News

Jul '21

Marie successfully defended her PhD thesis. Congratulations!

Marie and Alex got the article Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions published in Nature Machine Intelligence.

Jun '21

Eric and Christian joined our group as PhD students at Forschungszentrum Jülich. Welcome! Find more information about their projects here.

May '21

Mehari and Jakob successfully defended their PhD theses. Congratulations!

Jan '21

Marie and Alex got the article The trimeric major capsid protein of Mavirus is stabilized by its interlocked N-termini enabling core flexibility for capsid assembly published in Journal of Molecular Biology.

Dec '20

Momin successfully defended his PhD thesis. Congratulations! Due to the ongoing COVID-19 pandemic, both his defense and the celebration afterwards were organized as online meetings. 

Prof. Dr. Rochus Schmid from the Ruhr Universität Bochum gave a seminar talk on metallo-organic frameworks in our group meeting. The research of his goup is focused on the development and application of theoretical methods for the simulation of complex systems in materials chemistry on an atomistic level. They try to develop atomistic models to bridge the length- and time-scales and thus overcome the intrinsic problem in the simulation of materials systems.

Alex gave an online seminar talk on "The Computer as a Wet Lab: Predicting Biomolecular Structures via Data Inference". His talk was part of the virtual physics colloquium at the Bergische Universität Wuppertal.

In the context of their Research Training Group - Tailored Scale-Briding Approaches to Computational Nanoscience, Fathia and Marie organized a virtual seminar day on coarse graining. Our guest speaker, Prof. Dr. Christine Peter (University of Konstanz, Department of Chemistry, Computational and Theoretical Chemistry), talked about “Linking simulation scales for biomolecular systems”.

Alexander Hautke, a doctoral student in the group of Prof. Dr. Simon Ebbinghaus at Technische Universität Braunschweig, gave a seminar talk in our group meeting. He talked about "Fast Relaxation Imaging Studies on Huntington Exon 1 Model Hairpin RNA - Research towards RNA hairpin unfolding".

Jakob and Alex got the article Assembly of Multi-Spheroid Cellular Architectures by Programmable Droplet Merging published in Advanced Materials.

Nov '20

Arthur, Marie, and Alex got the article Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations published in PLOS ONE.

Oct '20

Momin and Alex got the article Design of Metal-Organic Framework Templated Materials Using High-Throughput Computational Screening published in Molecules.

Jakob and Alex got the article CellsInSilico - Introducing a High-performance Framework for Large-scale Tissue Modeling published in BMC Bioinformatics.

Aug '20

Emanuel and Alex got the article CORE-MD, a path-correlated Molecular Dynamics simulation method published in Journal of Chemical Physics.

Jeff Noel gave a seminar talk in our group meeting. As a Humboldt Fellow in Berlin, he is collaborating with Oliver Daumke and Alexander Mikhailov in an effort to provide a structure-based understanding of the dynamics and power stroke of the dynamin molecular motor.

Emanuel and Alex got the article The Inhibitory Effect of a Coronavirus Spike Protein Fragment with ACE2 published in Biophysical Journal.

Jul '20

After finishing his Master thesis in December, Julian joined our group as a PhD student. Welcome back!

In our weekly group meeting, Shachi Gosavi gave a seminar talk on using structure-based simulations to analyze domain swapping in proteins.

Jun '20

Ines, Marie, and Alex got the article FRET Dyes Significantly Affect SAXS Intensities of Proteins published in Israel Journal of Chemistry.

Jakob, Ines, Claude, and Alex got the article Modeling of Wnt-mediated Tissue Patterning in Vertebrate Embryogenesis published in PLoS Computational Biology.

Due to the Corona crisis, lots of Alex' invited talks got canceled, such as a physics colloquium on "The Computer as a Wet Lab: Predicting Biomolecular Structures via Data Inference" at the University of Darmstadt (originally planned for May) and an invited talk at the Cargèse conference on "Biological sequence variation: from statistical modeling to structure, function, and evolutionary dynamics" in Corsica, France (originally planned for April).

Maria Barbarossa from Frankfurt Institute for Advanced Studies gave a seminar talk in our group meeting. Her work is devoted to the development of mathematical models and methods for the understanding of multiscale processes in immunology and in the dynamics of infectious diseases.

May '20

Claude, a former PhD student in our group, and Alex got the article Pcdh 18a-positive tip cells orchestrate notochord formation accepted in Histochemistry and Cell Biology.

Birgit Strodel from Forschungszentrum Jülich gave a seminar talk in our group meeting.

Apr '20

Jochen Hub from Saarland University gave a seminar talk in our group meeting.

Mar '20

Fabrizio, Emanuel, Mehari, and Alex got their article Evaluating DCA-based method performances for RNA contact prediction by a well-curated dataset published in RNA.

Alex was invited as a speaker to the Germany Physical Society spring meeting. He gave a presentation on "Predicting Protein and RNA Structures via Data Inference: from Potts Models to Machine Learning". Due to the Corona crisis, the DPG meeting was organized as a virtual conference.

