Gerrit Groenhof

Affiliations

Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.

ORCID: 0000000181485334

Publications (28)

Multi-scale dynamics simulations of molecular polaritons: The effect of multiple cavity modes on polariton relaxation.

The Journal of chemical physics

Avec: Ruth H Tichauer , Johannes Feist , Gerrit Groenhof

Non-Hermitian molecular dynamics simulations of exciton-polaritons in lossy cavities.

The Journal of chemical physics

Avec: Ilia Sokolovskii , Gerrit Groenhof

Effect of molecular Stokes shift on polariton dynamics.

The Journal of chemical physics

Avec: E Hulkko , S Pikker , V Tiainen , R H Tichauer , G Groenhof , J J Toppari

The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.

The journal of physical chemistry letters

Avec: Dmitry Morozov , Vaibhav Modi , Vladimir Mironov , Gerrit Groenhof

Best Practices in Constant pH MD Simulations: Accuracy and Sampling.

Journal of chemical theory and computation

Avec: Pavel Buslaev , Noora Aho , Anton Jansen , Paul Bauer , Berk Hess , Gerrit Groenhof

Scalable Constant pH Molecular Dynamics in GROMACS.

Journal of chemical theory and computation

Avec: Noora Aho , Pavel Buslaev , Anton Jansen , Paul Bauer , Gerrit Groenhof , Berk Hess

gmXtal: Cooking Crystals with GROMACS.

The protein journal

Avec: Pavel Buslaev , Gerrit Groenhof

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations.

Current opinion in structural biology

Avec: Gerrit Groenhof , Vaibhav Modi , Dmitry Morozov

Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons in Strongly Coupled Molecule-Cavity Systems.

The journal of physical chemistry letters

Avec: Ruth H Tichauer , Dmitry Morozov , Ilia Sokolovskii , J Jussi Toppari , Gerrit Groenhof

phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.

Journal of chemical information and modeling

Avec: Anton Jansen , Noora Aho , Gerrit Groenhof , Pavel Buslaev , Berk Hess

Do All Paths Lead to Rome? How Reliable is Umbrella Sampling Along a Single Path?

Journal of chemical theory and computation

Avec: Noora Aho , Gerrit Groenhof , Pavel Buslaev

One molecule to couple them all: Toward realistic numbers of molecules in multiscale molecular dynamics simulations of exciton-polaritons.

The Journal of chemical physics

Avec: Ilia Sokolovskii , Dmitry Morozov , Gerrit Groenhof

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome.

The journal of physical chemistry. B

Avec: Vaibhav Modi , Serena Donnini , Gerrit Groenhof , Dmitry Morozov

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers.

Chemistry (Weinheim an der Bergstrasse, Germany)

Avec: Vladimir Mironov , Irina A Shchugoreva , Polina V Artyushenko , Dmitry Morozov , Nicola Borbone , Giorgia Oliviero , Tatiana N Zamay , Roman V Moryachkov , Olga S Kolovskaya , Kirill A Lukyanenko , Yanling Song , Iuliia A Merkuleva , Vladimir N Zabluda , Georgy Peters , Lyudmila S Koroleva , Dmitry V Veprintsev , Yury E Glazyrin , Ekaterina A Volosnikova , Svetlana V Belenkaya , Tatiana I Esina , Anastasiya A Isaeva , Valentina S Nesmeyanova , Daniil V Shanshin , Anna N Berlina , Nadezhda S Komova , Valery A Svetlichnyi , Vladimir N Silnikov , Dmitriy N Shcherbakov , Galina S Zamay , Sergey S Zamay , Tatyana Smolyarova , Elena P Tikhonova , Kelvin H-C Chen , U-Ser Jeng , Gerolama Condorelli , Vittorio de Franciscis , Gerrit Groenhof , Chaoyong Yang , Alexander A Moskovsky , Dmitri G Fedorov , Felix N Tomilin , Weihong Tan , Yuri Alexeev , Maxim V Berezovski , Anna S Kichkailo

Controlling Exciton Propagation in Organic Crystals through Strong Coupling to Plasmonic Nanoparticle Arrays.

ACS photonics

Avec: Anton Matthijs Berghuis , Ruth H Tichauer , Lianne M A de Jong , Ilia Sokolovskii , Ping Bai , Mohammad Ramezani , Shunsuke Murai , Gerrit Groenhof , Jaime Gómez Rivas

Optical control of ultrafast structural dynamics in a fluorescent protein.

