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Ursula Röthlisberger

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Publications associées (291)

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Ursula Röthlisberger, Paolo Carloni, Simone Meloni, Martin Peter Bircher, Jógvan Magnus Olsen, Viacheslav Bolnykh

We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computatio ...

2019

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Ursula Röthlisberger, Paolo Carloni, Siri Camee van Keulen, Daniele Narzi

Author summary Adenylyl cyclases (ACs) are enzymes that can translate extracellular signals into the intracellular molecule cAMP, which is thus a 2nd messenger of extracellular events. The brain expresses nine membrane-bound AC variants, and AC5 is the dom ...

2019

Crosslinking Allosteric Sites on the Nucleosome

Paul Joseph Dyson, Ursula Röthlisberger, Thibaud Edouard Alistair von Erlach, Lucinda Kate Batchelor

Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleos ...

Wiley-VCH Verlag GmbH2019

Pre-mRNA Splicing: The Gene Maturation Symphony of the Intron Lariat Spliceosome Revealed by Molecular Dynamics Simulations

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

CELL PRESS2019

Association of Both Inhibitory and Stimulatory G alpha Subunits Implies Adenylyl Cyclase 5 Deactivation

Ursula Röthlisberger, Siri Camee van Keulen, Daniele Narzi

Adenylyl cyclase (AC) generates cyclic AMP required for a variety of cellular functions, and its regulation plays a major role in cellular signal transduction in eukaryotes and prokaryotes. All membrane-bound AC isoforms in eukaryotes can be activated by s ...

AMER CHEMICAL SOC2019

Shedding Light on the Basis Set Dependence of the Minnesota Functionals: Differences Between Plane Waves, Slater Functions, and Gaussians

Ursula Röthlisberger, Pablo Lopez Tarifa, Martin Peter Bircher

The Minnesota family of exchange-correlation (xc) functionals are among the most popular, accurate, and abundantly used functionals available to date. However, their use in plane-wave based first-principles MD has been limited by their sparse availability. ...

2019

Cu–Al Spinel as a Highly Active and Stable Catalyst for the Reverse Water Gas Shift Reaction

Ursula Röthlisberger, Jeremy Luterbacher, Christophe Jean Baranowski, Oliver Kröcher, Florent Emmanuel Héroguel, Alimohammad Bahmanpour, Murat Kiliç

The reverse water gas shift reaction is considered to be a highly attractive catalytic route for CO2 recycling in a future sustainable economy. Copperbased catalysts are commonly used for this reaction due to their high activity and selectivity. However, t ...

2019

All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

National Academy of Sciences2018

Publisher's Note: “Implications of short time scale dynamics on long time processes” (Struct. Dyn. 4, 061507 (2017)]

Majed Chergui, Ursula Röthlisberger, Luigi Bonacina, Cédric Schmidt, Swarnendu Bhattacharyya

2018

Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations

Ursula Röthlisberger, Martin Peter Bircher

2018

Plane-Wave Implementation and Performance of à-la-Carte Coulomb-Attenuated Exchange-Correlation Functionals for Predicting Optical Excitation Energies in Some Notorious Cases

Ursula Röthlisberger, Martin Peter Bircher

2018

A Versatile Multiple Time Step Scheme for Efficient ab Initio Molecular Dynamics Simulations

Ursula Röthlisberger, Rocco Meli, Elisa Liberatore

2018

Effect of graphene oxide nanosheets on visible light-assisted antibacterial activity of vertically-aligned copper oxide nanowire arrays

Ursula Röthlisberger, Negar Ashari Astani, Ehsan Hashemi, Fateme Kiani Shahvandi

2018

A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein

Rudolf Hovius, Ursula Röthlisberger, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

The development of thermostable and solvent-tolerant metalloproteins is a long-sought goal for many applica- tions in synthetic biology and biotechnology. In this work, we were able to engineer a highly thermo- and organic solvent- stable metallo variant o ...

2018

The Structure of the Protonated Serine Octamer

Thomas Rizzo, Ursula Röthlisberger, Aurelien Stephen Arnaud Gregor, Marta Andreia Da Silva Perez, Valeriu Scutelnic, Stephan Warnke, Carsten Baldauf

The amino acid serine has long been known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretica ...

2018

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Sara Bonella, Mohammadhassan Valadan

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime ...

2017

Nonadiabatic effects in electronic and nuclear dynamics

Majed Chergui, Ursula Röthlisberger, Jiri Vanicek, Aurélien Kevin Fabrice Patoz, Tomas Zimmermann, Elisa Liberatore, Nicholas John Browning, Martin Peter Bircher

Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by th ...

2017

Stabilization of the Perovskite Phase of Formamidinium Lead Triiodide by Methylammonium, Cs, and/or Rb Doping

Ursula Röthlisberger, Michael Saliba, Olga Syzgantseva

In this work we perform a computational study comparing the influence of monovalent cation substitution by methylammonium (MA(+)), cesium (Cs+), and rubidium (Rb+) on the properties of formamidinium lead triiodide (FAPbI(3))based perovskites. The relative ...

2017

Charge separation and carrier dynamics in donor-acceptor heterojunction photovoltaic systems

Jacques-Edouard Moser, Majed Chergui, Joël Teuscher, Jean-Pierre Wolf, Ursula Röthlisberger, Jan Cornelius Brauer, Alicia Solano, Natalie Renuka Banerji, Ariadni Boziki

Electron transfer and subsequent charge separation across donor-acceptor heterojunctions remain the most important areas of study in the field of third-generation photovoltaics. In this context, it is particularly important to unravel the dynamics of indiv ...

2017

Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

The vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intr ...

2017

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