Publications
Displaying of publications. Sorted by year, then title.
Folding lattice proteins confined on minimal grids using a quantum-inspired encoding
Anders Irbäck, Lucas Knuthson, Sandipan Mohanty
(2025) Physical Review E: covering statistical, nonlinear, biological, and soft matter physics, 112
ArticleUsing quantum annealing to design lattice proteins
Anders Irbäck, Lucas Knuthson, Sandipan Mohanty, Carsten Peterson
(2024) Physical Review Research, 6
ArticleFolding lattice proteins with quantum annealing
Anders Irbäck, Lucas Knuthson, Sandipan Mohanty, Carsten Peterson
(2022) Physical Review Research, 4
ArticleLimitations of field-theory simulation for exploring phase separation: The role of repulsion in a lattice protein model
Daniel Nilsson, Behruz Bozorg, Sandipan Mohanty, Bo Söderberg, Anders Irbäck
(2022) The Journal of chemical physics, 156
ArticleFinite-size shifts in simulated protein droplet phase diagrams
Daniel Nilsson, Anders Irbäck
(2021) Journal of Chemical Physics, 154
ArticleFinite-size scaling analysis of protein droplet formation
Daniel Nilsson, Anders Irbäck
(2020) Physical Review E, 101
ArticleWhen a foreign gene meets its native counterpart : computational biophysics analysis of two PgiC loci in the grass Festuca ovina
Yuan Li, Sandipan Mohanty, Daniel Nilsson, Bengt Hansson, Kangshan Mao, et al.
(2020) Scientific Reports, 10
ArticlePeptide folding in cellular environments: a Monte Carlo and Markov modeling approach
Daniel Nilsson, Sandipan Mohanty, Anders Irbäck
(2019) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes , p.453-466
Book chapterStability and Local Unfolding of SOD1 in the Presence of Protein Crowders
Anna Bille, Kristine Steen Jensen, Sandipan Mohanty, Mikael Akke, Anders Irbäck
(2019) Journal of Physical Chemistry B, 123 p.1920-1930
ArticleFitting a function to time-dependent ensemble averaged data
Karl Fogelmark, Michael A. Lomholt, Anders Irbäck, Tobias Ambjörnsson
(2018) Scientific Reports, 8
ArticleMarkov modeling of peptide folding in the presence of protein crowders
Daniel Nilsson, Sandipan Mohanty, Anders Irbäck
(2018) Journal of Chemical Physics, 148
ArticleProtein folding/unfolding in the presence of interacting macromolecular crowders
Anders Irbäck, Sandipan Mohanty
(2017) European Physical Journal: Special Topics, 226 p.627-638
Review articlePeptide folding in the presence of interacting protein crowders
Anna Bille, Sandipan Mohanty, Anders Irbäck
(2016) Journal of Chemical Physics, 144
ArticleThermodynamics of amyloid formation and the role of intersheet interactions
Anders Irbäck, Jonas Wessén
(2015) Journal of Chemical Physics, 143
ArticleEquilibrium simulation of trp-cage in the presence of protein crowders.
Anna Bille, Björn Linse, Sandipan Mohanty, Anders Irbäck
(2015) Journal of Chemical Physics, 143
ArticleConformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I
Jitka Petrlova, Arnab Bhattacherjee, Wouter Boomsma, Stefan Wallin, Jens O Lagerstedt, et al.
(2014) Protein Science, 23 p.1559-71
ArticleRobust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling
Pengfei Tian, Sigurdur Jonsson, Jesper Ferkinghoff-Borg, Sergi V. Krivov, Kresten Lindorff-Larsen, et al.
(2014) Journal of Chemical Theory and Computation, 10 p.543-553
ArticleHybrid Monte Carlo with non-uniform step size
Christian Holzgräfe, Arnab Bhattacherjee, Anders Irbäck
(2014) Journal of Chemical Physics, 140
ArticleAggregate geometry in amyloid fibril nucleation.
