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Biological and Chemical Physics Commons™

Open Access. Powered by Scholars. Published by Universities.®

City University of New York (CUNY)

2017

Articles 1 - 4 of 4

Full-Text Articles in Biological and Chemical Physics

Stochastic Resonance In A Proton Pumping Complex I Of Mitochondria Membranes, Davneet Kaur, Ilan Filonenko, Lev Mourokh, Cornelius Fendler, Robert H. Blick Sep 2017

Stochastic Resonance In A Proton Pumping Complex I Of Mitochondria Membranes, Davneet Kaur, Ilan Filonenko, Lev Mourokh, Cornelius Fendler, Robert H. Blick

Publications and Research

We make use of the physical mechanism of proton pumping in the so-called Complex I within mitochondria membranes. Our model is based on sequential charge transfer assisted by conformational changes which facilitate the indirect electron-proton coupling. The equations of motion for the proton operators are derived and solved numerically in combination with the phenomenological Langevin equation describing the periodic conformational changes. We show that with an appropriate set of parameters, protons can be transferred against an applied voltage. In addition, we demonstrate that only the joint action of the periodic energy modulation and thermal noise leads to efficient uphill proton …

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Continuum Electrostatics Analysis Of The Kok Cycle Of Photosystem Ii, Witold Szejgis Sep 2017

Continuum Electrostatics Analysis Of The Kok Cycle Of Photosystem Ii, Witold Szejgis

Dissertations, Theses, and Capstone Projects

The Kok cycle is catalytic process by which the oxygen-evolving complex (OEC) of photosystem II (PSII) oxidizes two water molecules forming oxygen. Four OEC oxidation states (S0 to S3) in the Kok cycle precede the final product formation in the S4 state. Here a semi-empirical classical electrostatics analysis is applied to S0 to S3 states of the OEC is used to estimate the electrochemical midpoints for each S-state transition and the proton loss coupled to oxidation. To account for geometrical rearrangement within the cluster during Kok cycle optimized QM/MM geometries are used for each …

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Second Harmonic Generation – A Novel Approach In Retinal Imaging, Denis Y. Sharoukhov Feb 2017

Second Harmonic Generation – A Novel Approach In Retinal Imaging, Denis Y. Sharoukhov

Dissertations, Theses, and Capstone Projects

Here we present the utilization of Second Harmonic Generation (SHG) for label-free imaging of microtubules (MTs) in the retinal nerve fiber layer (RNFL). MTs are an important part of axonal cytoskeleton, providing structural support and serving as a railroad in intracellular transport. We demonstrate the application of SHG microscopy to the following studies: 1) Can changes in MT conformation be detected when treated with a stabilizing drug (Taxol); 2) if disruption in MT precedes loss of axons in a mouse model of glaucoma (DBA/2J); and 3) if elevated levels of intraocular pressure affect MT integrity. Our results validate SHG imaging …

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Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian Jan 2017

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

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