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Multiscale Simulations for Biological Signaling and Biomimetic Design

English title Multiscale Simulations for Biological Signaling and Biomimetic Design
Applicant Röthlisberger Ursula
Number 146645
Funding scheme Project funding (Div. I-III)
Research institution Laboratoire de chimie et biochimie computationnelles EPFL - SB - ISIC - LCBC
Institution of higher education EPF Lausanne - EPFL
Main discipline Physical Chemistry
Start/End 01.05.2013 - 30.04.2016
Approved amount 548'363.00
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Keywords (8)

Computational Biophysics; G-protein coupled receptors; QM/MM Car-Parrinello/TDDFT; Biological Signalling; multiscale modelling; Biomimetic Design; Biochemistry; Computational Chemistry

Lay Summary (French)

Lead
Approches de simulation à plusieurs échelles appliquées à la signalisation biologique et au design bio-inspirée
Lay summary

Par le truchement de millions d’années d’évolution, la nature a développé des processus aptes à maintenir des écosystèmes hautement efficaces et stables. Il n’est donc pas surprenant d’y puiser notre inspiration afin de développer des stratégies durables visant à produire des ressources matérielles et énergétiques dont la population mondiale grandissante a besoin. Cependant, une compréhension complète des fonctionnements internes de processus biologiques est très fréquemment une tâche ardue, vu que ce sont des événements complexes pouvant impliquer plusieurs ordres de grandeur tant en temps qu’en dimension et que les techniques expérimentales testant leur mode d’action ne fournissent souvent que des informations partielles ou indirectes.

La simulation par ordinateur donne de nos jours un aperçu direct de ces mécanismes biomoléculaires, mais la combinaison d’une taille étendue, d’un large espace des configurations disponibles et d’une haute précision, nécessaire afin de décrire les différences d’énergie faible de l’ordre de kT, reste un défi.

Dans cette recherche, nous proposons de (1) Repousser les limites courantes des simulations biologiques à plusieurs échelles, grâce au développement d’une approche hybride généralisée QM/(QM)/MM qui sera capable de résoudre simultanément l’exigence liée à la précision nécessaire en taille et en temps; (2) Développer et implémenter des techniques d’analyses de données efficaces et systématiques, basées sur la sélection de caractéristiques et l’inférence causale, qui nous permettront d’identifier les facteurs cruciaux responsables d’une transformation biologique donnée; (3) Utiliser cette information afin de guider la conception de systèmes bio-inspirés et (4) Optimiser les systèmes biomimétiques afin d’obtenir des propriétés sur mesure en utilisant l’exploration efficace d’un espace chimique grâce à des algorithmes évolutionnistes.

