chemistry. DLs near electrodes are different from DLs near charged objects carrying fixed surface charge (such as colloids, macromolecules, porous bodies) because the surface charge on the electrode can be controlled by applying an external voltage.
The electrical DL was a topic of extensive research using various methods from the Poisson-Boltzmann theory to state of the art statistical mechanical methods such as density functional theory. Recently, computer simulations became the dominant tool to study DLs according to their flexibility and accuracy. To exploit the advantages of symmetry, studies of DLs are commonly performed in the planar geometry where the elctrolyte is located between two charged surfaces. Monte Carlo simulations can be performed in the constant charge ensemble (where the surface charges on the elecrodes are fixed) or in the constant voltage ensemble (where the potential difference between the electrodes is fixed). It is advantageous to simulate the electrolyte in the grand canonical ensemble where the chemical potentials of the various ionic species are fixed. An overview of these various simulation techiques with a general introduction to Monte Carlo simulations will be given.
Simulations provide the charge density in the simulation cell from which the potential profile in the DL is computed by solving Poisson's equation using appropriate boundary conditions. The use of various boundary conditions (Neumann, Dirichlet) will be discussed in relation to the ensemble used in the simulation. Results for various situations and comparison with various theories will be presented.
Examples include the behavior of the DL capacitance at low temperatures, the effect of asymmetries of size and charge of ions on the DL potential, the competition of various ions at a higly charged electrode, the structure of the DL at dielectric interfaces, the effect of DL structure on the conductance of nanopores, and the importance of DLs in the behavior of ion channels.
  • Event: Workshop "Nanostructures in biology and physics" (2008)

Gillespie, Dirk WPI Seminarroom C 207 Thu, 24. Jul 08, 9:30
"Energetics of ion selectivity in a biological calcium-selective ion channel"
A model of the ryanodine receptor (RyR) calcium-selective biological ion channel is used to study the energetics of ion binding selectivity (i.e., ion adsorption). RyR is a calcium-selective channel with four aspartates (a DDDD locus) in the selectivity filter, similar to the four glutamates (the EEEE locus) of the L-type calcium channel. While the affinity of RyR for Ca2+ is in the millimolar range (as opposed to the micromolar range of Ca2+ the L-type channel), the ease of single-channel measurements compared to L-type and its similar selectivity filter make RyR an excellent candidate for studying calcium selectivity.
A Poisson-Nernst-Planck/Density Functional Theory model of RyR is used to calculate the energetics of selectivity. In RyR, ion selectivity is driven by the charge/space competition mechanism in which selectivity arises from a balance of electrostatics and the excluded volume of ions in the crowded selectivity filter.
While electrostatic terms dominate Ca2+ selectivity, the much smaller excluded-volume term also plays a substantial role. In the D4899N mutation of RyR that is analyzed, substantial changes in specific components of the chemical potential profiles are found far from the mutation site. These changes result in the significant reduction of Ca2+ selectivity found in both theory and experiments.
  • Event: Workshop "Nanostructures in biology and physics" (2008)

Karlic, Heidrun WPI, Seminarroom C 714 Thu, 24. Jul 08, 10:45
"Nano- targets in cancer stem cells"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Vasileska, Dragica WPI Seminarroom C 207 Thu, 24. Jul 08, 13:30
"Quantum and Thermal Effects in Nanoscale Devices"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Roth, Roland WPI Seminarroom C 207 Thu, 24. Jul 08, 14:45
"Density Funtional Theory as a Tool to study Nanostructures in Physics and Biology"
Density functional theory (DFT) of classical systems provides a versatile and powerful framework to study on equal footing inhomogeneous density distribution and thermodynamics of nanostructures. The key problem of DFT is to construct and to test the accuracy of a functional that allows one to describe the system of interest, characterized by its interparticle interaction. Once a DFT for a given system is constructed, the system can be studied in any external field by minimizing the DFT.

In this talk I will give a brief introduction into the general formalism of DFT and present a density functional for charged hard spheres. The DFT for charged hard spheres allows one to study packing effects at high densities and short distances as well as screening of the electric field at larger distances. Applications to biological problems are outlined.
  • Event: Workshop "Nanostructures in biology and physics" (2008)

Baurecht, Dieter WPI, Seminarroom C 714 Fri, 25. Jul 08, 9:30
"Investigation of the arrangement of biomolecules on Si and Ge surfaces by FTIR- ATR spectroscopy"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

Valisko, Monika WPI Seminarroom C 207 Fri, 25. Jul 08, 10:45
"Competition of Steric Repulsion and Electrostatic Attraction: Determines the Selectivity of Calcium Channels"
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  • Event: Workshop "Nanostructures in biology and physics" (2008)

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