Computational Biophysical Chemistry

Hansmann Group







Contact us at:
Dept. of Chemistry and Biochemistry
University of Oklahoma
101 Stephenson Parkway
Norman, OK 73019-5251,USA


Tel:  -405-325-2386
Fax:  -405-325-6111
E-mail: uhansmann at ou.edu
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Publication List

by

Ulrich H.E. Hansmann

221) H. Zhang, W. Xi, U.H.E. Hansmann and Y. Wei, Fibril-Barrel Transitions in Cylindrin Amyloids, J. Chem. Theor. Comp., accepted for publication.

220) W. Xi and U.H.E. Hansmann, Ring-like N-fold Models of Aβ42 fibrils, Scientific Report, 7 (2017) 6588.

219) E.J. Alred, M.V. Nguyen, M. Martin and U.H.E. Hansmann, Molecular dynamics simulations of early steps in RNA-mediated conversion of prions, Protein Science, 26 (2017) 1524.

218) N.A. Bernhardt, W. Xi, W. Wang and U.H.E. Hansmann, Simulating Protein Fold Switching by Replica-Exchange-with-Tunneling, J. Chem. Theor. Comp. 12 (2016) 5656; 13 (2017) 393.

217) E.J. Alred, M. Phillips, M. Bhavaraju and U.H.E. Hansmann, Stability Differences in the NMR ensembles of amyloid-β fibrils, J. Theor. Comp. Chem. 15 (2016), 1650059.

216) W. Xi, W.Wang, G.L. Abbott and U.H.E. Hansmann, Stability of a recently found triple-β-stranded Aβ1-42 fibril motif, J. Phys. Chem. B, 120 (2016) 4548.

215) F. Yasar, N.A. Bernhardt and U.H.E. Hansmann, Replica-Exchange-with-Tunneling for fast Exploration of Protein Landscapes, J. Chem. Phys., 143 (2015) 224102; 145 (2016) 057102.

214) W.M. Berhanu, E.J. Alred and U.H.E. Hansmann, Stability of Osaka mutant and wild-type fibril models, J. Phys. Chem. B, 119 (2015) 13063.

213) W.M. Berhanu, E.J. Alred, N.A. Bermhardt and U.H.E. Hansmann, All-atom simulation of amyloid aggregates, Physics Procedia, 68C (2015) 61.

212) M. Bhavaraju, M. Phillips, D. Bowman, J.M. Aceves-Herndez and U.H.E. Hansmann, Binding of ACE-inhibitors to In Vitro and Patient-derived Amyloid-β Fibril Models, J. Chem. Phys. 144 (2016) 015101.

211) M. Bhavaraju and U.H.E. Hansmann, Effect of single point mutations in a form of systemic amyloidosis, Protein Science, 24 (2015) 1451.

210) H.W. German, M. Bhavaraju, S. Uyaver and U.H.E. Hansmann, Computational Insights Into The Self-Assembly Of Phenylalanine-Based Molecules, TASK Quarterly, 18 (2014) 365.

209) E.J. Alred, E.G. Scheele, W. M. Berhanu, and U.H.E. Hansmann, Comparative Stability Analysis Of D23N Mutated Aβ, TASK Quarterly, 18 (2014) 365.

208) E.J. Alred, M. Phillips, W.M. Berhanu and U.H.E. Hansmann, On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains, Protein Science, 24 (2015) 923.

207) W.M. Berhanu and U.H.E. Hansmann, Stability of Amyloid Oligomers , in: T. Karabencheva-Christova (ed.), Advances in Protein Chemistry and Structural Biology - Bimolecular Modeling and Simulations,vol. 96, Academic Press, London, GB, (2014), p. 113 - 141.

206) H.W. German, S. Uyaver and U.H.E. Hansmann, Self-Assembly of Phenylalanine-Based Molecules, J. Phys. Chem. A, 119 (2015) 1609-1615.

205) E.J. Alred, E.G. Scheele, W.M. Berhanu and U.H.E. Hansmann, Stability of Iowa Mutant and Wild Type Aβ-peptide Aggregates, J. Chem. Phys., 141 (2014) 175101.

204) W.M. Berhanu and U.H.E. Hansmann, Inter-species cross-seeding: stability and assembly of rat - human amylin aggregates, PlosONE, 9 (2014) e97051.

203) F. Yasar, P. Jiang and U.H.E. Hansmann, Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9, Euro. Phys. Lett., 105 (2014) 30008.

202) S. Uyaver and U.H.E. Hansmann, Multicanonical Monte Carlo Simulations of a de novo designed protein with end-to-end β-sheet, J. Chem. Phys., 140 (2014) 065101.

201) N.A. Bernhardt, W.M. Berhanu and U.H.E. Hansmann, Mutations and cross-seeding of amylin fibril-like oligomers, J. Phys. Chem. B, 117 (2013) 16076.

200) W. M. Berhanu, P. Jiang and U.H.E. Hansmann, Enhanced Sampling for Biomolecular Simulations, in: Adam Liwo (ed.), Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - From Bioinformatics to Molecular Quantum Mechanics, Springer, Heidelberg (2014), p. 249-267.

199) F. Yasar, A.K. Sieradzan and U.H.E. Hansmann, Folding and Self-Assembly of a small Heterotetramer, J. Chem. Phys., 140 (2014) 105103.

198) W.M. Berhanu, F. Yasar and U.H.E. Hansmann, In Silico cross seeding of Aβ and amylin fibril-like oligomers, ACS Chem. Neurosci., 4 (2013) 1488.

