arXiv subjects

Hannes Jónsson

Publications and source records attributed to Hannes Jónsson.

At least 19 recordsLinked to original sources

arXiv2026

Network of localized magnetic textures revealed using a saddle-point search framework

A computational framework is presented for the exploration of energy surfaces of magnetic systems via systematic identification of first-order saddle points that connect local energy minima representing possible states of the system. The saddle points characterize the mechanism of transitions between states and, together with the energy of the local minima, provide estimates of the transition rates within harmonic transition state theory or Kramers/Langer theory. The calculations involve four stages: (1) the symmetry of a given energy-minimum configuration is identified and used to define subsystems whose eigenmodes provide relevant deformation directions. (2) These modes are then used to guide the system toward the neighborhoods of the various saddle points on the energy rim surrounding the given energy minimum. (3) Next, the geodesic minimum mode following method is employed to efficiently converge onto the saddle points. (4) Finally, the identified saddle points are embedded into the network describing the connectivity of the states of the system. This methodology is applied in a study of the metastable textures of two-dimensional chiral magnets described by a lattice Hamiltonian, where a hierarchy of transition mechanisms for the nucleation, annihilation, and rearrangement of various localized magnetic textures are identified, such as skyrmions, antiskyrmions, skyrmion bags, chiral droplet, etc. Transitions corresponding to homotopies that preserve the topological charge as well as transformations that change it are identified. By scaling the interaction parameters, the distinct behavior of these two classes is obtained as the continuum limit is approached. For some transitions, the topological charge changes during the transition even though it is the same for the initial and final states.

cond-mat.mtrl-sci↗

arXiv2026

Polaron Conductivity in $α$-Fe2O3 Quenched by Adsorbed NO2

Polaron-mediated charge transport in α-Fe2O3 plays a central role in its performance as a gas-sensing material, yet the atomistic interaction between surface adsorbates and polarons remains insufficiently understood. Here, density functional theory with Hubbard-U correction (DFT+U) combined with nudged elastic band calculations is used to investigate polaron formation, migration, and quenching at the Fe-terminated α-Fe2O3 (0001) surface. The calculated activation energy for small-polaron hopping in bulk α-Fe2O3 is found to be 0.12 eV, in excellent agreement with experimental measurements, confirming the validity of the computational approach. Slab calculations show that migration of the polaron from bulk to the surface lowers the energy by 0.12 eV, indicating preferential localization of charge carriers at the gas-solid interface. Adsorption of NO2 induces substantial electron transfer (0.72 e-) from the oxide to the molecule, eliminating the localized Fe2+ polaron state and thereby suppressing polaronic conductivity. These results provide a direct microscopic explanation for the resistance increase of hematite-based sensors upon exposure to oxidizing gases. More broadly, the study establishes how surface adsorption can modulate charge transport α-Fe2O3 through control of polaron populations, offering design principles for improved iron oxide gas sensors.

cond-mat.mtrl-sci↗

arXiv2026

ChemFit: A framework for automated high-dimensional model parameter optimization

The parameterization of simulation-based models is a central yet laborious task in computational chemistry and physics, often driven by human intuition and manual iteration. Automating this task necessitates the definition of suitable objective functions, which tend to be expensive to evaluate, noisy, non-differentiable, or composed of heterogeneous contributions originating from separate sets of simulations. Gradient-free and black-box optimization algorithms are powerful tools which are particularly well-suited to minimizing such objective functions. Here, we introduce ChemFit, a flexible Python framework for the definition, composition, and massively concurrent evaluation of simulation-based objective functions, which is designed to operate in conjunction with these algorithms. We demonstrate the broad applicability of this approach by using ChemFit for three representative examples of increasing complexity and real-world relevance. First, we obtain the parameters of the Lennard-Jones potential for liquid argon from experimental measurements of the density. Second, we parameterize a polarizable and flexible potential energy function to reproduce the structure of small H$_2$O clusters obtained from density functional theory calculations. Finally, we tune a small subset of the parameters of a residue-level coarse-grained protein force-field, with the goal to reproduce the experimental critical solution temperature of the low complexity domain of the wild-type hnRNPA1 sequence and an arginine-enriched mutant of this protein. hnRNPA1 is an RNA-binding protein linked to amyotrophic lateral sclerosis. Together, these examples illustrate how ChemFit enables scalable, reproducible, and optimizer-agnostic parameter fitting for broadly applicable multiscale models.

