Research graph
References from Molecular simulations of chromatin-associated biomolecular condensates. Local targets link to admitted publications; unresolved targets remain external evidence.
Liquid droplet formation by hp1α suggests a role for phase separation in heterochromatin
10.1038/nature22822 · 2017 · External reference
Mediator and rna polymerase ii clusters associate in transcription-dependent condensates
10.1126/science.aar4199 · 2018 · External reference
Coactivator condensation at super-enhancers links phase separation and gene control
10.1126/science.aar3958 · 2018 · External reference
Phase separation of 53bp1 determines liquid-like behavior of dna repair compartments
10.15252/embj.2018101379 · 2019 · External reference
Transcription factors activate genes through the phase-separation capacity of their activation domains
10.1016/j.cell.2018.10.042 · 2018 · External reference
Modeling biomolecular condensates across scales: atomistic, coarse-grained, and data-driven approaches
2025 · External reference
Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy
10.1038/s43588-021-00155-3 · 2021 · External reference
Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures
10.1016/j.bpj.2023.06.024 · 2024 · External reference
Decoding phase separation of prion-like domains through data-driven scaling laws
2025 · External reference
Chemically informed coarse-graining of electrostatic forces in charge-rich biomolecular condensates
10.1021/acscentsci.4c01617 · 2025 · External reference
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins
10.1016/j.cell.2018.06.006 · 2018 · External reference
Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains
10.1038/s41557-021-00840-w · 2022 · External reference
Kresten Lindorff-Larsen. Conformational ensembles of the human intrinsically disordered proteome
10.1038/s41586-023-07004-5 · 2024 · External reference
Chromatin heterogeneity modulates nuclear condensate dynamics and phase behavior
10.1038/s41467-025-60771-9 · 2025 · External reference
Decoding the genomic landscape of chromatin-associated biomolecular condensates
10.1038/s41467-024-51426-2 · 2024 · External reference
Multiscale modelling of chromatin organisation: resolving nucleosomes at near-atomistic resolution inside genes
2022 · External reference
Organization of chromatin by intrinsic and regulated phase separation
10.1016/j.cell.2019.08.037 · 2019 · External reference
Multiscale structure of chromatin condensates explains phase separation and material properties
10.1126/science.adv6588 · 2025 · External reference
Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation
2025 · External reference
Nucleosome spacing can fine-tune higher-order chromatin assembly
10.1038/s41467-025-61482-x · 2025 · External reference
Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
10.1038/s41467-021-23090-3 · 2021 · External reference
Multiscale physical effects of cpg methylation on dna mechanics, nucleosome wrapping, and chromatin condensates
2026 · External reference
Multifunctional histone variants in genome function
10.1038/s41576-024-00759-1 · 2025 · External reference
Chromatin liquid–liquid phase separation (llps) is regulated by ionic conditions and fiber length
10.3390/cells11193145 · 2022 · External reference
Explicit ion modeling predicts physicochemical interactions for chromatin organization
10.7554/elife.90073.3 · 2024 · External reference
OCT4 interprets and enhances nucleosome flexibility
10.1093/nar/gkac755 · 2022 · External reference
Oct4 clusters promote dna accessibility by enhancing chromatin plasticity
2025 · External reference
Two independent modes of chromatin organization revealed by cohesin removal
10.1038/nature24281 · 2017 · External reference
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
10.1038/s41467-024-49727-7 · 2024 · External reference
Functional partitioning of transcriptional regulators by patterned charge blocks
10.1016/j.cell.2022.12.013 · 2023 · External reference
Pi-pi contacts are an overlooked protein feature relevant to phase separation
2018 · External reference
Sequence determinants of protein phase behavior from a coarse-grained model
10.1371/journal.pcbi.1005941 · 2018 · External reference
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
2021 · External reference
Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles
10.1016/j.bpj.2023.10.030 · 2024 · External reference
Accurate prediction of thermoresponsive phase behavior of disordered proteins
10.1002/pro.70284 · 2025 · External reference
Breaths, twists, and turns of atomistic nucleosomes
10.1016/j.jmb.2020.166744 · 2021 · External reference
Energy-driven genome regulation by ATP-dependent chromatin remodellers
10.1038/s41580-023-00683-y · 2024 · External reference
Chromatin organization drives the search mechanism of nuclear factors
10.1038/s41467-023-42133-5 · 2023 · External reference
Current practices in the study of biomolecular condensates: a community comment
10.1038/s41467-025-62055-8 · 2025 · External reference
