Publications
For our complete publication profile, please check our Google Scholar profile.
2026:
2025:
– Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, Thomas E Cheatham III, Shi‐Jie Chen, Arne Elofsson, Masoud Amiri Farsani, Olivia N Fisher, M Michael Gromiha, Ayush Gupta, Michiaki Hamada, K Harini, Gang Hu, David Huang, Junichi Iwakiri, Anika Jain, Yuki Kagaya, Daisuke Kihara, Sebastian Kmiecik, Sowmya Ramaswamy Krishnan, Ikuo Kurisaki, Olivier Languin‐Cattoën, Jun Li, Shanshan Li, Karim Malekzadeh, Tsukasa Nakamura, Wentao Ni, Chandran Nithin, Michael Z Palo, Joon Hong Park, Smita P Pilla, Simón Poblete, Fabrizio Pucci, Pranav Punuru, Anouka Saha, Kengo Sato, Ambuj Srivastava, Genki Terashi, Emilia Tugolukova, Jacob Verburgt, Qiqige Wuyun, Gül H Zerze, Kaiming Zhang, Sicheng Zhang, Wei Zheng, Yuanzhe Zhou, Wah Chiu, David A Case, Rhiju Das. Blind prediction of complex water and ion ensembles around RNA in CASP16. Soft Matter. doi: 10.1002/prot.70079
– Nehil Shreyash, Maninderjeet Singh, Karan Kumar Paswan, Nour Bader, Mohammad K Hassan, Jack F Douglas, Gül H Zerze, Alamgir Karim. Glassy dynamics of model complex coacervate films with variable interaction strength quantified by the critical salt concentration. Soft Matter. doi: 10.1039/d5sm00969c
– Kosar Rahimi, Albert Halbing, Minh Ngoc Nguyen, Mehmet Sen, Richard C Willson, Gül H Zerze. Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A. bioRxiv. doi: 10.64898/2025.12.08.692973
– Eduardo Ayala, Ayush Gupta, Nehil Shreyash, Arvind Ramanathan, Gül H Zerze. Classification of Human Transcription Factors Based on Their Effector Domains via Unsupervised Learning. bioRxiv. doi: 10.1101/2025.10.26.684687
– Aliasghar Sepehri, Gül H Zerze. Nucleation Landscape of Biomolecular Condensates in the Grand Canonical Ensemble via Monte Carlo Simulations. bioRxiv. doi: 10.1101/2025.06.06.658304
– Alexander RJ Silalahi, Morgan G Murray,, Gül H Zerze. A Dynamical Density Functional Theory Framework for Non-Equilibrium Phase Dynamics in Biomolecular Condensates. bioRxiv. doi: 10.1101/2025.10.02.680159
– Karim Malekzadeh, Gül H Zerze. Optimizing on-the-fly probability enhanced sampling for complex RNA systems: sampling free energy surfaces of an H-type pseudoknot. bioRxiv. doi: 10.1101/2024.10.25.620366
– Yerragunta M, Veliz AC, Warzecha M, Hadjiev VG, Florence AJ, Zerze GH, Rimer JD and Vekilov PG. Mesoscopic solute-rich clusters in organic solutions. Crys Growth Des 2025, 25(11), 3958-3967. doi: 10.1021/acs.cgd.5c00370
– Zerze H, Gupta A, Baksi A, Chakraborty D, Vekilov PG, Rimer JD, Zerze GH.A coarse-graining approach to model molecular liquids for mesoscale problems. AICHE Journal, 2025, 71(3), e18700. doi: 10.1002/aic.18700
2024:
– Burton HG, Dong SS, Ghosh S, Gu B, Jackson NE, Keefer D, Lu Y, Monroe JI, Peng B, Pieri E, Spackman PR, Vacher M, Vuckovic S, Williams-Young D, Yang ZJ, Yue S, Zerze GH, Zhu T. JCTC Early Career Board Selects. J Chem Theory Comput, 2024, 20(14), 5785-5787. doi: 10.1021/acs.jctc.4c00787
– Rahimi K, Piaggi PM, Zerze GH. Comparison of On-the-Fly Probability Enhanced Sampling and Parallel Tempering Combined with Metadynamics for Atomistic Simulations of RNA Tetraloop Folding. J Phys Chem B (Pablo G. Debenedetti Festschrift) 2023, 127(21), 4722–4732. doi: 10.1021/acs.jpcb.3c00117
– Atanu Baksi, Hasan Zerze, Aman Agrawal, Alamgir Karim, Gül H Zerze (2024.01. 12.575416). The Molecular Picture of the Local Environment in a Stable Model Coacervate. bioRxiv. doi: 10.1101/2024.01.12.575416