physics.chem-ph↗

arXiv2026

Polarizable Embedding QM/MM for Periodic Systems

A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is coupled to a single center multipole expansion (SCME) model, characterising H$_2$O molecules in the MM region. In SCME the H$_2$O molecules are ascribed anisotropic dipole and quadrupole polarizabilities and permanent multipoles up to and including the hexadecapole. Our embedding scheme illustrates a smooth and efficient convergence pattern of the periodic interaction potential by introducing a single and clustered multipole expansion points in the far-field. By choosing the near- and far-field expansion of the potential carefully the PE-QM/MM calculation matches the level of accuracy of a the QM calculation. In the short range, the electrostatic interaction between the QM and MM subsystems is damped with a real-space and pair-wise isotropic damping functions - resulting in a screened interaction and preventing over-polarization. In molecular dynamics simulations the two subsystems are separated with the elastic scattering assisted flexible inner region [Kirchhoff et. al. JCTC, 2021, 17, 9, 5863] - ensuring a smooth transition in the radial distribution at the boundary between the two subsystems.

physics.chem-ph↗

arXiv2026

Surface sites drive Fe enrichment at reactive olivine interfaces

Calculations based on density functional theory and statistical mechanics reveal how Fe site preference in olivine is altered at interfaces. Although the M1 site is favoured in bulk olivine, surface metal sites provide greater stabilisation for high-spin Fe2+. This enrichment accounts for the enhanced reactivity of olivine interfaces towards dissolution, carbonation and catalysis.

cond-mat.mtrl-sci↗

arXiv2026

Enhanced Climbing Image Nudged Elastic Band method with Hessian Eigenmode Alignment

Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify the minimum energy path between the two and thereby the saddle point on the energy surface that is relevant for the given transition, thus providing an estimate of the transition state within the harmonic approximation of transition state theory. Such calculations can, however, incur high computational costs and may suffer stagnation on exceptionally flat or rough energy surfaces. Conversely, methods that only require specification of an initial set of atomic coordinates, such as the minimum mode following (MMF) method, offer efficiency but can converge on saddle points that are not relevant for transition of interest. Here, we present an adaptive hybrid algorithm that integrates the CI-NEB with the MMF method so as to get faster convergence to the relevant saddle point. The method is benchmarked for the Baker-Chan (BC) saddle point test set using the PET-MAD machine-learned potential as well as 59 transitions of a heptamer island on Pt(111) from the OptBench benchmark set. A Bayesian analysis of the performance shows a reduction in energy and force calculations of 57% [95% CrI: -64%, -50%] relative to CI-NEB for the BC set, while a 31% mean reduction is found for the transitions of the heptamer island. These results establish this hybrid method as a highly effective tool for high-throughput automated chemical discovery of atomic rearrangements.

physics.chem-ph↗

arXiv2026

Orbital Optimization and Neural-Network-Assisted Configuration Interaction Calculations of Rydberg States

Rydberg excited states of molecules pose a challenge for electronic structure calculations because of their highly diffuse electron distribution. Even large and elaborate atomic basis sets tend to underrepresent the long-range tail, overly confining the Rydberg state. An approach is presented here where the molecular orbitals are variationally optimized for the excited state using a plane wave basis set in a Hartree-Fock calculation, followed by a configuration interaction calculation. The use of excited state optimized orbitals greatly enhances the convergence of the many-body calculation, as illustrated by a full configuration interaction calculation of the $2s$ Rydberg state of H$_2$. A neural-network-based selective configuration interaction approach is then applied to calculations of $3s$ and $3p$ states of H$_2$O and NH$_3$. The obtained values of excitation energy are in close agreement with experimental measurements as well as previous many-body calculations where sufficiently diffuse atomic basis sets were used. Calculations using atomic basis sets lacking extra diffuse functions, such as aug-cc-pVTZ, give significantly higher estimates due to confinement of the Rydberg states.

physics.chem-ph↗

arXiv2026

Viscosity as a Smoking Gun for Complex Formation in Solution: Fe$^{2+}$ and Mg$^{2+}$ Chlorides as Examples

Electrolyte solutions at high concentration are indispensable and yet poorly understood. In particular, the extent of speciation -- the formation of complexes composed of multiple species -- in concentrated ionic solutions is very challenging to obtain theoretically and experimentally, but can have a strong effect on solution properties. The literature is rife with contradictory estimates of speciation from experiments. We find that speciation affects transport properties, and is therefore, a prerequisite to accurately model concentrated solutions. We turn this to our advantage by showing that the viscosity can be used to determine the extent of complexation in concentrated aqueous solutions. Results of simulations as well as experimental measurements are presented. The atomistic Madrid-2019 force-field is extended to model FeCl$_2$. Solutions of FeCl$_2$ and MgCl$_2$ are compared and the observed difference in viscosity explained by more complexation in the former, a conclusion supported by recently reported X-ray absorption and neutron scattering experiments.

physics.chem-ph↗

arXiv2026

Locally Scaled Self-Interaction Corrected Energy Functionals with Complex Optimal Orbitals