Arginine multivalency stabilizes protein/rna condensates
10.1002/pro.4109 · 2021 · External reference
Uncovering differences in hydration free energies and structures for model compound mimics of charged side chains of amino acids
10.1021/acs.jpcb.1c01073 · 2021 · External reference
Crossover in aromatic amino acid interaction strength between tyrosine and phenylalanine in biomolecular condensates
10.7554/elife.104950 · 2025 · External reference
Extreme dynamics in a biomolecular condensate
10.1038/s41586-023-06329-5 · 2023 · External reference
Molecular drivers of rna phase separation
10.1073/pnas.2511348122 · 2025 · External reference
Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
10.1073/pnas.2111696118 · 2021 · External reference
Surfactants or scaffolds? Rnas of varying lengths control the thermodynamic stability of condensates differently
10.1016/j.bpj.2023.03.006 · 2023 · External reference
Rna length has a non-trivial effect in the stability of biomolecular condensates formed by rna-binding proteins
10.1371/journal.pcbi.1009810 · 2022 · External reference
A coarse-grained model for disordered and multi-domain proteins
10.1002/pro.5172 · 2024 · External reference
Coarse-grained model of disordered rna for simulations of biomolecular condensates
10.1021/acs.jctc.4c01646 · 2025 · External reference
Driving forces of rna condensation revealed through coarse-grained modeling with explicit mg2+
2025 · External reference
Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions
10.1063/5.0062687 · 2021 · External reference
A coarse-grained model for disordered proteins under crowded conditions
2025 · External reference
Protein structural transitions critically transform the network connectivity and viscoelasticity of rna-binding protein condensates but rna can prevent it
10.1038/s41467-022-32874-0 · 2022 · External reference
Alphafold-guided simulations of multi-domain proteins at the proteome level
2025 · External reference
Rna2ps: a sequence-specific coarse-grained rna model linking structure, thermodynamics and phase separation
2026 · External reference
Condensates in rna repeat sequences are heterogeneously organized and exhibit reptation dynamics
10.1038/s41557-022-00934-z · 2022 · External reference
Accelerated simulations reveal physicochemical factors governing stability and composition of rna clusters
10.1021/acs.jctc.4c00803 · 2024 · External reference
Cg modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability
10.1063/5.0242509 · 2025 · External reference
Implicit solvent with explicit ions generalized born model in molecular dynamics: application to dna
10.1021/acs.jctc.4c00833 · 2024 · External reference
Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism
10.1016/j.molcel.2019.08.019 · 2019 · External reference
Regulation of chromatin architecture by protein binding: insights from molecular modeling
10.1007/s12551-024-01195-5 · 2024 · External reference
Nonspecific bridging-induced attraction drives clustering of dna-binding proteins and genome organization
10.1073/pnas.1302950110 · 2013 · External reference
Transcriptional condensates encode a “golden mean” to optimize enhancer–promoter communication across genomic distances
10.1073/pnas.2513371122 · 2025 · External reference
Heterogeneous condensates of transcription factors in embryonic stem cells: molecular simulations
10.1016/j.bpj.2025.04.001 · 2025 · External reference
Phase separation and inheritance of repressive chromatin domains
10.1016/j.gde.2024.102201 · 2024 · External reference
Hp1 reshapes nucleosome core to promote phase separation of heterochromatin
10.1038/s41586-019-1669-2 · 2019 · External reference
Hp1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation
10.1073/pnas.2211855120 · 2023 · External reference
Interplay between charge distribution and dna in shaping hp1 paralog phase separation and localization
2024 · External reference
Principles of assembly and regulation of condensates of polycomb repressive complex 1 through phase separation
10.1016/j.celrep.2023.113136 · 2023 · External reference
Loss of sumoylation drives aberrant prc1 clustering and 3d genome rewiring independent of h3k27me3
2026 · External reference
Biomolecular condensates at sites of dna damage: more than just a phase
2021 · External reference
Chromatin network retards nucleoli coalescence
10.1038/s41467-021-27123-9 · 2021 · External reference
Differential interactions determine anisotropies at interfaces of rna-based biomolecular condensates
10.1038/s41467-025-58736-z · 2025 · External reference
An electrostatic repulsion model of centromere organisation
2025 · External reference
Molecular dynamics-guided all-atom reconstruction of cryo-et maps reveals mechanisms of histone tail-mediated chromatin compaction
2025 · External reference
Histone h3 tail charge patterns govern nucleosome condensate formation and dynamics
10.1093/nar/gkag050 · 2026 · External reference
Biophysical experiments and biomolecular simulations: a perfect match?
