Condensed Matter

This article is based on lecture notes for the Marie Curie Training school "Initial Training on Numerical Methods for Active Matter". It provides an introductory overview of modeling approaches for active matter and is primarily targeted at PhD students (or other readers) who encounter some of these approaches for the first time. The aim of the article is to help put the described modeling approaches into perspective.

This paper studies numerically the Weeks-Chandler-Andersen (WCA) system, which is shown to obey hidden scale invariance with a density-scaling exponent that varies from below 5 to above 500. This unprecedented variation makes it advantageous to use the fourth-order Runge-Kutta algorithm for tracing out isomorphs. Good isomorph invariance of structure and dynamics is observed over more than three orders of magnitude temperature variation. For all state points studied, the virial potential-energy correlation coefficient and the density-scaling exponent are controlled mainly by the temperature. Based on the assumption of statistically independent pair interactions, a mean-field theory is developed that rationalizes this finding and provides an excellent fit to data at low temperatures and densities.

Organic semiconductors are indispensable for today's display technologies in form of organic light emitting diodes (OLEDs) and further optoelectronic applications. However, organic materials do not reach the same charge carrier mobility as inorganic semiconductors, limiting the efficiency of devices. To find or even design new organic semiconductors with higher charge carrier mobility, computational approaches, in particular multiscale models, are becoming increasingly important. However, such models are computationally very costly, especially when large systems and long time scales are required, which is the case to compute static and dynamic energy disorder, i.e. dominant factor to determine charge transport. Here we overcome this drawback by integrating machine learning models into multiscale simulations. This allows us to obtain unprecedented insight into relevant microscopic materials properties, in particular static and dynamic disorder contributions for a series of application-relevant molecules. We find that static disorder and thus the distribution of shallow traps is highly asymmetrical for many materials, impacting widely considered Gaussian disorder models. We furthermore analyse characteristic energy level fluctuation times and compare them to typical hopping rates to evaluate the importance of dynamic disorder for charge transport. We hope that our findings will significantly improve the accuracy of computational methods used to predict application relevant materials properties of organic semiconductors, and thus make these methods applicable for virtual materials design.

Understanding the dynamics of charge exchange between a solid surface and a liquid is fundamental to various situations, ranging from nanofiltration to catalysis and electrochemistry. Charge transfer is ultimately determined by physicochemical processes (surface group dissociation, ion adsorption, etc...) occurring in the few layers of molecules at the interface between the solid and the liquid. Unfortunately, these processes remain largely uncharted due to the experimental challenges in probing interfacial charge dynamics with sufficiently high spatial and temporal resolution. Here, we resolve at the single-charge scale, the dynamics of proton charges at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (e.g. alcohol), evidencing a dramatic influence of solvation on interfacial dynamics. Our observations rely on the application of spectral Single Molecule Localization Microscopy (sSMLM) to two types of optically active defects at the hBN surface, which act as intrinsic optical markers for both surface protonation and interaction with apolar alkyl groups of the organic solvent. We use sSMLM to reveal interfacial proton charge transport as a succession of jumps between the titratable surface defects, mediated by the transport of the solvated proton charge along the solid/liquid interface. By changing the relative concentration of water in binary mixtures, we evidence a non-trivial effect on interfacial proton charge dynamics, leading at intermediate water concentration to an increased affinity of the proton charge to the solid surface, accompanied by an increased surface diffusivity. These measurements confirm the strong role of solvation on interfacial proton charge transport and establish the potential of single-molecule localization techniques to probe a wide range of dynamic processes at solid/liquid interfaces.

Anions generally associate more favorably with the air-water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this bias. Here we assess quantitatively the role that intrinsic charge asymmetry of water's surface plays in ion adsorption, using computer simulations to compare model solutes of various size and charge. In doing so, we also evaluate the degree to which linear response theory for solvent polarization is a reasonable approach for comparing the thermodynamics of bulk and interfacial ion solvation. Consistent with previous works on bulk ion solvation, we find that the average electrostatic potential at the center of a neutral, sub-nanometer solute at the air-water interface depends sensitively on its radius, and that this potential changes quite nonlinearly as the solute's charge is introduced. The nonlinear response closely resembles that of the bulk. As a result, the net nonlinearity of ion adsorption is weaker than in bulk, but still substantial, comparable to the apparent magnitude of macroscopically nonlocal contributions from the undisturbed interface. For the simple-point-charge model of water we study, these results argue distinctly against rationalizing ion adsorption in terms of surface potentials inherent to molecular structure of the liquid's boundary.

