Ashok Deniz
@ashokdeniz.bsky.social
Professor, @scripps.edu
Interested in Single-molecule Biophysics, Soft matter physics,
Condensates, Protein disorder, Membranes, RNA, #smFRET, Physical Organic Chemistry
https://scholar.google.com/citations?user=bNzBCLYAAAAJ&hl=en
Interested in Single-molecule Biophysics, Soft matter physics,
Condensates, Protein disorder, Membranes, RNA, #smFRET, Physical Organic Chemistry
https://scholar.google.com/citations?user=bNzBCLYAAAAJ&hl=en
Pinned
Ashok Deniz
@ashokdeniz.bsky.social
· Dec 29
Biomolecular Condensates can Induce Local Membrane Potentials
Biomolecular condensates are a ubiquitous component of cells, known for their ability to selectively partition and compartmentalize biomolecules without the need for a lipid membrane. Nevertheless, co...
biorxiv.org
Excited to share our preprint, work by Anthony Gurunian, showing that #condensates can induce localized potentials in membranes + an analytical framework, with important biological implications, collaboration with @kerenlasker
biorxiv.org/cgi/content/...
biorxiv.org/cgi/content/...
Reposted by Ashok Deniz
A tremendous honor! Thrilled & humbled to receive 2025 Keio Medical Science Prize for launching LLPS #phaseseparation field (= #softmatter + #cellbio) w collaborators esp @HymanLab. & Congrats to Akiko Iwasaki @virusesimmunity.bsky.social. www.princeton.edu/news/2025/09...
#KeioMedicalSciencePrize
#KeioMedicalSciencePrize
Bioengineer Clifford Brangwynne wins Keio Medical Science Prize
Japan’s Keio University awards the prize annually to honor contributions in medicine and life sciences. Brangwynne is being recognized for groundbreaking work that has opened up a new field of cell bi...
www.princeton.edu
September 20, 2025 at 6:16 PM
A tremendous honor! Thrilled & humbled to receive 2025 Keio Medical Science Prize for launching LLPS #phaseseparation field (= #softmatter + #cellbio) w collaborators esp @HymanLab. & Congrats to Akiko Iwasaki @virusesimmunity.bsky.social. www.princeton.edu/news/2025/09...
#KeioMedicalSciencePrize
#KeioMedicalSciencePrize
Reposted by Ashok Deniz
Curious how biomolecular condensates can localize ions? Using NMR, we found that condensates selectively bind and localize both chaotropic anions and kosmotropic cations. This alters the condensate composition, interface potential and RNA duplex stability inside. By @irissmokers.bsky.social
Selective ion binding and uptake shape the microenvironment of biomolecular condensates
Biomolecular condensates modulate various ion-dependent cellular processes and can regulate subcellular ion distributions by selective uptake of ions. However, the molecular grammar governing condensa...
www.biorxiv.org
January 13, 2025 at 8:25 AM
Curious how biomolecular condensates can localize ions? Using NMR, we found that condensates selectively bind and localize both chaotropic anions and kosmotropic cations. This alters the condensate composition, interface potential and RNA duplex stability inside. By @irissmokers.bsky.social
Reposted by Ashok Deniz
I am super happy to share our latest article entitled "Decoding the molecular interplay of CD20 and therapeutic antibodies with fast volumetric nanoscopy", now published in Science www.science.org/doi/10.1126/...
It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!
It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!
January 10, 2025 at 2:07 PM
I am super happy to share our latest article entitled "Decoding the molecular interplay of CD20 and therapeutic antibodies with fast volumetric nanoscopy", now published in Science www.science.org/doi/10.1126/...
It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!
It was my postdoctoral work mit @sauer-lab.bsky.social Congrats to all the co-authors!
Reposted by Ashok Deniz
Happy new year! Our new preprint is live! We use single molecule imaging in live cells to show that activation domains can control how transcription factors bind to chromatin. SMT 1 TF Dogma 0 www.biorxiv.org/content/10.1...
Short activation domains control chromatin association of transcription factors
Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. It is generally assumed that DBDs are solely responsible for interacting with DNA and chromatin. ...
www.biorxiv.org
January 10, 2025 at 5:07 PM
Happy new year! Our new preprint is live! We use single molecule imaging in live cells to show that activation domains can control how transcription factors bind to chromatin. SMT 1 TF Dogma 0 www.biorxiv.org/content/10.1...
Reposted by Ashok Deniz
Happy to be on BlueSky!
For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...
For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...
Programming scheduled self-assembly of circadian materials - Nature Communications
Harnessing biomolecular systems to endow synthetic materials with life-like properties is a significant challenge. Here, the authors use the biomolecular KaiABC circadian clock proteins to control aut...
www.nature.com
January 11, 2025 at 3:37 AM
Happy to be on BlueSky!
For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...