Anders Irbäck, Sigurdur Jonsson, Niels Linnemann, Björn Linse, Stefan Wallin
(2013) Physical Review Letters, 110
ArticleMechanical resistance in unstructured proteins.
Sigurdur Jonsson, Simon Mitternacht, Anders Irbäck
(2013) Biophysical Journal, 104 p.2725-2732
ArticleAll-atom Monte Carlo simulations of protein folding and aggregation
Anders Irbäck, Sandipan Mohanty
(2013) Springer Series in Bio-/Neuroinformatics, 1 p.433-444
Book chapterLocal Unfolding and Aggregation Mechanisms of SOD1: A Monte Carlo Exploration.
Anna Bille, Sigurdur Jonsson, Mikael Akke, Anders Irbäck
(2013) The Journal of Physical Chemistry Part B, 117 p.9194-9202
ArticleDistinct phases of free α-synuclein - A Monte Carlo study.
Sigurdur Jonsson, Sandipan Mohanty, Anders Irbäck
(2012) Proteins, 80 p.2169-2177
ArticleMonte Carlo studies of protein aggregation
Sigurdur Jonsson, Iskra Staneva, Sandipan Mohanty, Anders Irbäck
(2012) Physics Procedia, 34 p.49-54
Paper in conference proceedingMonte Carlo Study of the Formation and Conformational Properties of Dimers of Aβ42 Variants.
Simon Mitternacht, Iskra Staneva, Torleif Härd, Anders Irbäck
(2011) Journal of Molecular Biology, 410 p.357-367
ArticleEffective all-atom potentials for proteins
Anders Irbäck, Sandipan Mohanty
(2011) Multiscale approaches to protein modeling , p.111-126
Book chapterMutation-induced fold switching among lattice proteins.
Christian Holzgräfe, Anders Irbäck, Carl Troein
(2011) Journal of Chemical Physics, 135
ArticleAccelerating atomic-level protein simulations by flat-histogram techniques.
Sigurdur Jonsson, Sandipan Mohanty, Anders Irbäck
(2011) Journal of Chemical Physics, 135
ArticleProtein folding, aggregation and unfolding in Monte Carlo Simulations
Sandipan Mohanty, Anders Irbäck, Simon Mitternacht, Giorgio Favrin, U. H E Hansmann
(2010) Physics Procedia, 7 p.68-71
Paper in conference proceedingUnfolding times for proteins in a force clamp
Stefano Luccioli, Alberto Imparato, Simon Mitternacht, Anders Irbäck, Alessandro Torcini
(2010) Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 81
ArticleMicroscopic Mechanism of Specific Peptide Adhesion to Semiconductor Substrates
Michael Bachmann, Karsten Goede, Annette G. Beck-Sickinger, Marius Grundmann, Anders Irbäck, et al.
(2010) Angewandte Chemie (International edition), 49 p.9530-9533
ArticleComparing the folding free-energy landscapes of Abeta42 variants with different aggregation properties.
Simon Mitternacht, Iskra Staneva, Torleif Härd, Anders Irbäck
(2010) Proteins, 78 p.2600-2608
ArticleAn effective all-atom potential for proteins
Anders Irbäck, Simon Mitternacht, Sandipan Mohanty
(2009) Food Biophysics, 2 p.2
ArticleChanging the Mechanical Unfolding Pathway of FnIII(10) by Tuning the Pulling Strength
Simon Mitternacht, Stefano Luccioli, Alessandro Torcini, Alberto Imparato, Anders Irbäck
(2009) Biophysical Journal, 96 p.429-441
ArticleFormation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
Da-Wei Li, Sandipan Mohanty, Anders Irbäck, Shuanghong Huo
(2008) PLoS Computational Biology, 4
ArticleSpontaneous beta-barrel formation: an all-atom study of Abeta(16-22) oligomerization
Anders Irbäck, Simon Mitternacht
(2008) Proteins, 71 p.207-214
ArticleProtein folding, unfolding and aggregation studied using an all-atom model with a simplified interaction potential
Anders Irbäck
(2008) Lecture Notes in Physics, volume "Rugged Free Energy Landscapes", 736 p.269-291
Book chapterHans-Uno Bengtsson - Docent i teoretisk fysik och folkbildare, dog den 18 maj 2007, 54 år gammal
Johan Bijnens, Gösta Gustafson, Anders Irbäck, Leif Lönnblad, Carsten Peterson, et al.
