Publications of Joseph F. Rudzinski

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)

Rudzinski, J. F.; Bereau, T.: Consistent representation of structural and dynamical properties from coarse-grained simulation models. In Abstracts of Papers of the American Chemical Society, 258, 22-COMP. ACS Fall National Meeting and Exposition, San Diego, CA, August 25, 2019 - August 29, 2019. (2019)

Rudzinski, J. F.; Kremer, K.; Bereau, T.: Characterization of Coarse-Grained Helix-Coil Transition Kinetics using Markov State Models. In Biophysical Journal, 112 (3), 958-Pos, pp. 194A - 194A . 61st Annual Meeting of the Biophysical-Society, New Orleans, LA, February 11, 2017 - February 15, 2017. Cell Press, Cambridge, Mass. (2017)