Joseph F. Rudzinski
Title
Cited by
Cited by
Year
Coarse-graining entropy, forces, and structures
JF Rudzinski, WG Noid
The Journal of chemical physics 135 (21), 214101, 2011
1182011
Influence of target concentration and background binding on in vitro selection of affinity reagents
J Wang, JF Rudzinski, Q Gong, HT Soh, PJ Atzberger
PLoS One 7 (8), e43940, 2012
502012
Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method
JF Rudzinski, WG Noid
The Journal of Physical Chemistry B 118 (28), 8295-8312, 2014
442014
Bottom-up coarse-graining of peptide ensembles and helix–coil transitions
JF Rudzinski, WG Noid
Journal of chemical theory and computation 11 (3), 1278-1291, 2015
402015
The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure
JF Rudzinski, WG Noid
The Journal of Physical Chemistry B 116 (29), 8621-8635, 2012
352012
Scaling behavior and local structure of ion aggregates in single-ion conductors
K Lu, JF Rudzinski, WG Noid, ST Milner, JK Maranas
Soft Matter 10 (7), 978-989, 2014
332014
Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information
JF Rudzinski, K Kremer, T Bereau
The Journal of chemical physics 144 (5), 051102, 2016
252016
A generalized-Yvon-Born-Green method for coarse-grained modeling
JF Rudzinski, WG Noid
The European Physical Journal Special Topics 224 (12), 2193-2216, 2015
232015
Generalized‐Yvon–Born–Green Model of Toluene
CR Ellis, JF Rudzinski, WG Noid
Macromolecular Theory and Simulations 20 (7), 478-495, 2011
222011
BOCS: Bottom-Up Open-Source Coarse-Graining Software
NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid
The Journal of Physical Chemistry B, 2017
182017
Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
JF Rudzinski, T Bereau
The European Physical Journal Special Topics 225 (8-9), 1373-1389, 2016
132016
Extended Ensemble Approach to Transferable Potentials for Low-Resolution Coarse-Grained Models of Ionomers
JF Rudzinski, K Lu, ST Milner, JK Maranas, WG Noid
Journal of Chemical Theory and Computation 13 (5), 2185-2201, 2017
102017
Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
T Bereau, JF Rudzinski
Physical Review Letters 121 (25), 256002, 2018
72018
Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models
JF Rudzinski, T Bereau
The Journal of Chemical Physics 148 (20), 204111, 2018
62018
Recent progress towards chemically-specific coarse-grained simulation models with consistent dynamical properties
JF Rudzinski
Computation 7 (3), 42, 2019
52019
The role of conformational entropy in the determination of structural-kinetic relationships for helix-coil transitions
JF Rudzinski, T Bereau
Computation 6 (1), 21, 2018
42018
Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders
YB Varolgüneş, T Bereau, JF Rudzinski
Machine Learning: Science and Technology 1 (1), 015012, 2020
22020
Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model
Y Zhao, R Cortes-Huerto, K Kremer, JF Rudzinski
The Journal of Physical Chemistry B 124 (20), 4097-4113, 2020
2020
Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations
SJ Wörner, T Bereau, K Kremer, JF Rudzinski
The Journal of Chemical Physics 151 (24), 244110, 2019
2019
Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics
JF Rudzinski, M Radu, T Bereau
The Journal of chemical physics 150 (2), 024102, 2019
2019
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Articles 1–20