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Publications
PEER-REVIEWED
- Shyu C, Ytreberg FM, Reducing bias and uncertainty of free energy estimates by using polynomial regression to analyze thermodynamic integration data, J Comput Chem, 30:2297 (2009) PDF
- Ytreberg FM, Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations, J Chem Phys, 130:164906 (2009) PDF
- Ytreberg FM, Zuckerman DM, A black-box re-weighting analysis can correct flawed simulation data, Proc Natl Acad Sci USA 105:7982 (2008) PDF Appendix
- Ytreberg FM, Using non-equilibrium simulations to estimate equilibrium binding affinities, AIP Conf Proc 978:65 (2008) PDF
- Ytreberg FM, Aroutioutian SK, Zuckerman DM, Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model, J Chem Theory Comput 3:1860 (2007) PDF
- Ytreberg FM, Zuckerman DM, Swendsen RH, Comparison of free energy methods for molecular systems, J Chem Phys 125:184114 (2006) PDF
- Ytreberg FM, Zuckerman DM, Simple estimation of absolute free energies for biomolecules, J Chem Phys 124:104015 (2006) PDF
- Lyman E, Ytreberg FM, Zuckerman DM, Resolution exchange simulation, Phys Rev Lett 96:028105 (2006) PDF
- Ytreberg FM, Zuckerman DM, Peptide conformational equilibria computed via a single-stage shifting protocol, J Phys Chem B 109:9096 (2005) PDF
- Ytreberg FM, Zuckerman DM, Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems, J Comput Chem 25:1749 (2004) PDF Software
- Ytreberg FM, Zuckerman DM, Single-ensemble nonequilibrium path-sampling estimates of free energy differences, J Chem Phys 120:10876 (2004) PDF Erratum
- Ytreberg FM, McKay SR, A quasi-equilibrium analysis to predict he dependence of ferrofluid aggregate properties on field ramping rate, IEEE Trans Magn 39:2648 (2003) PDF
- Ytreberg FM, McKay SR, Model for the effect of ramping rate on ferrofluid aggregates, IEEE Inter Mag Conf GA-01 (2003) PDF
- Ytreberg FM, McKay SR, Calculated properties of field-induced aggregates in ferrofluids, Phys Rev E 61:4107 (2000) PDF
- Ytreberg FM, McKay SR, A second mechanism for transitions in a reaction diffusion system, Phys Rev E 59:3376 (1999) PDF
SUBMITTED
- Shyu C, Ytreberg FM, Computational Estimates of Binding Affinities for Estrogen Receptor Isoforms in Rainbow Trout, submitted http://arxiv.org/abs/0909.0981
- Shyu C, Ytreberg FM, Use of polynomial interpolation to reduce bias and uncertainty of free energy estimates via thermodynamic integration, submitted http://arxiv.org/abs/0809.0882
OTHER
- Ytreberg FM, Pattern formation in reaction-diffusion and ferrofluid systems (Ph.D. Dissertation, The University of Maine, 2000) PDF
- Ytreberg FM, McKay SR, Scaling behavior of field-induced aggregates in ferrofluids, e-print available http://arxiv.org/abs/cond-mat/0308261
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