
ACERT Resources
last update: July 21, 2022


The National Resource facilities include:
ESR Spectrometers
 Pulsed, FT and 2DFT ESR spectrometer operating at 9 and 17 GHz: Dedicated mainly to PDS (PulseDipolar Spectroscopy)
(RA: Peter Borbat)
 Stateoftheart 218 GHz pulsed and 2DFT ESR spectrometer: Dedicated to 2DELDOR
(RA: Peter Borbat) (Nearing completion)
 35 GHz Pulsed, FT, and 2DFTESR Spectrometer: Dedicated mainly to PDS
(RA: Peter Borbat)
 95 GHz highpower pulsed, 2DFT ESR, and cw spectrometer with lowtemperature VTI
(RA: Curt Dunnam)
 93 GHz Pulsed ESR spectrometer: Mainly for microsamples
(RA: Curt Dunnam) (Nearing completion)
 170/240 GHz ESR cw spectrometer
(RA: Curt Dunnam)
 Bruker cwESR EMX spectrometer with XBand bridge: For standard ESR experiments
(RA: Curt Dunnam)
 Bruker cw & pulse spectrometer operating at 9 and 35 GHz: For PDS, ENDOR, and other standard ESR experiments
Additional;
 workstations for theoretical simulation of ESR spectra;
 wet chemistry and biochemistry lab for sample preparation, synthesis;
 electronics and machining facilities.
Downloadable Software
We have a number of useful programs available for FTP downloading. They are available here as ZIP files.
This software includes:

Software 
Function 
Programming Language 
Accessibility 
1. 
NERD 
Removes noise from cwESR and ENDOR data to greatly improve their signaltonoise ratio. 
Python 
Webserver and GUI 
2. 
WavPDS 
Removes noise from PDS data to greatly improve their signaltonoise. 
Python 
Webserver and GUI 
3. 
1D SFSVD 
Reconstructs distance distributions between nitroxide spin labels to determine protein structure from 1D PDS experiments. 
Python 
Webserver and GUI 
4. 
2D SFSVD 
Reconstructs distance distributions between nitroxide spin labels to determine protein structure from 2D PDS experiments. 
Python 
Webserver and GUI 
5a. 
nlsl.MOMD 
Performs nonlinear least squares fitting of slow motional CW ESR spectra to the microscopic order macroscopic disorder (MOMD) model 
Fortran 
downloadable package 
5b. 
nlsl.SRLS 
Performs nonlinear least squares fitting of slow motional CW ESR spectra to the advanced slowly relaxing local structure (SRLS) model 
Fortran 
downloadable package 
5c. 
EPRLL 
Simulates slow motional CW spectrum for dynamics studies with nitroxide labels. 
Fortran 
downloadable package 
6. 
lsld2 
Performs nonlinear least squares fitting of CW saturation spectra to the MOMD model 
Python + Fortran 90 
downloadable package 
7a. 
nlspmc 
Performs nonlinear least squares fitting of 2D ESR spectra to the MOMD model 
Fortran 
downloadable package 
7b. 
srls2d 
Performs nonlinear least squares fitting of 2D ESR spectra to the SRLS model 
Fortran 
downloadable package 
8a. 
nlspmc_resolvents 
Extends nlspmc to ultraslow motional rates and includes dynamic exchange between conformers 
Matlab 
downloadable package 
8b. 
sle_acert 
Python API for generating SLE matrices relevant to 1D and 2D ESR spectra 
Python + Fortran 90 
downloadable package 
Original versions of wellknown programs described in the papers "Calculating Slow Motional Magnetic Resonance Spectra: A User's Guide" by D.J. Schneider and J.H. Freed. Spin Labeling: Theory and Applications, Vol. III, Biological Magnetic Resonance 8, 176 (1989) (Plenum, NY) and "Nonlinear LeastSquares Analysis of SlowMotional EPR Spectra in One and Two Dimensions Using a Modified LevenbergMarquardt Algorithm" by David E. Budil, Sanghyuk Lee, Sunil Saxena and Jack H. Freed. J. Magn. Res. A 120, 155189 (1996) and their most recent updates: EPRLL, PC, NLSL, PC.NEW, NL2DR, NL2DC
Basic programs for CW spectral fitting using the SRLS model as described in "An Assessment of the Applicability of Multifrequency ESR to Study the Complex Dynamics of Biomolecules", Z. Liang and J.H. Freed, J. Phys. Chem. B, 103, 63846396 (1999): NLSL.SLRS
Software for Tikhonov regularization (TIKR) and maximum entropy (MEM) methods. The software was developed to extract pair distributions from pulsed ESR experiments. See: "The Determination of Pair Distance Distributions by Pulsed ESR Using Tikhonov Regularization" by Y.W. Chiang, P.P. Borbat, and J.H. Freed, J. Magn. Res. 172, 279295 (2005) and Maximum Entropy: “A Complement to Tikhonov Regularization for Determination of Pair Distances Distributions by Pulsed ESR” by Y.W. Chiang, P.P. Borbat, and J.H. Freed, J. Magn. Res. 177, 184196 (2005): PD_Tikhonov, DPD_Pkg
The programs are contained in the following subdirectories:
 EPRLL  the basic simulation programs for CW spectrum calculation including the program EPRBL used to determine the truncated basis sets. A detailed description of the method and Version 1.0 of the program is given in the “User’s guide” by Schneider and Freed (1989). See file UPDATE.DOC for cumulative changes through Version 1.6b that have been made in EPRLL and related programs since the publication of Version 1.0.
