Publications of Joseph F. Rudzinski

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)

Kanekal, K.; Rudzinski, J. F.; Bereau, T.: Broad chemical transferability in structure-based coarse-graining. The Journal of Chemical Physics 157 (10), 104102 (2022)

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)

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)

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)

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)

Rudzinski, J. F.; Bereau, T.: Coarse-grained conformational surface hopping: Methodology and transferability. The Journal of Chemical Physics 153 (21), 0031249 (2020)

Rudzinski, J. F.: Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. Computation 7 (3), 42 (2019)

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)

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)

Bereau, T.; Rudzinski, J. F.: Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Physical Review Letters 121 (25), 256002 (2018)

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)

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)

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)

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)

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)

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)

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)

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)

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)