# Simone MarrasNew Jersey Institute of Technology | NJIT · Department of Mechanical & Industrial Engineering

17.61

· M.Sc. Aerospace Engineering. Ph.D. Environmental Engineering and Scientific ComputingAbout

Introduction

**Current Institution**

Newark, New Jersey

**Current position**

Assistant professor (tenure track)

**Skills and Expertise**

34

Research items

4,225

Reads

113

Citations

Research Experience

**Jun 2014 - Oct 2016**

**Research Scientist**

Stanford University · Department of Geophysics

Stanford, United States

**Jul 2013 - Jun 2015**

**NRC Research Associate**

Naval Postgraduate School · Department of Applied Mathematics

Monterey, United States

**Mar 2008 - Aug 2012**

**Graduate student/junior researcher**

Barcelona Supercomputing Center · Department of Computer Applications in Science and Engineering

Barcelona, Spain

Education

**Jan 2008 - Dec 2012**

**Universitat Politècnica de Catalunya**

Applied Mathematics

**Sep 1998 - Apr 2004**

**Politecnico di Milano**

Aerospace Engineering

Current research

Projects (3)

Solve complex coupled multi-physics problems on supercomputers.

The debate about natural barriers to coastal hazards is at the sweet spot between being a fascinating scientific question and a significant real-world problem. The goal of this project is to advance our understanding of the role that nature-based features can and should play in coastal-risk reduction.

Research

Research Items

A rich heptane/air mixture was reacted in a porous medium burner consisting of a packed bed of alumina pellets. Measurements include the hydrogen mole fraction in the exhaust and the temperature at various points in the reactor. Experiments were conducted at different equivalence ratios. Specifically, the mixture was ignited at ! = 1.0 (stoichiometric) and then experiments were conducted at equivalence ratios ranging from 1.5 to 3.2. For this study the inlet mixture speed was kept constant at 50 cm/s for each equivalence ratio but future experiments will examine different inlet velocities. Experimental results show a reaction front propagating downstream and indicate that significant conversion of the hydrocarbon to hydrogen occurred in the reactor. The experimental measurements of H 2 are compared to equilibrium values.

Global circulation models (GCMs) are the best currentently available
tools to describe the complexity of atmospheric variability and climate
evolution on a global scale. However, the large number of existing
models shows a wide spectrum of approaches and results, as shown by the
intercomparison project of the Intergovernmental Panel on Climate Change
(IPCC); or, e.g. Garcia-Herrera et al. (2006), Schmidt at al. (2006),
Hansen et al. (2007) and Garcia et al. (2007), among others. Therefore,
this work compares side-by-side results from the ModelE GCM version of
the NASA Goddard Institute for Space Studies (GISS) at 2º x
2.5º horizontal resolution and 20 vertical layers and the NCAR
Whole-Atmosphere Community Climate Model (WACCM) at 2º x 2.5º
resolution against reanalysis products of the European Centre for
Medium-Range Weather Forecasts (ERA-40) available at 2.5º x
2.5º horizontal resolution and 23 pressure levels (obtained by the
ECMWF three-dimensional assimilation system based on satellite,
radiosondes and other conventional observations). Both GISS ModelE and
WACCM were implemented in a parallel high- performance computing
infrastructure, the Marenostrum supercomputer. Model outputs are
available for different decades (GISS ModelE simulations were run from
1950 to 2050 while results from WACCM cover the period 1950-2003), but
comparison focuses on the period 1957-2002, conditioned by the
availability of the ERA-40 re- analysis. The main aim of this study is
the definition of the degree of reliability of two specific models for
their use in climate prediction and to analyze their seasonal behavior
in several regions. Statistical comparisons are performed for global and
regional averaged distribution maps of sea level pressure,
2m-temperature, geopotential heights and precipitation at several time
scales. The Root Mean Square Error (RMSE) and bias with respect to
ERA-40 data have also been estimated and diagrammed for the years 1957-
2002 evolution. Averaged values are then analyzed for different seasons
and regions. Moreover, through the use of Taylor diagrams, we quantify
and discuss the different performances for each model simulated patterns
in terms of standard deviation, centered RMSE and their correlations.
Discrepancies between reanalysis and models emerge widely through the
study, especially for total cloud cover and precipitation. The global
behavior of both models is accurate when compared to ERA-40 re-analysis
in terms of low bias and RMSE for 2m-temperature computed by both
models, and very high correlations appear (greater than 0.95). Given
that the WACCM and the GISS simulations were run at specified sea
surface temperatures (SST), in the oceanic regions this result must be
expected. However, in terms of sea-level pressure larger differences
emerge, with RMSE as large as 0.45 (normalized value) and correlation
coefficients in the range between 0.8 and 0.9. In extremely complex
topography regions such as the Himalaya range, large differences in
error and tendencies appear for pressure and geopotential heights for
both models. Despite such problems, a detailed analysis of the results
coming shows that both GISS ModelE and WACCM results are within the
range of error estimates found in the revised scientific literature.