For my first post, I am excited to share a new collaborative paper combining experiments and simulations, where we used circadian clock proteins to engineer biomaterials with time-programmed self-assembly and disassembly www.nature.com/articles/s41...
Reposted by Ashok Deniz
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
January 6, 2025 at 11:19 AM
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Reposted by Ashok Deniz
After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month. We are very grateful for his service.
@jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases
Details: cdn.rcsb.org/rcsb-pd...
@jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases
Details: cdn.rcsb.org/rcsb-pd...
EDUCATION CORNER: Molecule of the Month: Celebrating 25 Years of Storytelling and Announcing New Beginnings
After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month series. Janet Iwasa will be continuing the series for PDB-101.
cdn.rcsb.org
January 6, 2025 at 5:12 PM
After a remarkable 300 columns, David Goodsell has retired from the Molecule of the Month. We are very grateful for his service.
@jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases
Details: cdn.rcsb.org/rcsb-pd...
@jiwasa.bsky.social will continue the series, beginning with January's article on Assembly Line Polyketide Synthases
Details: cdn.rcsb.org/rcsb-pd...
Rayleigh-Plateau instability in mitochondria? Exciting analysis of physics of mitochondria dynamics
Mitochondria consist of networks of cylindrical tubes, right? Not necessarily! - in our new preprint, @gavsturm.bsky.social investigates how mitochondria transiently adopt a beads-on-a-string morphology
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 31, 2024 at 4:13 AM
Rayleigh-Plateau instability in mitochondria? Exciting analysis of physics of mitochondria dynamics
Reposted by Ashok Deniz
For inspiration, here are the papers we discussed in 2023:
December 30, 2024 at 3:02 PM
For inspiration, here are the papers we discussed in 2023:
Reposted by Ashok Deniz
Visualizing Single V-ATPase Rotation Using Janus Nanoparticles
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Visualizing Single V-ATPase Rotation Using Janus Nanoparticles
Understanding the function of rotary molecular motors, such as rotary ATPases, relies on our ability to visualize single-molecule rotation. Traditional imaging methods often involve tagging those mot...
pubs.acs.org
December 15, 2024 at 4:30 AM
Visualizing Single V-ATPase Rotation Using Janus Nanoparticles
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Reposted by Ashok Deniz
1/ 🚨We’re thrilled to share our latest study:
"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟
www.biorxiv.org/content/10.1...
How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟
www.biorxiv.org/content/10.1...
How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure
Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We stud...
www.biorxiv.org
December 30, 2024 at 9:01 PM
1/ 🚨We’re thrilled to share our latest study:
"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟
www.biorxiv.org/content/10.1...
How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
"Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟
www.biorxiv.org/content/10.1...
How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
Excited to share our preprint, work by Anthony Gurunian, showing that #condensates can induce localized potentials in membranes + an analytical framework, with important biological implications, collaboration with @kerenlasker
biorxiv.org/cgi/content/...
biorxiv.org/cgi/content/...
Biomolecular Condensates can Induce Local Membrane Potentials
Biomolecular condensates are a ubiquitous component of cells, known for their ability to selectively partition and compartmentalize biomolecules without the need for a lipid membrane. Nevertheless, co...
biorxiv.org
December 29, 2024 at 9:02 AM
Excited to share our preprint, work by Anthony Gurunian, showing that #condensates can induce localized potentials in membranes + an analytical framework, with important biological implications, collaboration with @kerenlasker
biorxiv.org/cgi/content/...
biorxiv.org/cgi/content/...
Interesting porous material - rhodium metal-organic polyhedra (MOP) with tethered polymers.
Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes.
www.nature.com/articles/s41...
Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes.
www.nature.com/articles/s41...
Phase-transformable metal-organic polyhedra for membrane processing and switchable gas separation - Nature Communications
The capability of materials to interconvert between phases enables greater control over properties without additional chemical modification but can result in a sacrifice of porosity. Here, the authors...
www.nature.com
December 17, 2024 at 5:18 PM
Interesting porous material - rhodium metal-organic polyhedra (MOP) with tethered polymers.
Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes.
www.nature.com/articles/s41...
Tunable phase transition/gas adsorption-diffusion properties, applied to gas separation membranes.
www.nature.com/articles/s41...
Reposted by Ashok Deniz
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
December 11, 2024 at 9:35 PM
Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...
Interesting biomaterial engineering!- leveraging physical and chemical properties of gallium
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Sacrificial capillary pumps to engineer multiscalar biological forms - Nature
A patterning method using gallium-based engineered sacrificial capillary pumps for evacuation is described for generating structures in soft natural hydrogels across several length scales and enabling...
www.nature.com
December 11, 2024 at 8:11 PM
Interesting biomaterial engineering!- leveraging physical and chemical properties of gallium
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ashok Deniz
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
December 4, 2024 at 8:53 PM
First paper of our lab today @natureportfolio.bsky.social by Nussi!
