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://www.ruppweb.org/Xray/101index.html 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.
• Advanced discussion Links to an external site. about the details. 

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.
• https://www.youtube.com/watch?v=4Z0sQ_GhBkk Links to an external site.
• https://www.thermofisher.com/us/en/home/electron-microscopy/life-sciences/cryo-tomography.html Links to an external site.
• https://www2.mrc-lmb.cam.ac.uk/research/scientific-facilities-and-support-services/electron-microscopy/ Links to an external site.
• National Center for X-ray Tomography Links to an external site.
• Lecture by Carolyn Larabell Links to an external site., director of NCXT Links to an external site. at LBNL. Closed caption version Links to an external site..

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://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.
• 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.
• Solution of Poisson Boltzmann eqn for two spheres Links to an external site.
• Software Links to an external site. for solving Boltzmann eqn and use with proteins 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.

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.
• actin filament 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.. Closed caption version Links to an external site.
• Nanopore Sequencing video Links to an external site. by Oxford Nanopore Technologies Links to an external site.
• This uses a modified version of alpha-hemolysin Links to an external site.

Closed caption version 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  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.
• 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.Closed caption version Links to an external site.
• actin/myosin Links to an external site. gliding assays . Closed caption version Links to an external site.
• microtubule/kinesin Links to an external site. gliding assay
• Myosin V, and Links to an external site. this Links to an external site. (here Links to an external site. is the supplementary 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.Closed caption version Links to an external site.
• Kinesin/Microtubule motion explained with narration  Links to an external site.Closed caption version Links to an external site.
• Bacterial Flagellum video Links to an external site.Closed caption version 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.
• 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://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.
• 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.
• 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 gastrulation Links to an external site.
• and Drosophila gastrulation/ventral furrow formation 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.
• 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.
• Becoming: From zygote to tadpole, in six stunning minutes Links to an external site.

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.Closed caption version 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 wikipedia Links to an external site. entry.
• How they did it Links to an external site.Closed caption version Links to an external site., giant squid axon Links to an external site.Closed caption version Links to an external site.
• synapses in neurons Links to an external site.Closed caption version 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.
• https://web.stanford.edu/class/ee102/lectures/fourtran Links to an external site.

Online biophysics programs:

Molecular Workbench:

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

Future Directions

• 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.