Publications

+ = equal author contribution/co‑first author; * = corresponding/co‑corresponding author

Preprints

Interaction networks within biomolecular condensates feature topological cliques near the interface

Tan, D.⁺, Aierken, D.⁺, and Joseph, J.A.*, 2025. Interaction networks within biomolecular condensates feature topological cliques near the interface. bioRxiv preprint .

The Critical Role of the 2’-OH group in Phase Separation and Percolation Transitions of RNA

Wadsworth, G. M.⁺, Aierken, D.⁺, Thurston, G. M., Joseph, J. A.*, & Banerjee, P. R.* (2025). The Critical Role of the 2'-OH group in Phase Separation and Percolation Transitions of RNA. bioRxiv, 2025-02.

Accurate prediction of thermoresponsive phase behavior of disordered proteins

Chakravarti, A., & Joseph, J. A*. (2025). Accurate prediction of thermoresponsive phase behavior of disordered proteins. bioRxiv, 2025-03.

Biomolecular condensates control and are defined by RNA-RNA interactions that arise in viral replication

Aierken, D., Zhang, V., Sealfon, R., Marecki, J.C., Raney, K.D., Gladfelter, A.S., Joseph, J.A.* and Roden, C.A.*, 2024. Biomolecular condensates control and are defined by RNA-RNA interactions that arise in viral replication. bioRxiv, pp.2024-12…

Prediction of small-molecule partitioning into biomolecular condensates from simulation

Emelianova, A., Garcia, P. L., Tan, D., & Joseph, J. A*. (2025). Prediction of small-molecule partitioning into biomolecular condensates from simulation. bioRxiv, 2025-03.

Condensate Size Control by Charge Asymmetry

Luo, C.+, Hess, N.+, Aierken, D., Qiang, Y., Joseph, J.A.* and Zwicker, D.*, 2024. Condensate Size Control by Charge Asymmetry. arXiv preprint arXiv:2409.15599.

A Highly Conserved ABC Transporter Mediates Cello-Oligosaccharide Uptake in the Extremely Thermophilic, Lignocellulolytic Bacterium Anaerocellum (f. Caldicellulosiruptor) bescii.

Tjo, H., Jiang, V., Calvo, A., Joseph, J. A., & Conway, J. M. (2025). A Highly Conserved ABC Transporter Mediates Cello-Oligosaccharide Uptake in the Extremely Thermophilic, Lignocellulolytic Bacterium Anaerocellum (f. Caldicellulosiruptor) bescii. bioRxiv, 2025-02.

Maltodextrin Transport in the Extremely Thermophilic, Lignocellulose Degrading Bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii)

Tjo, H., Jiang, V., Joseph, J.A. and Conway, J.M., 2024. Maltodextrin Transport in the Extremely Thermophilic, Lignocellulose Degrading Bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii). bioRxiv, pp.2024-09.

Tandem-repeat proteins introduce tuneable properties to engineered biomolecular condensates

Ng, T.L.C., Hoare, M.P., Maristany, M.J., Wilde, E.J., Sneideris, T., Huertas, J., Agbetiameh, B.K., Furukawa, M., Joseph, J.A., Knowles, T.P. and Collepardo-Guevara, R., 2024. Tandem-repeat proteins introduce tuneable properties to engineered biomolecular…

2025 Publications

Structured protein domains enter the spotlight: modulators of biomolecular condensate form and function

Hess, N. and Joseph, J.A.*, 2025. Structured protein domains enter the spotlight: modulators of biomolecular condensate form and function. Trends in Biochemical Sciences.

Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws

Maristany, M.J., Aguirre Gonzalez, A., Espinosa, J. R., Huertas, J., Collepardo-Guevara, R., Joseph, J. A.*, (2025) Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws. eLife.

2024 Publications

Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters

Aierken, D. and Joseph, J.A.*, 2024. Accelerated Simulations Reveal Physicochemical Factors Governing Stability and Composition of RNA Clusters. Journal of Chemical Theory and Computation, 20(22), pp.10209-10222.

Aromatic and arginine content drives multiphasic condensation of protein–RNA mixtures

Chew, P.Y., Joseph, J.A., Collepardo-Guevara, R. and Reinhardt, A., 2024. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophysical Journal, 123(11), pp.1342-1355.

2023 Publications

Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity.

Nicy, Collepardo-Guevara, R., Joseph, J.A.* and Wales, D.J.*, 2023. Energy landscapes and heat capacity signatures for…

Thermodynamic origins of two-component multiphase condensates of proteins

Chew, P.Y., Joseph, J.A., Collepardo-Guevara, R. and Reinhardt, A., 2023. Thermodynamic origins of two-component multiphase condensates of proteins. Chemical Science, 14(7), pp.1820-1836.

2022

Garaizar A, Espinosa J, Joseph J, Collepardo-Guevara R. 2022. Kinetic interplay between droplet maturation and coalescence modulates shape of aged protein condensates. Scientific reports. 12(1):4390. doi:10.1038/s41598-022-08130-2.

Garaizar A, Espinosa J, Joseph J, Krainer G, Shen Y, Knowles T, Collepardo-Guevara R. 2022. Aging can transform single-component protein condensates into multiphase architectures. Proceedings of the National Academy of Sciences of the United States of America. 119(26):e2119800119. doi:10.1073/pnas.2119800119.

