Publications

"Development of boxed molecular dynamics for efficient simulations of structural transitions", CPGS report, Department of Chemistry, University of Cambridge, June 2013, advisor: David Wales, examiners: Daan Frenkel and Stuart Althorpe

"Development and application of computational methods for decomposition of large reaction networks and determination of their stability", Diploma thesis, Faculty of Chemical Engineering, Institute of Chemical Technology in Prague, August 2012, advisor: Igor Schreiber, examiner: Otto Hadač

"Intramolecular and intermolecular interactions in proteins", Diploma thesis, Faculty of Science, Charles University in Prague, June 2012, advisor: Jiří Vondrášek, examiner: Karel Berka

"Potential energy stabilizing a hydrophobic core of protein and its contribution to overall stability", Bachelor thesis, June 2010, advisor: Jiří Vondrášek, examiner: Vojěch Spiwok

"Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling", Boris Fačkovec, Eric Vanden-Eijnden and David J. Wales, 2015, J. Chem. Phys. 143, 044119

"Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications", Boris Fačkovec and Jiří Vondrášek, 2012, J. Phys. Chem. B, 116 (42), 12651-12660

"Systems and Computational Biology - Molecular and Cellular Experimental Systems", Chapter 20 "Decomposition Of Intramolecular Interactions Between Amino-acids In Globular Proteins - A Consequence For Structural Classes Of Proteins And Methods Of Their Classification", Boris Fačkovec and Jiří Vondrášek, September 2011, pp. 69-82.