Publications — Anders Irbäck

Original research papers

Conformational and aggregation properties of the 1‒93 fragment of apolipoprotein A-I
J. Petrlova, A. Bhattacherjee, W. Boomsma, S. Wallin, J.O. Lagerstedt and A. Irbäck
Protein Science, DOI: 10.1002/pro.2534

Robust estimation of diffusion-optimized ensembles for enhanced sampling
P. Tian, S.Æ. Jónsson, J. Ferkinghoff-Borg, S.V. Krivov, K. Lindorff-Larsen, A. Irbäck and W. Boomsma
Journal of Chemical Theory and Computation 10, 543–553 (2014)

Hybrid Monte Carlo with non-uniform step size
C. Holzgräfe, A. Bhattacherjee and A. Irbäck
Journal of Chemical Physics 140, 044105 (2014)

Local unfolding and aggregation mechanisms of SOD1: a Monte Carlo exploration
A. Bille, S.Æ. Jónsson, M. Akke and A. Irbäck
Journal of Physical Chemistry B 117, 9194–9202 (2013)

Mechanical resistance in unstructured proteins
S.Æ. Jónsson, S. Mitternacht and A. Irbäck
Biophysical Journal 104, 2725–2732 (2013)

Aggregate geometry in amyloid fibril nucleation
A. Irbäck, S.Æ. Jónsson, N. Linnemann, B. Linse and S. Wallin
Physical Review Letters 110, 058101 (2013)

Distinct phases of free α-synuclein — a Monte Carlo study
S.Æ. Jónsson, S. Mohanty and A. Irbäck
Proteins: Structure, Function, and Bioinformatics 80, 2169–2177 (2012)

Mutation-induced fold switching among lattice proteins
C. Holzgräfe, A. Irbäck and C. Troein
Journal of Chemical Physics 135, 195101 (2011)  data

Accelerating atomic-level protein simulations by flat-histogram techniques
S.Æ. Jónsson, S. Mohanty and A. Irbäck
Journal of Chemical Physics 135, 125102 (2011)

Monte Carlo study of the formation and conformational properties of dimers of Aβ42 variants
S. Mitternacht, I. Staneva, T. Härd and A. Irbäck
Journal of Molecular Biology 410, 357–367 (2011)

Microscopic mechanism of specific peptide adhesion to semiconductor substrates
M. Bachmann, K. Goede, A.G. Beck-Sickinger, M. Grundmann, A. Irbäck and W. Janke
Angewandte Chemie International Edition 49, 9530–9533 (2010)

Comparing the folding free-energy landscapes of Aβ42 variants with different aggregation properties
S. Mitternacht, I. Staneva, T. Härd and A. Irbäck
Proteins: Structure, Function, and Bioinformatics 78, 2600–2608 (2010)

Unfolding times for proteins in a force clamp
S. Luccioli, A. Imparato, S. Mitternacht, A. Irbäck and A. Torcini
Physical Review E 81, 010902(R) (2010)

An effective all-atom potential for proteins
A. Irbäck, S. Mitternacht and S. Mohanty
PMC Biophysics 2, 2 (2009)

Changing the mechanical unfolding pathway of FnIII-10 by tuning the pulling strength
S. Mitternacht, S. Luccioli, A. Torcini, A. Imparato and A. Irbäck
Biophysical Journal 96, 429–441 (2009)

Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment
D.-W. Li, S. Mohanty, A. Irbäck and S. Huo
PLoS Computational Biology 4, e1000238 (2008)

Spontaneous β-barrel formation: an all-atom Monte Carlo study of Aβ(16–22) oligomerization
A. Irbäck and S. Mitternacht
Proteins: Structure, Function, and Bioinformatics 71, 207–214 (2008)

Differences in solution behavior among four semiconductor-binding peptides
S. Mitternacht, S. Schnabel, M. Bachmann, W. Janke and A. Irbäck
Journal of Physical Chemistry B 111, 4355–4360 (2007)