Sanchez-Burgos I, Espinosa J, Joseph J, Collepardo-Guevara R. 2022. RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins. PLoS computational biology. 18(2):e1009810. doi:10.1371/journal.pcbi.1009810.

Welsh T, Krainer G, Espinosa J, Joseph J, Sridhar A, Jahnel M, Arter W, Saar K, Alberti S, Collepardo-Guevara R, et al. 2022. Surface Electrostatics Govern the Emulsion Stability of Biomolecular Condensates. Nano letters. 22(2):612–621. doi:10.1021/acs.nanolett.1c03138.

2021

Farr S, Woods E, Joseph J, Garaizar A, Collepardo-Guevara R. 2021. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nature communications. 12(1):2883. doi:10.1038/s41467-021-23090-3.

Joseph J, Espinosa J, Sanchez-Burgos I, Garaizar A, Frenkel D, Collepardo-Guevara R. 2021. Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model. Biophysical journal. 120(7):1219–1230. doi:10.1016/j.bpj.2021.01.031.

Joseph J, Reinhardt A, Aguirre A, Chew P, Russell K, Espinosa J, Garaizar A, Collepardo-Guevara R. 2021. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Nature computational science. 1(11):732–743. doi:10.1038/s43588-021-00155-3.

Krainer G, Welsh T, Joseph J, Espinosa J, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska M, et al. 2021. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nature communications. 12(1):1085. doi:10.1038/s41467-021-21181-9.

Sanchez-Burgos I, Espinosa J, Joseph J, Collepardo-Guevara R. 2021. Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components. Biomolecules. 11(2). doi:10.3390/biom11020278.

Sanchez-Burgos I, Joseph J, Collepardo-Guevara R, Espinosa J. 2021. Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients. Scientific reports. 11(1):15241. doi:10.1038/s41598-021-94309-y.

2020

Espinosa J, Joseph J, Sanchez-Burgos I, Garaizar A, Frenkel D, Collepardo-Guevara R. 2020. Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components. Proceedings of the National Academy of Sciences of the United States of America. 117(24):13238–13247. doi:10.1073/pnas.1917569117.

2019

Joseph J, Chakraborty D, Wales D. 2019. Energy Landscape for Fold-Switching in Regulatory Protein RfaH. Journal of chemical theory and computation. 15(1):731–742. doi:10.1021/acs.jctc.8b00912.

Röder K, Joseph JA, Husic BE, Wales DJ. 2019. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. Advanced Theory and Simulations. 2:1800175. Referenced from onlinelibrary.wiley.com.

2018

Joseph J, Wales D. 2018. Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide. The journal of physical chemistry. B. 122(50):11906–11921. doi:10.1021/acs.jpcb.8b08371.

2017

Joseph J, Röder K, Chakraborty D, Mantell R, Wales D. 2017. Exploring biomolecular energy landscapes. Chemical communications (Cambridge, England). 53(52):6974–6988. doi:10.1039/c7cc02413d.

2016

Joseph J, Whittleston C, Wales D. 2016. Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification. Journal of chemical theory and computation. 12(12):6109–6117.

2015

Joseph J, McDowell S. 2015. Comparative computational study of model halogen-bonded complexes of FKrCl. The journal of physical chemistry. A. 119(11):2568–77. doi:10.1021/jp5091262.

McDowell SA, Joseph JA. 2015. A comparative study of model halogen-bonded, π-hole-bonded and cationic complexes involving NCX AND H2O (X = F, Cl, Br). Molecular Physics. 113:16–21. doi:10.1080/00268976.2014.939116. Referenced from doi.org.

McDowell S, Joseph JA. 2015. Interplay of Hydrogen, Halogen, Lithium and Beryllium Bonds in Complexes of Thiirane. In: Scheiner S, editor. Cham: Springer International Publishing. pp. 357–389. Referenced from doi.org.

2014

McDowell S, Joseph J. 2014. Variation of sigma-hole magnitude with M valence electron population in MX(n)Y(4-n) molecules (n = 1-4; M = C, Si, Ge; X, Y = F, Cl, Br). Physical chemistry chemical physics : PCCP. 16(2):669–71. doi:10.1039/c3cp53738b.

McDowell SA, Joseph JA. 2014. Destabilization of the halogen bond in complexes of protonated NCX (X=F, Cl, Br) molecules. Chemical Physics Letters. 603:37–40. Referenced from www.sciencedirect.com.

McDowell S, Joseph J. 2014. The effect of atomic ions on model σ-hole bonded complexes of AH3Y (A = C, Si, Ge; Y = F, Cl, Br). Physical chemistry chemical physics : PCCP. 16(22):10854–60. doi:10.1039/c4cp01074d.

2013

McDowell S, Joseph J. 2013. Cooperative effects in novel LiF∕HF⋯LiF⋯XF (X = F, Cl, Br) clusters. The Journal of chemical physics. 138(16):164313. doi:10.1063/1.4801863.

2012

McDowell S, Joseph J. 2012. Cooperative effects of noncovalent bonds to the Br atom of halogen-bonded H3N.BrZ and HCN.BrZ (Z = F, Br) complexes. The Journal of chemical physics. 137(7):074310. doi:10.1063/1.4745838.

McDowell S, Joseph J. 2012. Communication: An unusual halogen-bonding motif: the LiBr···BrF dimer as a model system. The Journal of chemical physics. 137(17):171103. doi:10.1063/1.4766932.