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Chemistry

D-Index
50
Citations
11189
World Ranking
14257
National Ranking
1037

Overview

Cecilia Clementi is affiliated with Freie Universität Berlin in Germany. Their research spans topics in biochemistry, genetics, molecular biology, and materials science. Within these broad fields, their work focuses particularly on materials chemistry, molecular biology, atomic and molecular physics, optics, statistical and nonlinear physics, and computational theory and mathematics.

The research topics they have contributed to include:

  • Protein Structure and Dynamics
  • Machine Learning in Materials Science
  • Computational Drug Discovery Methods
  • Enzyme Structure and Function
  • Block Copolymer Self-Assembly
  • Model Reduction and Neural Networks
  • Vaccines and Immunoinformatics Approaches

Their recent publications illustrate an emphasis on molecular simulation, machine learning techniques, and coarse-graining approaches in molecular dynamics. Notable papers include:

  • Unsupervised Learning Methods for Molecular Simulation Data, 2021, Chemical Reviews
  • Data-driven approximation of the Koopman generator: Model reduction, system identification, and control, 2020, Physica D Nonlinear Phenomena
  • TorchMD: A Deep Learning Framework for Molecular Simulations, 2021, Journal of Chemical Theory and Computation
  • Coarse graining molecular dynamics with graph neural networks, 2020, Refubium (Universitätsbibliothek der Freien Universität Berlin)
  • Machine learning coarse-grained potentials of protein thermodynamics, 2023, Nature Communications

Frequent co-authors collaborating with Cecilia Clementi include:

  • Frank Noé
  • Yaoyi Chen
  • Andreas Krämer
  • Nicholas E. Charron
  • Félix Musil

The scientist's work has been published multiple times in prominent venues, demonstrating a consistent engagement with several key journals and repositories. These frequent publication venues include:

  • arXiv (Cornell University)
  • The Journal of Chemical Physics
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Nature Communications
  • Journal of Chemical Theory and Computation

Best Publications

  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

    Cecilia Clementi;Hugh Nymeyer;José Nelson Onuchic

  • Machine Learning for Molecular Simulation.

    Frank Noé;Frank Noé;Alexandre Tkatchenko;Klaus Robert Müller;Klaus Robert Müller;Klaus Robert Müller;Cecilia Clementi;Cecilia Clementi

  • Machine Learning of Coarse-Grained Molecular Dynamics Force Fields.

    Jiang Wang;Simon Olsson;Christoph Wehmeyer;Adrià Pérez

  • Coarse-grained models of protein folding: toy models or predictive tools?

    Cecilia Clementi

  • Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    Payel Das;Mark Moll;Hernán Stamati;Lydia E. Kavraki

  • Unsupervised Learning Methods for Molecular Simulation Data.

    Aldo Glielmo;Brooke E. Husic;Alex Rodriguez;Cecilia Clementi

  • AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

    Aram Davtyan;Nicholas P. Schafer;Weihua Zheng;Cecilia Clementi

  • Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates.

    Leslie L Chavez;José N Onuchic;Cecilia Clementi

  • Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

    Frank Noé;Cecilia Clementi

  • How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta.

    Cecilia Clementi;Patricia A. Jennings;José N. Onuchic

  • Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

    Mary A. Rohrdanz;Wenwei Zheng;Cecilia Clementi

  • Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globular proteins

    Cecilia Clementi;Hugh Nymeyer;Jose' Nelson Onuchic

  • TorchMD: A Deep Learning Framework for Molecular Simulations.

    Stefan Doerr;Maciej Majewski;Adrià Pérez;Andreas Krämer

  • Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

    Cecilia Clementi;Angel E. Garcı́a;José N. Onuchic

  • The effects of nonnative interactions on protein folding rates: theory and simulation.

    Cecilia Clementi;Cecilia Clementi;Steven S. Plotkin

  • Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods.

    Frank Noé;Cecilia Clementi

  • Dynamics of polymer translocation through nanopores: theory meets experiment.

    Silvina Matysiak;Alberto Montesi;Matteo Pasquali;Anatoly B. Kolomeisky

  • Coarse graining molecular dynamics with graph neural networks

    Brooke E Husic;Nicholas E Charron;Dominik Lemm;Jiang Wang

  • Adaptive resolution simulation of liquid water

    Matej Praprotnik;Silvina Matysiak;Luigi Delle Site;Kurt Kremer

  • From coarse-grain to all-atom: toward multiscale analysis of protein landscapes.

    Allison P. Heath;Lydia E. Kavraki;Cecilia Clementi;Cecilia Clementi

  • Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes

    Payel Das;Silvina Matysiak;Cecilia Clementi

Frequent Co-Authors

Lydia E. Kavraki
Lydia E. Kavraki Rice University
José N. Onuchic
José N. Onuchic Rice University
Klaus-Robert Müller
Klaus-Robert Müller Technical University of Berlin
Shantenu Jha
Shantenu Jha Rutgers, The State University of New Jersey
Kurt Kremer
Kurt Kremer Max Planck Institute for Polymer Research
Peter G. Wolynes
Peter G. Wolynes Rice University
Charles A. Laughton
Charles A. Laughton University of Nottingham
Mauro Maggioni
Mauro Maggioni Johns Hopkins University
Paolo Carloni
Paolo Carloni Forschungszentrum Jülich
Alexandre Tkatchenko
Alexandre Tkatchenko University of Luxembourg

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