Nature chemistry

Avec: Christopher D M Hutchison , James M Baxter , Ann Fitzpatrick , Gabriel Dorlhiac , Alisia Fadini , Samuel Perrett , Karim Maghlaoui , Salomé Bodet Lefèvre , Violeta Cordon-Preciado , Josie L Ferreira , Volha U Chukhutsina , Douglas Garratt , Jonathan Barnard , Gediminas Galinis , Flo Glencross , Rhodri M Morgan , Sian Stockton , Ben Taylor , Letong Yuan , Matthew G Romei , Chi-Yun Lin , Jon P Marangos , Marius Schmidt , Viktoria Chatrchyan , Tiago Buckup , Dmitry Morozov , Jaehyun Park , Sehan Park , Intae Eom , Minseok Kim , Dogeun Jang , Hyeongi Choi , HyoJung Hyun , Gisu Park , Eriko Nango , Rie Tanaka , Shigeki Owada , Kensuke Tono , Daniel P DePonte , Sergio Carbajo , Matt Seaberg , Andrew Aquila , Sebastien Boutet , Anton Barty , So Iwata , Steven G Boxer , Gerrit Groenhof , Jasper J van Thor

Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling.

Nature communications

Avec: Ilia Sokolovskii , Ruth H Tichauer , Dmitry Morozov , Johannes Feist , Gerrit Groenhof

Tuning the Coherent Propagation of Organic Exciton-Polaritons through the Cavity Q-factor.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Avec: Ruth H Tichauer , Ilia Sokolovskii , Gerrit Groenhof

What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations.

The journal of physical chemistry. B

Avec: Noora Aho , Gerrit Groenhof , Pavel Buslaev

Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Nadav Amdursky , Yiyang Lin , Noora Aho , Gerrit Groenhof

Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations.

The journal of physical chemistry letters

Avec: Gerrit Groenhof , Clàudia Climent , Johannes Feist , Dmitry Morozov , J Jussi Toppari

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.

eLife

Avec: Elin Claesson , Weixiao Yuan Wahlgren , Heikki Takala , Suraj Pandey , Leticia Castillon , Valentyna Kuznetsova , Léocadie Henry , Matthijs Panman , Melissa Carrillo , Joachim Kübel , Rahul Nanekar , Linnéa Isaksson , Amke Nimmrich , Andrea Cellini , Dmitry Morozov , Michał Maj , Moona Kurttila , Robert Bosman , Eriko Nango , Rie Tanaka , Tomoyuki Tanaka , Luo Fangjia , So Iwata , Shigeki Owada , Keith Moffat , Gerrit Groenhof , Emina A Stojković , Janne A Ihalainen , Marius Schmidt , Sebastian Westenhoff

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked.

The journal of physical chemistry letters

Avec: Satu Mustalahti , Dmitry Morozov , Hoi Ling Luk , Rajanish R Pallerla , Pasi Myllyperkiö , Mika Pettersson , Petri M Pihko , Gerrit Groenhof

Ultrafast structural changes within a photosynthetic reaction centre.

Nature

Avec: Robert Dods , Petra Båth , Dmitry Morozov , Viktor Ahlberg Gagnér , David Arnlund , Hoi Ling Luk , Joachim Kübel , Michał Maj , Adams Vallejos , Cecilia Wickstrand , Robert Bosman , Kenneth R Beyerlein , Garrett Nelson , Mengning Liang , Despina Milathianaki , Joseph Robinson , Rajiv Harimoorthy , Peter Berntsen , Erik Malmerberg , Linda Johansson , Rebecka Andersson , Sergio Carbajo , Elin Claesson , Chelsie E Conrad , Peter Dahl , Greger Hammarin , Mark S Hunter , Chufeng Li , Stella Lisova , Antoine Royant , Cecilia Safari , Amit Sharma , Garth J Williams , Oleksandr Yefanov , Sebastian Westenhoff , Jan Davidsson , Daniel P DePonte , Sébastien Boutet , Anton Barty , Gergely Katona , Gerrit Groenhof , Gisela Brändén , Richard Neutze

Covalent and non-covalent coupling of a Au

Nanoscale advances

Avec: Eero Hulkko , Tanja Lahtinen , Varpu Marjomäki , Emmi Pohjolainen , Ville Saarnio , Karolina Sokolowska , Ardra Ajitha , Mikael Kuisma , Lauri Lehtovaara , Gerrit Groenhof , Hannu Häkkinen , Mika Pettersson

Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.

Journal of the American Chemical Society

Avec: Alisia Fadini , Christopher D M Hutchison , Dmitry Morozov , Jeffrey Chang , Karim Maghlaoui , Samuel Perrett , Fangjia Luo , Jeslyn C X Kho , Matthew G Romei , R Marc L Morgan , Christian M Orr , Violeta Cordon-Preciado , Takaaki Fujiwara , Nipawan Nuemket , Takehiko Tosha , Rie Tanaka , Shigeki Owada , Kensuke Tono , So Iwata , Steven G Boxer , Gerrit Groenhof , Eriko Nango , Jasper J van Thor

Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits.

