Multispecies model with interconversion, chipping, and injection

Sachdeva, Himani; Barma, Mustansir; Rao, Madan

doi:10.1103/physreve.84.031106

Cited by 6 publications

(12 citation statements)

References 22 publications

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“…In fact, if the influx is too high, the vesicular outflux may fail to balance the influx near the peaks, leading to runaway growth of mass, as elaborated in ref. 33 (also pointed out in ref. 29).…”

Section: Resultsmentioning

confidence: 70%

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Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae

Sachdeva

Barma

Rao

2016

Sci Rep

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A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner–this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.

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Section: Resultsmentioning

confidence: 70%

“…This allows us to solve for the average mass of each species at each site in steady state, using the techniques described in ref. 33 (see S2.1, SI for details). While we have explored several functional forms of f [ m ] using numerical simulations (S2.2, SI), we discuss below properties of structures generated using Eq.…”

Section: Resultsmentioning

confidence: 99%

Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae

Sachdeva

Barma

Rao

2016

Sci Rep

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“…The studies in Refs. [11,12] and Ref. [13] of intermittency due to clustering at the cellular level, suggest that these methods may work well in the biological context as well.…”

Section: Discussionmentioning

confidence: 99%

“…These methods are of broad applicability and may fruitfully be used in a number of settings. For instance, in the context of biological systems which exhibit clustering, temporal intermittency has been studied for both molecular transport through Golgi [11,12], and protein aggregation on cell membranes [13].…”

Section: Introductionmentioning

confidence: 99%

Clustering, intermittency, and scaling for passive particles on fluctuating surfaces

Singha

Barma

2018

Phys. Rev. E

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We show that a scaling approach successfully characterizes clustering and intermittency in space and time, in systems of noninteracting particles driven by fluctuating surfaces. We study both the steady state and the approach to it, for passive particles sliding on one-dimensional Edwards-Wilkinson or Kardar-Parisi-Zhang (KPZ) surfaces, with particles moving either along (advection) or against (antiadvection) the growth direction in the latter case. Extensive numerical simulations are supplemented by analytical results for a sticky slider model in which particles coalesce when they meet. Results for single particle displacement versus time show to what extent particle dynamics is slaved to the surface, while scaling properties of the probability distribution of the separation of two particles determine the scaling form of average overlap of a pair of trajectories. For the manyparticle system, clustering in steady state is studied via moments of particle number fluctuations in a single stretch, revealing different degrees of spatial multiscaling with different drivings. Temporal intermittency in steady state is established by showing that the scaled flatness diverges as the stretch size scaled by system size approaches zero for all the three drivings, but with different exponents, reflecting strongest clustering for KPZ advection and weakest for KPZ antiadvection. Finally we consider the approach to the steady state, study both the flatness and the evolution of equal-time correlation functions as in coarsening of phase ordering systems. Our studies give clear evidence for a simple scaling description of the approach to steady state, with the scale set by a length which grows in time. An investigation of aging properties reveals that flatness is nonmonotonic in time with two distinct branches, and that a scaling description holds for each one.

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“…The phenomenon is akin to Bose condensation, but in real space.Does the condensation transition survive in a system when the total mass is not conserved, but can undergo large fluctuations due to the exit of clusters of all sizes? This question is important in a number of physical situations, ranging from formation of clouds and aerosols, to intracellular trafficking and organelle formation in living cells [4][5][6]. We address this within a simple but generic 1D model with aggregation and fragmentation (chipping) of masses in the bulk, and influx and outflux of masses at the boundaries.…”

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confidence: 99%

Condensation and Intermittency in an Open-Boundary Aggregation-Fragmentation Model

2013

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We study real space condensation in aggregation-fragmentation models where the total mass is not conserved, as in phenomena such as cloud formation and intracellular trafficking. We study the scaling properties of the system with influx and outflux of mass at the boundaries using numerical simulations, supplemented by analytical results in the absence of fragmentation. The system is found to undergo a phase transition to an unusual condensate phase, characterized by strong intermittency and giant fluctuations of the total mass. A related phase transition also occurs for biased movement of large masses, but with some crucial differences which we highlight.

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Multispecies model with interconversion, chipping, and injection

Cited by 6 publications

References 22 publications

Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae

Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae

Clustering, intermittency, and scaling for passive particles on fluctuating surfaces

Condensation and Intermittency in an Open-Boundary Aggregation-Fragmentation Model

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