Resonance Energy Transfer

Resonance energy transfer, also known as Förster- or fluorescence- resonance energy transfer, or electronic energy transfer, is a photonic process whose relevance in many major areas of science is reflected both by a wide prevalence of the effect and through numerous technical applications. The process, operating through an optical near-field mechanism, effects a transport of electronic excitation between physically distinct atomic or molecular components, based on transition dipole-dipole coupling. In this chapter a comprehensive survey of the process is presented, beginning with an outline of the history and highlighting the early contributions of Perrin and Förster. A review of the photophysics behind resonance energy transfer follows, and then a discussion of some prominent applications of resonance energy transfer. Particular emphasis is given to analysis and sensing techniques used in molecular biology, ranging from the ‘spectroscopic ruler’ measurements of functional group separation, to fluorescence lifetime microscopy. The chapter ends with a description of the role of energy transfer in photosynthetic light harvesting

Constructing A Flexible Likelihood Function For Spectroscopic Inference

We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically address the common problem of mismatches in model spectral line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line "outliers." By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high resolution $V$-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate resolution $K$-band spectrum of Gliese 51, an M5 field dwarf.Comment: Accepted to ApJ. Incorporated referees' comments. New figures 1, 8, 10, 12, and 14. Supplemental website: http://iancze.github.io/Starfish

The inconstancy of the transient climate response parameter under increasing CO₂

In the Coupled Model Intercomparison Project Phase 5 (CMIP5), the model-mean increase in global mean surface air temperature T under the 1pctCO2 scenario (atmospheric CO2 increasing at 1% yr−1) during the second doubling of CO2 is 40% larger than the transient climate response (TCR), i.e. the increase in T during the first doubling. We identify four possible contributory effects. First, the surface climate system loses heat less readily into the ocean beneath as the latter warms. The model spread in the thermal coupling between the upper and deep ocean largely explains the model spread in ocean heat uptake efficiency. Second, CO2 radiative forcing may rise more rapidly than logarithmically with CO2 concentration. Third, the climate feedback parameter may decline as the CO2 concentration rises. With CMIP5 data, we cannot distinguish the second and third possibilities. Fourth, the climate feedback parameter declines as time passes or T rises; in 1pctCO2, this effect is less important than the others. We find that T projected for the end of the twenty-first century correlates more highly with T at the time of quadrupled CO2 in 1pctCO2 than with the TCR, and we suggest that the TCR may be underestimated from observed climate change

Forcing and response in simulated 20th and 21st century surface energy and precipitation trends

A simple methodology is applied to a transient integration of the Met Office Hadley Centre Global Environmental Model version1 (UKMO-HadGEM1) fully coupled atmosphere-ocean general circulation model in order to separate forcing from climate response in simulated 20th century and future global mean surface energy and precipitation trends. Forcings include any fast responses that are caused by the forcing agent and that are independent of global temperature change. Results reveal that surface radiative forcing is dominated by shortwave forcing over the 20th and 21st centuries, which is strongly negative. However, when fast responses of surface turbulent heat fluxes are separated from climate feedbacks, and included in the forcing, net surface forcing becomes positive. The nonradiative forcings are the result of rapid surface and tropospheric adjustments and impact 20th century, as well as future, evaporation and precipitation trends. A comparison of energy balance changes in eight different climate models finds that all models exhibit a positive surface energy imbalance by the late 20th century. However, there is considerable disagreement in how this imbalance is partitioned between the longwave, shortwave, latent heat and sensible heat fluxes. In particular, all models show reductions in shortwave radiation absorbed at the surface by the late 20th century compared to the pre-industrial control state, but the spread of this reduction leads to differences in the sign of their latent heat flux changes and thus in the sign of their hydrological responses

Cloud adjustment and its role in CO 2 radiative forcing and climate sensitivity: a review

Understanding the role of clouds in climate change remains a considerable challenge. Traditionally, this challenge has been framed in terms of understanding cloud feedback. However, recent work suggests that under increasing levels of atmospheric carbon dioxide, clouds not only amplify or dampen climate change through global feedback processes, but also through rapid (days to weeks) tropospheric temperature and land surface adjustments. In this article, we use the Met Office Hadley Centre climate model HadGSM1 to review these recent developments and assess their impact on radiative forcing and equilibrium climate sensitivity. We estimate that cloud adjustment contributes ~0.8 K to the 4.4 K equilibrium climate sensitivity of this particular model. We discuss the methods used to evaluate cloud adjustments, highlight the mechanisms and processes involved and identify low level cloudiness as a key cloud type. Looking forward, we discuss the outstanding issues, such as the application to transient forcing scenarios. We suggest that the upcoming CMIP5 multi-model database will allow a comprehensive assessment of the significance of cloud adjustments in fully coupled atmosphere-ocean-general-circulation models for the first time, and that future research should exploit this opportunity to understand cloud adjustments/feedbacks in non-idealised transient climate change scenarios

The dependence of radiative forcing and feedback on evolving patterns of surface temperature change in climate models

