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At least 19 records

Umbrella sampling: a powerful method to sample tails of distributions

We present the umbrella sampling (US) technique and show that it can be used to sample extremely low-probability areas of the posterior distribution that may be required in statistical analyses of data. In this approach sampling of the target likelihood is split into sampling of multiple biased likelihoods confined within individual umbrella windows. We show that the US algorithm is efficient and highly parallel and that it can be easily used with other existing Markov Chain Monte Carlo (MCMC) samplers. The method allows the user to capitalize on their intuition and define umbrella windows and increase sampling accuracy along specific directions in the parameter space. Alternatively, one can define umbrella windows using an approach similar to parallel tempering. We provide a public code that implements US as a standalone PYTHON package. We present a number of tests illustrating the power of the US method in sampling low-probability areas of the posterior and show that this ability allows a considerably more robust sampling of multimodal distributions compared to standard sampling methods. We also present an application of the method in a real world example of deriving cosmological constraints using the supernova type Ia data. We show that US can sample the posterior accurately down to the approximate to 15 sigma credible region in the Omega(m) - Omega(Lambda) plane, while for the same computational effort the affine-invariant MCMC sampling implemented in the emcee code samples the posterior reliably only to approximate to 3 sigma.

cosmology: cosmological parameters↗

The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism

Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella particles that harbor distinct polymorphic toxin domains and an overlapping set of six diversified lectins. Here, we show that the exquisite specificity of umbrella particles derives from lectin-mediated species-specific binding to previously undescribed hypervariable surface glycoconjugates. A cryo-electron microscopy (cryo-EM) structure of one such lectin in complex with its oligosaccharide substrate defines the molecular basis for targeting through the coordinated recognition of multiple glycan features. Biochemical and genetic studies of several target species, in conjunction with lectin-swapping experiments, support a model whereby S. coelicolor umbrella toxin diversification at the levels of lectin composition and toxin polymorphism represents a unique, two-tiered bet-hedging strategy. Bioinformatic analyses support this as a means by which the unusual architecture of umbrella toxins offers Streptomyces a generalizable strategy to antagonize an unpredictable array of competitors.

59 BASIC BIOLOGICAL SCIENCES↗

Streptomyces umbrella toxin particles block hyphal growth of competing species

Abstract Streptomycesare a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive 1 . The production of these antibacterial molecules reflects the relentless competitionStreptomycesengage in with other bacteria, including otherStreptomycesspecies 1,2 . Here we show that in addition to small-molecule antibiotics,Streptomycesproduce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles.Streptomyces coelicolorencodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of selectStreptomycesspecies from among a diverse collection of bacteria screened. For one target,Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show thatStreptomycesumbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly 3,4 . Sequence analyses suggest that this role of umbrella particles extends beyondStreptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.

Science & Technology - Other Topics↗

Implementation of replica-exchange umbrella sampling in GAMESS

In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. Here, REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation.

97 MATHEMATICS AND COMPUTING↗

Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling

We compare the performance of two well-established computational algorithms for the calculation of free-energy landscapes of biomolecular systems, umbrella sampling and metadynamics. We look at benchmark systems composed of polyethylene and polypropylene oligomers interacting with lipid (phosphatidylcholine) membranes, aiming at the calculation of the oligomer water-membrane free energy of transfer. We model our test systems at two different levels of description, united-atom and coarse-grained. We provide optimized parameters for the two methods at both resolutions. We devote special attention to the analysis of statistical errors in the two different methods and propose a general procedure for the error estimation in metadynamics simulations. Metadynamics and umbrella sampling yield the same estimates for the water-membrane free energy profile, but metadynamics can be more efficient, providing lower statistical uncertainties within the same simulation time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile

Phthalocyanine (Pc) and its metal complexes (MPcs) have been used industrially since their discovery in the early 20th century. The phthalonitrile (PN) method is a well-known synthesis method in which Pc or MPc can be afforded by heating a mixture of PN and metal powders over 280 °C with only moderate yield. However, the formation mechanism of the phthalocyanines and the intermediate stages of this seemingly simple reaction have yet to be fully understood. To study this mechanism computationally, we carried out quantum chemical molecular dynamics (MD) simulations based on the density-functional tight-binding (DFTB) method, applying the replica-exchange umbrella sampling (REUS) method, starting from four PN molecules and one iron atom. The DFTB-REUS-MD simulations successfully yielded FePc, and a metastable structure very similar to FePc but with a reactive nitrene unit was also identified that might explain the incomplete conversion of the reactants into FePc. Furthermore, analysis of the MD trajectories reveals a three-step FePc formation mechanism for the PN method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A giant umbrella-like stellar stream around the tidal ring galaxy NGC 922

