Nucleic acid structure determination

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Advanced Computational Methods for NMR Crystallography

Knowledge of the atomic-level structure is key to understanding and predicting properties of materials. X-ray diffraction (XRD) is the methods of choice for structures containing well-defined long-range order. However, many materials contain various degree ...

EPFL2019

Quantifying the Limits of Detection of Surface-Enhanced Infrared Spectroscopy with Grating Order-Coupled Nanogap Antennas

Hatice Altug, Andreas Tittl, Aurélian Michel John-Herpin

Infrared spectroscopy is widely used for biomolecular studies, but struggles when investigating minute quantities of analytes due to the mismatch between vibrational cross sections and IR wavelengths. It is therefore beneficial to enhance absorption signal ...

2018

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A

Oleg Boyarkine, Aleksandr Pereverzev

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with s ...

Royal Society of Chemistry2017

Molecular Imaging of Biopolymers Enabled by Electrospray-Ion Beam Deposition

Sabine Abb

Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of ye ...

EPFL2017

Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process

Françoise Gisou van der Goot Grunberg, Matteo Dal Peraro, Mircea Ioan Iacovache, Nuria Cirauqui Diaz

Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-s ...

Nature Publishing Group2016

Probing chemical structures and physical processes with nanopores

Jiandong Feng

This thesis develops and applies the nanopore tool to probe chemical structures and physical processes at the single-molecule level: from single ions to DNA molecules. Nanopore experiments electrically measure the ionic transport through the pore and its m ...

EPFL2016

Discriminative adsorption of amphiphilic monolayer protected gold nanoparticles on amyloid fibers

Paulo Henrique Jacob Silva

This thesis presents a systematic study of how different types monolayer-protected AuNPs interact with amyloid fibers. We report a class of amphiphilic gold nanoparticles capable of adsorbing onto specific surface features on these types of protein fibers. ...

EPFL2016

'Seeing' Atoms: The Crystallographic Revolution

Dieter Schwarzenbach

Laue's experiment in 1912 of the diffraction of X-rays by crystals led to one of the most influential discoveries in the history of science: the first determinations of crystal structures, NaCl and diamond in particular, by W. L. Bragg in 1913. For the fir ...

Swiss Chemical Soc2014

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Fabio Pietrucci

We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially des ...

2012

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Fabio Pietrucci

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are dif ...

2011

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Quantifying the Limits of Detection of Surface-Enhanced Infrared Spectroscopy with Grating Order-Coupled Nanogap Antennas

Hatice Altug, Andreas Tittl, Aurélian Michel John-Herpin

2018