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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↗

Study of Umbrella-Type Erectable Paraboloidal Solar Concentrators for Generation of Spacecraft Auxiliary Power

An investigation was made of some aspects of erectable umbrella-type paraboloidal solar-energy concentrators for use in spacecraft auxiliary power systems. An analysis is presented for the design of concentrators employing radial ribs and membrane-type coverings. The rib stiffness necessary to give a desired parabolic curvature upon erection is determined. Rib contour measurements were made in an upright and inverted position on an experimental 10-foot-diameter concentrator giving a focal length of 30.78 inches and 30.6 inches, respectively, as compared with a design focal length of 30 inches. Calorimetric tests employing spherical heat receivers showed a maximum geometrical concentrator efficiency of 75.3 percent with a concentration ratio of 92.2 at a focal length of approximately 30.5 inches. Within the scope of this investigation, it was found that, as the concentrator size increases, the weight per unit projected area increases, time to damp to one-half amplitude increases, and the natural frequency decreases. Umbrella-type solar concentrators appear to be feasible for power conversion systems using low concentration ratios; however, for large concentrators the time required to damp out disturbances may be a problem.

SPACECRAFT↗

Measurements and Calculations of the Effects of Distortions in the Collector Surface on Efficiencies of Umbrella-Type Solar Collectors

The meridional tensions along the ribs in a Mylar-covered umbrella-type solar collector produce a distortion in the reflecting surface that is detrimental to the image in the focal plane. The investigation reported herein was made to obtain measured and calculated geometric efficiencies of umbrella-type collectors as affected by these surface distortions. These studies show that if the tension transverse to the ribs is increased relative to the meridional tensions, the distortion is reduced and higher efficiencies can be attained, and if the transverse tension is small, the number of ribs in the collector must be increased for higher efficiencies.

Bond, Victor R.↗

A Nanoscale Vacuum Field Emission Gated Diode with an Umbrella Cathode

A nanoscale field emission vacuum channel gated diode structure is proposed and a tungsten cathode with an umbrella-like geometry and sharp vertical edge is fabricated. The edge of the suspended cathode becomes the field emission surface. Unlike in the traditional transistor with the gate typically located between the source and the drain, the bottom silicon plate becomes the gate here and the anode terminal is located between the umbrella cathode and the gate. The fabricated devices show excellent diode characteristics and the gated diode structure is attractive for extremely low gate leakage.

Vacuum field emission diode↗

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↗