Welcome to TiddlyWiki created by Jeremy Ruston, Copyright © 2007 UnaMesa Association
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<link rel='alternate' type='application/rss+xml' title='RSS' href='index.xml' />
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Background: #fff
Foreground: #000
PrimaryPale: #8cf
PrimaryLight: #18f
PrimaryMid: #04b
PrimaryDark: #014
SecondaryPale: #ffc
SecondaryLight: #fe8
SecondaryMid: #db4
SecondaryDark: #841
TertiaryPale: #eee
TertiaryLight: #ccc
TertiaryMid: #999
TertiaryDark: #666
Error: #f88
/*{{{*/
body {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];}
a {color:[[ColorPalette::PrimaryMid]];}
a:hover {background-color:[[ColorPalette::PrimaryMid]]; color:[[ColorPalette::Background]];}
a img {border:0;}
h1,h2,h3,h4,h5,h6 {color:[[ColorPalette::SecondaryDark]]; background:transparent;}
h1 {border-bottom:2px solid [[ColorPalette::TertiaryLight]];}
h2,h3 {border-bottom:1px solid [[ColorPalette::TertiaryLight]];}
.button {color:[[ColorPalette::PrimaryDark]]; border:1px solid [[ColorPalette::Background]];}
.button:hover {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::SecondaryLight]]; border-color:[[ColorPalette::SecondaryMid]];}
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.headerForeground a {font-weight:normal; color:[[ColorPalette::PrimaryPale]];}
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background:[[ColorPalette::TertiaryPale]];
border-left:1px solid [[ColorPalette::TertiaryLight]];
border-top:1px solid [[ColorPalette::TertiaryLight]];
border-right:1px solid [[ColorPalette::TertiaryLight]];
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.tabUnselected {color:[[ColorPalette::Background]]; background:[[ColorPalette::TertiaryMid]];}
.tabContents {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::TertiaryPale]]; border:1px solid [[ColorPalette::TertiaryLight]];}
.tabContents .button {border:0;}
#sidebar {}
#sidebarOptions input {border:1px solid [[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel {background:[[ColorPalette::PrimaryPale]];}
#sidebarOptions .sliderPanel a {border:none;color:[[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel a:hover {color:[[ColorPalette::Background]]; background:[[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel a:active {color:[[ColorPalette::PrimaryMid]]; background:[[ColorPalette::Background]];}
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.wizard h2 {color:[[ColorPalette::Foreground]]; border:none;}
.wizardStep {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];
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.wizard .changedLocally {background:#80ff80;}
.wizard .changedServer {background:#8080ff;}
.wizard .changedBoth {background:#ff8080;}
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.wizard .putToServer {background:#ff80ff;}
.wizard .gotFromServer {background:#80ffff;}
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#messageArea .button {color:[[ColorPalette::PrimaryMid]]; background:[[ColorPalette::SecondaryPale]]; border:none;}
.popupTiddler {background:[[ColorPalette::TertiaryPale]]; border:2px solid [[ColorPalette::TertiaryMid]];}
.popup {background:[[ColorPalette::TertiaryPale]]; color:[[ColorPalette::TertiaryDark]]; border-left:1px solid [[ColorPalette::TertiaryMid]]; border-top:1px solid [[ColorPalette::TertiaryMid]]; border-right:2px solid [[ColorPalette::TertiaryDark]]; border-bottom:2px solid [[ColorPalette::TertiaryDark]];}
.popup hr {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::PrimaryDark]]; border-bottom:1px;}
.popup li.disabled {color:[[ColorPalette::TertiaryMid]];}
.popup li a, .popup li a:visited {color:[[ColorPalette::Foreground]]; border: none;}
.popup li a:hover {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; border: none;}
.popup li a:active {background:[[ColorPalette::SecondaryPale]]; color:[[ColorPalette::Foreground]]; border: none;}
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.title {color:[[ColorPalette::SecondaryDark]];}
.subtitle {color:[[ColorPalette::TertiaryDark]];}
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.toolbar a {color:[[ColorPalette::TertiaryLight]];}
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.tagging, .tagged {border:1px solid [[ColorPalette::TertiaryPale]]; background-color:[[ColorPalette::TertiaryPale]];}
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.footer {color:[[ColorPalette::TertiaryLight]];}
.selected .footer {color:[[ColorPalette::TertiaryMid]];}
.sparkline {background:[[ColorPalette::PrimaryPale]]; border:0;}
.sparktick {background:[[ColorPalette::PrimaryDark]];}
.error, .errorButton {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::Error]];}
.warning {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::SecondaryPale]];}
.lowlight {background:[[ColorPalette::TertiaryLight]];}
.zoomer {background:none; color:[[ColorPalette::TertiaryMid]]; border:3px solid [[ColorPalette::TertiaryMid]];}
.imageLink, #displayArea .imageLink {background:transparent;}
.annotation {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; border:2px solid [[ColorPalette::SecondaryMid]];}
.viewer .listTitle {list-style-type:none; margin-left:-2em;}
.viewer .button {border:1px solid [[ColorPalette::SecondaryMid]];}
.viewer blockquote {border-left:3px solid [[ColorPalette::TertiaryDark]];}
.viewer table, table.twtable {border:2px solid [[ColorPalette::TertiaryDark]];}
.viewer th, .viewer thead td, .twtable th, .twtable thead td {background:[[ColorPalette::SecondaryMid]]; border:1px solid [[ColorPalette::TertiaryDark]]; color:[[ColorPalette::Background]];}
.viewer td, .viewer tr, .twtable td, .twtable tr {border:1px solid [[ColorPalette::TertiaryDark]];}
.viewer pre {border:1px solid [[ColorPalette::SecondaryLight]]; background:[[ColorPalette::SecondaryPale]];}
