Thermodynamic Interpolation: A generative approach to molecular thermodynamics and kinetics

Authors: Moqvist, Selma, Chen, Weilong, Schreiner, Mathias, Nüske, Feliks, Olsson, Simon

Subject Terms: Physics - Chemical Physics

Access URL: http://arxiv.org/abs/2411.10075

Boltzmann priors for Implicit Transfer Operators

Authors: Diez, Juan Viguera, Schreiner, Mathias, Engkvist, Ola, Olsson, Simon

Subject Terms: Physics - Chemical Physics

Access URL: http://arxiv.org/abs/2410.10605

SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching

Authors: Irwin, Ross, Tibo, Alessandro, Janet, Jon Paul, Olsson, Simon

Subject Terms: Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Neural and Evolutionary Computing

Access URL: http://arxiv.org/abs/2406.07266

Navigating protein landscapes with a machine-learned transferable coarse-grained model

Authors: Charron, Nicholas E., Musil, Felix, Guljas, Andrea, Chen, Yaoyi, Bonneau, Klara, Pasos-Trejo, Aldo S., Venturin, Jacopo, Gusew, Daria, Zaporozhets, Iryna, Krämer, Andreas, Templeton, Clark, Kelkar, Atharva, Durumeric, Aleksander E. P., Olsson, Simon, Pérez, Adrià, Majewski, Maciej, Husic, Brooke E., Patel, Ankit, De Fabritiis, Gianni, Noé, Frank, Clementi, Cecilia

Subject Terms: Quantitative Biology - Biomolecules, Physics - Biological Physics, Physics - Chemical Physics, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2310.18278

Ecosystem Models Based on Artificial Intelligence

Authors: Strannegard, Claes, Engsner, Niklas, Eisfeldt, Jesper, Endler, John, Hansson, Amanda, Lindgren, Rasmus, Mostad, Petter, Olsson, Simon, Perini, Irene, Reese, Heather, Taylan, Fulya, Ulfsbacker, Simon, Nordgren, Ann

Source: 2022 Swedish Artificial Intelligence Society Workshop (SAIS) Artificial Intelligence Society Workshop (SAIS), 2022 Swedish. :1-9 Jun, 2022

Relation: 2022 Swedish Artificial Intelligence Society Workshop (SAIS)

Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics

Authors: Schreiner, Mathias, Winther, Ole, Olsson, Simon

Subject Terms: Physics - Chemical Physics, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2305.18046

AI Tool for Exploring How Economic Activities Impact Local Ecosystems

Authors: Strannegård, Claes, Engsner, Niklas, Lindgren, Rasmus, Olsson, Simon, Endler, John

Subject Terms: Computer Science - Multiagent Systems, 92B20, I.2.6, J.3

Access URL: http://arxiv.org/abs/2301.10507

Markov Field Models: scaling molecular kinetics approaches to large molecular machines

Authors: Hempel, Tim, Olsson, Simon, Noé, Frank

Subject Terms: Physics - Biological Physics

Access URL: http://arxiv.org/abs/2206.11620

Machine Learning in Molecular Dynamics Simulations of Biomolecular Systems

Authors: Kolloff, Christopher, Olsson, Simon

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2205.03135

Markov State Models of protein-protein encounters

Authors: Olsson, Simon

Subject Terms: Physics - Biological Physics, Physics - Chemical Physics, Physics - Computational Physics, Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2105.02767

Coarse Graining Molecular Dynamics with Graph Neural Networks

Authors: Husic, Brooke E., Charron, Nicholas E., Lemm, Dominik, Wang, Jiang, Pérez, Adrià, Majewski, Maciej, Krämer, Andreas, Chen, Yaoyi, Olsson, Simon, de Fabritiis, Gianni, Noé, Frank, Clementi, Cecilia

Subject Terms: Physics - Computational Physics, Physics - Biological Physics, Physics - Chemical Physics, Quantitative Biology - Biomolecules, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2007.11412

Boltzmann Generators -- Sampling Equilibrium States of Many-Body Systems with Deep Learning

Authors: Noé, Frank, Olsson, Simon, Köhler, Jonas, Wu, Hao

Subject Terms: Statistics - Machine Learning, Condensed Matter - Statistical Mechanics, Computer Science - Machine Learning, Physics - Chemical Physics

Access URL: http://arxiv.org/abs/1812.01729

Machine Learning of coarse-grained Molecular Dynamics Force Fields

Authors: Wang, Jiang, Olsson, Simon, Wehmeyer, Christoph, Perez, Adria, Charron, Nicholas E., de Fabritiis, Gianni, Noe, Frank, Clementi, Cecilia

Subject Terms: Physics - Computational Physics, Computer Science - Machine Learning, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/1812.01736

Thermodynamic Interpolation: A Generative Approach to Molecular Thermodynamics and Kinetics.

Authors: Moqvist, Selma, Chen, Weilong, Schreiner, Mathias, Nüske, Feliks, Olsson, Simon

Source: Journal of Chemical Theory & Computation; 3/11/2025, Vol. 21 Issue 5, p2535-2545, 11p

Motional clustering in supra-[formula omitted] conformational exchange influences NOE cross-relaxation rate

Authors: Kolloff, Christopher, Mazur, Adam, Marzinek, Jan K., Bond, Peter J., Olsson, Simon, Hiller, Sebastian

Source: In Journal of Magnetic Resonance May 2022 338

De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models

Authors: Atance, Sara Romeo, Diez, Juan Viguera, Engkvist, Ola, Olsson, Simon, Mercado, Rocío

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(20):4863-4872

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632699283&indx=1&recIds=ETOCRN632699283

Discovery of a hidden transient state in all bromodomain families

Authors: Raich, Lluís, Meier, Katharina, Günther, Judith, Christ, Clara D., Noé, Frank, Olsson, Simon

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Jan . 118(4), 1-7.

Access URL: https://www.jstor.org/stable/27006014

Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity

Authors: Hoffmann, Markus, Hofmann-Winkler, Heike, Smith, Joan C., Krüger, Nadine, Arora, Prerna, Sørensen, Lambert K., Søgaard, Ole S., Hasselstrøm, Jørgen Bo, Winkler, Michael, Hempel, Tim, Raich, Lluís, Olsson, Simon, Danov, Olga, Jonigk, Danny, Yamazoe, Takashi, Yamatsuta, Katsura, Mizuno, Hirotaka, Ludwig, Stephan, Noé, Frank, Kjolby, Mads, Braun, Armin, Sheltzer, Jason M., Pöhlmann, Stefan

Source: In EBioMedicine March 2021 65

Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration.

Authors: Pasarkar, Amey P., Bencomo, Gianluca M., Olsson, Simon, Dieng, Adji Bousso

Source: Journal of Chemical Physics; 10/14/2023, Vol. 159 Issue 14, p1-11, 11p

Subject Terms: MOLECULAR conformation, METASTABLE states, MOLECULAR dynamics, STATISTICAL sampling, SAMPLING (Process)

Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostatElectronic supplementary information (ESI) available. See DOI: 10.1039/d0sc05064d

Authors: Hempel, Tim, Raich, Lluís, Olsson, Simon, Azouz, Nurit P., Klingler, Andrea M., Hoffmann, Markus, Pöhlmann, Stefan, Rothenberg, Marc E., Noé, Frank

Source: Chemical science. 12(3):983-992

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100116424567.0x000001&indx=1&recIds=ETOCvdc_100116424567.0x000001