The fundamental pathways for tropical cyclone (TC) intensification are explored by considering axisymmetric and asymmetric impulsive thermal perturbations to balanced, TC-like vortices using
the dynamic cores of three different nonlinear numerical models. Attempts at reproducing the
results of previous work, which used the community model WRF (Nolan and Grasso 2003; NG03),
revealed a discrepancy with the impacts of purely asymmetric thermal forcing. The current study
finds that thermal asymmetries can have an important, largely positive role on the vortex
intensification whereas NG03 and other studies find that asymmetric impacts are negligible.
Analysis of the spectral energetics of each numerical model indicates that the vortex response to
asymmetric thermal perturbations is significantly damped in WRF relative to the other models.
Spectral kinetic energy budgets show that this anomalous damping is primarily due to the increased
removal of kinetic energy from the vertical divergence of the vertical pressure flux, which is
related to the flux of inertia-gravity wave energy. The increased kinetic energy in the other two
models is shown to originate around the scales of the heating and propagate upscale with time from
nonlinear effects. For very large thermal amplitudes (50 K), the anomalous removal of kinetic
energy due to inertia-gravity wave activity is much smaller resulting in good agreement between
models.
The results of this paper indicate that the numerical treatment of small-scale processes that
project strongly onto inertia-gravity wave energy can lead to significant differences in asymmetric
TC intensification. Sensitivity tests with different time integration schemes suggest that diffusion
entering into the implicit solution procedure is partly responsible for the anomalous damping of
energy.

Coastal communities around the world are being encouraged to plant or restore vegetation along their shores for the purpose of mitigating tsunami damage. A common setup for these projects is to develop ‘mitigation hills’ – an ensemble of vegetated hills along the coast – instead of one continuous stretch of vegetation. An example is depicted on the left.
The rationale behind a staggered-hill setup is to give tree roots more space to grow and deepen.
From a fluid-dynamical point of view, however, staggered mitigation hills may have significant drawbacks such as diverting the flow into the low-lying areas of the park, which could entail strong currents in the narrow channels between the hills and lead to erosion of the hills from the sides. The goal of this study is to quantify, via numerical simulation, how mitigation hills affect tsunami runup and to understand how channelization may really be a threat.
Our computations are based on the non-linear shallow water equation solved through a fully implicit, high-order, discontinuous Galerkin method (DG). A dynamic subgrid-scale eddy viscosity model for large eddy simulation (LES) is used for stabilization purposes and to capture the obstacle-generated turbulence.

This was published as "Variational multiscale stabilization of high-order spectral elements for the advection–diffusion equation", see "https://www.researchgate.net/publication/256375304_Variational_multiscale_stabilization_of_high-order_spectral_elements_for_the_advectiondiffusion_equation"

Histotripsy with ultrasound is an emerging non-invasive therapeutic modality that uses cavitation to precisely destroy diseased soft tissue. Accurate simulations of histotripsy are needed for treatment planning and device design. These simulations must model transient pressure fields, span hundreds of wavelengths, and must handle strong shocks and disconti-nuities between materials, such as the brain and the skull. The discontinuous Galerkin (DG) method is an outstanding candidate for such simulations. DG methods possess the following qualities: 1) high order accuracy, 2) geometric flexibility, 3) excellent dissipation properties, and 4) excellent scalability on massively parallel machines. The objective of this work is to introduce our efforts to develop a model nonlinear ultrasound simulations that are ultimately intended for histotripsy simulations in the brain. We have developed a 3D nonlinear wave equation solver using a time-explicit DG method [1]. The governing equations are expressed in first-order flux form, which models the effects of diffraction, attenuation, and nonlinearity. A Rusanov numerical flux is formulated and the eigenvalues of the flux Jacobian are calculated. A third-order, strong stability preserving Runge-Kutta (RK) time-integrator is used for time-discretization. Frequency-squared attenuation is modeled via a second-order diffusion term, which is evaluated using the local DG method. To stabilize the method and guarantee a non-oscillatory solution near shocks, a parameter-free stabilization scheme is implemented [2]. Full-wave 3D simulations are simulated for both linear and nonlinear problems. Numerical results for a planar waveguide and a pulsed rectangular piston are presented and compared to existing analytical solutions and to the FOCUS package [3]–[7]. Our nonlinear DG captures strong shocks and resolves diffrac-tion, absorption, and nonlinear for all problems considered. An approach for coupling DG with FOCUS is proposed. These results suggest DG is a competitive method for transient biomedical acoustics simulations.

A nodal discontinuous Galerkin (DG) code based on the nonlinear wave equation is developed to simulate transient ultrasound propagation. The DG method has high-order accuracy, geometric flexibility, low dispersion error, and excellent scalability on massively parallel machines, so DG is an ideal choice for solving this problem. A nonlinear acoustic wave equation is written in a first-order flux form and discretized using nodal DG. A dynamic sub-grid scale (dyn-SGS) stabilization method to reduce Gibbs oscillations to simulate acoustic shock waves is then established. Numerical results, both linear and nonlinear, from a 1D and 2D DG code are presented and compared to numerical solutions obtained from linear and KZK-based simulations in FOCUS. These numerical results indicate these nodal DG simulations capture nonlin-earity, thermoviscous absorption, and diffraction for both planar and focused pistons.