.viewer code {color:[[ColorPalette::SecondaryDark]];}
.viewer hr {border:0; border-top:dashed 1px [[ColorPalette::TertiaryDark]]; color:[[ColorPalette::TertiaryDark]];}
.highlight, .marked {background:[[ColorPalette::SecondaryLight]];}
.editor input {border:1px solid [[ColorPalette::PrimaryMid]];}
.editor textarea {border:1px solid [[ColorPalette::PrimaryMid]]; width:100%;}
.editorFooter {color:[[ColorPalette::TertiaryMid]];}
#backstageArea {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::TertiaryMid]];}
#backstageArea a {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::Background]]; border:none;}
#backstageArea a:hover {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; }
#backstageArea a.backstageSelTab {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];}
#backstageButton a {background:none; color:[[ColorPalette::Background]]; border:none;}
#backstageButton a:hover {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::Background]]; border:none;}
#backstagePanel {background:[[ColorPalette::Background]]; border-color: [[ColorPalette::Background]] [[ColorPalette::TertiaryDark]] [[ColorPalette::TertiaryDark]] [[ColorPalette::TertiaryDark]];}
.backstagePanelFooter .button {border:none; color:[[ColorPalette::Background]];}
.backstagePanelFooter .button:hover {color:[[ColorPalette::Foreground]];}
#backstageCloak {background:[[ColorPalette::Foreground]]; opacity:0.6; filter:'alpha(opacity=60)';}
/*}}}*/
/*{{{*/
* html .tiddler {height:1%;}
body {font-size:.75em; font-family:arial,helvetica; margin:0; padding:0;}
h1,h2,h3,h4,h5,h6 {font-weight:bold; text-decoration:none;}
h1,h2,h3 {padding-bottom:1px; margin-top:1.2em;margin-bottom:0.3em;}
h4,h5,h6 {margin-top:1em;}
h1 {font-size:1.35em;}
h2 {font-size:1.25em;}
h3 {font-size:1.1em;}
h4 {font-size:1em;}
h5 {font-size:.9em;}
hr {height:1px;}
a {text-decoration:none;}
dt {font-weight:bold;}
ol {list-style-type:decimal;}
ol ol {list-style-type:lower-alpha;}
ol ol ol {list-style-type:lower-roman;}
ol ol ol ol {list-style-type:decimal;}
ol ol ol ol ol {list-style-type:lower-alpha;}
ol ol ol ol ol ol {list-style-type:lower-roman;}
ol ol ol ol ol ol ol {list-style-type:decimal;}
.txtOptionInput {width:11em;}
#contentWrapper .chkOptionInput {border:0;}
.externalLink {text-decoration:underline;}
.indent {margin-left:3em;}
.outdent {margin-left:3em; text-indent:-3em;}
code.escaped {white-space:nowrap;}
.tiddlyLinkExisting {font-weight:bold;}
.tiddlyLinkNonExisting {font-style:italic;}
/* the 'a' is required for IE, otherwise it renders the whole tiddler in bold */
a.tiddlyLinkNonExisting.shadow {font-weight:bold;}
#mainMenu .tiddlyLinkExisting,
#mainMenu .tiddlyLinkNonExisting,
#sidebarTabs .tiddlyLinkNonExisting {font-weight:normal; font-style:normal;}
#sidebarTabs .tiddlyLinkExisting {font-weight:bold; font-style:normal;}
.header {position:relative;}
.header a:hover {background:transparent;}
.headerShadow {position:relative; padding:4.5em 0 1em 1em; left:-1px; top:-1px;}
.headerForeground {position:absolute; padding:4.5em 0 1em 1em; left:0px; top:0px;}
.siteTitle {font-size:3em;}
.siteSubtitle {font-size:1.2em;}
#mainMenu {position:absolute; left:0; width:10em; text-align:right; line-height:1.6em; padding:1.5em 0.5em 0.5em 0.5em; font-size:1.1em;}
#sidebar {position:absolute; right:3px; width:16em; font-size:.9em;}
#sidebarOptions {padding-top:0.3em;}
#sidebarOptions a {margin:0 0.2em; padding:0.2em 0.3em; display:block;}
#sidebarOptions input {margin:0.4em 0.5em;}
#sidebarOptions .sliderPanel {margin-left:1em; padding:0.5em; font-size:.85em;}
#sidebarOptions .sliderPanel a {font-weight:bold; display:inline; padding:0;}
#sidebarOptions .sliderPanel input {margin:0 0 0.3em 0;}
#sidebarTabs .tabContents {width:15em; overflow:hidden;}
.wizard {padding:0.1em 1em 0 2em;}
.wizard h1 {font-size:2em; font-weight:bold; background:none; padding:0; margin:0.4em 0 0.2em;}
.wizard h2 {font-size:1.2em; font-weight:bold; background:none; padding:0; margin:0.4em 0 0.2em;}
.wizardStep {padding:1em 1em 1em 1em;}
.wizard .button {margin:0.5em 0 0; font-size:1.2em;}
.wizardFooter {padding:0.8em 0.4em 0.8em 0;}
.wizardFooter .status {padding:0 0.4em; margin-left:1em;}
.wizard .button {padding:0.1em 0.2em;}
#messageArea {position:fixed; top:2em; right:0; margin:0.5em; padding:0.5em; z-index:2000; _position:absolute;}
.messageToolbar {display:block; text-align:right; padding:0.2em;}
#messageArea a {text-decoration:underline;}
.tiddlerPopupButton {padding:0.2em;}
.popupTiddler {position: absolute; z-index:300; padding:1em; margin:0;}
.popup {position:absolute; z-index:300; font-size:.9em; padding:0; list-style:none; margin:0;}
.popup .popupMessage {padding:0.4em;}
.popup hr {display:block; height:1px; width:auto; padding:0; margin:0.2em 0;}
.popup li.disabled {padding:0.4em;}
.popup li a {display:block; padding:0.4em; font-weight:normal; cursor:pointer;}
.listBreak {font-size:1px; line-height:1px;}
.listBreak div {margin:2px 0;}
.tabset {padding:1em 0 0 0.5em;}
.tab {margin:0 0 0 0.25em; padding:2px;}
.tabContents {padding:0.5em;}
.tabContents ul, .tabContents ol {margin:0; padding:0;}
.txtMainTab .tabContents li {list-style:none;}
.tabContents li.listLink { margin-left:.75em;}
#contentWrapper {display:block;}
#splashScreen {display:none;}
#displayArea {margin:1em 17em 0 14em;}
.toolbar {text-align:right; font-size:.9em;}
.tiddler {padding:1em 1em 0;}
.missing .viewer,.missing .title {font-style:italic;}
.title {font-size:1.6em; font-weight:bold;}
.missing .subtitle {display:none;}
.subtitle {font-size:1.1em;}
.tiddler .button {padding:0.2em 0.4em;}
.tagging {margin:0.5em 0.5em 0.5em 0; float:left; display:none;}
.isTag .tagging {display:block;}
.tagged {margin:0.5em; float:right;}
