| 1. |
- Agrawal, Vipin, 1994-, et al.
(författare)
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Active buckling of pressurized spherical shells : Monte Carlo simulation
- 2023
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Ingår i: Physical review. E. - : American Physical Society (APS). - 2470-0045 .- 2470-0053. ; 108:3
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Tidskriftsartikel (refereegranskat)abstract
- We study the buckling of pressurized spherical shells by Monte Carlo simulations in which the detailed balance is explicitly broken—thereby driving the shell to be active, out of thermal equilibrium. Such a shell typically has either higher (active) or lower (sedate) fluctuations compared to one in thermal equilibrium depending on how the detailed balance is broken. We show that, for the same set of elastic parameters, a shell that is not buckled in thermal equilibrium can be buckled if turned active. Similarly a shell that is buckled in thermal equilibrium can unbuckle if sedated. Based on this result, we suggest that it is possible to experimentally design microscopic elastic shells whose buckling can be optically controlled.
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| 2. |
- Agrawal, Vipin, 1994-, et al.
(författare)
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MeMC : A package for Monte Carlo simulations of spherical shells
- 2022
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Ingår i: Journal of Open Source Software. - : The Open Journal. - 2475-9066. ; 7:74
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Tidskriftsartikel (refereegranskat)abstract
- The MeMC is an open-source software package for Monte Carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The code is written in c++ and python. The code is customizable – new modules can be added in a straightforward manner.
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| 3. |
- Bhatnagar, Akshay, et al.
(författare)
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Rate of formation of caustics in heavy particles advected by turbulence
- 2022
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Ingår i: Philosophical Transactions. Series A. - : The Royal Society. - 1364-503X .- 1471-2962. ; 380:2219
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Tidskriftsartikel (refereegranskat)abstract
- The rate of collision and the relative velocities of the colliding particles in turbulent flows are a crucial part of several natural phenomena, e.g. rain formation in warm clouds and planetesimal formation in protoplanetary discs. The particles are often modelled as passive, but heavy and inertial. Within this model, large relative velocities emerge due to formation of singularities (caustics) of the gradient matrix of the velocities of the particles. Using extensive direct numerical simulations of heavy particles in both two (direct and inverse cascade) and three-dimensional turbulent flows, we calculate the rate of formation of caustics, J as a function of the Stokes number (St). The best approximation to our data is J similar to exp(-C/St), in the limit St -> 0 where C is a non-universal constant. This article is part of the theme issue 'Scaling the turbulence edifice (part 2)'.
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| 4. |
- Chiappino-Pepe, Anush, et al.
(författare)
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Genome reconstructions of metabolism of Plasmodium RBC and liver stages
- 2021
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Ingår i: Current Opinion in Microbiology. - : Elsevier. - 1369-5274 .- 1879-0364. ; 63, s. 259-266
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Forskningsöversikt (refereegranskat)abstract
- Genome scale metabolic models (GEMs) offer a powerful means of integrating genome and biochemical information on an organism to make testable predictions of metabolic functions at different conditions and to systematically predict essential genes that may be targeted by drugs. This review describes how Plasmodium GEMs have become increasingly more accurate through the integration of omics and experimental genetic data. We also discuss how GEMs contribute to our increasing understanding of how Plasmodium metabolism is reprogrammed between life cycle stages.
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| 5. |
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| 6. |
- Pandey, Vikash, et al.
(författare)
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Clustering and energy spectra in two-dimensional dusty gas turbulence
- 2019
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Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 100:1
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Tidskriftsartikel (refereegranskat)abstract
- We present direct numerical simulation of heavy inertial particles (dust) immersed in two-dimensional turbulent flow (gas). The dust particles are modeled as monodispersed heavy particles capable of modifying the flow through two-way coupling. By varying the Stokes number (St) and the mass-loading parameter (phi(m)), we study the clustering phenomenon and the gas phase kinetic energy spectra. We find that the dust-dust correlation dimension (d(2)) also depends on phi(m). In particular, clustering decreases as mass loading (phi(m)) is increased. In the kinetic energy spectra of gas we show (i) the emergence of a different scaling regime and that (ii) the scaling exponent in this regime is not universal but a function of both St and phi(m). Using a scale-by-scale enstrophy budget analysis we show that in this emerged scaling regime, which we call the dust-dissipative range, viscous dissipation due to the gas balances the back-reaction from the dust.