Journal of the American Chemical Society

Avec: Yong Rui Poh , Dmitry Morozov , Nathanael P Kazmierczak , Ryan G Hadt , Gerrit Groenhof , Joel Yuen-Zhou

Thermal disorder prevents the suppression of ultra-fast photochemistry in the strong light-matter coupling regime.

Nature communications

Avec: Arpan Dutta , Ville Tiainen , Ilia Sokolovskii , Luís Duarte , Nemanja Markešević , Dmitry Morozov , Hassan A Qureshi , Siim Pikker , Gerrit Groenhof , J Jussi Toppari

Réseau de co-auteurs

Dmitry Morozov 15 collaborations

Ilia Sokolovskii 7 collaborations

Pavel Buslaev 6 collaborations

Noora Aho 6 collaborations

Ruth H Tichauer 5 collaborations

Johannes Feist 3 collaborations

Vaibhav Modi 3 collaborations

Anton Jansen 3 collaborations

Berk Hess 3 collaborations

J Jussi Toppari 3 collaborations

Eriko Nango 3 collaborations

Rie Tanaka 3 collaborations

Shigeki Owada 3 collaborations

So Iwata 3 collaborations

Vladimir Mironov 2 collaborations

Paul Bauer 2 collaborations

Christopher D M Hutchison 2 collaborations

Alisia Fadini 2 collaborations

Samuel Perrett 2 collaborations

Karim Maghlaoui 2 collaborations

Violeta Cordon-Preciado 2 collaborations

Matthew G Romei 2 collaborations

Marius Schmidt 2 collaborations

Kensuke Tono 2 collaborations

Daniel P DePonte 2 collaborations

Sergio Carbajo 2 collaborations

Anton Barty 2 collaborations

Steven G Boxer 2 collaborations

Jasper J van Thor 2 collaborations

Elin Claesson 2 collaborations

Joachim Kübel 2 collaborations

Michał Maj 2 collaborations

Robert Bosman 2 collaborations

Sebastian Westenhoff 2 collaborations

Hoi Ling Luk 2 collaborations

Mika Pettersson 2 collaborations

E Hulkko 1 collaboration

S Pikker 1 collaboration

V Tiainen 1 collaboration

R H Tichauer 1 collaboration

G Groenhof 1 collaboration

J J Toppari 1 collaboration

Serena Donnini 1 collaboration

Irina A Shchugoreva 1 collaboration

Polina V Artyushenko 1 collaboration

Nicola Borbone 1 collaboration

Giorgia Oliviero 1 collaboration

Tatiana N Zamay 1 collaboration

Roman V Moryachkov 1 collaboration

Olga S Kolovskaya 1 collaboration

Kirill A Lukyanenko 1 collaboration

Yanling Song 1 collaboration

Iuliia A Merkuleva 1 collaboration

Vladimir N Zabluda 1 collaboration

Georgy Peters 1 collaboration

Lyudmila S Koroleva 1 collaboration

Dmitry V Veprintsev 1 collaboration

Yury E Glazyrin 1 collaboration

Ekaterina A Volosnikova 1 collaboration

Svetlana V Belenkaya 1 collaboration

Tatiana I Esina 1 collaboration

Anastasiya A Isaeva 1 collaboration

Valentina S Nesmeyanova 1 collaboration

Daniil V Shanshin 1 collaboration

Anna N Berlina 1 collaboration

Nadezhda S Komova 1 collaboration

Valery A Svetlichnyi 1 collaboration

Vladimir N Silnikov 1 collaboration

Dmitriy N Shcherbakov 1 collaboration

Galina S Zamay 1 collaboration

Sergey S Zamay 1 collaboration

Tatyana Smolyarova 1 collaboration

Elena P Tikhonova 1 collaboration

Kelvin H-C Chen 1 collaboration

U-Ser Jeng 1 collaboration

Gerolama Condorelli 1 collaboration

Vittorio de Franciscis 1 collaboration

Chaoyong Yang 1 collaboration

Alexander A Moskovsky 1 collaboration

Dmitri G Fedorov 1 collaboration

Felix N Tomilin 1 collaboration

Weihong Tan 1 collaboration

Yuri Alexeev 1 collaboration

Maxim V Berezovski 1 collaboration

Anna S Kichkailo 1 collaboration

Anton Matthijs Berghuis 1 collaboration

Lianne M A de Jong 1 collaboration

Ping Bai 1 collaboration

Mohammad Ramezani 1 collaboration

Shunsuke Murai 1 collaboration

Jaime Gómez Rivas 1 collaboration

James M Baxter 1 collaboration

Ann Fitzpatrick 1 collaboration

