| 1. |
- Baillie, C. F., et al.
(författare)
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Scaling in Steiner random surfaces
- 1994
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 325:1-2, s. 45-50
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Tidskriftsartikel (refereegranskat)abstract
- It has been suggested that the modified Steiner action functional has desirble properties for a random surface action. In this paper we investigate the scaling of the string tension and massgap in a variant of this action on dynamically triangulated random surfaces and compare the results with the gaussian plus extrinsic curvature actions that have been used previously.
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| 2. |
- Flensburg, M., et al.
(författare)
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Measurement of Tc in the scaling region of (2+1)-dimensional SU(2) lattice gauge theory
- 1986
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693. ; 175:2, s. 187-191
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Tidskriftsartikel (refereegranskat)abstract
- The deconfinement temperature Tc of (2+1)-dimensional SU(2) gauge theory is measured on lattice sizes varying from 2 × 202 to 6 × 602 and with β in the rate 3-9. Approximative scaling is found for β > 6.5 and Tc/√σ = 0.94 ± 0.03 is obtained. This value is in excellent agreement with (3/π) 1 2, as predicted from the breakdown of SU(2) confinement in terms of an effective scalar string theory.
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| 3. |
- Flensburg, M., et al.
(författare)
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The effective string and SU(2) lattice MC data
- 1987
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Ingår i: Zeitschrift für Physik C Particles and Fields. - 0170-9739. ; 36:4, s. 629-637
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Tidskriftsartikel (refereegranskat)abstract
- We present high statistics MC calculations of the static potential in three-dimensional SU(2) for a wide range of β values on a 243 lattice. The deviations from area law are unambiguously demonstrated by use of 2nd lattice R derivative. After a clear crossover at β=4.5 the data show signs of an effective string roughening up to β=6.5, while scaling is not strictly obeyed in this interval. Pure fermionic strings do not provide better fits. The effect of regularization prescription on the effective string model up to two-loop correction is discussed and is found to be small. We also make a comparative study of existing data on Z(2) and SU(3) together with new data on fourdimensional SU(2) presented here. It is pointed out that standard variance reduction methods as applied especially to Wilson lines are plagued by severe long range auto-correlations, whereas larger Wilson loops are less affected.
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| 4. |
- Fogelmark, Karl, et al.
(författare)
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Fitting a function to time-dependent ensemble averaged data
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Time-dependent ensemble averages, i.e., trajectory-based averages of some observable, are of importance in many fields of science. A crucial objective when interpreting such data is to fit these averages (for instance, squared displacements) with a function and extract parameters (such as diffusion constants). A commonly overlooked challenge in such function fitting procedures is that fluctuations around mean values, by construction, exhibit temporal correlations. We show that the only available general purpose function fitting methods, correlated chi-square method and the weighted least squares method (which neglects correlation), fail at either robust parameter estimation or accurate error estimation. We remedy this by deriving a new closed-form error estimation formula for weighted least square fitting. The new formula uses the full covariance matrix, i.e., rigorously includes temporal correlations, but is free of the robustness issues, inherent to the correlated chi-square method. We demonstrate its accuracy in four examples of importance in many fields: Brownian motion, damped harmonic oscillation, fractional Brownian motion and continuous time random walks. We also successfully apply our method, weighted least squares including correlation in error estimation (WLS-ICE), to particle tracking data. The WLS-ICE method is applicable to arbitrary fit functions, and we provide a publically available WLS-ICE software.
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| 5. |
- Gupta, Sourendu, et al.
(författare)
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Finite-size scaling at phase coexistence
- 1993
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Ingår i: Nuclear Physics, Section B. - 0550-3213. ; 409:3, s. 663-683
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Tidskriftsartikel (refereegranskat)abstract
- From a finite-size scaling (FSS) theory of cumulants of the order parameter at phase-coexistence points, we reconstruct the scaling of the moments. Assuming that the cumulants allow a reconstruction of the free energy density no better than as an asymptotic expansion, we find that FSS for moments of low order is still complete. We suggest ways of using this theory for the analysis of numerical simulations. We test these methods numerically through the scaling of cumulants and moments of the magnetisation in the low-temperature phase of the two-dimensional Ising model.
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| 6. |
- Irbäck, A.
(författare)
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A random surface representation of Wilson loops in Z(2) gauge theory
- 1988
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693. ; 211:1-2, s. 129-131
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Tidskriftsartikel (refereegranskat)abstract
- We study a random surface representation of Wilson loops in Z(2) gauge theory. The weights consist of an area factor, which dominates at strong coupling, and an excluded volume factor flavouring crumpled surfaces. We examine the latter one in some detail in three as well as four dimensions by use of Monte Carlo methods. In three dimensions, the critical behaviour of the surfaces is found to be determined to a large extent by the excluded volume factor.
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| 7. |
- Irbäck, A, et al.
(författare)
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Binary assignments of amino acids from pattern conservation
- 1997
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Ingår i: Protein Engineering. - : Oxford University Press (OUP). - 0269-2139. ; 10:9, s. 1013-1017
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The maximization is carried out at fixed composition. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlated with hydrophobicity. The stability of the procedure is demonstrated. Our calculations are based upon sequences in the SWISS-PROT database.
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| 8. |
- Irbäck, A., et al.