197) P. Jiang, F. Yasar and U.H.E. Hansmann, Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics, J. Chem. Theor. Comput., 9 (2013) 3816.

196) W.M. Berhanu and U.H.E. Hansmann, The stability of cylindrin β-barrel amyloid oligomer models - a molecular dynamics study, Proteins, 81 (2013) 1542.

195) W. M. Berhanu, P. Jiang and U.H.E. Hansmann, Simulation of folding and association of a home-tetrameric protein complex in an all-atom Go model, Phys. Rev. E, 87 (2013) 014701.

194) W.M. Berhanu and U.H.E. Hansmann, Side-chain hydrophobicity and the stability of Aβ(16-22) aggregates, Protein Science, 21 (2012) 1837.

193) A.K. Sieradzan, U.H.E. Hansmann, H.A. Scheraga and A. Liwo, Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues, J. Chem. Theor. Comp., 8 (2012) 4746.

192) A.K. Sieradzan, A. Liwo and U.H.E. Hansmann, Folding and self-assembly of a small protein complex, J. Chem. Theor. Comp, 8 (2012) 3416.

191) M. Kouza and U.H.E. Hansmann, An Optimized Replica Exchange Molecular Dynamics Approach, in: P. Carloni, U.H.E. Hansmann, Th. Lippert, J.H. Meinke, S. Mohanty, W. Nadler and O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB11) - Celebrating Harold Scheraga's 90th Birthday, Verlag des Forschungszentrums Jülich, IAS Series vol. 8, Jülich (2012), p. 91-94.

190) P. Carloni, U.H.E. Hansmann, Th. Lippert, J.H. Meinke, S. Mohanty, W. Nadler and O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB11) - Celebrating Harold Scheraga's 90th Birthday, Verlag des Forschungszentrums Jülich, IAS Series vol. 8, Jülich (2012).

189) W.M. Berhanu and U.H.E. Hansmann, Structure and dynamics of amyloid-β segmental polymorphism, PlosONE, 7 (2012) e41479.

188) P. Jiang and U.H.E. Hansmann, Modeling Structural Flexibility of Proteins with Go-Models, J. Chem. Theor. Comp, 8 (2012) 2127.

187) U.H.E. Hansmann, Proteins studied by Computer Simulations, in: Gh. Adam, J. Busa, M. Hnatic (eds.), Mathematical Modeling and Computational Science, Springer, Berlin - Heidelberg (2012), p. 56 - 65.

186) M. Kouza and U.H.E. Hansmann, Folding Simulations of the A and B domain of Protein G, J. Phys. Chem. B, 116 (2012) 6645.

185) M.L. Gaye, C. Hardwick, M. Kouza and U.H.E. Hansmann, Chamelonicity and folding of the C-fragment of TOP7, Eur. Phys. Let., 97 (2012) 68003.

184) J. Wang, W. Zhu, G. Li and U.H.E. Hansmann, Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent, J. Chem. Phys., 135 (2011) 084115..

183) Ming Han and U.H.E. Hansmann, Replica Exchange Molecular Dynamics of the Thermodynamics of Fibril Growth of Alzheimer's Abeta42-peptide, J. Chem. Phys., 135 (2011) 065101.

182) U.H.E. Hansmann, Sampling Protein Energy Landscapes - The Quest for Efficient Algorithms, in A. Kolinski (ed.), Multiscale Approaches to Protein Modeling, Springer, New York (2011), p. 209-230.

181) M. Kouza and U.H.E. Hansmann, Velocity scaling for optimizing replica exchange molecular dynamics, J. Chem. Phys., 134 (2011) 044124..

180) M. Kouza, S. Gowtham, M. Seel and U.H.E. Hansmann, A numerical investigation into possible mechanisms by that the A629P mutant of ATP7A causes Menkes Disease, Physical Chemistry - Chemical Physics, 12 (2010) 11390.

179) P. Anand and U.H.E. Hansmann Internal and environmental effects on folding and dimerization of the Alzheimer's Beta-amyloid peptide, Molecular Simulation, 37 (2011) 440.

178) U.H.E. Hansmann, Temperature Random Walk Sampling of Protein Configurations, Physica A, 389 (2010) 1400.

177) P. Kar, W. Nadler and U.H.E. Hansmann, Microcanonical Replica Exchange Molecular Dynamics Simulation of Proteins, Phys. Rev. E, 80 (2009) 056703.

176) J.H. Meinke and U.H.E. Hansmann, Thermodynamics and Free-energy driven Folding of the 67-residue protein GSαW - A large-scale Monte Carlo study, J. Comp. Chem., 30 (2009) 1642.

175) P. Anand, F.S. Nandel and U.H.E. Hansmann, The Alzheimer's β-amyloid Aβ(1-39) dimer in an implicit solvent, J. Chem. Phys., 129 (2008) 195102.

174) W. Nadler, J.A. Meinke and U.H.E. Hansmann, Folding Proteins by First-Passage-Times Optimized Replica Exchange, Phys. Rev. E, 78 (2008) 061905.

173) W. Nadler and U.H.E. Hansmann, Optimized explicit-solvent replica-exchange molecular dynamics from scratch, J. Phys.Chem. B,112 (2008) 10386.

172) U. H. E. Hansmann, J. Meinke, S. Mohanty, W. Nadler and O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB08), NIC Series Vol. 40, Jülich (2008).

171) S. Mohanty and U. H. E. Hansmann, A Non-Native Helix Extension Channels Folding, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB08), NIC Series Vol. 40, Jülich (2008), p. 329.

