Flexible Interface Research Articles

C-Coupler2: a flexible and user-friendly community coupler for model coupling and nesting

Abstract. The Chinese C-Coupler (Community Coupler) family aims primarily to develop coupled models for weather forecasting and climate simulation and prediction. It is targeted to serve various coupled models with flexibility, user-friendliness, and extensive coupling functions. C-Coupler2, the latest version, includes a series of new features in addition to those of C-Coupler1 – including a common, flexible, and user-friendly coupling configuration interface that combines a set of application programming interfaces and a set of XML-formatted configuration files; the capability of coupling within one executable or the same subset of MPI (message passing interface) processes; flexible and automatic coupling procedure generation for any subset of component models; dynamic 3-D coupling that enables convenient coupling of fields on 3-D grids with time-evolving vertical coordinate values; non-blocking data transfer; facilitation for model nesting; facilitation for increment coupling; adaptive restart capability; and finally a debugging capability. C-Coupler2 is ready for use to develop various coupled or nested models. It has passed a number of test cases involving model coupling and nesting, and with various MPI process layouts between component models, and has already been used in several real coupled models.

Client-side straggler-aware I/O scheduler for object-based parallel file systems

Abstract Object-based parallel file systems have emerged as promising storage solutions for high-performance computing (HPC) systems. Despite the fact that object storage provides a flexible interface, scheduling highly concurrent I/O requests that access a large number of objects still remains as a challenging problem, especially in the case when stragglers (storage servers that are significantly slower than others) exist in the system. An efficient I/O scheduler needs to avoid possible stragglers to achieve low latency and high throughput. In this paper, we introduce a log-assisted straggler-aware I/O scheduling to mitigate the impact of storage server stragglers. The contribution of this study is threefold. First, we introduce a client-side, log-assisted, straggler-aware I/O scheduler architecture to tackle the storage straggler issue in HPC systems. Second, we present three scheduling algorithms that can make efficient decision for scheduling I/Os while avoiding stragglers based on such an architecture. Third, we evaluate the proposed I/O scheduler using simulations, and the simulation results have confirmed the promise of the newly introduced straggler-aware I/O scheduler.

ABE-VIEW: Android Interface for Wireless Data Acquisition and Control.

Advances in scientific knowledge are increasingly supported by a growing community of developers freely sharing new hardware and software tools. In this spirit we have developed a free Android app, ABE-VIEW, that provides a flexible graphical user interface (GUI) populated entirely from a remote instrument by ascii-coded instructions communicated wirelessly over Bluetooth. Options include an interactive chart for plotting data in real time, up to 16 data fields, and virtual controls including buttons, numerical controls with user-defined range and resolution, and radio buttons which the user can use to send coded instructions back to the instrument. Data can be recorded into comma delimited files interactively at the user’s discretion. Our original objective of the project was to make data acquisition and control for undergraduate engineering labs more modular and affordable, but we have also found that the tool is highly useful for rapidly testing novel sensor systems for iterative improvement. Here we document the operation of the app and syntax for communicating with it. We also illustrate its application in undergraduate engineering labs on dynamic systems modeling, as well as for identifying the source of harmonic distortion affecting electrochemical impedance measurements at certain frequencies in a novel wireless potentiostat.

Common Spaces: Multi-Modal-Media Ecosystem for Live Performances

Common Spaces is an interface for real-time media convergence and live performance combining media, applications and devices. A multimodal media ecosystem was designed to respond to the requirement of a specific performance — how to mix multiple applications into a single environment. This collaborative environment provides a flexible interface for performers to negotiate, share, and mix media, applications, and devices. Common Spaces is a framework based on interoperability and data flow, a network of virtual wires connecting applications that “talk” to each other sharing resources through technologies such as OSC or Syphon. With this approach, media designers have the freedom to choose a set of applications and devices that best suit their needs and are not restricted to a unique environment. We have implemented and performed with this ecosystem in live events, demonstrating its feasibility. In our paper we describe the project's concept and methodology. In the proposed performance we will use the Digital Archive of Portuguese Experimental Literature (www.po-ex.net) as a framework, appropriating its database assets, remixing its contents, as well as the techniques and methods they imply, stimulating the understanding of the archive as variable and adaptable. These digital re-readings and re-codings of experimental poems further highlight the importance of the materialities of experimental writing, integrating self-awareness in the modes of exchanges between literature, music, animation, performance, and technology.

Simultaneous stimulation and recording of cell activity with reference-less sensors: Is it feasible?