Thermal versus mechanical unfolding of ubiquitin
A. Irbäck and S. Mitternacht
Proteins: Structure, Function, and Bioinformatics 65, 759–766 (2006)

PROFASI: a Monte Carlo simulation package for protein folding and aggregation
A. Irbäck and S. Mohanty
Journal of Computational Chemistry 27, 1548–1555 (2006)

Dissecting the mechanical unfolding of ubiquitin
A. Irbäck, S. Mitternacht and S. Mohanty
Proceedings of the National Academy of Sciences USA 102, 13427–13432 (2005)

Folding thermodynamics of peptides
A. Irbäck and S. Mohanty
Biophysical Journal 88, 1560–1569 (2005)

Oligomerization of amyloid Aβ(16–22) peptides using hydrogen bonds and hydrophobicity forces
G. Favrin, A. Irbäck and S. Mohanty
Biophysical Journal 87, 3657–3664 (2004); erratum 89, 754 (2005)

Folding thermodynamics of three β-sheet peptides: a model study
A. Irbäck and F. Sjunnesson
Proteins: Structure, Function, and Bioinformatics 56, 110–116 (2004)

Coupled folding-binding versus docking: a lattice model study
N. Gupta and A. Irbäck
Journal of Chemical Physics 120, 3983–3989 (2004)

Sequence-based study of two related proteins with different folding behaviors
G. Favrin, A. Irbäck and S. Wallin
Proteins: Structure, Function, and Bioinformatics 54, 8–12 (2004)

Thermodynamics of α- and β-structure formation in proteins
A. Irbäck, B. Samuelsson, F. Sjunnesson and S. Wallin
Biophysical Journal 85, 1466–1473 (2003)

Two-state folding over a weak free-energy barrier
G. Favrin, A. Irbäck, B. Samuelsson and S. Wallin
Biophysical Journal 85, 1457–1465 (2003)

Enumerating designing sequences in the HP model
A. Irbäck and C. Troein
Journal of Biological Physics 28, 1–15 (2002)  data

Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
G. Favrin, A. Irbäck and S. Wallin
Proteins: Structure, Function, and Genetics 47, 99–105 (2002)

Monte Carlo update for chain molecules: biased Gaussian steps in torsional space
G. Favrin, A. Irbäck and F. Sjunnesson
Journal of Chemical Physics 114, 8154–8158 (2001)

Three-helix-bundle protein in a Ramachandran model
A. Irbäck, F. Sjunnesson and S. Wallin
Proceedings of the National Academy of Sciences USA 97, 13614–13618 (2000)

On hydrophobicity correlations in protein chains
A. Irbäck and E. Sandelin
Biophysical Journal 79, 2252–2258 (2000)

Monte Carlo study of the phase structure of compact polymer chains
A. Irbäck and E. Sandelin
Journal of Chemical Physics 110, 12256–12262 (1999)

Design of sequences with good folding properties in coarse-grained protein models
A. Irbäck, C. Peterson, F. Potthast and E. Sandelin
Structure with Folding & Design 7, 347–360 (1999)

Monte Carlo procedure for protein design
A. Irbäck, C. Peterson, F. Potthast and E. Sandelin
Physical Review E 58, R5249–R5252 (1998)

Local interactions and protein folding: a model study on the square and triangular lattices
A. Irbäck and E. Sandelin
Journal of Chemical Physics 108, 2245–2250 (1998)

Local interactions and protein folding: a three-dimensional off-lattice approach
A. Irbäck, C. Peterson, F. Potthast and O. Sommelius
Journal of Chemical Physics 107, 273–282 (1997)

Identification of amino acid sequences with good folding properties in an off-lattice model
A. Irbäck, C. Peterson and F. Potthast
Physical Review E 55, 860–867 (1997)

Binary assignments of amino acids from pattern conservation
A. Irbäck and F. Potthast
Protein Engineering 10, 1013–1017 (1997)

Evidence for nonrandom hydrophobicity structures in protein chains
A. Irbäck, C. Peterson and F. Potthast
Proceedings of the National Academy of Sciences, USA 93, 9533–9538 (1996)

