ASU Scholarship Showcase

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

Human societies are unique in the level of cooperation among non-kin. Evolutionary models explaining this behavior typically assume pure strategies of cooperation and defection. Behavioral experiments, however, demonstrate that humans are typically conditional co-operators who have other-regarding preferences. Building on existing models on the evolution of cooperation and costly punishment, we use a utilitarian formulation of agent decision making to explore conditions that support the emergence of cooperative behavior. Our results indicate that cooperation levels are significantly lower for larger groups in contrast to the original pure strategy model. Here, defection behavior not only diminishes the public good, but also affects the expectations of group members leading conditional co-operators to change their strategies. Hence defection has a more damaging effect when decisions are based on expectations and not only pure strategies.

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth’s oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S₀ to S₄, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S₁ state and after double laser excitation (putative S₃ state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn₄CaO₅ core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the ‘dangler’ Mn) and the Mn₃CaO_x cubane in the S₂ to S₃ transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

Explosive extrusion of cold material from the interior of icy bodies, or cryovolcanism, has been observed on Enceladus and, perhaps, Europa, Triton, and Ceres. It may explain the observed evidence for a young surface on Charon (Pluto’s surface is masked by frosts). Here, we evaluate prerequisites for cryovolcanism on dwarf planet-class Kuiper belt objects (KBOs). We first review the likely spatial and temporal extent of subsurface liquid, proposed mechanisms to overcome the negative buoyancy of liquid water in ice, and the volatile inventory of KBOs. We then present a new geochemical equilibrium model for volatile exsolution and its ability to drive upward crack propagation. This novel approach bridges geophysics and geochemistry, and extends geochemical modeling to the seldom-explored realm of liquid water at subzero temperatures. We show that carbon monoxide (CO) is a key volatile for gas-driven fluid ascent; whereas CO₂ and sulfur gases only play a minor role. N₂, CH₄, and H₂ exsolution may also drive explosive cryovolcanism if hydrothermal activity produces these species in large amounts (a few percent with respect to water). Another important control on crack propagation is the internal structure: a hydrated core makes explosive cryovolcanism easier, but an undifferentiated crust does not. We briefly discuss other controls on ascent such as fluid freezing on crack walls, and outline theoretical advances necessary to better understand cryovolcanic processes. Finally, we make testable predictions for the 2015 New Horizons flyby of the Pluto-Charon system.

It has been suggested that the extended intensity profiles surrounding Bragg reflections that arise when a series of finite crystals of varying size and shape are illuminated by the intense, coherent illumination of an x-ray free-electron laser may enable the crystal’s unit-cell electron density to be obtained ab initio via well-established iterative phasing algorithms. Such a technique could have a significant impact on the field of biological structure determination since it avoids the need for a priori information from similar known structures, multiple measurements near resonant atomic absorption energies, isomorphic derivative crystals, or atomic-resolution data. Here, we demonstrate this phasing technique on diffraction patterns recorded from artificial two-dimensional microcrystals using the seeded soft x-ray free-electron laser FERMI. We show that the technique is effective when the illuminating wavefront has nonuniform phase and amplitude, and when the diffraction intensities cannot be measured uniformly throughout reciprocal space because of a limited signal-to-noise ratio.

Collective behaviors in social insect societies often emerge from simple local rules. However, little is known about how these behaviors are dynamically regulated in response to environmental changes. Here, we use a compartmental modeling approach to identify factors that allow harvester ant colonies to regulate collective foraging activity in response to their environment. We propose a set of differential equations describing the dynamics of: (1) available foragers inside the nest, (2) active foragers outside the nest, and (3) successful returning foragers, to understand how colony-specific parameters, such as baseline number of foragers, interactions among foragers, food discovery rates, successful forager return rates, and foraging duration might influence collective foraging dynamics, while maintaining functional robustness to perturbations. Our analysis indicates that the model can undergo a forward (transcritical) bifurcation or a backward bifurcation depending on colony-specific parameters. In the former case, foraging activity persists when the average number of recruits per successful returning forager is larger than one. In the latter case, the backward bifurcation creates a region of bistability in which the size and fate of foraging activity depends on the distribution of the foraging workforce among the model׳s compartments. We validate the model with experimental data from harvester ants (Pogonomyrmex barbatus) and perform sensitivity analysis. Our model provides insights on how simple, local interactions can achieve an emergent and robust regulatory system of collective foraging activity in ant colonies.

