2026
A Structure-Aware Generative Framework for Exploring Protein Sequence and Function Space

[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

A molecular grammar for programmable multiphase protein-RNA vesicles

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

V Ramachandran, DA Potoyan*

Biorxiv (2026) condensates

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

[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

Backbone Rigidity Encodes Universal Viscoelastic Signatures in Biomolecular Condensates

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

S Biswas, S Yang, DA Potoyan*

Biophys J (2026) condensates

Histone H3 tail charge patterns govern nucleosome condensate formation and dynamics

[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

2025
Molecular Drivers of RNA phase separation

[54] Molecular Drivers of RNA phase separation

V Ramachandran, DA Potoyan*

Proc Natl Acad Sci (2025) condensates

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

[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

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

[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

Decoding the dynamics of biomolecular condensates: An energy landscape approach

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

S Biswas, DA Potoyan*

PLoS Comp Bio (2025) condensates

Thermal Adaptation of Extremozymes: Temperature-Sensitive Contact Analysis of Serine Proteases
2024
On microscopic origins of flow activation energy in biomolecular condensates

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

S Yang, DA Potoyan*

J Phys Chem B (2024) condensates

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

[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

Illuminating protein allostery by Chemically Accurate Contact Response Analysis

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

D Burns, V Venditti*, DA Potoyan*

J Chem Theor Comp (2024) allostery

Molecular drivers of aging in biomolecular condensates: Desolvation, rigidification, and sticker lifetimes
4D Mesoscale liquid model of nucleus resolves chromatin's radial organization

[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

Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores
Mapping energy landscapes of homopolymeric RNAs via simulated tempering and deep unsupervised learning

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

V Ramachandran, DA Potoyan*

Biophys J (2024) condensates genai

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

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

V Ramachandran, DA Potoyan*

J Chem Phys (2024) condensates

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

[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

Determinants of Viscoelasticity and Flow Activation Energy in Biomolecular Condensates

[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

Protein thermal sensing regulates physiological amyloid aggregation

[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

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

[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

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

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

Vizcarra, C. L. et al

Nat Comp Sci (2024)

2023
Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

[35] Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

D Burns, V Venditti*, DA Potoyan*

PLoS Comp Bio (2023) allostery

Re-entrant transitions of locally stiff RNA chains in the presence of polycations leads to gelated architectures
Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

[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

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

[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

2022
Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity

[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

On the role of stoichiometry, salt and external crowding in protein-RNA phase separation

[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

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

[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

A Liquid State Perspective on Dynamics of Chromatin Compartments

[28] A Liquid State Perspective on Dynamics of Chromatin Compartments

R Laghmach, M Di Pierro, DA Potoyan*

Front. Mol. Biosci. (2022) chromatin

Multi-scale models of protein-RNA phase separation

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

R Laghmach, I Malhotra, DA Potoyan*

Methods in Molecular Biology (2022) condensates

2021
The interplay of chromatin phase separation and lamina interactions in nuclear organisation

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

R Laghmach, M Di Pierro, DA Potoyan*

Biophys J (2021) chromatin

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

[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

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

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

J Mueterthies, DA Potoyan*

Biomolecules (2021) chromatin condensates

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

[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

2020
Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm

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

R Laghmach, DA Potoyan*

Phys Biol (2020) chromatin condensates

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

[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

Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates

[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

2019
Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained computer simulations
Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes

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

R Laghmach, M Di Pierro, DA Potoyan

Biophys J (2019) chromatin

2018
A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

[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

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

[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

Work done prior to ISU (2010–2017)

[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

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

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

Methods (2010)