title: PJNMR: a platform-independent graphical simulation tool for NMR spectroscopy.
abstract: A new simulation program for multinuclear NMR is introduced. PJNMR (Pure Java NMR) 2.0, written entirely in the Java programming language, simulates pulse sequences on systems of up to three weakly coupled spins-1/2 with a command-driven, spectrometer-like interface. Users may simulate the effects of pulses, precessions, and pulsed field gradients on the spin system, with a graphical display showing the state of the density matrix (in a novel polar-coordinate representation) as well as the magnetization vectors for each nucleus. Relevant computations and optimizations as implemented in the code are detailed, along with the object-oriented structures used. A description of the simulation environment is given, illustrated with a series of example pulse sequences highlighting the insights gained in the graphical presentation.
authors.affiliation: Protein Engineering Network of Centres of Excellence, University of Alberta, Alta., Edmonton, Canada T6G 2H7.
authors.forename: Paul-Jean
authors.initials: PJ
authors.lastname: Letourneau
authors.forename: Robert
authors.initials: R
authors.lastname: Boyko
authors.forename: Brian D
authors.initials: BD
authors.lastname: Sykes
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy; D012984:Software