PRINCIPAL INVESTIGATOR
Bercem Dutagaci, PhD
Assistant Professor
Office: Science and Engineering Building 1, room 396
bdutagaci@ucmerced.edu
209-228-3603
Bercem Dutagaci received her bachelor degree in Chemistry at 2006 and her master degree at 2008 from the Bogazici University, Istanbul, Turkey. She then moved to Frankfurt, Germany to pursue her PhD in Biochemistry at Johann Wolfgang Goethe University, where she has worked on membrane biophysics using solid-state NMR techniques and computer simulations. After her graduation at 2013, she went back to Bogazici University in Istanbul for a postdoctoral training in in-silico drug research. In 2015, she started her postdoctoral research in Michigan State University, where she has worked on various projects including implicit membrane development, protein structure refinement, and predictions of membrane permeation of drug molecules. Lately, she started to be interested in larger scale biological questions related to eukaryotic transcription and phase separation events in cellular system. She joined UC Merced in January 2021 and her research focuses on transcription processes using computational techniques.
POSTDOCTORAL RESEARCHERS
Weththasinghage Don Amith, PhD
Postdoctoral researcher, 2021-2024
Volunteer researcher, 2024-present
wamith@ucmerced.edu
Amith received his B.Sc. degree in computational chemistry from the University of Colombo, Sri Lanka in 2014. Then he moved to the University of Iowa where he worked on investigating structural and dynamical properties of typical vs special ionic liquids in the bulk form and at interfaces. He received his PhD degree in 2021 from the University of Iowa. Between 2021 and 2024, he worked at UC Merced as a postdoctoral researcher and now he continues his work as a volunteer researcher. He is working on the dynamics and spatial organization of RNA polymerase during the transcription events using multi-scale molecular dynamics simulations and machine learning techniques.
GRADUATE STUDENTS
Negin Safaei Hashkavaei
Graduate Student, 2024-Present
Office: Science and Engineering Building 1, room 394
nsafaeihashkavaei@ucmerced.edu
Negin obtained her B.S. in cellular and molecular biology and genetics in 2019. Then, she obtained her M.Sc. in biochemistry at the Protein Research Center at Shahid Beheshti University in 2022, where she worked on the investigation into the structural peculiarities of the receptor binding domains of the spike protein from the SARS-CoV-2 using computational methods. Afterward, she started to pursue her research interests as a graduate student at the Quantitative and Systems Biology program at UC Merced in 2024. Here, she studies the effects of elongation factor proteins on the dynamics and conformation of the RNA polymerase enzyme and link these effects to the function of the enzyme to develop new hypotheses.
Adan Gallardo
Graduate Student, 2021-Present
Office: Science and Engineering Building 1, room 394
agallardo10@ucmerced.edu
Adan obtained his B.S in biology with a concentration on human emphasis in May of 2022. He enrolled into UC Merced with a concrete goal of becoming a doctor and pursuing his degree in medicine. During his years at UC Merced, he encountered a newly developed passion towards deepening his knowledge on molecular systems and research. As a result, he started to pursue a PhD degree at the Quantitative and Systems Biology program at UC Merced in 2024. Here, he studies protein nucleic acid interactions between DNA/RNA and elongation factors that form an elongation complex with RNA polymerase II during transcription.
UNDERGRADUATE STUDENTS
Shashank Shriram
Undergraduate Student, 2022-Present
Office: Science and Engineering Building 1, room 398
sshriram2@ucmerced.edu
FORMER MEMBERS
Vincent Chen, undergraduate student, 2022-2024
Bereinda Younan Anhar, undergraduate student, 2023
Oliver Cantrell, undergraduate Student at Bakersfield College, UROC CV PATH Scholar, Summer 2023
Shiwani Limbu, graduate student, 2021-2022
Brandon M. Bogart, graduate student, 2021-2022
JOIN US
Graduate and undergraduate students interested in transcription events and computer simulations are welcome to join!