Abstract The study of neuronal and neurodegenerative diseases requires the development of new tools and technologies to create functional neuroelectronics allowing both stimulation and recording of cellular electrical activity. We present a model that describes electrolyte-gated organic field-effect transistors (EGOFETs) as neural interfaces. We show that our model can be successfully applied to understand the behaviour of a more general class of devices, including both organic and inorganic transistors. We introduce the reference-less (RL-) EGOFET and we show that it might be successfully used as a low cost and flexible neural interface for extracellular recording in vivo without the need of a reference electrode, making the implant less invasive and easier to use. The working principle underlying RL-EGOFETs involves self-polarization and back-gate stimulation, which we show experimentally to be feasible. Our results open the door to using and optimizing EGOFETs and RL-EGOFETs for neural interfaces.

Calculations of free energy of surface interactions in crystalline polyethylene.

The surface free energy of the crystalline polyethylene (PE) is an important property related with wettability, adhesion, and crystal growth. We investigated the profiles of free energy of surface interactions in the fully thermalized crystalline PE during debonding and shearing with atomistic molecular dynamics simulations using steered molecular dynamics and umbrella sampling techniques. The stress profiles during debonding and shearing processes were also estimated and compared with those obtained from analogous deformation simulations. We estimated the vacuum surface free energies of two different crystallographic surfaces (100) and (010) of the crystalline PE from the free energy changes during the debonding process. The estimated surface free energies were insensitive to the choice of simulation protocols after combining estimates from both forward and backward processes and were in excellent agreement with those obtained from an experiment on PE single crystal aggregates, which underscores the importance of the inclusion of the entropic contribution in the free energy calculated with the fully flexible interface adopted in this study.

Maplab: An Open Framework for Research in Visual-Inertial Mapping and Localization

Robust and accurate visual-inertial estimation is crucial to many of today's challenges in robotics. Being able to localize against a prior map and obtain accurate and driftfree pose estimates can push the applicability of such systems even further. Most of the currently available solutions, however, either focus on a single session use-case, lack localization capabilities or an end-to-end pipeline. We believe that only a complete system, combining state-of-the-art algorithms, scalable multi-session mapping tools, and a flexible user interface, can become an efficient research platform. We therefore present maplab, an open, research-oriented visual-inertial mapping framework for processing and manipulating multi-session maps, written in C++. On the one hand, maplab can be seen as a ready-to-use visual-inertial mapping and localization system. On the other hand, maplab provides the research community with a collection of multisession mapping tools that include map merging, visual-inertial batch optimization, and loop closure. Furthermore, it includes an online frontend that can create visual-inertial maps and also track a global drift-free pose within a localization map. In this paper, we present the system architecture, five use-cases, and evaluations of the system on public datasets. The source code of maplab is freely available for the benefit of the robotics research community.

Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery

The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.

Elastic waves induced transport along slab-like solid-gouge interfaces

Theoretical derivation of the perturbed transport due to a sudden weak impact in a presumed slab-like region filled with solid-gouge and vacancies was conducted. The induced transport which is of the second order is created by a small-amplitude surface elastic wave propagating along the flexible interface by considering the weakly nonlinear coupling between the interfaces and the slip effect. We simplify the original system of lower-order partial differential equations (related to the momentum and mass transport) to one single higher-order quasi-linear partial differential equation in terms of the unknown stream function. Via numerical searching we identify the possible critical threshold values for zero-flux states corresponding to certain Navier-slip parameter and wave number which could be relevant to the possible seismic reversal or disappearance of moving of solid-gouge. Our numerical results are useful to the seismic pattern recognition together with synthetic earthquake catalogs.

Bayonet: probabilistic inference for networks

Network operators often need to ensure that important probabilistic properties are met, such as that the probability of network congestion is below a certain threshold. Ensuring such properties is challenging and requires both a suitable language for probabilistic networks and an automated procedure for answering probabilistic inference queries. We present Bayonet, a novel approach that consists of: (i) a probabilistic network programming language and (ii) a system that performs probabilistic inference on Bayonet programs. The key insight behind Bayonet is to phrase the problem of probabilistic network reasoning as inference in existing probabilistic languages. As a result, Bayonet directly leverages existing probabilistic inference systems and offers a flexible and expressive interface to operators. We present a detailed evaluation of Bayonet on common network scenarios, such as network congestion, reliability of packet delivery, and others. Our results indicate that Bayonet can express such practical scenarios and answer queries for realistic topology sizes (with up to 30 nodes).

Research on VSC-LVDC with DC Energy Storage to Improve the Stability of Microgrid Connected to Grid Operation

In order to improve stability of the microgrid operation connected to distribute network, the power flow fluctuations are smoothed. In this paper, a kind of flexible interconnection interface was studied in this paper, based on voltage source converter low voltage direct current(VSC-LVDC) containing energy storage. According to the mathematical model of VSC-LVDC and battery, a dual vector decoupling three-loop control strategy consisted of stages charging is proposed, and the battery charging and discharging switch control is offered, for charging and discharging of the energy storage, the bidirectional power transmission and suppressing power fluctuations. A simulation model is built that microgrid connected to distribute network using the flexible interconnection interface, and the conditions of power fluctuation, battery charging and discharging switch and the short-circuit fault at the microgrid side AC bus are simulated. The simulation results show that the control strategy effectively suppresses the power fluctuations of point of common coupling(PCC), guarantee the stability of the power flow.

