Uncertainty quantification of dynamic earthquake rupture simulations.

We present a tutorial demonstration using a surrogate-model based uncertainty quantification (UQ) approach to study dynamic earthquake rupture on a rough fault surface. The UQ approach performs model calibration where we choose simulation points, fit and validate an approximate surrogate model or emulator, and then examine the input space to see which inputs can be ruled out from the data. Our approach relies on the mogp_emulator package to perform model calibration, and the FabSim3 component from the VECMA toolkit to streamline the workflow, enabling users to manage the workflow using the command line to curate reproducible simulations on local and remote resources.

Effective temperature dynamics of shear bands in metallic glasses.

We study the plastic deformation of bulk metallic glasses with shear transformation zone (STZ) theory, a physical model for plasticity in amorphous systems, and compare it with experimental data. In STZ theory, plastic deformation occurs when localized regions rearrange due to applied stress and the density of these regions is determined by a dynamically evolving effective disorder temperature. We compare the predictions of STZ theory to experiments that explore the low-temperature deformation of Zr-based bulk metallic glasses via shear bands at various thermal temperatures and strain rates.

Stick-slip instabilities and shear strain localization in amorphous materials.

We study the impact of strain localization on the stability of frictional slipping in dense amorphous materials. We model the material using shear transformation zone (STZ) theory, a continuum approximation for plastic deformation in amorphous solids. In the STZ model, the internal state is quantified by an effective disorder temperature, and the effective temperature dynamics capture the spontaneous localization of strain.

Quantifying optimal accuracy of local primary sequence bioinformatics methods.

Motivation: Traditional bioinformatics methods scan primary sequences for local patterns. It is important to assess how accurate local primary sequence methods can be.

Results: We study the problem of donor pre-mRNA splice site recognition, where the sequence overlaps between real and decoy datasets can be quantified, exposing the intrinsic limitations of the performance of local primary sequence methods.