Lesson 1. Introducton to Biophysics.
Introduction to Biophysics
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Biology studies living things, whereas Physics studies nonliving matter
Biophysics is the application of physics to biology
Biophysics helps in understanding biological systems
Biophysics covers various domains such as statics, bone and tissue, dynamics, motility, transport, fluid mechanics, electrodynamics, cells and membrane, thermodynamics, metabolism, quantum mechanics, chemical and molecular bonds, statistical mechanics, protein folding, chaos and nonlinear dynamics
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Biophysics enables the production of new devices and instruments for biological research, medical diagnosis, and treatment
Biophysical methods examine the structure-function connection in proteins, organelles, cells, and body parts
Scientists Feynman and Zhabotinsky emphasized the importance of atoms and vibrations in understanding biological processes
The human body emits electromagnetic waves and can be studied using biophysical methods
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Biophysics formulates and explains problems of living organisms using the concepts and principles of physics
Ibn-i Sina and Leonardo da Vinci made early applications of mechanics to understand the movements of living things
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Ibn-i Sina classified mechanics under mathematics and described various machines involved in human and skeletal movements
Ibn-i Sina's work included the study of the blood circulatory system
Leonardo da Vinci analyzed human movement, including joints, muscles, bones, ligaments, tendons, and cartilages
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Biophysics provides tools and methods for biology and medicine
Biophysics formulates and explains problems of living organisms using physics concepts and principles
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Early applications of mechanics to understand the movements of living things can be seen in the works of Ibn-i Sina and Leonardo da Vinci
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Ibn-i Sina, also known as Avicenna, classified mechanics under mathematics and described various machines involved in human and skeletal movements
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Ibn-i Sina's work included the study of the blood circulatory system
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Avicenna's books on medicine were published in Venice in the 16th century
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Leonardo da Vinci analyzed human movement, including joints, muscles, bones, ligaments, tendons, and cartilages
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Leonardo da Vinci's famous drawing depicted the muscles and their connections in the human body
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All bodies, living and non-living, are made up of atoms
Biomolecules, cells, and tissues can be understood through the movements and interactions of atoms and molecules
The structure of atoms and the properties of the water molecule are important in understanding living and non-living matter
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Rutherford's model of an atom explained the existence of the atomic nucleus
The planetary model of an atom explained the orbiting of electrons around the nucleus
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Bohr's model proposed that atoms have stationary energy states
Transition of electrons between energy orbits causes emission or absorption of electromagnetic radiation
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Atoms are electrically neutral because the positive charge of the nucleus and the negative charge of electrons compensate each other.
Atomic nucleus consists of protons with a positive charge and neutrons with a neutral charge.
Proton and neutron masses are very close and about 2000 times that of an electron.
Electron charge is negative.
Electron cloud is the distribution of the electron space probability density within the atom.
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The water molecule (H2O) determines the polarity of water and its interaction mechanism with other molecules.
The water molecule consists of two hydrogen (H) atoms and one oxygen (O) atom.
The angle between the H atoms in the water molecule is 105°3'.
The distance between the centers of the H and O atoms is 0.1nm.
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Water vapor is a gas consisting of water molecules.
Water vapor molecules are chaotically moving and do not interact with each other except for random collisions.
The concentration of H2O vapor molecules in air at 60% humidity and 22°C temperature is approximately 1%.
The distance between the H atoms in the water molecule can be calculated using the given angle and distance between the H and O atoms.
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Liquid water molecules are in limiting motion and weakly bound.
The force between water molecules is attractive at relatively large distances and repulsive at small distances.
Molecules of ice are strongly bound and form a crystalline structure.
The hexagonal structure is seen in ice and tiny pieces of snow.
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At the triple point temperature and pressure, matter can exist in three states: gas, liquid, and solid.
The critical point is the end point of the liquid-gas phase transition.
The phase states of water (or other matter) depend on temperature and pressure.
The phase diagram illustrates the transitions between different states of matter.
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At pressures higher than the critical point, the vapor state is not realized.
At temperatures higher than the critical point, the liquid state is not realized.
Water is the most important component of living cells.
About 70% of the weight of animals consists of water.
Bones carry solid properties due to the solidification of cells with calcium.
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Control questions related to the forces between molecules, pT phase diagram, triple point, values of p and T for water at the triple point, and solid-liquid phase equilibrium curve.
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Physical models are used to study biological systems.
Animals are composed of 70% water by weight, exhibiting fluid properties.
Cell membranes have properties similar to liquid crystals.