170) P. Anand, F. Nandel and U. H. E. Hansmann, Conformational Study of Alzheimer's Aβ Wild Type Peptide and Flemish Mutant, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB08), NIC Series Vol. 40, Jülich (2008), p. 149.

169) S. Mohanty and U.H.E. Hansmann, Caching of a Chameleon Segment facilitates Folding of a Protein with End-to-End β -sheet, J. Phys. Chem. B, 112 (2008) 15134.

168) U.H.E. Hansmann, Toward reliable simulations of protein folding, misfolding and aggregation, in: Michael Conn (Ed.), Progress in Molecular Biology and Translational Science vol. 84 Molecular Biology of Protein Folding, Part B, Elsevier (2008), p. 39 - 56.

167) O. Zimmermann and U.H.E. Hansmann, LOCUSTRA: Accurate prediction of local protein structure using a two-layer SVM approach, J. Chem. Inf. Mod.,48 (2008) 1903.

166) P. Anand, N.S. Nandel and U.H.E. Hansmann, The Alzheimer's β-amyloid Aβ(1-39) monomer in an implicit solvent, J. Chem. Phys.,128 (2008) 165102.

165) J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann and U.H.E. Hansmann, Computer Simulation of Proteins - Thermodynamics and Structure Prediction, Eur. Phys. J. D, 51 (2009) 33.

164) J.H. Meinke, S. Mohanty, W. Nadler,T. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Protein Simulations on Massively Parallel Computers, in: G. Münster, D. Wolf, M. Kremer, NIC Symposium 2008, Jülich (2008), p. 9-16.

163) O. Zimmermann and U.H.E. Hansmann, Understanding protein folding: Small proteins in silico, Biochimica et Biophysica Acta - Proteins and Proteomics, 1784 (2008) 252.

162) Y. Wei, W. Nadler and U.H.E. Hansmann, Backbone and Sidechain Ordering in a small Protein, J. Chem. Phys. 128 (2008) 025105.

161) S. Mohanty, J.H. Meinke, O. Zimmermann and U.H.E. Hansmann, Simulation of Top7-CFr: a transient helix extension guides folding, Proc. Nat. Acad. Scie. (USA), 105 (2008) 8004.

160) W. Nadler and U.H.E. Hansmann, Optimizing Replica Exchange Moves For Molecular Dynamics, Phys.Rev. E 76 (2007) 057102.

159) J. H. Meinke, S. Mohanty, F. Eisenmenger and U. H. E. Hansmann, SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran, Comp. Phys. Comm., (2008) 459.

158) W. Nadler and U.H.E. Hansmann, Dynamics and optimal number of replicas in parallel tempering simulations, Phys. Rev. E 76 (2007) 065701.

157) U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007).

156) E. Arashiro, J. R. Drugowich de Felício and U. H. E. Hansmann, Global Persistence Exponent of the Helix-Coil Transition in Polypeptides, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 79-82.

155) T. Eitrich, S. Mohanty, X. Xiao and U. H. E. Hansmann, Dimensionality Reduction Techniques for Protein Folding Trajectories, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 99-102.

154) F. Fredel, J. Meinke, S. Mohanty, O. Zimmermann and U. H. E. Hansmann, Semiautomatic Workflow for Fold Recognition - Results from the CASP 2006 Competition, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 113-116.

153) P. Kar, M. Seel, U. H. E. Hansmann and S. Höfinger, Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 155-158.

152) P. Kar, M. Seel, U. H. E. Hansmann and S. Höfinger, Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 173-176.

151) J. H. Meinke and U. H. E. Hansmann, Parallelization of ECEPP/3 in SMMP, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 219-222.

150) S. Mohanty and U. H. E. Hansmann, Folding and Aggregation of Proteins with Monte Carlo Simulations, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 227-229.

149) M. Magiera, T. Neuhaus and U. H. E. Hansmann, Efficient Parallel Tempering with Multiple Gaussian Modified Ensembles, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 243-245.

148) Y. Wei, W. Nadler and U. H. E. Hansmann, Side-Chain Ordering in Homopolymers, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 297-300.

147) O. Zimmermann and U. H. E. Hansmann, Dihedral Angle Patterns in Coil Regions of Protein Structures, in: U. H. E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB07), NIC Series Vol. 36, Jülich (2007), p. 301-303.

146) T. Neuhaus, M.P. Magiera, and U.H.E. Hansmann, Efficient Parallel Temperingt for First Order Phase Transitions, Phys. Rev. E,76 (2007) 045701.

145) S. Trebst and U.H.E. Hansmann, Optimized Folding Simulations of Protein A, Eur. Phys. J. E, 24 (2007) 311.

144) S. Mohanty and U.H.E. Hansmann, Folding of a Miniprotein with mixed Fold, J. Chem. Phys.,127 (2007) 035102.

143) P. Kar, M. Seel, U.H.E. Hansmann and S. Höfinger, Dispersion Terms and Analysis of Size- and Charge Dependence in an Enhanced Poisson-Boltzmann Approach, J. Phys. Chem. B,111 (2007) 8910.

142) O. Zimmermann, L. Wang and U.H.E. Hansmann, BETTY: Prediction of beta-strand type from sequence, In Silico Biology, <7> (2007) 0037.

141) S. Mohanty, A. Irbaeck, S. Mitternacht, G. Favrin and U.H.E. Hansmann, Protein folding, aggregation and unfolding in Monte Carlo Simulations, Physica Procedia 7 (2010) 68-71

140) S. Mohanty and U.H.E. Hansmann, Improving an all-atom force field, Phys. Rev. E, 76 (2007) 012901.

