A NOTE ON COARSE GRAINED PARALLEL INTEGER SORTING

1999 ◽  
Vol 09 (04) ◽  
pp. 533-538 ◽  
Author(s):  
A. CHAN ◽  
F. DEHNE
Keyword(s):  
Experimental Data ◽  
Coarse Grained ◽  
Sorting Algorithm ◽  
Local Computation ◽  
Integer Sorting

We observe that for n/p ≥ p, which is usually the case in practice, there exists a very simple, deterministic, optimal coarse grained parallel integer sorting algorithm with 24 communication rounds (6 [Formula: see text]-relations and 18 p-relations), O (n/p) memory per processor and O (n/p) local computation. Experimental data indicates that the algorithm has very good performance in practice.

scholarly journals Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies

2018 ◽  
Author(s):  
Jukka Intosalmi ◽  
Adrian C. Scott ◽  
Michelle Hays ◽  
Nicholas Flann ◽  
Olli Yli-Harja ◽  
...  
Keyword(s):  
Experimental Data ◽  
Time Course ◽  
Model Development ◽  
Growth Dynamics ◽  
Colony Growth ◽  
Data Driven ◽  
Coarse Grained ◽  
Intercellular Signaling ◽  
Growth Data ◽  
Metabolic Coupling

AbstractMotivationMulticellular entities, such as mammalian tissues or microbial biofilms, typically exhibit complex spatial arrangements that are adapted to their specific functions or environments. These structures result from intercellular signaling as well as from the interaction with the environment that allow cells of the same genotype to differentiate into well-organized communities of diversified cells. Despite its importance, our understanding on how cell–cell and metabolic coupling produce functionally optimized structures is still limited.ResultsHere, we present a data-driven spatial framework to computationally investigate the development of one multicellular structure, yeast colonies. Using experimental growth data from homogeneous liquid media conditions, we develop and parameterize a dynamic cell state and growth model. We then use the resulting model in a coarse-grained spatial model, which we calibrate using experimental time-course data of colony growth. Throughout the model development process, we use state-of-the-art statistical techniques to handle the uncertainty of model structure and parameterization. Further, we validate the model predictions against independent experimental data and illustrate how metabolic coupling plays a central role in colony formation.AvailabilityExperimental data and a computational implementation to reproduce the results are available athttp://research.cs.aalto.fi/csb/software/multiscale/[email protected],[email protected]

scholarly journals Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Tobias Schneider ◽  
Andrej Berg ◽  
Zeynel Ulusoy ◽  
Martin Gamerdinger ◽  
Christine Peter ◽  
...  
Keyword(s):  
Experimental Data ◽  
Functional Characterization ◽  
Isotopic Labeling ◽  
Md Simulations ◽  
Conformational Space ◽  
Coarse Grained ◽  
Covalent Attachment ◽  
Binding Studies ◽  
Polyubiquitin Chains ◽  
Polypeptide Chains

AbstractUbiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.

scholarly journals Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jukka Intosalmi ◽  
Adrian C. Scott ◽  
Michelle Hays ◽  
Nicholas Flann ◽  
Olli Yli-Harja ◽  
...  
Keyword(s):  
Experimental Data ◽  
Time Course ◽  
Growth Dynamics ◽  
Colony Growth ◽  
Data Driven ◽  
Coarse Grained ◽  
Colony Development ◽  
Intercellular Signaling ◽  
Metabolic Coupling ◽  
The Impact

Abstract Background Multicellular entities like mammalian tissues or microbial biofilms typically exhibit complex spatial arrangements that are adapted to their specific functions or environments. These structures result from intercellular signaling as well as from the interaction with the environment that allow cells of the same genotype to differentiate into well-organized communities of diversified cells. Despite its importance, our understanding how this cell–cell and metabolic coupling lead to functionally optimized structures is still limited. Results Here, we present a data-driven spatial framework to computationally investigate the development of yeast colonies as such a multicellular structure in dependence on metabolic capacity. For this purpose, we first developed and parameterized a dynamic cell state and growth model for yeast based on on experimental data from homogeneous liquid media conditions. The inferred model is subsequently used in a spatially coarse-grained model for colony development to investigate the effect of metabolic coupling by calibrating spatial parameters from experimental time-course data of colony growth using state-of-the-art statistical techniques for model uncertainty and parameter estimations. The model is finally validated by independent experimental data of an alternative yeast strain with distinct metabolic characteristics and illustrates the impact of metabolic coupling for structure formation. Conclusions We introduce a novel model for yeast colony formation, present a statistical methodology for model calibration in a data-driven manner, and demonstrate how the established model can be used to generate predictions across scales by validation against independent measurements of genetically distinct yeast strains.

