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Previous COMPUTE seminars

30 May 2017, 13:30, Lundmarksalen (Astronomy)

Michel Defrise (Vrije Universiteit, Brussel): Statistical reconstruction methods in medical imaging

Abstract:
Statistical reconstruction methods are probably today the most common methods to obtain tomographic images from SPECT/PET measurements. The methods are based on modelling the camera systems and thereby iteratively find a good estimate of the internal radionuclide distribution from the similarity of the calculated and measured projection data. The main advantage is here that if physical problems, associated with the measurement of the radiation, such as, non-homogeneous photon attenuation, contribution from scattered photons, partial volume problems due to collimator resolution, septal penetration etc, can be modelled accurately then this naturally comes out as a compensation for the problems. The lecture will cover the fundamental mathematical parts of the procedures describe above.

14 November 2016

INTEGRATE meeting -- see the INTEGRATE website for more details.

26 October 2016

INTEGRATE math-hack day -- see the INTEGRATE website for more details.

5 October 2016

INTEGRATE hack day -- see the INTEGRATE website for more details.

26 September 2016

INTEGRATE meeting -- see the INTEGRATE website for more details.

11 May 2016

INTEGRATE meeting -- see the INTEGRATE website for more details.

25 April 2016

INTEGRATE math-hack day -- see the INTEGRATE website for more details.

12 April 2016

Patrick Farrell (Oxford University): Automated adjoint simulations with FEniCS and dolfin-adjoint

Abstract:
The derivatives of PDE models are key ingredients in many important algorithms of computational science. They find applications in diverse areas such as sensitivity analysis, PDE-constrained optimisation, continuation and bifurcation analysis, error estimation, and generalised stability theory.

These derivatives, computed using the so-called tangent linear and adjoint models, have made an enormous impact in certain scientific fields (such as aeronautics, meteorology, and oceanography). However, their use in other areas has been hampered by the great practical difficulty of the derivation and implementation of tangent linear and adjoint models. Naumann (2011) describes the problem of the robust automated derivation of parallel tangent linear and adjoint models as ``one of the great open problems in the field of high-performance scientific computing''.

In this talk, we present an elegant solution to this problem for the (common) case where the original discrete forward model may be written in variational form, and discuss some of its applications.

11 April 2016

INTEGRATE hack day -- see the INTEGRATE website for more details.

14 March

INTEGRATE meeting -- see the INTEGRATE website for more details.

12 October 2015

Volker Springel (Heidelberg Institute for Theoretical Studies): Cosmic structure formation on a moving mesh

Abstract:
Recent years have seen impressive progress towards hydrodynamic cosmological simulations of galaxy formation that try to account for much of the relevant physics in a realistic fashion. At the same time, numerical uncertainties and scaling limitations in the available simulation codes have been recognized as important challenges. I will review the state of the field in this area, highlighting a number of recent results obtained with large particle-based and mesh based simulations. I will in particularly describe a novel moving-mesh methodology for gas dynamics in which a fully dynamic and adaptive Voronoi tessellation is used to formulate a finite volume discretization of hydrodynamics which offers numerous advantages compared with traditional techniques. The new approach is fully Galilei-invariant and gives much smaller advection errors than ordinary Eulerian codes, while at the same time offering comparable accuracy for treating shocks and an improved treatment of contact discontinuities. The scheme adjusts its spatial resolution to the local clustering of the flow automatically and continuously, and hence retains a principle advantage of SPH for simulations of cosmological structure growth. Applications of the method in large production calculations that aim to produce disc galaxies similar to the Milky Way will be discussed.

16 April 2015

Derek Richardson (University of Maryland): Asteroids: Modeling the future of space exploration

Abstract:
Over the past 2 decades since the first spacecraft images were returned from an asteroid, we have learned that these potentially hazardous objects not only often support satellites but are likely themselves loose collections of fragmented material. Numerical simulations assist in understanding the evolution of these leftover building blocks of the terrestrial planets, planning for the mitigation of their threat to Earth, and for advising space mission designers on the challenges of sample return and possible astronaut landing. Our group uses an adapted high-performance parallelized gravity tree code (PKDGRAV) to simulate gravitational and collisional processes among small bodies in space. Basic features of the code will be presented, along with their application to selected topics in small-body evolution. The talk will feature our latest simulations of granular flow in microgravity, a key tool for modeling sample-return mechanisms.

23 March 2015

Thomas Neuhaus (Jülich Supercomputing Centre): Quantum computing via quantum annealing from a physics point of view

Abstract:
I present an overview on the theory of quantum annealing for the use of solving so called intractable mathematical problems. I will introduce satisfiability problems consisting of a number of simple constraints (clauses) on a set of Boolean variables (e.g., 2SAT and 3SAT) and report on today's knowledge on the usefulness of quantum annealing in such theories. I will also give an introduction to the existing Dwave Quantum Computer and present a few computer experiments on the machine. As of today theoretical physics has not yet identified a class of mathematical problems, nor physical theories, that really benefits from quantum annealing with certainty. A search for such problems is under way.

