News

July 2021

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.

May 2021

Mehari and Jakob successfully defended their PhD theses. Congratulations!

January 2021

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.

December 2020

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.

November 2020

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.

October 2020

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.

August 2020

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.

July 2020

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.

June 2020

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 2020

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.

April 2020

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

March 2020

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.

February 2020

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.

December 2019

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

November 2019

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.

October 2019

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.

August 2019

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

July 2019

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

June 2019

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 2019

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.

March 2019

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.

December 2018

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

April 2018

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.

March 2018

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.

January 2018

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

December 2017

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

November 2017

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

October 2017

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!

September 2017

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

June 2017

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.

April 2017

Lars joined our group as a Bachelor student. Welcome!

March 2017

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

February 2017

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.

January 2017

Claude finished his PhD. Congratulations!

Oskar joined our group as a Master student. Welcome!

​November 2016

Arthur joined our group as a Master student. Welcome!

Jakob joined our group as a Master student. Welcome!

​October 2016

Alexander gave a presentation at "Nacht der Wissenschaft".

Marie joined our group as a Master student. Welcome!

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

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

​September 2016

Alexander gave a presentation at GridKa School Karlsruhe.

​June 2016

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 2016

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.

​April 2016

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.

December 2015

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

November 2015

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

October 2015

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

September 2015

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.

August 2015

Sebastian finished his Master thesis. Congratulations!

Fabian finished his Bachelor thesis. Congratulations!

Jan joined our group as HiWi. Welcome!

Carlos joined our group as HiWi. Welcome!

Alexander presented our research at the Stadtfest Karlsruhe.

June 2015

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

http://www.kit.edu/kit/english/pi_2015_062_erna-scheffler-sponsorship-award.php 

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 2015

Fabian joined our group as a Bachelor student. Welcome!

April 2015

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

March 2015

Alexander got a publication accepted in Methods Enzymology.

January 2015

The lecture "Theoretical molecular Biophysics" (WS2014/2015) got top grades from students (LQI 100/100, graded "very good" as total grade).

December 2014

Ilaria joined our group. Welcome!

November 2014

Claude got a publication accepted in Nature Communication.

Update:

Links http://www.nature.com/ncomms/2015/150105/ncomms6846/abs/ncomms6846.html

Press releases: http://www.kit.edu/kit/english/pi_2015_16157.php

Ines finished her master thesis.

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

May 2014

March 2014

February 2014

Abhinav finished his postdoc with us and joined Shell.

November 2013

Benny got an article accepted in Nucleic Acids Research.

October 2013

Shalini John Lovis joined our group as a postdoc. Ines Reinartz joined our group as a master student. Claude Sinner started his PhD. Welcome!

August 2013

Benny got an article accepted in Bioinformatics.

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

July 2013

Visit of Prof. A. Möglich.

June 2013

Claude finished his Diploma thesis. Congratulations!

June 2013

Application for WE-Heraeus seminar accepted.

January 2013

Prof M. Weigt visited our group.

December 2012

Visit of Dr. A. Stadler (FZ Jülich).

Visit of Thomas-Otavio Peulen (HHU Düsseldorf).

October 2012

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

October 2012

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

April 2012

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

July 2011

Abhinav joined our group.

June 2011

Benjamin joined our group as a PhD student.

April 2011

The group started @KIT.