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Basic Physics and Chemistry
1. The Atom and Subatomic Particles
• Quantum Theory (=quantum mechanics, QM)
– most fundamental framework for understanding nature
– marked the end of scientific determinism (there is always some
unpredictability)
– basis for electronics, nanotechnology and structural biology,
may be also thinking?
– quantum – indivisible packet of energy, for ex. photon (for EM
radiation such as light); from Latin "quantus," for "how much“
– Atomic Theory:
• first conceptualized by philosophers: the Hindu Kanda in 6th
century BCE, and the Greek Democritus in 5th century BCE:
“atom” means “indivisible”
• concept borrowed by chemists in 19th century
• physicists in early 20th century discovered atoms are made of
subatomic particles
– Elements of quantum mechanics:
• wave / particle duality of matter (for ex. light: wave / photons, but
applies to any object)
• Heisenberg uncertainty principle: cannot measure simultaneously the
position and momentum of a particle - the greater the precision in one,
the less precise the other (uses probabilities)
• pairs of particle + antiparticle pop into existence out of nothing, then
annihilate (vacuum fluctuations) – cause gradual evaporation of black
holes over time via Hawking radiation
• particle entanglement (quantum teleportation)– information passes
instantly between 2 particles in a pair, regardless of distance (faster
than light speed)
• “observer effect” – the act of observing may change the system – what
is reality?
• can be very strange, counterintuitive, and different from our
“macroworld”, even Einstein had problems accepting some aspects of
QM (Einstein’s disagreement: “God does not play dice”)
• Atoms
– nucleus: protons [p+] + neutrons [n]
• each p+ or n is made of 3 quarks
• quark flavors: up, down, top, bottom, charm, strange
– electrons [e-]
– antimatter: antiprotons, antineutrons, positrons, anti-atoms
• Medical PET scanners (positron emission tomography)
• Chemical elements
• (collection of) atoms with same number of protons in nucleus
• elements cannot be reduced to simpler chemical substances
• elements are unique and have specific chemical properties
• Examples: hydrogen (H), carbon (C), oxygen (O), gold (Au)
• Ions – positive (+) and negative (-)
– plasma (ionized gas) – 4th state of matter (along with solids, liquids & gases)
with unique properties, the most common state in the Universe; behavior
similar to fluid, conducts electricity and interacts with magnetic fields
– natural occurrences: ionosphere, lightning (incl. ball), St. Elmo’s fire, polar
aurorae, stars, interplanetary / interstellar / intergalactic medium
– practical applications: fluorescent & neon lights, electric/plasma arc in
welding torches, ion engine for space probes; fusion reactors, plasma TV,
plasma lamp
• The importance of electrons
– exist as orbitals (= electron clouds), where position & speed are described as
probabilities (cannot be known precisely, only approximately; described by
wave function equations)
– completeness of electron shells (= levels): 2 or 8
– form chemical bonds (oxidation = loss of e-, reduction = gain of e-)
– valence – the # of electrons in outermost shell that participate in chemical
bonding
– electricity
2. The Universe
All space + time, matter + energy, physical laws + constants (for ex.
mass and charge of elementary particles)
Cosmology – science of the universe
– Big Bang Theory, Quantum Theory, Theory of Relativity (space-time
warped by matter & energy);
– will there be Theory of Everything (“Quantum Gravity”)?
~ 14 billion years old, ~93 billion light years across, mostly empty space
Composition: matter + forces (E=mc2)
– Dark matter and dark energy (unknown nature)
– Visible matter (stars, gas, and dust form large galaxies)
4 or 5 Fundamental Forces:
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2 nuclear forces: strong and weak
electromagnetic
gravity – still poorly understood
dark energy – new force? – a repellent force (“anti-gravity”)
The Universe
• Evidence leading to the Big Bang Theory
– space growing and galaxies flying apart
• very rapid expansion at first (inflation), slow down later
– cosmic microwave background – red-shifted (Doppler effect)
remnant of original Big Bang radiation
– percentages of the light chemical elements (H, He, Li)
• Ultimate fate of the Universe
– expansion is accelerating (overwhelming the attraction of
gravity) and will continue indefinitely
– thermodynamic (heat) death: all particles will ultimately
dissipate and lose their energy and stop moving
Galaxies, Stars and Elements
Chemical elements and star evolution
• The life and evolution of a star depend on its mass
– All start with H, most abundant element in Universe
– Gas and dust cloud coalesces under its own gravity to form a star and
planets; compression increases temp. until thermonuclear burning
starts; size of a star is result of its mass & action of gravity vs. burning
– Switch from burning (fusing) one element to the next, heavier one (HHe-C-Ne-O-Si-Fe)
– Largest stars burn most intensely at highest temperature, have shortest
lives, explode as supernovae, leave neutron stars (pulsars) or black
holes
• Elements heavier than iron (Fe) form only in supernova explosions
• Galaxies
– Enormous, rotating systems of stars, gas, dust (and dark matter?)
