Projects

Virolab

The HIV virus genome consists of only 9 genes that code for 19 proteins. The complexity of HIV infection and virus reproduction in the human host is a result of the multitude of interactions that HIV has with its host. Many of these interactions have been studied on a protein level and can be collected in a so called protein interaction network where these 19 HIV proteins interact with thousands of human proteins. Visualization and analysis of this complex network using a graph-theoretic approach can bring new insight into the workings of the HIV virus and its relation to the human host. Where classical biology looks at individual interactions, in complex systems we study the system as a whole. Using this integrated approach and with the help of state-of-the-art computational techniques we envisage today what biological and medical research will be like in the future.

Multi-scale modelling of calcification in scleractinian corals

The project is financed by the Netherlands Organisation for Scientific Research, NWO, research program Computational Life Sciences. The project is a collaboration with the research groups from Prof. R.P.M. Bak (Netherlands Institute for Sea Research (NIOZ) and Prof. D.J. Miller (James Cook University, Australia The central research question we propose to investigate in this project is to characterize the genes that control the differences in coral morphology for related coral species. We do this by a quantitative comparison of gene expression patterns. We especially focus on genes involved in the process of calcification. To test the hypothesis that these genes can explain the differences in morphology, we plan to use the estimated quantities in a simulated network controlling calcification. We want to study the emergence of the micro-morphology structure and link gene expression patterns to the corallite structure. This polyp (corallite) based model will be coupled with a macroscopic growth form model describing Ca2+ and HCO3- fluxes from the environment. A better understanding of calcification in corals is of fundamental importance in research on the potentially detrimental impact of increasing atmospheric carbon dioxide concentrations, reducing ocean pH and carbonate ion concentrations on the calcification process in corals and other calcifying organisms.

HemoSolve

Provide an environment for simulation of blood flow in patient specific arteries.

Sparse Grid Finite-Difference Methods for Pricing of Multi-Asset Options

Numerical approximations of the Libor Market Model by using Sparse Grid techniques.

Understanding Volatility Smile in Option Markets

It is well known that the Black-Scholes model cannot account for the volatility smile observed in financial markets. To explain the deviations of option prices from the Black-Scholes formula, models based on processes other than the geometric Brownian motion, such as stochastic volatility and jump diffusion processes, have been proposed. While these models can include the smile effect on the valuation of options to some extent, they do not explain the origin of the smile phenomenon.

UvA-DRIVE

The UvA Distributed Real-time Interactive Virtual Environment

ACGT

Advancing Clinico-Genomic Trials on cancer

COAST

Complex Automata Simulation Technique

Epiwork

The EPIWORK project proposes a multidisciplinary research effort aimed at developing the appropriate framework of tools and components-epiwork knowledge needed for the design of epidemic forecast infrastructures to be used in by epidemiologists and public health scientists. The project is a truly interdisciplinary effort, anchored to the research questions and needs of epidemiology research by the participation in the consortium of leading epidemiologists, public health specialists and mathematical biologists.

MeDDiCa

Medical Devices Design in Cardiovascular Applications

Multi-Vis

A Multi-modal Visualisation Environment for Interactive Analysis of Medical Data

DynaNets

DynaNets studies and develops a new paradigm of computing through Dynamically Changing Complex Networks reproducing the way nature processes information.

Advanced Visualisation

A collaboration between the visualization groups of SARA and Computational Science.

VEARD

A Visual Exploration environment for Analyzing Gene Regulation in Developmental Processes

MORPHEX

Morphogenesis and gene regulatory networks in plants and animals: a complex systems modelling approach

QosCosGrid

Quasi Opportunistic Supercomputing for Complex Systems in Grid Environments

Genetic and Cellular Mechanisms for Controlled Growth

 

BIOMINTEC

Biomineralization: understanding of basic mechanisms for the design of novel strategies in nanobiotechnology (BIOMINTEC)

From individuals to emergence

 

Direct gravitational N-body simulations on graphics processing units

Mapping of a N-body code on a GPU using NVIDIA's CUDA.

Lattice Boltzmann Research

Overview of Lattice Boltzmann Research in Computational Science research group

CellMath

Mathematics and Computation for the Systems Biology of Cells

Simulation of developmental regulatory networks

Simulation of developmental regulatory networks

Grid-enabled workflow management system for scientific applications

grid-enabled workflow management system (WS-VLAM) following the OGSA/WSRF

Urban Flood

UrbanFlood is a project supported by the EC 7th Framework Programme, investigating the use of sensors within flood embankments to support an online early warning system, real time emergency management and routine asset management.

MAPPER

Multiscale Applications on European e-Infrastructures

VPH-Share

Virtual Physiological Human: Sharing for Healthcare - A Research Environment

THROMBUS

Development of a multiscale computational model for stent-induced thrombosis in intracranial aneurysms: understanding the biology, model the crucial processes, validate the model (In Vitro – In Vivo – In Silico), and develop an end-user software providing a virtual simulation of the thrombosis leading to the optimal stent for a specific patient’s aneurysm.

Twilight

Twilight is an interactive workbench for the visualization and exploration of graphs/networks.