Importance sampling large deviations in nonequilibrium steady states. I

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states, and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult, because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.Comment: Published in JC

Exact fluctuations of nonequilibrium steady states from approximate auxiliary dynamics

We describe a framework to significantly reduce the computational effort to evaluate large deviation functions of time integrated observables within nonequilibrium steady states. We do this by incorporating an auxiliary dynamics into trajectory based Monte Carlo calculations, through a transformation of the system's propagator using an approximate guiding function. This procedure importance samples the trajectories that most contribute to the large deviation function, mitigating the exponentially complexity of such calculations. We illustrate the method by studying driven diffusions and interacting lattice models in one and two dimensions. Our work offers an avenue to calculate large deviation functions for high dimensional systems driven far from equilibrium.Comment: Accepted in Physical Review Letters (2018). v1: Main document: 5 pages, 3 figures. Supplementary information: 5 pages, 3 figures. v2: Main document: 5 pages, 3 figures. Supplementary information: 6 pages, 3 figures. Fixed some typos and notational inconsistencies. Expanded continuum tilted operator derivation in supplementary sectio

Flight Reynolds Number Testing of the Orion Launch Abort Vehicle in the NASA Langley National Transonic Facility

A 6%-scale unpowered model of the Orion Launch Abort Vehicle (LAV) ALAS-11-rev3c configuration was tested in the NASA Langley National Transonic Facility to obtain static aerodynamic data at flight Reynolds numbers. Subsonic and transonic data were obtained for Mach numbers between 0.3 and 0.95 for angles of attack from -4 to +22 degrees and angles of sideslip from -10 to +10 degrees. Data were also obtained at various intermediate Reynolds numbers between 2.5 million and 45 million depending on Mach number in order to examine the effects of Reynolds number on the vehicle. Force and moment data were obtained using a 6-component strain gauge balance that operated both at warm temperatures (+120 . F) and cryogenic temperatures (-250 . F). Surface pressure data were obtained with electronically scanned pressure units housed in heated enclosures designed to survive cryogenic temperatures. Data obtained during the 3-week test entry were used to support development of the LAV aerodynamic database and to support computational fluid dynamics code validation. Furthermore, one of the outcomes of the test was the reduction of database uncertainty on axial force coefficient for the static unpowered LAV. This was accomplished as a result of good data repeatability throughout the test and because of decreased uncertainty on scaling wind tunnel data to flight

The 105-kDa Basement Membrane Autoantigen p105 Is N-Terminally Homologous to a Tumor-Associated Antigen

Certain constitutive skin basement membrane components, such as bullous pemphigoid antigens and epidermolysis bullosa acquisita antigen, were discovered because they were targeted by an autoimmune reaction. We aimed to purify and characterize a 105-kDa skin basement membrane protein termed p105 recognized by autoantibodies (anti-p105) from patients with a unique immune-mediated subepidermal blistering skin disease. A simian virus 40-transformed human fibroblast cell line that synthesizes and secretes p105 was utilized as the protein source. p105 was partially purified by salt-gradient fractionation of serum-free conditioned medium through a Mono Q anion-exchange column and by examining each fraction with protein staining and immunoblotting against anti-p105. p105 was isolated from polyacrylamide gel electrophoresis gels, blotted onto polyvinylidene difluoride membrane, and subjected to protein microsequencing. The 20 microsequenced N-terminal amino acids exhibited no homology to known basement membrane proteins but exhibited a 70% homology to a 90-kDa tumor-associated antigen. Antibodies raised against a peptide generated from these amino acid sequences reacted to a 105-kDa western-blotted keratinocyte and fibroblast protein and a basement membrane component. p105 resisted digestion by glycosidases chondroitinase ABC, neuraminidase, and N-glycosidase F but was cleaved by protease V8 to antigenic fragments of 22kDa and 14kDa. The synthesis of p105 was inhibited by cycloheximide. We conclude that p105 is a unique basement membrane component produced by both keratinocytes and fibroblasts

“Fecal microbiome in epidemiologic studies” - Letter

We congratulate Sinha et al. on their recent report (1) comparing fecal sample collection methods for epidemiologic studies of the gut microbiome. These data contribute to the increasing body of literature describing robust methodological frameworks for specimen collection and processing (2, 3). However, their claim that fixation of stool using RNAlater® results in “considerable changes to the microbiome diversity” contrasts with previous findings (2, 3), including those from their earlier reports (4, 5). We have previously demonstrated that self-collected stool stabilized with RNAlater® or other fixatives yields high fidelity and reproducibility in compositional profiling of DNA and RNA from shotgun sequence data, compared to immediately-frozen specimens (3). Additionally, fixation offers several distinct advantages crucial for large-scale population-based studies: a straightforward self-collection procedure; sample stabilization without deep-freezing during shipping, receiving, and processing; and versatility for multiple molecular analyses. The authors’ finding that specimens preserved in RNAlater® had poor correlation with immediately frozen specimens (1) could be explained, for example, by improper fixation resulting from an excess of specimen relative to preservative volume (1–2 g:2.5 ml, compared to the manufacturer-recommended ratio of 1 g:5–10 ml; Thermo Fisher Scientific Inc., Waltham, MA)

