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ATP seminars 2010-2015

Seminars 2015

11 November 2015, 15.15

Mapping fungal genes to decomposition of soil organic matter (pdf)
Tomas Martin-Bertelsen


Globally, more carbon (C) is stored in soil organic matter (SOM) than is present in the terrestrial biomass and the atmosphere combined. Whether soils will capture, store or release carbon will be critical for regulating the atmospheric carbon dioxide level and thus the Earth's climate. The molecular interactions between SOM, microorganisms and the physicochemical environment are not well understood thus limits our ability to predict how SOM will respond to environmental changes. Plant-litter (dead leaves, roots) is the main input source to SOM and litter-decomposing fungi play an important role in the degradation of SOM. Within the multidisciplinary MICCS research program ( we aim to characterize the enzyme pathways that mediate SOM decomposition. Wetlab experimentalists produce high-dimensional transcriptomic (gene expression) and spectroscopic (chemical modifications) data. In this talk I will describe the computational approaches we are adapting for discovery of links between genes and the mediated chemical modifications of SOM extracts.

9 September 2015, 15.15

Dynamic exoplanets (pdf)
Alexander Mustill


Planetary systems change: over long time-scales planets perturb each others' orbits away from perfect Keplerian motion. Planets can experience both regular orbital variations and more violent instabilities that can lead to collisions between planets or their ejection from their system. In this talk I will describe the diversity of dynamical behaviour that planetary systems can exhibit, and explain why a knowledge of their orbital dynamics is necessary for a full understanding of the planets themselves.

13 May 2015, 15.15

Parton distribution functions and Monte Carlo simulations of photon-photon collisions (pdf)
Ilkka Helenius


When colliding hadrons at high energies, e.g. protons at the LHC, the interactions happen between the quarks and gluons which are the constituents of the hadrons. The distribution of these partons inside the hadron cannot be computed from the first principles of QCD but can be determined using experimental data as an input. In the first part of the talk I will introduce the theoretical framework that is used in the parton distribution function (PDF) analyses and briefly discuss about the experimental data that are included in the analyses. I will also describe how the PDFs are modified in nuclear collisions. In the second part I will discuss why one should consider also the partonic structure of photons and show some preliminary results from our Monte Carlo simulations of photon-photon collisions with PYTHIA8 event generator.

15 April 2015, 15.15

Evolution of protoplanetary discs and why it is important for planet formation (pdf)
Bertram Bitsch


The birthplace of planets around newly born stars is the protoplanetary disc surrounding the star. In these discs dust particles can collide, grow and form ever bigger objects, the so-called planetesimals, which form by dust particles collapsing due to gravity. These planetesimals can then collide and form even bigger objects, the cores of giant planets, which can attract gas from the protoplanetary disc and become gas giants like Jupiter. The movement and growth of dust and the formation planetesimals depends on the structure of the protoplanetary discs. In this talk I will discuss the influence of the structure and evolution of protoplanetary discs on the formation of planetesimals and planets.

25 February 2015, 15.15

When the hay looks like needles — statistical challenges in omics data mining (pdf)
Patrik Edén


Standard statistical methods, preferably involving test sets, can control false discovery rates in the enormously flexible microarray data analysis. However, it is normally assumed that a similar flexibility in pre-processing (e.g. quality control and noise filter) was not exploited with knowledge of sample properties. This leaves the typical research group with the unpleasent choice to either abstain from pre-processing optimization or lose formal control of their statistical tests. I will discuss a possible solution and present preliminary results.

Seminars 2014

7 May 2014, 15.15

Formation of galactic bars and bulges (pdf)
Lia Athanassoula


Like many other disc galaxies, the Milky Way has a bar and a boxy bulge in its central parts. I will use N-body simulations to discuss the formation, evolution and properties of such structures, with emphasis in our Milky Way bar/bulge region. I will also discuss the role of the dark matter and of gas in these processes, and how baryonic and dark matter interact.