 PC  the original PC version of the CW spectrum simulation programs. (11/3/95).
 NLSL.MOMD  the least squares version of the above CW MOMD program described by Budil et al. (1996). See the subdirectory EXAMPLES for fitting examples to test.
 PC.NEW  a version of the NLSL programs suitable for running on a PC with WINDOWS 98/2000/NT/XP. Besides executables and calculation examples the folder contains files, which are necessary for Fortran Powerstation 4.0 to compile and link the source files from NLSL.MOMD folder. See README.TXT in this directory.
The source code files for the 2DFTESR programs below are designed for running under LINUX. They are stored in uncompressed or zipped format and may be obtained by ASCII ftp transfer. Tar files are provided for compressed data transfer and contain all files in the specific directories and subdirectories except the executables to save space.
READ.ME files are provided in each of the above directories giving further information on their contents and usage.
 NL2DC  Contains the twodimensional Fourier Transform (2DFT) version of the least squares program using the conjugate gradients matrix solution method. For 2D basis set pruning see the subdirectory BASIS in NL2DR.
 NL2DR  Contains the 2DFT version of the least squares program using the Rutishauser matrix solution method. For 2D basis set pruning see the subdirectory BASIS.
 NLSPMC  Contains the 2DFT version of the leastsquares program using the conjugategradient method. This version is capable of simultaneously fitting multiple spectral components and multiple spectra of different mixing times. This is an upgraded version of the NL2DC. See "LipidGramicidin Interactions: Dynamic Structure of the Boundary Lipid by 2DELDOR" by A. J. CostaFilho, R. H. Crepeau, P. P. Borbat, M. Ge, and J. H. Freed.
 NLSPMC_ri  Contains the full Sc 2DFT version of the leastsquares program using the conjugategradient method. This version is modified from the NLSPMC. The fitting is performed in the full Sc domain as described in "TwoDimensional ELDOR in the Study of Model and Biological Membranes", by Y.W. Chiang, A. J. CostaFilho, and J. H. Freed.
 NLSPMC_qmr  Contains the 2DFT version of the leastsquares program using the quasiminimal residuals (QMR) method. This program was developed and optimized for fitting 2DELDOR spectra at highfrequencies in the very slowmotional regime. See "A New LanczosBased Algorithm for Calculation HighFrequency TwoDimensional ELDOR Spectra in the SlowMotional Regime" by Y.W. Chiang and J. H. Freed.
 NLSL.SRLS  Contains the basic programs for CW spectral fitting using the SRLS model as described by Liang and J.H. Freed (1999). NLSL.SRLS is the fitting program, and ESRBS.SRLS is used to prune the basis set. LBSR.SRLS is for inputting all the parameters used in an ESRBS.SRLS calculation.
 NLSL.SRLS.EXCH  Contains updates of NLSL.SRLS for dynamic exchange of the nitroxide between two conformers. NLSL.SRLS.EXCH can be used to perform spectral simulations. Basis set pruning and parameter inputing programs are the same as those listed in NLSL.SRLS.
 PD_Tikhonov  Package includes all necessary functions required to extract the pair distributions from pulsed ESR experiments using the Tikhonov regularization method. MATLAB version 6.5 or higher is required to perform the task. PD_Tikhonov requires the use of the Regularization Toolbox package obtainable from the website: http://www2.imm.dtu.dk/~pch/Regutools/index.html. The toolbox is well documented with a detailed manual and illustrated with numerous examples. We strongly suggest users should first get acquainted with the Regularization Toolbox. After unzipping the package, please read README.pdf file.
 DPD_pkg  Package includes all necessary functions required to perform Tikhonov regularization (TIKR) method and maximum entropy method (MEM) to extract the pair distributions from pulsed ESR experiments. DPD_pkg can be considered an upgraded version of PD_Tikhonov package since both TIKR and MEM are included in the package. MATLAB version 6.5 or higher is required to perform the task. DPD_pkg requires the use of the Regularization Toolbox package obtainable from the website: http://www2.imm.dtu.dk/~pch/Regutools/index.html and which is very well documented with a manual and illustrated with numerous examples. We strongly suggest users should first get acquainted with the Regularization Toolbox. After unzipping the package, please read PD_demo.m file.
Also available are C2S, LITTLEJ, and NLSL.
The Readme and Corrections information is available in the Supplements package.
Every effort has been made to ensure that these programs are correct and thoroughly tested. However, the programs are distributed "AS IS", and all warranties, whether expressed or implied, as to correctness or fitness for any specific purpose are specifically disclaimed. In no event shall the authors be liable for any direct, consequential or incidental damages arising from the use of these programs. Free use and distribution of these programs is permitted with suitable reference to the original publication (see above) in any published work resulting from the use of these programs or programs derived from them. The programs may be copied and distributed, so long as, 1) due credit is given by retaining the comment lines at the beginning of each source file in all copies; and 2) all copies must be distributed free of charge.
Questions and comments may be directed to ACERT at acert@cornell.edu, which will forward the correspondence to the most appropriate person.