– Kosar Rahimi, Pablo M Piaggi, Gül H Zerze (127 (21), 4722-4732). Comparison of on-the-fly probability enhanced sampling and parallel tempering combined with metadynamics for atomistic simulations of RNA tetraloop folding. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.3c00117
– Gül H Zerze (20 (4), 1646-1655). Optimizing the Martini 3 Force Field Reveals the Effects of the Intricate Balance between Protein–Water Interaction Strength and Salt Concentration on Biomolecular Condensate Formation. Journal of Chemical Theory and Computation. doi: 10.1021/acs.jctc.2c01273
2021:
– Gül H Zerze, Pablo M Piaggi, Pablo G Debenedetti (2021/12/10 125 (50), 13685-13695). A computational study of RNA tetraloop thermodynamics, including misfolded states. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.1c08038
– Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (2021/1/12 125 (3), 771-779). Thermodynamics of DNA Hybridization from Atomistic Simulations. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.0c09237
2020:
– Pablo G Debenedetti, Francesco Sciortino, Gül H Zerze (369 (6501), 289-292 2020/7/17). Second critical point in two realistic models of water. American Association for the Advancement of Science. doi: 10.1126/science.abb9796
– Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (124 (26), 5362-5369 2020/6/5). The handedness of DNA assembly around carbon nanotubes is determined by the chirality of DNA. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.0c02816
– Alexander E Conicella, Gregory L Dignon, Gül H Zerze, Hermann Broder Schmidt, Alexandra M D’Ordine, Young C Kim, Rajat Rohatgi, Yuna M Ayala, Jeetain Mittal, Nicolas L Fawzi (117 (11), 5883-5894 2020/3/17). TDP-43 α-helical structure tunes liquid–liquid phase separation and function. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1912055117
– Alexander E Conicella, Gregory Dignon, Gül H Zerze, Broder Schmidt, MD Alexandra, Youngchan Kim, Rajat Rohatgi, Yuna M Ayala, Jeetain Mittal, Nicolas L Fawzi (118 (3), 5a-6a 2020/2/7). Alpha-Helical Structure in TDP-43 Tunes Liquid-liquid Phase Separation and Cellular Function. Biophysical Journal. doi: 10.1016/j.bpj.2019.11.223
– Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (594 (1), 104-113 2020/1). Computational investigation of retro-isomer equilibrium structures: Intrinsically disordered, foldable, and cyclic peptides. FEBS letters. doi: 10.1002/1873-3468.13558
2019:
– Anastasia C Murthy, Gregory L Dignon, Yelena Kan, Gül H Zerze, Sapun H Parekh, Jeetain Mittal, Nicolas L Fawzi (26 (7), 637-648 2019/7). Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain. Nature structural & molecular biology. doi: 10.1038/s41594-019-0250-x
– Gül H Zerze, Frank H Stillinger, Pablo G Debenedetti (87 (7), 569-578 7/1/2019). Effect of heterochiral inversions on the structure of a β-hairpin peptide. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.25680
– Daniel A Heller, Hanan Baker, Januka Budhathoki-Uprety, Christian Cupo, Jackson Harvey, Prakrit Vaibhav Jena, Rachel E Langenbacher, Jeetain Mittal, Daniel Roxbury, Janki Shah, Ryan M Williams, Gül H Zerze, Ming Zheng ( 235, 721-721 2019/5/1). Carbon Nanotube Photoluminescence Solvatochromism in Biomedicine: Spectroscopy, Imaging, and Modulation. Electrochemical Society Meeting Abstracts 235. doi: 10.1149/MA2019-01/9/721
– Gül H Zerze, Wenwei Zheng, Robert B Best, Jeetain Mittal (10 (9), 2227-2234 2019/4/16). Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. The journal of physical chemistry letters. doi: 10.1021/acs.jpclett.9b00850