5 March 2014, 15.15

How can we understand the strong force? (pdf)
Gösta Gustafson

5 February 2014, 15.15

Modeling of survival data and some nice applications in clinical medicine (pdf)
Mattias Ohlsson

Seminars 2013

13 November 2013, 15.15
Sal F (K404)

Cosmic explosions from compact binaries (pdf)
Ross Church


The majority of observed high-energy transient astrophysical events are associated with massive stars, and these massive stars are in the most part in binaries: gravitationally bound systems in which two stars orbit their common centre of mass. Interactions between the two stars can profoundly change their evolution and lead directly to explosive events such as gamma-ray bursts. I will briefly review the evolution of single and binary stars and discuss three examples of binary interactions leading to high-energy transients: long-duration gamma-ray bursts from black-hole binaries, short-duration gamma-ray bursts from neutron star-binaries and calcium-rich explosions from white-dwarf--neutron-star binaries.

23 October 2013, 15.15
sal F (K404)

Modeling protein aggregation - from sticks to atomic representation (pdf)
Anders Irbäck

2 October 2013, 15.15

Connecting Inner Space & Outer Space
Subir Sarkar, Niels Bohr Institute and University of Oxford


We have just celebrated the centenary of the finding that the Earth is constantly bombarded by high energy `cosmic rays' from outer space. This initiated a glorious era of discovery of many new elementary particles (positron, muon, pion, ...) and developed into accelerator-based research in high energy physics. A century later this has given us the triumphant `Standard Model' of particle physics which provides a precise quantum description of all fundamental processes in terrestrial laboratories, including (with the recent discovery of "a Higgs boson") an understanding of how particles acquire mass. Unfortunately the Standard Model does not explain any of the salient features of the universe as a whole - Why there is matter but no antimatter? Why there is so much more `dark matter' of unknown origin? Why is the expansion rate apparently accelerating, as if driven by a Cosmological Constant-like, dominant component of `dark energy'? I will describe how new experiments and theoretical developments at the rapidly growing interface of astro-particle physics are attempting to answer these cosmic questions, by linking them to possible new physics beyond the Standard Model.

10 April 2013, 15.15

The three colours of the strong force (pdf)
Malin Sjödahl

6 March 2013, 15.15
sal F

Turbulent Mixing in Galactic Disks (pdf)
Chao-Chin Yang


Observations show that radial metallicity gradients in disk galaxies are relatively shallow, if not flat, especially at large galactocentric distances and for galaxies in the high-redshift universe. Given that star formation and metal production are centrally concentrated, this requires a mechanism to redistribute metals. However, the nature of this mechanism is poorly understood, let alone quantified. I will present my first-principle calculations of turbulent mixing driven by thermal instability, and argue that this is an efficient process in redistributing metals on large scales. And then I will discuss the on-going extension of this work to understand the chemical homogeneity in old star clusters.

6 February 2013, 15.15
sal F

Quasiperiodic Patterns in Biology (pdf)
Bo Söderberg


There has been some interest lately in certain mechanisms for pattern formation in biological tissue, where the dynamics is based not only on diffusion and local production/deletion, as in conventional reaction- diffusion models, but also on so called active transport. Some of the related equations bear relations to Newton's and Schrödinger's equations, and the dynamics sometimes allow for quasiperiodic patterns due to the existence of a non-trivial spatial conservation law.

Seminars 2012

14 November 2012, 15.15

Lithium in the Cosmos (pdf)
Greg Ruchti

17 October 2012, 15.15
sal F

The "Higgs" discovery - a portal to new physics (pdf)
Johan Rathsman


Starting from the experimental discovery of a Higgs-like particle, I will recapitulate the role of the Higgs boson in the standard model of particle physics. Then I move on to discuss the implications of the discovery, and how the detailed properties of the "Higgs" particle can tell us something about physics beyond the standard model, such as supersymmetric theories.

19 September 2012, 15.15
sal F

Modelling the plant circadian clock (pdf)
Carl Troein


The vast majority of living organisms are exposed to daily cycles in temperature, sunlight and other environmental factors. The ability to anticipate these rhythmic changes is highly beneficial: clocks with a 24-hour period are found in many different lifeforms, including both animals and plants.
In the plant model organism Arabidopsis thaliana, more than a dozen genes form the core of the clock. Together they form a complex network of interactions, with positive and negative feedbacks and many inputs and outputs. Over the past decade, more and more complete models clock have been created, typically in the form of ordinary differential equations, based on a vast number of experiments.
In this talk, I will present the biological background and building blocks of circadian clocks, and show how the models have been - and, despite their complexity, are still being - iteratively improved through feedback between modelling and experimentation.