139) Y. Wei, W. Nadler and U.H.E. Hansmann, On the Helix-coil Transition in Alanine-based Polypeptides in Gas Phase, J. Chem. Phys., 126 (2007) 204307.

138) P. Kar, Y. Wei, U.H.E. Hansmann and S. Höfinger, Systematic Study of the Boundary Composition in Poisson Boltzmann Calculations, J. Comp. Chem., 28 (2007) 2538.

137) E. Arashiro, J.R. Drugowich de Felicio and U.H.E. Hansmann, Short-Time Dynamics of Polypeptides, J. Chem. Phys., 126 (2007) 045107.

136) J. Skrivanek and U.H.E. Hansmann, A method of faster in silico folding of proteins, Particles and Nuclei, Letters,5 (2008) 236.

135) R. Mahajan, D. Krazmüller, J. Volkert, U.H.E. Hansmann and S. Höfinger, Detecting Secondary Bottlenecks in Scientific MPI-Applications, Int. J. Mod. Phys. C 19 (2008) 1-13.

134) Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain and backbone ordering in homopolymers, J. Phys. Chem. B, 111 (2007) 4244.

133) J. Meinke and U.H.E. Hansmann, Protein Simulations combining an All-Atom Force Field with a Go-Term, J. Phys.:Cond. Mat. 19 (2007) 285215.

132) T. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Ring Polymer Simulations with Global Radius of Curvature, Phys. Rev. E., 75 (2007) 051803.

131) J. Meinke and U.H.E. Hansmann, Aggregation of beta-Amyloid Fragments, J. Chem. Phys., 126 (2007) 014706.

130) J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computtional Biophysics to Systems Biology 2006, NIC Series Vol. 34, Jülich (2006).

129) Ch. Junghans and U.H.E. Hansmann, Cross-Check Methods in Protein Simulations, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 157 - 160.

128) Y. Wei, W. Nadler and U.H.E. Hansmann, Side-chain Ordering in PolyGlutamic Acid, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 205 - 209.

127) Parimal Kar, Yanjie Wei,Ulrich H.E. Hansmann and Siegfried Höfinger, The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 161 - 164.

126) L. Wang, O. Zimmermann and U.H.E. Hansmann, Prediction of Parallel and Antiparallel Beta Sheets Based on Sequence Profiles Using Support Vector Machines, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 201 - 204.

125) Th. Neuhaus, O. Zimmermann and U.H.E. Hansmann, Simulations of thick polymers, in: J. Meinke, S. Mohanty, O. Zimmermann and U.H.E. Hansmann (Eds), From Computational Biophysics to Systems Biology 2006 , NIC Series Vol. 34, Jülich (2006); p. 177 - 180.

124) Y. Wei, W. Nadler and U.H.E. Hansmann, Side chain and backbone ordering in a polypeptide, J. Chem. Phys. 125 (2006) 164902.

123) W. Nadler and U.H.E. Hansmann, Generalized Ensemble and Tempering Simulations: A Unified View, Phys. Rev. E, 75 (2007) 026109.

122) S. Höfinger, B. Almeida and U.H.E. Hansmann, Parallel Tempering Molecular Dynamics Folding Simulation of a Signal Peptide in Explicit Water , Proteins, 68 (2007) 662.

121) S. Mohanty and U.H.E. Hansmann, Folding of Proteins with diverse folds, Biophysical Journal 91 (2006) 3573.

120) U.H.E. Hansmann, All-Atom Simulation of Proteins,in: W. Janke (Ed.) Rugged Free Energy Landscapes, Lect. Notes Phys. 736 (2008) 293.

119) O. Zimmermann and U.H.E. Hansmann, Support Vector Machines for Prediction of Dihedral Angle Regions, Bioinformatics 22 (2006) 3009.

118) U.H.E. Hansmann, Protein Folding in Silico, inSide 3 (2005) 12-13

117) U.H.E. Hansmann, Computational Biology and Biophysics at NIC, in: G. Münster, D. Wolf, M. Kremer, NIC Symposium 2006, Jülich (2006), p.13-20.

116) U.H.E. Hansmann, How to fold proteins on a computer? in: S. Blügel,G. Gompper, H. Müller-Krumbhaar, E. Koch, R.G. Winkler and R. Spatschek, 37th IFF Spring School "Computational Condensed Matter Physics, Jülich (2006), B11.1-14.

115) S. Trebst, D.A. Huse, E. Gull, H.G. Katzgraber, U.H.E. Hansmanns and M. Troyer, Ensemble optimization techniquesfor the simulation of slowly equilibrating systems, in D. P. Landau, S. P. Lewis and H. B. Schöttler (Eds), Computer Simulation Studies in Condensed-Matter Physics XIX Proceedings of the NineteenthWorkshop Athens, GA, USA, February 20-24, 2006; Springer Proceedings in Physics, vol 123, Springer Berlin Heidelberg (2008), pp. 33-47.

114) R. Mahajan, D. Krazmüller, U.H.E. Hansmann, J. Volkert and S. Höfinger, Computational assesment of the entropy of solvation of small-sized hydrophobic entities, Physical Chemistry Chemical Physics, 8 (2006) 5515.

113) C. Junghans and U.H.E. Hansmann, Numerical Comparison of Wang-Landau Sampling and Parallel Tempering for Met-enkephalin, Int. J. Mod. Phys. C,17 (2006) 817.

112) S. Trebst, M. Troyer and U.H.E. Hansmann, Optimized parallel tempring simulations of Proteins, J. Chem. Phys., 124 (2006) 174903.

