Nanocapillaries combined with optical tweezers as a single molecule technique for studying DNA-protein complexes

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Mitochondria play essential metabolic roles and are increasingly understood to interact with other organelles, influencing cellular function and disease. Primary cilia, as sensory and signalling organelles, are crucial for neuronal communication and functi ...

Although the dynamics of collisions between a molecule and a solid surface are ultimately quantum mechanical, decohering effects owing to the large number of interacting degrees of freedom typically obscure the wavelike nature of these events. However, a p ...

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

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Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial specie ...

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

This work focuses on understanding and identifying the drag forces applied to a rotary-wing Micro Aerial Vehicle (MAV). We propose a lumped drag model that concisely describes the aerodynamical forces the MAV is subject to, with a minimal set of parameters ...

The development of protein-tagging techniques such as SunTag has given unprecedented opportunities to measure translation dynamics in living cells. In this study we leveraged the SunTag system to investigate the regulatory role of translation elongation in ...

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

Pump-probe experiments with subfemtosecond resolution are the key to understanding electronic dynamics in quantum systems. Here we demonstrate the generation and control of subfemtosecond pulse pairs from a two-colour X-ray free-electron laser. By measurin ...

Hydrogen clathrate hydrates are ice-like crystalline substances in which hydrogen molecules are trapped inside polyhedral cages formed by the water molecules. Small cages can host only a single H-2 molecule, while each large cage can be occupied by up to f ...

Nanocapillaries combined with optical tweezers as a single molecule technique for studying DNA-protein complexes

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Quantum interference observed in state-resolved molecule-surface scattering

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Mechanisms and functions of protein S-acylation

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Computational drug development for membrane protein targets

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Lumped Drag Model Identification and Real-Time External Force Detection for Rotary-Wing Micro Aerial Vehicles

Characterisation of EIF5A perturbations on ribosome dynamics with single-molecule imaging

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Experimental demonstration of attosecond pump-probe spectroscopy with an X-ray free-electron laser

Large-cage occupation and quantum dynamics of hydrogen molecules in sII clathrate hydrates