Tracer diffusion in active suspensions

We study the diffusion of a Brownian probe particle of size $R$ in a dilute dispersion of active Brownian particles (ABPs) of size $a$, characteristic swim speed $U_0$, reorientation time $\tau_R$, and mechanical energy $k_s T_s = \zeta_a U_0^2 \tau_R /6$, where $\zeta_a$ is the Stokes drag coefficient of a swimmer. The probe has a thermal diffusivity $D_P = k_B T/\zeta_P$, where $k_B T$ is the thermal energy of the solvent and $\zeta_P$ is the Stokes drag coefficient for the probe. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. In competition with this steric hindrance is an enhancement driven by the activity of the swimmers. The strength of swimming relative to thermal diffusion is set by $Pe_s = U_0 a /D_P$. The active contribution to the diffusivity scales as $Pe_s^2$ for weak swimming and $Pe_s$ for strong swimming, but the transition between these two regimes is nonmonotonic. When fluctuations in the probe motion decay on the time scale $\tau_R$, the active diffusivity scales as $k_s T_s /\zeta_P$: the probe moves as if it were immersed in a solvent with energy $k_s T_s$ rather than $k_B T$.Comment: 5 pages, 3 figures, submitted for publication. Please contact authors regarding supplemental informatio

Fluctuation-dissipation in active matter

In a colloidal suspension at equilibrium, the diffusive motion of a tracer particle due to random thermal fluctuations from the solvent is related to the particle’s response to an applied external force, provided this force is weak compared to the thermal restoring forces in the solvent. This is known as the fluctuation-dissipation theorem (FDT) and is expressed via the Stokes-Einstein-Sutherland (SES) relation D = k_BT/ζ, where D is the particle’s self-diffusivity (fluctuation), ζ is the drag on the particle (dissipation), and k_BT is the thermal Boltzmann energy. Active suspensions are widely studied precisely because they are far from equilibrium—they can generate significant nonthermal internal stresses, which can break the detailed balance and time-reversal symmetry—and thus cannot be assumed to obey the FDT a priori. We derive a general relationship between diffusivity and mobility in generic colloidal suspensions (not restricted to near equilibrium) using generalized Taylor dispersion theory and derive specific conditions on particle motion required for the FDT to hold. Even in the simplest system of active Brownian particles (ABPs), these conditions may not be satisfied. Nevertheless, it is still possible to quantify deviations from the FDT and express them in terms of an effective SES relation that accounts for the ABPs conversion of chemical into kinetic energy

Fluctuation-dissipation in active matter

In a colloidal suspension at equilibrium, the diffusive motion of a tracer particle due to random thermal fluctuations from the solvent is related to the particle’s response to an applied external force, provided this force is weak compared to the thermal restoring forces in the solvent. This is known as the fluctuation-dissipation theorem (FDT) and is expressed via the Stokes-Einstein-Sutherland (SES) relation D = k_BT/ζ, where D is the particle’s self-diffusivity (fluctuation), ζ is the drag on the particle (dissipation), and k_BT is the thermal Boltzmann energy. Active suspensions are widely studied precisely because they are far from equilibrium—they can generate significant nonthermal internal stresses, which can break the detailed balance and time-reversal symmetry—and thus cannot be assumed to obey the FDT a priori. We derive a general relationship between diffusivity and mobility in generic colloidal suspensions (not restricted to near equilibrium) using generalized Taylor dispersion theory and derive specific conditions on particle motion required for the FDT to hold. Even in the simplest system of active Brownian particles (ABPs), these conditions may not be satisfied. Nevertheless, it is still possible to quantify deviations from the FDT and express them in terms of an effective SES relation that accounts for the ABPs conversion of chemical into kinetic energy

The photochemistry of acetone in the upper troposphere: A source of odd-hydrogen radicals

This paper summarizes measured photodissociation quantum yields for acetone in the 290-320 nm wavelength region for pressures and temperatures characteristic of the upper troposphere. Calculations combine this laboratory data with trace gas concentrations obtained during the NASA and NOAA sponsored Stratospheric Tracers of Atmospheric Transport (STRAT) field campaign, in which measurements of OH, HO_(2), odd-nitrogen, and other compounds were collected over Hawaii, and west of California during fall and winter of 1995/1996. OH and HO_(2) concentrations within 2 to 5 km layers just below the tropopause are ∼50% larger than expected from O_(3), CH_(4), and H_(2)O chemistry alone. Although not measured during STRAT, acetone is inferred from CO measurements and acetone-CO correlations from a previous field study. These inferred acetone levels are a significant source of odd-hydrogen radicals that can explain a large part of the discrepancy in the upper troposphere. For lower altitudes, the inferred acetone makes a negligible contribution to HO_(x) (HO+HO_(2)), but influences NO_(y) partitioning. A major fraction of HO_(x) production by acetone is through CH_(2)O formation, and the HO_(x) discrepancy can also be explained by CH_(2)O levels in the 20 to 50 pptv range, regardless of the source

Pulsed Feedback Defers Cellular Differentiation

Environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well-characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable “polyphasic” positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a “timer” that operates over timescales much longer than a cell cycle

ruvA Mutants that resolve Holliday junctions but do not reverse replication forks

RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination

Effects of external nutrient sources and extreme weather events on the nutrient budget of a Southern European coastal lagoon

The seasonal and annual nitrogen (N), phosphorus (P), and carbon (C) budgets of the mesotidal Ria Formosa lagoon, southern Portugal, were estimated to reveal the main inputs and outputs, the seasonal patterns, and how they may influence the ecological functioning of the system. The effects of extreme weather events such as long-lasting strong winds causing upwelling and strong rainfall were assessed. External nutrient inputs were quantified; ocean exchange was assessed in 24-h sampling campaigns, and final calculations were made using a hydrodynamic model of the lagoon. Rain and stream inputs were the main freshwater sources to the lagoon. However, wastewater treatment plant and groundwater discharges dominated nutrient input, together accounting for 98, 96, and 88 % of total C, N, and P input, respectively. Organic matter and nutrients were continuously exported to the ocean. This pattern was reversed following extreme events, such as strong winds in early summer that caused upwelling and after a period of heavy rainfall in late autumn. A principal component analysis (PCA) revealed that ammonium and organic N and C exchange were positively associated with temperature as opposed to pH and nitrate. These variables reflected mostly the benthic lagoon metabolism, whereas particulate P exchange was correlated to Chl a, indicating that this was more related to phytoplankton dynamics. The increase of stochastic events, as expected in climate change scenarios, may have strong effects on the ecological functioning of coastal lagoons, altering the C and nutrient budgets.Portuguese Science and Technology Foundation (FCT) [POCI/MAR/58427/2004, PPCDT/MAR/58427/2004]; Portuguese Science and Technology Foundation (FCT