Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 37) Show all publications
Wang, W., Díaz-Méndez, R., Wallin, M., Lidmar, J. & Babaev, E. (2019). Melting of a two-dimensional monodisperse cluster crystal to a cluster liquid. Physical review. E, 99(4), Article ID 042140.
Open this publication in new window or tab >>Melting of a two-dimensional monodisperse cluster crystal to a cluster liquid
Show others...
2019 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 99, no 4, article id 042140Article in journal (Refereed) Published
Abstract [en]

Monodisperse ensembles of particles that have cluster crystalline phases at low temperatures can model a number of physical systems, such as vortices in type-1.5 superconductors, colloidal suspensions, and cold atoms. In this work, we study a two-dimensional cluster-forming particle system interacting via an ultrasoft potential. We present a simple mean-field characterization of the cluster-crystal ground state, corroborating with Monte Carlo simulations for a wide range of densities. The efficiency of several Monte Carlo algorithms is compared, and the challenges of thermal equilibrium sampling are identified. We demonstrate that the liquid to cluster-crystal phase transition is of first order and occurs in a single step, and the liquid phase is a cluster liquid. © 2019 American Physical Society.

Place, publisher, year, edition, pages
American Physical Society, 2019
Keywords
Ground state, Intelligent systems, Liquids, Suspensions (fluids), Colloidal suspensions, Crystal phase transition, Crystalline phasis, Monodisperse clusters, Monte carlo algorithms, Particle systems, Thermal equilibriums, Two-dimensional clusters, Monte Carlo methods
National Category
Materials Chemistry
Identifiers
urn:nbn:se:kth:diva-255902 (URN)10.1103/PhysRevE.99.042140 (DOI)2-s2.0-85064828694 (Scopus ID)
Note

Export Date: 24 May 2019; Article; Funding details: 621-2012-3984; Funding details: Vetenskapsrådet, 642-2013-7837; Funding text 1: W.W. and E.B. acknowledge support from the Swedish Research Council Grant No. 642-2013-7837 and the Goran Gustafsson Foundation for Research in Natural Sciences and Medicine. M.W. and R.D.M. acknowledge support from the Swedish Research Council Grant No. 621-2012-3984. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at the National Supercomputer Centre (NSC) and the High Performance Computing Center North (HPC2N).

Available from: 2019-08-22 Created: 2019-08-22 Last updated: 2019-08-22Bibliographically approved
Diaz-Mendez, R., Pupillo, G., Mezzacapo, F., Wallin, M., Lidmar, J. & Babaev, E. (2019). Phase-change switching in 2D via soft interactions. Soft Matter, 15(3), 355-358
Open this publication in new window or tab >>Phase-change switching in 2D via soft interactions
Show others...
2019 (English)In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 15, no 3, p. 355-358Article in journal (Refereed) Published
Abstract [en]

We present a new type of phase-change behavior relevant for information storage applications, that can be observed in 2D systems with cluster-forming ability. The temperature-based control of the ordering in 2D particle systems depends on the existence of a crystal-to-glass transition. We perform molecular dynamics simulations of models with soft interactions, demonstrating that the crystalline and amorphous structures can be easily tuned by heat pulses. The physical mechanism responsible for this behavior is a self-assembled polydispersity, that depends on the cluster-forming ability of the interactions. Therefore, the range of real materials that can perform such a transition is very wide in nature, ranging from colloidal suspensions to vortex matter. The state of the art in soft matter experimental setups, controlling interactions, polydispersity and dimensionality, makes it a very fertile ground for practical applications.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-244117 (URN)10.1039/c8sm01738g (DOI)000457278300001 ()30556570 (PubMedID)2-s2.0-85060062234 (Scopus ID)
Note