16 February 2015

Gregor Gassner (University of Cologne): A massively parallel model for fluid dynamics simulations

Abstract:
In this talk, I will consider the numerical simulation of non-linear advection-diffusion problems, particularly of the compressible Navier-Stokes equations used to model turbulent fluid flows in engineering applications and problems appearing in natural sciences.

For this, we develop stable and accurate methods for conservation laws and incorporate other important physical aspects, such as e.g. entropy stability. Examples include the Burgers equation, the shallow water equations, Maxwell's equations and the Euler equations.

A special emphasis is on the computational implementation of these mathematical models such that they are well suited for realistic applications. Due to the multi-scale character of the considered problems, a large amount of spatial and temporal resolution is needed for an accurate approximation. The number of spatial degrees of freedom are as high as one billion with over one hundred thousand time steps. Such simulations are only feasible, when the power of today's largest supercomputers are unleashed.

I will present a special parallelization strategy which is tailored directly to the mathematical model in use and allows simulations on over one hundred thousand cores with near perfect parallel efficiency. Scaling results on different machines are demonstrated, where the absolute limit of MPI is tested with only one grid cell left on a processor.

At the end of the talk, some applications simulated with this framework are illustrated.

15 December 2014

Anna-Karin Tornberg (KTH): Accelerated boundary integral simulations of particulate and two-phase flows

Abstract:
In micro-fluidic applications where the scales are small and viscous effects dominant, the Stokes equations are often applicable. The suspension dynamics of fluids with immersed rigid particles and fibers are very complex also in this Stokesian regime, and surface tension effects are strongly pronounced at interfaces of immiscible fluids - such as surfaces of water drops in oil.

Simulation methods can be developed based on boundary integral equations, which leads to discretizations of the boundaries of the domain only, and hence fewer unknowns compared to a discretization of the PDE. This involves evaluating integrals containing the fundamental solution (Green's function) for the PDE. This will result in both singular and nearly singular integrals that need to be evaluated, and the construction of accurate quadrature methods is a main challenge. The Green's functions decay slowly, which results in dense or full system matrices. To reduce the cost of the solution of the linear system, an acceleration method must be used. If these two issues - accurate quadrature methods and acceleration of the solution of the linear system - are properly addressed, boundary integral based simulations can be both highly accurate and very efficient.

I will give an introduction to boundary integral methods - discussing the concepts starting with the simplest formulation for rigid particles, before discussing the more well-conditioned formulations that we actually use. I will give the main ideas for a spectrally accurate FFT based Ewald method developed for the purpose of accelerating simulations, and for quadrature treatment in two and three dimensions. I will show results for periodic suspensions of rigid particles in 3D and of interacting drops in 2D.

17 November 2014

Debora Sijacki (University of Cambridge): Simulating galaxy formation: numerical and physical uncertainties

Abstract:
Hydrodynamical cosmological simulations are one of the most powerful tools to study the formation and evolution of galaxies in the fully non-linear regime. Despite several recent successes in simulating Milky Way look-alikes, self-consistent, ab-initio models are still a long way off. In this talk I will review numerical and physical uncertainties plaguing current state-of-the-art cosmological simulations of galaxy formation. I will then present global properties of galaxies as obtained with novel cosmological simulations with the moving mesh code Arepo and discuss which physical mechanisms are needed to reproduce realistic galaxy morphologies in the present day Universe.

20 October 2014

Lund University Humanities Lab — Why the humanities needs a lab and what we do in it

Marianne Gullberg, Director of the Humanities Lab:
Why on earth do the Humanities need a lab?

Tea/coffee

Annika Andersson:
What the recording of brainwaves can tell us about language processing
Marcus Nyström:
What are eye movements? Looking into the elastic eye
Victoria Johansson:
Are we reading during writing? What does the combination of keystroke logging and eyetracking reveal?
Nicolo dell'Unto:
The use of 3D models for intra-site investigation in Archaeology

Abstract:
Lund University Humanities Lab is an interdisciplinary research and training facility whose aim is to enable scholars (mainly) in the humanities to combine traditional and novel methods, and to interact with other disciplines in order to meet the scientific challenges ahead. The Lab hosts technology, methodological know-how, and archiving expertise, and a wide range of research projects. Activities are centered around issues of communication, culture, cognition and learning, but many projects are interdisciplinary and conducted in collaboration with the social sciences, medicine, the natural sciences, engineering, and e-Science locally (Lund University), nationally, and internationally. We start with a brief overview of the lab and its facilities, followed by four short talks exemplifying the kind of research that takes place in the Lab.