We present a fully variational locally scaled self-interaction corrected (SIC) energy functional using complex optimal orbitals. This represents an important milestone for fully variational SIC energy functionals, which have been shown to improve the prediction of the properties of atomic, molecular and solid state systems in general, in both ground and excited states. However, it depends on the system and property of the system whether it is beneficial to scale the SIC correction by a factor of one-half, which makes the application of SIC inconsistent. In the limit of a single electron the SIC exactly cancels the self interaction error, but overcorrects the error in regions of high density where there is large overlap between occupied orbitals. The newly implemented local scaling function, $z(\mathbf{r})$, which is based on an iso-orbital indicator derived from considering the kinetic energy density in the iso-electron and many electron case, and takes into account that the orbitals are complex, naturally scales the SIC correction from $0\leq z(\mathbf{r}) \leq 1$ in regions of high and low (isolated orbital) electron density. The locally scaled and fully variational SIC framework is general and applicable to atomic, molecular and solid-state systems.

physics.chem-ph↗

arXiv2025

Silver electrodes are highly selective for CO in CO$_2$ electroreduction due to interplay between voltage dependent kinetics and thermodynamics

Electrochemical reduction is a promising way to make use of CO$_2$ as feedstock for generating renewable fuel and valuable chemicals. Several metals can be used in the electrocatalyst to generate CO and formic acid but hydrogen formation is an unwanted side reaction that can even be dominant. The lack of selectivity is in general a significant problem, but silver-based electrocatalysts have been shown to be highly selective for CO with over over 90% faradaic efficiency when the applied voltage is below -1 V vs. RHE. Hydrogen formation is then insignificant and little formate is formed even though it is thermodynamically favored. We present calculations of the activation free energy for the various elementary steps as a function of applied voltage at the three low index facets, Ag(111), Ag(100) and Ag(110), as well as experimental measurements on polycrystalline electrodes, to identify the reason for this high selectivity. The formation of formic acid is suppressed because of the low coverage of adsorbed hydrogen and kinetic hindrance to the formation of the HCOO* intermediate, while *COOH, a key intermediate in CO formation, is thermodynamically unstable until the applied voltage reaches -1 V vs. RHE, at which point the kinetics for its formation are more favorable than for hydrogen. The calculated results are consistent with experimental measurements carried out for acidic conditions and provide an atomic scale insight into the high CO selectivity of silver-based electrocatalysts.

cond-mat.mtrl-sci↗

arXiv2025

Adaptive Pruning for Increased Robustness and Reduced Computational Overhead in Gaussian Process Accelerated Saddle Point Searches

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

physics.chem-ph↗

arXiv2025

Natural-Orbital-Based Neural Network Configuration Interaction

Selective configuration interaction methods approximate correlated molecular ground- and excited states by considering only the most relevant Slater determinants in the expansion. While a recently proposed neural-network-assisted approach efficiently identifies such determinants, the procedure typically relies on canonical Hartree-Fock orbitals, which are optimized only at the mean-field level. Here we assess approximate natural orbitals - eigenfunctions of the one-particle density matrix computed from intermediate many-body eigenstates - as an alternative. Across our benchmarks for H$_2$O, NH$_3$, CO, and C$_3$H$_8$ we see a consistent reduction in the required determinants for a given accuracy of the computed correlation energy compared to full configuration interaction calculations. Our results confirm that even approximate natural orbitals constitute a simple yet powerful strategy to enhance the efficiency of neural-network-assisted configuration interaction calculations.

physics.chem-ph↗

arXiv2025

Variational Calculations of the Excited States of the Charged NV-center in Diamond Using a Hybrid Functional

The excited electronic states involved in the optical cycle preparation of a pure spin state of the negatively charged NV-defect in diamond are calculated using the HSE06 hybrid density functional and variational optimization of the orbitals. This includes the energy of the excited triplet as well as the two lowest singlet states with respect to the ground triplet state. In addition to the vertical excitation, the effect of structural relaxation is also estimated using analytical atomic forces. The lowering of the energy in the triplet excited state and the resulting zero-phonon line triplet excitation energy are both within 0.1 eV of the experimental estimates. An analogous relaxation in the lower energy singlet state using spin purified atomic forces is estimated to be 0.06 eV. These results, obtained with a hybrid density functional, improve on previously published results using local and semi-local functionals, which are known to underestimate the band gap. The good agreement with experimental estimates demonstrates how time-independent variational calculations of excited states using density functionals can give accurate results and, thereby, provide a powerful screening tool for identifying other defect systems as candidates for quantum technologies.

cond-mat.mtrl-sci↗

arXiv2025

Fine Tuning of the Rotational Rate of Light-Driven, Second Generation Molecular Motors by Fluorine Substitutions