– Gül H Zerze, Pablo Debenedetti, Frank Stillinger (116 (3), 46a 2019/2/15). Computational Investigation of the Effect of Backbone Chiral Inversions on Polypeptide Structure. Biophysical Journal. doi: 10.1016/j.bpj.2018.11.292
2018:
– Jackson D Harvey, Gül H Zerze, Kathryn M Tully, Jeetain Mittal, Daniel A Heller (122 (19), 10592-10599 2018/5/7). Electrostatic Screening Modulates Analyte Binding and Emission of Carbon Nanotubes. The Journal of Physical Chemistry C. doi: 10.1021/acs.jpcc.8b01239
– Fanjie Meng, Mathias MJ Bellaiche, Jae-Yeol Kim, Gül H Zerze, Robert B Best, Hoi Sung Chung (114 (4), 870-884 2018/2/27). Highly disordered amyloid-β monomer probed by single-molecule FRET and MD simulation. Biophysical journal. doi: 10.1016/j.bpj.2017.12.025
– Brandon G Horan, Gül H Zerze, Young C Kim, Dimitrios Vavylonis, Jeetain Mittal (263566 2018/2/11). Computational modeling highlights disordered Formin Homology 1 domain’s role in profilin-actin transfer. bioRxiv. doi: 10.1101/263566
– Wenwei Zheng, Gül Zerze, Alessandro Borgia, Jeetain Mittal, Benjamin Schuler, Robert B Best (114 (3), 367a 2018/2/2). Inferring Properties of Disordered Chains From FRET Transfer Efficiencies. Biophysical Journal. doi: 10.1016/j.bpj.2017.11.2036
– Brandon G Horan, Gül Zerze, Gregory L Dignon, Young C Kim, Dimitrios Vavylonis, Jeetain Mittal (114 (3), 144a 2018/2/2). Multiscale Model of the Formin Homology 1 Domain Illustrates its Role in Regulation of Actin Polymerization. Biophysical Journal. doi: /10.1016/j.bpj.2017.11.810
– Veronica H Ryan, Gregory L Dignon, Gül H Zerze, Charlene V Chabata, Rute Silva, Alexander E Conicella, Joshua Amaya, Kathleen A Burke, Jeetain Mittal, Nicolas L Fawzi (69 (3), 465-479. e7 2018/2/1). Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation. Molecular cell. doi: 10.1016/j.molcel.2017.12.022
2017:
– Zachary Monahan, Veronica H Ryan, Abigail M Janke, Kathleen A Burke, Shannon N Rhoads, Gül H Zerze, Robert OMeally, Gregory L Dignon, Alexander E Conicella, Wenwei Zheng, Robert B Best, Robert N Cole, Jeetain Mittal, Frank Shewmaker, Nicolas L Fawzi (36 (20), 2951-2967 2017/10/16). Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity’. The EMBO journal. doi: 10.15252/embj.201696394
– Gregory L Dignon, Gül H Zerze, Jeetain Mittal (121 (37), 8661-8668 2017/9/21). Interplay between membrane composition and structural stability of membrane-bound hIAPP. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.7b05689
– Daniel A Heller, Jackson D Harvey, Prakrit V Jena, Ryan M Williams, Thomas V Galassi, Hanan A Baker, Daniel Roxbury, Gül Zerze, Jeetain Mittal (77 (13_Supplement), LB-222-LB-222 2017/7/1). Abstract LB-222: A nanoscale optical reporter implant for miRNA biomarkers in vivo. Cancer Research. doi: 10.1158/1538-7445.AM2017-LB-222
– Jackson D Harvey, Prakrit V Jena, Hanan A Baker, Gül H Zerze, Ryan M Williams, Thomas V Galassi, Daniel Roxbury, Jeetain Mittal, Daniel A Heller (1 (4), 0041 2017/3/13). A carbon nanotube reporter of microRNA hybridization events in vivo. Nature biomedical engineering. doi: 10.1038/s41551-017-0041
– Tushar Modi, Gül H Zerze, Jeetain Mittal, Sara M Vaiana, S Banu Ozkan (112 (3), 208a-209a 2017/2/3). Intrinsically Disordered Protein Dynamics Uncovered through Dynamic Flexibility Index (DFI) Analysis. Biophysical Journal. doi: 10.1016/j.bpj.2016.11.1152
2016:
– Alexander E Conicella, Gül H Zerze, Jeetain Mittal, Nicolas L Fawzi (24 (9), 1537-1549 2016/9/6). ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain. Structure. doi: 10.1016/j.str.2016.07.007