111) E. Arashiro, J.R. Drugowich de Felicio and U.H.E. Hansmann, Short-Time Dynamics of Helix-Coil Transition in Polypeptides, Phys. Rev. E., 73 (2006) 040902.

110) D. Gront, A. Kolinski and U.H.E. Hansmann, Protein Structure Prediction by Tempering Spatial Constraints, J. Comp.-aid. Mol. Des., 19 (2005) 603.

109) F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan and C.-K. Hu, An Enhanced Version of SMMP - Open-Source Software Package for Simulation of Proteins, Comp. Phys. Comm., 174 (2006) 422.

108) D. Gront, U.H.E. Hansmann and A. Kolinski, Exploring Protein Energy Landscapes with Hierachical Clustering, Int. J. Quant. Chem., 105 (2005) 826.

107) W. Kwak and U.H.E. Hansmann, Efficient Sampling of Protein Structures by Model Hopping, Phys. Rev. Lett. 95 (2005) 138102.

106) A. Schug, W. Wenzel and U.H.E. Hansmann, Energy Landscape Paving Simulations of the trp-cage Protein, J. Chem. Phys., 122 (2005) 194711.

105) N.A. Alves, V. Aleksenko and U.H.E. Hansmann, A Simple Hydrophobicity-Based Score for Profiling Protein Structures, J. Phys.: Cond. Mat., 17 (2005) 1595.

104) V. Aleksenko, W. Kwak and U.H.E. Hansmann, Generalized-ensemble simulations of all-atom protein models, Physica A, 350 (2005) 28.

103) N.A. Alves, V. Aleksenko, W. Kwak and U.H.E. Hansmann, Protein folding as studied in generalized-ensemble simulations of all-atom protein models, in: X-G. Zhao, S. Jiang and X-J.Yu, Computational Physics Paramus (NJ,USA) (2005) 1-11

102) U.H.E. Hansmann, Generalized-Ensemble Simulations of Small Proteins, in: D.P. Landau, S.P. Lewis and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics XVII, Springer Verlag (Berlin 2006), p. 87.

101) U.H.E. Hansmann, Simulations of a Small Protein in a specifically designed Generalized Ensemble, Phys. Rev. E, 70 (2004) 01290.

100) N.A. Alves, Y. Peng and U.H.E. Hansmann, All-atom protein-folding simulations in generalized-ensembles, Braz. J. Phys., 34 (2004) 363.

99) Y. Peng and U.H.E. Hansmann, Helix vs. Sheet Formation in a Small Peptide, Phys. Rev. E, 68 (2003) 041911.

98) B.S. Kinnear, M.F. Jarrold and U.H.E. Hansmann, All-Atom Generalized-Ensemble Simulations of Small Proteins, J. Mol. Graph. Mod., 22 (2004) 397.

97) N.A. Alves and U.H.E. Hansmann, Helix-formation and folding as studied in generalized-ensemble simulations, Braz. J. Phy. 33 (2003) 600.

96) U.H.E. Hansmann, Protein folding in silico - The Quest for Better Algorithms, in: A. Hartmann and H. Rieger (eds), New Optimization Algorithms in Physics, VCH-Wiley (2004), p. 275.

95) U.H.E. Hansmann, Generalized-Ensemble Simulations of the Human Parathyroid Hormone Fragment PTH(1-34), J. Chem. Phys., 120 (2004) 417.

94) U.H.E. Hansmann, Protein Folding in silico : An overview, Comp. Sci. Eng., 5 (2003) 64.

93) N.A.~Alves and U.H.E. Hansmann, Solution effects and the Folding of an Artificial Peptide, J. Phys. Chem. B, 107 (2003) 10284.

92) C.Y. Lin, C.K. Hu and U.H.E. Hansmann, Parallel Tempering Simulations of HP-36, Proteins:Structure, Function and Genetics, 52 (2003) 436.

91) Y. Peng, U.H.E. Hansmann and N.A. Alves, Solution effects and the order of the helix-coil transition in polyalanine , J. Chem. Phys, 118 (2003) 2374.

90) U.H.E. Hansmann, New Algorithms and the Physics of Proteins, Physica A, 321 (2003) 152.

89) U.H.E. Hansmann, Protein-folding simulations in generalized-ensemble, Int. J. Quant. Chem., 90 (2002) 1515.

88) N.A. Alves and U.H.E. Hansmann, Helix formation and folding in an artifical peptide , J. Chem. Phys., 117 (2002) 2337.

87) N.A. Alves, U.H.E. Hansmann and Y. Peng, Structural transitions in biomolecules - a numerical comparison of two approaches for the study of phase transitions in small systems, Int. J. Mol. Sci., 3 (2002) 17-29.

86) Y. Peng and U.H.E. Hansmann, Solvation model dependency of helix-coil transition in polyalanine, Biophysical Journal, 82 (2002) 3269.

85) N.A. Alves, J.P.N. Ferrite and U.H.E. Hansmann, Numerical comparison of two approaches for the study of phase transitions in small systems, Phys. Rev. E, 65 (2002) 036110.

84) U.H.E. Hansmann , Generalized Ensemble Techniques and Protein Folding Simulations, Comp. Phys. Comm., 147 (2002) 604.

83) H.P. Hsu, S.C. Lin and U.H.E. Hansmann, Energy Landscape Paving for X-Ray Structure Prediction of Macromolecules , Acta Cryst. A, 58 (2002) 259.

82) U.H.E. Hansmann, New Algorithms and the Physics of Protein Folding, in L.T. Wille (Ed.), ``New Directions in Statistical Physics - Econophysics, Bioinformatics and Pattern Recognition", Springer Verlag (Berlin 2004), 173.