The relaxation time of several second generation molecular motors is analysed by calculating the minimum energy path between the metastable and stable states and evaluating the transition rate within harmonic transition state theory based on energetics obtained from density functional theory. Comparison with published experimental data shows remarkably good agreement and demonstrates the predictive capability of the theoretical approach. While previous measurements by Feringa and coworkers [Chem.\,Eur.\,J.\,(2017) 23, 6643] have shown that a replacement of the stereogenic hydrogen by a fluorine atom increases the relaxation time because of destabilization of the transition state for the thermal helix inversion, we find that a replacement of CH$_3$ by a CF$_3$ group at the same site shortens the relaxation time because of elevated energy of the metastable state without a significant shift in the transition state energy. Since these two fluorine substitutions have an opposite effect on the relaxation time, the two combined can provide a way to fine tune the rotational speed of a molecular motor.

physics.chem-ph↗

arXiv2025

The Effect of Chlorine Substitution on Rotational Speed and Light Absorption of Second Generation Molecular Motors

The effect of substituting a hydrogen atom by a chlorine atom or a methyl group by a trichloromethyl (CCl3) group at the stereogenic center of light-driven second generation molecular motors is calculated in order to assess the effect on rotational speed and the separation of the absorption peaks of the isomers. While experimental and theoretical studies have previously been carried out for fluorine substitution, this is the first study of chlorine substitution. Five well-characterized base molecules are studied and the trends are compared with the effect of fluorine substitution. The trichloromethyl substitution is found to accelerate the rotation more than a trifluoromethyl (CF3) substitution by reducing the life-time of the metastable state, due to larger steric hindrance in the metastable state than in the transition state for the thermal helix inversion (THI). A larger increase in the separation of the absorption peaks of the two isomers is also obtained. The Cl atom substitution, however, changes the energy landscape significantly, making the M isomer lower in energy than the P isomer, and raising the energy barrier for THI beyond that of the back transition, thus quenching the rotation.

physics.chem-ph↗

arXiv2025

Tuning Molecular Motors with Tert-Butyl and Fluorinated Tert-Butyl Groups

The effect of modifying substituents in the rotor group of five second generation molecular motors is estimated by theoretical calculations. The rotational speed is estimated by calculating the rate limiting step, the thermal helix inversion, as well as the competing backward transition using harmonic transition state theory with energy and atomic forces obtained from density functional theory. First, a methyl group at the stereogenic center is replaced with a tert-butyl (tBu) group and the rotational speed is found to increase due to reduced lifetime of the metastable state. For two of the rotors, comparison can be made with experimental measurements and the calculated half-life is in close agreement. Secondly, the effect of substituting the nine hydrogen atoms in the tBu group with fluorine atoms is studied and this is found to increase the rotational rate further without significantly altering the molecular structure. The excitation wavelength of both the stable and metastable states is calculated and the separation of the absorption peaks is found to increase by the tBu substitution and even more so by the fluorinated tBu substitution, up to 40 nm. These findings can help develop a strategy for designing molecular motors with a rotational speed that best fits a given application.

physics.chem-ph↗

arXiv2025

Time Reversible Integration of the Landau-Lifshitz-Gilbert Equation

A method for time-reversible numerical integration of the deterministic Landau-Lifshitz Gilbert equation by means of a second order Suzuki-Trotter decomposition is presented and tested against commonly used second order predictor-corrector methods. We find the time-reversibility of the Suzuki-Trotter integrator to be superior by several orders of magnitude while the computational effort is similar. Calculations of trajectories backwards in time are useful, for example, when evaluating dynamical corrections to transition state theory.

physics.comp-ph↗

arXiv2025

Multiple Adsorption of CO Molecules on Transition Metal Substitutional Impurities in Copper Surfaces

Copper-based catalysts are of particular interest for electrochemical reduction of CO$_2$ (CO2RR) as products beyond CO can form. To improve activity and selectivity, several studies have focused on the addition of other elements as substitutional impurities. Although the adsorption of a single CO molecule has often been used as a descriptor for CO2RR activity, our recent calculations using the RPBE functional showed that multiple CO molecules can bind to first-row transition metal impurities. Here, we extend the study to second-row transition metals and also to a functional that explicitly includes dispersion interaction, BEEF-vdW. The binding energy of the first CO molecule on the impurity atom is found to be significantly larger than on the clean Cu(111) and Cu(100) surfaces, but the differential binding energy generally drops as more CO molecules adsorb. The dispersion interaction is found to make a significant contribution to the binding energy, in particular for the last and weakest bound CO molecule, the one that is most likely to participate in CO2RR. In some cases, four CO admolecules can bind more strongly on the impurity atom than on the clean copper surface. The adsorption of CO causes the position of the impurity atom to shift outwards and in some cases, even escape from the surface layer. The C-O stretch frequencies are calculated in order to identify possible experimental signatures of multiple CO adsorption.

cond-mat.mtrl-sci↗