(2007)
MiscellaneousDifferences in solution behavior among four semiconductor-binding peptides
Simon Mitternacht, Stefan Schnabel, Michael Bachmann, Wolfhard Janke, Anders Irbäck
(2007) The Journal of Physical Chemistry Part B, 111 p.4355-4360
ArticleProtein aggregation and unfolding studied using an all-atom model with a simplified energy function
Anders Irbäck, Simon Mitternacht
(2006) John von Neumann Institute for Computing, NIC Series, 34 p.15-20
Paper in conference proceedingPROFASI: A Monte Carlo simulation package for protein folding and aggregation
Anders Irbäck, Sandipan Mohanty
(2006) Journal of Computational Chemistry, 27 p.1548-1555
ArticleThermal versus mechanical unfolding of ubiquitin
Anders Irbäck, Simon Mitternacht
(2006) Proteins, 65 p.759-766
ArticlePeptide folding and aggregation studied using a simplified atomic model
Anders Irbäck
(2005) Journal of Physics: Condensed Matter, 17 p.S1553-S1564
ArticleFolding thermodynamics of peptides
Anders Irbäck, Sandipan Mohanty
(2005) Biophysical Journal, 88 p.1560-1569
ArticleDissecting the mechanical unfolding of ubiquitin
Anders Irbäck, Simon Mitternacht, Sandipan Mohanty
(2005) Proceedings of the National Academy of Sciences, 102 p.13427-13432
ArticleCoupled folding-binding versus docking: A lattice model study
N Gupta, Anders Irbäck
(2004) Journal of Chemical Physics, 120 p.3983-3989
ArticleOligomerization of amyloid A beta(16-22) peptides using hydrogen bonds and hydrophobicity forces
Giorgio Favrin, Anders Irbäck, Sandipan Mohanty
(2004) Biophysical Journal, 87 p.3657-3664
ArticleFolding thermodynamics of three beta-sheet peptides: A model study
Anders Irbäck, Fredrik Sjunnesson
(2004) Proteins, 56 p.110-116
ArticleSequence-based study of two related proteins with different folding behaviors
Giorgio Favrin, Anders Irbäck, Stefan Wallin
(2004) Proteins, 54 p.8-12
ArticleTwo-state folding over a weak free-energy barrier
Giorgio Favrin, Anders Irbäck, Björn Samuelsson, Stefan Wallin
(2003) Biophysical Journal, 85 p.1457-1465
ArticleProtein folding in the absence of a clear free-energy barrier
Anders Irbäck
(2003) Acta Physica Polonica. Series B: Elementary Particle Physics, Nuclear Physics, Statistical Physics, Theory of Relativity, Field Theory, 34 p.4867-4878
ArticleA minimalistic all-atom approach to protein folding
Anders Irbäck
(2003) Journal of Physics: Condensed Matter, 15 p.S1797-S1807
ArticleThermodynamics of α- and β-structure formation in proteins
Anders Irbäck, Björn Samuelsson, Fredrik Sjunnesson, Stefan Wallin
(2003) Biophysical Journal, 85 p.1466-1473
ArticleEnumerating designing sequences in the HP model
Anders Irbäck, Carl Troein
(2002) Journal of Biological Physics, 28 p.1-15
ArticleFolding of a small helical protein using hydrogen bonds and hydrophobicity forces.