Gabriel Dorlhiac 1 collaboration

Salomé Bodet Lefèvre 1 collaboration

Josie L Ferreira 1 collaboration

Volha U Chukhutsina 1 collaboration

Douglas Garratt 1 collaboration

Jonathan Barnard 1 collaboration

Gediminas Galinis 1 collaboration

Flo Glencross 1 collaboration

Rhodri M Morgan 1 collaboration

Sian Stockton 1 collaboration

Ben Taylor 1 collaboration

Letong Yuan 1 collaboration

Chi-Yun Lin 1 collaboration

Jon P Marangos 1 collaboration

Viktoria Chatrchyan 1 collaboration

Tiago Buckup 1 collaboration

Jaehyun Park 1 collaboration

Sehan Park 1 collaboration

Intae Eom 1 collaboration

Minseok Kim 1 collaboration

Dogeun Jang 1 collaboration

Hyeongi Choi 1 collaboration

HyoJung Hyun 1 collaboration

Gisu Park 1 collaboration

Matt Seaberg 1 collaboration

Andrew Aquila 1 collaboration

Sebastien Boutet 1 collaboration

Nadav Amdursky 1 collaboration

Yiyang Lin 1 collaboration

Clàudia Climent 1 collaboration

Weixiao Yuan Wahlgren 1 collaboration

Heikki Takala 1 collaboration

Suraj Pandey 1 collaboration

Leticia Castillon 1 collaboration

Valentyna Kuznetsova 1 collaboration

Léocadie Henry 1 collaboration

Matthijs Panman 1 collaboration

Melissa Carrillo 1 collaboration

Rahul Nanekar 1 collaboration

Linnéa Isaksson 1 collaboration

Amke Nimmrich 1 collaboration

Andrea Cellini 1 collaboration

Moona Kurttila 1 collaboration

Tomoyuki Tanaka 1 collaboration

Luo Fangjia 1 collaboration

Keith Moffat 1 collaboration

Emina A Stojković 1 collaboration

Janne A Ihalainen 1 collaboration

Satu Mustalahti 1 collaboration

Rajanish R Pallerla 1 collaboration

Pasi Myllyperkiö 1 collaboration

Petri M Pihko 1 collaboration

Robert Dods 1 collaboration

Petra Båth 1 collaboration

Viktor Ahlberg Gagnér 1 collaboration

David Arnlund 1 collaboration

Adams Vallejos 1 collaboration

Cecilia Wickstrand 1 collaboration

Kenneth R Beyerlein 1 collaboration

Garrett Nelson 1 collaboration

Mengning Liang 1 collaboration

Despina Milathianaki 1 collaboration

Joseph Robinson 1 collaboration

Rajiv Harimoorthy 1 collaboration

Peter Berntsen 1 collaboration

Erik Malmerberg 1 collaboration

Linda Johansson 1 collaboration

Rebecka Andersson 1 collaboration

Chelsie E Conrad 1 collaboration

Peter Dahl 1 collaboration

Greger Hammarin 1 collaboration

Mark S Hunter 1 collaboration

Chufeng Li 1 collaboration

Stella Lisova 1 collaboration

Antoine Royant 1 collaboration

Cecilia Safari 1 collaboration

Amit Sharma 1 collaboration

Garth J Williams 1 collaboration

Oleksandr Yefanov 1 collaboration

Jan Davidsson 1 collaboration

Sébastien Boutet 1 collaboration

Gergely Katona 1 collaboration

Gisela Brändén 1 collaboration

Richard Neutze 1 collaboration

Eero Hulkko 1 collaboration

Tanja Lahtinen 1 collaboration

Varpu Marjomäki 1 collaboration

Emmi Pohjolainen 1 collaboration

Ville Saarnio 1 collaboration

Karolina Sokolowska 1 collaboration

Ardra Ajitha 1 collaboration

Mikael Kuisma 1 collaboration

Lauri Lehtovaara 1 collaboration

Hannu Häkkinen 1 collaboration

Jeffrey Chang 1 collaboration

Fangjia Luo 1 collaboration

Jeslyn C X Kho 1 collaboration

R Marc L Morgan 1 collaboration

Christian M Orr 1 collaboration

Takaaki Fujiwara 1 collaboration

Nipawan Nuemket 1 collaboration

Takehiko Tosha 1 collaboration

Yong Rui Poh 1 collaboration

Nathanael P Kazmierczak 1 collaboration

Ryan G Hadt 1 collaboration

Joel Yuen-Zhou 1 collaboration

Arpan Dutta 1 collaboration

Ville Tiainen 1 collaboration

Luís Duarte 1 collaboration

Nemanja Markešević 1 collaboration

Hassan A Qureshi 1 collaboration

Siim Pikker 1 collaboration