scholarly journals The Replication Domain Model: Regulating Replicon Firing in the Context of Large-Scale Chromosome Architecture

2013 ◽  
Vol 425 (23) ◽  
pp. 4690-4695 ◽  
Author(s):  
Benjamin D. Pope ◽  
David M. Gilbert
Keyword(s):  
Large Scale ◽  
Domain Model ◽  
Chromosome Architecture ◽  
Replication Domain

scholarly journals A massively scalable distributed multigrid framework for nonlinear marine hydrodynamics

2019 ◽  
Vol 33 (5) ◽  
pp. 855-868 ◽  
Author(s):  
Stefan Lemvig Glimberg ◽  
Allan Peter Engsig-Karup ◽  
Luke N Olson
Keyword(s):  
Potential Flow ◽  
Large Scale ◽  
Data Locality ◽  
High Order ◽  
Domain Model ◽  
Processing Unit ◽  
Parallel Scalability ◽  
Marine Hydrodynamics ◽  
Practical Applications ◽  
Oak Ridge

The focus of this article is on the parallel scalability of a distributed multigrid framework, known as the DTU Compute GPUlab Library, for execution on graphics processing unit (GPU)-accelerated supercomputers. We demonstrate near-ideal weak scalability for a high-order fully nonlinear potential flow (FNPF) time domain model on the Oak Ridge Titan supercomputer, which is equipped with a large number of many-core CPU-GPU nodes. The high-order finite difference scheme for the solver is implemented to expose data locality and scalability, and the linear Laplace solver is based on an iterative multilevel preconditioned defect correction method designed for high-throughput processing and massive parallelism. In this work, the FNPF discretization is based on a multi-block discretization that allows for large-scale simulations. In this setup, each grid block is based on a logically structured mesh with support for curvilinear representation of horizontal block boundaries to allow for an accurate representation of geometric features such as surface-piercing bottom-mounted structures—for example, mono-pile foundations as demonstrated. Unprecedented performance and scalability results are presented for a system of equations that is historically known as being too expensive to solve in practical applications. A novel feature of the potential flow model is demonstrated, being that a modest number of multigrid restrictions is sufficient for fast convergence, improving overall parallel scalability as the coarse grid problem diminishes. In the numerical benchmarks presented, we demonstrate using 8192 modern Nvidia GPUs enabling large-scale and high-resolution nonlinear marine hydrodynamics applications.

scholarly journals FARUL3S: a New Framework for Agile Regulated Ultra-Large-Scale Software Systems

2021 ◽  
Author(s):  
Amira KSIKSI
Keyword(s):  
System Design ◽  
Smart City ◽  
Large Scale ◽  
Complex Adaptive System ◽  
Systems Design ◽  
Domain Model ◽  
Design Rule ◽  
Software Systems ◽  
Management And Development ◽  
Complex Adaptive

<div>The Ultra-Large-Scale Software (ULSS) systems development challenges today’s software management and development approaches. Northrop et al. (2006) revealed three broad areas of challenges [1]. To deal with those challenges, they propose an interdisciplinary portfolio of research. In particular, we address the design and evolution challenge by focusing on the design area of research. In order to regulate the ULSS systems, the traditional software engineering tools face challenges as they are top-down so they deal with each domain model separately. To address the domain diversity like in the smart city systems, we propose the Framework for Agile Regulated Ultra Large Scale Software System (FARUL3S) to look at the ULSS system from bottom-up. The FARUL3S is a user-centered solution that aims at combining the complex adaptive system, the financial economics as well as the engineering systems design. Our contribution aims to regulate and constrain the ULSS systems by using architectural agreements and other rules. In this paper, we provide a detailed description of the FARUL3S steps. Our Framework generates a system Design Rule Hierarchy (DRH) so it can be used to constrain the entire system design. In the future, we will provide an illustration of the FARUL3S adoption on the management and design of different smart city services to ensure the efficiency of our solution.</div>