Tidal ring galaxies (TRGs) are rarely observed in the local universe due to their intrinsically transient nature. The tidal ring structures are the result of strong interactions between gas-rich stellar disks and smaller galactic systems, and do not last longer than ~500 Myr. Therefore, these are perfect scenarios in which to look for the debris of recently accreted dwarf galactic systems. Our goal is to study the low surface brightness stellar structures around the TRG NGC 922 and to revise the hypothesis of its formation in light of these new data. We present new deep images of the TRG NGC 922 and its surroundings from the DESI Legacy survey data and from our observations with an amateur telescope. These observations are compared with results from high-resolution N-body simulations that were designed to reproduce an alternative formation scenario for this peculiar galaxy. Our new observations unveil that the low surface brightness stellar tidal structures around NGC 922 are much more complex than reported in previous works. In particular, the formerly detected tidal spike-like structure at the north-east of the central galaxy disk is not connected with the dwarf companion galaxy PGC 3080368, which has been suggested as the intruder triggering the ring formation of NGC 922. The deep images reveal that this tidal structure mainly has a fainter giant umbrella-like shape, and thus it was formed from the tidal disruption of a different satellite. Using the broad-band g, r, and z DESI LS images, we measured the photometric properties of this stellar stream, estimating a total absolute magnitude in the r band of M r = -17.0 ± 0.03 mag and a total stellar mass for the stream of between 6.9 and 8.5×10 8 M ⊙ . We performed a set of N-body simulations to reproduce the observed NGC922-intruder interaction, suggesting a new scenario for the formation of its tidal ring from the infall of a gas-rich satellite around 150 Myr ago. Finally, our deep images also reveal a tidal shell around the dwarf galaxy PGC 3080368, a possible fossil of a recent merger with a smaller satellite, which may suggest it is in its first infall towards NGC 922.

79 ASTRONOMY AND ASTROPHYSICS↗

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up” all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Laser-induced electron diffraction of the ultrafast umbrella motion in ammonia

Visualizing molecular transformations in real-time requires a structural retrieval method with Ångström spatial and femtosecond temporal atomic resolution. Imaging of hydrogen-containing molecules additionally requires an imaging method sensitive to the atomic positions of hydrogen nuclei, with most methods possessing relatively low sensitivity to hydrogen scattering. Laser-induced electron diffraction (LIED) is a table-top technique that can image ultrafast structural changes of gas-phase polyatomic molecules with sub-Ångström and femtosecond spatiotemporal resolution together with relatively high sensitivity to hydrogen scattering. Here, we image the umbrella motion of an isolated ammonia molecule (NH3) following its strong-field ionization. Upon ionization of a neutral ammonia molecule, the ammonia cation (NH3+) undergoes an ultrafast geometrical transformation from a pyramidal (ΦHNH=107°) to planar (ΦHNH=120°) structure in approximately 8 femtoseconds. Using LIED, we retrieve a near-planar (ΦHNH=117 ± 5°) field-dressed NH3+ molecular structure 7.8−9.8 femtoseconds after ionization. Our measured field-dressed NH3+ structure is in excellent agreement with our calculated equilibrium field-dressed structure using quantum chemical ab initio calculations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-point nonequilibrium umbrella sampling and associated fluctuation relations

We describe a simple method of umbrella trajectory sampling for Markov chains. The method allows the estimation of large-deviation rate functions, for path-extensive dynamic observables, for an arbitrary number of models within a certain family. The general relationship between probability distributions of dynamic observables of members of this family is an extended fluctuation relation. When the dynamic observable is chosen to be entropy production, members of this family include the forward Markov chain and its time reverse, whose probability distributions are related by the expected simple fluctuation relation.

97 MATHEMATICS AND COMPUTING↗

Rare behavior of growth processes via umbrella sampling of trajectories

We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space, in terms of their typical and atypical trajectories. Thus key features of growth processes can be insensitive to the precise form of the rate constants used to generate them, recalling the insensitivity to microscopic details of certain equilibrium behavior. We obtained these results using a sampling method, inspired by the "s-ensemble" large-deviation formalism, that amounts to umbrella sampling in trajectory space. The method is a simple variant of existing approaches, and applies to ensembles of trajectories controlled by the total number of events. It can be used to determine large-deviation rate functions for trajectory observables in or out of equilibrium.

