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Ivano Tavernelli

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Publications associées (123)

Two Misfolding Routes for the Prion Protein around pH 4.5

Ursula Röthlisberger, Ivano Tavernelli

Using molecular dynamics simulations, we show that the prion protein (PrP) exhibits a dual behavior, with two possible transition routes, upon protonation of H187 around pH 4.5, which mimics specific conditions encountered in endosomes. Our results suggest ...

Public Library Science2013

On trajectory-based nonadiabatic dynamics: Bohmian dynamics versus trajectory surface hopping

Ivano Tavernelli, Basile Curchod

In this work, we present a complete derivation of the NonAdiabatic Bohmian DYnamics (NABDY) equations of motion. This approach naturally emerges from a transformation of the molecular time-dependent Schrodinger equation in the adiabatic representation of t ...

Amer Inst Physics2013

Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Manuel Dömer, Thomas James Penfold

We present an ab initio Born-Oppenheimer molecular dynamics study of the early time solvent dynamics after electron abstraction from aqueous iodide. An initial response occurs within ∼75 fs, corresponding to a water molecule sharing almost one electron wit ...

Elsevier2013

Local Control Theory using Trajectory Surface Hopping and Linear-Response Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold

The implementation of local control theory using nonadiabatic molecular dynamics within the framework of linear-response time-dependent density functional theory is discussed. The method is applied to study the photoexcitation of lithium fluoride, for whic ...

Schweizerische Chemische Gesellschaft2013

Solvent Induced Luminescence Quenching: Static and Time-Resolved X-Ray Absorption Spectroscopy of a Copper(I) Phenanthroline Complex

Majed Chergui, Olivier Christian Bräm, Ursula Röthlisberger, Ivano Tavernelli, Frederico Alves Lima, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold, Lotta Susanne Karlsson, Jochen Rittmann, Gloria Capano

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) (Cu(dmp)(2); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photolumi ...

Amer Chemical Soc2013

Nonadiabatic ab initio molecular dynamics using linear-response time-dependent density functional theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold

We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we descr ...

Versita2013

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos

Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of ...

Amer Chemical Soc2013

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules

Ivano Tavernelli, Basile Curchod

Recent advances in algorithms and computational hardware have enabled the calculation of excited states with time-dependent density functional theory (TDDFT) for large systems of O(1000) atoms. Unfortunately, the aqueous charge transfer problem in TDDFT (w ...

American Chemical Society2013

Ab initio-driven trajectory-based nuclear quantum dynamics in phase space

Ivano Tavernelli

We derive a Bohmian trajectory-based quantum dynamics approach for the calculation of adiabatic and nonadiabatic quantum effects in ab initio on-the-fly molecular dynamics simulations. The method is designed for calculations in the full, unconstrained, pha ...

Amer Physical Soc2013

Intricacies of Describing Weak Interactions involving Halogen Atoms within Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Manuel Dömer

In this work we assess the performance of different dispersion-corrected DFT approaches (M06, M06-2X, DFT-D3 and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers (X2)2 and X2-Ar (for X=F,Cl,Br,I ...

Amer Chemical Soc2013

Prion versus Doppel Protein Misfolding: New Insights from Replica-Exchange Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli

The doppel (Dpl) and prion (PrP) proteins share a very similar fold (three helices and two short beta-strands), while they differ significantly in sequence (only 25% homologous) and in disease-related beta-rich conformations that occur for PrP only. In a p ...

American Chemical Society2013

In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion

Ursula Röthlisberger, Ivano Tavernelli, Manuel Dömer, Elisa Liberatore

The parameterisation of accurate and transferable repulsive potentials is a key ingredient for the self-consistent-charge density functional tight-binding method (SCC-DFTB). In the conventional parameterisation scheme the balanced description of different ...

Taylor & Francis2013

A wavelet analysis for the X-ray absorption spectra of molecules

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Amal El Nahhas, Marco Eli Reinhard, Thomas James Penfold

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to ...

American Institute of Physics2013

Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecula ...

Wiley-Blackwell2013

Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Oleg Boyarkine, Thomas Rizzo, Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Natalia Nagornova, Manuel Dömer

We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test ...

Wiley-Blackwell2013

Photodynamics of Lys+-Trp Protein Motifs: Hydrogen Bonds Ensure Photostability

Ursula Röthlisberger, Ivano Tavernelli, Matteo Guglielmi, Manuel Dömer

Cation-pi interactions such as Lys(+)-Trp, are highly abundant structural motifs in proteins. Both, experimental and theoretical studies of small prototypical gas phase systems, H(+)Trp, H(+)Trp center dot(H2O)(n) and H+ Gly-Trp, indicate such an arrangeme ...

Royal Soc Chemistry2013

Molecular Engineering of a Fluorene Donor for Dye-Sensitized Solar Cells

Michael Graetzel, Jacques-Edouard Moser, Mohammad Khaja Nazeeruddin, Robin Humphry-Baker, Joël Teuscher, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Negar Ashari Astani, Aswani Yella, Julien Edouard Frey, Simon Mathew, Lauren Elizabeth Polander

To improve their efficiency beyond the state-of-the-art, D-pi-A dyes must display increased spectral breadth and account for the physical limitations observed in the dye. sensitized solar cells. In particular, they should be designed to control the electro ...

Amer Chemical Soc2013

Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells

Two D−π−A dyes based on the dithieno[3,2-b:2′,3′-d]pyrrole π-bridge (DTP) were synthesized, characterized using UV−vis absorption spectroscopy and electrochemistry, modeled using quantum chemical calculations, and used as sensitizers in dye-sensitized sola ...

Amer Chemical Soc2013

Excited State Dynamics with Quantum Trajectories

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod

Nuclear quantum dynamics beyond the Born-Oppenheimer approximation is performed using quantum trajectories. Within the adiabatic representation of the electronic states, NABDY (NonAdiabatic Bohmian DYnamics) is used in combination with DFT and LR-TDDFT to ...

Schweizerische Chemische Gesellschaft2012

Structure and dynamics of liquid water from ab initio molecular dynamics - Comparison of BLYP, PBE and revPBE density functionals with and without van der Waals corrections

Ursula Röthlisberger, Ivano Tavernelli, I-Chun Lin

We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using ab initio molecular dynamics simulations with density functional theor ...

Amer Chemical Soc2012

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