24 May 2012, 15.15
Ecology House

Improving the precision of high-energy simulation and analysis tools (pdf)
Honorary Doctor's Seminar by Bryan Webber

18 April 2012, 15.15

Stellar Clusters: Factories Producing Exotic Objects (pdf)
Melvyn Davies

14 March 2012, 15.15

Status of the LHC and Anatomy of LHC Events (pdf)
Torbjörn Sjöstrand

22 February 2012, 15.15
sal F, theoretical physics

The European Spallation Source: What is it and what can I do with it !
Dimitri Argyriou (Director of Science, ESS)


In this talk I will discuss briefly what is the European Spallation Source and why it is different from other sources. Apart from highlighting how neutrons are used in science today, the talk will also focus on some of the special opportunities that ESS offers.

25 January 2012, 15.15
sal F, theoretical physics

Simulation of Structure & Function of Biological Macromolecules (pdf)
Erik Lindahl (KTH)


Biological macromolecules are fascinating machines with highly complex functional roles determined by their structure, but this in turn is determined by fairly simple physical interactions. In principle it is possible to simulate the folding of e.g. a protein in a computer, but the very high computational complexity has limited this to small systems even when using special-purpose hardware. I will discuss how we are trying to address this problem by using different approaches to computation that originally came out of our work on the Folding@Home project, and how it might be possible to model quite complex and general biological processes with large numbers of simulations running as an ensemble on extremely large future "exascale" computers, in particular by using Markov State Models. I will also present how we are applying these techniques to model functions and drug interactions for ligand-gated ion channel membrane proteins to illustrate how current simulations provide concrete functional conclusions for proteins that complement and guide other experimental methods.

Seminars 2011

7 December 2011, 15.15

The chemical history of the Galactic bulge and disk (pdf)
Thomas Bensby

16 November 2011, 15.15

The Physical Vacuum: Where Particle Physics Meets Cosmology (pdf)
Roman Pasechnik


The Nobel Prize in Physics this year has been awarded "for the discovery of the accelerating expansion of the Universe through observations of distant supernovae". Such a fundamental discovery together with up-to-date results from the Large Hadron Collider poses even more fundamental questions to our understanding of the structure of the Physical Vacuum, both at micro and macro scales. Many diverse unsolved problems ranging from e.g. the Supersymmetry breaking mechanism giving a natural candidate for the Dark Matter, the Higgs issue in the Standard Model and the confinement issue in the Quantum Chromodynamics up to the Dark Energy issue leading to observable acceleration of the Universe originate from poorly understood structure of the Physical Vacuum. In this talk, I make an attempt to review this very complicated problem from different perspectives, as well as to go through major current and possible theoretical developments at frontiers of Particle Physics and Cosmology.

2 November 2011, 15.00

Monte Carlo simulation of proteins: from folding to "nonfolding" to interactions (pdf)
Stefan Wallin

4 May 2011, 15.15
sal F

Imaging possibilities at Lund University BioImaging Center
Sven-Erik Strand and Freddy Ståhlberg

2 February 2011, 15.15

The physics of musical instruments
Gösta Gustafson


Why does a clarinet sound one octave lower than an oboe or a saxophone of the same length, and why is the first overtone missing in the clarinet?
Why should you not hit a drum in the center?
What is the motion of a violin string?
Why can you have finger holes in a flute but not in a trumpet?
These are some of the questions to be discussed in the talk.

Seminars 2010

8 December 2010, 15.15
sal F

The art of moving when you are stuck - from Darwins' research on plants to state of the art methods for resolving the underlying mechanisms of multicellular life (pdf)
Henrik Jönsson


The differentiation of stem cells into different cell types and the possibility of guiding cells back to stem cells are currently attracting much attention within developmental biology and medical research. Plants, unable to move around, rely on an ability to respond to the environment and continue the production of organs throughout their lives. Hence they have developed the competence to regulate stem cells and growth depending on intrinsic and external signals. I will discuss our research on combining mathematical models and live imaging techniques to gain insights in the mechanisms regulating multicellular development. I will show that a combination of gene regulation, hormone signaling, and mechanical stresses are important for development.

17 November 2010, 15.15

How migrating geese and falling pens inspire planet formation (pdf)
Anders Johansen


Planets form in gaseous discs around young stars as tiny dust grains collide to form larger and larger bodies. This paradigm however faces major problems as particles reach cm sizes, as macroscopic bodies are more prone to bouncing and shattering than to sticking. I will talk about my computational work on explaining the formation of km-sized planetesimals from cm-sized pebbles. Particles fall at their terminal velocity towards the point of highest pressure, like objects on earth falling to the floor. High-pressure regions in circumstellar discs collect particles this way. An aerodynamical streaming instability causes particles to clump further, analogous to how migrating geese and bicycle riders travel in groups to reduce their common air resistance. The local particle density can become high enough to initiate a gravitational collapse of the pebble component. This planet formation picture has widespread implications for observations of exoplanets and for explaining why the solar system formed when it did.

3 November 2010, 15.15
sal F

Dark matter searches in the sky and underground (pdf)
Joakim Edsjö (Stockholm University)


Finding the dark matter in the Universe is one of the big questions in science today. I will here go through various ways to search for dark matter and discuss the current status both from a particle physics and astrophysics point of view. I will also discuss future searches that will take place in the near future.

20 October 2010, 15.15

Near field cosmology, now and in the Gaia era (pdf)
Sofia Feltzing


I will review the current status of the field often referred to as near field cosmology, i.e. the study of cosmologically interesting process but in the local volume. In particular I will focus on our understanding of the Milky Way as a galaxy and how it constrains the cosmological models. The advent of Gaia will radically change the impact of near field cosmology on cosmology in general.

9 June 2010, 15.15
sal F

Computational modeling of the living cell biochemistry: What statistical physicists are not but should do
Zoran Konkoli (Department of Microtechnology and Nanoscience - MC2, Chalmers University of Technology, Sweden)


The talk will discuss how Statistical Physics tools can be used to understand biochemistry of the living cell. Structures found in the living cell are rather special and to achieve such task tchniques used in the field of Statistical Physics need to be slightly modified. A critical reflection is needed on which techniques to use and for what purpose. As an example the theory of diffusion controlled reactions will be reviewed with a purpose of using it for understanding spatio-temporal organization of the living cell.
It will be argued that formalism of diffusion controlled reactions is a suitable framework for describing living cell and the scope and the limitations of such approach will be discussed. Informal discussion will be given around problems (and possible traps) one meets when trying to compute properties of biochemical reactions in the cell interior. For example, assumption of perfect mixing is frequently used for modeling. However, large number of processes in the cell exists to battle precisely lack of perfect mixing. Few selected issues related to validity of mean field equations (perfect mixing) in describing intracellular kinetics will be discussed.
The last part of the talk will cover more applied topics. It will be shown how framework of diffusion controlled reactions (and Markov chains) can be used to analyze spatio-temporal organization of the living cell. A platform for doing such analysis, Geometry-Reaction InterPlay (GRIP), will be presented. If the time allows some issues related to complex noise formation will be discussed.

26 May 2010, 15.15
sal F

Boson Interferometry: From astronomy to particle physics, and back (pdf)
Dainis Dravins

28 April 2010, 14.15

(Two seminars, thereby the early start!)
Justin Read and Sandipan Mohanty

14 April 2010, 15.15
sal F

Hadrons, Flavours and Effective Theories (pdf)
Johan Bijnens

17 March 2010,, 15.15

Black holes and cosmic explosions (pdf)
Magnus Axelsson


Stellar mass black holes are the end product of massive stars. Their formation may be accompanied by spectacular events such as supernovae and gamma-ray bursts. In this presentation I will briefly outline this connection and show how observational results from studies of black holes in binary systems can be used to probe their formation.

3 March 2010 14.15
sal F

ACCELERATED COSMIC EXPANSION: Observations, theoretical ideas (pdf)
Bengt E Y Svensson


I will review the present understanding of the accelerated expansion of the universe, the "dark energy" enigma, observationally discovered about a decade ago and still without a satisfactory explanation. To try to get everyone on-board, I will start with a "crash course" in cosmology by presenting all the basics needed (so if you are unfamiliar with the topic, you will have a cheap chance to get updated!) After giving a brief summary of the relevant observational data, I will then dwell on some of the theoretical ideas that have been put forward to explain the phenomenon.

17 February 2010, 15.15

The physics of subcellular processes (pdf)
Tobias Ambjörnsson

3 February 2010,, 15.15
sal F

Gaia: A brief overview of the ESA space astrometry project (pdf)
Lennart Lindegren