.tagging, .tagged {font-size:0.9em; padding:0.25em;}
.tagging ul, .tagged ul {list-style:none; margin:0.25em; padding:0;}
.tagClear {clear:both;}
.footer {font-size:.9em;}
.footer li {display:inline;}
.annotation {padding:0.5em; margin:0.5em;}
* html .viewer pre {width:99%; padding:0 0 1em 0;}
.viewer {line-height:1.4em; padding-top:0.5em;}
.viewer .button {margin:0 0.25em; padding:0 0.25em;}
.viewer blockquote {line-height:1.5em; padding-left:0.8em;margin-left:2.5em;}
.viewer ul, .viewer ol {margin-left:0.5em; padding-left:1.5em;}
.viewer table, table.twtable {border-collapse:collapse; margin:0.8em 1.0em;}
.viewer th, .viewer td, .viewer tr,.viewer caption,.twtable th, .twtable td, .twtable tr,.twtable caption {padding:3px;}
table.listView {font-size:0.85em; margin:0.8em 1.0em;}
table.listView th, table.listView td, table.listView tr {padding:0px 3px 0px 3px;}
.viewer pre {padding:0.5em; margin-left:0.5em; font-size:1.2em; line-height:1.4em; overflow:auto;}
.viewer code {font-size:1.2em; line-height:1.4em;}
.editor {font-size:1.1em;}
.editor input, .editor textarea {display:block; width:100%; font:inherit;}
.editorFooter {padding:0.25em 0; font-size:.9em;}
.editorFooter .button {padding-top:0px; padding-bottom:0px;}
.fieldsetFix {border:0; padding:0; margin:1px 0px;}
.sparkline {line-height:1em;}
.sparktick {outline:0;}
.zoomer {font-size:1.1em; position:absolute; overflow:hidden;}
.zoomer div {padding:1em;}
* html #backstage {width:99%;}
* html #backstageArea {width:99%;}
#backstageArea {display:none; position:relative; overflow: hidden; z-index:150; padding:0.3em 0.5em;}
#backstageToolbar {position:relative;}
#backstageArea a {font-weight:bold; margin-left:0.5em; padding:0.3em 0.5em;}
#backstageButton {display:none; position:absolute; z-index:175; top:0; right:0;}
#backstageButton a {padding:0.1em 0.4em; margin:0.1em;}
#backstage {position:relative; width:100%; z-index:50;}
#backstagePanel {display:none; z-index:100; position:absolute; width:90%; margin-left:3em; padding:1em;}
.backstagePanelFooter {padding-top:0.2em; float:right;}
.backstagePanelFooter a {padding:0.2em 0.4em;}
#backstageCloak {display:none; z-index:20; position:absolute; width:100%; height:100px;}
.whenBackstage {display:none;}
.backstageVisible .whenBackstage {display:block;}
/*}}}*/
/***
StyleSheet for use when a translation requires any css style changes.
This StyleSheet can be used directly by languages such as Chinese, Japanese and Korean which need larger font sizes.
***/
/*{{{*/
body {font-size:0.8em;}
#sidebarOptions {font-size:1.05em;}
#sidebarOptions a {font-style:normal;}
#sidebarOptions .sliderPanel {font-size:0.95em;}
.subtitle {font-size:0.8em;}
.viewer table.listView {font-size:0.95em;}
/*}}}*/
/*{{{*/
@media print {
#mainMenu, #sidebar, #messageArea, .toolbar, #backstageButton, #backstageArea {display: none !important;}
#displayArea {margin: 1em 1em 0em;}
noscript {display:none;} /* Fixes a feature in Firefox 1.5.0.2 where print preview displays the noscript content */
}
/*}}}*/
<!--{{{-->
<div class='header' macro='gradient vert [[ColorPalette::PrimaryLight]] [[ColorPalette::PrimaryMid]]'>
<div class='headerShadow'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
<div class='headerForeground'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
</div>
<div id='mainMenu' refresh='content' tiddler='MainMenu'></div>
<div id='sidebar'>
<div id='sidebarOptions' refresh='content' tiddler='SideBarOptions'></div>
<div id='sidebarTabs' refresh='content' force='true' tiddler='SideBarTabs'></div>
</div>
<div id='displayArea'>
<div id='messageArea'></div>
<div id='tiddlerDisplay'></div>
</div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
<div class='tagging' macro='tagging'></div>
<div class='tagged' macro='tags'></div>
<div class='viewer' macro='view text wikified'></div>
<div class='tagClear'></div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::EditToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='editor' macro='edit title'></div>
<div macro='annotations'></div>
<div class='editor' macro='edit text'></div>
<div class='editor' macro='edit tags'></div><div class='editorFooter'><span macro='message views.editor.tagPrompt'></span><span macro='tagChooser excludeLists'></span></div>
<!--}}}-->
To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers:
* [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* [[MainMenu]]: The menu (usually on the left)
* [[DefaultTiddlers]]: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>
These [[InterfaceOptions]] for customising [[TiddlyWiki]] are saved in your browser
Your username for signing your edits. Write it as a [[WikiWord]] (eg [[JoeBloggs]])
<<option txtUserName>>
<<option chkSaveBackups>> [[SaveBackups]]
<<option chkAutoSave>> [[AutoSave]]
<<option chkRegExpSearch>> [[RegExpSearch]]
<<option chkCaseSensitiveSearch>> [[CaseSensitiveSearch]]
<<option chkAnimate>> [[EnableAnimations]]
----
Also see [[AdvancedOptions]]
Students are encouraged to work in groups, however, ''all work turned in must be your own''.
All students of the University of Colorado at Boulder are responsible for knowing and adhering to the academic integrity policy of this institution. Violations of this policy may include: cheating, plagiarism, aid of academic dishonesty, fabrication, lying, bribery, and threatening behavior. All incidents of academic misconduct shall be reported to the Honor Code Council (honor@colorado.edu; 5-2273).
Students who are found to be in violation of the academic integrity policy will be subject to both academic sanctions (a final grade of F in this course) and non-academic sanctions (including but not limited to university probation, suspension, or expulsion). See policies [[here|http://www.colorado.edu/academics/honorcode]].
