Master of

Computational Science Projects

Cellular simulation of blood flow

Blood is a complex suspension constituted of various components suspended in plasma. Many of its intriguing properties originate from this cellular nature. Red blood cells are the major component, they transport oxygen and determine the bulk behaviour of blood. Platelets, the second most numerous cells, form the link between transport dynamics and several vital biochemical processes such as clot formation. With the recent advancement of micro-medical devices modelling the small-scale behaviour gains more importance. Accurate modelling of blood flow related phenomena on this scale requires a description of the dynamics at the level of individual cells. This, however, presents several computational challenges that can only be addressed by high performance computing. We developed HemoCell (www.hemocell.eu), a parallel computing framework which implements validated mechanical models for red blood cells and is capable of reproducing the emergent transport characteristics of such a complex cellular system. It is computationally capable of handling large domain sizes, thus it is able to bridge the cell-based micro-scale and macroscopic domains. Using HemoCell as a tool, we pursue the answers to numerous open questions around the human circulatory system.

Keywords : Computational Biomedicine,

Track : Computational Bio-Medicine

Contact 1 : Alfons Hoekstra A.G.Hoekstra@uva.nl

Valid Date : Jan. 25, 2019

Computational Origins Simulator

As part of a project for the Dutch Origins Center, and in parallel with the development of an experimental Origins Simulator (http://www.origins-center.nl/the-origins-simulator-a-preliminary-description), we will take initial steps to build a computational Origins Simulator. This will be partly based on previous work on autocatalytic sets (https://evolution-institute.org/article/the-origin-of-life-a-selfish-act-or-a-cooperative-effort), and on ongoing work on modeling biomineralization (https://staff.fnwi.uva.nl/j.a.kaandorp/research.html). Within this project, we will develop and run new simulation models to extend the existing research, in the context of origin of life studies.

Keywords : Agent Based Model, Network-based modelling, Chemical reaction networks,

Track : Complex Sytems Theory

Contact 1 : Peter Sloot p.m.a.sloot@uva.nl
Contact 2 : Wim Hordijk wim@WorldWideWanderings.net

Valid Date : June 29, 2018

What is the role of vasoconstriction in initial platelet aggregation?

Our blood vessels contain smooth muscles cells (in circumferential direction) to regulate the diameter of the blood vessel. The vessels can in this way regulate the blood pressure in our body. Moreover, the regulation of the diameter of a blood vessel is also important when a vessel is damaged. To reduce the loss of blood smooth muscle cells will contract, a process which is called vasoconstriction. This contraction of the vessel is part of hemostasis, the process of blood clot formation. Vasoconstriction causes also an increase in shear rate that could be of value during initial platelet aggregation. Under high shear rates a protein called von Willebrand factor is important in the binding of platelets to the vessel wall and to each other. In our current study we found the appearance of a cell-free layer (CFL) at the place where a platelet aggregation is initialized. Additionally, we think that this CFL is needed for the von Willebrand factor to uncoil and bind platelets. Therefore, in this study we are interested in the relationship between the amount of vessel constriction and the thickness of the CFL. In addition, we want to know if the vasoconstriction is only important in hemostasis or also in thrombus formation. During this project you will work with the cell-based model Hemocell on this topic. If you are interested, please contact Alfons Hoekstra or Britt van Rooij.

Keywords : Computational Biomedicine,

Track : Computational Bio-Medicine

Contact 1 : Alfons Hoekstra A.G.Hoekstra@uva.nl
Contact 2 : Britt van Rooij b.j.m.vanrooij@uva.nl

Valid Date : Dec. 31, 2019

Self-organized criticality in an interest-rate swap market model

The interest-rate swap market (and similar hedging activities) is a large financial derivatives market. Here, agents (banks, funds, others) build up risk internally, which they 'swap' with other agents to make the total risk in total 'zero'. It is thus an agent-based networked model. The problem is that if one agent cannot meet its obligations and defaults then the swaps it holds with other agents reverse, leading potentially to a cascade or avalanche. The initial simulation results of a previous Master thesis project reveals a self-organized critical regime in the parameter space, or even a 'super' self-organized critical regime where system-wide crashes are inevitable. It is written in a thesis report and an optimized software package is available. This project will continue on this work and work towards a scientific publication. Remaining open questions include a mathematical mean-field approach to better understand the process and critical regimes, but also a comparison of the theoretical model parameters with real data or knowledge. Also more simulations are likely needed.The end goal is to bring the important message out into the world that these types of markets are potentially very dangerous to the systemic stability of our economy. We are looking for a mathematically or physics oriented student.

Keywords : Agent Based Model, Economics, Risk Management, Network-based modelling, Computational Finance,

Track : Computational Finance Complex Sytems Theory

Contact 1 : Rick Quax r.quax@uva.nl

Valid Date : Jan. 25, 2019