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Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts…
The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new…
High-fidelity electron microscopy simulations required for quantitative crystal structure refinements face a fundamental challenge: while physical interactions are well-described theoretically, real-world experimental effects are…
Dynamical structural defects exist naturally in a wide variety of solids. They fluctuate temporally, and hence can deteriorate the performance of many electronic devices. Thus far, the entities of such dynamic objects have been identified…
The stochastic dynamics of small elastic objects in fluid are central to many important and emerging technologies. It is now possible to measure and use the higher modes of motion of elastic structures when driven by Brownian motion alone.…
Discrete element modelling (DEM) is one of the most efficient computational approaches to the fracture processes of heterogeneous materials on mesoscopic scales. From the dynamics of single crack propagation through the statistics of crack…
Electron tomography has become a commonly used tool to investigate the three-dimensional (3D) structure of nanomaterials, including colloidal nanoparticle assemblies. However, electron microscopy is typically carried out under high vacuum…
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the…
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current…
Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which…
In this thesis, a computational framework for microstructural modelling of transverse behaviour of heterogeneous materials is presented. The context of this research is part of the broad and active field of Computational Micromechanics,…
Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
Cryo-electron microscopy (cryo-EM) enables single-particle analysis of biological macromolecules under strict low-dose imaging conditions, but the resulting micrographs often exhibit extremely low signal-to-noise ratios and weak particle…
Non-equilibrium assembly, driven by fluxes controllable by continuous external energy inputs, enables dynamic and reconfigurable structures. Such controlled 3D assembly is desired for the design of adaptive materials that exploit…
In the past decade, deep conditional generative models have revolutionized the generation of realistic images, extending their application from entertainment to scientific domains. Single-particle cryo-electron microscopy (cryo-EM) is…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
FEMSIM, a Fortran code, has been developed to simulate the fluctuation electron microscopy signal, the variance, V(k), from a model atomic structure. FEMSIM has been incorporated into a hybrid-reverse Monte Carlo code that combines an…
Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly…
Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological…