Mechanisms of kinetic trapping in self-assembly and phase transformation

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions

Challenges in the development of the orbiter radiator system

Major technical challenges which were met in the design and development of the Space Shuttle Orbiter Radiator System are discussed. This system rejects up to 30 kW of waste heat from eight individual radiators having a combined surface area of 175 sq m. The radiators, which are deployable, are mounted on the inside of the payload bay doors for protection from aerodynamic heating during ascent and re-entry. While in orbit the payload bay doors are opened to expose the radiators for operation. An R21 coolant loop accumulates waste heat from various components in the Orbiter and delivers the heat to the radiators for rejection to space. Specific challenges included high acoustically induced loads during lift-off, severe radiating area constraints, demanding heat load control requirements, and long life goals. Details of major design and analysis efforts are discussed. The success of the developed hardware in satisfying mission objectives showed how well the design challenge was met

Opportunistic linked data querying through approximate membership metadata

Between URI dereferencing and the SPARQL protocol lies a largely unexplored axis of possible interfaces to Linked Data, each with its own combination of trade-offs. One of these interfaces is Triple Pattern Fragments, which allows clients to execute SPARQL queries against low-cost servers, at the cost of higher bandwidth. Increasing a client's efficiency means lowering the number of requests, which can among others be achieved through additional metadata in responses. We noted that typical SPARQL query evaluations against Triple Pattern Fragments require a significant portion of membership subqueries, which check the presence of a specific triple, rather than a variable pattern. This paper studies the impact of providing approximate membership functions, i.e., Bloom filters and Golomb-coded sets, as extra metadata. In addition to reducing HTTP requests, such functions allow to achieve full result recall earlier when temporarily allowing lower precision. Half of the tested queries from a WatDiv benchmark test set could be executed with up to a third fewer HTTP requests with only marginally higher server cost. Query times, however, did not improve, likely due to slower metadata generation and transfer. This indicates that approximate membership functions can partly improve the client-side query process with minimal impact on the server and its interface

Feedforward Inhibition Underlies the Propagation of Cholinergically Induced Gamma Oscillations from Hippocampal CA3 to CA1.

Gamma frequency (30-80 Hz) oscillations are implicated in memory processing. Such rhythmic activity can be generated intrinsically in the CA3 region of the hippocampus from where it can propagate to the CA1 area. To uncover the synaptic mechanisms underlying the intrahippocampal spread of gamma oscillations, we recorded local field potentials, as well as action potentials and synaptic currents in anatomically identified CA1 and CA3 neurons during carbachol-induced gamma oscillations in mouse hippocampal slices. The firing of the vast majority of CA1 neurons and all CA3 neurons was phase-coupled to the oscillations recorded in the stratum pyramidale of the CA1 region. The predominant synaptic input to CA1 interneurons was excitatory, and their discharge followed the firing of CA3 pyramidal cells at a latency indicative of monosynaptic connections. Correlation analysis of the input-output characteristics of the neurons and local pharmacological block of inhibition both agree with a model in which glutamatergic CA3 input controls the firing of CA1 interneurons, with local pyramidal cell activity having a minimal role. The firing of phase-coupled CA1 pyramidal cells was controlled principally by their inhibitory inputs, which dominated over excitation. Our results indicate that the synchronous firing of CA3 pyramidal cells rhythmically recruits CA1 interneurons and that this feedforward inhibition generates the oscillatory activity in CA1. These findings identify distinct synaptic mechanisms underlying the generation of gamma frequency oscillations in neighboring hippocampal subregions

Holographic U(1)_A and String Creation

We analyze the resolution of the U(1)_A problem in the Sakai-Sugimoto holographic dual of large N_c QCD at finite temperature. It has been shown that in the confining phase the axial symmetry is broken at order 1/N_c, in agreement with the ideas of Witten and Veneziano. We show that in the deconfined phase the axial symmetry remains unbroken to all orders in 1/N_c. In this case the breaking is due to instantons which are described by spacelike D0-branes, in agreement with 'tHooft's resolution. The holographic dual of the symmetry breaking fermion condensate is a state of spacelike strings between the D0-brane and the flavor D8-branes, which result from a spacelike version of the string creation effect. In the intermediate phase of deconfinement with broken chiral symmetry the instanton gas approximation is possibly regulated in the IR, which would imply an eta' mass-squared of order exp(-N_c).Comment: 18 pages, 19 figures, minor change

Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable

Development and Pilot of a Checklist for Management of Acute Liver Failure in the Intensive Care Unit

Introduction Acute liver failure (ALF) is an ideal condition for use of a checklist. Our aims were to develop a checklist for the management of ALF in the intensive care unit (ICU) and assess the usability of the checklist among multiple providers. Methods The initial checklist was developed from published guidelines and expert opinion. The checklist underwent pilot testing at 11 academic liver transplant centers in the US and Canada. An anonymous, written survey was used to assess the usability and quality of the checklist. Written comments were used to improve the checklist following the pilot testing period. Results We received 81 surveys involving the management of 116 patients during the pilot testing period. The overall quality of the checklist was judged to be above average to excellent by 94% of users. On a 5-point Likert scale, the majority of survey respondents agreed or agreed strongly with the following checklist characteristics: the checklist was easy to read (99% agreed/agreed strongly), easy to use (97%), items are categorized logically (98%), time to complete the checklist did not interfere with delivery of appropriate and safe patient care (94%) and was not excessively burdensome (92%), the checklist allowed the user the freedom to use his or her clinical judgment (80%), it is a useful tool in the management of acute liver failure (98%). Web-based and mobile apps were developed for use of the checklist at the point of care. Conclusion The checklist for the management of ALF in the ICU was shown in this pilot study to be easy to use, helpful and accepted by a wide variety of practitioners at multiple sites in the US and Canada

D-brane interactions in type IIB plane-wave background

The cylinder diagrams that determine the static interactions between pairs of Dp-branes in the type IIB plane wave background are evaluated. The resulting expressions are elegant generalizations of the flat-space formulae that depend on the value of the Ramond-Ramond flux of the background in a non-trivial manner. The closed-string and open-string descriptions consistently transform into each other under a modular transformation only when each of the interacting D-branes separately preserves half the supersymmetries. These results are derived for configurations of euclidean signature D(p+1)-instantons but also generalize to lorentzian signature Dp-branes.Comment: 24 pages, Normalisation of boundary states correcte

Environmental entrainment demonstrates natural circadian rhythmicity in the cnidarian Nematostella vectensis

Author Posting. © Company of Biologists, 2019. This article is posted here by permission of Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 222(21), (2019): jeb.205393, doi:10.1242/jeb.205393.Considerable advances in chronobiology have been made through controlled laboratory studies, but distinct temporal rhythms can emerge under natural environmental conditions. Lab-reared Nematostella vectensis sea anemones exhibit circadian behavioral and physiological rhythms. Given that these anemones inhabit shallow estuarine environments subject to tidal inputs, it was unclear whether circadian rhythmicity would persist following entrainment in natural conditions, or whether circatidal periodicity would predominate. Nematostella were conditioned within a marsh environment, where they experienced strong daily temperature cycles as well as brief tidal flooding around the full and new moons. Upon retrieval, anemones exhibited strong circadian (∼24 h) activity rhythms under a light–dark cycle or continuous darkness, but reduced circadian rhythmicity under continuous light. However, some individuals in each light condition showed circadian rhythmicity, and a few individuals showed circatidal rhythmicity. Consistent with the behavioral studies, a large number of transcripts (1640) exhibited diurnal rhythmicity compared with very few (64) with semidiurnal rhythmicity. Diurnal transcripts included core circadian regulators, and 101 of 434 (23%) genes that were previously found to be upregulated by exposure to ultraviolet radiation. Together, these behavioral and transcriptional studies show that circadian rhythmicity predominates and suggest that solar radiation drives physiological cycles in this sediment-dwelling subtidal animal.A.M.T., R.R.H. and O.L. were supported by the Gordon and Betty Moore Foundation (grant number 4598 to A.M.T. and O.L.). H.E.R. was funded by a Martin Family Fellowship for Sustainability at Massachusetts Institute of Technology and an American dissertation grant from the American Association of University Women.2020-10-1