Biophysics

Courses on Biophysics provide students with physical basis of selected biological and physiological processes and with experimental skill in laboratory practice. Contemporary methods of instrumentation are also included in curricula. The education is focused on scientific method in theoretical as well as practical parts of subject.

Syllabus

Theory of Errors

Absolute error, relative error, gross error, systematic errors, random errors, mean value, standard deviation of mean value, graphic processing of results of measurements

The Measurement of Some Physical Quantities

Mass measurement – mass, weight, equal-arm balance, spring balance, torsion balance, tensometric balance – the mechanism of measurement

Density measurement –the pycnometric method of measurement of solutions and solids, hydrometer, immersed – body method - the mechanism of measurement

Measurement of viscosity – viscosity, Newton´s law of viscosity, capillary viscometers, Hagen – Poiseuille´s equation, body viscometers, Stoke´s law, Höppler´s viscometer, rotational and torsion viscometers

Heat and its measurements – heat, specific heat capacity, law of conservation of energy, electric calorimeter, heat capacity of the calorimeter

Refractometry – Snell´s law, absolute refractive index, refraction towards the perpendicular line, refraction from the perpendicular line, critical angle, Abbe´s refractometer – principle of measurement

Polarimetry – linearly polarized light, optical activity, angle of optical rotation, circle polarimeter – the principle of measurement

Spectrophotometry (measurement of light absorption) – Lambert´s law, Lambert – Beer´s law, absorptivity, absorption spectrum, calibration curve, spectrophotometer – principle of measurement

Free Radicals and the Matter

Matter - atom structure, subatomic particles, quantum numbers, the four fundamental forces of nature, energy of particles

Free radicals – the formation of free radicals, reactive oxygen and nitrogen species and the characterization of the most important representatives, the reaction of free radicals with biomolecules (lipids, proteins and DNA), Oxidative stress, Fenton´s reaction for copper and iron

Radioactivity

Radioactivity – radioactivity definitions and characterization, activity (quantity) and physical half-time, atomic number, mass number; isotopes, isobars, isotones and isomers definitions

Rays – alpha, beta and gamma radiation and their characterization

Interactions – the interaction of radiation with either atom shell or atom nucleus

Ionizing Radiation – Biological Effects and the Application in Medicine

Dosimetry – the basic dosimetry quantities

Radiobiological effects – 4-step radiobiological effect and its pathological effects on cells and tissue/organ, cell cycle, direct and indirect effects of ionizing radiation, stochastic versus deterministic effects (ARS and CRS)

Radiotherapy – sealed and open sources, Irradiators – i) gamma radiation sources, ii) particle accelerators

Radiodiagnosis – 3D scintigraphy (PET and SPECT)

X-rays

X-rays – the physical properties, X-ray tube, types of X-ray radiation, the interaction of X-ray with the matter, fluoroscopy and radiography, contrast agents

Computed Tomography – the description of the principle of the method, voxel, Hounsfield units

Ultrasound

The physical principle – the physical properties of ultrasound, transverse and longitudinal waves, acoustic impedance, the generation of echoes, intensity decrease of echoes

The imaging – A-scan, B-scan, piezoelectric and magnestrictive transducers, Motion Mode, TRSU and IVUS

Doppler shift – characterization of Doppler shift, its application in medicine (Doppler shift formula), CW and PW flowmeter, PW methods (CDI, SDR, CDE)

Ultrasound therapy – biological effects, therapy application, ATDD

Magnetic Resonance Imaging (MRI)

Magnetic properties of nucleus, electromagnetic impulse, T1 and T2 time, TR, the principle of the resonance generation, weighted images, image reconstruction principle, MRA, FMRI, MRI application

Biomembranes and transport of substances across membranes 

Biomembranes – model of fluid mosaic, function, lipid bilayer – composition and structure, micelles and liposomes – structure and importance

Transport of substances across membranes – passive transport - diffusion, Fick´s law, osmosis, osmosis pressure, Donnan´s equilibrium, active transport, group translocation, vesicular transport, facilitated transport through specific transporters 

Fluid mechanics and mechanics of flow of body fluids

Liquid dynamics - classification of liquids, flow of fluids, basic equations for ideal and Newtonian fluids – equation of continuity, Bernoulli equation, Navier – Stokes equation, viscosity, Newton law of viscosity, Hagen – Poiseuille´s law, Stoke´s law

Flow of body fluids – heart and circulatory system, cardiac cycle, blood, hydromechanical laws important for description of flow and pressure conditions in circulatory system

Mechanics of solids and basics of rheology

Solids mechanics  - classification of solids, structure of solids, deformations and mechanical stress, normal stress, tangential stress, relationship strain-stress (strain- stress curve), Hooke´s law for different types of loading 

Basics of rheology – importance, rheological classifications of bodies, viscoelasticity, rheological axioms, elementary rheological bodies and rheological models, rheological diagrams – creep curves 

Thermodynamics

State functions, process (path) functions, thermodynamics systems, ideal gas, temperature, heat, work, isothermal process, isobaric process, isochoric process, adiabatic process, reversible and irreversible processes, cyclic process, Carnot cycle 

Optics and biophysics of vision

Optics – spectrum and properties of electromagnetic radiation, electromagnetic spectrum, propagation of light, reflection and refraction of light, interference of light, diffraction of light, Huygens principle, polarization

Biophysics of vision  – structure of eye, optical system of the eye, near point, distant point, accommodation range, visual acuity, structure and function of  retina, mechanism of function of cone cells and rods cells, vision defects – myopia, hyperopia, presbyopia, astigmatism 

Acoustic and biophysics of hearing

Acoustic – acoustic waves, interference of waves, speed of propagation of acoustic waves, acoustic quantities, intensity of sound waves, loudness, acoustic impedance

Biophysics of hearing – structure and function of inner, middle and outer ear, organ of Corti, theories of hearing, hearing deficiency

Literature

  • Biophysics An Introduction (Second Edition), Roland Glaser, Springer-Verlag Berlin Heidelberg, 2012; ISBN 978-3-662-49596-4
  • Physics, Gettys et al., Mc Grow Hill Book Company, 1989, ISBN 0-07-033555-9
  • Biophysics Demystified, Daniel Goldfarb, Mc Grow Hill Book Company, 2011, ISBN 978-0-07-163364-2

Practical trainings:

  • Practical Exercises in Biophysics, Charles University, Department of Biophysics and Physical Chemistry (own edition)

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