Direct link to Lay Summary Last update: 08.04.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations
Bircher Martin P., Rothlisberger Ursula (2018), Exploiting Coordinate Scaling Relations To Accelerate Exact Exchange Calculations, in The Journal of Physical Chemistry Letters, 9(14), 3886-3890.
A Versatile Multiple Time Step Scheme for Efficient ab Initio Molecular Dynamics Simulations
Liberatore Elisa, Meli Rocco, Rothlisberger Ursula (2018), A Versatile Multiple Time Step Scheme for Efficient ab Initio Molecular Dynamics Simulations, in Journal of Chemical Theory and Computation, 14(6), 2834-2842.
Plane-Wave Implementation and Performance of à-la-Carte Coulomb-Attenuated Exchange-Correlation Functionals for Predicting Optical Excitation Energies in Some Notorious Cases
Bircher Martin P., Rothlisberger Ursula (2018), Plane-Wave Implementation and Performance of à-la-Carte Coulomb-Attenuated Exchange-Correlation Functionals for Predicting Optical Excitation Energies in Some Notorious Cases, in Journal of Chemical Theory and Computation, 14(6), 3184-3195.
Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein
Bozkurt Esra, Perez Marta A. S., Hovius Ruud, Browning Nicholas J., Rothlisberger Ursula (2018), Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein, in Journal of the American Chemical Society, 140(13), 4517-4521.
Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective
Bozkurt Esra, Soares Thereza A., Rothlisberger Ursula (2017), Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective, in Journal of Chemical Theory and Computation, 13(12), 6382-6390.
Computational Characterization of the Dependence of Halide Perovskite Effective Masses on Chemical Composition and Structure
Ashari-Astani Negar, Meloni Simone, Salavati Amir Hesam, Palermo Giulia, Grätzel Michael, Rothlisberger Ursula (2017), Computational Characterization of the Dependence of Halide Perovskite Effective Masses on Chemical Composition and Structure, in The Journal of Physical Chemistry C, 121(43), 23886-23895.
How Rhodopsin Tunes the Equilibrium between Protonated and Deprotonated Forms of the Retinal Chromophore
van Keulen Siri C., Solano Alicia, Rothlisberger Ursula (2017), How Rhodopsin Tunes the Equilibrium between Protonated and Deprotonated Forms of the Retinal Chromophore, in Journal of Chemical Theory and Computation, 13(9), 4524-4534.
Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties
Browning Nicholas J., Ramakrishnan Raghunathan, von Lilienfeld O. Anatole, Roethlisberger Ursula (2017), Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties, in The Journal of Physical Chemistry Letters, 8(7), 1351-1359.
Stabilization of the Perovskite Phase of Formamidinium Lead Triiodide by Methylammonium, Cs, and/or Rb Doping
Syzgantseva Olga A., Saliba Michael, Grätzel Michael, Rothlisberger Ursula (2017), Stabilization of the Perovskite Phase of Formamidinium Lead Triiodide by Methylammonium, Cs, and/or Rb Doping, in The Journal of Physical Chemistry Letters, 8(6), 1191-1196.
Does Proton Conduction in the Voltage-Gated H + Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues?
van Keulen Siri C., Gianti Eleonora, Carnevale Vincenzo, Klein Michael L., Rothlisberger Ursula, Delemotte Lucie (2017), Does Proton Conduction in the Voltage-Gated H + Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues?, in The Journal of Physical Chemistry B, 121(15), 3340-3351.
Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO 2
Brunk Elizabeth, Perez Marta A. S., Athri Prashanth, Rothlisberger Ursula (2016), Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO 2, in ChemPhysChem, 17(23), 3831-3835.
Origin of unusual bandgap shift and dual emission in organic-inorganic lead halide perovskites
Dar M. I., Jacopin G., Meloni S., Mattoni A., Arora N., Boziki A., Zakeeruddin S. M., Rothlisberger U., Gra tzel M. (2016), Origin of unusual bandgap shift and dual emission in organic-inorganic lead halide perovskites, in Science Advances, 2(10), e1601156-e1601156.
