Publications of Joseph F. Rudzinski

Journal Article (18)

2023
Journal Article
Krevert, C. S.; Chavez, D.; Chatterjee, S.; Stelzl, L. S.; Pütz, S.; Roeters, S. J.; Rudzinski, J. F.; Fawzi, N. L.; Girard, M.; Parekh, S. H. et al.; Hunger, J.: Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. The Journal of Physical Chemistry Letters 14 (49), pp. 11224 - 11234 (2023)
2022
Journal Article
Kanekal, K.; Rudzinski, J. F.; Bereau, T.: Broad chemical transferability in structure-based coarse-graining. The Journal of Chemical Physics 157 (10), 104102 (2022)
Journal Article
Banerjee, A.; Sevilla, M.; Rudzinski, J. F.; Cortes Huerto, R.: Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions. Soft Matter 18 (12), pp. 2373 - 2382 (2022)
2021
Journal Article
Rudzinski, J. F.; Kloth, S.; Woerner, S.; Pal, T.; Kremer, K.; Bereau, T.; Vogel, M.: Dynamical properties across different coarse-grained models for ionic liquids. Journal of Physics: Condensed Matter 33 (22), 224001 (2021)
2020
Journal Article
Zhao, Y.; Cortes-Huerto, R.; Kremer, K.; Rudzinski, J. F.: Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model. The Journal of Physical Chemistry B 124 (20), pp. 4097 - 4113 (2020)
Journal Article
Bozkurt Varolgunes, Y.; Bereau, T.; Rudzinski, J. F.: Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders. Machine Learning: Science and Technology 1 (1), 015012 (2020)
Journal Article
Rudzinski, J. F.; Bereau, T.: Coarse-grained conformational surface hopping: Methodology and transferability. The Journal of Chemical Physics 153 (21), 0031249 (2020)
2019
Journal Article
Rudzinski, J. F.: Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. Computation 7 (3), 42 (2019)
Journal Article
Rudzinski, J. F.; Radu, M.; Bereau, T.: Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics. The Journal of Chemical Physics 150 (2), 024102 (2019)
Journal Article
Wörner, S. J.; Bereau, T.; Kremer, K.; Rudzinski, J. F.: Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations. The Journal of Chemical Physics 151 (24), 244110 (2019)
2018
Journal Article
Bereau, T.; Rudzinski, J. F.: Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Physical Review Letters 121 (25), 256002 (2018)
Journal Article
Dunn, N. J. H.; Lebold, K. M.; DeLyser, M.R.; Rudzinski, J. F.; Noid, W. G.: BOCS: Bottom-up Open-source Coarse-graining Software. The Journal of Physical Chemistry B 122 (13), pp. 3363 - 3377 (2018)
Journal Article
Rudzinski, J. F.; Bereau, T.: The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions. Computation 6 (1), 21 (2018)
Journal Article
Rudzinski, J. F.; Bereau, T.: Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. The Journal of Chemical Physics 148 (20), 204111 (2018)
2017
Journal Article
Rudzinski, J. F.; Lu, K.; Milner, S. T.; Maranas, J. K.; Noid, W. G.: Extended Ensemble Approach to Transferable Potentials for Low Resolution Coarse-Grained Models of Ionomers. Journal of Chemical Theory and Computation 13 (5), pp. 2185 - 2201 (2017)
2016
Journal Article
Rudzinski, J. F.; Bereau, T.: Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields. European Physical Journal - Special Topics 225 (8-9), pp. 1373 - 1389 (2016)
Journal Article
Rudzinski, J. F.; Kremer, K.; Bereau, T.: Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information. The Journal of Chemical Physics 144 (5), 051102 (2016)
2015
Journal Article
Rudzinski, J. F.; Noid, W. G.: A generalized-Yvon-Born-Green method for coarse-grained modeling Advances, Challenges, and Insight. European Physical Journal 224 (12), pp. 2193 - 2216 (2015)

Meeting Abstract (6)

2021
Meeting Abstract
Bozkurt Varolgunes, Y.; Bereau, T.; Rudzinski, J. F.: Automated Identification of Collective Variables and Metastable States from Molecular Dynamics Data. In Biophysical Journal, 120, 382-Pos, p. 79A - 79A. 65th Biophysical Society Annual Meeting, Virtual, Online, February 22, 2021 - February 26, 2021. Cell Press, Cambridge, Mass. (2021)
2020
Meeting Abstract
Zhao, Y.; Cortes Huerto, R.; Kremer, K.; Rudzinski, J. F.: Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model. In Biophysical Journal, 118 3 Ed., 286-Pos, p. 58A. 64th Annual Meeting of the Biophysical-Society, San Diego, CA, February 15, 2020 - February 19, 2020. Cell Press, Cambridge, Mass. (2020)
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