The occurrence of coarse-grained massive tilleyite in the Redcap Creek magmatic skarn, North Queensland

1985 ◽  
Vol 49 (350) ◽  
pp. 71-75 ◽  
Author(s):  
M. J. Rubenach ◽  
C. Cuff
Keyword(s):  
Experimental Data ◽  
Mass Transfer ◽  
Close Agreement ◽  
Igneous Rocks ◽  
Coarse Grained ◽  
Reverse Direction ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Activity Diagrams ◽  
Grey Colour

AbstractEndoskarns formed where a swarm of diorite dykes have intruded calcite marble at Redcap Creek include an inner melilite-dominated, a wollastonite-dominated, and an outer massive tilleyite zone in contact with marble. The massive tilleyite is unusual in that it is coarse-grained (prisms 2–15 cm in length) and its deep grey colour contrasts with the lighter coloured varieties described elsewhere. A chemical analysis gives a formula close to ideal, with only minor substitution of Al, Ti, and Mg. Refined unit cell parameters are in close agreement with those quoted in the literature. The skarns have clearly formed by transport of Si, Mg, Fe, Al, and Ti from the igneous rocks, and Ca in the reverse direction from the marble. Activity diagrams derived from experimental data are most useful in interpreting the zonal sequence of endoskarns, and preliminary results suggest mass transfer at low Xco2 and temperature of the order of 800°C or higher for the formation of the massive tilleyite.

scholarly journals Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations

2012 ◽  
Vol 8 (9) ◽  
pp. e1002683 ◽  
Author(s):  
Evelyne Deplazes ◽  
Martti Louhivuori ◽  
Dylan Jayatilaka ◽  
Siewert J. Marrink ◽  
Ben Corry
Keyword(s):  
Experimental Data ◽  
Structural Investigation ◽  
Md Simulations ◽  
Coarse Grained

scholarly journals Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins

2017 ◽  
Author(s):  
Lam T. Nguyen ◽  
Matthew T. Swulius ◽  
Samya Aich ◽  
Mithilesh Mishra ◽  
Grant J. Jensen
Keyword(s):  
Experimental Data ◽  
Cell Division ◽  
Fluorescence Microscopy ◽  
Actin Filaments ◽  
Coarse Grained ◽  
Eukaryotic Cells ◽  
Ring Assembly ◽  
Assembly Result ◽  
Coarse Grained Simulations ◽  
Electron Cryotomography

AbstractCytokinesis in most eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by existing literature and new 3D molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin crosslinkers, and membranes and simulate their nteractions. Exploring a matrix of possible actomyosin configurations suggested that node-based architectures ike those presently described for ring assembly result in membrane puckers not seen in EM images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly-distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.Significance StatementIn most eukaryotes, a ring of actin and myosin drives cell division, but how the elements of the ring are arranged and constrict remain unclear. Here we use 3D coarse-grained simulations to explore various possibilities. Our simulations suggest that if actomyosin is arranged in nodes (as suggested by a popular model of ring assembly), the membrane distorts in ways not seen experimentally. Instead, actin and myosin are more ikely uniformly distributed around the ring. In the model that best fits experimental data, ring tension is generated by interactions between bipolar myosins and actin, and transmitted to the membrane via unipolar myosins. Technologically the study highlights how coarse-grained simulations can test specific mechanistic hypotheses by comparing their predicted outcomes to experimental results.

scholarly journals Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

2016 ◽  
Vol 49 (6) ◽  
pp. 1861-1875 ◽  
Author(s):  
Stephen J. Perkins ◽  
David W. Wright ◽  
Hailiang Zhang ◽  
Emre H. Brookes ◽  
Jianhan Chen ◽  
...  
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
High Performance ◽  
Solution Structure ◽  
Small Angle Scattering ◽  
Coarse Grained ◽  
Scattering Data ◽  
Structural Constraints ◽  
Atomistic Modelling ◽  
Angle Scattering

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.

scholarly journals An Efficient Parallel VLSI Sorting Architecture

VLSI Design ◽  
2000 ◽  
Vol 11 (2) ◽  
pp. 137-147 ◽  
Author(s):  
Yanjun Zhang ◽  
S. Q. Zheng
Keyword(s):  
Experimental Data ◽  
Theoretical Analysis ◽  
Constant Time ◽  
Sorting Algorithm ◽  
Fixed Size ◽  
Parallel Sorting ◽  
Termination Detection ◽  
Linear Arrays ◽  
Arbitrary Size ◽  
Sorting Network

We present a new parallel sorting algorithm that uses a fixed-size sorter iteratively to sort inputs of arbitrary size. A parallel sorting architecture based on this algorithm is proposed. This architecture consists of three components, linear arrays that support constant-time operations, a multilevel sorting network, and a termination detection tree, all operating concurrently in systolic processing fashion. The structure of this sorting architecture is simple and regular, highly suitable for VLSI realization. Theoretical analysis and experimental data indicate that the performance of this architecture is likely to be excellent in practice.

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