Compressing nearly hard sphere fluids increases glass fragility

We use molecular dynamics to investigate the glass transition occurring at large volume fraction, phi, and low temperature, T, in assemblies of soft repulsive particles. We find that equilibrium dynamics in the (phi, T) plane obey a form of dynamic scaling in the proximity of a critical point at T=0 and phi=phi_0, which should correspond to the ideal glass transition of hard spheres. This glass point, `point G', is distinct from athermal jamming thresholds. A remarkable consequence of scaling behaviour is that the dynamics at fixed phi passes smoothly from that of a strong glass to that of a very fragile glass as phi increases beyond phi_0. Correlations between fragility and various physical properties are explored.Comment: 5 pages, 3 figures; Version accepted at Europhys. Let

Loss of control in pattern-directed nucleation: a theoretical study

The properties of template-directed nucleation are studied close to the transition where full nucleation control is lost and additional nucleation occurs beyond the pre-patterned regions. First, kinetic Monte Carlo simulations are performed to obtain information on a microscopic level. Here the experimentally relevant cases of 1D stripe patterns and 2D square lattice symmetry are considered. The nucleation properties in the transition region depend in a complex way on the parameters of the system, i.e. the flux, the surface diffusion constant, the geometric properties of the pattern and the desorption rate. Second, the properties of the stationary concentration field in the fully controlled case are studied to derive the remaining nucleation probability and thus to characterize the loss of nucleation control. Using the analytically accessible solution of a model system with purely radial symmetry, some of the observed properties can be rationalized. A detailed comparison to the Monte Carlo data is included

Tunneling dynamics of side chains and defects in proteins, polymer glasses, and OH-doped network glasses

Simulations on a Lennard-Jones computer glass are performed to study effects arising from defects in glasses at low temperatures. The numerical analysis reveals that already a low concentration of defects may dramatically change the low temperature properties by giving rise to extrinsic double-well potentials (DWP's). The main characteristics of these extrinsic DWP's are (i) high barrier heights, (ii) high probability that a defect is indeed connected with an extrinsic DWP, (iii) highly localized dynamics around this defect, and (iv) smaller deformation potential coupling to phonons. Designing an extension of the Standard Tunneling Model (STM) which parametrizes this picture and comparing with ultrasound experiments on the wet network glass $a$-B$_2$O$_3$ shows that effects of OH-impurities are accurately accounted for. This model is then applied to organic polymer glasses and proteins. It is suggested that side groups may act similarly like doped impurities inasmuch as extrinsic DWP's are induced, which possess a distribution of barriers peaked around a high barrier height. This compares with the structurlessly distributed barrier heights of the intrinsic DWP's, which are associated with the backbone dynamics. It is shown that this picture is consistent with elastic measurements on polymers, and can explain anomalous nonlogarithmic line broadening recently observed in hole burning experiments in PMMA.Comment: 34 pages, Revtex, 9 eps-figures, accepted for publication in J. Chem. Phy

The bumpy road of purinergic inhibitors to clinical application in immune-mediated diseases

Purinergic signaling plays important roles throughout the body in the regulation of organ functions during and following the disruption of homeostasis. This is also reflected by the widespread expression of two families of purinergic receptors (P1 and P2) with numerous subtypes. In the last few decades, there has been increasing evidence that purinergic signaling plays an important role in the regulation of immune functions. Mainly, signals mediated by P2 receptors have been shown to contribute to immune system-mediated pathologies. Thus, interference with P2 receptors may be a promising strategy for the modulation of immune responses. Although only a few clinical studies have been conducted in isolated entities with limited success, preclinical work suggests that the use of P2 receptor inhibitors may bear some promise in various autoimmune diseases. Despite the association of P2 receptors with several disorders from this field, the use of P2 receptor antagonists in clinical therapy is still very scarce. In this narrative review, we briefly review the involvement of the purinergic system in immunological responses and clinical studies on the effect of purinergic inhibition on autoimmune processes. We then open the aperture a bit and show some preclinical studies demonstrating a potential effect of purinergic blockade on autoimmune events. Using suramin, a non-specific purinergic inhibitor, as an example, we further show that off-target effects could be responsible for observed effects in immunological settings, which may have interesting implications. Overall, we believe that it is worthwhile to further investigate this hitherto underexplored area

The PACE 2022 Parameterized Algorithms and Computational Experiments Challenge: Directed Feedback Vertex Set

The Parameterized Algorithms and Computational Experiments challenge (PACE) 2022 was devoted to engineer algorithms solving the NP-hard Directed Feedback Vertex Set (DFVS) problem. The DFVS problem is to find a minimum subset $X ⊆ V$ in a given directed graph $G = (V,E)$ such that, when all vertices of $X$ and their adjacent edges are deleted from $G$, the remainder is acyclic. Overall, the challenge had 90 participants from 26 teams, 12 countries, and 3 continents that submitted their implementations to this year’s competition. In this report, we briefly describe the setup of the challenge, the selection of benchmark instances, as well as the ranking of the participating teams. We also briefly outline the approaches used in the submitted solvers