Advanced aeroservoelastic stabilization techniques for hypersonic flight vehicles

Advanced high performance vehicles, including Single-Stage-To-Orbit (SSTO) hypersonic flight vehicles, that are statically unstable, require higher bandwidth flight control systems to compensate for the instability resulting in interactions between the flight control system, the engine/propulsion dynamics, and the low frequency structural modes. Military specifications, such as MIL-F-9490D and MIL-F-87242, tend to limit treatment of structural modes to conventional gain stabilization techniques. The conventional gain stabilization techniques, however, introduce low frequency effective time delays which can be troublesome from a flying qualities standpoint. These time delays can be alleviated by appropriate blending of gain and phase stabilization techniques (referred to as Hybrid Phase Stabilization or HPS) for the low frequency structural modes. The potential of using HPS for compensating structural mode interaction was previously explored. It was shown that effective time delay was significantly reduced with the use of HPS; however, the HPS design was seen to have greater residual response than a conventional gain stablized design. Additional work performed to advance and refine the HPS design procedure, to further develop residual response metrics as a basis for alternative structural stability specifications, and to develop strategies for validating HPS design and specification concepts in manned simulation is presented. Stabilization design sensitivity to structural uncertainties and aircraft-centered requirements are also assessed

The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA

Tfam (transcription factor A, mitochondrial), a DNA-binding protein with tandem high-mobility group (HMG)-box domains, has a central role in the expression, maintenance and organization of the mitochondrial genome. It activates transcription from mitochondrial promoters and organizes the mitochondrial genome into nucleoids. Using X-ray crystallography, we show that human Tfam forces promoter DNA to undergo a U-turn, reversing the direction of the DNA helix. Each HMG-box domain wedges into the DNA minor groove to generate two kinks on one face of the DNA. On the opposite face, a positively charged α-helix serves as a platform to facilitate DNA bending. The structural principles underlying DNA bending converge with those of the unrelated HU family proteins, which have analogous architectural roles in organizing bacterial nucleoids. The functional importance of this extreme DNA bending is promoter specific and seems to be related to the orientation of Tfam on the promoters

Transmission of viruses via our microbiomes.

BackgroundBacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts.ResultsHere, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts.ConclusionsBecause bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household

Icosahedral metallacarborane/carborane species derived from 1,1′-bis(o-carborane)

We thank ORSAS (GS) and the EPSRC (DE and DMcK supported by project EP/E02971X/1, WYM supported by project EP/I031545/1) for funding.Examples of singly-metallated derivatives of 1,1[prime or minute]-bis(o-carborane) have been prepared and spectroscopically and structurally characterised. Metallation of [7-(1[prime or minute]-1[prime or minute],2[prime or minute]-closo-C2B10H11)-7,8-nido-C2B9H10]2- with a {Ru(p-cymene)}2+ fragment affords both the unisomerised species [1-(1[prime or minute]-1[prime or minute],2[prime or minute]-closo-C2B10H11)-3-(p-cymene)-3,1,2-closo-RuC2B9H10] (2) and the isomerised [8-(1[prime or minute]-1[prime or minute],2[prime or minute]-closo-C2B10H11)-2-(p-cymene)-2,1,8-closo-RuC2B9H10] (3), and 2 is easily transformed into 3 with mild heating. Metallation with a preformed {CoCp}2+ fragment also affords a 3,1,2-MC2B9-1[prime or minute],2[prime or minute]-C2B10 product [1-(1[prime or minute]-1[prime or minute],2[prime or minute]-closo-C2B10H11)-3-Cp-3,1,2-closo-CoC2B9H10] (4), but if CoCl2/NaCp is used followed by oxidation the result is the 2,1,8-CoC2B9-1[prime or minute],2[prime or minute]-C2B10 species [8-(1[prime or minute]-1[prime or minute],2[prime or minute]-closo-C2B10H11)-2-Cp-2,1,8-closo-CoC2B9H10] (5). Compound 4 does not convert into 5 in refluxing toluene, but does do so if it is reduced and then reoxidised, perhaps highlighting the importance of the basicity of the metal fragment in the isomerisation of metallacarboranes. A computational study of 1,1[prime or minute]-bis(o-carborane) is in excellent agreement with a recently-determined precise crystallographic study and establishes that the {1[prime or minute],2[prime or minute]-closo-C2B10H11} fragment is electron-withdrawing compared to H.Publisher PDFPeer reviewe