Extended Intermolecular Interactions Governing Photocurrent–Voltage Relations in Ternary Organic Solar Cells
Tress Wolfgang, Beyer Beatrice, Ashari Astani Negar, Gao Feng, Meloni Simone, Rothlisberger Ursula (2016), Extended Intermolecular Interactions Governing Photocurrent–Voltage Relations in Ternary Organic Solar Cells, in The Journal of Physical Chemistry Letters, 7(19), 3936-3944.
Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
Casalino Lorenzo, Palermo Giulia, Rothlisberger Ursula, Magistrato Alessandra (2016), Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns, in Journal of the American Chemical Society, 138(33), 10374-10377.
Ionic polarization-induced current–voltage hysteresis in CH3NH3PbX3 perovskite solar cells
Meloni Simone, Moehl Thomas, Tress Wolfgang, Franckevičius Marius, Saliba Michael, Lee Yong Hui, Gao Peng, Nazeeruddin Mohammad Khaja, Zakeeruddin Shaik Mohammed, Rothlisberger Ursula, Graetzel Michael (2016), Ionic polarization-induced current–voltage hysteresis in CH3NH3PbX3 perovskite solar cells, in Nature Communications, 7, 10334-10334.
Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics
Dreyer Jens, Brancato Giuseppe, Ippoliti Emiliano, Genna Vito, De Vivo Marco, Carloni Paolo, Rothlisberger Ursula (2016), Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics, in Tunon Inaki, Moliner Vicent (ed.), Royal Society of Chemistry, Cambridge, 294-339.
Synthesis, characterization and ab initio investigation of a panchromatic ullazine–porphyrin photosensitizer for dye-sensitized solar cells
Mathew Simon, Astani Negar Ashari, Curchod Basile F. E., Delcamp Jared H., Marszalek Magdalena, Frey Julien, Rothlisberger Ursula, Nazeeruddin Mohammad Khaja, Grätzel Michael (2016), Synthesis, characterization and ab initio investigation of a panchromatic ullazine–porphyrin photosensitizer for dye-sensitized solar cells, in Journal of Materials Chemistry A, 4(6), 2332-2339.
Valence and conduction band tuning in halide perovskites for solar cell applications
Meloni Simone, Palermo Giulia, Ashari-Astani Negar, Grätzel Michael, Rothlisberger Ursula (2016), Valence and conduction band tuning in halide perovskites for solar cell applications, in Journal of Materials Chemistry A, 4(41), 15997-16002.
The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase
Campomanes Pablo, Rothlisberger Ursula, Alfonso-Prieto Mercedes, Rovira Carme (2015), The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase, in Journal of the American Chemical Society, 137(34), 11170-11178.
Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets
Palermo Giulia, Bauer Inga, Campomanes Pablo, Cavalli Andrea, Armirotti Andrea, Girotto Stefania, Rothlisberger Ursula, De Vivo Marco (2015), Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets, in PLOS Computational Biology, 11(6), e1004231-e1004231.
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
Brunk Elizabeth, Rothlisberger Ursula (2015), Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States, in Chemical Reviews, 115(12), 6217-6263.
Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling
Aseev Oleg, Perez Marta A. S., Rothlisberger Ursula, Rizzo Thomas R. (2015), Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling, in The Journal of Physical Chemistry Letters, 6(13), 2524-2529.
In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO 2 Surface of Dye-Sensitized Solar Cells
Voïtchovsky Kislon, Ashari-Astani Negar, Tavernelli Ivano, Tétreault Nicolas, Rothlisberger Ursula, Stellacci Francesco, Grätzel Michael, Harms Hauke A. (2015), In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO 2 Surface of Dye-Sensitized Solar Cells, in ACS Applied Materials & Interfaces, 7(20), 10834-10842.
Computational insights into function and inhibition of fatty acid amide hydrolase
Palermo Giulia, Rothlisberger Ursula, Cavalli Andrea, De Vivo Marco (2015), Computational insights into function and inhibition of fatty acid amide hydrolase, in European Journal of Medicinal Chemistry, 91, 15-26.
