[65] Coevolution-informed Bayesian optimization for sample-efficient protein design

DP Kulathunga, D Shukla, DA Potoyan*

bioRxiv (2026) genai allostery

[64] Amyloid nucleation at condensate interfaces is facilitated by rigid motifs and protein influx

S Biswas, DA Potoyan*

bioRxiv (2026) condensates

[63] Synthetic Biomolecular Condensates as Tunable Microtubule Assembly Hubs

S Srinivasan, A Singh, DA Potoyan*, PR Banerjee*

bioRxiv (2026) condensates

[62] 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes

A Das, R Cheng, DA Potoyan, M Di Pierro

bioRxiv (2026) chromatin

[60] A Structure-Aware Generative AI Framework for Exploring Protein Functional Space

D Shukla, J Martin, F Morcos*, DA Potoyan*

Proc. Natl. Acad. Sci. (accepted) (2026) genai allostery

[59] A Language Model-Informed Minimalistic Design of Functional Coacervate Vesicles

W Guo, Y Wang, S Biswas, F Wiertz, G Chakraborty, G Chen, S Liu, Y Song, A Herrmann*, DA Potoyan*, HC Shum*

Nat Comm (accepted) (2026) condensates genai

[58] Integrating NMR and contact-response analysis reveals the allosteric network driving domain closure in Enzyme I

A Singh, D Burns, S Sedinkin, SS Das, DA Potoyan*, V Venditti*

Proc. Natl. Acad. Sci. (2026) allostery

[57] A molecular grammar for programmable multiphase protein–RNA vesicles

V Ramachandran, DA Potoyan*

JACS Au (2026) condensates

[56] Backbone Rigidity Encodes Universal Viscoelastic Signatures in Biomolecular Condensates

S Biswas, S Yang, DA Potoyan*

Biophys. J. (2026) condensates

[55] Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics

EF Hammonds, A Singh, KK Suresh, S Yang, SSM Zahorodny, R Gupta, DA Potoyan*, PR Banerjee*, EA Morrison*

Nucleic Acids Res. (2026) chromatin condensates

[61] Viscoelasticity and Interface Properties of Multi-Component Condensates Govern Protein Sequestration and Suppression of Amyloid Formation

TS Mahendran, X Gui, A Bremer, A Singh, FK Zaidi, G Tesei, JL Basalla, S Chittori, MR Marzahn, B Gindra, RB Davis, T Das, K Lindorff-Larsen, DA Potoyan, T Mittag, PR Banerjee

bioRxiv (2025) condensates

[54] Molecular Drivers of RNA Phase Separation

V Ramachandran, DA Potoyan*

Proc. Natl. Acad. Sci. (2025) condensates

[53] Mechanisms of Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis

D Shukla, J Martin, F Morcos, DA Potoyan*

J. Chem. Theory Comput. (2025) allostery genai

[52] Decoding the dynamics of biomolecular condensates: An energy landscape approach

S Biswas, DA Potoyan*

PLoS Comput. Biol. (2025) condensates

[51] Thermal Adaptation of Extremozymes: Temperature-Sensitive Contact Analysis of Serine Proteases

DP Kulathunga, DA Potoyan*

Biophys. J. (2025) allostery

[50] Chromatin binding regulates phase behavior and morphology of condensates formed by prion-like domains

A Suprakar, RB Davis, S Biswas, S Yang, DA Potoyan*, PR Banerjee*

J. Mol. Biol. (2025) condensates chromatin

[49] Conformational landscape of the transcription factor ATF4 is dominated by disordered-mediated inter-domain coupling

U Patel, S Siang, DA Potoyan, J Roche

Biochemistry (2025) allostery

[48] Illuminating protein allostery by Chemically Accurate Contact Response Analysis

D Burns, V Venditti*, DA Potoyan*

J. Chem. Theory Comput. (2024) allostery

[47] Molecular Drivers of Aging in Biomolecular Condensates: Desolvation, Rigidification, and Sticker Lifetimes

S Biswas, DA Potoyan*

Phys. Rev. X Life (2024) condensates

[46] On microscopic origins of flow activation energy in biomolecular condensates

S Yang, DA Potoyan*

J. Phys. Chem. B (2024) condensates

[45] 4D Mesoscale liquid model of nucleus resolves chromatin's radial organization

