124 citations · 971 across the 28 of their papers we have counts for
28 papers
Joint Bayesian inference of Earth's magnetic field and core surface flow on millennial timescales
Andreas Nilsson, Neil Suttie, Marie Troyano +3
Understanding Earth's core dynamics over millennial timescales requires models that jointly describe the evolution of the geomagnetic field and core surface flow, while accommodati…
Designing lattice proteins with variational quantum algorithms
Hanna Linn, Lucas Knuthson, Anders Irbäck +3
Quantum heuristics have shown promise in solving various optimization problems, including lattice protein folding. Equally relevant is the inverse problem, protein design, where on…
Using quantum annealing to design lattice proteins
Anders Irbäck, Lucas Knuthson, Sandipan Mohanty +1
Quantum annealing has shown promise for finding solutions to difficult optimization problems, including protein folding. Recently, we used the D-Wave Advantage quantum annealer to…
Folding lattice proteins with quantum annealing
Anders Irbäck, Lucas Knuthson, Sandipan Mohanty +1
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure…
Markov modeling of peptide folding in the presence of protein crowders
Daniel Nilsson, Sandipan Mohanty, Anders Irbäck
We use Markov state models (MSMs) to analyze the dynamics of a -hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different type…
Thermodynamics of amyloid formation and the role of intersheet interactions
Anders Irbäck, Jonas Wessén
The self-assembly of proteins into -sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastabl…
Mechanical resistance in unstructured proteins
S. Æ. Jónsson, S. Mitternacht, A. Irbäck
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To in…
Unfolding times for proteins in a force clamp
Stefano Luccioli, Alberto Imparato, Simon Mitternacht +2
The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfoldi…
Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space
Giorgio Favrin, Anders Irbäck, Fredrik Sjunnesson
We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conform…
Three-helix-bundle Protein in a Ramachandran Model
Anders Irbäck, Fredrik Sjunnesson, Stefan Wallin
We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types of amino acids and fi…
On Hydrophobicity Correlations in Protein Chains
Anders Irbäck, Erik Sandelin
We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from r…
Monte Carlo Study of the Phase Structure of Compact Polymer Chains
Anders Irbäck, Erik Sandelin
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not une…
Design of Sequences with Good Folding Properties in Coarse-Grained Protein Models
Anders Irbäck, Carsten Peterson, Frank Potthast +1
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish thi…
Monte Carlo Procedure for Protein Design
Anders Irbäck, Carsten Peterson, Frank Potthast +1
A new method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Le…
Local Interactions and Protein Folding: A Model Study on the Square and Triangular Lattices
Anders Irbäck, Erik Sandelin
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the m…
Local Interactions and Protein Folding: A 3D Off-Lattice Approach
Anders Irbäck, Carsten Peterson, Frank Potthast +1
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence…
Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
Anders Irbäck, Carsten Peterson, Frank Potthast
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo pr…
Comment on `Avalanche Dynamics in Evolution, Growth and Depinning Models'
Mats Dahlbom, Anders Irbäck
This paper is withdrawn.
Binary Assignments of Amino Acids from Pattern Conservation
Anders Irbäck, Frank Potthast
We develop a simple optimization procedure for assigning binary values to the amino acids. The binary values are determined by a maximization of the degree of pattern conservation…
Evidence for Non-Random Hydrophobicity Structures in Protein Chains
Anders Irbäck, Carsten Peterson, Frank Potthast
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed…
Sequence Dependence in an Off-Lattice Model for Protein Folding
Anders Irbäck, Frank Potthast
See chem-ph/9505003.
Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature
Anders Irbäck, Frank Potthast
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulatio…
Hybrid Monte Carlo simulation of polymer chains
A. Irbäck
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The per…
Scaling in Steiner Random Surfaces
C. F. Baillie, A. Irback, W. Janke +1
It has been suggested that the modified Steiner action functional has desirable properties for a random surface action. In this paper we investigate the scaling of the string tensi…