@article {156899, title = {Temperature switchable self-propulsion activity of liquid crystalline microdroplets.}, journal = {Soft Matter}, year = {2025}, month = {2025 Apr 17}, abstract = {

We report on a switchable emulsion droplet microswimmer by utilizing a temperature-dependent transition of the droplet phase. The droplets, made from a liquid crystalline (LC) smectic phase material ( = 25 {\textdegree}C), self-propel only in their nematic and isotropic phases at elevated temperatures ( >= 33.5 {\textdegree}C). This transition between motile and non-motile states is fully reversible - in the motile state, the droplets exhibit persistent motion and directional memory over multiple heating-cooling cycles. Furthermore, we distinguish the state of rest from the state of motion by characterizing the chemical and hydrodynamic fields of the droplets. Next, we map the motility behaviour of the droplets across varying surfactant concentrations and temperatures, observing that swimming occurs only at sufficiently high surfactant concentrations and temperatures above the smectic-nematic phase transition temperature >= 33.5 {\textdegree}C. Our work envisions the potential of LC emulsion droplets as temperature tunable microswimmers.

}, issn = {1744-6848}, doi = {10.1039/d4sm01382d}, url = {https://pubs.rsc.org/en/content/articlelanding/2025/sm/d4sm01382d}, author = {Kumar, Manoj and Sane, Siddharth and Murali, Aniruddh and Thutupalli, Shashi} } @article {139054, title = {Constrained dynamics of DNA oligonucleotides in phase-separated droplets.}, journal = {Biophys J}, year = {2024}, month = {2024 Jan 02}, abstract = {

Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in\ vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.

}, issn = {1542-0086}, doi = {10.1016/j.bpj.2023.12.025}, author = {Singh, Anupam and Thutupalli, Shashi and Kumar, Manoj and Ameta, Sandeep} } @article {144789, title = {Emergent dynamics due to chemo-hydrodynamic self-interactions in active polymers.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Jun 08}, pages = {4903}, abstract = {

The field of synthetic active matter has, thus far, been led by efforts to create point-like, isolated (yet interacting) self-propelled objects (e.g. colloids, droplets, microrobots) and understanding their collective dynamics. The design of flexible, freely jointed active assemblies from autonomously powered sub-components remains a challenge. Here, we report freely-jointed active polymers created using self-propelled droplets as monomeric units. Our experiments reveal that the self-shaping chemo-hydrodynamic interactions between the monomeric droplets give rise to an emergent rigidity (the acquisition of a stereotypical asymmetric C-shape) and associated ballistic propulsion of the active polymers. The rigidity and propulsion of the chains vary systematically with their lengths. Using simulations of a minimal model, we establish that the emergent polymer dynamics are a generic consequence of quasi two-dimensional confinement and auto-repulsive trail-mediated chemical interactions between the freely jointed active droplets. Finally, we tune the interplay between the chemical and hydrodynamic fields to experimentally demonstrate oscillatory dynamics of the rigid polymer propulsion. Altogether, our work highlights the possible first steps towards synthetic self-morphic active matter.

}, issn = {2041-1723}, doi = {10.1038/s41467-024-49155-7}, author = {Kumar, Manoj and Murali, Aniruddh and Subramaniam, Arvin Gopal and Singh, Rajesh and Thutupalli, Shashi} } @article {147304, title = {Rigid flocks, undulatory gaits, and chiral foldamers in a chemically active polymer}, journal = {NEW JOURNAL OF PHYSICS}, volume = {26}, year = {2024}, month = {08/2024}, abstract = {

Active matter systems-such as a collection of active colloidal particles-operate far from equilibrium with complex inter-particle interactions that govern their collective dynamics. Predicting the collective dynamics of such systems may aid the design of self-shaping structures comprised of active colloidal units with a prescribed dynamical function. Here, using simulations and theory, we study the collective dynamics of a chain consisting of active Brownian particles with internal interactions via trail-mediated chemicals, connected by harmonic springs in two dimensions to obtain design principles for active colloidal molecules. We show that two-dimensional confinement and chemo-repulsive interactions between the freely-jointed particles lead to an emergent rigidity of the chain in the steady-state dynamics. In the chemo-attractive regime, the chain collapses into crystals that abruptly halt their motion. Further, in a chain consisting of a binary mixture of monomers, we show that non-reciprocal chemical affinities between distinct species give rise to novel phenomena, such as chiral molecules with tunable dynamics, sustained undulatory gaits and reversal of the direction of motion. Our results suggest a novel interpretation of the role of trail-mediated interactions, in addition to providing active self-assembly principles arising due to non-reciprocal interactions.