81) U.H.E. Hansmann and L. Wille, Global Optimization by Energy Landscape Paving , Phys. Rev. Let., 88 (2002) 068105.

80) H.P. Hsu, U.H.E. Hansmann and S.C. Lin, X-Ray Structure determination of organic molecules from diffraction data by simulated annealing, Phys. Rev. E., 64 (2001) 056707.

79) U.H.E. Hansmann and J.N. Onuchic, Thermodynamic and Kinetic of Folding of a Small Peptide, J. Chem. Phys., 115 (2001) 1601.

78) C.Y. Lin, C.K. Hu and U.H.E. Hansmann, Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass, Phys. Rev. E., 64 (2001) 052903.

77) F. Eisenmenger,U.H.E. Hansmann , Sh. Hayryan and C.-K. Hu, [SMMP] A Modern Package for Simulation of Proteins, Comp. Phys. Comm., 138 (2001) 192.

76) Y. Okamoto and U.H.E. Hansmann, Protein folding simulations by a generalized-ensemble algorithm based on Tsallis statistics, in: Lecture notes in Physics: Nonextensive Statistical Mechanics and Its Applications , S. Abe and Y. Okamoto (Eds.) (Springer Verlag, Berlin, 2001), pp. 259-274.

75) U.H.E. Hansmann, New Techniques for Protein Simulations - The Generalized-Ensemble Approach, J.Comp.Meth.Sci.Eng. 2 (2002) 95.

74) U.H.E. Hansmann, New Algorithms and the Statistical Physics of Protein Folding , in: Proceedings of the 8th Asia - Pacific Physics Conference APPC 2000, edited by Y.-D. Yao, H.-Y. Cheng, C.-S. Chang and S.-F. Lee, World Scientific 2001, p. 30 - 35.

73) N.A. Alves and U.H.E. Hansmann, Yang-Lee zeros and the helix-coil transition in a continuum model of polyalanine, Physica A, 292 (2001) 509.

72) U.H.E. Hansmann, Protein Energy Landscapes as studied by a Generalized-Ensemble Approach with Tsallis Statistics, Chaos, Solitons and Fractals, 13 (2002) 507.

71) N.A. Alves, J.R. Drugowich de Felicio and U.H.E. Hansmann, Partition function zeros and leading order scaling correction of the 3D Ising model from multicanonical simulations, J. Phys. A 33 (2000) 7489.

70) N.A. Alves and U.H.E. Hansmann, Glass Transition Temperature and Fractal Dimension of Protein Free Energy Landscapes, Int. J. Mod. Phys. C, 11 (2000) 301.

69) J.P. Kemp, U.H.E. Hansmann and Zh.Y.~Chen, Is there a universality of the helix-coil transition in protein models?, Eur. Phy. J. B, 15 (2000) 371.

68) U.H.E. Hansmann, Protein Folding Simulations in a Deformed Energy Landscape, Eur. Phy. J. B, 12 (1999) 607.

67) Nelson A. Alves and U.H.E. Hansmann, Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide, Phys. Rev. Let., 84 (2000) 1836.

66) U.H.E. Hansmann, Computer Simulation of Biological Macromolecules in Generalized Ensembles, Int. J. Mod. Phys. C 10 (1999) 1521.

65) U.H.E. Hansmann and Y. Okamoto, Protein folding: generalized-ensemble algorithms, in: Encyclopedia of Optimization, edited by C.A. Floudas and P.M. Pardalos (Kluwer Academic, Norwell), vol. IV (2001) 392.

64) U.H.E. Hansmann, Thermodynamics of Protein Folding - The Generalized-Ensemble Approach , in Optimization in Computational Chemistry and Molecular Biology, edited by C.A. Floudas and P.M. Pardalos (Kluwer Academic Publishers) (2000) 91.

63) U.H.E. Hansmann and Y. Okamoto, Tackling the Protein Folding Problem by a Generalized-Ensemble Approach with Tsallis Statistics, Bras. J. Phys. 29 (1999) 187.

62) A. Mitsutake, U.H.E. Hansmann and Y. Okamoto, Temperature Dependence of Distributions of Conformations of a Small Peptide, J. Mol. Graph. Mod. 16 (1999) 226.

61) U.H.E. Hansmann and Y. Okamoto, New Monte Carlo Algorithms for Protein Folding , Curr. Opin. Struc. Biol. 9 (1999) 177.

60) U.H.E. Hansmann, Recent Results from Generalized-Ensemble Protein-Folding Simulations, Comp. Phys. Comm. 121 - 122 (1999) 129.

59) U.H.E. Hansmann, F. Eisenmenger and Y. Okamoto, Stochastic dynamics simulations in a new generalized ensemble, Chem. Phys. Lett. 297 (1998) 374.

58) U.H.E. Hansmann and Y. Okamoto, Effects of side-chain charges on 1#1 -helix stability in C-peptide of ribonuclease A studied by multicanonical algorithm, J. Phys. Chem. B 103 (1999) 1595.

57) U.H.E. Hansmann and Y. Okamoto, Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations, J. Chem. Phys. 110 (1999) 1267, 111 (1999) 1339(E).

56) U.H.E. Hansmann, Y. Okamoto and J.N. Onuchic, The Folding Funnel Landscape for the Peptide Met-Enkephalin, Proteins: Structure, Function and Genetics 34 (1999) 472.

55) B.A. Berg and U.H.E. Hansmann, Configuration Space for Random Walk Dynamics, Euro. Phy. J. B. 6 (1998) 395.

