J. A. Joseph

Accelerated simulations of RNA clustering: a systematic study of repeat sequences

This study uses a coarse-grained model to simulate RNA repeat clustering, finding that base pairing and entropy drive cluster formation and that odd repeats cluster more strongly than even repeats.

Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws

The paper uses a coarse-grained model to analyze how amino acid mutations affect the stability of prion-like domains across multiple proteins, revealing scaling laws that predict condensate behavior.

Energy landscapes and heat capacity signatures for peptides correlate with phase separation propensity

Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures

This study uses simulations to show that aromatic and arginine residues drive multiphasic condensation of protein-RNA mixtures, enabling design of synthetic condensates.

A 2D Fragment-Assisted Protein Mimetic Approach to Rescue α-Synuclein Aggregation Mediated Early and Post-Disease Parkinsons Phenotypes

This paper develops a 2D-FAST method to identify antagonists of α-synuclein aggregation, showing efficacy in C. elegans models of Parkinson's disease.

Foldamers Reveal and Validate Novel Therapeutic Targets Associated with Toxic α-Synuclein Self-Assembly

This study identifies and validates novel therapeutic targets for Parkinson's disease by analyzing α-Synuclein self-assembly using foldamers and multiple assays.

Designing multiphase biomolecular condensates by coevolution of protein mixtures

This study designs protein pairs that form multiphase biomolecular condensates using a computational method combining genetic algorithms and coarse-grained models.

The chromatin regulator HMGA1a undergoes phase separation in the nucleus

This study shows HMGA1a undergoes phase separation in the nucleus, driven by protein-DNA interactions and its disordered C-terminal tail.

Can single-component protein condensates form multiphase architectures?

This study investigates how single-component protein condensates can transform into multiphase architectures during ageing through non-conservative inter-molecular interactions.

RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins

This study investigates how RNA length affects the stability of RNA-binding protein condensates through computational simulations of homotypic and heterotypic interactions.

Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients

The paper shows that size-conserved biomolecular condensates can form spontaneously through phase separation of scaffolds and surfactant clients, depending on their concentration ratios.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

The paper shows that proteins forming liquid condensates can reenter a phase-separated state at high salt concentrations due to hydrophobic and non-ionic interactions, distinct from low-salt electrostatic-driven phase separation.

Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions

This study develops a multiscale chromatin model to show that nucleosome plasticity drives chromatin LLPS and multivalent interactions.

Surface electrostatics govern the emulsion stability of biomolecular condensates

The paper investigates how surface electrostatics influence the stability of biomolecular condensates by comparing their fusion propensity using zeta potential measurements and molecular modeling.

Oligonucleotides can act as superscaffolds that enhance liquid-liquid phase separation of intracellular mixtures

This study shows oligonucleotides enhance liquid-liquid phase separation by acting as superscaffolds, increasing molecular connectivity and reducing barriers for phase separation in protein-oligonucleotide mixtures.