Search Results - "Roet, Sander"

Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms by Chaillet, Marten L, van der Schot, Gijs, Gubins, Ilja, Roet, Sander, Veltkamp, Remco C, Förster, Friedrich

“…Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often…”
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Exact non-Markovian permeability from rare event simulations by Ghysels, An, Roet, Sander, Davoudi, Samaneh, van Erp, Titus S.

“…Permeation of compounds through membranes is important in biological and engineering processes, e.g., drug delivery through lipid bilayers, anesthetics, or…”
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Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning by Roet, Sander, Daub, Christopher D, Riccardi, Enrico

“…We propose to analyze molecular dynamics (MD) output via a supervised machine learning (ML) algorithm, the decision tree. The approach aims to identify the…”
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Exchanging Replicas with Unequal Cost, Infinitely and Permanently by Roet, Sander, Zhang, Daniel T., van Erp, Titus S.

“…We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are…”
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Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps by Zhang, Daniel T, Baldauf, Lukas, Roet, Sander, Lervik, Anders, van Erp, Titus S

“…Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue…”
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PyRETIS 3: Conquering rare and slow events without boundaries by Vervust, Wouter, Zhang, Daniel T, Ghysels, An, Roet, Sander, van Erp, Titus S, Riccardi, Enrico

“…We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation,…”
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Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas by Roet, Sander, Hooft, Ferry, Bolhuis, Peter G., Swenson, David W. H., Vreede, Jocelyne

“…Flexibility is essential for many proteins to function, but can be difficult to characterize. Experiments lack resolution in space and time, while the time…”
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PyRETIS 2: An improbability drive for rare events by Riccardi, Enrico, Lervik, Anders, Roet, Sander, Aarøen, Ola, Erp, Titus S.

“…The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method…”
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Chemistrees: data driven identification of reaction pathways via machine learning by Roet, Sander, Daub, Christopher David, Riccardi, Enrico

“…J. Chem. Theory Comput. 2021, 17, 10, 6193-6202 We propose a supervised machine learning algorithm, decision trees, to analyze molecular dynamics output. The…”
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Exchanging replicas with unequal cost, infinitely and permanently by Roet, Sander, Zhang, Daniel T, van Erp, Titus S

“…We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are…”
Get full text