Author Archives: Dan Gezelter

SimThyr – simulation software for pituitary thyroid feedback

This is a bit outside our normal area of expertise, but it looks interesting. Thyroid hormones play an important role in metabolism, growth and differentiation. Therefore, exact regulation of thyroid hormone levels is vital for most organisms. The mechanism for the feedback … Continue reading

Posted in Science, Software | Tagged , | Leave a comment

Not a kickstarter for science, a prize clearinghouse

Yesterday’s post on the reversible random number generators received some interesting reactions from my colleagues.  They were uniformly impressed with the solution to what everyone thought was a hard problem, but surprisingly, most of the scientists I talked to were … Continue reading

Posted in open science, Policy, Science | Tagged , , | Leave a comment

Reversible Random Number Generators

This news comes by way of John Parkhill, my new colleague here at Notre Dame. William G. Hoover (of the Nosé-Hoover Thermostat) and Carol G. Hoover issued a $500 challenge on arXiv to generate a time-reversible random number generator.  The … Continue reading

Posted in Science, Software | Tagged , , , | 3 Comments

Relax – Molecular dynamics by NMR data analysis

Edward d’Auvergne pointed out the relax program, which looks like a useful way to connect experimental NMR spectra with molecular dynamics simulations. relax is designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other … Continue reading

Posted in NMR spectroscopy, open science, Science, Software | Tagged , | Leave a comment

The Tyranny of Pi day

March 14th is -day in the US (and perhaps day in Europe). The idea of a day devoted to celebrating an important irrational number is wonderful — I’d love to see schools celebrate e-day as well, but February 71st isn’t on … Continue reading

Posted in education, Science | Leave a comment

Fantastic news on the Open Access front

The White House just posted a new policy memorandum in response to the Open Access petition:  Expanding Public Access to the Results of Federally Funded Research.   This is great news for Open Science!

Posted in Open Access, open science, Policy, Science | Leave a comment

Do.abl.es

Do you want to know how to measure DNA contour lengths using ImageJ?  Perhaps you want to stain a C. Elegans embryo for imaging?  Or possibly, you might want to test whether or not you have gotten an immune response using ELISA? Martin … Continue reading

Posted in Open Access, open science, Science | Tagged , , , , , , | 1 Comment

The Up-Goer Five Research Challenge

I thought this was silly at first, but after struggling to do it for my own research, I now think it can be a profound exercise that scientists should attempt before writing their NSF broader impact statements. Here’s the challenge: … Continue reading

Posted in education, Fun, Science | 2 Comments

Overture – A C++ toolkit for Solving PDEs in Complex Geometries

This looks useful!   The partial differential equations (PDEs) we solve in my lab are the equations of motion for atoms in molecular dynamics.  These are relatively easy to integrate numerically.  Lots of labs work with harder PDE problems  (like … Continue reading

Posted in Adaptive grids, Applied Mathematics, PDEs, Science, Software | Tagged , , , , , , | Leave a comment

SASSIE – Create atomistic models from Small Angle scattering data

Here’s a neat bit of “bridge” or “glue” software for today – SASSIE is a python-based suite for creating atomistic models of molecular systems in order to compare those models directly to data from small-angle X-ray scattering (SAXS) and small-angle … Continue reading

Posted in Science, Small-angle Scattering, Software | Leave a comment