Giorgio Favrin, Anders Irbäck, Stefan Wallin
(2002) Proteins, 47 p.99-105
ArticleMonte Carlo update for chain molecules: Biased Gaussian steps in torsional space
Giorgio Favrin, Anders Irbäck, Fredrik Sjunnesson
(2001) Journal of Chemical Physics, 114 p.8154-8158
ArticleHydrogen bonds, hydrophobicity forces and the character of the collapse transition
A Irbäck, F Sjunnesson, S Wallin
(2001) Journal of Biological Physics, 27 p.169-79
ArticleOn hydrophobicity correlations in protein chains
A Irbäck, E Sandelin
(2000) Biophysical Journal, 79 p.2252-8
ArticleThree-helix-bundle protein in a Ramachandran model
A Irbäck, F Sjunnesson, S Wallin
(2000) Proceedings of the National Academy of Sciences, 97 p.13614-8
ArticleSequence design in coarse-grained protein models
Anders Irbäck
(2000) Progress of Theoretical Physics Supplement, 138 p.273-281
Paper in conference proceedingDesign of sequences with good folding properties in coarse-grained protein models
A Irbäck, C Peterson, F Potthast, E Sandelin
(1999) Structure, 7 p.347-60
ArticleMonte Carlo study of the phase structure of compact polymer chains
Anders Irbäck, Erik Sandelin
(1999) Journal of Chemical Physics, 110 p.12256-12262
ArticleLocal interactions and protein folding : A model study on the square and triangular lattices
Anders Irbäck, Erik Sandelin
(1998) Journal of Chemical Physics, 108 p.2245-2250
ArticleMonte Carlo procedure for protein design
Anders Irbäck, Carsten Peterson, Frank Potthast, Erik Sandelin
(1998) Physical Review E, 58
ArticleBinary assignments of amino acids from pattern conservation
A Irbäck, F Potthast
(1997) Protein Engineering, 10 p.1013-1017
ArticleLocal interactions and protein folding : A three-dimensional off-lattice approach
Anders Irbäck, Carsten Peterson, Fránk Potthast, Ola Sommelius
(1997) Journal of Chemical Physics, 107 p.273-282
ArticleIdentification of amino acid sequences with good folding properties in an off-lattice model
Anders Irbäck, Carsten Peterson, Frank Potthast
(1997) Physical Review E, 55 p.860-867
ArticleEvidence for nonrandom hydrophobicity structures in protein chains
A Irbäck, C Peterson, F Potthast
(1996) Proceedings of the National Academy of Sciences, 93 p.9533-8
ArticleSequence dependence of self-interacting random chains
Anders Irbäck, H. Schwarze
(1995) Journal of Physics A: Mathematical and General, 28 p.2121-2132
ArticleStudies of an off-lattice model for protein folding : Sequence dependence and improved sampling at finite temperature
Anders Irbäck, Frank Potthast
(1995) Journal of Chemical Physics, 103 p.10298-10305
ArticleScaling in Steiner random surfaces
C. F. Baillie, A. Irbäck, W. Janke, D. A. Johnston
(1994) Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics, 325 p.45-50
ArticleHybrid Monte Carlo simulation of polymer chains
A. Irbäck
(1994) Journal of Chemical Physics, 101 p.1661-1667
ArticleFinite-size scaling at phase coexistence
Sourendu Gupta, A. Irbäck, M. Ohlsson
(1993) Nuclear Physics, Section B, 409 p.663-683
ArticleThe theory of dynamical random surfaces with extrinsic curvature
J. Ambjørn, A. Irbäck, J. Jurkiewicz, B. Petersson
(1993) Nuclear Physics, Section B, 393 p.571-600
ArticleFinite-size scaling on the Ising coexistence line
Sourendu Gupta, A. Irbäck
(1993) Nuclear Physics B - Proceedings Supplements, 30 p.861-864
ArticlePhysics beyond instantons. Measuring the physical correlation length
Sourendu Gupta, A. Irbäck
(1992) Physics Letters B, 286 p.112-117
ArticleSpectral density analysis of the chiral transition in nf=4 finite temperature QCD
Nelson A. Alves, Bernd A. Berg, Dennis W. Duke, Anders Irbäck, Sergiu Sanielevici
(1992) Physics Letters B, 280 p.261-266
ArticleCritical properties of the dynamical random surface with extrinsic curvature
J. Ambjørn, J. Jurkiewicz, S. Varsted, A. Irbäck, B. Petersson
(1992) Physics Letters B, 275 p.295-303
ArticleScaling properties at the crumpling transition
Anders Irbäck
(1992) Nuclear Physics B (Proceedings Supplements), 26 p.572-574
Paper in conference proceedingMeasuring the string tension in random surface models with extrinsic curvature
A. Irbäck, J. Jurkiewicz, S. Varsted
(1992) Computer Physics Communications, 70 p.59-68
ArticleHadronic correlation functions in the QCD plasma phase
Anders Irbäck
(1991) Nuclear Physics B (Proceedings Supplements), 20 p.280-283
Paper in conference proceedingHadronic correlation functions in the QCD plasma phase
K.D. Born, S. Gupta, Anders Irbäck, F. Karsch, E. Laermann, et al.
