Chapter 3 Lecture

Biological Physics
Nelson
Updated 1st Edition

The Molecular Dance

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Announcements
Study methods
Read each chapter BEFORE class
Pair study groups (if class big enough)
Grading format
Participation 30%
Midterm report/presentation 35%
Final report/presentation 35%
Those of you taking Advanced Physics 1 (AP1)
will be encouraged to take AP2, sorry.

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Summary Chapter 1
Dont forget: The BelousovZhabotinskii experiment

Free energy transducers and reverse osmosis

High to low quality energy in plants and
animals

The 1st law: dEtherm=dU= dQ - dWext

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Summary Chapter 1
The First Law of thermodynamics:
Etherm= Q - Wext
can be rephrased for different cases as:

Just depends on what youre interested in ...

Well discuss the chemical potential later
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Chapter 1 Homework
You should have:
Made a presentation on Chapter 2 or your
own them and pleas upload to Goggle Drive
Homework Problems
1.4 (Earths temperature)
1.5 (Franklins experiment)

Example solutions later please ...

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Chapter 3: The Molecular Dance

Cover previous material to tie in with the
beginning of chapter 2 and chapter 4
3.1 Probability & normalization
3.2 Gaussian, Maxwell & Boltzmann
distributions (Kinetic Theory of Gases)
3.3 Physical carrier of genetic information
(extra reading)

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Question?
Heat is disorganized molecular motion and
hence the lower the temperature the more
organized things are (lower entropy)
So, do cells work best at the coldest
temperatures? No, then what is happening?
It is amazing that a tiny cell can contain your
own personal database (the genome) without
loss of information over many generations ...

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3.1 Probability

1991 by Larry Gonick.

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Probability Rules
Discrete measurements xi , x1, x2,.... with each
measurement made N times then probability is

, large

For the continuous case we have

where we divide the range x into small bins x+dx

They are normalized as (cf. quantum mechanics)

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Mean, Variance
Mean

Variance
For a Gaussian: mean = x0 and var =
Exclusive events add:
and independent event multiply:
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Gaussians

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Useful Mathware
Maxima is a free Computer Algebra System
(CAS) unlike Maple or Mathematica
Octave is a (Matlab-like) free package which
uses GnuPlot to make plots
Finally we will also try Wolfram Alpha an
online free version of Mathematica
Alternatively use a graphical calculator ... :-)

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2D Gaussian: Shooting Arrows

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Homework 1: 3D Case & 3D Gaussian

distribution?

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3.2 Kinetic-molecular model of ideal gas

The assumptions of the kinetic-molecular

model are:
A container contains a very large number
of identical molecules.
The molecules behave like point particles
that are small compared to the size of the
container and the average distance
between molecules.
The molecules are in constant motion and
undergo perfectly elastic collisions.
The container walls are perfectly rigid and
do not move.
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Molecular Pressure

= 2 / = 2 =
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Molecular speeds
The Maxwell-Boltzmann
distribution f(v) gives distribution
of molecular speeds.
Figure right helps interpret f(v):
Part (a) shows how the shape
of the curve depends on
temperature.
Part (b) shows the fraction of
molecules within certain speed
ranges. The most probable
speed for a given temperature
is at the peak of the curve.

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Theory vs. Experiment

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An experimental apparatus*

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The Boltzmann Distribution

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The Boltzmann Equation

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IN CLASS DISCUSSION
Discuss the following Figures 3.8 and 3.9:
Why does evaporating water cool?
How does an activation barrier affect the cooling of
evaporating water or chemical reaction rates?

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Activation barriers

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Relaxation to equilibrium

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Homework/In class time

1. Make 2D/3D Gaussians with plots for different
using Wolfram or similar software.
2. Derive Your Turn 3E/3F (darts in 1D & 3D)
3. Do Problem 3.1 (The Dodgy Bakery)
4. Suppose you role 3 fair dice. What is the
probability that you will get a 5 on at least one
dice?
5. Read Excursion 3.3. and think about Mendels
rules of heredity information.
See slides for Chapter 4 for next week.
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3.3 How is bio-information stored?

First how is the information replicated?
Aristotle correctly argued (roughly) that life is
copied/created through
software stored in a carrier to direct own
construction (genotype)
duplicates/outputs the software (and carrier)
for transmission of offspring (phenotype)

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Heredity Information

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Mendels Peas

1961. Used by permission of Dover Publications.

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Meiosis

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1961. Used by permission of Dover Publications.

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(b) Andrew Syred/Science Photo Library/Photo Researchers, Inc.

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