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The development of a quasi-linear gyrokinetic transport model for tokamak plasmas, ultimately designed to provide physically comprehensive predictions of the time evolution of the thermodynamic relevant quantities, is a task that requires…
We report about a study of the ordinary muon capture in nuclei belonging to the sd shell, an electroweak process that occurs with exchange momenta far larger than ordinary beta decays (approximately 100 MeV). Such a characteristic places…
Plasma technology has found widespread applications in numerous domains, yet the techniques to manipulate plasma transport predominantly rely on magnetic control. In this review, we present a streamlined diffusion-migration method to…
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 introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
The method of using neural networks (NNs) for turbulent transport prediction in a simplified model of tokamak plasmas is explored. The NNs are trained on a database obtained via test-particle simulations of a transport model in the…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Electroporation method is a useful tool for delivering drugs into various diseased tissues in the human body. As a result of an applied electric field, drug particles enter the intracellular compartment through the temporarily permeabilized…
Collective cell migration is a multicellular phenomenon that arises in various biological contexts, including cancer and embryo development. "Collectiveness" can be promoted by cell-cell interactions such as co-attraction and contact…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather…
The nature of light-induced structures in attosecond transient absorption spectroscopy of molecular systems is investigated theoretically. It is shown how nuclear dynamics affect these structures. We find that a theoretical three-surface…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
The radiative capture process $n p \to d \gamma$ is considered within the framework of a recently developed six-quark dressed-bag model for the nucleon-nucleon interaction. The calculations presented here include both the nucleon current…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
This thesis provides an overview of an approach to quantum simulations using magnesium-25 ions stored in a linear Paul trap as the carriers of quantum information. Their quantum state is manipulated and read out using ultraviolet laser…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
It is increasingly common to encounter data from dynamic processes captured by static cross-sectional measurements over time, particularly in biomedical settings. Recent attempts to model individual trajectories from this data use optimal…
The electron spin transport in condensed matter, Spintronics, is a subject of rapidly growing interest both scientifically and from the point of view of applications to modern and future electronics. In many cases the electron spin…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…