Useful Links

• Xray-Crystallography
• Tomography
• FRAP
• Protein Structure
• NMR
• Optical Tweezers
• Electrophoresis
• Time Dependent Effects
• Motor Proteins
• Diffusion
• Pattern Formation
• Development
• Neurons
• Fourier Transforms

General Bio:

• http://www.biology.arizona.edu/DEFAULT.html Links to an external site.

Biophysics lectures:

• Biophysics Lectures Links to an external site. from Berkeley

X-ray Crystallography:

• Ewald sphere movie: http://escher.epfl.ch/x-ray/diff.mpeg Links to an external site.
• http://escher.epfl.ch/eCrystallography/ Links to an external site.
• Berkeley Lecture Links to an external site.
• Intuitive discussion Links to an external site. of xray crystallography by Kevin Cowtan Links to an external site..
• For the ambitious: How to solve protein structures on your computer, by Bill Scott of UCSC.

Tomography

• http://en.wikipedia.org/wiki/Tomography Links to an external site.
• http://en.wikipedia.org/wiki/Tomographic_reconstruction Links to an external site.
• http://en.wikipedia.org/wiki/Projection-slice_theorem Links to an external site.
• http://www.lce.hut.fi/~engelhar/csc/CSC-94.html Links to an external site.
• National Center for X-ray Tomography Links to an external site.
• http://www.msg.ucsf.edu/agard/research/microscopy.html Links to an external site.
• Lecture by Carolyn Larabell Links to an external site., director of NCXT Links to an external site. at LBNL.

Fluorescence Recovery After Photobleaching

• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1334945/pdf/biophysj00300-0068.pdf Links to an external site.
• http://www.math.ualberta.ca/~devries/reprints/methods2003.pdf Links to an external site.

Fluorescence Resonance Energy Transfer

• http://bio.physics.illinois.edu/newTechnique.html Links to an external site.
• http://www.nature.com/nmeth/journal/v5/n6/full/nmeth.1208.html Links to an external site.

Protein Structure

Alpha Helix Links to an external site.

• Helices Links to an external site.
• Protein Data Bank Links to an external site.
• Helix coil transition Links to an external site.
• Protein Structure Links to an external site. and power point Links to an external site..
• papers and talks Links to an external site. on protein folding.
• Solutions for the HP model Links to an external site.
• travelling salesman Links to an external site.
• http://en.wikipedia.org/wiki/Traveling_salesman_problem Links to an external site.
• Derivation of the Poisson-Boltzmann Eqn Links to an external site. and here Links to an external site.
• Solution of Poisson Boltzmann eqn for parallel cylinders Links to an external site. and two spheres Links to an external site.

DNA and RNA

• http://en.wikipedia.org/wiki/DNA Links to an external site.
• http://en.wikipedia.org/wiki/RNA Links to an external site.
• http://en.wikipedia.org/wiki/DNA_melting Links to an external site.

NMR

http://www.nmr2.buffalo.edu/resources/edu/matr/Edison_Bloch_Paper.pdf Links to an external site.

Imaging:

• http://www.math.upenn.edu/~cle/notes/Lect1.pdf Links to an external site.
• http://www.math.upenn.edu/~cle/notes/Lect2.pdf Links to an external site.
• http://www.imaios.com/en/e-Courses/e-MRI Links to an external site.
• Notes at http://www.radiology.georgiahealth.edu Links to an external site.

Spectroscopy:

• http://www.cis.rit.edu/htbooks/nmr/inside.htm Links to an external site.
• NMR lecture Links to an external site. by David Wemmer, Berkeley.

Cell Bio Intro

• http://www.johnkyrk.com/ Links to an external site.
• http://www.biology.arizona.edu/cell_bio/cell_bio.html Links to an external site. (downloadable)
• http://www.cellsalive.com/ Links to an external site.

Microtubules:

• http://en.wikipedia.org/wiki/Microtubule Links to an external site.

Actin

• http://en.wikipedia.org/wiki/Actin Links to an external site.
• http://www.youtube.com/watch?v=ks2C9FJ9pFY&NR=1 Links to an external site.