<<option chkGenerateAnRssFeed>> GenerateAnRssFeed
<<option chkOpenInNewWindow>> OpenLinksInNewWindow
<<option chkSaveEmptyTemplate>> SaveEmptyTemplate
<<option chkToggleLinks>> Clicking on links to tiddlers that are already open causes them to close
^^(override with Control or other modifier key)^^
<<option chkHttpReadOnly>> HideEditingFeatures when viewed over HTTP
<<option chkForceMinorUpdate>> Treat edits as MinorChanges by preserving date and time
^^(override with Shift key when clicking 'done' or by pressing Ctrl-Shift-Enter^^
<<option chkConfirmDelete>> ConfirmBeforeDeleting
Maximum number of lines in a tiddler edit box: <<option txtMaxEditRows>>
Folder name for backup files: <<option txtBackupFolder>>
<<option chkInsertTabs>> Use tab key to insert tab characters instead of jumping to next field
Welcome to the home page for Physics 4810/7810, Introduction to Biophysics.
* Thank you for a great semester. Enjoy your winter holiday.
* Final exams have been graded and final grades submitted to the Registrar.
** If you would like to know your final exam grade, final homework grade, or other grades, you can email me to request them. Please remember that email is not a secure form of communication and that my email to you could be read by people other than you.
* Extra exam review material and review problems added to [[Final Exam]].
[[Old Announcements]]
/***
|Name|BetterTimelineMacro|
|Created by|SaqImtiaz|
|Location|http://lewcid.googlepages.com/lewcid.html#BetterTimelineMacro|
|Version|0.5 beta|
|Requires|~TW2.x|
!!!Description:
A replacement for the core timeline macro that offers more features:
*list tiddlers with only specfic tag
*exclude tiddlers with a particular tag
*limit entries to any number of days, for example one week
*specify a start date for the timeline, only tiddlers after that date will be listed.
!!!Installation:
Copy the contents of this tiddler to your TW, tag with systemConfig, save and reload your TW.
Edit the ViewTemplate to add the fullscreen command to the toolbar.
!!!Syntax:
{{{<<timeline better:true>>}}}
''the param better:true enables the advanced features, without it you will get the old timeline behaviour.''
additonal params:
(use only the ones you want)
{{{<<timeline better:true onlyTag:Tag1 excludeTag:Tag2 sortBy:modified/created firstDay:YYYYMMDD maxDays:7 maxEntries:30>>}}}
''explanation of syntax:''
onlyTag: only tiddlers with this tag will be listed. Default is to list all tiddlers.
excludeTag: tiddlers with this tag will not be listed.
sortBy: sort tiddlers by date modified or date created. Possible values are modified or created.
firstDay: useful for starting timeline from a specific date. Example: 20060701 for 1st of July, 2006
maxDays: limits timeline to include only tiddlers from the specified number of days. If you use a value of 7 for example, only tiddlers from the last 7 days will be listed.
maxEntries: limit the total number of entries in the timeline.
!!!History:
*28-07-06: ver 0.5 beta, first release
!!!Code
***/
//{{{
// Return the tiddlers as a sorted array
TiddlyWiki.prototype.getTiddlers = function(field,excludeTag,includeTag)
{
var results = [];
this.forEachTiddler(function(title,tiddler)
{
if(excludeTag == undefined || tiddler.tags.find(excludeTag) == null)
if(includeTag == undefined || tiddler.tags.find(includeTag)!=null)
results.push(tiddler);
});
if(field)
results.sort(function (a,b) {if(a[field] == b[field]) return(0); else return (a[field] < b[field]) ? -1 : +1; });
return results;
}
//this function by Udo
function getParam(params, name, defaultValue)
{
if (!params)
return defaultValue;
var p = params[0][name];
return p ? p[0] : defaultValue;
}
window.old_timeline_handler= config.macros.timeline.handler;
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Students and faculty each have responsibility for maintaining an appropriate learning environment. As part of this responsibility, you are expected to
* turn off cell phone ringers during class,
* not use laptop computers, cell phones, pagers, or other electronic devices in class, and
* not read newspapers or magazines in class.
Students who fail to adhere to behavioral standards may be subject to discipline.
Faculty have the professional responsibility to treat students with understanding, dignity and respect, to guide classroom discussion and to set reasonable limits on the manner in which students express opinions. For more information, see the [[University|http://www.colorado.edu/policies/classbehavior.html]] and [[student affairs|http://www.colorado.edu/studentaffairs/judicialaffairs/code.html#student_code]] policies on classroom behavior.
Professional courtesy and sensitivity are especially important with respect to individuals and topics dealing with differences of race, culture, religion, politics, sexual orientation, gender variance, and nationalities. Class rosters are provided to me with the student's legal name. I will gladly honor your request to address you by an alternate name or gender pronoun. Please advise me of this preference early in the semester so that I may make appropriate changes to my records.
*This course is an introduction to the physics of living systems for students with a physics, engineering, or chemistry background, developing the biology background as required.
* The central theme of the course will be how living systems are able to generate order, with a focus on both physical principles and biological examples.
* A second course theme will be the development of quantitative models and estimates for biological systems.
* Topics will include the properties of biomolecules, physics of random walks and diffusion, low-Reynolds number hydrodynamics, entropy and free energy of biomolecules, entropic forces, and biological self assembly.
* Selected biophysics applications will be discussed based on student interest, potentially including polymer elasticity, cooperative transitions in proteins, enzymes, molecular motors, transport across membranes, and nerve impulses.
* For more details, see the [[Course Outline]] and [[Detailed Schedule]].
!!!Prerequisites
*Prerequisites for 4810: PHYS 2210 or instructor permission. PHYS 4230 helpful but not required.
* Prerequisites for 7810: undergraduate statistical mechanics or instructor permission. PHYS 7230 helpful but not required.
!General information
* [[Instructor]]''s''
* [[Textbooks]]
* [[Resources]]
* [[Course Goals]]
* [[Course Outline]]
* [[Detailed Schedule]]
!Course components
* [[Lectures]]
* [[Homework]]
* [[Exams]]
* [[Term Paper]]
!Grading
* [[Grading Policy]]
!Policies and requirements
* [[Dropping the course]]
* [[Extra help]]
* [[Exams]]
* [[Academic honesty]]
* [[Classroom behavior]]
* [[Disabilities]]
* [[Religious observances]]
* [[Equity and discrimination]]
PDF file of the [[syllabus|syllabus.pdf]] distributed on the first day of class.