– Zachary A Levine, Michael V Rapp, Wei Wei, Ryan Gotchy Mullen, Chun Wu, Gül H Zerze, Jeetain Mittal, J Herbert Waite, Jacob N Israelachvili, Joan-Emma Shea (113 (16), 4332-4337 2016/4/19). Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1603065113
– Hande Güneş, Erdem Boy, Özge Ata, Gül H Zerze, Pınar Çalık, Tunçer H Özdamar (91 (3), 664-671 2016/3). Methanol feeding strategy design enhances recombinant human growth hormone production by Pichia pastoris. Journal of Chemical Technology & Biotechnology. doi: 10.1002/jctb.4619
– Gül H Zerze, Robert B Best, Jeetain Mittal (110 (3), 557a 2016/2/16). Dynamics of Contact Formation in Disordered Polypeptides. Biophysical Journal. doi: 10.1016/j.bpj.2015.11.2979
– Gül H Zerze, Jeetain Mittal, Robert B Best (116 (6), 068102 2016/2/12). Diffusive Dynamics of Contact Formation in Disordered Polypeptides. Physical review letters. doi: 10.1103/PhysRevLett.116.068102
2015:
– Gül H Zerze, Jeetain Mittal (119 (51), 15583-15592 2015/12/24). Effect of O-Linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.5b10022
– Gül H Zerze, Robert B Best, Jeetain Mittal (119 (46), 14622-14630 2015/11/19). Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations. The Journal of Physical Chemistry B. doi: 10.1021/acs.jpcb.5b08619
– Gül H Zerze, Ryan G Mullen, Zachary A Levine, Joan-Emma Shea, Jeetain Mittal (31 (44), 12223-12230 2015/11/10). To What Extent Does Surface Hydrophobicity Dictate Peptide Folding and Stability near Surfaces?. Langmuir. doi: 10.1021/acs.langmuir.5b03814
– Gül H Zerze, Bilge Uz, Jeetain Mittal (83 (7), 1307-1315 2015/7). Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.24827
– Gül H Zerze, Cayla M Miller, Daniele Granata, Jeetain Mittal (11 (6), 2776-2782 2015/6/9). Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics. Journal of chemical theory and computation. doi: 10.1021/acs.jctc.5b00047
– Pınar Çalık, Özge Ata, Hande Güneş, Aslan Massahi, Erdem Boy, Abdullah Keskin, Sibel Öztürk, Gül H Zerze, Tunçer H Özdamar (95, 20-36 2015/3/15). Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters. Biochemical engineering journal. doi: 10.1016/j.bej.2014.12.003
– Sara M Sizemore, Gül H Zerze, Stephanie M Cope, Jeetain Mittal, Sara M Vaiana (108 (2), 388a-389a 2015/1/27). Comparing Solution Structures of Amylin and CGRP by Nanosecond Laser-Pump Spectroscopy and Atomistic Simulations. Biophysical Journal. doi: 10.1016/j.bpj.2014.11.2129
– Gül H Zerze, Robert B Best, Jeetain Mittal (108 (2), 194a 2015/1/27). Molecular Simulations of Unfolded and Intrinsically Disordered Proteins. Biophysical Journal. doi: 10.1016/j.bpj.2014.11.1072
2014:
– Gül H Zerze, Robert B Best, Jeetain Mittal (107 (7), 1654-1660 2014/10/7). Modest Influence of FRET Chromophores on the Properties of Unfolded Proteins. Biophysical Journal. doi: 10.1016/j.bpj.2014.07.071
– Gül H Zerze, Cayla Miller, Jeetain Mittal (106 (2), 483a 2014/1/28). Correlation of Helical Propensity in Amylin Sequences with Known Aggregation Propensity. Biophysical Journal. doi: 10.1016/j.bpj.2013.11.2728
2013:
– Cayla Miller, Gül H Zerze, Jeetain Mittal (117 (50), 16066-16075 2013/12/19). Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity. The Journal of Physical Chemistry B. doi: 10.1021/jp409755y
– Pınar Çalık, Bahar Bozkurt, Gül H Zerze, Bahar İnankur, Eda Bayraktar, Erdem Boy, Mehmet Ali Orman, Eda Açık, Tunçer H Özdamar (88 (9), 1631-1640 2013/9). Effect of co-substrate sorbitol different feeding strategies on human growth hormone production by recombinant Pichia pastoris. Journal of Chemical Technology & Biotechnology. doi: 10.1002/jctb.4011