Lessons from Nature: Computational Design of Biomimetic Compounds and Processes
Bozkurt Esra, Ashari Negar, Browning Nicholas, Brunk Elizabeth, Campomanesa Pablo, Perez Marta A. S., Rothlisberger Ursula (2014), Lessons from Nature: Computational Design of Biomimetic Compounds and Processes, in CHIMIA International Journal for Chemistry, 68(9), 642-647.
Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion
Palermo Giulia, Campomanes Pablo, Cavalli Andrea, Rothlisberger Ursula, De Vivo Marco (2014), Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion, in The Journal of Physical Chemistry B, 119(3), 789-801.
A Mechanochemical Switch to Control Radical Intermediates
Brunk Elizabeth, Kellett Whitney F., Richards Nigel G. J., Rothlisberger Ursula (2014), A Mechanochemical Switch to Control Radical Intermediates, in Biochemistry, 53(23), 3830-3838.
Study of the Redox Properties of Singlet and Triplet Tris(2,2′-bipyridine)ruthenium(II) ([Ru(bpy) 3 ] 2+ ) in Aqueous Solution by Full Quantum and Mixed Quantum/Classical Molecular Dynamics Simulations
Diamantis Polydefkis, Gonthier Jérôme Florian, Tavernelli Ivano, Rothlisberger Ursula (2014), Study of the Redox Properties of Singlet and Triplet Tris(2,2′-bipyridine)ruthenium(II) ([Ru(bpy) 3 ] 2+ ) in Aqueous Solution by Full Quantum and Mixed Quantum/Classical Molecular Dynamics Simulations, in The Journal of Physical Chemistry B, 118(14), 3950-3959.
Dye-sensitized solar cells with 13% efficiency achieved through the molecular engineering of porphyrin sensitizers
Mathew Simon, Yella Aswani, Gao Peng, Humphry-Baker Robin, Curchod Basile F. E., Ashari-Astani Negar, Tavernelli Ivano, Rothlisberger Ursula, Nazeeruddin Md. Khaja, Grätzel Michael (2014), Dye-sensitized solar cells with 13% efficiency achieved through the molecular engineering of porphyrin sensitizers, in Nature Chemistry, 6(3), 242-247.
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle
Campomanes Pablo, Neri Marilisa, Horta Bruno A. C., Röhrig Ute F., Vanni Stefano, Tavernelli Ivano, Rothlisberger Ursula (2014), Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle, in Journal of the American Chemical Society, 136(10), 3842-3851.
Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations
Campomanes Pablo, Kellett Whitney F., Easthon Lindsey M., Ozarowski Andrew, Allen Karen N., Angerhofer Alexander, Rothlisberger Ursula, Richards Nigel G. J. (2014), Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations, in Journal of the American Chemical Society, 136(6), 2313-2323.
Structure–property relationships based on Hammett constants in cyclometalated iridium( iii ) complexes: their application to the design of a fluorine-free FIrPic-like emitter
Frey Julien, Curchod Basile F. E., Scopelliti Rosario, Tavernelli Ivano, Rothlisberger Ursula, Nazeeruddin Mohammad K., Baranoff Etienne (2014), Structure–property relationships based on Hammett constants in cyclometalated iridium( iii ) complexes: their application to the design of a fluorine-free FIrPic-like emitter, in Dalton Trans., 43(15), 5667-5679.
Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory
Doemer Manuel, Tavernelli Ivano, Rothlisberger Ursula (2013), Intricacies of Describing Weak Interactions Involving Halogen Atoms within Density Functional Theory, in Journal of Chemical Theory and Computation, 9(2), 955-964.
Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis
Palermo Giulia, Campomanes Pablo, Neri Marilisa, Piomelli Daniele, Cavalli Andrea, Rothlisberger Ursula, De Vivo Marco (2013), Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis, in Journal of Chemical Theory and Computation, 9(2), 1202-1213.
In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion
Doemer Manuel, Liberatore Elisa, Knaup Jan M., Tavernelli Ivano, Rothlisberger Ursula (2013), In situ parameterisation of SCC-DFTB repulsive potentials by iterative Boltzmann inversion, in Molecular Physics, 111(22-23), 3595-3607.
