Anda Trifan

  • Program Year: 4
  • Academic Institution: University of Illinois at Urbana-Champaign
  • Field of Study: Theoretical and Computational Biophysics
  • Academic Advisor: Emad Tajkhorshid
  • Practicum(s):
    Argonne National Laboratory (2020)
    Argonne National Laboratory (2021)
  • Degree(s):
    B.S. Chemistry, DePaul University, 2012

Publications

Anda Trifan, Defne Gorgun, ..., Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, Arvind Ramanathan. Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action. IJHPCA, 2022 (Accepted) Gordon Bell COVID Special Prize Finalist.

Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, ..., Arvind Ramanathan, Lillian Chong, Rommie Amaro. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. IJHPCA, 2022 (Accepted) Gordon Bell COVID Special Prize Finalist.

Anda Trifan, Till Rudak, Joshua Vermaas, and Emad Tajkhorshid. Systematic study of the K-Ras functional regions: HVR's important role in orienting the G-domain. ?Biophys Journal, 2021 (In Progress).

Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, ..., John E.Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro.AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. IJHPCA, 2021. Gordon Bell COVID Special Prize Winner.

Austin Clyde, Daniel Kneller, ..., Anda Trifan, ..., Shantenu Jha, Arvind Ramanathana, and Rick Stevens. High Throughput Virtual Screening and Validation of a Non-Covalent Inhibitor of the SARS-CoV-2 Main Protease. JCIM, 2021 (cover)

Agastya P. Bhati, ..., Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V. Coveney. Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics based Simulations on High Performance Computers. Interface Focus, 2021

Alexander Brace, Hyungro Lee, Heng Ma, Anda Trifan, Matteo Turilli, Igor Yaskushin, Todd Munson, Ian Foster, Shantenu Jha, Arvind Ramanathan. Achieving 1000X faster simulations of complex biological phenomena by coupling ML to HPC ensembles. IPDPS, 2021 (review)

Alexander Brace, Michael Salim, Vishal Subbiah, HengMa, Murali Emani,Anda Trifan, Corey Adams, Thomas Uram, Hyunseung Yoo, Andrew Hock, Jessica Liu, Venkatram Vishwanath, Arvind Ramanathan. Stream-AI-MD: Streaming AI-driven Adaptive Molecular Simulations for Heterogeneous Computing Platforms. PASC21, 2021.

Aymen Al Saadi, ...,Anda Trifan, ... Arvind Ramanathan, Ashka Shah, Abraham Stern, Rick Stevens, Li Tan, Mikhail Titov, Aristeidis Tsaris, Matteo Turilli, Huub Van Dam, Shunzhou Wan, David Wifling. IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. PASC21, 2021.

Hyungro Lee, Andre Merzky, ...,Anda Trifan, ... , Shantenu Jha. Scalable HPC & AI Infrastructure for COVID-19 Therapeutics. https://arxiv.org/abs/2010.10517

Janina Sprenger, Anda Trifan, Neal Patel, Ashley Vanderbeck, Jenny Bredtfelt, Emad Tajkhorshid, Roger Rowlett, LeilaLo Leggio, Karin Akerfeldt, Sara Linse. Calmodulin complexes with brain and muscle creatine kinase peptides. Current Research in Structural Biology, 2020.

Heng Ma, Austin Clyde, Anda Trifan, Venkatram Vishwanath, Debsindhu Bhowmik, Shantenu Jha, Arvind Ramanathan. Benchmarking Machine Learning Workloads in Structural Bioinformatics Applications. Challenge20, 2020.

Muller, M.P., Jiang, T., Sun C., Lihan M., Pant S., Mahinthinchaichan, P.,Trifan, A., Tajkhorshid, E. Characterization of Lipids. Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chemical Reviews. 119, 9, 6086-6161, 2019.

G.B. Kharas, N.E. Anderson, A. Bajor, A.C. Colbert, A. Coleman, C.E. Gregory, J. Hayes, J. Lantin, J.M. Malecki, T.C.Murphy,A. Oprescu, B.F. Rydzon, and I. Timoshevskaya.Novel Copolymers of Di- and Trialkoxy Ring-substituted Ethyl2-Cyano-3-phenyl-2-propenoates and Styrene. J. Macromol. Sci, 2013



Talks

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action. Supercomputing '21. Gordon Bell COVID Special Prize Finalist Talk.

Alumni Speaker DePaul University Awards symposium, June, 2021 (Invited)

Great Promise in COMP talk- Deep learning reveals wild-type and mutant Ras dimer interface formation in membranes, ACS Fall, August, 2021 (Award)

Deep learning driven adaptive sampling methods for targeting SARS-CoV-2 proteins, ACS Fall, August 2021 (Invited)

Awards

ACM Gordon Bell Special Prize Finalist for HPC-Based COVID-19 Research, SC21 Conference, 2021
ACM Gordon Bell Special Prize Finalist for HPC-Based COVID-19 Research, SC21 Conference, 2021
Promise in Computational Chemistry Award, ACS 2021
College of Liberal Arts and Science (UIUC) Impact Award, 2021
Secretary of Energy Achievement Honor Award, National Virtual Biotechnology Laboratory (NVBL)
ACM Gordon Bell Special Prize for HPC-Based COVID-19 Research, SC20 Conference, 2020
Impact Argonne Award for Discovery, Argonne National Laboratory, 2020
Impact Argonne Award for Innovation, Argonne National Laboratory, 2020
Impact Argonne Award for Extraordinary Effort, Argonne National Laboratory, 2020
BIOCHEMISTRY TRAVEL AWARD (2019)
BIOPHYSICS TRAVEL AWARD (2019)
Colin A Wraight Graduate Award (2017)
Biophysics Fellowship (2017)
Kelly Services Emerald Award (2014)
C. and K. Jonaitis Chemistry Award (2012)
DePaul University Department of Chemistry Scholarship (2011)
DePaul University Presidential Scholarship (2009-2012)
DePaul University Dean's List (2009-2012)