}, doi = {10.1088/1367-2630/ad6a7c}, author = {Gopal Subramaniam, Arvin and Kumar, Manoj and Thutupalli, Shashi and Singh, Rajesh} } @article {129505, title = {A molecular rotor FLIM probe reveals dynamic coupling between mitochondrial inner membrane fluidity and cellular respiration.}, journal = {Proc Natl Acad Sci U S A}, volume = {120}, year = {2023}, month = {2023 Jun 13}, pages = {e2213241120}, abstract = {

The inner mitochondrial membrane (IMM), housing components of the electron transport chain (ETC), is the site for respiration. The ETC relies on mobile carriers; therefore, it has long been argued that the fluidity of the densely packed IMM can potentially influence ETC flux and cell physiology. However, it is unclear if cells temporally modulate IMM fluidity upon metabolic or other stimulation. Using a photostable, red-shifted, cell-permeable molecular-rotor, Mitorotor-1, we present a multiplexed approach for quantitatively mapping IMM fluidity in living cells. This reveals IMM fluidity to be linked to cellular-respiration and responsive to stimuli. Multiple approaches combining in\ vitro experiments and live-cell fluorescence (FLIM) lifetime imaging microscopy (FLIM) show Mitorotor-1 to robustly report IMM {\textquoteright}microviscosity{\textquoteright}/fluidity through changes in molecular free volume. Interestingly, external osmotic stimuli cause controlled swelling/compaction of mitochondria, thereby revealing a graded Mitorotor-1 response to IMM microviscosity. Lateral diffusion measurements of IMM correlate with microviscosity reported via Mitorotor-1 FLIM-lifetime, showing convergence of independent approaches for measuring IMM local-order. Mitorotor-1 FLIM reveals mitochondrial heterogeneity in IMM fluidity; between-and-within cells and across single mitochondrion. Multiplexed FLIM lifetime imaging of Mitorotor-1 and NADH autofluorescence reveals that IMM fluidity positively correlates with respiration, across individual cells. Remarkably, we find that stimulating respiration, through nutrient deprivation or chemically, also leads to increase in IMM fluidity. These data suggest that modulating IMM fluidity supports enhanced respiratory flux. Our study presents a robust method for measuring IMM fluidity and suggests a dynamic regulatory paradigm of modulating IMM local order on changing metabolic demand.

}, keywords = {Cell Respiration, Membrane Fluidity, Microscopy, Fluorescence, Mitochondrial Membranes, Molecular Probes}, issn = {1091-6490}, doi = {10.1073/pnas.2213241120}, author = {Singh, Gaurav and George, Geen and Raja, Sufi O and Kandaswamy, Ponnuvel and Kumar, Manoj and Thutupalli, Shashi and Laxman, Sunil and Gulyani, Akash} } @article {128092, title = {Multispecies autocatalytic RNA reaction networks in coacervates.}, journal = {Communications Chemistry}, volume = {6}, year = {2023}, month = {2023 May 08}, pages = {91}, abstract = {

Robust localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of the Azoarcus ribozyme system within charge-rich coacervates where catalytic ribozymes are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates-both in micron-sized droplets as well as in a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, due to differential molecular transport, these phase-separated compartments endow robustness to the composition of the collectively autocatalytic networks against external perturbations. Altogether, our results establish the formation of multispecies self-reproducing reaction networks in phase-separated compartments which in turn render transient robustness to the network composition.