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
Doemer Manuel, Maurer Patrick, Campomanes Pablo, Tavernelli Ivano, Rothlisberger Ursula (2013), Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin, in Journal of Chemical Theory and Computation, 10(1), 412-422.
Towards Compatibility between Ruthenium Sensitizers and Cobalt Electrolytes in Dye-Sensitized Solar Cells
Polander Lauren E., Yella Aswani, Curchod Basile F. E., Ashari Astani Negar, Teuscher Joël, Scopelliti Rosario, Gao Peng, Mathew Simon, Moser Jacques-E., Tavernelli Ivano, Rothlisberger Ursula, Grätzel Michael, Nazeeruddin Md. Khaja, Frey Julien (2013), Towards Compatibility between Ruthenium Sensitizers and Cobalt Electrolytes in Dye-Sensitized Solar Cells, in Angewandte Chemie International Edition, 52(33), 8731-8735.
Towards Compatibility between Ruthenium Sensitizers and Cobalt Electrolytes in Dye-Sensitized Solar Cells
Polander Lauren E., Yella Aswani, Curchod Basile F. E., Ashari Astani Negar, Teuscher Joël, Scopelliti Rosario, Gao Peng, Mathew Simon, Moser Jacques-E., Tavernelli Ivano, Rothlisberger Ursula, Grätzel Michael, Nazeeruddin Md. Khaja, Frey Julien (2013), Towards Compatibility between Ruthenium Sensitizers and Cobalt Electrolytes in Dye-Sensitized Solar Cells, in Angewandte Chemie International Edition, 52(33), 8731-8735.
Molecular Engineering of a Fluorene Donor for Dye-Sensitized Solar Cells
Yella Aswani, Humphry-Baker Robin, Curchod Basile F. E., Ashari Astani Negar, Teuscher Joël, Polander Lauren E., Mathew Simon, Moser Jacques-E., Tavernelli Ivano, Rothlisberger Ursula, Grätzel Michael, Nazeeruddin Md. Khaja, Frey Julien (2013), Molecular Engineering of a Fluorene Donor for Dye-Sensitized Solar Cells, in Chemistry of Materials, 25(13), 2733-2739.
Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells
Polander Lauren E., Yella Aswani, Teuscher Joël, Humphry-Baker Robin, Curchod Basile F. E., Ashari Astani Negar, Gao Peng, Moser Jacques-E., Tavernelli Ivano, Rothlisberger Ursula, Grätzel Michael, Nazeeruddin Md. Khaja, Frey Julien (2013), Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells, in Chemistry of Materials, 25(13), 2642-2648.
Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls
Valsson Omar, Campomanes Pablo, Tavernelli Ivano, Rothlisberger Ursula, Filippi Claudia (2013), Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls, in Journal of Chemical Theory and Computation, 9(5), 2441-2454.
Mechanism to Trigger Unfolding in O 6 -Alkylguanine-DNA Alkyltransferase
Brunk Elizabeth, Mollwitz Birgit, Rothlisberger Ursula (2013), Mechanism to Trigger Unfolding in O 6 -Alkylguanine-DNA Alkyltransferase, in ChemBioChem, 14(6), 703-710.
Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide
Doemer Manuel, Guglielmi Matteo, Athri Prashanth, Nagornova Natalia S., Rizzo Thomas R., Boyarkin Oleg V., Tavernelli Ivano, Rothlisberger Ursula (2013), Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide, in International Journal of Quantum Chemistry, 113(6), 808-814.
Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase
Kellett Whitney F., Brunk Elizabeth, Desai Bijoy J., Fedorov Alexander A., Almo Steven C., Gerlt John A., Rothlisberger Ursula, Richards Nigel G. J. (2013), Computational, Structural, and Kinetic Evidence That Vibrio vulnificus FrsA Is Not a Cofactor-Independent Pyruvate Decarboxylase, in Biochemistry, 52(11), 1842-1844.
Charge transfer relaxation in donor–acceptor type conjugated materials
Scarongella Mariateresa, Laktionov Andrey, Rothlisberger Ursula, Banerji Natalie (2013), Charge transfer relaxation in donor–acceptor type conjugated materials, in Journal of Materials Chemistry C, 1(12), 2308-2308.
Photodynamics of Lys+-Trp protein motifs: Hydrogen bonds ensure photostability
Guglielmi Matteo, Doemer Manuel, Tavernelli Ivano, Rothlisberger Ursula (2013), Photodynamics of Lys+-Trp protein motifs: Hydrogen bonds ensure photostability, in Faraday Discussions, 163, 189-189.