Self-assembly of Janus (or `patchy') particles is dependent on the precise interaction between neighbouring particles. Here, the orientations of two amphiphilic Janus spheres within a dimer in an explicit fluid are studied with high geometric resolution. Molecular dynamics simulations and first-principles energy calculations are used with hard- and soft-sphere Lennard-Jones potentials, and temperature and hydrophobicity are varied. The most probable centre-centre-pole angles are in the range 40° to 55°, with pole-to-pole alignment not observed due to orientational entropy. Angles near 90° are energetically unfavoured due to solvent exclusion, and we unexpectedly found that the relative azimuthal angle between the spheres is affected by solvent ordering.

The modelling of off-axis simple tension experiments on transversely isotropic nonlinearly elastic materials is considered. A testing protocol is proposed where normal force is applied to one edge of a rectangular specimen with the opposite edge allowed to move laterally but constrained so that no vertical displacement is allowed. Numerical simulations suggest that this deformation is likely to remain substantially homogeneous throughout the specimen for moderate deformations. It is therefore further proposed that such tests can be modelled adequately as a homogenous deformation consisting of a triaxial stretch accompanied by a simple shear. Thus the proposed test should be a viable alternative to the standard biaxial tests currently used as material characterisation tests for transversely isotropic materials in general and, in particular, for soft, biological tissue. A consequence of the analysis is a kinematical universal relation for off-axis testing that results when the strain-energy function is assumed to be a function of only one isotropic and one anisotropic invariant, as is typically the case. The universal relation provides a simple test of this assumption, which is usually made for mathematical convenience. Numerical simulations also suggest that this universal relation is unlikely to agree with experimental data and therefore that at least three invariants are necessary to fully capture the mechanical response of transversely isotropic materials.

In this article, the mechanism of the unexpected high fluidity in SiOx nanowire under modest irradiation was proposed, the high fluidity is attributed to the long lifetime of irradiation-induced holes, which arise from formation of small polarons. The holes created in irradiation could have a long lifetime, and localized in space, such missing of bonding electron could suppress the energy barrier(athermal activation effect) for a Pachner move of the network. The atomic level dynamics of the system is proposed by interaction of phonon and local configuration, the activation effect was then studied with passing rate of corresponding stochastic dynamic equation, calculation shows an exponential dependent of the time-lapse of Pachner move to lifetime of the activation, furthermore, connection between the local configuration time and viscosity of the fluid indicates a strong sensitivity of viscosity to lifetime of the athermal activation, such mechanism would give an effective interpretation to the unexpected high fluidity together with the passivation effect of the conductor on the material.

We study athermal jamming as well as the thermal glassy dynamics in systems composed of spheres that interact according to repulsive interactions that exponentially decay as a function of distance. As usual, a cutoff is employed in the simulations. While the athermal jamming transition that is determined by trying to remove overlaps is found to depend on the arbitrary and therefore unphysical choice of the cutoff, we do not find any athermal jamming transition or crossover that only relies on the physical decay length. In contrast, the glassy dynamics mainly depends on the decay length. Our findings constitute another demonstration of the fact that the athermal jamming transition is not related to thermal glassy dynamics. In addition, we argue that interactions without sharp physical cutoff should be considered more often as a model system in jamming. By exploring how widely-used theoretical approaches or methods of analysis in the field of jamming have to be changed in order to not depend on unphysical cutoffs will lead to deeper insights into the nature of athermal and thermal jamming.

Understanding the degradation mechanisms of aliphatic polymers by thermal oxidation and radio-oxidation is very important in order to assess their lifetime in a variety of industrial applications. We focus here on polyethylene as a prototypical aliphatic polymer. Kinetic models describing the time evolution of the concentration of chain defects and radicals species in the material identify a relevant step in the formation and subsequent decomposition of transient hydroperoxides species, finally leading to carbonyl defects, in particular ketones. In this paper we first summarize the most relevant mechanistic paths proposed in the literature for hydroperoxide formation and decomposition and, second, revisit them using first principles calculations based on Density Functional Theory (DFT). We investigate the reaction paths for several chemical reactions, for both isolated alkane molecules and a crystalline model of polyethylene, and confirm, in some cases, the accepted activation energies; in some other cases, we challenge the accepted view finding alternative, more favourable, reaction paths for which we estimate the activation energy. We highlight the infuence of the environment -- crystalline or not -- on the outcome of some of the studied chemical reactions. A remarkable results of our calculations is that hydroxyl radicals play an important role in the decomposition of hydroperoxides. Based on our findings, it should be possible to improve the set of equations and parameters used in current kinetic simulations of polyethylene radio-oxidation.