LASSI: A lattice model for simulating phase transitions of multivalent proteins

Stoichiometry controls activity of phase-separated clusters of actin signaling proteins

(2019) Lindsay B. Case et al.   SCIENCE

Complete Phase Diagram for Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins

(2019) James McCarty et al.   Journal of Physical Chemistry Letters

Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

(2019) Steven Boeynaems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designing Electrostatic Interactions via Polyelectrolyte Monomer Sequence

(2019) Tyler K. Lytle et al.   ACS Central Science

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates

(2018) Yi-Hsuan Lin et al.   BIOCHEMISTRY

Functional Implications of Intracellular Phase Transitions

(2018) Alex S. Holehouse et al.   BIOCHEMISTRY

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers

(2018) Ammon E. Posey et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantum theory of multiscale coarse-graining

(2018) Yining Han et al.   JOURNAL OF CHEMICAL PHYSICS

Interfacial properties of polymeric complex coacervates from simulation and theory

(2018) Tyler K. Lytle et al.   JOURNAL OF CHEMICAL PHYSICS

A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase Separation

(2018) Suman Das et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior

(2018) Tarique Khan et al.   MOLECULAR CELL

Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

(2018) Tyler S Harmon et al.   NEW JOURNAL OF PHYSICS

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

(2018) Diana M. Mitrea et al.   Nature Communications

Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation

(2018) Valery Nguemaha et al.   Scientific Reports

Sequence determinants of protein phase behavior from a coarse-grained model

(2018) Gregory L. Dignon et al.   PLoS Computational Biology

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

Reconstituted Postsynaptic Density as a Molecular Platform for Understanding Synapse Formation and Plasticity

(2018) Menglong Zeng et al.   CELL

Kinase-controlled phase transition of membraneless organelles in mitosis

(2018) Arpan Kumar Rai et al.   NATURE

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

(2018) Gregory L. Dignon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds

(2018) Dan Bracha et al.   CELL

Injectable tissue integrating networks from recombinant polypeptides with tunable order

(2018) Stefan Roberts et al.   NATURE MATERIALS

Compositional adaptability in NPM1-SURF6 scaffolding networks enabled by dynamic switching of phase separation mechanisms

(2018) Mylene C. Ferrolino et al.   Nature Communications

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics

(2017) Steven Boeynaems et al.   MOLECULAR CELL

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles

(2017) Ming-Tzo Wei et al.   Nature Chemistry

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

(2017) Yi-Hsuan Lin et al.   NEW JOURNAL OF PHYSICS

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation

(2017) Jacob P. Brady et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Transfer matrix theory of polymer complex coacervation

(2017) Tyler K. Lytle et al.   Soft Matter

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules

(2016) Hao Wu et al.   CELL

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism

(2016) Shambaditya Saha et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Recent Developments in Fully Fluctuating Field-Theoretic Simulations of Polymer Melts and Solutions

(2016) Kris T. Delaney et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fast Method for Computing Chemical Potentials and Liquid–Liquid Phase Equilibria of Macromolecular Solutions

(2016) Sanbo Qin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles

(2016) Yi-Hsuan Lin et al.   PHYSICAL REVIEW LETTERS

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

(2016) Diana M Mitrea et al.   eLife

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

(2015) Kiersten M. Ruff et al.   JOURNAL OF CHEMICAL PHYSICS

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

A multi-species exchange model for fully fluctuating polymer field theory simulations

(2014) Dominik Düchs et al.   JOURNAL OF CHEMICAL PHYSICS

Structural polymorphism in the N-terminal oligomerization domain of NPM1

(2014) D. M. Mitrea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase transitions of multivalent proteins can promote clustering of membrane receptors

(2014) Sudeep Banjade et al.   eLife

Fitting coarse-grained distribution functions through an iterative force-matching method

(2013) Lanyuan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Monte Carlo simulations of a polymer chain conformation. The effectiveness of local moves algorithms and estimation of entropy

(2013) Agnieszka Mańka et al.   JOURNAL OF MOLECULAR MODELING

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

A Bayesian statistics approach to multiscale coarse graining

(2008) Pu Liu et al.   JOURNAL OF CHEMICAL PHYSICS

On the relationship between two popular lattice models for polymer melts

(2008) Gopinath Subramanian et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Graining in Interaction Space:  A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials

(2008) Sergei Izvekov et al.   JOURNAL OF PHYSICAL CHEMISTRY B