Author

S. Samantray

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· 3

Signature Assays, Organisms & Methods

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Approach:mechanistic / dynamical model· 3 Research Focus:protein folding & dynamics· 1 Assay:protein structure· 1

Frequent Co-Authors

B. Strodel· 3 shared A. Paul· 2 shared A.-M. Illig· 1 shared B. Barz· 1 shared B. Kav· 1 shared F. Yin· 1 shared M. Anteghini· 1 shared M. Carballo-Pacheco· 1 shared

Activity by Year

2020-2020 · peak 3/yr

Co-Author Collaboration Network

9 top collaborators · 20 mutual co-author links

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3 shared papersBiophysics

B. Strodel

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3 papers

Recent·Most cited

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations

S. Samantray, F. Yin, B. Kav, B. Strodel

This study evaluates new force fields for simulating amyloid-beta peptide aggregation, finding that force field choice significantly affects aggregation pathways and that CHARMM36m performs best.

bioRxiv · Sep 9, 2020Biophysics

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

A. Paul, S. Samantray, M. Anteghini, B. Strodel

This study uses 30-microsecond MD simulations with seven force fields to analyze the thermodynamics and kinetics of Aβ40, identifying suitable force fields and equilibrium times.

bioRxiv · Jul 27, 2020Biophysics

Molecular dynamics simulations of protein aggregation: protocols for simulation setup and analysis with Markov state models and transition networks

S. Samantray, W. Schumann, A.-M. Illig, M. Carballo-Pacheco, A. Paul, B. Barz, B. Strodel

The paper provides protocols for setting up and analyzing molecular dynamics simulations of peptide aggregation using GROMACS, including tools for determining oligomer size and deriving Markov state models and transition networks.

bioRxiv · Apr 25, 2020 · PreprintBiophysics