Feb '20

Alex gave a popular-scientific talk on "Von der Proteinfaltung bis zur Krebsentwicklung: Computersimulationen der Maschinerie des Lebens" at KIT in Karlsruhe. He also was invited to the University of Brussels to give a seminar talk on "Predicting Proteind and RNA Structures via Data Inference".

Alex and Arthur went to the NIC Symposium in Jülich, which is held biennially to give an overview on activities and results obtained by the NIC projects in the last two years. Alex was the chair of one session there and Arthur presented a poster.

Dec '19

Julian finished his Master thesis on "Accelerating Molecular Dynamics Simulations Using Convolutional Variational Autoencoders". Congratulations!

Nov '19

Mehari, Fabrizio, and Alex got the article pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences published in Bioinformatics.

Oct '19

Marie won the Erna Scheffler Sponsorship Award for her Master thesis. The ceremony took place at the German Federal Constitutional Court. Congratulations!

Marie and Ines gave popular scientific presentations at the "Bunte Nacht der Digitalisierung", a public event organized by the city of Karlsruhe.

Alexander and Jan got the article Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase published in Biological Chemistry.

Ines and Marie presented their work at the CECAM workshop "Protein simulations - current state of the art" at Tel Aviv University, Israel.

Aug '19

Ines and Alexander got the article Identification of evolutionary and kinetic drivers of NAD-dependent signaling published in PNAS.

Jul '19

Oskar got the article diSTruct v1.0: generating biomolecular structures from distance constraints published in Bioinformatics.

Jun '19

Fabrizio got the article Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction published in Methods.

May '19

Ines successfully defended her PhD thesis. Congratulations! She will continue to work in our group as a PostDoc for some months.

Fathia joined our group as a PhD student. Welcome!

Momin got the article Rising Up: Hierarchical Metal-Organic Frameworks in Experiments and Simulations published in Advanced Materials.

Mar '19

Marie got the article Rapid interpretation of small-angle X-ray scattering data published in PLOS Computational Biology.

For 2019's  "Girls' Day", ten interested girls from various high schools in and near Karlsruhe visited our group at SCC. Together with some collegues, Marie gave a short overview to our work at the institute's 3D visualization room and organized a workshop with programming games and a virtual-reality framework.

Dec '18

Julian joined our group as a Master student. He has already worked with us as a Hiwi some time ago, so welcome back!

Apr '18

Marie and Oskar started their work as PhD students in our group. Welcome back!

Alexander, Arthur, Marie, and Oskar attended a Helmholtz Analytics Framework meeting for the usecase "Structural Biology" together with the groups of Prof. Michael Sattler from Technical University of Munich and Prof. Gunnar Schröder from Forschungszentrum Jülich at the Bavarian NMR center, Forschungscampus Garching.

For 2018's  "Girls' Day", ten interested young ladies from different high schools in Karlsruhe area visited our group at SCC. Marie and Oskar gave a short introduction to our work at the institute's 3D visualization room and organized a workshop with programming games and small simulations.

Mar '18

The whole group went to the DPG Spring Meeting of the Condensed Matter Section (SKM) together with the EPS in Berlin. Alexander organized a focus session on statistical physics-based methods in molecular evolution together with Prof. Martin Weigt from Institut de Biologie, Paris. Ines and Marie gave talks about their work and Arthur, Lars, Mehari, and Oskar presented their projects in the poster sessions.

Jan '18

Arthur continues his work as a PhD student in our group. Oskar finished his Master thesis. Congratulations!

Dec '17

Ines got the article Simulation of FRET dyes allows quantitative comparison against experimental data accepted in Journal of Chemical Physics. 

Nov '17

Marie and Arthur finished their Master theses. Lars finished his Bachelor thesis. Congratulations!

Oct '17

Kickoff meeting of the Helmholtz Analytics Framework at Forschungszentrum Jülich. We are leading the use case "Structural Biology" with partners at KIT, Forschungszentrum Jülich, and Helmholtz Zentrum München.

Mehari got the review article Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function published in Biochemical Society Transactions. Congratulations!

Sep '17

Alexander started his work as a NIC group leader at Forschungszentrum Jülich. The group MBS will continue their work at KIT.

Jun '17

Linda finished her Bachelor thesis 'Analysis of the Importance of the Score Value, Calculated by Direct Coupling Analysis, for Protein Folding' and continues her work as a HiWi.

Apr '17

Lars joined our group as a Bachelor student. Welcome!

Mar '17

The group attended the workshop 'Computer Simulation and Theory of Macromolecules 2017' in Huenfeld and Marie won a poster prize. Congratulations!

Feb '17

Momin joined our group as a PhD student. Welcome!

Ines got the article "Bi-functional nanopatterned hydrogels control hematopoietic stem cell maintenance and proliferation" accepted in Advanced Functional Materials. 

Alexander got the article Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis accepted in PNAS. 

Ines gave a presentation at the Biophysical Society Meeting in New Orleans, USA.

Alexander gave a presentation at Google, Mountainview, USA.

Alexander gave a presentation at CTBP, Rice University, USA.

Jan '17

Claude finished his PhD. Congratulations!

Oskar joined our group as a Master student. Welcome!

​Nov '16

Arthur and Jakob joined our group as Master students. Welcome!