Dynamic effects on the loss of control in template-directed nucleation

Full nucleation control for deposited functional molecules on pre-patterned surfaces is of major technological relevance. To understand the nucleation behavior we combine the numerical solution for the evolution of the adatom concentration with standard nucleation theory. From the qualitative change in nucleation behavior upon variation of the pattern spacing and coverage we show why the quality of nucleation control can vary significantly in different parameter regimes. In some limits analytical expressions can be formulated for the nucleation control. Our analysis provides a theoretical explanation for previous experimental observations [Wang et al, PRL 98, 225504 (2007)]

Backward correlations and dynamic heterogeneities: a computer study of ion dynamics

We analyse the correlated back and forth dynamics and dynamic heterogeneities, i.e. the presence of fast and slow ions, for a lithium metasilicate system via computer simulations. For this purpose we define, in analogy to previous work in the field of glass transition, appropriate three-time correlation functions. They contain information about the dynamics during two successive time intervals. First we apply them to simple model systems in order to clarify their information content. Afterwards we use this formalism to analyse the lithium trajectories. A strong back-dragging effect is observed, which also fulfills the time-temperature superposition principle. Furthermore, it turns out that the back-dragging effect is long-ranged and exceeds the nearest neighbor position. In contrast, the strength of the dynamic heterogeneities does not fulfill the time-temperature superposition principle. The lower the temperature, the stronger the mobility difference between fast and slow ions. The results are then compared with the simple model systems considered here as well as with some lattice models of ion dynamics.Comment: 12 pages, 10 figure

Thermodynamic Fingerprints of Disorder in Flux Line Lattices and other Glassy Mesoscopic Systems

We examine probability distributions for thermodynamic quantities in finite-sized random systems close to criticality. Guided by available exact results, a general ansatz is proposed for replicated free energies, which leads to scaling forms for cumulants of various macroscopic observables. For the specific example of a planar flux line lattice in a two dimensional superconducting film near H_c1, we provide detailed results for the statistics of the magnetic flux density, susceptibility, heat capacity, and their cross-correlations.Comment: 4 page

On the Growth of Al_2 O_3 Scales

Understanding the growth of Al2O3 scales requires knowledge of the details of the chemical reactions at the scale–gas and scale–metal interfaces, which in turn requires specifying how the creation/annihilation of O and Al vacancies occurs at these interfaces. The availability of the necessary electrons and holes to allow for such creation/annihilation is a crucial aspect of the scaling reaction. The electronic band structure of polycrystalline Al2O3 thus plays a decisive role in scale formation and is considered in detail, including the implications of a density functional theory (DFT) calculation of the band structure of a Σ7 View the MathML source bicrystal boundary, for which the atomic structure of the boundary was known from an independent DFT energy-minimization calculation and comparisons with an atomic-resolution transmission electron micrograph of the same boundary. DFT calculations of the formation energy of O and Al vacancies in bulk Al2O3 in various charge states as a function of the Fermi energy suggested that electronic conduction in Al2O3 scales most likely involves excitation of both electrons and holes, which are localized on singly charged O vacancies, View the MathML source and doubly charged Al vacancies, View the MathML source, respectively. We also consider the variation of the Fermi level across the scale and bending (“tilting”) of the conduction band minimum and valence band maximum due to the electric field developed during the scaling reaction. The band structure calculations suggest a new mechanism for the “reactive element” effect—a consequence of segregation of Y, Hf, etc., to grain boundaries in Al2O3 scales, which results in improved oxidation resistance—namely, that the effect is due to the modification of the near-band edge grain-boundary defect states rather than any blocking of diffusion pathways, as previously postulated. Secondly, Al2O3 scale formation is dominated by grain boundary as opposed to lattice diffusion, and there is unambiguous evidence for both O and Al countercurrent transport in Al2O3 scale-forming alloys. We postulate that such transport is mediated by migration of grain boundary disconnections containing charged jogs, rather than by jumping of isolated point defects in random high-angle grain boundaries

Memetic Multilevel Hypergraph Partitioning

Hypergraph partitioning has a wide range of important applications such as VLSI design or scientific computing. With focus on solution quality, we develop the first multilevel memetic algorithm to tackle the problem. Key components of our contribution are new effective multilevel recombination and mutation operations that provide a large amount of diversity. We perform a wide range of experiments on a benchmark set containing instances from application areas such VLSI, SAT solving, social networks, and scientific computing. Compared to the state-of-the-art hypergraph partitioning tools hMetis, PaToH, and KaHyPar, our new algorithm computes the best result on almost all instances