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| 7. |
- Pandey, Vikash, et al.
(författare)
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Kolmogorov Turbulence Coexists with Pseudo-Turbulence in Buoyancy-Driven Bubbly Flows
- 2023
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Ingår i: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 131:11
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the spectral properties of buoyancy-driven bubbly flows. Using high-resolution numerical simulations and phenomenology of homogeneous turbulence, we identify the relevant energy transfer mechanisms. We find (a) at a high enough Galilei number (ratio of the buoyancy to viscous forces) the velocity power spectrum shows the Kolmogorov scaling with a power-law exponent -5/3 for the range of scales between the bubble diameter and the dissipation scale (η). (b) For scales smaller than η, the physics of pseudo-turbulence is recovered.
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| 8. |
- Pandey, Vikash, et al.
(författare)
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Turbulence modulation in buoyancy-driven bubbly flows
- 2021
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 932
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Tidskriftsartikel (refereegranskat)abstract
- We present a direct numerical simulation (DNS) study of buoyancy-driven bubbly flows in the presence of large-scale driving that generates turbulence. On increasing the turbulence intensity: (a) the bubble trajectories become more curved and (b) the average rise velocity of the bubbles decreases. We find that the energy spectrum of the flow shows a pseudo-turbulence scaling for length scales smaller than the bubble diameter and a Kolmogorov scaling for scales larger than the bubble diameter. We conduct a scale-by-scale energy budget analysis to understand the scaling behaviour observed in the spectrum. Although our bubbles are weakly buoyant, the statistical properties of our DNS are consistent with the experiments that investigate turbulence modulation by air bubbles in water.
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| 9. |
- Ramadugu, Rashmi, et al.
(författare)
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Energy spectra of buoyancy-driven bubbly flow in a vertical Hele-Shaw cell
- 2023
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Ingår i: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- We present direct numerical simulations (DNS) study of confined buoyancy-driven bubbly flows in a Hele-Shaw setup. We investigate the spectral properties of the flow and make comparisons with experiments. The energy spectrum obtained from the gap-averaged velocity field shows E(k) similar to k for k < k (d) , E(k) similar to k(-5) for k > k (d) , and an intermediate scaling range with E(k) similar to k(-3) around k similar to k(d) . We perform an energy budget analysis to understand the dominant balances and explain the observed scaling behavior. For k < k(d) , energy injection balances dissipation due to drag, whereas for k > k(d) , the net injection balances net dissipation. We also show that the Navier-Stokes equation with a linear drag can be used to approximate large scale flow properties of bubbly Hele-Shaw flow.
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| 10. |
- Russell, Andrew J.C., et al.
(författare)
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Regulators of male and female sexual development are critical for the transmission of a malaria parasite
- 2023
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Ingår i: Cell Host and Microbe. - : Cell Press. - 1931-3128 .- 1934-6069. ; 31:2, s. 305-319.e10
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Tidskriftsartikel (refereegranskat)abstract
- Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of ten mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in the determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain as well as the protein interactors of a female-determining zinc-finger protein indicate that germ-granule-like ribonucleoprotein complexes complement transcriptional processes in the regulation of both male and female development of a malaria parasite.
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| 11. |
- Stanway, Rebecca R., et al.
(författare)
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Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
- 2019
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 179:5, s. 1112-1128.e1-e15
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Tidskriftsartikel (refereegranskat)abstract
- Plasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We discover 461 genes required for efficient parasite transmission to mosquitoes through the liver stage and back into the bloodstream of mice. We analyze the screen in the context of genomic, transcriptomic, and metabolomic data by building a thermodynamic model of P. berghei liver-stage metabolism, which shows a major reprogramming of parasite metabolism to achieve rapid growth in the liver. We identify seven metabolic subsystems that become essential at the liver stages compared with asexual blood stages: type II fatty acid synthesis and elongation (FAE), tricarboxylic acid, amino sugar, heme, lipoate, and shikimate metabolism. Selected predictions from the model are individually validated in single mutants to provide future targets for drug development.
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