}, issn = {2399-3669}, doi = {10.1038/s42004-023-00887-5}, author = {Ameta, Sandeep and Kumar, Manoj and Chakraborty, Nayan and Matsubara, Yoshiya J and S, Prashanth and Gandavadi, Dhanush and Thutupalli, Shashi} } @article {105899, title = {Assembling anisotropic colloids using curvature-mediated lipid sorting.}, journal = {Soft Matter}, year = {2022}, month = {2022 Jan 24}, abstract = {

The use of colloid supported lipid bilayers (CSLBs) for assembling colloidal structures has been of recent interest. Here, we use multi-component lipid bilayer membranes formed around anisotropic colloids and show that the curvature anisotropy of the colloids drives a sorting of the lipids in the membrane along the colloids. We then exploit this curvature-sensitive lipid sorting to create "shape-anisotropic patchy colloids" - specifically, we use colloids with six rods sticking out of a central cubic core, "hexapods", for this purpose and demonstrate that membrane patches self-assemble at the tip of each of the six colloidal rods. The membrane patches are rendered sticky using biotinylated lipids in complement with a biotin-binding streptavidin protein. Finally, using these "shape-anisotropic patchy colloids", we demonstrate the directed assembly of colloidal links, paving the way for the creation of heterogeneous and flexible colloidal structures.

}, issn = {1744-6848}, doi = {10.1039/d1sm01517f}, author = {Kumar, Manoj and Singh, Anupam and Del Secco, Benedetta and Baranov, Maksim V and van den Bogaart, Geert and Sacanna, Stefano and Thutupalli, Shashi} } @article {120165, title = {Irregular particle morphology and membrane rupture facilitate ion gradients in the lumen of phagosomes.}, journal = {Biophys Rep (N Y)}, volume = {2}, year = {2022}, month = {2022 Sep 14}, pages = {100069}, abstract = {

Localized fluxes, production, and/or degradation coupled to limited diffusion are well known to result in stable spatial concentration gradients of biomolecules in the cell. In this study, we demonstrate that this also holds true for small ions, since we found that the close membrane apposition between the membrane of a phagosome and the surface of the cargo particle it encloses, together with localized membrane rupture, suffice for stable gradients of protons and iron cations within the lumen of the phagosome. Our data show that, in phagosomes containing hexapod-shaped silica colloid particles, the phagosomal membrane is ruptured at the positions of the tips of the rods, but not at other positions. This results in the confined leakage at these positions of protons and iron from the lumen of the phagosome into the cytosol. In contrast, acidification and iron accumulation still occur at the positions of the phagosomes nearer to the cores of the particles. Our study strengthens the concept that coupling metabolic and signaling reaction cascades can be spatially confined by localized limited diffusion.

}, issn = {2667-0747}, doi = {10.1016/j.bpr.2022.100069}, author = {Baranov, Maksim V and Ioannidis, Melina and Balahsioui, Sami and Boersma, Auke and de Boer, Rinse and Kumar, Manoj and Niwa, Masato and Hirayama, Tasuku and Zhou, Qintian and Hopkins, Terrence M and Grijpstra, Pieter and Thutupalli, Shashi and Sacanna, Stefano and van den Bogaart, Geert} } @article {90597, title = {Modulation of Immune Responses by Particle Size and Shape.}, journal = {Front Immunol}, volume = {607945}, year = {2021}, month = {2020}, abstract = {

The immune system has to cope with a wide range of irregularly shaped pathogens that can actively move (e.g., by flagella) and also dynamically remodel their shape (e.g., transition from yeast-shaped to hyphal fungi). The goal of this review is to draw general conclusions of how the size and geometry of a pathogen affect its uptake and processing by phagocytes of the immune system. We compared both theoretical and experimental studies with different cells, model particles, and pathogenic microbes (particularly fungi) showing that particle size, shape, rigidity, and surface roughness are important parameters for cellular uptake and subsequent immune responses, particularly inflammasome activation and T cell activation. Understanding how the physical properties of particles affect immune responses can aid the design of better vaccines.

}, issn = {1664-3224}, doi = {10.3389/fimmu.2020.607945}, author = {Baranov, Maksim V and Kumar, Manoj and Sacanna, Stefano and Thutupalli, Shashi and van den Bogaart, Geert} }