Author

A. Bogetti

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6

Signature Assays, Organisms & Methods

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Approach:deep learning· 4 Research Focus:benchmarking· 2 Approach:statistical model· 2 Organism:virus· 2 Research Focus:clustering· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Assay:imaging· 1

Frequent Co-Authors

L. Chong· 4 shared J. Russo· 3 shared A. Brace· 2 shared A. Stern· 2 shared A. Trifan· 2 shared D. Hardy· 2 shared D. LeBard· 2 shared D. M. Zuckerman· 2 shared

Activity by Year

2020-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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4 shared papersBiophysics

L. Chong

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6 papers

Recent·Most cited

LPATH: A semi-automated Python tool for clustering molecular pathways

A. Bogetti, J. M. Leung, L. Chong

The paper introduces LPATH, a Python tool for clustering molecular pathways using linguistics-assisted methods, demonstrating its effectiveness on alanine dipeptide conformational transitions.

bioRxiv · Aug 17, 2023 · PreprintBiophysics

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

A. Bogetti, J. Leung, J. Russo, S. Zhang, J. Thompson, A. Saglam, D. Ray, R. Abraham, J. Faeder, I. Andricioaei, J. Adelman, M. Zwier, D. LeBard, D. M. Zuckerman, L. Chong

The paper provides advanced tutorials for WESTPA 2.0, demonstrating new features for rare-events sampling in molecular simulations.

bioRxiv · Oct 4, 2022 · PreprintBiophysics

WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications

J. Russo, S. Zhang, J. Leung, A. Bogetti, J. Thompson, A. DeGrave, P. Torrillo, A. J. Pratt, K. Wong, J. Xia, J. T. Copperman, J. Adelman, M. Zwier, D. LeBard, D. M. Zuckerman, L. Chong

The paper introduces WESTPA 2.0, an upgraded software package for weighted ensemble simulations, enhancing efficiency and analysis of longer-timescale applications.

bioRxiv · Dec 5, 2021Biophysics

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

A. Dommer, L. Casalino, F. Kearns, M. Rosenfeld, N. Wauer, S.-H. Ahn, J. Russo, S. Oliveira, C. Morris, A. Bogetti, A. Trifan, A. Brace, T. Sztain, A. Clyde, H. Ma, , Muholland

This paper uses AI-enabled multiscale computational microscopy to study SARS-CoV-2 Delta variant in respiratory aerosols, revealing atomic-level insights into airborne transmission.

bioRxiv · Nov 12, 2021Biophysics

The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations

A. J. DeGrave, A. Bogetti, L. T. Chong

The RED scheme improves rate-constant estimation from simulations by using event duration distributions, achieving up to 50% greater efficiency than existing methods.

bioRxiv · Dec 21, 2020Biophysics

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

L. Casalino, A. C. Dommer, Z. Gaieb, E. P. Barros, T. Sztain, S.-H. Ahn, A. Trifan, A. Brace, H. Ma, H. Lee, M. Turilli, A. Bogetti, S. Khalid, L. Chong, C. Simmerling, , R. E. Amaro

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

bioRxiv · Nov 19, 2020Biophysics