Effective all-atom potentials for proteins
A. Irbäck and S. Mohanty
LU TP 09-16, to appear in Multiscale approaches to protein folding:
structure prediction, dynamics, thermodynamics and macromolecular
assemblies, ed. A. Kolinski
Comparing the folding free-energy
landscapes of Aβ42 variants: differences
in conformational diversity and stability
S. Mitternacht, I. Staneva, T. Härd and A. Irbäck
LU TP 09-04
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)
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An effective all-atom potential for proteins
A. Irbäck, S. Mitternacht and S. Mohanty
PMC Biophysics 2, 2 (2009)
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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)
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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)
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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)
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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)
Volume `Rugged Free Energy Landscapes',
ed. W. Janke (Springer, Berlin Heidelberg)
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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)
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Thermal versus mechanical unfolding of ubiquitin
A. Irbäck and S. Mitternacht
Proteins: Structure, Function, and Bioinformatics
65, 759-766 (2006)
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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 2006, Jülich, eds. U.H.E. Hansmann et al.,
pp. 15-20 (2006)
[Full text (PDF)]
PROFASI: a Monte Carlo simulation package for protein folding and
aggregation
A. Irbäck and S. Mohanty
Journal of Computational Chemistry
27, 1548-1555 (2006)
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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)
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Peptide folding and aggregation studied using a simplified atomic model
A. Irbäck
Journal of Physics: Condensed Matter 17, S1553-S1564 (2005)
Proceedings of the Workshop `Function and Structure of
Biomolecules', Bedlewo, eds. M. Cieplak and A. Sienkiewicz
[HTML at journal]
Folding thermodynamics of peptides
A. Irbäck and S. Mohanty
Biophysical Journal 88, 1560-1569 (2005)
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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)
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Folding thermodynamics of three β-sheet peptides: a model study
A. Irbäck and F. Sjunnesson
Proteins: Structure, Function, and Bioinformatics
56, 110-116 (2004)
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Coupled folding-binding versus docking: a lattice model study
N. Gupta and A. Irbäck
Journal of Chemical Physics 120, 3983-3989 (2004)
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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)
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Protein folding in the absence of a clear free-energy barrier
A. Irbäck
Acta Physica Polonica B 34, 4867-4878 (2003)
Proceedings of Workshop on `Random Geometry', Krakow,
eds. Z. Burda and J. Jurkiewicz
[Full text (PDF)]
Thermodynamics of α-
and β-structure formation in proteins
A. Irbäck, B. Samuelsson, F. Sjunnesson and S. Wallin
Biophysical Journal 85, 1466-1473 (2003)
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Two-state folding over a weak free-energy barrier
G. Favrin, A. Irbäck, B. Samuelsson and S. Wallin
Biophysical Journal 85, 1457-1465 (2003)
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A minimalistic all-atom approach to protein folding
A. Irbäck
Journal of Physics: Condensed Matter 15, S1797-S1807 (2003)
Proceedings of the EPS Meeting on `Nano Physics in Life Systems', Copenhagen,
ed. P.-A. Lindgård
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Enumerating designing sequences in the HP model
A. Irbäck and C. Troein
Journal of Biological Physics 28, 1-15 (2002)
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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)
[HTML at journal]
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)
Proceedings of the ISI workshop on
`Protein Folding: Simple Models and Experiments', Torino,
eds. P. Bruscolini et al.
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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)
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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)
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On hydrophobicity correlations in protein chains
A. Irbäck and E. Sandelin
Biophysical Journal 79, 2252-2258 (2000)
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Sequence design in coarse-grained protein models
A. Irbäck
Progress of Theoretical Physics Supplement 138, 273-281 (2000)
Proceedings of the Fifth International Conference on Computational Physics,
Kanazawa, eds. Y. Hiwatari et al.
[Preprint
full text (PDF)]
Monte Carlo study of the phase structure of compact polymer chains
A. Irbäck and E. Sandelin
Journal of Chemical Physics 110, 12256-12262 (1999)
[Full text (PDF)]
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)
[Full text (PDF)]
Monte Carlo procedure for protein design
A. Irbäck, C. Peterson, F. Potthast and E. Sandelin
Physical Review E 58, R5249-R5252 (1998)
[Full text (PDF)]
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)
[Full text (PDF)]
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
full text (PDF)]
Simulations of toy proteins
A. Irbäck
in Field Theoretical Tools for Polymer and Particle Physics,
eds. H. Meyer-Ortmanns and A. Klümper, pp. 143-153 (Springer, Berlin, 1998)
[Preprint
full text (PDF)]
The hybrid Monte Carlo method for polymer chains
A. Irbäck
in Field Theoretical Tools for Polymer and Particle Physics,
eds. H. Meyer-Ortmanns and A. Klümper, pp. 133-142 (Springer, Berlin, 1998)
[Preprint
full text (PDF)]
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)
[Full text (PDF)]
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)
[Full text (PDF)]
Binary assignments of amino acids from pattern conservation
A. Irbäck and F. Potthast
Protein Engineering 10, 1013-1017 (1997)
[Full text (PDF)]
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)
[Full text (PDF)]
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)
[ Full text (PDF)]
Sequence dependence of self-interacting random chains
A. Irbäck and H. Schwarze
Journal of Physics A 28, 2121-2132 (1995)
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Hybrid Monte Carlo simulation of polymer chains
A. Irbäck
Journal of Chemical Physics 101, 1661-1667 (1994)
[Full text (PDF)]
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)
Finite-size scaling on the Ising coexistence line
S. Gupta and A. Irbäck
Nuclear Physics B (Proc. Suppl.) 30, 861-864 (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)
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)
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)
[Full text (PDF)]
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)
Hadronic correlation functions in the QCD plasma phase
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 20, 280-283 (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)
Hybrid Monte Carlo simulation of four flavour QCD at
finite temperature
A. Irbäck
Nuclear Physics B (Proc. Suppl.) 17, 210-213 (1990)
The correlation lengths and the order of the phase
transition in three-dimensional Z3 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)
[Full text (PDF)]