27 May 2014

Freddy Ståhlberg (Dept. of Medical Radiation Physics): What is LBIC?

Abstract:
The overall goal of Lund University Bioimaging Center (LBIC) is to pursue in-depth knowledge of human metabolism and function by developing and combining advanced imaging techniques, primarily high-field MRI, PET and SPECT). The goal is accomplished by a step-by-step establishment of the above mentioned bio-imaging center at our University, using already well-established research groups in the field as the core structure.

To achieve this goal, we provide technical platforms, knowledge and support in the development of new diagnostic methods from experimental models, while at the same time taking unmet clinical problems to device patient-specific tailored therapies. Technically, MRI and PET will be advanced both as individual modalities and also towards a merged use. We envision future simultaneous extraction of physiological and molecular information in a multimodal imaging environment for better understanding the impact of molecular events on cellular/tissue behavior. We believe that the development of the Lund University Bioimaging Center will have a significant impact on the research at Lund University. Locally, the center is a powerful resource for translational research at the medical faculty and at Skåne university hospital, with strong connections to planned larger research facilities in Lund, e.g. MAXIV and ESS Scandinavia. On a national and international level, the buildup of the proposed center can be foreseen to become an asset to the whole biomedical research community.

5 May 2014

Martin Rosvall (Umeå University): Memory in network flows and its effects on community detection, ranking, and spreading

Abstract:
It is a paradigm to capture the spread of information and disease with random flow on networks. This conventional approach ignores an important feature of the dynamics: where flow moves to depends on where it comes from. That is, memory matters. We analyze multi-step pathways from different systems and show that ignoring memory has profound consequences for community detection. Compared to analysis without memory, community detection with memory generally reveals system organizations with more and smaller modules that overlap to a greater extent. For example, we show that including memory reveals actual travel patterns in air traffic and multidisciplinary journals in scientific communication. These results suggest that we can use only more data and not more elaborate algorithms to identify real modules in integrated systems.

23 April 2014

Paul Segars (Duke University): The XCAT phantom based on NURBS to create realistic anatomical computer models for use in Medical Imaging simulations

Talks on research involving voxel-based phantoms at Dept of Medical Radiation Physics, Lund University:

1) Michael Ljungberg: Nuclear medicine and the use of voxel-phantoms in Monte Carlo research

2) Gustav Brolin: A national quality assurance study of dynamic 99Tcm-MAG3 renography using Monte Carlo simulations and the XCAT phantom

3) Katarina Sjögreen Gleisner: An introduction to image-based dosimetry

4) Johan Gustafsson: A procedure for evaluation of accuracy in Image-Based dosimetrical caculations using the XCAT Phantom

9 December 2013

Thomas Curt (Irstea): Modelling fire behaviour and simulating fire-landscape relationships: Possibilities and Challenges

Abstract:
Fire is one of the major disturbances on the global scale, shaping landscapes and vegetation, and affecting the global carbon cycle (Gill et al., 2013). Global changes (land use changes and climate change) are predicted to modify fire regimes and fire distribution in many parts of the world (Krawchuk et al., 2009). In this context assessing fire risk and simulating fire-landscape interactions become crucial to sustainable land management. In the recent period, important progress has been made to model fire behavior and to simulate fires on various spatial scales. A variety of models and simulators now exist, which have specific abilities and limitations (see http://www.fire.org/). We propose to review some of these models, and to sum up their purpose, potential, and challenges. Fire behavior models (e.g. BehavePlus, Firetec) allow simulating fire behavior for almost all ecosystems using quite simple field data. They also permit to assess fire effects on the ecosystems, notably postfire tree mortality. Some of these models are fully physics-based (2D or 3D), while others use empirical equations. They have been used or adapted to a large array of ecosystems and climate conditions worldwide, and examples will be presented. Landscape-fire models (e.g. Farsite, FlamMap) are spatially-explicit and designed to simulate fires with different weather scenarios in sufficiently realistic landscapes (Cary et al., 2006). Thus they consider the combined effects of weather, fuels, and topography. Recently, high performance fire simulation systems have been developed to permit the simulation of hundreds of thousands of fires. They provides large-scale maps of burn probability or flame length, thus allowing to assess which ecosystems and areas are at risk and should be monitored and managed preferentially. Some applications based on this type of models will be presented. Coupling fire behavior models with vegetation into Dynamic Global Vegetation Model (e.g. LPJ, Sierra) allows studying the role of fire disturbance for global vegetation dynamics. Their application at regional scale requires an approach which is explicit enough to simulate geographical patterns, but general enough to be applicable to each vegetation type at large scales. We shall present how the Sierra model can be used at local scale, in order to predict vegetation shifts according to different scenarios of future fire regime.