R Laghmach, M Di Pierro, DA Potoyan*

Phys. Rev. X Life (2024) chromatin

[44] Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning

V Ramachandran, DA Potoyan*

Biophys. J. (2024) condensates genai

[43] Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores

W Brown, DA Potoyan*

Biophys. J. (2024) condensates

[42] Nucleoprotein phase-separation affinities revealed via atomistic simulations of short peptide and RNA fragments

V Ramachandran, W Brown, C Gayvert, DA Potoyan*

J. Phys. Chem. Lett. (2024) condensates

[41] Atomistic insights into the reentrant phase-transitions in polyuracil and polylysine mixtures

V Ramachandran, DA Potoyan*

J. Chem. Phys. (2024) condensates

[40] An α-ketoglutarate conformational switch controls iron accessibility, activation and substrate selection of the human FTO protein

D Burns, B Khatiwada, A Singh, JA Purslow, DA Potoyan*, V Venditti*

Proc. Natl. Acad. Sci. (2024) allostery

[39] Determinants of Viscoelasticity and Flow Activation Energy in Biomolecular Condensates

I Alshareedah, A Singh, S Yang, V Ramachandran, A Quinn, DA Potoyan*, PR Banerjee*

Sci. Adv. (2024) condensates

[38] Protein Thermal Sensing Regulates Physiological Amyloid Aggregation

D Marijan, EA Momchilova, D Burns, S Chandhok, R Zapf, H Wille, DA Potoyan, TE Audas

Nat. Commun. (2024) condensates allostery

[37] An interdisciplinary effort to integrate coding into science courses

Vizcarra, C. L. et al

Nat. Comput. Sci. (2024)

[36] Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions

JD Levengood, DA Potoyan, S Penumutchu, A Kumar, Y Wang, AL Hansen, S Kutluay, J Roche, Blanton S Tolbert

Sci. Adv. (2024) allostery

[35] Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

D Burns, V Venditti*, DA Potoyan*

PLoS Comput. Biol. (2023) allostery

[34] Re-entrant transitions of locally stiff RNA chains in the presence of polycations leads to gelated architectures

I Malhotra, DA Potoyan*

Soft Matter (2023) condensates

[33] Solution structure ensembles of the open and close forms of the 130 kDa Enzyme I via AlphaFold modeling, Coarse-Grained simulations, and NMR

A Singh, S Sedinkin, D Burns, D Shukla, DA Potoyan*, V Venditti*

J. Am. Chem. Soc. (2023) allostery genai

[32] Protein conformational dynamics underlay selective recognition of thermophilic over mesophilic Enzyme I by a substrate analogue

A Singh, D Burns, S Sedinkin, B Van Veller, DA Potoyan*, V Venditti*

Biomolecules (2023) allostery

[31] Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity

D Burns, A Singh, V Venditti*, DA Potoyan*

Proc. Natl. Acad. Sci. (2022) allostery

[30] RNA chain length and stoichiometry govern surface tension and stability of protein-RNA condensates

R. Laghmach, I. Alshareedah, M. Pham, M. Raju, P.R. Banerjee*, DA Potoyan*

iScience (2022) condensates

[29] BIAPSS: A comprehensive physicochemical analyzer of proteins undergoing liquid-liquid phase separation

AE Badaczewska-Dawid, VA Uversky*, DA Potoyan*

Int. J. Mol. Sci. (2022) condensates

[28] Liquid state perspective on dynamics of chromatin compartments

R Laghmach, M Di Pierro, DA Potoyan*

Front. Mol. Biosci. (2022) chromatin

[27] Multi-scale modeling of protein-RNA condensation in and out of equilibrium

R Laghmach, I Malhotra, DA Potoyan*

Methods Mol. Biol. (2022) condensates

[26] Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides

I Alshareedah, M M Moosa, M Pham, DA Potoyan*, PR Banerjee*

Nat. Commun. (2021) condensates

[25] Interplay of chromatin phase separation and lamina interactions in nuclear organization

R Laghmach, M Di Pierro, DA Potoyan*

Biophys. J. (2021) chromatin

[24] Solvent Exposure and Ionic Condensation Drive Fuzzy Dimerization of Disordered Heterochromatin Protein Sequence