Plasmonic and metamaterial based nano/micro-structured materials enable spectrally selective resonant absorption, where the resonant bandwidth and absorption intensity can be engineered by controlling the size and geometry of nanostructures. Here, we demonstrate a simple, lithography-free approach for obtaining a resonant and dynamically tunable broadband absorber based on vanadium dioxide (VO2) phase transition. Using planar layered thin film structures, where top layer is chosen to be an ultrathin (20 nm) VO2 film, we demonstrate broadband IR light absorption tuning (from similar to 90% to similar to 30% in measured absorption) over the entire mid-wavelength infrared spectrum. Our numerical and experimental results indicate that the bandwidth of the absorption bands can be controlled by changing the dielectric spacer layer thickness. Broadband tunable absorbers can find applications in absorption filters, thermal emitters, thermophotovoltaics, and sensing.

Most studies on the response of socioeconomic systems to a sudden shift focus on long-term equilibria or end points. Such narrow focus forgoes many valuable insights. Here we examine the transient dynamics of regime shift on a divided population, exemplified by societies divided ideologically, politically, economically, or technologically. Replicator dynamics is used to investigate the complex transient dynamics of the population response. Though simple, our modeling approach exhibits a surprisingly rich and diverse array of dynamics. Our results highlight the critical roles played by diversity in strategies and the magnitude of the shift. Importantly, it allows for a variety of strategies to arise organically as an integral part of the transient dynamics-as opposed to an independent process-of population response to a regime shift, providing a link between the population's past and future diversity patterns. Several combinations of different populations' strategy distributions and shifts were systematically investigated. Such rich dynamics highlight the challenges of anticipating the response of a divided population to a change. The findings in this paper can potentially improve our understanding of a wide range of socio-ecological and technological transitions.

A major conundrum in evolution is that, despite natural selection, polymorphism is still omnipresent in nature: Numerous species exhibit multiple morphs, namely several abundant values of an important trait. Polymorphism is particularly prevalent in asymmetric traits, which are beneficial to their carrier in disruptive competitive interference but at the same time bear disadvantages in other aspects, such as greater mortality or lower fecundity. Here we focus on asymmetric traits in which a better competitor disperses fewer offspring in the absence of competition. We report a general pattern in which polymorphic populations emerge when disruptive selection increases: The stronger the selection, the greater the number of morphs that evolve. This pattern is general and is insensitive to the form of the fitness function. The pattern is somewhat counterintuitive since directional selection is excepted to sharpen the trait distribution and thereby reduce its diversity (but note that similar patterns were suggested in studies that demonstrated increased biodiversity as local selection increases in ecological communities). We explain the underlying mechanism in which stronger selection drives the population towards more competitive values of the trait, which in turn reduces the population density, thereby enabling lesser competitors to stably persist with reduced need to directly compete. Thus, we believe that the pattern is more general and may apply to asymmetric traits more broadly. This robust pattern suggests a comparative, unified explanation to a variety of polymorphic traits in nature.

Background: While prior studies have quantified the mortality burden of the 1957 H2N2 influenza pandemic at broad geographic regions in the United States, little is known about the pandemic impact at a local level. Here we focus on analyzing the transmissibility and mortality burden of this pandemic in Arizona, a setting where the dry climate was promoted as reducing respiratory illness transmission yet tuberculosis prevalence was high.

Methods: Using archival death certificates from 1954 to 1961, we quantified the age-specific seasonal patterns, excess-mortality rates, and transmissibility patterns of the 1957 H2N2 pandemic in Maricopa County, Arizona. By applying cyclical Serfling linear regression models to weekly mortality rates, the excess-mortality rates due to respiratory and all-causes were estimated for each age group during the pandemic period. The reproduction number was quantified from weekly data using a simple growth rate method and assumed generation intervals of 3 and 4 days. Local newspaper articles published during 1957–1958 were also examined.

Results: Excess-mortality rates varied between waves, age groups, and causes of death, but overall remained low. From October 1959-June 1960, the most severe wave of the pandemic, the absolute excess-mortality rate based on respiratory deaths per 10,000 population was 16.59 in the elderly (≥65 years). All other age groups exhibit very low excess-mortality and the typical U-shaped age-pattern was absent. However, the standardized mortality ratio was greatest (4.06) among children and young adolescents (5–14 years) from October 1957-March 1958, based on mortality rates of respiratory deaths. Transmissibility was greatest during the same 1957–1958 period, when the mean reproduction number was estimated at 1.08–1.11, assuming 3- or 4-day generation intervals with exponential or fixed distributions.

Conclusions: Maricopa County exhibited very low mortality impact associated with the 1957 influenza pandemic. Understanding the relatively low excess-mortality rates and transmissibility in Maricopa County during this historic pandemic may help public health officials prepare for and mitigate future outbreaks of influenza.