10.1126/science.aat4010 · 2018 · External reference
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells
2025 · External reference
Non-equilibrium modeling of directed flux through biomolecular condensates
2026 · External reference
Compositional control of aging kinetics in tdp-43 condensates
10.1103/w7g3-6rsd · 2025 · External reference
Arginine multivalency stabilizes protein/rna condensates
10.1002/pro.4109 · ExternalCitation · doi-reference
A coarse-grained model for disordered and multi-domain proteins
10.1002/pro.5172 · ExternalCitation · doi-reference
Accurate prediction of thermoresponsive phase behavior of disordered proteins
10.1002/pro.70284 · ExternalCitation · doi-reference
Regulation of chromatin architecture by protein binding: insights from molecular modeling
10.1007/s12551-024-01195-5 · ExternalCitation · doi-reference
Surfactants or scaffolds? Rnas of varying lengths control the thermodynamic stability of condensates differently
10.1016/j.bpj.2023.03.006 · ExternalCitation · doi-reference
Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures
10.1016/j.bpj.2023.06.024 · ExternalCitation · doi-reference
Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles
10.1016/j.bpj.2023.10.030 · ExternalCitation · doi-reference
Heterogeneous condensates of transcription factors in embryonic stem cells: molecular simulations
10.1016/j.bpj.2025.04.001 · ExternalCitation · doi-reference
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins
10.1016/j.cell.2018.06.006 · ExternalCitation · doi-reference
Transcription factors activate genes through the phase-separation capacity of their activation domains
10.1016/j.cell.2018.10.042 · ExternalCitation · doi-reference
Organization of chromatin by intrinsic and regulated phase separation
10.1016/j.cell.2019.08.037 · ExternalCitation · doi-reference
Functional partitioning of transcriptional regulators by patterned charge blocks
10.1016/j.cell.2022.12.013 · ExternalCitation · doi-reference
Principles of assembly and regulation of condensates of polycomb repressive complex 1 through phase separation
10.1016/j.celrep.2023.113136 · ExternalCitation · doi-reference
Phase separation and inheritance of repressive chromatin domains
10.1016/j.gde.2024.102201 · ExternalCitation · doi-reference
Breaths, twists, and turns of atomistic nucleosomes
10.1016/j.jmb.2020.166744 · ExternalCitation · doi-reference
Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism
10.1016/j.molcel.2019.08.019 · ExternalCitation · doi-reference
Accelerated simulations reveal physicochemical factors governing stability and composition of rna clusters
10.1021/acs.jctc.4c00803 · ExternalCitation · doi-reference
Implicit solvent with explicit ions generalized born model in molecular dynamics: application to dna
10.1021/acs.jctc.4c00833 · ExternalCitation · doi-reference
Coarse-grained model of disordered rna for simulations of biomolecular condensates
10.1021/acs.jctc.4c01646 · ExternalCitation · doi-reference
Uncovering differences in hydration free energies and structures for model compound mimics of charged side chains of amino acids
10.1021/acs.jpcb.1c01073 · ExternalCitation · doi-reference
Chemically informed coarse-graining of electrostatic forces in charge-rich biomolecular condensates
10.1021/acscentsci.4c01617 · ExternalCitation · doi-reference
Liquid droplet formation by hp1α suggests a role for phase separation in heterochromatin
10.1038/nature22822 · ExternalCitation · doi-reference
Two independent modes of chromatin organization revealed by cohesin removal
10.1038/nature24281 · ExternalCitation · doi-reference
Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
10.1038/s41467-021-23090-3 · ExternalCitation · doi-reference
Chromatin network retards nucleoli coalescence
10.1038/s41467-021-27123-9 · ExternalCitation · doi-reference
Protein structural transitions critically transform the network connectivity and viscoelasticity of rna-binding protein condensates but rna can prevent it
10.1038/s41467-022-32874-0 · ExternalCitation · doi-reference
Chromatin organization drives the search mechanism of nuclear factors
10.1038/s41467-023-42133-5 · ExternalCitation · doi-reference
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
10.1038/s41467-024-49727-7 · ExternalCitation · doi-reference
Decoding the genomic landscape of chromatin-associated biomolecular condensates
10.1038/s41467-024-51426-2 · ExternalCitation · doi-reference