Collaboration

Group / person Country
Types of collaboration
Prof. Thereza Soares, Universidade Federal de Pernambuco Brazil (South America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Anatole O. von Lilienfeld Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Paolo Carloni, GRS Jülich, RWTH Aachen Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Michael Graetzel, Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Thomas Rizzo, EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Kai Johnsson, EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Nigel Richards, Indiana University- Purdue University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
ACS Meeting Talk given at a conference Multiple Time Step Schemes for First-Principles Based Multiscale Simulations 12.03.2016 San Diego, United States of America Röthlisberger Ursula;
International Chemical Congress of Pacific Basin Societies (Pacifichem) Talk given at a conference 1. Allosteric Regulation of Nucleosome Core Particle by Transition Metal Anticancer Drugs 2. Multiscale Modelling and Design of Biological Systems in Ground and Excited States 15.12.2015 Honolulu, United States of America Röthlisberger Ursula;
Psi-K Conference 2015 Talk given at a conference 1. Origin of the Spectral Shifts Among the Early Intermediate of the Rhodopsin Photocycle 2. Origin of Hysteresis in Hybrid Lead Halide Perovskites 06.10.2015 Barcelona, Switzerland Röthlisberger Ursula;
CECAM conference on "Computational Advances in Drug Discovery" Talk given at a conference Ru-Based Anticancer Compounds and their Interactions with DNA and Protein Targets 20.09.2015 EPFL Lausanne, Switzerland Röthlisberger Ursula;
CECAM workshop on “Perovskite solar cells: the quest for a theoretical description” Talk given at a conference What’s so Special about Hybrid Halide Perovskites? 25.08.2015 EPFL Lausanne, Switzerland Röthlisberger Ursula;
CECAM Workshop on "Next generation quantum based molecular dynamics: challenges and perspectives Talk given at a conference Higher Accuracy Simulations with the Cost of Lower Level Methods 14.07.2015 Bremen, Germany Röthlisberger Ursula;
CECAM workshop on "Modeling activity vs selectivity in metalloproteins" Talk given at a conference The role of dispersion-correction for the description of metal compounds in density functional theory 29.06.2015 Paris, France Bircher Martin Peter;
Invited talk at the Satellite meeting on quantum simulations of macromolecules associated with the 2015 International Congress of Quantum Chemistry Talk given at a conference QM/MM Simulations of Biological and Biomimetic Systems 04.06.2015 Changchun, China Röthlisberger Ursula;
ACS Physical Chemistry Symposium in honor of Don Truhlar "Computational Chemical Dynamics: advancing our understanding of chemical processes in gas-phase, biomolecular, and condensed-phase systems" Talk given at a conference QM/MM Excited State Simulations of Complex Systems 22.03.2015 Denver, United States of America Röthlisberger Ursula;
Energy Workshop Muenster Talk given at a conference Characterization and Design of Biomimetic Systems 09.03.2015 Muenster, Germany, Switzerland Röthlisberger Ursula;
CECAM Tutorial on Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond Talk given at a conference Lecture I: Interaction between QM and MM Subsystem Lecture II: Advanced Techniques: QM/MM Enhanced Sampling Methods 09.02.2015 EPFL Lausanne, Switzerland Röthlisberger Ursula;
Symposium in Honor of Wanda Andreoni Talk given at a conference Computational Modelling of Photovoltaic Materials 06.02.2015 EPFL Lausanne, Switzerland Röthlisberger Ursula;
9th International Conference on Computational Physics Talk given at a conference QM/MM Simulations in Ground and Excited States 06.01.2015 National University of Singapore, Singapore Röthlisberger Ursula;
Multiscale Modeling of Biomolecular Systems Talk given at a conference Keynote talk: Multiscale Modeling and Design of Biological Systems in Ground and Excited States 28.11.2014 Amsterdam, Netherlands Röthlisberger Ursula;
Talk at the Department of Chemistry, University of Basel Individual talk Lessons from Nature: Computational Design of Biomimetic Systems 29.10.2014 Basel, Switzerland Röthlisberger Ursula;
CCMX Summer School 2014 "Atomistic Scale Modelling of Materials" Talk given at a conference Multiscale Modelling of Biological Matter 01.09.2014 EPFL Lausanne, Switzerland Röthlisberger Ursula;
CCP2014 Conference on Computational Talk given at a conference Mixed QM/MM Simulations of Biological Systems: From Understanding to Control and Design 11.08.2014 Boston, United States of America Röthlisberger Ursula;
Seminar at the University of Oslo Individual talk Lessons from Nature: Computational Design of Biomimetic Systems 17.06.2014 Oslo, Norway Röthlisberger Ursula;
Conference on "Promoting Female Excellence in Theoretical and Computational Chemistry" Talk given at a conference Plenary talk: QM/MM Car-Parrinello Simulations in Ground and Excited States 13.06.2014 Oslo, Norway Röthlisberger Ursula;
