Ion Permeation through the α-Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory

This is the published version. Copyright 2004 by Elsevier.Identification of the molecular interaction governing ion conduction through biological pores is one of the most important goals of modern electrophysiology. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) and three-dimensional Poisson-Nernst-Plank (3d-PNP) electrodiffusion algorithms offer powerful and general approaches to study of ion permeation through wide molecular pores. A detailed analysis of ion flows through the staphylococcal α-hemolysin channel based on series of simulations at different concentrations and transmembrane potentials is presented. The position-dependent diffusion coefficient is approximated on the basis of a hydrodynamic model. The channel conductance calculated by GCMC/BD is ∼10% higher than (electrophysiologically measured) experimental values, whereas results from 3d-PNP are always 30–50% larger. Both methods are able to capture all important electrostatic interactions in equilibrium conditions. The asymmetric conductance upon the polarity of the transmembrane potential observed experimentally is reproduced by GCMC/BD and 3d-PNP. The separation of geometrical and energetic influence of the channel on ion conduction reveals that such asymmetries arise from the permanent charge distribution inside the pore. The major determinant of the asymmetry is unbalanced charge in the triad of polar residues D127, D128, and K131. The GCMC/BD or 3d-PNP calculations reproduce also experimental reversal potentials and permeability rations in asymmetric ionic solutions. The weak anionic selectivity of the channel results from the presence of the salt bridge between E111 and K147 in the constriction zone. The calculations also reproduce the experimentally derived dependence of the reversible potential to the direction of the salt gradient. The origin of such effect arises from the asymmetrical distribution of energetic barriers along the channel axis, which modulates the preferential ion passage in different directions

Ion Permeation through the α-Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory

This is the published version. Copyright 2004 by Elsevier.Identification of the molecular interaction governing ion conduction through biological pores is one of the most important goals of modern electrophysiology. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) and three-dimensional Poisson-Nernst-Plank (3d-PNP) electrodiffusion algorithms offer powerful and general approaches to study of ion permeation through wide molecular pores. A detailed analysis of ion flows through the staphylococcal α-hemolysin channel based on series of simulations at different concentrations and transmembrane potentials is presented. The position-dependent diffusion coefficient is approximated on the basis of a hydrodynamic model. The channel conductance calculated by GCMC/BD is ∼10% higher than (electrophysiologically measured) experimental values, whereas results from 3d-PNP are always 30–50% larger. Both methods are able to capture all important electrostatic interactions in equilibrium conditions. The asymmetric conductance upon the polarity of the transmembrane potential observed experimentally is reproduced by GCMC/BD and 3d-PNP. The separation of geometrical and energetic influence of the channel on ion conduction reveals that such asymmetries arise from the permanent charge distribution inside the pore. The major determinant of the asymmetry is unbalanced charge in the triad of polar residues D127, D128, and K131. The GCMC/BD or 3d-PNP calculations reproduce also experimental reversal potentials and permeability rations in asymmetric ionic solutions. The weak anionic selectivity of the channel results from the presence of the salt bridge between E111 and K147 in the constriction zone. The calculations also reproduce the experimentally derived dependence of the reversible potential to the direction of the salt gradient. The origin of such effect arises from the asymmetrical distribution of energetic barriers along the channel axis, which modulates the preferential ion passage in different directions

Parity effect in Al and Nb single electron transistors in a tunable environment

Two different types of Cooper pair transistors, with Al and Nb islands, have been investigated in a tunable electromagnetic environment. The device with an Al island demonstrates gate charge modulation with 2e-periodicity in a wide range of environmental impedances at bath temperatures below 340 mK. Contrary to the results of the Al sample, we were not able to detect 2e-periodicity under any conditions on similar samples with Nb island. We attribute this to the material properties of Nb.Comment: 3 pages, 3 figure

Detection of mechanical resonance of a single-electron transistor by direct current

We have suspended an Al based single-electron transistor whose island can resonate freely between the source and drain leads forming the clamps. In addition to the regular side gate, a bottom gate with a larger capacitance to the SET island is placed underneath to increase the SET coupling to mechanical motion. The device can be considered as a doubly clamped Al beam that can transduce mechanical vibrations into variations of the SET current. Our simulations based on the orthodox model, with the SET parameters estimated from the experiment, reproduce the observed transport characteristics in detail.Comment: 4 pages, 3 figure

Mu-synthesis PID control of full-car with parallel active link suspension under variable payload

This paper presents a combined μ -synthesis PID control scheme, employing a frequency separation paradigm, for a recently proposed novel active suspension, the Parallel Active Link Suspension (PALS). The developed μ -synthesis control scheme is superior to the conventional H∞ control, previously designed for the PALS, in terms of ride comfort and road holding (higher frequency dynamics), with important realistic uncertainties, such as in vehicle payload, taken into account. The developed PID control method is applied to guarantee good chassis attitude control capabilities and minimization of pitch and roll motions (low frequency dynamics). A multi-objective control method, which merges the aforementioned PID and μ -synthesis-based controls is further introduced to achieve simultaneously the low frequency mitigation of attitude motions and the high frequency vibration suppression of the vehicle. A seven-degree-of-freedom Sport Utility Vehicle (SUV) full car model with PALS, is employed in this work to test the synthesized controller by nonlinear simulations with different ISO-defined road events and variable vehicle payload. The results demonstrate the control scheme's significant robustness and performance, as compared to the conventional passive suspension as well as the actively controlled PALS by conventional H∞ control, achieved for a wide range of vehicle payload considered in the investigation

Fabrication and optical properties of nano-structured semipolar InGaN/GaN quantum wells on c-plane GaN template

High density self-assembled nanostructured semipolar (NSSP) GaN pyramids are fabricated based on c-plane GaN template by in situ silane treatment followed by high temperature treatment. Semipolar InGaN/GaN multiple quantum wells (MQWs) were subsequently grown on the NSSP GaN. Optical properties of the MQWs were studied by temperature- dependent and excitation density varied photoluminescence. It was found that the internal electric field in the NSSP MQWs were remarkably reduced in comparison with planar c-plane MQWs. The internal quantum efficiency of the NSSP MQWs was measured to be > 30% which showed potential applications in III-nitride light emitters. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58655/1/1618_ftp.pd

Study of lead adsorption on activated carbons

In this study, the removal of lead (II) from water using commercial  activated carbons from wood and coconut shell were investigated in acidic medium (pH = 4). Atomic absorption spectrometer (AAS) was used to investigate initial (C0) and (equilibrium) (Ce) solution concentrations. Powder and granular activated carbons showed different adsorption capacity. The amount of Pb2+ adsorbed reached44.58, 38.96 and 39.06 mg/g for CPA, CGA 830 and CGA 1230 respectively at 25 °C. Langmuir and Freundlich adsorption models were used to represent the equilibrium data. Despite the high value of coefficient (R2) from Freundlich model, the best interpretation for the experimental data was given by the Langmuir model. The work showed that using powder activated carbon from wood exhibited relatively high adsorption capacity than activated carbon from coconut shell.Keywords: Lead, activated carbon, adsorption, Langmuir, isotherm