Optical Tweezers

• Block Lab, Stanford Links to an external site.
• sophisticated manipulation Links to an external site. video
• more manipulation Links to an external site. (video)
• fluorescent stretched DNA Links to an external site. video
• neutrophil chemotaxis Links to an external site. video
• DNA condensation Links to an external site. video
• Single Molecule Force Spectroscopy for RNA Links to an external site.
• Lecture Links to an external site. by Steven Smith.

Electrophoresis

• Virtual Electrophoresis Links to an external site.
• Explanation Links to an external site. with lab photos
• wikipedia Links to an external site.
• papers Links to an external site.
• Short video Links to an external site. of DNA electrophoresis by Carlos Bustamante Links to an external site..
• Nanopore Sequencing video Links to an external site. by Oxford Nanopore Technologies Links to an external site.

Time dependent effects

• James Sethna has a great book on stat mech http://pages.physics.cornell.edu/sethna/StatMech/EntropyOrderParametersComplexity.pdf Links to an external site. that has a lot of discussion of many things including the fluctuation dissipation theorem
• The Langevin equation http://cbp.tnw.utwente.nl/PolymeerDictaat/node29.html Links to an external site.
• More Langevin eqn stuff http://units.physics.uwa.edu.au/__data/page/115450/lecture3_(brownian_motion)-NF.pdf Links to an external site. (or here Links to an external site.) and http://www.pmaweb.caltech.edu/~mcc/Ph127/b/Lecture15.pdf Links to an external site. , http://www.pmaweb.caltech.edu/~mcc/Ph127/b/Lecture16.pdf Links to an external site.
• Relation to the Fokker-Planck eqn http://www.phys.au.dk/~fogedby/statphysII/fokker-planck.pdf Links to an external site.
• http://mathworld.wolfram.com/Wiener-KhinchinTheorem.html Links to an external site.
• Fluorescence correlation spectroscopy Links to an external site.
• Stochastic Gene Expression Links to an external site.

Motor Proteins

• 
  Muscle contractile proteins Links to an external site.
• actin/myosin Links to an external site. gliding assays
• microtubule/kinesin Links to an external site. gliding assay
• Myosin V Links to an external site. and this Links to an external site., or this Links to an external site. with supplemental Links to an external site. information: Spudich Lab
• Myosin V simulation Links to an external site. with movies Links to an external site.
• Myosin/Actin motion explained with narration Links to an external site.
• Kinesin/Microtubule motion explained with narration Links to an external site.
• Bacterial Flagellum video Links to an external site.
• in vitro Links to an external site. cilia-like motion and videos Links to an external site.
• Life at low Reynolds number Links to an external site. by E.M. Purcell
• Lecture Links to an external site.by Yimin Zou Links to an external site. from UCSD.

Diffusion

• Reference material for Random walks and diffusion Links to an external site.
• Diffusion in external potentials and Kramer's theory. Enzyme kinetics Links to an external site.. From biological and soft systems at the Cavendish Laboratory.

Pattern Formation

• http://www.sjsu.edu/faculty/watkins/murray.htm Links to an external site.
• A paper by Evelyn Sanders on pattern formation Links to an external site.
• http://www.resnet.wm.edu/~jxshix/math490/Turing%20Patterns%20in%20Animal%20Coat.ppt Links to an external site.
• Papers Links to an external site.
• Check out youtube movies of the Belousov-Zhabotinsky Links to an external site. reaction
• http://biology.kenyon.edu/courses/biol114/Chap13/Chapter_13C.html Links to an external site.
• http://herbie.ucsd.edu/~levine/ Links to an external site.
• http://www.cmp.caltech.edu/~mcc/Patterns/index.html Links to an external site.
• http://www.scholarpedia.org/article/Barkley_model Links to an external site.
• http://en.wikipedia.org/wiki/Fractals Links to an external site.
• Scale invariance Links to an external site.
• fractals in physiology Links to an external site.
• The Snowflake: Winter's Secret Beauty Links to an external site.
• Diffusion-Limited Aggregation and its Simulation Links to an external site.
• http://markjstock.org/dla3d/ Links to an external site.
• Self Assembly in Nature Links to an external site. by Radhika Nagpal Links to an external site.
• L-systems online generator Links to an external site.
• electrical Links to an external site. analogy

In Bacterial Colonies

• • Papers on diffusion limited bacterial morphogenesis Links to an external site.