|! Nelson|! Phillips, Kondev, and Theriot|
|''Chapter 1: What the ancients knew.'' The central question of this course: how are living systems able to generate order? Energy and heat, free energy transduction, dimensional analysis, properties of molecules. |Section 1.3-1.4: Modeling in biology. Section 5.2: Biological systems as minimizers. Section 6.2: On being ideal. |
|''Chapter 2: What's inside cells.'' Anatomy of a cell, biomolecules, macromolecular assemblies, examples of cellular components. |Section 1.1: Biomolecules. Chapter 2: Ingredients of a cell. Chapter 3: Biological timescales. Chapter 4: Model organisms. |
|''Chapter 3: The molecular dance.'' Probability distributions, heat and kinetic energy, the Boltzmann distribution, genetic information. |Chapter 6: Entropy. |
|''Chapter 4: Random walks, friction, and diffusion.'' Brownian motion and random walks, diffusion, biological examples. |Chapter 8: Random walks. Chapter 13: Diffusion. |
|''Chapter 5: Life in the slow lane: the low Reynolds-number world.'' Viscous drag, Reynolds number, biological fluid flow. |Chapter 12: Water |
|''Chapter 6: Entropy, temperature, and free energy.'' Entropy and temperature, the second law of thermodynamics, free energy transduction, microscopic systems. |Chapter 6: Entropy. |
|''Chapter 7: Entropic forces at work.'' Entropic forces, osmotic pressure, osmotic flow, solution electrostatics, properties of water. |Chapter 9: Solution electrostatics. Chapter 14: Crowding. |
|''Chapter 8: Chemical forces and self assembly.'' Chemical potential and chemical reactions, dissociation, self assembly, cellular examples. |Chapter 7: Two-state systems. Chapter 11: Membranes. |
The remaining material covered at the end of the course will be chosen based on student interest.
[[Announcements]]
[[Course Information]]
For the big picture, see the [[Course Outline]].
This is the course schedule, reading assignments, and links to homework and exam information. [[Textbooks]]: N refers to Nelson, PKT refers to Phillips, Kondev, and Theriot.The topics listed for each day are preliminary and may change (some material may be covered more quickly or slowly than listed in the schedule).
| Week | Date | Topic | Reading |
| 1 | 8/25 |Class overview. Things you should know from introductory physics. Start ''Nelson Chapter 1: What the ancients knew''. Heat and energy, order and disorder. Key physics concepts in biology. Philosophy of modeling. |Nelson 1.1-1.3, PKT 1.3|
| 1 | 8/27 |Dimensional analysis and scaling. Estimation. Molecules and the ideal gas law. |Nelson 1.4-1.5, PKT 1.4|
| 2 | 9/1 |Start ''Nelson Chapter 2: What's inside cells''. Essential biology background I: Cell anatomy. |Nelson 2.1, PKT 2.1-2.2 |
| 2 | 9/3 |Essential biology background II: Biomolecules. [[Homework 1 due|Homework]]. |Nelson 2.2, PKT 1.2 |
| 3 | 9/8 |Essential biology background III: Molecular devices and organisms. |Nelson 2.3, PKT 2.3, 4.1-4.8 |
| 3 | 9/10 |Essential biology background IV: Biological timescales. [[Homework 2 due|Homework]]. |PKT 3.1-3.4|
| 4 | 9/15 |Probability distributions, ideal gas law, Boltzmann distribution, activation barriers. |Nelson 3.1-3.2 |
| 4 | 9/17 |Basics of genetics. Probability and genetics. Mendelian inheritance, chromosome maps. [[Homework 3 due|Homework]]. |Nelson 3.3 |
| 5 | 9/22 |Random walks and diffusion, part 1. Simple random walk model, diffusion law. Discrete random walk and the binomial distribution. Large N limit, Gaussian distribution. |Nelson 4.1-4.2 |
| 5 | 9/24 |Random walks and diffusion, part 2. Model independence of diffusion. Friction and diffusion, the Einstein relation. Random walks and polymer conformation. Derivation of the diffusion equation. [[Homework 4 due|Homework]]. |Nelson 4.3-4.5 |
| 6 | 9/29 |Biological applications of diffusion, part 1. Diffusive limits on metabolism. Membrane permeability. |Nelson 4.6 |
| 6 | 10/1 |Biological applications of diffusion, part 2. Membrane electrical potential. Conductivity of solutions. Start low Reynolds-number fluid dynamics. [[Homework 5 due|Homework]]. |Nelson 5.1 |
| 7 | 10/6 |Low Reynolds-number fluid dynamics. |Nelson 5.2 |
| 7 | 10/8 |Biological applications of low Reynolds-number fluid dynamics. Swimming, pumping, and stirring. [[Homework 6 due|Homework]]. |Nelson 5.3-5.4 |
| 8 | 10/13 |Biological applications of low Reynolds-number fluid dynamics. Foraging, attack, and escape. Blood flow. | |
| 8 | 10/15 |[[Midterm Exam|Exams]]. ||
| 9 | 10/20 |Class cancelled. ||
| 9 | 10/23 |||
| 10 | 10/27 |||
| 10 | 10/29 |[[Homework 7 due|Homework]]. ||
| 11 | 11/3 |||
| 11 | 11/5 | ||
| 12 | 11/10 |||
| 12 | 11/12 |[[Homework 8 due|Homework]]. ||
| 13 | 11/17 |||
| 13 | 11/19 |[[Homework 9 due|Homework]]. ||
| 14 | 12/1 |||
| 14 | 12/3 |[[Homework 10 due|Homework]]. [[Final paper|Term Paper]] due Friday at 5 pm.||
| 15 | 12/8 |||
| 15 | 12/10 |[[Homework 11 due|Homework]]. ||
| 16 | 12/12 |[[Final exam|Exams]]. |7:30 - 10:00 PM|
If you qualify for accommodations because of a disability, please submit a letter to me from Disability Services in a timely manner (within the first two weeks of class) so that your needs may be addressed. Disability Services determines accommodations based on documented disabilities. Contact: 303-492-8671, Willard 322, or [[this site|http://www.Colorado.EDU/disabilityservices]].
Advice from the Dean's office is recommended before dropping any course. After 10/7 (for Engineering students) or 10/30 (for Arts and Sciences students) dropping the course is possible only with a petition approved by the Dean's office.
* The University of Colorado at Boulder policy on Discrimination and Harassment (available at [[this site|http://www.colorado.edu/policies/discrimination.html]]), the University of Colorado policy on Sexual Harassment and the University of Colorado policy on Amorous Relationships applies to all students, staff and faculty.
* Any student, staff or faculty member who believes s/he has been the subject of discrimination or harassment based upon race, color, national origin, sex, age, disability, religion, sexual orientation, or veteran status should contact the Office of Discrimination and Harassment (ODH) at 303-492-2127 or the Office of Judicial Affairs at 303-492-5550.
