
@article {106556,
	title = {Glycan processing in the Golgi: optimal information coding and constraints on cisternal number and enzyme specificity.},
	journal = {Elife},
	volume = {11},
	year = {2022},
	month = {2022 Feb 17},
	abstract = {<p>Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we construct a simplified chemical synthesis model to quantitatively analyse the tradeoffs between the number of cisternae, and the number and specificity of enzymes, required to synthesize a prescribed target glycan distribution of a certain complexity to within a given fidelity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity (promiscuity) of enzymes that achieves the target distribution with high fidelity. The geometry of the fidelity landscape in the multidimensional space of the number and specificity of enzymes, inter-cisternal transfer rates, and number of cisternae, provides a measure for robustness and identifies stiff and sloppy directions. Our results show how the complexity of the target glycan distribution and number of glycosylation enzymes places functional constraints on the Golgi cisternal number and enzyme specificity.</p>
},
	issn = {2050-084X},
	doi = {10.7554/eLife.76757},
	author = {Yadav, Alkesh and Vagne, Quentin and Sens, Pierre and Iyengar, Garud and Rao, Madan}
}
@article {29622,
	title = {Glassy swirls of active dumbbells.},
	journal = {Phys Rev E},
	volume = {96},
	year = {2017},
	month = {2017 Oct},
	pages = {042605},
	abstract = {<p>Is an active glass different from a conventional passive glass? To address this, we study the dynamics of a dense binary mixture of soft dumbbells, each subject to an active propulsion force and thermal fluctuations. This dense assembly shows dynamical arrest, first to a translational and then to a rotational glass, as one reduces temperature T or the self-propulsion force f. We monitor the dynamics along an iso-relaxation-time contour in the (T-f) plane. We find dramatic differences both in the fragility and in the nature of dynamical heterogeneity, which characterize the onset of glass formation-the activity-induced glass exhibits large swirls or vortices, whose scale is set by activity, and it appears to diverge as one approaches the glass transition. This large collective swirling movement should have implications for collective cell migration in epithelial layers. We construct continuum hydrodynamic equations for the simulated system, and we show that the observed behavior of this growing dynamic length scale can be understood from these equations.</p>
},
	issn = {2470-0053},
	doi = {10.1103/PhysRevE.96.042605},
	author = {Mandal, Rituparno and Bhuyan, Pranab Jyoti and Chaudhuri, Pinaki and Rao, Madan and Dasgupta, Chandan}
}