Studies of an off-lattice model for protein folding: sequence dependence and improved sampling at finite temperature
A. Irbäck and F. Potthast
Journal of Chemical Physics 103, 10298–10305 (1995)

Sequence dependence of self-interacting random chains
A. Irbäck and H. Schwarze
Journal of Physics A 28, 2121–2132 (1995)

Hybrid Monte Carlo simulation of polymer chains
A. Irbäck
Journal of Chemical Physics 101, 1661–1667 (1994)

Scaling in Steiner random surfaces
C.F. Baillie, A. Irbäck, W. Janke and D. Johnston
Physics Letters B 325, 45–50 (1994)

Finite-size scaling at phase coexistence
S. Gupta, A. Irbäck and M. Ohlsson
Nuclear Physics B 409, 663–683 (1993)

The theory of dynamical random surfaces with extrinsic curvature
J. Ambjørn, A. Irbäck, J. Jurkiewicz and B. Petersson
Nuclear Physics B 393, 571–600 (1993)

Physics beyond instantons. Measuring the physical correlation length
S. Gupta and A. Irbäck
Physics Letters B 286, 112–117 (1992)

Spectral density analysis of the chiral transition in nf=4 finite temperature QCD
N.A. Alves, B.A. Berg, D.W. Duke, A. Irbäck and S. Sanielevici
Physics Letters B 280, 261–266 (1992)

Measuring the string tension in random surface models with extrinsic curvature
A. Irbäck, J. Jurkiewicz and S. Varsted
Computer Physics Communications 70, 59–68 (1992)

Critical properties of the dynamical random surface with extrinsic curvature
J. Ambjørn, J. Jurkiewicz, S. Varsted, A. Irbäck and B. Petersson
Physics Letters B 275, 295–303 (1992)

The heavy quark potential in SU(2) gauge theory at high temperature
A. Irbäck, P. LaCock, D. Miller, B. Petersson and T. Reisz
Nuclear Physics B 363, 34–64 (1991)

Hadronic correlation functions in the QCD plasma phase
K.D. Born, S. Gupta, A. Irbäck, F. Karsch, E. Laermann, B. Petersson and H. Satz
Physical Review Letters 67, 302–305 (1991)

Dynamics near a first-order phase transition with the Metropolis and Swendsen-Wang algorithms
A. Billoire, R. Lacaze, A. Morel, S. Gupta, A. Irbäck and B. Petersson
Nuclear Physics B 358, 231–248 (1991)

Comment on `Finite-size effects at temperature-driven phase transitions'
A. Billoire, R. Lacaze, A. Morel, S. Gupta, A. Irbäck and B. Petersson
Physical Review B 42, 6743–6744 (1990)

The acceptance probability in the hybrid Monte Carlo method
S. Gupta, A. Irbäck, F. Karsch and B. Petersson
Physics Letters B 242, 437–443 (1990)

Flavour degrees of freedom and the transition temperature in QCD
R.V. Gavai, S. Gupta, A. Irbäck, F. Karsch, S. Meyer, B. Petersson, H. Satz and H.W. Wyld
Physics Letters B 241, 567–573 (1990)

The correlation lengths and the order of the phase transition in three-dimensional Z(3) symmetric models
R.V. Gavai, S. Gupta, A. Irbäck, F. Karsch and B. Petersson
Nuclear Physics B 329, 263–284 (1990)

The finite temperature phase transition in four flavour QCD on an 8x123 lattice
R.V. Gavai, S. Gupta, A. Irbäck, F. Karsch, S. Meyer, B. Petersson H. Satz and H.W. Wyld
Physics Letters B 232, 491–497 (1989)

Lattice QCD with small number of flavours
A. Irbäck, F. Karsch, B. Petersson and H.W. Wyld
Physics Letters B 216, 177–183 (1989)

A random surface representation of Wilson loops in Z(2) gauge theory
A. Irbäck
Physics Letters B 211, 129–131 (1988)