(författare)
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Compact three-dimensional U(1) gauge theory reexamined
- 1987
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Ingår i: Physical Review D. - 0556-2821. ; 36:12, s. 3804-3808
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Tidskriftsartikel (refereegranskat)abstract
- Convincing evidence of a nonvanishing string tension in the continuum limit of compact three-dimensional U(1) gauge theory is presented. It is based on Monte Carlo measurements of Wilson loops on a 323 lattice at =2.0 and 2.2. The observed string tensions at these couplings are consistent with the Polyakov theory. Also, a very clean signal of a string vibrational contribution to the potential is observed.
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| 9. |
- Irbäck, A, et al.
(författare)
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Design of sequences with good folding properties in coarse-grained protein models
- 1999
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Ingår i: Structure. - 0969-2126. ; 7:3, s. 60-347
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplishing this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences; this requires excessive computational demand. Several approximate attempts to remedy this situation, based on energy minimization for fixed structure or high-T expansions, have been proposed. These methods are fast but often not accurate, as folding occurs at low T.RESULTS: We have developed a multisequence Monte Carlo procedure where both sequence and conformational space are simultaneously probed with efficient prescriptions for pruning sequence space. The method is explored on hydrophobic/polar models. First we discuss short lattice chains in order to compare with exact data and with other methods. The method is then successfully applied to lattice chains with up to 50 monomers and to off-lattice 20mers.CONCLUSIONS: The multisequence Monte Carlo method offers a new approach to sequence design in coarse-grained models. It is much more efficient than previous Monte Carlo methods, and is, as it stands, applicable to a fairly wide range of two-letter models.
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| 10. |
- Irbäck, A, et al.
(författare)
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Evidence for nonrandom hydrophobicity structures in protein chains
- 1996
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Ingår i: Proceedings of the National Academy of Sciences. - 0027-8424. ; 93:18, s. 8-9533
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Tidskriftsartikel (refereegranskat)abstract
- 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 by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistically significant way. By performing Fourier transforms on the random walks, one obtains additional evidence for nonrandomness of the distributions. We have also analyzed results from a synthetic model containing only two amino acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from some previous investigations using other methods, might have impact on how permissive with respect to sequence specificity protein folding process is-only sequences with nonrandom hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.
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| 11. |
- Irbäck, A.
(författare)
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Hybrid Monte Carlo simulation of polymer chains
- 1994
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 101:2, s. 1661-1667
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Tidskriftsartikel (refereegranskat)abstract
- 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 performance of the algorithm is tested on models for homopolymers with short- or long-range self-repulsion, using chains with 16≤N≤512 monomers. Without excessive fine tuning, we find that the computational cost grows as N2+z′ with 0.641N∼Nν(ln N)-α.
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| 12. |
- Irbäck, A, et al.
(författare)
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Hydrogen bonds, hydrophobicity forces and the character of the collapse transition
- 2001
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Ingår i: Journal of Biological Physics. - 0092-0606. ; 27:2-3, s. 79-169
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Tidskriftsartikel (refereegranskat)abstract
- We study the thermodynamic behavior of a model protein with 54 amino acidsthat is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom.The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.
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| 13. |
- Irbäck, A., et al.
(författare)
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Lattice QCD with small number of flavours
- 1989
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693. ; 216:1-2, s. 177-183
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Tidskriftsartikel (refereegranskat)abstract
- The finite temperature behaviour of lattice QCD with dynamical quarks for small number of flavours Nf is investigated. Simulations have been performed on lattices of size N3σ·4 with Nσ=8 and 12 and staggered fermions of mass ma=0.1 using a hybrid algorithm. We find that the two state signal at the critical point of the pure gauge theory, which is taken as sign for a fiorst order phase transition, persists for the values of Nf we have investigated, namely Nf=0.5, 1 and 2. It is, however, considerably weaker for Nf=1 and 2. Moreover, for Nf=2 the discontinuity at βc decreases with increasing lattice size. Thid puts doubt o order nature of the Nf=2 transition at intermediate masses.
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| 14. |
- Irbäck, A., et al.
(författare)
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Numerical evidence for a mass gap in three-dimensional SU(2)
- 1986
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693. ; 174:1, s. 99-103
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Tidskriftsartikel (refereegranskat)abstract
- Numerical evidence for a nonvanishing 0++ glueball mass in three-dimensional SU(2) is presented. By using a long-distance correlation Monte Carlo method we obtain m0++ = (4.7±1.2)√σ in the β-range 4.0-6.5. The measurements are consistent with 1/β-scaling. The relevance of this result for SU(2) in four dimensions at finite temperature is briefly discussed.
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| 15. |
- Irbäck, A, et al.
(författare)
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On hydrophobicity correlations in protein chains
- 2000
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Ingår i: Biophysical Journal. - 0006-3495. ; 79:5, s. 8-2252
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Tidskriftsartikel (refereegranskat)abstract
- 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 random sequences in significant ways in terms of both the distribution of hydrophobicity along the chains and total hydrophobicity. Whenever statistically feasible, the analogous calculations are performed for a set of real enzymes, too.
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| 16. |
- Irbäck, A, et al.
(författare)
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Three-helix-bundle protein in a Ramachandran model
- 2000
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 97:25, s. 8-13614
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Tidskriftsartikel (refereegranskat)abstract
- 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 five to six atoms per amino acid and has the Ramachandran torsional angles phi(i), psi(i) as its degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. For a suitable choice of the relative strength of these interactions, we find that the three-helix-bundle protein undergoes an abrupt folding transition from an expanded state to the native state. Also shown is that the corresponding one- and two-helix segments are less stable than the three-helix sequence.
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