<commit_before>Introduction To Biophysics (PHYS 225/BIOL 225) (3 credits, SI non-lab, A-QR)
========================================================

**TODO**

  1. Add [CHARMMing][CHARMMing] custom lessons

  1. decide if Demian should cover ENM (benefit: dead simple physical
     model + a touch of linear algebra = deep insight) or QM/MM
     (benefit: MGL does MD, LW does QM+DFT, DR does QM/MM is a really
     nice sequence)

  1. Add accommodations, plagiarism policy, etc.

  1. Refer frequently to [Physical Lens on the Cell][PLotC].


When people ask me what it means to be a Biophysicist, my stock answer
is "I like to think like a physicist, but am fascinated by problems
that come from biology." **Introduction to Biophysics** is an
introduction to that mindset, summed up wonderfully by the back-cover
of [Physical Biology of the Cell][PBoC]:

> *Physical Biology of the Cell* maps the huge and complex landscape
> of cell and molecular biology from the distinct perspective of
> physical biology. As a key organizing principle, the proximity of
> topics is based on the physical concepts that unite a given set of
> biological phenomena. Herein lies the central premise: that the
> appropriate application of a few fundamental physical models can
> serve as the foundation of whole bodies of quantitative biological
> intuition, useful across a wide range of biological problems.

What sorts of patterns do we expect to find in biology? Can physics
let us determine whether a process in the cell is governed by random
diffusion, or whether active transport (molecular motors) are needed
to move things from one part of a cell to another? How does dialysis
work (spoiler: entropy!)? What are the main forces governing protein
folding? We'll develop a small number of fundamental physical models,
and apply them to a broad range of biological problems. These physical
models give us both a new perspective on biology and a way of gaining
quantitative biological intuition across that range of problems.

## Learning Goals ##

In addition to specific content-related learning objectives, the
course has several non-content, "course-scale" learning
objectives. You can see the evolution of one of those goals
[here](http://www.mglerner.com/blog/?p=45).

  * Given a biological system, students will be able to predict relevant
    physical models.
    * Students will mature in knowledge organization and
      communication, gaining in ability to justify and explain
      approches and solutions to problems, both in written or oral
      form; be able to articulate big ideas from each content area.
  * Given a biological system and a physical model, students will be
    able to adapt the model to the system through quantitative
    analysis.
    * Students will develop problem solving skills and the ability to
      connect concepts between physics, biology, chemistry and
      mathematics to understand how biological systems function.
    * Students will mature in knowledge organization and
      communication, gaining in ability to justify and explain
      approches and solutions to problems, both in written or oral
      form; be able to articulate big ideas from each content area.
  * Students will gain exposure to the important questions in the
    modern field of molecular biophysics, and evaluate current
    research on a system of their choice.


## Textbook(s) ##

The primary (and *required*) textbook will be [Nelson][BiolPhys]. It's
most definitely a physics book, but it's less math-intensive and more
readable than many other physics texts, and has gotten great reviews
from classes just like this one. There are (at least!) two other
excellent books that I considered using:

 * [Physical Biology of the Cell, Second Edition][PBoC] does a
   masterful job of laying things out from a physics perspective, but
   most readers will want to have a bit more than one semester of<commit_msg>learning proficiencies<commit_after>Introduction To Biophysics (PHYS 225/BIOL 225) (3 credits, SI non-lab, A-QR)
========================================================

**TODO**

  1. Add [CHARMMing][CHARMMing] custom lessons

  1. decide if Demian should cover ENM (benefit: dead simple physical
     model + a touch of linear algebra = deep insight) or QM/MM
     (benefit: MGL does MD, LW does QM+DFT, DR does QM/MM is a really
     nice sequence)

  1. Add accommodations, plagiarism policy, etc.

  1. Refer frequently to [Physical Lens on the Cell][PLotC].


When people ask me what it means to be a Biophysicist, my stock answer
is "I like to think like a physicist, but am fascinated by problems
that come from biology." **Introduction to Biophysics** is an
introduction to that mindset, summed up wonderfully by the back-cover
of [Physical Biology of the Cell][PBoC]:

> *Physical Biology of the Cell* maps the huge and complex landscape
> of cell and molecular biology from the distinct perspective of
> physical biology. As a key organizing principle, the proximity of
> topics is based on the physical concepts that unite a given set of
> biological phenomena. Herein lies the central premise: that the
> appropriate application of a few fundamental physical models can
> serve as the foundation of whole bodies of quantitative biological
> intuition, useful across a wide range of biological problems.

What sorts of patterns do we expect to find in biology? Can physics
let us determine whether a process in the cell is governed by random
diffusion, or whether active transport (molecular motors) are needed
to move things from one part of a cell to another? How does dialysis
work (spoiler: entropy!)? What are the main forces governing protein
folding? We'll develop a small number of fundamental physical models,
and apply them to a broad range of biological problems. These physical
models give us both a new perspective on biology and a way of gaining
quantitative biological intuition across that range of problems.

## Learning Goals ##

In addition to specific content-related learning objectives, the
course has several non-content, "course-scale" learning
objectives. You can see the evolution of one of those goals
[here](http://www.mglerner.com/blog/?p=45).

  * Given a biological system, students will be able to predict relevant
    physical models.
  * Given a biological system and a physical model, students will be
    able to adapt the model to the system through quantitative
    analysis.
  * Students will gain exposure to important questions in the
    modern field of molecular biophysics, and evaluate current
    research on a system of their choice.

The list of learning proficiencies is much larger. Some broad examples include

  * Students will mature in knowledge organization and
    communication, gaining in ability to justify and explain
    approches and solutions to problems, both in written or oral
    form; be able to articulate big ideas from each content area.
  * Students will develop problem solving skills and the ability to
    connect concepts between physics, biology, chemistry and
    mathematics to understand how biological systems function.

## Textbook(s) ##

The primary (and *required*) textbook will be [Nelson][BiolPhys]. It's
most definitely a physics book, but it's less math-intensive and more
readable than many other physics texts, and has gotten great reviews
from classes just like this one. There are (at least!) two other
excellent books that I considered using:

 * [Physical Biology of the Cell, Second Edition][PBoC] does a
   masterful job of laying things out from a physics perspective, but
   most readers will want to have a bit more than one semester of
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