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New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

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Nonadiabatic Molecular Dynamics Simulations: Synergies between Theory and Experiments

Ivano Tavernelli

CONSPECTUS: Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by ...

Amer Chemical Soc2015

The physical chemical principles underlying,enzymatic thermostability are keys to understand the way evolution has shaped proteins,to adapt to a broad range of temperatures. Understanding the molecular determinants at the basis of protein thermostability i ...

Amer Chemical Soc2015

A virtual or in silico screening approach makes it much easier to identify the molecular structure that best combines efficacy for a specific task with safety and minimum environmental or health impacts. In this approach, software is used to generate a lar ...

Royal Soc Chemistry2015

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

Alessandro Barducci

Molecular chaperones are an essential part of the machinery that avoids protein aggregation and misfolding in vivo. However, understanding the molecular basis of how chaperones prevent such undesirable interactions requires the conformational changes withi ...

Natl Acad Sciences2014

Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013

Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins

Matteo Dal Peraro, Michele Cascella, Matteo Thomas Degiacomi, Davide Alemani, Enrico Spiga

We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, p ...

Amer Chemical Soc2013

Programming Hierarchical Supramolecular Nanostructures by Molecular Design

Klaus Kern, Magalí Alejandra Lingenfelder, Giovanni Costantini

Supramolecular nanostructures with tunable dimensionalities are fabricated by deposition of benzene carboxylic acids on the Cu(110) surface. By tailoring the number and position of the functional moieties, the structure of the final molecular assemblies ca ...

Amer Chemical Soc2013

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism

Henning Paul-Julius Stahlberg, Françoise Gisou van der Goot Grunberg, Matteo Dal Peraro, Matteo Thomas Degiacomi

Aerolysin is the founding member of a superfamily of (beta-pore-forming toxins whose pore structure is unknown. We have combined X-ray crystallography, cryo-EM, molecular dynamics and computational modeling to determine the structures of aerolysin mutants ...

Nature Publishing Group2013

Integrated Plasmonic NanoBiosensors

Hatice Altug, Serap Aksu

We will demonstrate plasmonic and metamaterial based integrated nano-biosensors and ultrasensitive infrared absorption spectroscopy. These systems by enabling monitoring of molecular-protein interactions in real-time within aqueous solutions can be importa ...

IEEE2013

Molecular Modeling of Bacterial Nanomachineries

Matteo Thomas Degiacomi

Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...

EPFL2012