J Mueterthies, DA Potoyan*

Biomolecules (2021) chromatin condensates

[23] Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies

T Kaur, M Raju, I Alshareedah, RB Davis, DA Potoyan*, P Banerjee*

Nat. Commun. (2021) condensates

[22] Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm

R Laghmach, DA Potoyan*

Phys. Biol. (2020) chromatin condensates

[21] Hybrid thermophilic/mesophilic enzymes reveal a role for conformational disorder in regulation of bacterial Enzyme I

RR Dotas, TT Nguyen, CE Stewart Jr, R Ghirlando, DA Potoyan*, V Venditti*

J. Mol. Biol. (2020) allostery

[20] Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates

I Alshareedah, MM Moosa, M Raju, DA Potoyan*, P Banerjee*

Proc. Natl. Acad. Sci. (2020) condensates

[19] Mesoscale liquid model of chromatin recapitulates large-scale organization of eukaryotic cell nuclei

R. Laghmach, M. Di Pierro, DA Potoyan*

Biophys. J. (2020) chromatin

[18] Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained molecular dynamics simulations

J Roche, DA Potoyan

J. Phys. Chem. B (2019) condensates

[17] Stochastic and dynamical view of pluripotency in mouse embryonic stem cells

YT Lin, PG Hufton, EJ Lee, DA Potoyan

PLoS Comput. Biol. (2018) chromatin

[16] Anomalous Diffusion, Spatial Coherence, and Viscoelasticity from the Energy Landscape of Human Chromosomes

M Di Pierro*, DA Potoyan*, PG Wolynes, JN Onuchic

Proc. Natl. Acad. Sci. (2018) chromatin

[15] Stochastic Resonances in a Distributed Genetic Broadcasting System: The NFκB/IκB paradigm

Z Wang*, DA Potoyan*, PG Wolynes

J. R. Soc. Interface (2018) chromatin

[14] Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides

Z Wang, DA Potoyan, PG Wolynes

BMC Syst. Biol. (2018) chromatin

[13] Resolving the NFκB heterodimer binding paradox: Strain and frustration guide the binding of dimeric transcription factors

DA Potoyan, C Bueno, W Zheng, EA Komives, PG Wolynes

J. Am. Chem. Soc. (2017) allostery

[12] Stochastic dynamics of genetic broadcasting networks

DA Potoyan, PG Wolynes

Phys. Rev. E (2017) chromatin

[11] PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites

DA Potoyan, W Zheng, DU Fereiro, PG Wolynes, EA Komives

J. Phys. Chem. B (2016) allostery

[10] Molecular stripping in the NFκB/IκB/DNA genetic switch

DA Potoyan, W Zheng, EA Komives, PG Wolynes

Proc. Natl. Acad. Sci. (2016) allostery

[9] Molecular stripping, targets and decoys as modulators of oscillations in the NFκB/IκBα/DNA genetic network

Z Wang*, DA Potoyan*, PG Wolynes

J. R. Soc. Interface (2016) chromatin

[8] Dichotomous noise based models of genetic switching

DA Potoyan, PG Wolynes

J. Chem. Phys. (2015) chromatin

[7] The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects

D Winogradoff, I Echeverria, DA Potoyan, GA Papoian

J. Am. Chem. Soc. (2015) chromatin

[6] On the dephasing of genetic oscillators

DA Potoyan, PG Wolynes

Proc. Natl. Acad. Sci. (2014) chromatin

[5] Recent successes in coarse-grained modeling of DNA

DA Potoyan, A. Savelyev, G.A. Papoian

WIREs Comput. Mol. Sci. (2013)

[4] Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation

DA Potoyan, G Papoian

Proc. Natl. Acad. Sci. (2012) chromatin

[3] Computing free energy of a large-scale allosteric transition in Adenylate Kinase using all atom explicit solvent simulations

DA Potoyan, P Zhuravlev, G Papoian

J. Phys. Chem. B (2012) allostery

[2] Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

DA Potoyan, G Papoian

J. Am. Chem. Soc. (2011) chromatin

[1] Computing free energies of protein conformations from explicit solvent simulations

P Zhuravlev, S Wu, DA Potoyan, M Rubinstein, G Papoian

Methods (2010)