* Information about the ODH and the campus resources available to assist individuals regarding discrimination or harassment can be obtained [[here|http://www.colorado.edu/odh]].
The midterm exam will be held in class on
* [[Midterm Exam]], Thursday, 10/15
The final exam will take place from 7:30-10:00 PM on
* [[Final Exam]], Saturday 12/12
!Exam policies
* There will be ''no'' make-up exams or early exams. If you are sick during an exam, please bring a note from your doctor verifying your illness. Your course grade will then be determined by the rest of your course work.
* Calculators are not allowed on the exams.
* Crib sheets are allowed on the exams. For the midterm exam, you may bring one letter size (8 1/2" x 11") sheet with anything written on both sides. For the final exam you may bring two letter size sheets.
* A special needs room for people with documented [[Disabilities]] will be provided for each exam. See me for more information.
You are encouraged to get extra help whenever you need it.
* Office hours are an excellent place to get help on the homework or ask questions about the course in general. See the [[Instructor]] page.
* Tutoring may be available through the dorms.
* Tutoring help is available through the Student Academic Services Center, see [[this site|http://www.colorado.edu/sasc/]].
* The final exam has been graded.
** The median grade was 64, the standard deviation 14, the range of scores 40-90.
* [[Final solutions|final-solns.pdf]] (PDF).
* The final exam will take place Saturday 12/12 7:30-10:00 PM.
** 4810 students with an overall A+ average as of HW 10 will be exempted from the final exam. I will tell you on Tuesday 12/8 if this applies to you.
** Students with 3 exams on that date will take the exam on Sunday afternoon, 1:00-3:30 PM.
* You can bring a 2-page formula sheet to the exam, with any notes written on it (both sides).
* Other than the formula sheet, the exam will be closed-book and closed-device.
* The exam will be comprehensive, but will emphasize material covered since the midterm: about 75% of the exam will focus on the second half of the course. This includes material from [[HW 7-11|Homework]], roughly chapters 5-8 and 11-12 of Nelson. The topics to focus on are:
**Low Reynolds-number hydrodynamics.
**Entropy, temperature, and free energy.
**The Boltzmann distribution.
**Two-state systems.
**Osmotic pressure.
**Solution electrostatics and Poisson Boltzmann.
**The hydrophobic effect.
**Chemical potential and chemical reactions.
*** Definition of chemical potential
*** Chemical potential of an ideal gas
*** The grand canonical distribution
***Condition for chemical equilibrium
*** Equilibrium constant
*** Determining concentration at equilibrium
*** Direction of chemical reactions
**Self-assembly of amphiphiles.
*** Qualitative explanation of amphiphile self assembly
**Micelles and bilayers.
*** Ingredients of the micelle model
*** Bilayer bending energy
**Donnan equilibrium and the Nernst potential.
**Ion channels and membrane conductance.
* Material to review from the first half of the course is [[HW 1-6|Homework]], roughly chapters 1-4 of Nelson, including:
** Heat and energy, order and disorder.
** Dimensional analysis and scaling.
** Estimation.
** Molecules and the ideal gas law.
** Biology basics:
*** Cell anatomy.
*** Biomolecules.
*** Molecular devices and organisms.
*** Biological timescales.
** Probability distributions.
** Ideal gas law, Boltzmann distribution, activation barriers.
** Basics of genetics.
*** Probability and genetics.
*** Mendelian inheritance, chromosome maps.
** Random walks and diffusion
*** Simple random walk model, diffusion law.
*** Discrete random walk and the binomial distribution.
*** Large N limit, Gaussian distribution.
*** Model independence of diffusion.
*** Friction and diffusion, the Einstein relation.
*** Random walks and polymer conformation.
*** Derivation of the diffusion equation.
** Biological applications of diffusion.
*** Diffusive limits on metabolism.
*** Membrane permeability.
*** Membrane electrical potential.
*** Conductivity of solutions.
* Problems on the exam will be similar to the homework problems.
* One of the best ways to study is to write your own exam: what topics would you want to test if you were teaching this class? What type of problems would you put on the exam? How many points would you assign to each?
** Here are a few review problems you can try if you like:
*** Consider a sodium ion moving through water driven by an electric field. What is the drift velocity of the ion? Estimate a numerical value assuming the electric field magnitude is similar to that across a neuron cell membrane.
*** Consider a simple model of a hard-sphere gas: consider n particles in a volume divided up into N "boxes", where each box can contain zero particles or 1 particle. How many arrangements of the particles are possible? What is the entropy of the system? Calculate the free energy and chemical potential.
*** Consider a square patch of bilayer membrane of length L on a side. Now suppose the membrane is "rippled" in one direction only with ripples of radius of curvature R. What is the total elastic energy cost of the ripples? Compare to kT, and explain what your result means for membrane structure.
** For additional exam preparation, you should solve problems in the book sections we covered; see the [[Detailed Schedule]] for the reading schedule.
* The exam will be challenging, with an average score of approximately 75%.
* Please review the general information about the [[Exams]].
!Point breakdown for 4810 (undergraduate)
|!Category|!Percentage |!Points|
|Homework | 50% |500 points |
|Midterm exam | 20% |200 points |
|Final exam | 30% |300 points |
|>|Total |1000 points |
!Point breakdown for 7810 (graduate)
|!Category|!Percentage |!Points|
|Homework | 40% |400 points |
|Midterm exam | 15% |150 points |
|Final paper | 25% |250 points |
|Final exam | 20% |200 points |
|>|Total |1000 points |
/%!Extra Credit
|!Category|!Points|
|Clicker questions |Up to 100 points|%/
!Grade determination
|!Points|!Grade|
|>900|A|
|>800, <900|B|
|>700, <800|C|
|>600, <700|D|
|<600|F|
These are the strictest possible grading standards. In other words, if you receive more than 900 points, you are guaranteed an A for the course. However, the grading standards may be relaxed (curved): the cutoff for an A may be lower than 900 points, but it will never be higher than 900 points.