– have giant black holes in center
– form galactic clusters and superclusters, with enormous empty spaces
between them
• Our galaxy: The Milky Way
– 100,000 light years across, relatively large barred spiral galaxy
– 200-400 billion stars
– Sun is 30,000 light years from the giant black hole in the galactic
center, competes orbit every 220 million years
– has small satellite galaxies around it (may be tens of them)
– closest large neighbor: Andromeda Galaxy, 2 million light years
away; together are part of the Local Group of galaxies
• Solar System
– Formed 4.7 billion years ago from a large dust and gas cloud
– Sun is at least 3rd generation star (has heavy elements)
– Sun will burn for another ~5 billion years and then enlarge into a
red giant, engulfing Earth
– Terrestrial planets (inner) vs. gas giants (outer planets)
Our Universe and Life
•
Our Universe has certain physical laws and constants that appear to be valid
universally, i.e. everywhere and in the same way
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These laws determine how the Universe works and that life is possible (at least in its
terrestrial variant)
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The existing physical laws & constants limit the number of possible organisms
– Why all animals see only in the same narrow part of the electromagnetic spectrum we call “visible
light”?
– Strength of gravity – when would flight be possible?
– Determine chemistry: fundamental properties of water and other compounds depend on basic
constants such as mass and charge of the electrons, protons and neutrons; make some reactions more
likely than others
– Is quantum mechanics important in neurobiology and thinking?
– Not to be confused with developmental and design/selection constraints, such as “why no animal
evolved wheels?”
General Phenomena / Laws
Higher-level laws of the Universe, esp. for complex systems?
Seen across many different systems and levels
• Emergence
– not to be confused with any complex system that has numerous components & interactions
• Self-Organization
– system with increase in complexity without being guided or managed by an outside
source
– In biology: spontaneous folding of biomolecules; formation of lipid bilayer; origin of
life; homeostasis; embryological pattern formation and morphogenesis; flocking
behavior
• Evolution: a type of emergence & self-organization?
Fulfilled prerequisite: resources are always limited. Only 2 basic conditions are needed:
1. entities consuming resources to survive
2. entities capable of change
• Evolution as kludge
– pragmatic, usually not the most elegant/optimal solutions (blindly finds a working
solution)
– example: vertebrate retina is covered by blood supply, reducing light; ‘correct’ design
in cephalopods
General Phenomena / Laws
• Evolution: a type of emergence & self-organization?
Fulfilled prerequisite: resources are always limited.
Only 2 basic conditions are needed for evolution to occur:
1. entities consuming resources to survive
2. entities capable of change
Examples: biological systems, artificial life, business, ideas, language
• Evolution as kludge
– pragmatic, usually not the most elegant/optimal solutions - blindly finds a working
solution
– example: vertebrate retina is covered by blood supply, reducing light; ‘correct’ design
in cephalopods (squid, octopus); many other, incl. human anatomy
Emergence
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Simple interactions → complex systems; caused by interconnectivity (intricate causal relations across
different scales and feedback)
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Present in non-linear systems, and is irreducible (information is ‘lost’ as changes progress, i.e. one cannot
reconstruct the starting conditions by observing only the later stages/end results; “The whole is greater
and different than the sum of its parts”)
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Essential properties (Jeffrey Goldstein 1999):
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Related to other phenomena: self-organization, chaos theory
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there may be instances of self-organization without emergence and emergence without self-organization, and it is clear from the
literature that the phenomena are not the same. The link between emergence and self-organization remains an active research
question.