54) U.H.E. Hansmann and Y. Okamoto, The Generalized-Ensemble Approach for Protein Folding Simulations, in: Annual Reviews of Computational Physics VI, edited by D. Stauffer, World Scientific, Singapore (1999) 129.

53) U.H.E. Hansmann, Recent Results from Protein-Folding Simulations in Generalized Ensembles, in: D.P. Landau and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics XI, Springer Verlag 1999, 62.

52) U.H.E. Hansmann, Multicanonical and other generalized-ensemble Algorithms in Protein Simulations, in: P. Grassberger, G.T. Barkema, W. Nadler (eds.), ``Monte Carlo approach to biopolymers and protein folding'' , World Scientific 1998, p. 81

51) U.H.E. Hansmann, Simulation of Peptides and Proteins, in: ``Annual Reports ZiF: 96/97'', published by the Center for Interdisciplinary Research (Zif) of the Universität Bielefeld (Germany), 1998, p. 46.

50) U.H.E. Hansmann, Parallel Tempering Algorithm for Conformational Studies of Biological Molecules, Chem. Phys. Lett. 281 (1997) 140.

49) U.H.E. Hansmann, Generalized Ensembles - A New Way of Simulating Proteins, Physica A 254 (1998) 15.

48) U.H.E. Hansmann and Ph. de Forcrand, A Simple Ansatz to Describe Thermodynamic Quantities of Peptides and Proteins at Low Temperatures, Int. J. Mod. Phys. C 8 (1997) 1085.

47) U.H.E. Hansmann, Monte Carlo Simulations of Proteins and Peptides in Generalized Ensembles, in: L. Luo,Q. Li and W. Lee (Eds.), Theoretical Biophysics and Biomathematics, Inner Mongolia University Press 1997, 84.

46) U.H.E. Hansmann and Y. Okamoto, Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm, J. Phys. Chem. B 102 (1998) 653.

45) U.H.E. Hansmann, M. Masuya and Y. Okamoto, Characteristic Temperatures of Folding of a Small Peptide, Proc. Nat. Aca. Sci. U.S.A. 94 (1997) 10652.

44) U.H.E. Hansmann, An Effective Way for Determination of Multicanonical Weights, Phy. Rev. E 56 (1997) 6000.

43) U.H.E. Hansmann and Y. Okamoto, Generalized Ensemble Simulations of Peptides and Proteins, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics X, Springer Verlag 1998, 180.

42) U.H.E. Hansmann, Simulated Annealing with Tsallis Weights - A Numerical Comparison, Physica A 242 (1997) 250.

41) U.H.E. Hansmann and Y. Okamoto, New Generalized-Ensemble Monte Carlo Method for Systems with Rough Energy Landscape, Phys. Rev. E 56 (1997) 2228.

40) U.H.E. Hansmann, Simulation of Peptides and Proteins in Generalized Ensembles, in: F. Karsch, B. Monien and H. Satz, Multiscale Phenomena and Their Simulation, World Scientific 1997, 114.

39) F. Eisenmenger and U.H.E. Hansmann, Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3, J. Phys. Chem. B 101 (1997) 3304.

38) N. Alves, J.R. Drugowich de Felicio and U.H.E. Hansmann, A new look at the 2D Ising Model from exact partion function zeros for large lattice sizes, Int. J. Mod. Phys. C 8 (1997) 1063.

37) F. Eisenmenger and U.H.E. Hansmann, Global Minimum Configuration of a Small Peptide for the ECEPP/2 and ECEPP/3 Force Field, Chem. Phys. Lett. 268 (1997) 86.

36) U.H.E. Hansmann and Y. Okamoto, Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem, J. Comp. Chem. 18 (1997) 920.

35) U.H.E. Hansmann and Y. Okamoto, Monte Carlo Simulations in Generalized Ensemble: Multicanonical Algorithm versus Simulated Tempering, Phys. Rev. E 54 (1996) 5863.

34) U.H.E. Hansmann, Y. Okamoto and F. Eisenmenger, Molecular dynamics, Langevin and Hybrid Monte Carlo simulations in multicanonical ensemble, Chem. Phys. Lett. 259 (1996) 321.

33) U.H.E. Hansmann and Y. Okamoto, Thermodynamics of Helix-Coil Transitions in Amino-Acid Homopolymers Studied by Multicanonical Algorithms, Nucl. Phys. B (Proc. Suppl.) 47 (1996) 842.i

32) U.H.E. Hansmann, On the Protein Folding Problem, Nucl. Phys. B (Proc. Suppl.) 47 (1996) 188.

31) Y. Okamoto and U.H.E. Hansmann, Thermodynamics of Helix-Coil Transition Studied by Multicanonical Algorithms, J. Phys. Chem. 99 (1995) 11276.

30) B.A. Berg, U.H.E. Hansmann and Y. Okamoto, Comment on ``Monte Carlo Simulation of a First-Order Transition for Protein Folding'', J. Phys. Chem. 99 (1995) 2236.

29) B.A. Berg, U.H.E. Hansmann and T. Celik, Groundstates of the 3d Edwards-Anderson spin glass model, Nucl. Phys. B (Proc. Suppl.) 42 (1995) 905.

28) U.H.E. Hansmann and Y. Okamoto, Multicanonical Approach in Statistical Mechanics of Peptides, Nucl. Phys. B (Proc. Suppl.) 42 (1995) 914.

