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

Strain Partitioning and Frictional Behavior of Opalinus Clay During Fault Reactivation

The Opalinus Clay (OPA) formation is considered a suitable host rock candidate for nuclear waste storage. However, the sealing integrity and long-term safety of OPA are potentially compromised by pre-existing natural or artificially induced faults. Therefore, characterizing the mechanical behavior and microscale deformation mechanisms of faults and the surrounding rock is relevant for predicting repository damage evolution. In this study, we performed triaxial tests using saw-cut samples of the shaly and sandy facies of OPA to investigate the influence of pressure and mineral composition on the deformation behavior during fault reactivation. Dried samples were hydrostatically pre-compacted at 50 MPa and then deformed at constant strain rate, drained conditions and confining pressures (pc) of 5–35 MPa. Mechanical data from triaxial tests was complemented by local strain measurements to determine the relative contribution of bulk deformation and fault slip, as well as by acoustic emission (AE) monitoring, and elastic P-wave velocity measurements using ultrasonic transmissions. With increasing pc, we observe a transition from brittle deformation behavior with highly localized fault slip to semi-brittle behavior characterized by non-linear strain hardening with increasing delocalization of deformation. We find that brittle localization behavior is limited by pc at which fault strength exceeds matrix yield strength. AEs were only detected in tests performed on sandy facies samples, and activity decreased with increasing pc. Microstructural analysis of deformed samples revealed a positive correlation between increasing pc and gouge layer thickness. This goes along with a change from brittle fragmentation and frictional sliding to the development of shear zones with a higher contribution of cataclastic and granular flow. Friction coefficient at fault reactivation is only slightly higher for the sandy (µ ~ 0.48) compared to the shaly facies (µ ~ 0.4). Slide-hold-slide tests performed after ~ 6 mm axial shortening suggest stable creeping and long-term weakness of faults at the applied conditions. Our results demonstrate that the mode of fault reactivation highly depends on the present stress field and burial history

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

The Impact of Composition and Morphology on Ionic Conductivity of Silk/Cellulose Bio-Composites Fabricated from Ionic Liquid and Varying Percentages of Coagulation Agents.

Blended biocomposites created from the electrostatic and hydrophobic interactions between polysaccharides and structural proteins exhibit useful and unique properties. However, engineering these biopolymers into applicable forms is challenging due to the coupling of the material’s physicochemical properties to its morphology, and the undertaking that comes with controlling this. In this particular study, numerous properties of the Bombyx mori silk and microcrystalline cellulose biocomposites blended using ionic liquid and regenerated with various coagulation agents were investigated. Specifically, the relationship between the composition of polysaccharide-protein bio-electrolyte membranes and the resulting morphology and ionic conductivity is explored using numerous characterization techniques, including scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray scattering, atomic force microscopy (AFM) based nanoindentation, and dielectric relaxation spectroscopy (DRS). The results revealed that when silk is the dominating component in the biocomposite, the ionic conductivity is higher, which also correlates with higher β-sheet content. However, when cellulose becomes the dominating component in the biocomposite, this relationship is not observed; instead, cellulose semicrystallinity and mechanical properties dominate the ionic conduction

Studies of new Higgs boson interactions through nonresonant HH production in the b¯bγγ fnal state in pp collisions at √s = 13 TeV with the ATLAS detector

A search for nonresonant Higgs boson pair production in the b ¯bγγ fnal state is performed using 140 fb−1 of proton-proton collisions at a centre-of-mass energy of 13 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. This analysis supersedes and expands upon the previous nonresonant ATLAS results in this fnal state based on the same data sample. The analysis strategy is optimised to probe anomalous values not only of the Higgs (H) boson self-coupling modifer κλ but also of the quartic HHV V (V = W, Z) coupling modifer κ2V . No signifcant excess above the expected background from Standard Model processes is observed. An observed upper limit µHH &lt; 4.0 is set at 95% confdence level on the Higgs boson pair production cross-section normalised to its Standard Model prediction. The 95% confdence intervals for the coupling modifers are −1.4 &lt; κλ &lt; 6.9 and −0.5 &lt; κ2V &lt; 2.7, assuming all other Higgs boson couplings except the one under study are fxed to the Standard Model predictions. The results are interpreted in the Standard Model efective feld theory and Higgs efective feld theory frameworks in terms of constraints on the couplings of anomalous Higgs boson (self-)interactions

Measurement of exclusive pion pair production in proton–proton collisions at √s=7 TeV with the ATLAS detector

The exclusive production of pion pairs in the process pp→ ppπ+π- has been measured at s=7TeV with the ATLAS detector at the LHC, using 80μb-1 of low-luminosity data. The pion pairs were detected in the ATLAS central detector while outgoing protons were measured in the forward ATLAS ALFA detector system. This represents the first use of proton tagging to measure an exclusive hadronic final state at the LHC. A cross-section measurement is performed in two kinematic regions defined by the proton momenta, the pion rapidities and transverse momenta, and the pion–pion invariant mass. Cross-section values of 4.8±1.0(stat)-0.2+0.3(syst)μb and 9±6(stat)-2+2(syst)μb are obtained in the two regions; they are compared with theoretical models and provide a demonstration of the feasibility of measurements of this type