QC 20190219

Available from: 2019-02-19 Created: 2019-02-19 Last updated: 2019-05-10Bibliographically approved
Wang, W., Wallin, M. & Lidmar, J. (2018). Chaotic temperature and bond dependence of four-dimensional Gaussian spin glasses with partial thermal boundary conditions. Physical review. E, 98(6), Article ID 062122.
Open this publication in new window or tab >>Chaotic temperature and bond dependence of four-dimensional Gaussian spin glasses with partial thermal boundary conditions
2018 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 6, article id 062122Article in journal (Refereed) Published
Abstract [en]

Spin glasses have competing interactions and complex energy landscapes that are highly susceptible to perturbations, such as the temperature or the bonds. The thermal boundary condition technique is an effective and visual approach for characterizing chaos and has been successfully applied to three dimensions. In this paper, we tailor the technique to partial thermal boundary conditions, where the thermal boundary condition is applied in a subset (three out of four in this work) of the dimensions for better flexibility and efficiency for a broad range of disordered systems. We use this method to study both temperature chaos and bond chaos of the four-dimensional Edwards-Anderson model with Gaussian disorder to low temperatures. We compare the two forms of chaos, with chaos of three dimensions, and also the four-dimensional +/- J model. We observe that the two forms of chaos are characterized by the same set of scaling exponents, bond chaos is much stronger than temperature chaos, and the exponents are also compatible with the +/- J model. Finally, we discuss the effects of chaos on the number of pure states in the thermal boundary condition ensemble.

Place, publisher, year, edition, pages
American Physical Society, 2018
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-240711 (URN)10.1103/PhysRevE.98.062122 (DOI)000453472900001 ()2-s2.0-85059435644 (Scopus ID)
Note

QC 20190104

Available from: 2019-01-04 Created: 2019-01-04 Last updated: 2019-03-18Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2018). Riemann metric approach to optimal sampling of multidimensional free-energy landscapes. Physical review. E, 98(2), Article ID 023312.
Open this publication in new window or tab >>Riemann metric approach to optimal sampling of multidimensional free-energy landscapes
2018 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 2, article id 023312Article in journal (Refereed) Published
Abstract [en]

Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%-70%.

Place, publisher, year, edition, pages
American Physical Society, 2018
Keywords
Bioinformatics, Boltzmann equation, Computational chemistry, Mathematical transformations, Molecular dynamics, Reaction kinetics, Boltzmann distribution, Computational overheads, Conformational transitions, Free-energy calculations, High-dimensional models, Molecular dynamics simulations, Multidimensional free energy, Nonlinear coordinate transformation, Free energy
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-236741 (URN)10.1103/PhysRevE.98.023312 (DOI)000443145500007 ()2-s2.0-85052735453 (Scopus ID)
Note

Export Date: 22 October 2018; Article; Correspondence Address: Hess, B.; Department of Physics, Swedish E-Science Research Center, KTH Royal Institute of TechnologySweden; email: hess@kth.se; Funding details: HPC2N; Funding details: SNIC 2016/10-47; Funding details: 2017/11-25; Funding details: 2016/1-562; Funding details: 258980, ERC, European Research Council; Funding details: 2014-4505, VR, Vetenskapsrådet; Funding text: This research was supported by the European Research Council (grant no. 258980) and the Swedish Research Council (grant no. 2014-4505). The simulations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC 2016/1-562, SNIC 2016/10-47, and 2017/11-25) at the PDC Centre for High Performance Computing (PDC-HPC) and the High Performance Computing Center North (HPC2N). QC 20181022

Available from: 2018-10-22 Created: 2018-10-22 Last updated: 2019-05-10Bibliographically approved
Diaz-Mendez, R., Lidmar, J. & Wallin, M. (2018). Scaling of the magnetic permeability at the Berezinskii–Kosterlitz–Thouless transition from Coulomb gas simulations. Journal of Statistical Mechanics: Theory and Experiment, 2018(12), Article ID 123203.
Open this publication in new window or tab >>Scaling of the magnetic permeability at the Berezinskii–Kosterlitz–Thouless transition from Coulomb gas simulations
2018 (English)In: Journal of Statistical Mechanics: Theory and Experiment, ISSN 1742-5468, E-ISSN 1742-5468, Vol. 2018, no 12, article id 123203Article in journal (Refereed) Published
Abstract [en]

