Computational Cell Biology

Ram Bhaskara received his bachelor's degree in Chemistry and Biochemistry from Osmania University, India. He then joined the Integrated Ph.D. program in Biological Sciences at the Indian Institute of Science, India. During this period, he gained research experience in various labs (from field ecology to molecular biophysics). He then joined Prof. N. Srinivasan's group for his Master's and Ph.D. During this period, he developed novel computational tools and analysis schemes to understand the "Structure, Stability, and Evolution of Multi-domain proteins." Ram was honored with the B. H. Iyer Gold Medal for the best doctoral thesis from the Molecular Biophysics Unit (2014). He then began his post-doctoral stint with Prof. Gerhard Hummer at the Max-Planck Institute of Biophysics, Frankfurt. Ram worked on diverse membrane remodeling processes: curvature induction, budding, fusion, & poration, primarily using physics-based modeling and simulation approaches. He developed and pioneered novel simulation methods to model dynamic processes inaccessible to experiments. Ram moved to the Institute of Biochemistry II, Goethe University, in September 2020 as a team leader for Computational Cell Biology to work on Data integration problems, modeling, and simulations of complex systems. He is interested in understanding biophysical mechanisms shaping the complex cellular architecture at various scales. His research focuses on developing computational tools to analyze and decipher molecular mechanisms.

Alberto Cristiani studied at the University of Trieste, Italy, and graduated with a degree in Nano-Biotechnology. For his bachelor’s thesis, he worked on identifying inhibitors of Pin1 at the LNCIB laboratory, Italy. He then switched fields to study Computational Biology by joining the Master’s program in Systems Biology at Newcastle University. During this period, he acquired an interdisciplinary skillset and an interest in the quantitative modeling of biological systems. As part of his thesis, he developed a method to automatically detect a set of functional Boolean Networks within the larger gene regulatory networks. After his Master’s degree, he worked briefly as a programmer (AI and Gameplay) at Symmetrical and later as an ETL developer in the Business Intelligence unit of NTT Data, Italy. Alberto then returned to academics and is now a Ph.D. student at the Computational Cell Biology group. He is currently developing pipelines for data acquisition and machine learning in order to explore the biology of the autophagy, ubiquitin, and SUMO systems.

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After finishing high school in Vietnam, Duy studied and graduated in Bachelor Biophysics at the University of Frankfurt am Main. Since then he is pursuing his Master's degree in Biochemistry, also from Goethe University Frankfurt am Main. His main focus is on Bioinformatics, Data Science and Autophagy. For his Master thesis, he is using data science approaches to identify novel autophagy receptors.

Izabela is a Master student (Biophysics) at the Johann Wolfgang von Goethe University in Frankfurt. For her bachelor's thesis, she studied simulations of strongfield ionization processes in three-dimensional laserfields at the Institute of Atomic Physics. She is currently pursuing an internship in the CCB group and is interested in image processing approaches to quantify organelle morphology.

Kateryna Lohachova obtained both her Bachelor and Master degrees in Chemistry from V.N. Karazin Kharkiv National University under the supervision of Prof. Oleg Kalugin. She studied the electrochemical applications of binary non-aqueous systems based on 1:1 electrolytes, ionic liquids, and molecular liquids. Her research was dedicated to exploring the features of molecular dynamics modeling as a method for predicting the behavior of ion-molecular systems, as well as the peculiarities of transport properties and ionic aggregation in such systems. During the SARS-CoV-2 pandemic, she worked with Prof. Alexander Kyrychenko as part of Prof. Oleg Kalugin’s team, on a project dedicated to the molecular design and computer modeling of new inhibitors of the SARS-CoV-2 coronavirus. In April 2022, Kateryna joined the CCB team as a fellow of IBC2 first and since August 2023 as a PhD student under the supervision of Dr. Ramachandra M. Bhaskara, focusing on the membrane remodeling. Her main work is related to quantification of membrane curvature induced by membrane remodelling proteins.

Plamen Kondev is currently pursuing his Master's degree in Biochemistry, Goethe University, Frankfurt.  He was intern in the CCB group in 2021–2022. He pursued another internship in the Münch group and returned to the CCB group in Decmber 2024 to work on his MS theisis. He is interested in Reticulon proteins and how their membrane remodeling signatures. 

Alejandro received his bachelor's degree in biology from the Pedagogical and Technological University of Colombia. He continued his academic journey by earning a Master's in Bioinformatics from the University of São Paulo (USP), where he conducted research on cancer-related protein complexes and the refinement of force-field models for coarse-grained systems. He later pursued doctoral studies at USP, focusing his thesis on investigating the NS1 protein of the Zika virus. His research, utilizing molecular simulations, explored critical aspects such as protein oligomerization, membrane binding affinity, epitope estimation, and glycosylation, providing invaluable insights into molecular mechanisms and virulence of Zika virus. Currently, Alejandro is a post-doctoral researcher at the Computational Cell Biology lab, where he studies the biophysical properties of proteins involved in autophagy, with a particular emphasis on selective autophagy receptors. His primary research focuses on understanding the intrinsically disordered region (IDR) of the ER-phagy receptor FAM134B and its role in large-scale membrane remodeling events. His work revealed how the context-dependent, or "Janus-like" ensemble properties of the IDR actively influence membrane properties to both induce and sense positive membrane curvature, as well as facilitate the clustering and sorting of proteins during spontaneous budding processes. 

Siddhanta completed her Bachelor's degree (Biotechnology) from Fergusson College, Pune, India. She then pursued a Master's degree in Bioinformatics at the Bioinformatics Centre, Savitribai Phule Pune University (2016). For her Master's thesis, she worked with Dr. Manali Joshi to study the interactions of novel antimicrobial peptides with membranes. She then began her Ph.D. at the National Chemical Laboratory, Pune, in affiliation with the Academy of Scientific and Innovative Research, India under the guidance of Dr. Durba Sengupta. Her doctoral research focused on G-protein-coupled receptors (GPCRs), investigating how amino acid residues, dynamic domains, and lipid environments modulate receptor function. Following her Ph.D., she worked as a DBT-Research associate with Dr. Arnab Gupta at IISER-Kolkata, India, exploring complex aspects of membrane proteins for a brief period. Currently, Siddhanta is a postdoctoral researcher in the Computational Cell Biology (CCB) Lab, where her interests lie in the structural modeling, molecular docking, and simulation of E3 ligases, with a focus on their roles in cellular signaling and targeted protein degradation.

Postdoc (2021–2024).

Arghya is currently an Assistant professor at the Department of Physics, SRM University, India.

BS Intern & BS Thesis (2021–2023).

Carolin is currently an Education Content Manager at Seneca Learning.

MS Intern (2021).

Jonathan moved to Merck Healthcare as an intern and is currently pursuing his PhD at TU Darmstadt.

MS Intern (2024).

Karling Tan is currently finishing her Masters in Physical Biology of Cells and Cell Interactions at Goethe University Frankfurt. 

BS Intern (2024).

Leo Jankovic is currently completeing his undergraduate studies at Stanford University.