27) U.H.E. Hansmann, Towards Ab Initio Prediction of Protein Conformations - The Multicanonical Approach, preprint SC-94-21, in: F. Haubensak and J. Sühnel (Eds.), Bioinformatik - Computereinsatz in den Biowissenschaften, IMB Jena 1994, p. 103-108.

26) U.H.E. Hansmann and Y. Okamoto, Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem, Physica A 212 (1994) 415.

25) U.H.E. Hansmann and Y. Okamoto, Sampling Groundstate Configurations of a Peptide by Multicanonical Annealing, J. Phys. Soc. (Japan) 63 (1994) 3945.

24) U.H.E. Hansmann and Y. Okamoto, A Multicanonical Study of Nonpolar Amino Acids, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics VII, Springer Verlag 1994, 183.

23) Y. Okamoto, U.H.E. Hansmann and T. Nakazawa, alpha-Helix Propensities of Nonpolar Amino Acids Studied by Multicanonical Algorithms, Chem. Lett. (1995) 391.

22) B.A. Berg and U.H.E. Hansmann, Multicanonical Study of the 3d Ising Spin Glass at Zero Temperature, Nucl. Phys. B (Proc. Suppl.) 34 (1994) 664.

21) U.H.E. Hansmann, Y. Okamoto and M. Katoot, Approaching the Protein Folding Problem, Nucl. Phys. B (Proc. Suppl.) 34 (1994) 792.

20) U.H.E. Hansmann and B.A. Berg, Spin Glas Groundstate Investigation by Multicanonical Ensemble, Int. J. Mod. Phys. C,5 (1994) 263.

19) U.H.E. Hansmann and Y. Okamoto, A Multicanonical Study of the Protein Folding Problem, Int. J. Mod. Phys. C, 5 (1994) 271.

18) B.A. Berg, T. Celik and U.H.E. Hansmann, Groundstate Properties of the 3D Ising Spin Glass, Phys. Rev. B 50 (1994) 16444.

17) U.H.E. Hansmann, Multicanonical Simulations, FSU-SCRI-93-119, D.-Y.~Li, D.-H.~Feng, M.R.~Strayer and T.~Y.~Zhang (eds.), The Second International Conference on Computational Physics , Campridge, Mass.: International Press (1994) p.~454-462.

16) T. Celik, U.H.E. Hansmann and M. Katoot, The van Hemmen Spin Glass Revisited, J. Stat. Phys. 73 (1993) 775.

15) U.H.E. Hansmann, T. Celik and M. Katoot, A Multicanonical Study of the van Hemmen Model, Tr. J. Phys. 18 (1994) 149.

14) U.H.E. Hansmann and Y. Okamoto, Prediction of Peptide Conformation by the Multicanonical Algorithm, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics VI, Springer Verlag 1993, 168.

13) M. Katoot, U.H.E. Hansmann and T. Celik, Multicanonical Simulation of the Van Hemmen Spin Glass Model, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics VI, Springer Verlag 1993, 152.

12) T. Celik, U.H.E. Hansmann and B.A. Berg, Study of +/-J Ising Spin Glasses via Multicanonical Ensemble, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics VI, Springer Verlag 1993, 173.

11) U.H.E. Hansmann and Y. Okamoto, Prediction of Peptide Conformation by Multicanonical Algorithm: A new Approach to the Multiple-Minima Problem, J. Comp. Chem. 14 (1993) 1333.

10) U.H.E. Hansmann, Multicanonical and Multimagnetical Simulations, in: C.H. Albright,P. H.Kasper,Raitendran Raja and John Yoh (ed.), The Fermilab Meeting DPF92, World Scientific Publishing (1993), 1507.

9) B.A. Berg, T. Celik and U.H.E. Hansmann Multicanonical Study of the 3D Ising Spin Glass, Europhys. Lett. 22 (1993) 63.

8) U.H.E. Hansmann, Multimagnetical Simulation of the Ising Model, Nucl. Phys. B (Proc. Suppl.) 30 (1993) 285.

7) U.H.E. Hansmann, B.A. Berg and T. Neuhaus, Multimagnetical Simulation of the Ising Model in Two and Three Dimensions, in: Robert A. de Groot and Jaroslav Nadrchal (eds.), Physics Computing '92, World Scientific Publishing (1993), 340.

6) U.H.E. Hansmann, B.A. Berg and T. Neuhaus, Recent Results from Multimagnetical Simulations of the Ising Model, Int. J. Mod. Phys. C 3 (1992) 1155.

5) B.A. Berg, U.H.E. Hansmann and T. Neuhaus, Properties of Interfaces in the two and three dimensional Ising Model, Z. Phys. B 90 (1993) 229.

4) U.H.E. Hansmann, B.A. Berg and T. Neuhaus, Multimagnetical Simulations, in: D.P. Landau, K.K Mon and H.-B. Schüttler (Eds.), Computer Simulation Studies in Condensed Matter Physics V, Springer Verlag 1993, 145.

3) B.A. Berg, U.H.E. Hansmann and T. Neuhaus, Simulation of an Ensemble with varying magnetic Field: a Numerical Determination of the Order-Order Interface Tension in the D=2 Ising Model, Phys. Rev. B 47 (1993), 497.

2) U.H.E. Hansmann, Monte Carlo Simulation von Gittereichtheorien mit Fermionen (A Monte Carlo Study of Lattice Gauge Theories with Fermions), Ph. D. thesis, 1990, Freie Universität Berlin.

1) U.H.E. Hansmann, Hamiltonsche Formulierung von Superraum Theorien (A Hamilton Formalism for Superspace Theories), Diplom thesis, 1985, Freie Universität Berlin.