A new approach to the Berezinskii–Kosterlitz–Thouless transition in the two-dimensional Coulomb gas model is explored by Monte Carlo simulation and finite size scaling. The usual mapping of a neutral two-dimensional superconductor in zero magnetic field to a Coulomb gas leads to an unscreened logarithmic interaction between the vortices, and with periodic boundary conditions vortex configurations are always vorticity neutral with an equal number of plus and minus vortices. We demonstrate that relaxing the neutrality condition has certain advantages. It leads to non-neutral vortex configurations that can appear in real systems with open boundary conditions and permits calculation of the compressibility, which for thin film superconductors corresponds to the magnetic permeability. The vortex-number fluctuation has remarkable scaling properties at and below the Berezinskii–Kosterlitz–Thouless transition. The fugacity variable becomes dangerously irrelevant in the low-temperature phase and leads to a multiplicative scaling correction to the mean-square vortex-number fluctuation and to the magnetic permeability. This multiplicative correction strongly affects the scaling properties of the vorticity fluctuation at and below the transition. Consequences of these findings are demonstrated using Monte Carlo simulations. Inclusion of the next-higher order correction to scaling is found to play an important role in the analysis of numerical data for the vortex number fluctuation and permits accurate determination of the critical properties.

Place, publisher, year, edition, pages
IOP Publishing, 2018
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-248133 (URN)10.1088/1742-5468/aae855 (DOI)000452045600003 ()2-s2.0-85059878709 (Scopus ID)
Note

QC 20190513

Available from: 2019-04-04 Created: 2019-04-04 Last updated: 2019-05-13Bibliographically approved
Andersson, A. & Lidmar, J. (2015). Modeling and simulations of quantum phase slips in ultrathin superconducting wires. Physical Review B. Condensed Matter and Materials Physics, 91(13), Article ID 134504.
Open this publication in new window or tab >>Modeling and simulations of quantum phase slips in ultrathin superconducting wires
2015 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 91, no 13, article id 134504Article in journal (Refereed) Published
Abstract [en]

We study quantum phase slips (QPS) in ultrathin superconducting wires. Starting from an effective one-dimensional microscopic model, which includes electromagnetic fluctuations, we map the problem to a (1+1)-dimensional gas of interacting instantons. We introduce a method to calculate the tunneling amplitude of quantum phase slips directly from Monte Carlo simulations. This allows us to go beyond the dilute instanton gas approximation and study the problem without any limitations of the density of QPS. We find that the tunneling amplitude shows a characteristic scaling behavior near the superconductor-insulator transition. We also calculate the voltage-charge relation of the insulating state, which is the dual of the Josephson current-phase relation in ordinary superconducting weak links. This evolves from a sinusoidal form in the regime of dilute QPS to more exotic shapes for higher QPS densities, where interactions are important.

Place, publisher, year, edition, pages
American Physical Society, 2015
Keywords
Quantum phase slips, superconductivity
National Category
Condensed Matter Physics
Research subject
Physics
Identifiers
urn:nbn:se:kth:diva-165381 (URN)10.1103/PhysRevB.91.134504 (DOI)000352588900005 ()2-s2.0-84928780607 (Scopus ID)
Note

QC 20150518

Available from: 2015-04-27 Created: 2015-04-27 Last updated: 2017-12-04Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2015). Sampling rare biomolecular events with adaptive pulling simulations. Paper presented at 10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY. European Biophysics Journal, 44, S144-S144
Open this publication in new window or tab >>Sampling rare biomolecular events with adaptive pulling simulations
2015 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S144-S144Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER, 2015
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-243669 (URN)000380001400390 ()
Conference
10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY
Note