Development

• http://en.wikipedia.org/wiki/Drosophila_embryogenesis Links to an external site.
• Drosophila Development Links to an external site.
• Drosophila gastrulation Links to an external site.
• and http://www.youtube.com/watch?v=1MnwHRURKns&feature=related Links to an external site.
• Early mitotic divisions Links to an external site.
• More details of mitosis Links to an external site.
• FlyMove Links to an external site.

• Regeneration of the hydra Links to an external site.
• http://www.npr.org/blogs/krulwich/2014/09/26/351440526/everything-dies-right-but-does-everything-have-to-die-here-s-a-surprise Links to an external site.
• modelling development of the Hydra Links to an external site. or here Links to an external site.
• Matrix elasticity directs stem cell lineage specification Links to an external site.
• Early drosophila development Links to an external site.
• Cytoplasmic Streaming Links to an external site. in drosophila oocytes (Serbus et al)
• cytoplasmic streaming Links to an external site. in Elodea Links to an external site.
• Talk Links to an external site. by Josh Deutsch on ooplasmic streaming.

Neurons

• 
  3D animation of firing neurons Links to an external site.
• Action potential animation Links to an external site.
• Action potential explanation Links to an external site.
• Na/K pump Links to an external site.
• potassium channel Links to an external site.
• The origin of the membrane resting potential Links to an external site.
• Hodgkin Huxley's classic paper Links to an external site. on nerve conduction
• and http://hebb.mit.edu/courses/9.29/2004/readings/hodgin-huxley%20model%206.pdf Links to an external site.
• Lecture Links to an external site. on Hodgkin Huxley eqns.
• and wikipedia Links to an external site. entry.
• How they did it Links to an external site., giant squid axon Links to an external site.
• synapses in neurons Links to an external site.
• Simultaneous recording of hundreds of neurons

Polymer Physics

• Notes Links to an external site.

Math:

• http://www.falstad.com/fourier/ Links to an external site.
• http://www.westga.edu/~jhasbun/osp/Fourier.htm Links to an external site.
• http://www.jcrystal.com/steffenweber/JAVA/jfourier/jfourier.html Links to an external site.
• http://sepwww.stanford.edu/oldsep/hale/FftLab.html Links to an external site.

Various Properties:

• http://www.cs.unm.edu/~williams/cs530/theorems6.pdf Links to an external site.
• http://www.phys.cwru.edu/courses/p431/notes-2003/node78.html Links to an external site.
• Nice intuitive discussion of Fourier Transforms Links to an external site. and xray crystallography by Kevin Cowtan Links to an external site..
• Discrete Fourier Transforms (DFT's Links to an external site.)
• Wiener-Khinchin Theorem Links to an external site.

Online biophysics programs:

Molecular Workbench:

• http://mw.concord.org/modeler/ Links to an external site.

Future Directions

• http://www.illumina.com/pages.ilmn?ID=203 Links to an external site.
• http://www.nature.com.oca.ucsc.edu/nbt/journal/v26/n10/full/nbt1485.html
• http://en.wikipedia.org/wiki/Systems_biology Links to an external site.
• http://en.wikipedia.org/wiki/Bioinformatics Links to an external site.
• http://en.wikipedia.org/wiki/Neuroscience Links to an external site.
• http://en.wikipedia.org/wiki/Origin_of_life Links to an external site.

Science Sociology

• Most Published Research Findings Are False Links to an external site. by John Ioannidis, Stanford
• How many papers are right Links to an external site.?
• http://www.ncbi.nlm.nih.gov/pubmed/23706263 Links to an external site.
• http://www.nature.com/nature/journal/v483/n7391/full/483531a.html Links to an external site.
• Scientific journals accept gibberish Links to an external site.