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Supercooled water is expected to exhibit a liquid--liquid phase transition between low- and high-density liquid states, possibly terminating in a liquid--liquid critical point in the experimentally difficult no man's land. Because the…

Accurate simulations of atomistic systems from first principles are limited by computational cost. In high-throughput settings, machine learning can reduce these costs significantly by accurately interpolating between reference…

Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…

Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…

In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…

Understanding the mechanisms underlying crystal formation is crucial. For most systems, crystallization typically goes through a nucleation process that involves dynamics that happen at short time and length scales. Due to this, molecular…

In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…

In recent decades, computer simulations have found increasingly widespread use as powerful tools of studying phase transitions in wide variety of systems. In the particular and very important case of aqueous systems, the commonly used…

Algebraic or geometric multigrid methods are commonly used in numerical solvers as they are a multi-resolution method able to handle problems with multiple scales. In this work, we propose a modification to the commonly-used U-Net neural…

Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…

Ice nucleation is a process of great relevance in physics, chemistry, technology and environmental sciences, much theoretical and experimental efforts have been devoted to its understanding, but still it remains a topic of intense research.…

Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…

Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…

We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…

The solvation structures and ion dynamics of CaCl$_2$ aqueous electrolytes have been investigated using ab initio molecular dynamics simulations and molecular dynamics simulations with deep learning potentials. We found multiple solvation…

Crystallization is one of the most important physicochemical processes which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental…

The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…

In this study, molecular dynamic simulations are employed to investigate the nucleation of NaCl crystal in solutions. According to the simulations, the dissolved behaviors of NaCl in water are dependent on ion concentrations. With…

The interplay between crystal nucleation and the structure of the metastable fluid has been a topic of significant debate over recent years. In particular, it has been suggested that even in simple model systems such as hard or charged…

The main subject of this thesis rests on the study ---at different levels of description--- of instabilities in systems which are driven, i.e., maintained far from equilibrium by an external forcing. We focus here on two main classes,…