Numerical Weather Prediction (NWP) is in a period of transition. As resolutions increase, global models are moving towards fully nonhydrostatic dynamical cores, with the local and global models using the same governing equations; therefore we have reached a point where it may be possible to use a single model for both applications. These new dynamical cores are designed to scale efficiently on clusters with hundreds of thousands or even millions of CPU cores and GPUs. Operational and research NWP codes currently use a wide range of numerical methods: finite difference, spectral transform, finite volume and, increasingly, finite/spectral elements and discontinuous Galerkin, which constitute element-based Galerkin (EBG) methods. Due to their important role in this transition, will EBGs be the dominant power behind NWP in the next 10 years, or will they just be one of many methods to chose from? One decade after the review of numerical methods for atmospheric modeling by Steppeler et al. (2003) [{\it Review of numerical methods for nonhydrostatic weather prediction models} Meteorol. Atmos. Phys. 82, 2003], this review discusses EBG methods as a viable numerical approach for the next-generation NWP models.
One well-known weakness of EBG methods is the generation of unphysical oscillations in advection-dominated flows; special attention is hence devoted to dissipation-based stabilization methods. % such as, but not limited to, variational multi-scale stabilization (VMS) or dynamic Large Eddy Simulation (LES) used for stabilization.
Since EBGs are geometrically flexible and allow both conforming and non-conforming meshes, as well as grid adaptivity, this review is concluded with a short overview of how mesh generation and dynamic mesh refinement are becoming as important for atmospheric modeling as they have been for engineering applications for many years.

The stabilization of high order spectral elements to solve the transport equations for tracers
in the atmosphere remains a relevant topic of research among atmospheric modelers.
This paper builds on our previous work on variational multiscale stabilization (VMS) and
discontinuity capturing (DC) [Variational multiscale stabilization of high-order spectral elements for the advection-diffusion equation, J. Comput. Phys. 231 (2012) 7187-7213]
and shows the applicability of VMS+DC to realistic atmospheric problems that involve physics coupling
with phase change in the simulation of 3D deep convection.
We show that the VMS+DC approach is a robust
technique that can damp the high order modes characterizing the spectral element
solution of coupled transport problems. The method has three important properties that
techniques of more common use typically lack: 1) it is free of a user-defined parameter, 2) it is anisotropic,
and 3) it is numerically consistent.
The proposed method is compared against the classical fourth-order hyper-viscosity scheme. The
main conclusion that arises is that tuning can be fully avoided without loss of accuracy if the dissipative scheme is
properly designed. Finally, 4) the cost of parallel communication is that of a second order operator
which means that fewer communications are required by VMS+DC than by a hyper-viscosity method;
fewer communications translate into a faster and more scalable code, which is of vital importance as we approach the
exascale range of computing. (Accepted for publication on J. Comput. Phys.)

The high order spectral element approximation of the Euler equations is stabilized via a dynamic sub-grid scale model (Dyn-SGS). This model was originally designed for linear finite elements to solve compressible flows at large Mach numbers. We extend its application to high-order spectral elements to solve the Euler equations of low Mach number stratified flows. The major justification of this work is twofold: stabilization and large eddy simulation are achieved via one scheme only.
Because the diffusion coefficients of the regularization stresses obtained via Dyn-SGS are residual-based, the effect of the artificial diffusion is minimal in the regions where the solution is smooth. The direct consequence is that the nominal convergence rate of the high-order solution of smooth problems is not degraded. To our knowledge, this is the first application in atmospheric modeling of a spectral element model stabilized by an eddy viscosity scheme that, by construction, may fulfill stabilization requirements, can model turbulence via LES, and is completely free of a user-tunable parameter.
From its derivation, it will be immediately clear that Dyn-SGS is independent of the numerical method; it could be implemented in a discontinuous Galerkin, finite volume, or other environments alike. Preliminary discontinuous Galerkin results are reported as well. The straightforward extension to non-linear scalar problems is also described. A suite of 1D, 2D, and 3D test cases is used to assess the method, with some comparison against the results obtained with the most known Lilly-Smagorinsky SGS model.

We report on the application of a SGS model for large eddy simulation as a tool to move towards a high-order, yet positivity-preserving solution to the scalar transport equation.

Video information:
- Test case reported in Fig. 15(b) of the paper, but with final time at t=24 days.
- The simulation in the video was obtained using the discontinuity capturing method described in the paper.
- The vorticity field is plotted on the adaptive cubed-sphere grid.
- Author of the video: Dr. Andreas M\"uller, Applied Mathematics, Naval Postgraduate School, amueller@nps.edu
- Video made using the open source software VisIt by the LLNL (https://wci.llnl.gov/simulation/computer-codes/visit/)

Spectral element simulation of a 2.5D density current using a dynamic LES scheme.
Resolution: dx=dz=25 m
The subgrid scale model serves as a stabilization method; no additional dissipation or filtering of high order modes is used.