Alireza Mashaghi

Delighted to share our new study, "Topological Investigation of Protein Folding and Intrinsic Disorder". We ask whether topology provides a unifying structural language across the order–disorder continuum!

doi.org/10.64898/202...

#ChemSky #Protein #IDP #Topology #Biophysics

Mashaghi Lab - Vacancies Community science: Since 1996, Alireza Mashaghi has actively advocated for collaborations between disciplines to explore new ways of addressing scientific and societal challenges. The team has a long...

My laboratory has an open postdoctoral position in the field of biomolecular condensate mechanochemistry! Please inquire if you are interested in interdisciplinary, cutting-edge research!

www.mashaghilab.org/vacancies
(Deadline: February 8, 2026)

#ChemSky #Mechanobiology #Biomolecular_Condensate

RNA topology: from simple loops to complex circuits

chemrxiv.org/engage/chemr...

#ChemSky #RNA #Biophysics

Learning capacity and function of stochastic reaction networks

iopscience.iop.org/article/10.1...

#ChemSky #Network #Physics #Stochasticity #Learning

Interplay of coil–globule transitions and aggregation in homopolymer aqueous solutions: Simulation and topological insights We investigate the structural and topological properties of hydrophobic homopolymer chains in aqueous solutions using molecular dynamics simulations and circuit

Impressive work by Dr. Jonas Berx and co-workers in the Journal of Chemical Physics on the topological organization of polymeric aggregates!
doi.org/10.1063/5.02...

#ChemSky #Topology #Polymer #Biophysics #SoftMatter

Good luck, Tony! You have been an inspiration to many! Thank you!

@hymanlab.bsky.social

On circuit topology of knots!

Circuit topology for bottom-up engineering of molecular knots
doi.org/10.3390/sym1...

A tile model of circuit topology for entangled biopolymers
www.nature.com/articles/s41...

Polynomial invariant of molecular circuit topology
doi.org/10.3390/sym1...
#ChemSky #knot

Our protocol on "Scanning probe microscopy for rheological analysis of biomolecular condensates" is now available for interested users!

doi.org/10.1016/j.xp...

#ChemSky #Biphysics #Biomolecular_Condensates #IDP #Rheology #AFM

Vasily from our team was invited to present at the #NRRN meeting on “Conformational Dynamics and Chromatin Assembly of #Glucocorticoid Receptor Using Topological Modeling and Single-Molecule Analysis.” Looking forward to connecting with researchers on advances in nuclear receptor research.
#ChemSky

Many congrats!

We discovered that the "orphan" nuclear receptor Nur77 binds DNA under regulation by #glucocorticoid receptor & glucocorticoids. The synthetic glucocorticoid dexamethasone directly interacts with Nur77, revealing a new function for this drug & a potential ligand for Nur77.

doi.org/10.1101/2025...

We’re excited to share our new #PyMOL plugin for protein topology analysis, now available!

doi.org/10.1101/2025...

Link to the report and the GitHub repository:

We’d appreciate your feedback — please try it out in PyMOL and report any bugs or suggestions!

#ChemSky #IDP #Topology #Bioinformatics

An interview with Stanford scientist Jonathan Chen on Medical #AI!

Also, see the piece we co-authored on Statistical #Physics and its applications in #Medicine:

pubmed.ncbi.nlm.nih.gov/33228143/

Our postdoctoral researcher Aida Naghilou presented our lab’s development of SPM-based technology for biomolecular condensate analysis at the Erwin Schrödinger Institute during the workshop “Charged Soft Matter: Bridging Theory and Experiment”!

www.youtube.com/playlist?lis...
#ChemSky #SoftMatter

Protamine Drives Liquid and Solid Condensation of DNA and Glycosaminoglycans Phase-separated biomolecular condensates play a crucial role in cellular organization. In the nucleus, phase separation regulates the assembly and function of nuclear proteins and the genome. Here, we...

We recently had some fun with protamine, which we used to model the Aggregate-to-Condensate transition in polyelectrolyte systems!

pubs.acs.org/doi/10.1021/...
#ChemSky #Bioengineering

Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment Single molecule experiments aimed at probing protein folding are typically performed in buffer conditions and cannot therefore be representative of the multi-faceted and complex cooperative interacti...

We recently carried out the first single-molecule analysis of protein folding & unfolding in a cytosolic environment using optical tweezers—moving beyond simplistic buffer conditions to study proteins where they actually function.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
#ChemSky #Biophysics

PhD student Vasily Akulov from our group is presenting our collaborative research with Eva Estébanez-Perpiñá’s group at the EMBO Workshop in Palermo, Italy!

meetings.embo.org/event/25-str...

