Rule-based multi-level modeling of cell biological systems

<p>Abstract</p> <p>Background</p> <p>Proteins, individual cells, and cell populations denote different levels of an organizational hierarchy, each of which with its own dynamics. Multi-level modeling is concerned with describing a system at these different levels and relating their dynamics. Rule-based modeling has increasingly attracted attention due to enabling a concise and compact description of biochemical systems. In addition, it allows different methods for model analysis, since more than one semantics can be defined for the same syntax.</p> <p>Results</p> <p>Multi-level modeling implies the hierarchical nesting of model entities and explicit support for downward and upward causation between different levels. Concepts to support multi-level modeling in a rule-based language are identified. To those belong rule schemata, hierarchical nesting of species, assigning attributes and solutions to species at each level and preserving content of nested species while applying rules. Further necessities are the ability to apply rules and flexibly define reaction rate kinetics and constraints on nested species as well as species that are nested within others. An example model is presented that analyses the interplay of an intracellular control circuit with states at cell level, its relation to cell division, and connections to intercellular communication within a population of cells. The example is described in ML-Rules - a rule-based multi-level approach that has been realized within the plug-in-based modeling and simulation framework JAMES II.</p> <p>Conclusions</p> <p>Rule-based languages are a suitable starting point for developing a concise and compact language for multi-level modeling of cell biological systems. The combination of nesting species, assigning attributes, and constraining reactions according to these attributes is crucial in achieving the desired expressiveness. Rule schemata allow a concise and compact description of complex models. As a result, the presented approach facilitates developing and maintaining multi-level models that, for instance, interrelate intracellular and intercellular dynamics.</p

High‐Temperature Deformation Behavior of Synthetic Polycrystalline Magnetite

Post-print (lokagerð höfundar)We performed a series of deformation experiments on synthetic magnetite aggregates to characterize the high‐temperature rheological behavior of this mineral under nominally dry and hydrous conditions. Grain growth laws for magnetite were additionally determined from a series of static annealing tests. Synthetic magnetite aggregates were formed by hot isostatic pressing of fine‐grained magnetite powder at 1,100 °C temperature and 300‐MPa confining pressure for 20 hr, resulting in polycrystalline material with a mean grain size around 40 μm and containing 2–4% porosity. Samples were subsequently deformed to axial strains of up to 10% under constant load conditions at temperatures between 900 and 1,150 °C in a triaxial deformation apparatus under 300‐MPa confining pressure at applied stresses in the range of 8–385 MPa or in a uniaxial creep rig at atmospheric pressure with stresses of 1–15 MPa. The aggregates exhibit typical power‐law creep behavior with a mean stress exponent of 3 at high stresses, indicating a dislocation creep mechanism and a transition to near‐Newtonian creep with a mean stress exponent of 1.1 at lower stresses. The presence of water in the magnetite samples resulted in significantly enhanced static grain growth and strain rates. Best‐fit flow laws to the data indicate activation energies of around 460 and 310 kJ/mol for dislocation and diffusion creep of nominally dry magnetite, respectively. Based on the experimentally determined flow laws, magnetite is predicted to be weaker than most major silicate phases in relatively dry rocks such as oceanic gabbros during high‐temperature crustal deformation.Alexander von Humboldt-Stiftun

Influence of time, temperature, confining pressure and fluid content on the experimental compaction of spherical grains

Theoretical models of compaction processes, such as for example intergranular pressure-solution (IPS), focus on deformation occurring at the contacts between spherical grains that constitute an aggregate. In order to investigate the applicability of such models, and to quantify the deformation of particles within an aggregate, isostatic experiments were performed in cold-sealed vessels on glass sphere aggregates at 200 MPa confining pressure and 350 degrees C with varying amounts of fluid

Searches for lepton-flavour-violating decays of the Higgs boson into eτ and μτ in \sqrt{s} = 13 TeV pp collisions with the ATLAS detector

Abstract This paper presents direct searches for lepton flavour violation in Higgs boson decays, H → eτ and H → μτ, performed using data collected with the ATLAS detector at the LHC. The searches are based on a data sample of proton-proton collisions at a centre-of-mass energy s $$\sqrt{s}$$ = 13 TeV, corresponding to an integrated luminosity of 138 fb−1. Leptonic (τ → ℓνℓντ) and hadronic (τ → hadrons ντ) decays of the τ-lepton are considered. Two background estimation techniques are employed: the MC-template method, based on data-corrected simulation samples, and the Symmetry method, based on exploiting the symmetry between electrons and muons in the Standard Model backgrounds. No significant excess of events is observed and the results are interpreted as upper limits on lepton-flavour-violating branching ratios of the Higgs boson. The observed (expected) upper limits set on the branching ratios at 95% confidence level, B $$\mathcal{B}$$ (H → eτ) < 0.20% (0.12%) and B $$\mathcal{B}$$ (H → μτ ) < 0.18% (0.09%), are obtained with the MC-template method from a simultaneous measurement of potential H → eτ and H → μτ signals. The best-fit branching ratio difference, B $$\mathcal{B}$$ (H → μτ) → B $$\mathcal{B}$$ (H → eτ), measured with the Symmetry method in the channel where the τ-lepton decays to leptons, is (0.25 ± 0.10)%, compatible with a value of zero within 2.5σ