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The driving of vibrational motion by external electric fields is a topic of continued interest, due to the possibility of assessing new or metastable material phases with desirable properties. Here, we combine ab initio molecular dynamics…
Molecular crystals play a central role in a wide range of scientific fields, including pharmaceuticals and organic semiconductor devices. However, they are challenging systems to model accurately with computational approaches because of a…
Electrostatic correlations play an important role in physics, chemistry and biology. In plasmas they lead to thermodynamic instability similar to the liquid-gas phase transition of simple molecular fluids. For charged colloidal suspensions…
We present a non-reactive force field for molecular dynamics simulations of interfaces between passivated amorphous surfaces and their interaction with water. The force field enables large-scale dynamic simulations of dry and lubricated…
The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
We investigate the role of the Coulomb interaction in strong field processes. We find that the Coulomb field of the ion makes its presence known even in highly intense laser fields, in contrast to the assumptions of the strong field…
Plasmonic nanocavities enable the confinement of molecules and electromagnetic fields within nano-metric volumes. As a consequence, the molecules experience a remarkably strong interaction with the electromagnetic field, to such an extent…
The electric microfield distribution at charged particles is studied for two-component electron-ion plasmas using molecular dynamics simulation and theoretical models. The particles are treated within classical statistical mechanics using…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
This perspective paper deals with an overview of particle-in-cell / Monte Carlo collision models applied to different plasma-propulsion configurations and scenarios, from electrostatic (E x B and pulsed arc) devices to electromagnetic (RF…
Electric field plays an important role in ferroelectric phase transition. There have been numerous phase field formulations attempting to account for electrostatic interactions subject to different boundary conditions. In this paper, we…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
We consider a phase field crystal modeling approach for binary mixtures of interacting active and passive particles. The approach allows to describe generic properties for such systems within a continuum model. We validate the approach by…
Previous studies have used numerical methods to optimize the hyperpolarizability of a one-dimensional quantum system. These studies were used to suggest properties of one-dimensional organic molecules, such as the degree of modulation of…
We study the ionic distribution near a charged surface. A new method for performing Monte Carlo simulations in this geometry is discussed. A theory is then presented that allows us to accurately reproduce the density profiles obtained in…
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory for an efficient and accurate description of the electrostatic interactions between molecules and…
Particle-in-Cell (PIC) methods employ particle representations of unknown fields, but also employ continuum fields for other parts of the problem. Thus projection between particle and continuum bases is required. Moreover, we often need to…
Interactions between crawling cells, which are essential for many biological processes, can be quantified by measuring cell-cell collisions. Conventionally, experiments of cell-cell collisions are conducted on two-dimensional flat…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…