QC 20190304

Available from: 2019-03-04 Created: 2019-03-04 Last updated: 2019-05-20Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2014). Accelerated weight histogram method for exploring free energy landscapes. Journal of Chemical Physics, 141(4), 044110
Open this publication in new window or tab >>Accelerated weight histogram method for exploring free energy landscapes
2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 4, p. 044110-Article in journal (Refereed) Published
Abstract [en]

Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a beta-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

Keywords
Ensemble Monte-Carlo, Molecular-Dynamics, Multicanonical Ensemble, Force-Field, Protein, Simulation, Systems, Distributions, Transitions, Chignolin
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-151349 (URN)10.1063/1.4890371 (DOI)000340712200018 ()2-s2.0-84905648018 (Scopus ID)
Funder
EU, European Research Council, 258980
Note

QC 20140919

Available from: 2014-09-19 Created: 2014-09-18 Last updated: 2017-12-05Bibliographically approved
Ergül, A., Lidmar, J., Johansson, J., Azizoglu, Y., Schaeffer, D. & Haviland, D. B. (2013). Localizing quantum phase slips in one-dimensional Josephson junction chains. New Journal of Physics, 15, 095014
Open this publication in new window or tab >>Localizing quantum phase slips in one-dimensional Josephson junction chains
Show others...
2013 (English)In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 15, p. 095014-Article in journal (Refereed) Published
Abstract [en]

We studied quantum phase-slip (QPS) phenomena in long one-dimensional Josephson junction series arrays with tunable Josephson coupling. These chains were fabricated with as many as 2888 junctions, where one sample had a separately tunable link in the middle of the chain. Measurements were made of the zero-bias resistance, R-0, as well as current-voltage characteristics (IVC). The finite R-0 is explained by QPS and shows an exponential dependence on root E-J/E-C with a distinct change in the exponent at R-0 = R-Q = h/4e(2). When R-0 > R-Q, the IVC clearly shows a remnant of the Coulomb blockade, which evolves to a zero-current state with a sharp critical voltage as E-J is tuned to a smaller value. The zero-current state below the critical voltage is due to coherent QPSs and we show that these are enhanced when the central link is weaker than all other links. Above the critical voltage, a negative, differential resistance is observed, which nearly restores the zero-current state.

Keywords
Small Tunnel-Junctions, Charge Solitons, Arrays, Superconductivity, Transition, Nanowires, Vortices
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-131716 (URN)10.1088/1367-2630/15/9/095014 (DOI)000324795400004 ()2-s2.0-84885158666 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20131018

Available from: 2013-10-18 Created: 2013-10-17 Last updated: 2017-12-06Bibliographically approved
Ergül, A., Schaeffer, D., Lindblom, M., Haviland, D. B., Lidmar, J. & Johansson, J. (2013). Phase sticking in one-dimensional Josephson junction chains. Physical Review B. Condensed Matter and Materials Physics, 88(10), 104501
Open this publication in new window or tab >>Phase sticking in one-dimensional Josephson junction chains
Show others...
2013 (English)In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 88, no 10, p. 104501-Article in journal (Refereed) Published
Abstract [en]

We studied current-voltage characteristics of long one-dimensional Josephson junction chains with Josephson energy much larger than charging energy, E-J >> E-C. In this regime, typical I-V curves of the samples consist of a supercurrent-like branch at low-bias voltages followed by a voltage-independent chain current branch, I-chain at high bias. Our experiments showed that I-chain is not only voltage-independent but it is also practically temperature-independent up to T = 0.7T(C). We have successfully model the transport properties in these chains using a capacitively shunted junction model with nonlinear damping.

Keywords
Superconducting Circuits, Coulomb-Blockade, Tunnel-Junctions, Arrays, Transition, Slips
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-129444 (URN)10.1103/PhysRevB.88.104501 (DOI)000323890700005 ()2-s2.0-84884886402 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20131002

Available from: 2013-10-02 Created: 2013-09-30 Last updated: 2017-12-06Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9881-7857

Search in DiVA

Show all publications