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# BIF

**Course:** Biophysics

**Department/Abbreviation:** KBF/BIF

**Year:** 2021

**Guarantee:** 'prof. RNDr. Jan Nauš, CSc.'

**Annotation:** The goal of this course is to present the basics of biophysics for students of other specializations. The basic disciplines of physics are repeated and necessary mathematical tools introduced. The introductory parts and examples of biomechanics, equilibrium and non-equilibrium thermodynamics, synergetics and theory of information are presented. Physical properties and effect in biological membranes are described together with the membrane transport, electrical phenomena including action potential, electrostatic interaction of molecules and electric organs of fishes. Magnetic phenomena and the principles of magnetic resonance spectroscopies are described, the optical effects in living matter and the effect of polarized light explained. The basic ideas of quantum mechanics, excitation energy transport and spectroscopies are formulated.

**Course review:**

1) Mathematical basics.
2) Biomechanics. Newton´s laws. Work, potential energy, potential. Conservation laws of energy and momentum. ? and stability. Rotational movement. Conservation of the angular momentum. Vibrational movement. Linear harmonic oscillator. Relaxation and resonance. Statics and kinematics of bones and joints. The muscular contraction. Molecular dynamics. Friction. Elastic deformation of solids. Models of visco-elastic behavior of matter. Sound and hearing.
3) Biophysics of fluids. Surface tension and capillary forces. Laws of the fluid streaming. Viscosity. Biophysics of the blood circulation. Biophysics of lungs.
4) Biothermodynamics. Classic equilibrium thermodynamics. First law of thermodynamics. Derivation and properties of entropy. Statistical interpretation of entropy. Thermodynamic potentials. Chemical potential. Water potential and water transport in plants. Reversible and irreversible processes. The third law of thermodynamics. Phase transitions. Non-equilibrium thermodynamics. Onsager´s law of reciprocity. Entropy in biology. The Prigogine´s postulate. The LeChatelier principle. Theoretical formulation of J´and X´. Diffusion , conduction and generation of heat.
5) Statistical physics. The distribution functions. Fluctuations and evolution.
6) Synergetics. The evolutionary equations, systems of one or two components. Bifurcation. Limit cycle. Dissipative structures. Solitons. Oscillations in biology. Information.
7) Biological membranes. Membrane structure. Phase transitions in lipid layer, arrangement. Motions of the membrane (diffusion, rotation, fluctuations). Membrane transport, selective channels, porins. Conjugated transports.
8) Electrical phenomena. Electric potential, voltage, current and capacity. Electrical properties of membranes. Concept of membrane potential. Nernst equation and other equations. Action potential and its spreading. Voltage-gated ion channels. Electrostatic interactions of biomolecules. Electric organs.
9) Magnetic phenomena. The nature of magnetic field and its properties. Magnetic moment of an atom and of electronic systems. Magnetic resonance and imaging.
10) Optical phenomena. Electromagnetic radiation. Quantum (photoelectric effect). Effect on living systems (UV, VIS, IR). Absorption and scattering effects. Classical optics in biology (focus, light guides, total reflection). Optical equations. Polarized light (detection in biology). Spectroscopic methods ATR, CD, and ORD. Laser and laser spectroscopy. Holography.
11) Quantum mechanics. The nature of the theory. Wave function and its significance. Schroedinger equation. Tunnel effect. Perturbation theory. Fermi golden rule. Uncertainty relations.
12) Excitation energy transfer. Resonance and non-resonance energy transfer.
13) Transfer of electrons and protons. Redox potential. Electron transport in protein systems. Chemiosmotic hypothesis. Principles of bioenergetics.
14) Spectroscopies. Translational, rotational, vibrational and electronic states of molecules and related spectroscopies.
15) Luminescence. Types of luminescence. Jablonski scheme. Fluorescence and phosphorescence, chemiluminescence and bioluminescence. Thermoluminescence. Parameters of luminescence and their measurements. Quantum yield. Quenching of luminescence. Recombination phenomena.