​Oct '16

Alexander gave a presentation at "Nacht der Wissenschaft".

Marie joined our group as a Master student. Welcome!

Michael finished his Master thesis in computer science (jointly with group of Prof. H. Meyerhenke).

Alexander gave a presentation at International Study Group for Systems Biology in Jena, Germany.

​Sep '16

Alexander gave a presentation at GridKa School Karlsruhe.

​Jun '16

Alexander was an oppenent of PhD candidate Anna Bille at Lund University (Sweden). Anna succesfully defended. Congratulations!

Alexander gave a presentation at Lund University, Sweden.

​May '16

Alexander gave a presentation at From Computational Biophysics to Systems Biology, Ankara, Turkey.

Alexander gave a presentation at Biomolecular Simulations across Scales, East China Normal University, Shanghai, China.

​Apr '16

Hannah Rickmann and Ralf Schnaterer finished their project "Proteinfaltung am Computer" inside our high-school outreach program "Simulierte Welten". We hope you enjoyed the experience!

Alexander gave a presentation at Coevolutionas in proteins and RNA, Cargese, France.

Dec '15

Claude got the article Revealing the Global Map of Protein Folding Space by Large-Scale Simulations accepted in Journal of Chemical Physics. 

Nov '15

Alexander got the article Constructing a folding model for protein S6 guided by dynamics deduced from NMR structures accepted in Journal of Chemical Physics.

Oct '15

Claude was given a best talk award at the XIXth European Contress of Lepidopterology.

Sep '15

Benjamin and Sebastian got the article Direct-Coupling Analysis of nucleotide coevolution facilitates RNA tertiary structure prediction published in Nucleic Acids Research.

Alexander got the publication "Coevolutionary inference of mutational landscapes: Capturing the context-dependence of mutations in the beta-lactamase TEM-1" accepted in Molecular Biology and Evolution.

Aug '15

Sebastian finished his Master thesis. Congratulations!

Fabian finished his Bachelor thesis. Congratulations!

Jan and Carlos joined our group as HiWis. Welcome!

Alexander presented our research at the Stadtfest Karlsruhe.

Jun '15

Ines won the Erna Scheffler Sponsorship Award for her Master thesis. The ceremony took place at the German Federal Constitutional Court. Congratulations, Ines!

David Oberacker (Gymnasium Neureut) and Joshua Hellinger (Bismark-Gymnasium) finished their project "Proteinfaltung am Computer" inside our high-school outreach program "Simulierte Welten". We hope you enjoyed the experience!

School Colloquium „Simulierte Welten“ at SCC

May '15

Fabian joined our group as a Bachelor student. Welcome!

Apr '15

Ines continues her studies as a PhD student in our group. Welcome back!

Mar '15

Alexander got a publication accepted in Methods Enzymology.

Jan '15

The lecture "Theoretical molecular Biophysics" (WS 2014/2015) got top grades from students (LQI 100/100, graded "very good" as total grade).

Claude got the article Filopodia-based Wnt transport during vertebrate tissue patterning published in Nature Communication.

Dec '14

Ilaria joined our group. Welcome!

Nov '14

Ines finished her Master thesis. Congratulations!

Aug '14

Sebastian joined our group. Welcome!

Jul '14

Ramneek did a very nice video clip on protein folding simulations.

May '14

Prof. Hendrik Szurmant (TSRI, La Jolla, USA) visited our group.

Harsh joined our group as an intern for two months.

Mar '14

Ramneek joined our group as an intern for six months.

Feb '14

Organization of the 552nd Heraeus Seminar "Physics of Biomolecular Folding and Assembly: Theory meets Experiment" went rather smoothly. Thank you everyone for a great conference!

Claude got a review article accepted in Israel Journal of Chemistry.

Dr. Matteo Figliuzzi (U Pierre et Marie Curie) visited our group for a month.

Jan '14

Abhinav finished his PostDoc with us and joined Shell.

Nov '13

Benny got an article accepted in Nucleic Acids Research.

Oct '13

Shalini John Lovis joined our group as a PostDoc.

Ines Reinartz joined our group as a master student.

Claude Sinner started his PhD. Welcome!

Aug '13

Benny got an article accepted in Bioinformatics.

An article together with the group of Prof. Wolfgang Wenzel got accepted in FEBS Letters.

Jul '13

Prof. A. Möglich visited our group.

Jun '13

Claude finished his Diploma thesis. Congratulations!

Jun '13

Our application for the WE-Heraeus seminar got accepted.

Jan '13

Prof. Martin Weigt visited our group.

Dec '12

Dr. A. Stadler from Forschungszentrum Jülich visited our group.

Thomas-Otavio Peulen from HHU Düsseldorf visited our group.

Oct '12

Dr. Jeff Noel (Rice University, TX, USA) visited our group for a month.

Prof. Changbong Hyeon (KIAS, Korea) visited our group for two weeks.

Apr '12

Our article Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics and mutagenesis has been accepted for publication in PNAS.

Jul '11

Abhinav joined our group as a PostDoc. Welcome!

Jun '11

Benjamin joined our group as a PhD student. Welcome!

Apr '11

The group started @ KIT.