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

2021 ◽  
Vol 118 (42) ◽  
pp. e2107092118
Author(s):  
Anna Lappala ◽  
Chen-Yu Wang ◽  
Andrea Kriz ◽  
Hunter Michalk ◽  
Kevin Tan ◽  
...  
Keyword(s):  
X Chromosome ◽  
Large Scale ◽  
Three Dimensions ◽  
Rna Molecules ◽  
Chromosome Architecture ◽  
Inactive X Chromosome ◽  
Mixing Dynamics ◽  
Chromosome Reconstruction ◽  
Slow Mixing ◽  
3D Information

Chromosomes are segmented into domains and compartments, but how these structures are spatially related in three dimensions (3D) is unclear. Here, we developed tools that directly extract 3D information from Hi-C experiments and integrate the data across time. With our “4DHiC” method, we use X chromosome inactivation (XCI) as a model to examine the time evolution of 3D chromosome architecture during large-scale changes in gene expression. Our modeling resulted in several insights. Both A/B and S1/S2 compartments divide the X chromosome into hemisphere-like structures suggestive of a spatial phase-separation. During the XCI, the X chromosome transits through A/B, S1/S2, and megadomain structures by undergoing only partial mixing to assume new structures. Interestingly, when an active X chromosome (Xa) is reorganized into an inactive X chromosome (Xi), original underlying compartment structures are not fully eliminated within the Xi superstructure. Our study affirms slow mixing dynamics in the inner chromosome core and faster dynamics near the surface where escapees reside. Once established, the Xa and Xi resemble glassy polymers where mixing no longer occurs. Finally, Xist RNA molecules initially reside within the A compartment but transition to the interface between the A and B hemispheres and then spread between hemispheres via both surface and core to establish the Xi.

A Domain Model-Centric Approach for the Development of Large-Scale Office Lighting Systems

2018 ◽  
pp. 109-120
Author(s):  
Richard Doornbos ◽  
Bas Huijbrechts ◽  
Jack Sleuters ◽  
Jacques Verriet ◽  
Kristina Ševo ◽  
...  
Keyword(s):  
Large Scale ◽  
Domain Model ◽  
Lighting Systems ◽  
Office Lighting

Two-Port Characteristic Analysis for Transformers with the Large Scale Windings Based on Sparse Matrix

2014 ◽  
Vol 986-987 ◽  
pp. 2035-2038
Author(s):  
Xu Dong Zhang ◽  
Jian Ye Yuan ◽  
Jing Ping Zhang ◽  
Jian Ying Feng
Keyword(s):  
Transmission Lines ◽  
Large Scale ◽  
Sparse Matrix ◽  
Domain Model ◽  
Computation Method ◽  
Characteristic Analysis ◽  
Matrix Operation ◽  
Large Matrix ◽  
Calculation Results ◽  
Block Storage

In order to calculate the two-port wide frequency parameters of a large transformer quickly and accurately, parameter calculation of multi-conductor transmission lines model is proposed based on the sparse matrix operation. It solved the problem caused by the large matrix. Firstly, multi-conductor transmission lines model of the transformer windings is established. Secondly, matrix characteristics ofYandZis analyzed, based on which the block storage and computation method is applied. Then the frequency-domain model is solved based on sparse matrix operation. At last, taking a SS11-20000/110 transformer as an example, the correctness of this method has been verified by comparing calculation results with measurement results.

scholarly journals Telomeres act autonomously in maize to organize the meiotic bouquet from a semipolarized chromosome orientation

2002 ◽  
Vol 157 (2) ◽  
pp. 231-242 ◽  
Author(s):  
Peter M. Carlton ◽  
W. Zacheus Cande
Keyword(s):  
Large Scale ◽  
Nuclear Periphery ◽  
Small Region ◽  
Homologous Chromosomes ◽  
Cis Acting ◽  
Chromosome Architecture ◽  
Meiotic Chromosomes ◽  
Ring Chromosomes ◽  
Bouquet Stage ◽  
Chromosome Regions