(1991) Physical Review Letters, 67 p.302-305
ArticleDynamics near a first-order phase transition with the Metropolis and Swendsen-Wang algorithms
A. Billoire, R. Lacaze, A. Morel, Sourendu Gupta, A. Irbäck, et al.
(1991) Nuclear Physics, Section B, 358 p.231-248
ArticleThe heavy quark potential in SU(2) gauge theory at high temperature
A. Irbäck, P. Lacock, D. Miller, B. Petersson, T. Reisz
(1991) Nuclear Physics, Section B, 363 p.34-64
ArticleA 3-dimensional Z 3 symmetric model : Correlation lengths at a first order phase transition
Sourendu Gupta, A. Irbäck, B. Petersson, R. V. Gavai, F. Karsch
(1990) Nuclear Physics B (Proceedings Supplements), 17 p.199-203
Paper in conference proceedingFlavour degrees of freedom and the transition temperature in QCD
R. V. Gavai, Sourendu Gupta, A. Irbäck, F. Karsch, S. Meyer, et al.
(1990) Physics Letters B, 241 p.567-573
ArticleThe correlation lengths and the order of the phase transition in three-dimensional Z 3 symmetric models
Sourendu Gupta, A. Irbäck, B. Petersson, R. V. Gavai, F. Karsch
(1990) Nuclear Physics, Section B, 329 p.263-284
ArticleHybrid Monte Carlo simulation of four flavour QCD at finite temperature
Anders Irbäck
(1990) Nuclear Physics B (Proceedings Supplements), 17 p.210-213
Paper in conference proceedingThe finite temperature phase transition in four flavour QCD on an 8×12 3 lattice
R. V. Gavai, Sourendu Gupta, A. Irbäck, F. Karsch, S. Meyer, et al.
(1989) Physics Letters B, 232 p.491-497
ArticleLattice QCD with small number of flavours
A. Irbäck, F. Karsch, B. Petersson, H. W. Wyld
(1989) Physics Letters B, 216 p.177-183
ArticleA random surface representation of Wilson loops in Z(2) gauge theory
A. Irbäck
(1988) Physics Letters B, 211 p.129-131
ArticleThe effective string and SU(2) lattice MC data
M. Flensburg, A. Irbäck, C. Peterson
(1987) Zeitschrift für Physik C Particles and Fields, 36 p.629-637
ArticleCompact three-dimensional U(1) gauge theory reexamined
A. Irbäck, C. Peterson
(1987) Physical Review D, 36 p.3804-3808
ArticleMeasurement of Tc in the scaling region of (2+1)-dimensional SU(2) lattice gauge theory
M. Flensburg, A. Irbäck
(1986) Physics Letters B, 175 p.187-191
ArticleNumerical evidence for a mass gap in three-dimensional SU(2)
A. Irbäck, C. Peterson
(1986) Physics Letters B, 174 p.99-103
ArticleMixed-Symmetry interacting-Boson-Model states in the nuclei Ba140, Ce142, and Nd144 with N=84
W. D. Hamilton, A. Irbäck, J. P. Elliott
(1984) Physical Review Letters, 53 p.2469-2472
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