arXiv subjects

Domagoj Fijan

Publications and source records attributed to Domagoj Fijan.

6 recordsLinked to original sources

arXiv2026

Anatomy of a Complex Crystallization Pathway

Using molecular dynamics simulations, we investigate the crystallization pathways of two exemplary systems that form the same complex crystal structure but differ fundamentally in the nature of their particle interactions. One system is composed of point particles interacting via an isotropic pair potential characteristic of metallic compounds, while the other system contains hard polyhedra whose interactions arise from emergent entropic forces. Despite the stark difference in the origins of the particle interactions, we find that both systems are polymorphic and share the same crystal polymorphs. Moreover, the two systems follow the same multistep crystallization pathways, and by examining the complex crystallization pathways on the single particle level, we find that the local structure evolution of the two systems is also similar. By mapping the hard particle system's interaction to an effective pairwise potential, we find that such resemblance arises from the particle interactions being effectively similar.

cond-mat.soft↗

arXiv2026

Quantifying Local Point-Group-Symmetry Order in Complex Particle Systems

Crystals and other condensed phases are defined primarily by their inherent symmetries, which play a crucial role in dictating their structural properties. In crystallization studies, local order parameters (OPs) that describe bond orientational order are widely employed to investigate crystal formation. Despite their utility, these traditional metrics do not directly quantify symmetry, an important aspect for understanding the development of order during crystallization. To address this gap, we introduce a new set of OPs, called Point Group Order Parameters (PGOPs), designed to continuously quantify point group symmetry order. We demonstrate the strength and utility of PGOP in detecting order across different crystalline systems and compare its performance to commonly used bond-orientational order metrics. PGOP calculations for all non-infinite point groups are implemented in the open-source package SPATULA (Symmetry Pattern Analysis Toolkit for Understanding Local Arrangements), written in parallelized C++ with a Python interface. The code is publicly available on GitHub at https://github.com/glotzerlab/spatula.

physics.comp-ph↗

arXiv2026

Entropic Colloidal Crystal Prediction: A Quantum Density Functional Theory Inspired Approach

In pursuit of a colloidal analogue to quantum density functional theory (DFT) predictions of atomic crystal structures, we report a new, classical DFT that predicts the relative thermodynamic stability of colloidal crystals of hard, convex particle shapes. In contrast to standard classical DFT approaches, our theory maps the hard particle system to an auxiliary system in which we treat the particles as fixed "nuclei" embedded in a fictitious, spatially varying density field that distributes throughout the auxiliary system. By minimizing the free energy of the auxiliary system, and through comparison with known equations of state and free energy calculations using thermodynamic integration, we show that the auxiliary system with the lowest free energy corresponds to the most probable crystal of hard shapes in the original system.

cond-mat.soft↗

arXiv2024

Change Point Detection of Events in Molecular Simulations using dupin

Particle tracking is commonly used to study time-dependent behavior in many different types of physical and chemical systems involving constituents that span many length scales, including atoms, molecules, nanoparticles, granular particles, etc. Behaviors of interest studied using particle tracking information include disorder-order transitions, thermodynamic phase transitions, structural transitions, protein folding, crystallization, gelation, swarming, avalanches and fracture. A common challenge in studies of these systems involves change detection. Change point detection discerns when a temporal signal undergoes a change in distribution. These changes can be local or global, instantaneous or prolonged, obvious or subtle. Moreover, system-wide changes marking an interesting physical or chemical phenomenon (e.g. crystallization) are often preceded by events (e.g. pre-nucleation clusters) that are localized and can occur anywhere at anytime in the system. For these reasons, detecting events in particle trajectories generated by molecular simulation is challenging and typically accomplished via ad hoc solutions unique to the behavior and system under study. Consequently, methods for event detection lack generality, and those used in one field are not easily used by scientists in other fields. Here we present a new Python-based tool, dupin, that allows for event detection from particle trajectory data irrespective of the system details. dupin works by creating a signal representing the simulation and partitioning the signal based on events (changes within the trajectory). This approach allows for studies where manual annotating of event boundaries would require a prohibitive amount of time. Furthermore, dupin can serve as a tool in automated and reproducible workflows. We demonstrate the application of dupin using two examples and discuss its applicability to a wider class of problems.

physics.comp-ph↗

arXiv2016

Numerical Evidence for Thermally Induced Monopoles

Electrical charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of non-equilibrium thermodynamics, combined with Maxwell's equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electrical/magnetic charge [J. Phys. Chem. B $\textbf{120}$, 5987 (2016)]. Here we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electrical or magnetic monopoles. However, in other respects, the non-equilibrium colloids do not behave as monopoles: they cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloids is crucial because the experimental and numerical determination of forces between such colloids would be complicated by the presence of other effects, such as thermophoresis.

physics.comp-ph↗

arXiv2016

Non-equilibrium simulations of thermally induced electric fields in water

Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between $2 \times 10^7$ and $5 \times 10^7~\text{V/m}$ for a temperature gradient of $5.2~\text{K/}\unicode{x212B}$. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. Chem. Phys. 139, 014504 (2013) and 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.

physics.comp-ph↗