Differential interactions determine anisotropies at interfaces of rna-based biomolecular condensates
10.1038/s41467-025-58736-z · ExternalCitation · doi-reference
Chromatin heterogeneity modulates nuclear condensate dynamics and phase behavior
10.1038/s41467-025-60771-9 · ExternalCitation · doi-reference
Nucleosome spacing can fine-tune higher-order chromatin assembly
10.1038/s41467-025-61482-x · ExternalCitation · doi-reference
Current practices in the study of biomolecular condensates: a community comment
10.1038/s41467-025-62055-8 · ExternalCitation · doi-reference
Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains
10.1038/s41557-021-00840-w · ExternalCitation · doi-reference
Condensates in rna repeat sequences are heterogeneously organized and exhibit reptation dynamics
10.1038/s41557-022-00934-z · ExternalCitation · doi-reference
Multifunctional histone variants in genome function
10.1038/s41576-024-00759-1 · ExternalCitation · doi-reference
Energy-driven genome regulation by ATP-dependent chromatin remodellers
10.1038/s41580-023-00683-y · ExternalCitation · doi-reference
Hp1 reshapes nucleosome core to promote phase separation of heterochromatin
10.1038/s41586-019-1669-2 · ExternalCitation · doi-reference
Extreme dynamics in a biomolecular condensate
10.1038/s41586-023-06329-5 · ExternalCitation · doi-reference
Kresten Lindorff-Larsen. Conformational ensembles of the human intrinsically disordered proteome
10.1038/s41586-023-07004-5 · ExternalCitation · doi-reference
Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy
10.1038/s43588-021-00155-3 · ExternalCitation · doi-reference
Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions
10.1063/5.0062687 · ExternalCitation · doi-reference
Cg modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability
10.1063/5.0242509 · ExternalCitation · doi-reference
Nonspecific bridging-induced attraction drives clustering of dna-binding proteins and genome organization
10.1073/pnas.1302950110 · ExternalCitation · doi-reference
Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
10.1073/pnas.2111696118 · ExternalCitation · doi-reference
Hp1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation
10.1073/pnas.2211855120 · ExternalCitation · doi-reference
Molecular drivers of rna phase separation
10.1073/pnas.2511348122 · ExternalCitation · doi-reference
Transcriptional condensates encode a “golden mean” to optimize enhancer–promoter communication across genomic distances
10.1073/pnas.2513371122 · ExternalCitation · doi-reference
OCT4 interprets and enhances nucleosome flexibility
10.1093/nar/gkac755 · ExternalCitation · doi-reference
Histone h3 tail charge patterns govern nucleosome condensate formation and dynamics
10.1093/nar/gkag050 · ExternalCitation · doi-reference
Compositional control of aging kinetics in tdp-43 condensates
10.1103/w7g3-6rsd · ExternalCitation · doi-reference
Coactivator condensation at super-enhancers links phase separation and gene control
10.1126/science.aar3958 · ExternalCitation · doi-reference
Mediator and rna polymerase ii clusters associate in transcription-dependent condensates
10.1126/science.aar4199 · ExternalCitation · doi-reference
Biophysical experiments and biomolecular simulations: a perfect match?
10.1126/science.aat4010 · ExternalCitation · doi-reference
Multiscale structure of chromatin condensates explains phase separation and material properties
10.1126/science.adv6588 · ExternalCitation · doi-reference
Sequence determinants of protein phase behavior from a coarse-grained model
10.1371/journal.pcbi.1005941 · ExternalCitation · doi-reference
Rna length has a non-trivial effect in the stability of biomolecular condensates formed by rna-binding proteins
10.1371/journal.pcbi.1009810 · ExternalCitation · doi-reference
Phase separation of 53bp1 determines liquid-like behavior of dna repair compartments
10.15252/embj.2018101379 · ExternalCitation · doi-reference
Chromatin liquid–liquid phase separation (llps) is regulated by ionic conditions and fiber length
10.3390/cells11193145 · ExternalCitation · doi-reference
Crossover in aromatic amino acid interaction strength between tyrosine and phenylalanine in biomolecular condensates
10.7554/elife.104950 · ExternalCitation · doi-reference
Explicit ion modeling predicts physicochemical interactions for chromatin organization
10.7554/elife.90073.3 · ExternalCitation · doi-reference
