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Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of…
With the advantages of high-speed parallel processing, quantum computers can efficiently solve large-scale complex optimization problems in future networks. However, due to the uncertain qubit fidelity and quantum channel noise, distributed…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
Population protocols are a model of distributed computation intended for the study of networks of independent computing agents with dynamic communication structure. Each agent has a finite number of states, and communication opportunities…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Nowadays, tiered architectures are widely accepted for constructing large scale information systems. In this context application servers often form the bottleneck for a system's efficiency. An application server exposes an object oriented…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
Top-tier parallel computing clusters continue to accumulate more and more computational power with more and better CPUs and Networks. This allows, especially for environmental simulations, computations with larger domain sizes and better…
At high energies, in particle-capture processes between ions and atoms, classical kinematic requirements show that generally double collision Thomas processes dominate. However, for certain mass-ratios these processes are kinematically…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
While machine learning (ML) models have been able to achieve unprecedented accuracies across various prediction tasks in quantum chemistry, it is now apparent that accuracy on a test set alone is not a guarantee for robust chemical modeling…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Atomic ensembles have many potential applications in quantum information science. Owing to collective enhancement, working with ensembles at high densities increases the overall efficiency of quantum operations, but at the same time also…
Many drug delivery systems suffer from undesirable interactions with the host immune system. It has been experimentally established that covalent attachment (irreversible adsorption) of suitable macromolecules to the surface of the drug…
Understanding interfacial phenomena in confined systems is important for optimizing CO2 capture technologies. Here, we present a comprehensive investigation of CO2 adsorption in hydrated amorphous silica nanopores through an integrated…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We present a scalable, robust approach to creating quantum programs of arbitrary size and complexity. The approach is based on the true abstraction of the problem. The quantum program is expressed in terms of a high-level model together…
Physical social encounters are governed by a set of socio-psychological behavioral rules with a high degree of uniform validity. Past research has shown how these rules or the resulting properties of the encounters (e.g. the geometry of…