Emergence properties may be predictable or unpredictable
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Creates radical novelty (new properties/patterns appear on each level of complexity)
Coherence (an integrated whole that maintains itself over time)
Global level (“wholeness”)
Dynamic process (changes/evolves over time)
Perceivable
One reason it’s hard to predict is that the number of interactions between components of a system increases combinatorially with
the number of components. However, a large number of interactions is not enough by itself to guarantee emergent behavior
it is impossible for a computer to even count the number of arrangements for a system with only 20 molecules
Examples:
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Physics → Chemistry → Biology → Behavior/Psychology (psychology is not simply applied biology, etc.)
Color, self-assembling/configuring molecules (incl. proteins), fractals, weather, evolution, swarming (flocks, ant colonies),
mind/intelligence, human organizations (bureaucracies behave differently from individuals), stock market, internet
Important Characteristics of the Atom
– Atomic Number
• the number of protons in the nucleus
• determines the element
– Atomic Mass
• the number of protons + neutrons;
– Isotopes
• # of neutrons can differ in atoms of the same chemical element
• normally # protons = # neutrons (in most atoms)
• each isotope has a unique number of neutrons
• some isotopes can be radioactive (= unstable)
Radioactivity
Some isotopes have an inherent instability that leads to spontaneous breakdown
(radioactive decay) of the atom, accompanied by energy emission.
Usage:
• Atomic bomb (fission, A-bomb): radioactive fission (atom splitting) of uranium or
plutonium
• Hydrogen bomb (thermonuclear, H-bomb) : fusion of 2 hydrogen atoms into one helium
atom; the energy source of stars; x1000 more powerful
• Nuclear (fission) and thermonuclear (fusion, so far only experimental) reactors
Types of radioactive emissions:
( Alpha particles
• energized nucleus of a helium atom (relatively large particles)
• have low penetration
( Beta particles
• energized electrons (small particles)
• high penetration
( Gamma rays and X-rays
• highly energetic photons (tiny particles (quanta) of pure energy, with no mass, that transmit
electromagnetic radiation)
• considerable penetration
Radioactive Dating
• Radioactive decay occurs at a constant speed
– it is not affected by temperature, pressure or chemicals
– used in atomic clocks and to date precisely rocks and organic matter
– many types: uranium-lead, potassium-argon, argon-argon, etc.
– can date materials as old as 4.5 billion years (age of Solar System)
• Radiocarbon dating
– Only for organic matter
– Radioactive isotope C14 decays to C12
– Live organisms maintain same proportion of C14 / C12 as in
environment
– After death the amount of C14 starts to decrease as it decays to C12
– This method can be used only for the past 60,000 years (history &
archeology)
Molecules and Chemical Bonds
• Molecules
• oxygen and ozone
• Chemical Bonds
– ionic
– covalent
– hydrogen
Ionic Bonds
• when an atom gains or loses electrons (to fill or
empty outer energy levels, making it more stable)
• the gained or lost electron interacts with another
atom to form the ionic bond (example: NaCl)
• relatively strong
• not directional
Covalent Bonds
• Bond by sharing a pair of e• Shared pair forms a new orbital that envelops the nuclei of both atoms
• The strongest of all chemical bonds (involves a lot of energy)
• Directional (between 2 specific atoms)
• Examples: H2, inert gases: helium, neon, argon, krypton, xenon
Polar covalent bond:
• Bond in which the two e- are shared unequally; this leads to the atoms
having either a partial positive or partial negative charge
• Strong bond
• Example: H2O
Hydrogen Bonds
Attraction between partial positive and negative charges of atoms
• produce polar molecules (H2O)
• individually very weak
• highly directional
• work only in short distances
• combined, can be important for:
• structure of macromolecules like DNA and proteins
• water and ice
• water has unique properties, making it the basis of life:
• the best solvent (under the conditions on Earth)
• absorbs a lot of heat
• solid phase is less dense than liquid (ice floats, insulating below)
• adhesion to charged particles (and walls of capillaries)
Free Radicals
• Have unpaired e- and thus are highly reactive
• Normal product of metabolism using oxygen
• Examples: reactive oxygen - causes a chain reaction; NO
• Production increased by smoking, alcohol and radiation (incl. sunlight)
• Cause mutations, irritate artery walls, aging, cancer
• Weapons against them: vitamins C and E, beta carotene