Liquid crystal models are used to learn the functions of cell membranes.
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Cell extrusion and its underlying mechanism are explored using the model of an active nematic liquid crystal.
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Comparison of the structures of cell membrane and liquid crystal.
Lipid molecules, phosphate heads, fatty acid tails, membrane proteins, and water molecules in the cell membrane.
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The cell membrane acts as an insulating capacitor surrounded by intracellular and extracellular ions.
The membrane capacitance and resistance are required for studying the propagation of electrical signals in nerve cells.
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Physical model of the electrical signal traveling across the cell membrane via ion transport.
Resistance and capacitance of the membrane, intracellular substance resistance, and extracellular resistance.
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Examples of applications such as the light microscope, X-ray structure analysis, and X-ray imaging technique.
The resolution of the optical microscope is limited by diffraction effects.
X-ray structure analysis allows imaging of objects in smaller sizes.
The diffraction condition of X-rays in the crystal is expressed by the Bragg formula.
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Typical light microscope can resolve features as small as 2x10^-7m
Comparable to the wavelength of light
View of water bacteria in light microscope with typical magnification of 2000 times
Image of single-celled organisms (freshwater algae) of size 0.2mm seen in microscope
Eyepiece or Ocular
Objective
Object
Light source
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X-ray structure analysis technique
Dark bands arranged in the shape of a cross are the first evidence of the helical structure of the DNA molecule
Diffraction condition of X-rays in the crystal expressed by the Bragg formula 2d sinθ = mλ (m = 1, 2, 3, ...)
λ is the wavelength of the X-rays
d is the interatomic distance
θ is the characteristic angle
X-rays have wavelengths about 1000 times shorter than optical rays
Electron microscope uses electron beam to take images like a beam of light
Resolution of the image is limited by the de-Brogle wavelength λ=h/p of the electron beam
h is Planck's constant
p is linear momentum
Diffraction image of DNA molecule with X-rays
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Question 1: Which image size (in mm) will be seen an object in the light microscope if its real size is at the limit of the resolvable size of 2x10^-7m?
Answer 1: Microscope with 2000 times of magnification will give an image of the object of size 2x10^-7m as: 2000 x 2x10^-7m = 4x10^-4 x 10^3 mm = 0.4mm
Question 2: In the figure, it is shown an image of the freshwater algae of size 0.2mm. Vertical size of the photo (the black background) is such that it may contain an image of five algae. What is the size of the inspected part of a sample (object)?
Answer 2: Inspected part of a sample has a size of 5 x 0.2mm = 1mm
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X-Ray Absorption and Medical Imaging
X-ray image of a human
Emission and absorption of photons (or electromagnetic waves) by the atom based on Bohr's postulates
Atomic electrons can absorb photons of varying wavelengths, including X-rays
Atoms with many electrons absorb X-rays better than atoms with few electrons
X-ray imaging shows dark regions where the rays are slightly absorbed (soft tissues containing H, C, O atoms with few electrons) and bright regions where the rays are absorbed more (bone tissues with more electrons, P and Ca)
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Panoramic x-ray is a type of tomographic x-ray
All teeth and jawbone are viewed together with less radiation
Used to show parts of the teeth, bones, and gums not visible by clinical examination
Use of digital system increases image quality and significantly reduces radiation received by the person
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Literature:
Physics in Biology and Medicine, Paul Davidovits, Academic Press, Elsevier, 2008.
Intermediate Physics for Medicine and Biology, Second edition, R.K. Hobbia, John Willey and Sons, 1988
Biophysics, An introduction, R.M.J. Cotterill, Danish Technical University, Denmark, John Wiley and Sons, 2002.
Biophysics: A Physiological Approach, P.F. Dillon, Cambridge University Press, 2012.
Methods in Modern Biophysics, Second edition, B.Nölting, Springer, 2006.
Ferit Pehlivan, Biyofizik. Yenilenmiş 8. Baskı, Pelikan Kitabevi, Ankara, 2015.
Additional Literature:
The Feynman Lectures on Physics, volume I-II, R.P. Feynman, B. Leigh-ton, M. Sands, Addison-Wesley, 1963.
University Physics with Modern Physics, Thirteen edition, H.D. Young, R. A. Freedman, A. Lewis Ford, Addison-Wesley, 2012.
Molecular Biology of The Cell, Fourth edition, A Problems Approach. John Wilson and Tim Hunt, Garland Science, New York and Londaon, W.H.Freeman and Company, New York, 2002.