For help on the homework problems, you are encouraged to attend my ''office hours'' (Tuesday 1-3 pm and Wednesday 2-3 pm).
|!HW |!Due Date|!Problems|!Hints|!Solutions (PDF)|
| 1 | 9/3 |[[Homework 1|hw1.pdf]] | |[[HW 1 solutions|hw1-solns.pdf]] |
| 2 | 9/10 |[[Homework 2|hw2.pdf]] | |[[HW 2 solutions|hw2-solns.pdf]] |
| 3 | 9/17 |[[Homework 3|hw3.pdf]] | |[[HW 3 solutions|hw3-solns.pdf]] |
| 4 | 9/24 |[[Homework 4|hw4.pdf]] |For problem 3, use a simple model that the probability of finding a gas molecule at a given altitude is related to the gravitational potential energy at that altitude (if temperature is constant). For problem 4, note that the specific k mutations must occur at k specific sites, not just anywhere in the genome. |[[HW 4 solutions|hw4-solns.pdf]] |
| 5 | 10/1 |[[Homework 5|hw5.pdf]] | |[[HW 5 solutions|hw5-solns.pdf]] |
| 6 | 10/8 |[[Homework 6|hw6.pdf]] |Typo correction: the diffusion coefficient of oxygen in water is about 10^(-9) meters squared per second, not 10^9 as I originally wrote. Suggested reference to use in finding the sodium ion current: Patlak and Horn, Journal of General Physiology Vol 79 (333) 1982. |[[HW 6 solutions|hw6-solns.pdf]] |
| 7 | 10/29 |[[Homework 7|hw7.pdf]] ||[[HW 7 solutions |hw7-solns.pdf]] |
| 8 | 11/12 |[[Homework 8|hw8.pdf]] |[[Data for problem 4|channel_data.xls]] |[[HW 8 solutions|hw8-solns.pdf]] |
| 9 | 11/19 |[[Homework 9|hw9.pdf]] ||[[HW 9 solutions|hw9-solns.pdf]] |
| 10 | 12/3 |[[Homework 10|hw10.pdf]] ||[[HW 10 solutions|hw10-solns.pdf]] |
| 11 | 12/10 |[[Homework 11|hw11.pdf]] ||[[HW 11 solutions|hw11-solns.pdf]] |
To do well in this course, you should do (and understand) the homework. Ask questions. Homework is due Thursday in class. Late homework will ''not be accepted or graded''. Homework will be graded and then returned in class the following week.
To receive full credit for a homework problem you must ''show all your work.'' The correct answer with no work shown will receive no credit. Homework must
* have ''your name'' written on the first page,
* be ''legible'',
* be ''stapled'',
otherwise your homework will not be graded.
| Instructor | Meredith Betterton |
| Office | Duane F629 |
| Office Hours | T 1-3 pm, W 2-3 pm |
| Phone | 5-6135 |
| Email | mdb at colorado dot edu |
Email availability: I will respond to email sent to me during office hours by the end of office hours. At other times, I make every effort to respond to email within 24-48 hours. I typically do not reply to email at night or on weekends.
You can find more information about my background and research at [[my web page|http://spot.colorado.edu/~mdb]].
| Grader | Quan Zhang |
| Office | |
| Phone | |
| Email | quan dot zhang at colorado dot edu |
*Lectures meet TR 11:00 am - 12:15 pm, in Duane ~G1B31 (the cookie room).
!!Lecture notes
* This is a list of PDF files of the slides, from lectures that used them. Note that these files are fairly large: the approximate size is listed for each files.
| Week | Date | Topic | Slides |
| 2 | 9/1 |Biology background: what's inside cells. |[[Lecture 2-1 notes|lecture2-1.pdf]] (2.9 MB)|
| 2 | 9/3 |Biology background: biomolecules. |[[Lecture 2-2 notes|lecture2-2.pdf]] (2.5 MB)|
| 3 | 9/8 |Biology background: macromolecules. |[[Lecture 3-1 notes|lecture3-1.pdf]] (2.4 MB)|
| 3 | 9/10 |Biology background: time. |[[Lecture 3-2 notes|lecture3-2.pdf]] (1 MB)|
[[Course Goals]]
[[Course Outline]]
[[Detailed Schedule]]
[[Homework]]
[[Course Information]]
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* The exam had a median score of 63.5, standard deviation 16, range 34-87.
* Midterm exam [[solutions|exam1_solns.pdf]] (PDF).
* The midterm exam will take place Thursday 10/15 in class.
* You can bring a 1-page formula sheet to the exam, with any notes written on it (both sides).
* Other than the formula sheet, the exam will be closed-book and closed-device.
* The exam will cover material from [[HW 1-6|Homework]], roughly chapters 1-4 of Nelson. The material covered includes:
** Heat and energy, order and disorder.
** Dimensional analysis and scaling.
** Estimation.
** Molecules and the ideal gas law.
** Biology basics:
*** Cell anatomy.
*** Biomolecules.
*** Molecular devices and organisms.
*** Biological timescales.
** Probability distributions.
** Ideal gas law, Boltzmann distribution, activation barriers.
** Basics of genetics.
*** Probability and genetics.
*** Mendelian inheritance, chromosome maps.
** Random walks and diffusion
*** Simple random walk model, diffusion law.
*** Discrete random walk and the binomial distribution.
*** Large N limit, Gaussian distribution.
*** Model independence of diffusion.
*** Friction and diffusion, the Einstein relation.
*** Random walks and polymer conformation.
*** Derivation of the diffusion equation.
** Biological applications of diffusion.
*** Diffusive limits on metabolism.
*** Membrane permeability.
*** Membrane electrical potential.
*** Conductivity of solutions.
* Problems on the exam will be similar to the homework problems.
* One of the best ways to study is to write your own exam: what topics would you want to test if you were teaching this class? What type of problems would you put on the exam? How many points would you assign to each?
** For additional exam preparation, you should solve problems in the book sections we covered; see the [[Detailed Schedule]] for the reading schedule.
* The exam will be challenging, with an average score of approximately 75%.
* Please review the general information about the [[Exams]].
/%[>img[exam_1.png]]
* The exam had a median score of 66, standard deviation 23.
* Exam 1 [[solutions|exam_1_solns.pdf]].
* The first exam will take place Wednesday 2/7 in class.%/
* [[Homework]] 11 solutions added.
* [[Homework]] 9 and 10 solutions added; typo corrected in homework 8 solution.
* [[Final Exam]] information added.
* [[Homework]] 11 added.
* [[Homework]] 10 added.
* Updated version of homework 9 added with more information for problem 5.
* [[Homework]] 8 solutions added.
* [[Homework]] 9 added.
* [[Homework]] 7 solutions added.
* [[Homework]] 8 added.
* There is no homework due Thursday 11/5. Homework 8 is deferred until 11/12.
* The midterm exams are graded and will be returned in class Thursday 11/5. See [[Midterm Exam]] for grade distribution and solutions.
* [[Homework]] 7 added.