Compact three-dimensional U(1) gauge theory reexamined
A. Irbäck and C. Peterson
Physical Review D 36, 3804–3808 (1987)

The effective string and SU(2) lattice MC data
M. Flensburg, A. Irbäck and C. Peterson
Zeitschrift für Physik C 36 629–637 (1987)

Measurement of Tc in the scaling region of (2+1)-dimensional SU(2) lattice gauge theory
M. Flensburg and A. Irbäck
Physics Letters B 175, 187–191 (1986)

Numerical evidence for a mass gap in three-dimensional SU(2)
A. Irbäck and C. Peterson
Physics Letters B 174, 99–103 (1986)

Mixed-symmetry Interacting-Boson-Model states in the nuclei 140Ba, 142Ce and 144Nd with N=84
W.D. Hamilton, A. Irbäck and J.P. Elliott
Physical Review Letters 53, 2469–2472 (1984)


Book chapters, conference papers

All-atom Monte Carlo simulations of protein folding and aggregation
A. Irbäck and S. Mohanty
In Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, ed. A. Liwo, pp. 433–444 (Springer, 2013)

Monte Carlo simulations of protein aggregation
S.Æ. Jónsson, I. Staneva, S. Mohanty and A. Irbäck
Physics Procedia 34, 49–54 (2012)

Effective all-atom potentials for proteins
A. Irbäck and S. Mohanty
In Multiscale Approaches to Protein Modeling, ed. A. Kolinski, pp. 111–126 (Springer, 2011)

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

Protein folding, unfolding and aggregation studied using an all-atom model with a simplified interaction potential
A. Irbäck
Lecture Notes in Physics 736, 269–291 (2008)

Protein aggregation and unfolding studied using an all-atom model with a simplified energy function
A. Irbäck and S. Mitternacht
In Proceedings of the Workshop From Computational Biophysics to Systems Biology, Jülich, eds. U.H.E. Hansmann et al., pp. 15–20 (2006)

Peptide folding and aggregation studied using a simplified atomic model
A. Irbäck
Journal of Physics: Condensed Matter 17, S1553–S1564 (2005)

Protein folding in the absence of a clear free-energy barrier
A. Irbäck
Acta Physica Polonica B 34, 4867–4878 (2003)

A minimalistic all-atom approach to protein folding
A. Irbäck
Journal of Physics: Condensed Matter 15, S1797–S1807 (2003)

Hydrogen bonds, hydrophobicity forces and the character of the collapse transition
A. Irbäck, F. Sjunnesson and S. Wallin
Journal of Biological Physics 27, 169–179 (2001)

Sequence design in coarse-grained protein models
A. Irbäck
Progress of Theoretical Physics Supplement 138, 273–281 (2000)

Dynamical-parameter algorithms for protein folding
A. Irbäck
In Monte Carlo Approach to Biopolymers and Protein Folding, eds. P. Grassberger, G.T. Barkema and W. Nadler, pp. 98–109 (World Scientific, Singapore, 1998)     preprint

Simulations of toy proteins
A. Irbäck
Lecture Notes in Physics 508, 143–154 (1998)

The hybrid Monte Carlo method for polymer chains
A. Irbäck
Lecture Notes in Physics 508, 133–142 (1998)

Finite-size scaling on the Ising coexistence line
S. Gupta and A. Irbäck
Nuclear Physics B (Proc. Suppl.) 30, 861–864 (1993)

Finite-size scaling on the Ising coexistence line
S. Gupta and A. Irbäck
International Journal of Modern Physics C 3 (Proc. Suppl.), 1119–1124 (1992)

Scaling properties at the crumpling transition
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 26, 572–574 (1992)

Hadronic correlation functions in the QCD plasma phase
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 20, 280–283 (1991)

Hybrid Monte Carlo simulation of four flavour QCD at finite temperature
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 17, 210–213 (1990)

Mixed symmetry states in the vibrational limit of the IBA model
W.D. Hamilton, A. Irbäck and J.P. Elliott
AIP Conference Proceedings 125, 106–108 (1985)

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