During meiosis, chromosomes undergo large-scale reorganization to allow pairing between homologues, which is necessary for recombination and segregation. In many organisms, pairing of homologous chromosomes is accompanied, and possibly facilitated, by the bouquet, the clustering of telomeres in a small region of the nuclear periphery. Taking advantage of the cytological accessibility of meiosis in maize, we have characterized the organization of centromeres and telomeres throughout meiotic prophase. Our results demonstrate that meiotic centromeres are polarized prior to the bouquet stage, but that this polarization does not contribute to bouquet formation. By examining telocentric and ring chromosomes, we have tested the cis-acting requirements for participation in the bouquet. We find that: (a) the healed ends of broken chromosomes, which contain telomere repeats, can enter the bouquet; (b) ring chromosomes enter the bouquet, indicating that terminal position on a chromosome is not necessary for telomere sequences to localize to the bouquet; and (c) beginning at zygotene, the behavior of telomeres is dominant over any centromere-mediated chromosome behavior. The results of this study indicate that specific chromosome regions are acted upon to determine the organization of meiotic chromosomes, enabling the bouquet to form despite large-scale changes in chromosome architecture.

A frequency domain model for analysing vibrations in large-scale integrated building–bridge structures induced by running trains

2019 ◽  
Vol 234 (2) ◽  
pp. 226-241 ◽  
Author(s):  
Xun Zhang ◽  
Linghui Ruan ◽  
Yu Zhao ◽  
Xiaogang Zhou ◽  
Xiaozhen Li
Keyword(s):  
Frequency Domain ◽  
High Speed ◽  
Large Scale ◽  
Computation Time ◽  
Domain Model ◽  
Vibration Source ◽  
Force Transmission ◽  
Train Track ◽  
Building Bridge ◽  
Bridge Structures

Integrated building–bridge structures are increasingly common in high-speed railway stations, where the elevated track floor is directly subjected to train–track dynamic forces that result in excessive vibrations. The common methods of predicting the train-induced vibrations in large-scale IBBS are implemented in the time domain and can have prohibitively long computation times. This paper presents a frequency domain model for the vibration analysis of large-scale IBBS, with the aim of reducing the computation time while retaining sufficient accuracy. The model consists of three coupled subsystems: train, track, and IBBS. The train and track subsystems are investigated analytically, and the IBBS subsystem is solved numerically using a finite element method. The receptance technique is introduced to obtain the wheel/rail force. The force transmitted to the floor slab is treated as the vibration source of the IBBS subsystem. The simulated vibration levels in the IBBS subsystem are compared with those obtained from in situ measurements, and a good agreement is observed in terms of both magnitude and frequency dependence. The vibration responses of the IBBS subsystem at different locations of the track floor and the waiting floor are compared, and the influence of the track position is investigated. Finally, a parametric analysis is conducted with the aim of formulating anti-vibration measures, in which the carbody acceleration, rail displacement, and ballast acceleration are considered as key indicators. The force transmission, vibration transmission and IBBS vibrations are also investigated. The results indicate that using a ballast mat and enlarging the column cross-section are the two most promising measures for reducing the vibration levels.

Experimental Tests of a 1:16th-Scale Model of the Spar-Buoy OWC in a Large Scale Wave Flume in Regular Waves

2018 ◽  
Author(s):  
R. P. F. Gomes ◽  
J. C. C. Henriques ◽  
L. M. C. Gato ◽  
A. F. O. Falcão
Keyword(s):  
Large Scale ◽  
Experimental Tests ◽  
Domain Model ◽  
Scale Model ◽  
Chamber Pressure ◽  
Viscous Drag ◽  
Regular Waves ◽  
Mooring Lines ◽  
Wave Flume ◽  
Free Surface Displacement