Seminar at the Department of Fundamental Chemistry Individual talk Lessons from Nature: Computational Design of Biomimetic Systems 22.05.2014 Recife, Brazil Röthlisberger Ursula;
43rd Meeting of SBBQ Talk given at a conference QM/MM Car-Parrinello Simulations of Biological and Biomimetic Systems 15.05.2014 Foz do Igaucu, Brazil Röthlisberger Ursula;
HOPV 2014 Talk given at a conference Computational Studies of Perovskites: Structural, Electronic & Transport Properties 11.05.2014 EPFL Lausanne, Switzerland Röthlisberger Ursula;
Workshop on "Computer Simulations of Biological Systems Talk given at a conference I. Simulating Biological Systems with QM/MM Car-Parrinello Simulations II. Simulating Biological Systems with QM/MM Car-Parrinello Simulations: Applications 29.04.2014 Teheran, Iran Röthlisberger Ursula;
CECAM Workshop Talk given at a conference Bridging the Gap between Molecular Simulations and Systems Biology 19.04.2014 EPFL Lausanne, Switzerland Röthlisberger Ursula;
Nanoscience Days Talk given at a conference Plenary talk: Computational Design of Biomimetic Devices 19.04.2014 Jyvaeskylae, Finland Röthlisberger Ursula;
ACS 247th National Meeting, Ultrafast Processes in Proteins: Theory and Experiment Talk given at a conference Mixed QM/MM Simulations of Biological Systems: From Understanding to Control and Design 25.03.2014 Dallas, United States of America Röthlisberger Ursula;
Austrian Chemical Society Talk given at a conference QM/MM Car-Parrinello Simulations in Ground and Excited States 03.03.2014 Innsbruck, Austria Röthlisberger Ursula;
Novartis Chemical Science Lecture Talk given at a conference QM/MM Car-Parrinello Simulations in Ground and Excited States 20.02.2014 Yale, United States of America Röthlisberger Ursula;
58th Biophysical Society Meeting Talk given at a conference Classical and Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations of G Protein Coupled Receptors 15.02.2014 San Francisco, United States of America Röthlisberger Ursula;
Spring Meeting of the Swiss Association of Computational Chemistry: Chemical Reactivity and Dynamics Talk given at a conference 40 Years of QM/MM and what now? 13.02.2014 Basel, Switzerland Röthlisberger Ursula;
9th International Conference on Computational Physics at National University of Singapore Talk given at a conference QM/MM Simulations in Ground and Excited States 29.01.2014 Basel, Switzerland Röthlisberger Ursula;
Five pieces and a do in computational physics, chemistry, biology, mathematics and engineering Talk given at a conference Controlling Nature: QM/MM and Trajectory Surface Hopping Simulations of Reactions in Complex Environments 18.12.2013 Rome, Italy Röthlisberger Ursula;
Talk at the Bernese Chemical Society Talk given at a conference Lessons from Nature: Computer Simulations of Biological and Biomimetic Processes 11.12.2013 Bern, Switzerland Röthlisberger Ursula;
CECAM Workshop on Innovative Approaches to Computational Drug Discovery Talk given at a conference Optimizing Systems for Target Properties 01.10.2013 EPFL Lausanne, Switzerland Röthlisberger Ursula;
15th International Conference on Density Functional Theory and its Application Talk given at a conference Trajectory Surface Hooping Simulations and Local Control of Reactions in Complex Environments 09.09.2013 Durhamn, Great Britain and Northern Ireland Röthlisberger Ursula;
FisMat 2013 – Italian National Conference on Condensed Matter Physics Talk given at a conference Doing it the Natural Way: Developing Biomimetic Systems via Multiscale Simulations 09.09.2013 Milan, Italy Röthlisberger Ursula;
CPMD 2013 Talk given at a conference Towards DFT Heaven: Minnesota Functionals and more.. 01.09.2013 Leipzig, Germany Röthlisberger Ursula;
CECAM Workshop Many-Dimensional Quantum Dynamics with (non)Classical Trajectories Talk given at a conference On-the-fly QM/MM Excited State Dynamics with Classical Trajectories 17.06.2013 EPFL Lausanne, Switzerland Röthlisberger Ursula;
International Opening Symposium for the Cluster of Excellence RESOLV Talk given at a conference Learning from Nature: QM/MM Car-Parrinello Simulations of Biological and Biomimetic Systems 02.06.2013 Bochum, Germany Röthlisberger Ursula;
Seminar at the National Institute of Chemistry Talk given at a conference Seminar at the National Institute of Chemistry, Ljubljana, Slovenia, 23 May (2013) Dynamics of Complex Systems by Mixed quantum Mechanical/Moelcular mechanical Simulations 23.05.2013 Ljubljana, Slovenia Röthlisberger Ursula;
Hybrid and Organic Photovoltaics Conference HOPV2013 Talk given at a conference Modeling Porphyrin-Based Dye-Sensitized Solar Cells with Classical and Mixed Quantum Mechanical/Molecular mechanical Simulations 06.05.2013 Sevilla, Spain Röthlisberger Ursula;
HPC Symposium Talk given at a conference Mixed Quantum Mechanical/Molecular Mechanical Simulations in Ground and Electronically Excited States 02.05.2013 Lugano, Switzerland Röthlisberger Ursula;