27 May 2013

Kevin Heng (University of Bern): Exoplanetary Atmospheres and Climates: Theory and Simulation

Abstract:
Exoplanet discovery is now an established enterprise. The next frontier is the in-depth characterization of the atmospheres and interiors of exoplanets, in preparation for next-generation observatories such as CHEOPS, TESS and JWST. In this presentation, I will review the astronomical, astrophysical and computational aspects of this nascent field of exoplanet science. I will begin by reviewing the observations of transit (absorption) and eclipse (emission) spectra and phase curves, emphasizing the importance of understanding clouds/hazes. Next, I will review the astrophysical aspects of understanding exoplanetary atmospheres, including the need to elucidate the complex interplay between dynamics, radiation and magnetic fields. Finally, I will discuss the Exoclimes Simulation Platform (ESP), an open-source set of simulational tools currently being constructed by my Exoplanets and Exoclimes Group at the University of Bern, reviewing the technical challenges faced by the ESP team. Advancing the theoretical state of the art requires a hierarchical (1D models versus 3D simulations) and multi-disciplinary approach, drawing from astronomy, astrophysics, geophysics, atmospheric and climate science, applied mathematics and planetary science.

7 May 2013

Susanna C. Manrubia (Centro de Astrobiología, Madrid): Tinkering in an RNA world and the origins of life

Abstract:
Life arose on Earth some 3.8 billion years ago. Despite tremendous experimental and theoretical efforts in the last 60 years to uncover how the first protocells could have originated from abiotic matter, we are still facing many more unknowns than answers. Two main players in the process are self-replicating molecules and metabolic cycles, whose emergence requires the presence of chemical species with the ability to code genetic information and catalyze chemical reactions. In current living organisms, DNA performs the former function and proteins the latter. But there is one molecule, RNA, able to perform both functions. This fact has led to the hypothesis that an ancient RNA world could have preceded modern cellular organization. That attractive scenario opens the possibility of carrying out computational studies on issues such as how RNA molecules could have been selected for simple chemical functions, what is the probability that such a molecule would arise in prebiotic environments in the absence of faithful template replication, or how populations of molecules explore the space of sequences and disclose evolutionary innovations.

10 December 2012

Bernhard Mehlig (Göteborg University): Turbulent aerosols: clustering, caustics, and collisions

Abstract:
Turbulent aerosols (particles suspended in a turbulent fluid or a random flow) are fundamental to understanding chemical and kinetic processes in many areas in the Natural Sciences, and in technology. Examples are the problem of rain initiation in turbulent clouds, and the problem of describing the collisions and aggregation of dust grains in circumstellar accretion disks.

In this talk I summarise recent progress in our understanding of the dynamics of turbulent aerosols. I discuss how the suspended particles may cluster together, and describe their collision dynamics in terms of singularities in the particle motion (so-called caustics).



25 October 2012

Chris Lintott (Oxford University): What to do with 600,000 scientists

Abstract:
'Citizen science' - the involvement of hundreds of thousands of internet-surfing volunteers in the scientific process - is a radical solution to the problem of Big Data. The largest and most successful such project, Galaxy Zoo, has seen volunteers provided more than 200 million classifications of more than 1 million galaxies, going beyond simple classification task to make and even follow-up serendipitous discoveries of their own. As PI of Zooniverse.org, astronomer Chris Lintott leads a team that has enabled volunteers to sort through a million galaxies, discover planets of their own, determine whether whales have accents and even transcribe ancient papyri. In this talk, he will review some of the highlights of their work, explore the technology needed to keep such a large group of volunteers busy and look forward to a future when man and machine can work in harmony once more...

7 June 2012

Cristian Micheletti (International School for Advanced Studies, Trieste): Coarse-grained simulations of DNA in confined geometries.

Abstract:
Biopolymers in vivo are typically subject to spatial restraints, either as a result of molecular crowding in the cellular medium or of direct spatial confinement. DNA in living organisms provides a prototypical example of a confined biopolymer. Confinement prompts a number of biophysics questions. For instance, how can the high level of packing be compatible with the necessity to access and process the genomic material? What mechanisms can be adopted in vivo to avoid the excessive geometrical and topological entanglement of dense phases of biopolymers? These and other fundamental questions have been addressed in recent years by both experimental and theoretical means. Based on the recent reviews of refs. [1,2] we shall given an overview of these studies and report on general simulation techniques that can be effectively used to characterize the equilibrium properties of coarse-grained models of confined biomolecules.

References:
[1] D. Marenduzzo et al. J. Phys.: Condens. Matter 22 (2010) 283102
http://iopscience.iop.org/0953-8984/22/28/283102/
[2] C. Micheletti et al. Physics Reports, 504 (2011) 1-73
http://www.sciencedirect.com/science/article/pii/S0370157311000640

Download a PDF of the slides here.

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This page was last modified on 27 August 2017.