#EMBO #StructuralBiology #IDP #Topology

On extracellular #biomolecular condensates!

We demonstrate that phase-separated #condensate #droplets can form and function in the #extracellular environment and may interact with cells!
www.sciencedirect.com/science/arti...
#CellBiology #Biophysics #ChemicalEngineering #SyntheticBiology #ChemSky

Check out our research on Semantic Topology at the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025) in Vienna next week!

#ACL2025 #Interdisciplinary #Semantics

Semantic Topology: a New Perspective for Communication Style Characterization

aclanthology.org/2025.finding...

#Linguistics #NLProc #ACL2025NLP #ACL2025

On disordered topologically compact states in intrinsically disordered proteins! We explored this concept in the context of the human Glucocorticoid Receptor.
pubs.acs.org/doi/10.1021/...

#ChemSky #IDP #Protein #Biophysics #Topology #CompChem

New Boltzmann Medalist Mehran Kardar at StatPhys29 in Florence, showing the first handmade slide that led to the #KPZ equation. #StatisticalPhysics #Physics Photo: Andrea Gabrielli

Team snapshot after our regular group meeting — this time with a great talk by Muriel Hammond on intrinsically disordered proteins!

For those interested in topological analysis of biomolecular condensates!

Article 1: link.springer.com/article/10.1...
Article 2: www.sciencedirect.com/science/arti...

#Topology #Condensate #PhaseSeparation #Aggregation #ChemSky #Biophysics #Polymer #Nanoscience

Polyglutamine expansion induced dynamic misfolding of androgen receptor Spinal bulbar muscular atrophy (SBMA) is caused by a polyglutamine expansion (pQe) in the N-terminal transactivation domain of the human androgen receptor (AR-NTD), resulting in a combination of toxi...

The first model of full length human androgen receptor and its polyQ expanded variant!

onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com/doi/full/10....

#endocrinology #androgen #hormone #receptor #SBMA #polyglutamine #prostate

PhD student Laurens Heling from my laboratory will be presenting a the #LACDR Spring Symposium!

"Single Molecule Analysis Reveals Allosteric Regulation of #Androgen #Receptor DNA Binding​"

#SingleMolecule #Biophysics #Endocrinology

Leiden scientists create first-ever dengue-on-a-chip to study this deadly virus Researchers at Leiden University have created a unique model that mimics how disease develops after a dengue infection. This 'dengue-on-a-chip' model helps them study the virus more effectively. The t...

Researchers at Leiden University have created a unique model that mimics how disease develops after a dengue infection. This 'dengue-on-a-chip' model helps them study the virus more effectively. The timing is crucial, as climate change is causing dengue to spread worldwide.
Read more:

Revealing Mechanopathology Induced by Dengue NS1 Using Organ Chips and Single-Cell Force Spectroscopy Capillary leakage is a hallmark of severe dengue, yet its precise mechanisms remain elusive. Emerging evidence highlights the dengue virus’s targeting of mechanically active endothelial cells as a key contributor to dengue shock syndrome. The viral nonstructural protein 1 (NS1) has been identified as a central player, disrupting endothelial integrity and inducing vascular hyperpermeability independently of pro-inflammatory cytokines. This study provides a direct assessment of NS1-induced endothelial pathology by combining single-cell force spectroscopy and a microvessel-on-a-chip platform. We demonstrate that NS1 significantly alters endothelial cell mechanics, reducing cell stiffness and compromising junctional integrity, thereby directly linking these mechanical alterations to vascular dysfunction. These findings establish a framework for understanding the mechano-pathology of dengue and offer a platform for developing targeted therapeutic strategies to mitigate severe disease outcomes.

Research update from our lab: Dengue-on-a-chip and single-cell rheology reveal that Dengue is a "disease of mechanics"!

#Bioengineering #Virology #Infection #Mechanobiology
pubs.acs.org/doi/10.1021/...

From liquid to solid: revolutionary technique uncovers disease-related changes in tiny droplets within our cells Understanding the behaviour of tiny droplets in our cells could aid the search for new treatments. A team of Leiden researchers has developed a groundbreaking method to study how these droplets transi...

Research update from our lab:
We reported the first use of Scanning Probe Microscopy in biomolecular condensate research!

#ChemSky #Interdisciplinary #Biophysics #Mechanics #Rheology

www.universiteitleiden.nl/en/news/2025...