* Midterm exam comment:
** It was clear from people's questions and comments that the exam was fairly long and difficult. Please remember that the exam is graded on a curve, and don't be depressed about it.
* [[Homework]] 6 solutions added.
* Suggested reference to use in finding the sodium ion current: Patlak and Horn, Journal of General Physiology Vol 79 (333) 1982.
* Updated [[Homework]] 6 to correct a typo in the first problem: the diffusion coefficient of oxygen in water is about 10^(-9) meters squared per second, not 10^9 as I originally wrote.
* [[Midterm Exam]] information added.
** The midterm exam is next Thursday 10/15 in class.
* [[Detailed Schedule]] updated with reading assignments for this week.
* [[Homework]] 4 and 5 solutions added.
* [[Homework]] 6 added.
* [[Homework]] 5 added.
* [[Homework]] 4 hints added.
* [[Homework]] 3 solutions added.
* [[Homework]] 4 added.
* [[Homework]] 2 solutions updated to correct typos.
* Wednesday office hours changed to 2-3 pm (used to be 3-4 pm).
* Office hours will be different ''this week only'' because of a thesis committee meeting I have to attend on Tuesday.
** Tuesday 3:30-4:30 pm (rather than the usual 1-3)
** Wednesday 2-4 pm (rather than the usual 2-3)
*[[Homework]] 1 and 2 solutions added.
* Slides from class on 9/8 and 9/10 added to [[Lectures]].
* [[Resources]] on biological imaging and animations added.
* [[Homework]] 3 added.
* Slides from class on 9/3 added to [[Lectures]].
** Note that I made a mistake in chemical terminology in lecture when I used the terms "amino acid" and "residue" to refer to the variable side group of an amino acid. The terms amino acid and residue in fact refer to the entire chemical group, not just the side chain. I've corrected this in the posted slides. Thanks to the biochemists in the class for pointing this out.
* Slides from class on 9/1 added to [[Lectures]].
* [[Homework]] 1, problem 6, contained an error: the scaling of heart rate with body mass had the wrong sign in the exponent. I've posted a corrected version.
* [[Homework]]s 1 and 2 added.
* [[Syllabus|syllabus.pdf]] added.
* [[Resources]] updated.
* [[Textbook|Textbooks]] information available.
* The room for the [[Lectures]] is now set.
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Campus policy regarding religious observances requires that faculty make every effort to reasonably and fairly deal with all students who, because of religious obligations, have conflicts with scheduled exams, assignments or required attendance.
In this class, you should speak with me at least two weeks before any anticipated class absences. See policy details at [[this site|http://www.colorado.edu/policies/fac_relig.html]].
Here are some useful resources for the course and for learning about biology and biophysics.
* Animations
**[[Molecular animations|http://wehi.edu.au/education/wehi-tv/]] by Drew Barry of the Walter and Eliza Hall Institute. See in particular these animations (direct links to quicktime .mov files)
*** [[Transcription|http://wehi.edu.au/uploads/wehi-tv/CentralDogma_Part1.mov]]
*** [[Translation|http://wehi.edu.au/uploads/wehi-tv/CentralDogma_Part2.mov]]
* Images
**[[Morphbank|http://www.morphbank.net/About/Introduction/]] database of biological images of plants and animals.
* Biological imaging information
** [[Web educational resources|http://swehsc.pharmacy.arizona.edu/exppath/micro/index.php]] from the University of Arizona imaging center. Includes links to information on optical, electron, and scanning probe microscopy.
** [[Primer on optical microscopy|http://micro.magnet.fsu.edu/primer/]] from Molecular Expressions.
** [[Optical microscopy information|http://www.microscopyu.com/articles/stereomicroscopy/]] from Nikon.
* Molecular viewing programs
** [[Rasmol|http://www.umass.edu/microbio/rasmol/]]
** [[VMD|http://www.ks.uiuc.edu/Research/vmd/]]
** [[DeepView|http://spdbv.vital-it.ch/]]
* Molecular structure databases
** [[Protein Data Bank|http://www.rcsb.org/pdb/home/home.do]] (PDB)
** [[Molecules to go|http://molbio.info.nih.gov/cgi-bin/pdb]] PDB search page
** [[Nucleic Acid Database|http://ndbserver.rutgers.edu/]]
** [[Cambridge Structural Database|http://www.ccdc.cam.ac.uk/products/csd/]] of small molecules
** [[Lipid bilayer for RasMol|http://www.umass.edu/microbio/rasmol/bilayers.htm]] page
* [[Bionumbers|http://bionumbers.hms.harvard.edu/default.aspx]]: web site with quantitative information about organisms, with references. A treasure trove of useful data.
* The [[Online biology book|http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html]] by Michael Farabee has a good introduction to many biology topics.
* [[Select topics in biophysics|http://www.biophysics.org/education/topics.htm]] from the Biophysical Society.
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<<timeline better:true firstDay:20090815 maxDays:30 maxEntries:30>>
*The term paper is required for the graduate version of the course (7810) and not for the undergraduate version.
*The paper due date is Friday, December 4 at 5 pm.
*The paper is a review of a current topic of biophysics research.
**You choose the paper topic, with suggestions from me if necessary.
**Please have your choice of topic approved by me no later than Thursday, 10/23 in class.
*The paper should be 5-10 pages (double spaced, not including figures and references) , approximately 2,000 to 2,500 words.
*The approach and format should be similar to a Comps II paper. From the department's Comps II paper guidelines:
** "The paper is a summary of the student's understanding of a broad research topic, its history, importance, ongoing efforts, outstanding issues, directions, etc. The paper is a formal, publication-ready document, complete with title, abstract figures, references, etc. It should be typeset, use 12-pt font, one-inch margins, and be double-spaced. Candidates are not to report on their own, original research. Rather, the paper is a well-referenced summary of the student's understanding of a broad research topic. The appropriate level of the paper is that of a summary article in, for example, Physics Today or the American Journal of Physics."
This course will use one primary textbook:
* "Biological Physics: Energy, Information, Life" (1st edition), by Nelson,
and one supplementary textbook:
* "Physical Biology", by Phillips, Kondev, and Theriot.
The primary text (Nelson) is essential for the course and you should own a copy. The supplementary text is recommended for students doing (or preparing to do) research in biophysics.
See also the information on [[Resources]].
Reading assignments are posted on the [[Detailed Schedule]].
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<div class='subtitle' align='right'>modified <span macro='view modified date [[DD MMM YYYY]]'></span> </div>