Experiments with CO2 instantaneously quadrupled and then held constant are used to show that the relationship between the global-mean net heat input to the climate system and the global-mean surface-air-temperature change is nonlinear in Coupled Model Intercomparison Project phase 5 (CMIP5) Atmosphere-Ocean General Circulation Models (AOGCMs). The nonlinearity is shown to arise from a change in strength of climate feedbacks driven by an evolving pattern of surface warming. In 23 out of the 27 AOGCMs examined the climate feedback parameter becomes significantly (95% confidence) less negative – i.e. the effective climate sensitivity increases – as time passes. Cloud feedback parameters show the largest changes. In the AOGCM-mean approximately 60% of the change in feedback parameter comes from the topics (30N-30S). An important region involved is the tropical Pacific where the surface warming intensifies in the east after a few decades. The dependence of climate feedbacks on an evolving pattern of surface warming is confirmed using the HadGEM2 and HadCM3 atmosphere GCMs (AGCMs). With monthly evolving sea-surface-temperatures and sea-ice prescribed from its AOGCM counterpart each AGCM reproduces the time-varying feedbacks, but when a fixed pattern of warming is prescribed the radiative response is linear with global temperature change or nearly so. We also demonstrate that the regression and fixed-SST methods for evaluating effective radiative forcing are in principle different, because rapid SST adjustment when CO2 is changed can produce a pattern of surface temperature change with zero global mean but non-zero change in net radiation at the top of the atmosphere (~ -0.5 Wm-2 in HadCM3)

Silicate versus carbonate weathering in Iceland: New insights from Ca isotopes

) to trace sources of Ca in Icelandic rivers. We report elemental and Ca isotope data for rivers, high- and low-temperature groundwater, basalt, hydrothermal calcite (including Iceland Spar), and stilbite and heulandite, which are two types of zeolites commonly formed during low-grade metamorphism of basalt. In agreement with previous research, we find that rivers have higher ?44/40Ca values than basalt, with a maximum difference of ?0.40‰. This difference may reflect isotope fractionation in the weathering zone, i.e., preferential uptake of 40Ca during clay mineral formation, adsorption, and other geochemical processes that cycle Ca. However, calcite ?44/40Ca values are also up to ?0.40‰?higher than bedrock values, and on a diagram of ?44/40Ca versus Sr/Ca, nearly all waters plot within a plausible mixing domain bounded by the measured compositions of basalt and calcite, with glacial rivers plotting closer to calcite than non-glacial rivers. Calcite and heulandite form during hydrothermal alteration of basalt in the deep lava pile and often occur together in metabasalts now exposed at the surface. Because heulandite ?44/40Ca values are ?1–2‰?lower than basalt, we suggest that 40Ca uptake by heudlandite explains the relatively high ?44/40Ca values of calcite and that calcite weathering in turn elevates riverine ?44/40Ca values. High mechanical erosion rates are known to facilitate the exposure and weathering of calcite, which explains the isotopic contrast between glacial and non-glacial watersheds. Using a mixing model, we find that calcite weathering provides ?0–65% of the Ca in non-glacial rivers and ?25–90% of the Ca in glacial rivers, with silicate weathering providing the remainder. Icelandic hydrothermal calcite contains mantle carbon. Noting that zeolite facies metamorphism and hydrothermal fluid circulation are ubiquitous characteristics of basaltic eruptions and assuming that hydrothermal calcite in other basaltic settings also contains mantle carbon, we suggest that the contribution of basalt weathering to long-term CO2 drawdown and climate regulation may be less significant than previously realized

An ALMA Constraint on the GSC 6214-210 B Circum-Substellar Accretion Disk Mass

We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of GSC 6214-210 A and B, a solar-mass member of the 5-10 Myr Upper Scorpius association with a 15 $\pm$ 2 Mjup companion orbiting at $\approx$330 AU (2.2"). Previous photometry and spectroscopy spanning 0.3-5 $\mu$m revealed optical and thermal excess as well as strong H$\alpha$ and Pa~$\beta$ emission originating from a circum-substellar accretion disk around GSC 6214-210 B, making it the lowest mass companion with unambiguous evidence of a subdisk. Despite ALMA's unprecedented sensitivity and angular resolution, neither component was detected in our 880 $\mu$m (341 GHz) continuum observations down to a 3-$\sigma$ limit of 0.22 mJy/beam. The corresponding constraints on the dust mass and total mass are <0.15 Mearth and <0.05 Mjup, respectively, or <0.003% and <0.3% of the mass of GSC 6214-210 B itself assuming a 100:1 gas-to-dust ratio and characteristic dust temperature of 10-20 K. If the host star possesses a putative circum-stellar disk then at most it is a meager 0.0015% of the primary mass, implying that giant planet formation has certainly ceased in this system. Considering these limits and its current accretion rate, GSC 6214-210 B appears to be at the end stages of assembly and is not expected to gain any appreciable mass over the next few Myr.Comment: Accepted to ApJ