97 MATHEMATICS AND COMPUTING↗

api-umbrella-cookbook [SWR-12-16]

This is the repository for api-umbrella-cookbook developed at National Renewable Energy Laboratory. This repository has been archived by the owner, as it is no longer used. The files are now available as read-only.

Muerdter, Nick↗

Abstract for Joint Work Statement 5 (AGMT-1005) between National Energy Technology Laboratory (NETL) and ExxonMobil Research and Engineering Company (EMRE) to Umbrella CRADA (AGMT-0922)

NETL and EMRE will focus on fundamental questions aimed at understanding the controlling factors on tight oil production flow paths and how those flow paths are impacted by the hydraulic fracturing fluids and processes. Key questions for the Parties to explore include the following: Are there geochemical reactions between hydrocarbon producing tight reservoir rocks and water from the hydraulic fracturing process? To what extent does this alteration impact oil production? By further characterizing the flow paths near the fracture-matrix interface, what is the relative impact of geochemical process compared to geomechanical changes on production? This research focuses on rock types found in the Permian Basin. The research drives along two main thrusts: 1) Inorganic geochemistry studies involving representative rock types, connate fluids (hydrocarbons and water), and injected fluids (fracturing water) will be conducted in order to bound the kinetics of key mineral reactions; 2) Computed tomography (CT) for characterization of flow paths as a function of geochemical and geomechanical processes associated with hydraulic fracture creation and reservoir production. The objective of this characterization is to ultimately develop new insights into the role geochemical and geomechanical effects play on production. The work will include studying mechanical damage near the rock-fracture interface and how it impacts flow properties.

02 PETROLEUM↗

Virginia Tech Center for Neutrino Physics HEP Umbrella. Final report

This DOE-supported project of Virginia Tech's Center for Neutrino Physics (VT-CNP), funded for a two-year period from July 1, 2017 through April 30, 2019. Supported the efforts our group in the Intensity Frontier, Theory programs. The Intensity Frontier program Prof. Link and his group included continued efforts on the Daya Bay Reactor Neutrino Experiment, starting of a new effort with the COHERENT collaboration studying coherent elastic neutrino scattering at the Oak Ridge National Laboratory's Spallation Neutrino Source, and an advanced reactor neutrino detector development effort known as CHANDLER, which was only partially supported by this grant. In the theory/phenomenology program of Profs. Huber and Horiuchi and their groups pursued independent (but interconnected) research activities including astrophysical searches for particle dark matter with a focus on combining gamma rays with multiple probes, supernova neutrinos, neutrino phenomenology with an emphasis on physics beyond three flavor oscillation, and further development of the GLoBES neutrino oscillation sensitivity tool kit. This group has strong synergy between its efforts in neutrino phenomenology and neutrino-related experimental research, which is the intellectual foundation for the Center for Neutrino Physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Abstract for Umbrella CRADA between NETL and Susteon, Inc. (AGMT-0983)

NETL and Susteon will develop new technologies involving catalysts, sorbents, and membrane materials. These materials will be incorporated into chemical processes, scaled up, and evaluated for commercialization potential. Areas of interest include technologies for shale and natural gas processing and utilization; hydrogen production and processing; coal and syngas processing; and CO 2 capture and utilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Project Task Statement 2 to Umbrella Cooperative Research and Development Agreement between National Energy Technology Laboratory and Ramaco Carbon [Abstract]

NETL and Ramaco will collaborate to characterize domestic coal, beneficiated coal, and coal byproducts to evaluate these materials for rare earth element (REE) content and ease of extraction. Ramaco will provide samples of coal, beneficiated coal, and coal byproducts to NETL, as well as provide research expertise on coal extraction and processing. NETL will characterize these feedstocks using the chemical/physical methods being utilized in its research laboratories. The objectives of this project are: identify promising coal-related REE reserves by testing and analysis of core samples from coal bearing formations; provide insights and expertise into opportunities for the extraction of REEs and other value-added products from domestic coal; and collect data that will be used to create quantitative modeling tools for predicting the likelihood of successful prospecting for REEs in coal, beneficiated and processed coal, and related geologic formation.

01 COAL, LIGNITE, AND PEAT↗