Tag Archives: international

Course on molecular dynamics simulations in Concepción, Chile

Posted by 28 de January de 2026

In January 15-19th, invited by the lab of Verónica Andrea Jimenez Curihual, at the Universidad Andrés Bello in its Concepción campus, Jordi Villà-Freixa taugth a course on molecular dynamics simulations with OpenMM and the posterior basic through advanced data analysis using standard tools like MDraj, MDAnalysis, pyemma or deeptime. Several PhD students and postdoctoral researchers (some shown in the picture) attended the course, that served as a way to build on the foundations of a long time collaborative bridge between the two labs.

The course web site and the source github repository are available under a MIT license.

Roger Casals presents his doctoral research at scverse 2025

Posted by 1 de December de 2025

Last November, Roger Casals, PhD candidate at the Computational Biochemistry and Biophysics Lab (CBBL), travelled to Stanford University to take part in scverse 2025, one of the key gatherings for the single-cell and multi-omics community.

During the conference, Roger presented a poster with some of the latest results from his PhD. His project focuses on building gene regulatory networks from single-cell data to understand cell state transitions, a line of work that is becoming increasingly important as we try to make sense of complex biological systems.

Beyond the science, the conference gave Roger the chance to meet many members of the scverse community, discuss ideas in person, and learn from researchers developing cutting-edge tools. Topics like agentic AI and virtual cell models were especially exciting, forecasting us where the field is heading.

Roger’s participation was possible thanks to a travel grant from the conference, along with support from the Department of Biosciences (FCTE), the BI-Squared Group, and IRIS-CC.

 

PhD Student Nayanika Das Begins Research Visit at the University of Groningen

Posted by 10 de October de 2025

We are delighted to share that our PhD student Nayanika Das has embarked on a research visit to the laboratory of Prof. Gerard Roelfes at the University of Groningen, The Netherlands. This visit marks an exciting step forward in her doctoral work on understanding and optimizing the function of enzymes, this time for proteins containing artificial amino acids.

During her stay, Nayanika will collaborate closely with the Roelfes group to investigate the incorporation of the noncanonical amino acid para-aminophenylalanine (pAF) into the nonenzymatic protein scaffold LmrR. Remarkably, this modification transforms LmrR into a proficient and stereoselective artificial enzyme (LmrR_pAF) — an elegant example of how chemical innovation can endow proteins with entirely new catalytic functions.

Nayanika’s research will combine experimental validation in the laboratory with computational modeling efforts. Specifically, she will contribute to the development of an Empirical Valence Bond (EVB) model aimed at uncovering the molecular details of the mechanism of action of pAF in the reactions catalyzed by LmrR_pAF. By integrating theoretical and experimental approaches, her work will help elucidate how artificial amino acids expand the functional landscape of proteins and open new avenues for biocatalysis and synthetic biology.

We wish Nayanika a productive and inspiring stay in Groningen and look forward to the exciting results that will emerge from this collaboration with the Roelfes Lab.

Visit of professor Yuk Sham, University of Minnesota

Posted by 6 de September de 2024

Professor Yuk Sham visits the CBBL for a collection of meetings and seminar.

Professor Sham is an expert in molecular simulations, in particular protein-protein and protein-ligand interactions. The work of his laboratory focuses on tools conducting to the rational discovery of drugs, and has a long trajectory in the field of computational biochemistry. During his visit, the current research projects of the CBBL and the ShamLab were explored, in search of synergies and possible collaborations.