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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…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little…
Static disorder plays a crucial role in the electronic dynamics and spectroscopy of complex molecular systems. Traditionally, obtaining observables averaged over static disorder requires thousands of realizations via direct sampling of the…
We describe how Monte Carlo simulation within the grand canonical ensemble can be applied to the study of phase behaviour in polydisperse fluids. Attention is focused on the case of fixed polydispersity in which the form of the `parent'…
In a recent experiment [Vochezer {\it et al.,} Phys. Rev. Lett. \textbf{120}, 073602 (2018)], a novel kind of hybrid atom-opto-mechanical system has been realized by coupling atoms in a lattice to a membrane. While such system promises a…
The advances in materials and biological sciences have necessitated the use of molecular simulations to study polymers. The Markov chain Monte Carlo simulations enable the sampling of relevant microstates of polymeric systems by traversing…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
We present a multilevel Monte Carlo simulation method for analysing multi-scale physical systems via a hierarchy of coarse-grained representations, to obtain numerically-exact results, at the most detailed level. We apply the method to a…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
Real-time satellite imaging has a central role in monitoring, detecting and estimating the intensity of key natural phenomena such as floods, earthquakes, etc. One important constraint of satellite imaging is the trade-off between…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…