Awards

Title Year
Doron Prize 2016 2016
Elected to be a member of the International Academy of Quantum Molecular Science 2015
EuCheMS Lecture Award 2015 2015
Elected to be a Board member of the World Association of Theoretically Oriented Chemists WATOC 2014

Associated projects

Number Title Start Funding scheme
165863 Next Generation First-Principles Based Molecular Dynamics with Application to Biomimetic and Materials Design 01.05.2016 Project funding (Div. I-III)
164011 Acquisition of the Central Computational Equipment for the Laboratory of Computational Chemistry and Biochemistry 01.10.2016 R'EQUIP
130082 Multiscale Modelling of Electronically Triggered Biological Signalling 01.05.2010 Project funding (Div. I-III)
116294 Multiscale Modelling of Electronically Triggered Biological Signalling 01.05.2007 Project funding (Div. I-III)

Abstract

The long-term survival of our society may critically depend on our ability to find and implement sustainable strategies that are able support our ever-increasing demands for material and energy resources while maintaining an intact environment. Through millions of years of evolution, Nature has managed to develop processes that are able to maintain highly efficient and stable ecosystems. It is therefore not surprising to seek inspiration from Nature to develop sustainable strategies to produce the material and energy resources needed for the world’s growing population. The first step towards the development of biomimetic systems is to understand how Nature ‘is doing it’. However, a comprehensive understanding of the inner workings of biological processes is often a very difficult task since they tend to be notoriously complex events that can involve several orders in length and time scales and experimental techniques probing their mode of action can often provide only indirect and partial information. Computer simulations can nowadays give direct insights into biomolecular mechanisms but the combined challenge of extended size, large available configurational space and high accuracy required to describe small energy differences of the order of kT remains a challenge.Here we propose to (1) push forward the current frontiers of multiscale biological simulations through the development of a generalized QM/(QM)/MM hybrid approach that will be able to address the combined challenge of size-time-accuracy requirements simultaneously; (2) Develop and implement systematic and efficient data analysis techniques based on feature selection and causality inference that allow us to identify the crucial factors that are responsible for a given biological transformation; (3) use this information to guide the design of bioinspired systems and (4) Optimize biomimetic systems for tailored properties via an efficient exploration of chemical space based on evolutionary algorithms.In continuation of our current SNF grant 200020-120082, we will apply methods (1) and (2) to two electronically triggered biological signaling cascades, electron-transfer induced DNA repair and signal transduction in G protein - coupled receptors. Since these biological signaling processes span many orders of length and time scales, from the electronic/atomic level to the mesoscopic/microscopic domain with accompanying time windows that range from 10-15 to 10-3s, these are two problems par excellence to test the performance of new multiscale methods. Furthermore, dysregulation of signaling cascades lie at the heart of a large variety of diseases such as cancer and neurodegeneration and a better understanding of the underlying molecular mechanisms of these processes might ultimately assist in the development of efficacious therapeutic approaches against these diseases.The newly developed methods (3) and (4), we will apply for the computational design of a biomimetic system for CO2 fixation and to the optimization of biomimetic porphyrin dyes in dye-sensitized solar cells (DSSCs). Both projects will be performed in close collaboration with experimental groups. The requested resources for this project are 4 PhD positions for 3 years. With this research, we expect to (i) make major advances in the development of computer simulation methods for biological systems; (ii) gain fundamental understanding of the molecular mechanisms involved in DNA repair and GPCR signaling; and (iii) contribute to the development of biomimetic compounds for CO2 fixation and DSSCs with higher efficiencies.
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