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Cellular Biophysics

 

Elective Course for undergraduate students (Semester A, Semesters 5/7)

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  • Introduction: basic concepts in thermodynamics, combinatorics and statistics and biology, Miller Urey experiment, hydrophobicity, hydrogen bonds, Gibbs free energy.

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  • Experimental Systems/techniques: FRAP, Diffusion weighted NMR, Function MRI (fMRI), voltage clamp, current clamp, space clamp, magnetoencephalography (MEG), electroencephalography (EEG).

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  • Water: Fick's equation, diffusion equation, diffusion to capture, Einstein's relation, mass conservation law, Einstein-Smoluchowski equation, Newtonian fluids, Navier-Stokes equations, Reynolds number, viscosity, density, material derivative, low Reynolds number, Stokes Equation, reciprocal motion.

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  • Salty water: Electrostatics in Salty water, Poisson Boltzmann Equation, Debye-Hückel equation, Debye length, Bjerrum length, mean-field theory.

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  • Statistical Mechanics: microstates, macrostates, ensembles, canonical partition function, grand canonical partition function, Boltzmann distribution, Gibbs distribution, average energy, chemical potential, two-state systems, multiple state systems, cooperativitym, Pauling model, Hill equation.

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  • Electro-diffusion: Nernst-Planck equation, electrical mobility, Nernst potential, Faraday constant, Goldman-Hodgkin-Katz equation, permeability, ionic flux, ion pumps, ion channels.

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  • Hodgkin-Huxley equation: first order ion channel dynamics, rate equations, ion channels conductance, action potential, depolarization, repolarization, voltage gated ion channels, passive cable model, Saltatory conduction.

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  • Molecular Motors: translational motors, rotary motors, molecular transport, average displacement, Randomness parameter.

 

Multi-cellular networks (if time permits):

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  • Immunology: evolution and ecology, immune system, system of differential equations, equilibrium points – stable/unstable, Lotka-Volterra model.

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  • Neural Networks: basic concepts in graph theory, connectivity, Perceptron model, adaptiveness, Small World networks, Gradient Descent.

 

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Introduction To Magnetic Resonance Imaging

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Elective Course for undergraduate students (Semester B, Semesters 6/8)

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The objective of the course is to familiarize the students with the MRI technology and its principles of operation. Students will learn about the physical basis, the engineering, and the clinical and research-wise applications of MRI.
Students will understand pulse-sequences, will know how to analyze the results of MRI experiments, will calculate the MR decay coefficients and will be 'smart users' in MRI experiments.
The course will be based on frontal lectures, and exercises that will include analysis of real MRI data.

The course covers the following subjects:

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  • Physical basis: the nuclear spin, classical and quantum description of the NMR phenomenon, Bloch equation, decay mechanisms (T1, T2, T2*).

  • Pulse sequences (Hahn spin echo, CP, CPMG, IR, Gradient echo), measurement of NMR parameters.

  • MRI: Fourier imaging, the concept of k-space, frequency and phase encoding, k-space in time domain and in spatial frequencies domain, imaging noise and artifacts, techniques for fast imaging.

  • Specific MRI applications: Diffusion weighted and Diffusion tensor imaging, functional imaging using the BOLD contrast, flow imaging and angiography, contrast agents.

  • Hardware: basic MR hardware (magnets, RF and gradient coils, receiver and A2D conversion, cooling), parallel coils, safety.

  • Basic MR Spectroscopy: Chemical shift, J-coupling, H-coupling experiment, COSY.

 

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Advanced Lab in Biomedical Engineering ​

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Lab Goals:

  • Direct and practical experience in biomedical systems and signals, including their challenges (e.g complex and time variant signals, signal and noise and multiple signal sources)

  • Learning advanced subjects in bio-medical engineering 

  • Acquiring Experience in open-end problem solution, as in academia and the industry 

  • Acquiring Experience in comprehension of scientific literature and scientific research writing format        

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Work Standards:

  • Work is conducted in pairs, each pair will conduct three experiments each is 3-4 weeks in length, the work includes:

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  • A week of learning relevant theory, done before the lab.

  • Two weeks of conducting the experiment, including an entry exam

  • A week to write a report, in English and in academic format

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Experiments:

  • The experiments include built experiments, as well as experiments designed by the students. Emphasis is put on solving open ended problems, and unique challenges for each pair. The experiments include:

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  • Video Processing

  • NMR

  • Bio - Signal processing

  • Ultrasound

  • Heart rate measurements

  • Interference microscopy  

  • Optical property measurements

  • Tissue 3D printing

  • Cell microscopy

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Grading:

  • The course has no final exam, the final grade is the average grade over the three experiments, grades are composed of:  

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  • Entry exam grade

  • Lab performance grade 

  • Final report grade

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Research Seminar​

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  • This course is offered only for graduate students in the track for a Master's degree with no thesis. Students perform a mid-size research project over a whole year. Grades will be based on the student's performance in conducting the research.

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