An integral part of our development of biophysical techniques at LDMA is the dissemination of tools. Supporting our workshops and publications, the present page has links to supporting material, including movies, protocols, and demo data sets.
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3D Printing for AUC
These are some of the centerpieces and spacer models used by us, as described in detail in https://pubmed.ncbi.nlm.nih.gov/30933465/ and https://pubmed.ncbi.nlm.nih.gov/27525659/. Additional models can be found at 3d.nih.gov , including three-channel centerpieces and fluorescence optics centerpieces. We have printed all centerpieces successfully by stereolithography using high-resolution materials like Accura Xtreme, or MicroFine Green.
3mm_doublegasket_0.scad5.21 KB
3mm_doublegasket_0.stl976.13 KB
3mm_spacers_0.scad2.9 KB
3mm_spacers.stl332.63 KB
new1p75mm_dome.scad6.94 KB
new1p75mm_dome.stl1.24 MB
new4mm_dome3.scad6.9 KB
new4mm_dome3.stl1.37 MB
new12mm_dome3.scad6.96 KB
new12mm_dome3.stl1.35 MB
EVILFIT Demo
Here are instructions for how to install and use EVILFIT, including a video and sample data.
Introductory Analytical Ultracentrifugation Reviews
For reviews of analytical ultracentrifugation, see https://pubmed.ncbi.nlm.nih.gov/23682298/ (general review from 2013), https://doi.org/10.1002/0471140864.ps2012s71 (detailed SE and SV protocols, 2013), https://doi.org/10.1002/cpps.109 (SV for self-associating systems, 2020), https://pubmed.ncbi.nlm.nih.gov/12192063/ (an introductory review from 2002), and https://pubmed.ncbi.nlm.nih.gov/34986360/ (2022 recommendations on quantitating aggregates of antibody therapeutics by the CASSS Biophysical Working Group). For detailed information see our books "Basic Analytical Ultracentrifugation", "Sedimentation Velocity Analytical Ultracentrifugation: Discrete Species and Size-Distributions of Macromolecules and Particles", and "Sedimentation Velocity Analytical Ultracentrifugation: Interacting Systems". Below are some reviews that may be harder to find.
CPI_2008_PracticalIntroSE.pdf318.42 KB
CPI_2008_PracticalIntroSV.pdf563.72 KB
CSHLP_2005_AUC_intro.pdf704.14 KB
Mixer
These are instructions and movies of a Lego cell mixer to resuspend samples after a sedimentation velocity run. For a detailed description and performance see https://pubmed.ncbi.nlm.nih.gov/32407733/.
Mixer_AnalBiochemNotes.pdf178.01 KB
SupportingMaterial_Partslist.pdf222.99 KB
Protocols
These materials contain some step-by-step protocols and other practical information for SE and SV analytical ultracentrifugation. See also the protocols listed above in the section on Reviews.
FlowChartAUC.pdf138.72 KB
SedimentationEquilibrium.pdf138.86 KB
SedimentationVelocity.pdf67.24 KB
Step-by-step_nonideal_c(s).docx14.55 KB
Step-by-step_nonideal_c(s).pdf76.85 KB
TOSE_implementation.wmv34.44 MB
TOSE_optimization.wmv38.86 MB
Reaction Boundary Movies
These movies and legends belong to the publication introducing the effective particle model for reaction boundaries, published in https://pubmed.ncbi.nlm.nih.gov/20441765/ . In the meantime, a tool has been incorporated into SEDPHAT (in the Options->Interaction Calculator menu) that will generate movies for conditions corresponding to a binding model and concentrations entered by the user.
Sedimentation-Diffusion Movies
These are movies illustrating the picture of Brownian motion with a bias to describe analytical ultracentrifugation experiments.
diffusion-sedimentation.zip2.85 MB
newmovies.pdf458 KB
Analytical Ultracentrifugation Tutorials
In addition to the above reviews and protocols, here are some tutorial videos and screenshot sequences for different data analysis tasks.
basic_c(s)_analysis.wmv15.81 MB
TestApproach2Equilibrium.pdf970.55 KB
Video demo_c(s) bimodal ff0.wmv25.97 MB
Using Fluorescence Detection for AUC
For a more recent protocol, see Nature Protocols volume 12, pages1777–1791 (2017) https://www.nature.com/articles/nprot.2017.064
FDSProtocol.pdf271.43 KB
youtube.docx13.37 KB
SEDFIT Command Line Interface
For a detailed description of the automated user interface of SEDFIT, see https://pubmed.ncbi.nlm.nih.gov/37669309/, and the extension described in https://pubmed.ncbi.nlm.nih.gov/38967176/. Below are example input files and MATLAB scripts that may be used as a template for serial analyses.
ExampleInput.xml1.85 KB
ExampleOutput.zip996.83 KB
MATLAB scripts mlSEDFIT.zip6.92 KB
ListOfCommandLineInputParameters_SEDFIT17.pdf222.8 KBJune 11, 2024
mlSEDFIT2.zip7.49 KBMay 23, 2023