[59] A Structure-Aware Generative Framework for Exploring Protein Sequence and Function Space

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

Biorxiv (2026) genai allostery

[58] A molecular grammar for programmable multiphase protein-RNA vesicles

V Ramachandran, DA Potoyan*

Biorxiv (2026) condensates

[57] 3D genome architecture regulates the traffic of transcription factors throughout human chromosomes

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

Biorxiv (2026) chromatin

[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*

Nuc Acid Res (2026) chromatin condensates

[54] Molecular Drivers of RNA phase separation

V Ramachandran, DA Potoyan*

Proc Natl Acad Sci (2025) condensates

[53] 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

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

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

J Chem Theor Comp (2025) allostery genai

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

S Biswas, DA Potoyan*

PLoS Comp Bio (2025) condensates

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

DP Kulathunga, DA Potoyan*

Biophys J (2025) allostery

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

S Yang, DA Potoyan*

J Phys Chem B (2024) condensates

[48] 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

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

D Burns, V Venditti*, DA Potoyan*

J Chem Theor Comp (2024) allostery

[46] Molecular drivers of aging in biomolecular condensates: Desolvation, rigidification, and sticker lifetimes

S Biswas, DA Potoyan*

Phys Rev X Life (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] Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores

W Brown, DA Potoyan*

Biophys J (2024) condensates

[43] Mapping energy landscapes of homopolymeric RNAs via simulated tempering and deep unsupervised learning

V Ramachandran, DA Potoyan*

Biophys J (2024) condensates genai

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

V Ramachandran, DA Potoyan*

J Chem Phys (2024) condensates

[41] 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

[40] 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

[39] Protein thermal sensing regulates physiological amyloid aggregation

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

Nat Comm (2024) condensates allostery

[38] 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

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

U Patel, S Siang, DA Potoyan, J Roche

Biochemistry (2024) allostery

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

Vizcarra, C. L. et al

Nat Comp Sci (2024)

[35] Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

D Burns, V Venditti*, DA Potoyan*

PLoS Comp Bio (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 Closed 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] On the role of stoichiometry, salt and external crowding in protein-RNA phase separation

R Laghmach, I Alshareedah, M Pham, M Raju, P 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] A Liquid State Perspective on Dynamics of Chromatin Compartments

R Laghmach, M Di Pierro, DA Potoyan*

Front. Mol. Biosci. (2022) chromatin

[27] Multi-scale models of protein-RNA phase separation

R Laghmach, I Malhotra, DA Potoyan*

Methods in Molecular Biology (2022) condensates

[26] The interplay of chromatin phase separation and lamina interactions in nuclear organisation

R Laghmach, M Di Pierro, DA Potoyan*

Biophys J (2021) chromatin

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

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

Nat Comm (2021) condensates

[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 Comm (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] Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained computer simulations

J Roche, DA Potoyan

J Phys Chem B (2019) condensates

[18] Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes

R Laghmach, M Di Pierro, DA Potoyan

Biophys J (2019) chromatin

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

YT Lin, PG Hufton, EJ Lee, DA Potoyan

PLoS Comp Bio (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] Modeling the therapeutic efficacy of NFkB synthetic decoy oligodeoxynucleotides

Z Wang, DA Potoyan, PG Wolynes

BMC Sys. Biol. (2018) chromatin

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

Z Wang*, DA Potoyan*, PG Wolynes

J. Roy. Soc. Int. (2018) chromatin

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

Z Wang*, DA Potoyan*, PG Wolynes

J. Roy. Soc. Int. (2016) chromatin

[10] PEST control of molecular stripping of NFkB from DNA transcription sites

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

J. Phys. Chem. B (2016) allostery

[9] Molecular stripping in the NFkB-IkB-DNA genetic switch

DA Potoyan, W Zheng, EA Komives, PG Wolynes

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

[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 Papoian

WIRES Comp. Mol. Sci. (2013) chromatin

[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. (2012) chromatin

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

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

Methods (2010)