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!
@embl.org #RNAbiology #RNASky
t.co/a24Xxcxdo0
December 11, 2024 at 5:33 AM
Reposted by Ashok Deniz
Published in @science.org, scientists at Scripps Research have uncovered a mutation in the H5N1 “bird flu” virus that enhances its ability to bind to human cells—emphasizing the need to monitor H5N1 to prepare for potential pandemic threats. More:
Scripps Research scientists identify mutation that could facilitate H5N1 “bird flu” virus infection and potential transmission in humans
www.scripps.edu
December 5, 2024 at 9:42 PM
Published in @science.org, scientists at Scripps Research have uncovered a mutation in the H5N1 “bird flu” virus that enhances its ability to bind to human cells—emphasizing the need to monitor H5N1 to prepare for potential pandemic threats. More:
Reposted by Ashok Deniz
Do you find yourself curious about the eating habits of macrophages? Check out our new preprint to discover the biophysical principles that guide macrophage behavior.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 5, 2024 at 9:48 PM
Do you find yourself curious about the eating habits of macrophages? Check out our new preprint to discover the biophysical principles that guide macrophage behavior.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Nice work! Also includes some interesting work with lipid chirality/racemic mixtures.
🥳 A tuneable minimal cell membrane reveals that two lipid species suffice for life: www.nature.com/articles/s41... We chemically minimized the membrane of the Minimal Cell...they survived, but with some interesting shapes, like this 'Death Star' phenotype @jcvi.bsky.social @jcv.bsky.social
December 7, 2024 at 12:22 AM
Nice work! Also includes some interesting work with lipid chirality/racemic mixtures.
Neat!
If you like total synthesis and Wordle, check out Synthordle, a retrosynthetic analysis game created by Shenvi Lab associates Kevin Zong (GS 2) and Jonah Luo (HS sophomore!).
shenvilab.github.io/Synthordle/
Easy problems for Sophomore OChem, hard problems for advanced practitioners.
shenvilab.github.io/Synthordle/
Easy problems for Sophomore OChem, hard problems for advanced practitioners.
December 5, 2024 at 2:45 PM
Neat!
Reposted by Ashok Deniz
We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
November 10, 2024 at 2:19 PM
We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
Reposted by Ashok Deniz
As the chair of the Intrinsically Disordered Proteins Subgroup of @biophysicalsoc.bsky.social I'm happy to announce the exciting scientific program put together by program co-chairs Dorothee Dormann & Lukasz Joachimiak.
Looking forward to seeing you in Los Angeles!
www.biophysics.org/2025meeting/...
Looking forward to seeing you in Los Angeles!
www.biophysics.org/2025meeting/...
December 5, 2024 at 6:54 AM
As the chair of the Intrinsically Disordered Proteins Subgroup of @biophysicalsoc.bsky.social I'm happy to announce the exciting scientific program put together by program co-chairs Dorothee Dormann & Lukasz Joachimiak.
Looking forward to seeing you in Los Angeles!
www.biophysics.org/2025meeting/...
Looking forward to seeing you in Los Angeles!
www.biophysics.org/2025meeting/...
Reposted by Ashok Deniz
Happy to share that my former PhD student, Debapriya Das (now doing her postdoc with my postdoc advisor, Ashok Deniz, at the Scripps Research Institute, California) has been selected for a platform talk at the Biophysical Society meeting to be held in Los Angeles in Feb 2025. Congrats, Debapriya!
December 3, 2024 at 3:57 PM
Happy to share that my former PhD student, Debapriya Das (now doing her postdoc with my postdoc advisor, Ashok Deniz, at the Scripps Research Institute, California) has been selected for a platform talk at the Biophysical Society meeting to be held in Los Angeles in Feb 2025. Congrats, Debapriya!
Reposted by Ashok Deniz
Latest #CDlab paper: Synchronization of E. coli Bacteria Moving in Coupled Microwells: onlinelibrary.wiley.com/doi/epdf/10....
E. coli bacteria swim in sync in weakly coupled neighboring microcavities!
Great work led by @AleksandreJapa from from Farbod Alijani's lab, to which I also contributed
E. coli bacteria swim in sync in weakly coupled neighboring microcavities!
Great work led by @AleksandreJapa from from Farbod Alijani's lab, to which I also contributed
November 27, 2024 at 12:06 PM
Latest #CDlab paper: Synchronization of E. coli Bacteria Moving in Coupled Microwells: onlinelibrary.wiley.com/doi/epdf/10....
E. coli bacteria swim in sync in weakly coupled neighboring microcavities!
Great work led by @AleksandreJapa from from Farbod Alijani's lab, to which I also contributed
E. coli bacteria swim in sync in weakly coupled neighboring microcavities!
Great work led by @AleksandreJapa from from Farbod Alijani's lab, to which I also contributed