This paper presents the experimental tests of a 16th-scale model of the Spar-buoy oscillating water column (OWC) carried out at a large scale wave flume. The model is slack-moored to the flume floor by two mooring lines. The turbine effect is replicated using calibrated orifice plates. The device six degree-of-freedom motion, inner free surface displacement and air chamber pressure are measured. The influence of wave height, turbine damping and mass distribution on the system dynamics is analysed for regular waves. An in-house developed numerical time-domain model is used to simulate the motion and power absorption under the same wave conditions as the physical model tests. The formulation considers linear hydrodynamic forces, viscous drag effects and drift forces. The floater is assumed to oscillate in six degrees of freedom and the OWC can move vertically in the tube. The mooring system is simulated using a quasi-static model. The comparison between experiments and numerical simulations shows a good agreement for wave periods outside the zone where parametric resonance in roll and pitch occurs.

scholarly journals FARUL3S: a New Framework for Agile Regulated Ultra-Large-Scale Software Systems

2021 ◽  
Author(s):  
Amira KSIKSI ◽  
Onsa Lazzez ◽  
Adel Khlifi ◽  
Hela Ltifi ◽  
Adel M. Alimi
Keyword(s):  
System Design ◽  
Smart City ◽  
Large Scale ◽  
Complex Adaptive System ◽  
Systems Design ◽  
Domain Model ◽  
Design Rule ◽  
Software Systems ◽  
Management And Development ◽  
Complex Adaptive

<div>The Ultra-Large-Scale Software (ULSS) systems development challenges today’s software management and development approaches. Northrop et al. (2006) revealed three broad areas of challenges [1]. To deal with those challenges, they propose an interdisciplinary portfolio of research. In particular, we address the design and evolution challenge by focusing on the design area of research. In order to regulate the ULSS systems, the traditional software engineering tools face challenges as they are top-down so they deal with each domain model separately. To address the domain diversity like in the smart city systems, we propose the Framework for Agile Regulated Ultra Large Scale Software System (FARUL3S) to look at the ULSS system from bottom-up. The FARUL3S is a user-centered solution that aims at combining the complex adaptive system, the financial economics as well as the engineering systems design. Our contribution aims to regulate and constrain the ULSS systems by using architectural agreements and other rules. In this paper, we provide a detailed description of the FARUL3S steps. Our Framework generates a system Design Rule Hierarchy (DRH) so it can be used to constrain the entire system design. In the future, we will provide an illustration of the FARUL3S adoption on the management and design of different smart city services to ensure the efficiency of our solution.</div>

Modeling the closing behavior of a smart hydrogel micro-valve

2017 ◽  
Vol 30 (9) ◽  
pp. 1409-1418 ◽  
Author(s):  
Philipp J Mehner ◽  
Merle Allerdißen ◽  
Sebastian Haefner ◽  
Andreas Voigt ◽  
Uwe Marschner ◽  
...  
Keyword(s):  
Finite Element ◽  
Large Scale ◽  
Chemical Concentration ◽  
Simulation Tools ◽  
Smart Hydrogel ◽  
Fluid Systems ◽  
Circuit Representation ◽  
Essential Components ◽  
Network Methods ◽  
Replication Domain

Smart hydrogel micro-valves are essential components of micro-chemo-mechanical fluid systems. These valves are based on phase-changeable polymers. They can open and close micro-fluidic channels depending on the chemical concentration or the temperature in the fluid. A concept of finite element–based modeling in combination with network methods to simulate concentration-triggered, phase-changeable hydrogels is proposed. We introduce a temperature domain as a replication domain to substitute insufficiently implemented domains. With the used simulation tools, problems are highlighted and their solutions are presented. The computed parameters of such valves are included in a circuit representation, which is capable of efficiently computing large-scale micro-fluidic systems. These methods will help predict, visualize, and understand polymeric swelling behavior as well as the performance of large-scale chip applications before any complex experiment is performed.

Sign in / Sign up

Export Citation Format

Share Document