Behaviour of an Integrated EV Based on Renewable Energy Linked to the Distribution Grid: An Educational Tool

Electric Vehicles (EVs) are one of the renewable energy sources that can bring significant positive impacts to power system during their charging and discharging operations. According to this research an educational tool has been created to show students/users the Electric Vehicle’s behavior when integrated to the distribution grid. This research helps students/users to develop new algorithms for renewable energy and energy storage applications. A Matlab/Simulink module has been utilized to implement the integrated systems with simple, easy and flexible Graphical User Interface (GUI) for experimentation purposes. Furthermore, the developed educational tool aims to show that EVs can be efficiently charged by renewable energy sources connected to the grid with reduced charging costs. In addition, users can understand how those results can be sustainable for further studies and development. Unlike commercial wise tools, such a tool would add a promising methodology for the research methods and educational systems due to availability and user friendly approach.

SOFTWARE FOR LINE OF BALANCE IN PROJECTS OF HIGHWAYS

Highways play an important role in countries’ economy improvement as they are the major transportation facilities. Highway construction project needs effective planning method to overcome its complicity. Line of Balance is the most effective technique for scheduling such projects. Computerization of this technique to cover highway construction is very powerful to obtain the full advantages of this technique as computer-based program can simplify the mission of end users. The software was build using Visual Basic to ensure flexible code and interactive user-interface. The developed software was verified and validated through extensive testing during and after its building. The result of test showed its correctness and effectiveness to attain objectives

Numerical study with OpenFOAM on heat conduction problems in heterogeneous media

OpenFOAM was used to numerically investigate heat conduction in heterogeneous media. The main advantage of this platform is that it offers an open flexible interface with great convenience for mesh generation and solver modification. Cases of 1D and 2D heat conduction problems in media with different levels of heterogeneity were considered to check the performance of OpenFOAM. The results were compared with references and other commercial software and showed good accuracy. Note that all of the processes, including the mesh generation, numerical simulation, and post-processing, relied on free open-source codes.

Simflowny 2: An upgraded platform for scientific modelling and simulation

Simflowny is an open platform for scientific dynamical models which automatically generates parallel code for different simulation frameworks. Here we present major upgrades on this software to support an extended set of model families, in particular: (i) a new family for the evolution of partial differential equations, which can include spatial derivatives of any order, (ii) a new family for agent based models to study complex phenomena — either on a spatial domain or on a graph. Additionally we introduce an upgraded flexible graphical user interface to accommodate these and future families of equations and models. This paper describes the new architecture and summarizes the formal representation and implementation of these new families, providing several validation results. Program summaryProgram Title: SimflownyProgram Files doi:http://dx.doi.org/10.17632/g9mcw8s64f.1Licensing provisions: Apache License, 2.0Programming language: Java, C++ and JavaScriptJournal Reference of previous version: Comput. Phys. Comm. 184 (2013) 2321–2331Does the new version supersede the previous version?: YesReasons for the new version: Additional featuresSummary of revisions: Expanded support for Partial Differential Equations, Support for Agent Based Models, New Graphical User Interface.Nature of problem: Simflowny generates numerical simulation code for a wide range of models.Solution method: Any discretization scheme based on either Finite Volume Methods, Finite Difference Methods, or meshless methods for Partial Differential Equations. Agent Based Model simulations execute their own algorithm as set in their models.Additional comments: The software architecture is easily extensible for future additional model families and simulation frameworks. Full documentation is available in the wiki home of the Simflowny project [2].

Real-time free spectral range measurement based on optical single-sideband technique.

We demonstrate a real-time scheme for measuring the free spectral range (FSR) of a high-aspect-ratio Si3N4 waveguide ring resonator with a fiber-based hybrid unbalanced Mach-Zehnder modulator (MZM) using an optical single-sideband technique. Resonance-tracking loops were established with the Pound-Drever-Hall technique for locking resonance modes. A relative precision of 3.25 × 10-6 was achieved for a 35-mm waveguide ring resonator with FSR = 1,844,628 kHz and Q = 3.211 × 106. Furthermore, the Si3N4 resonator FSR coefficient of thermal expansion was measured as -16.735±0.002 kHz/°C. This method will provide a flexible photonic interface for realizing advanced photonic systems.

An All-Programmable 16-nm RFSoC for Digital-RF Communications

The Xilinx RFSoC is the first product to integrate cutting-edge RF data converters with an FPGA SoC. This breakthrough integration delivers a dramatic reduction in system power and footprint, while offering increased flexibility for wide-bandwidth communications applications. The RFSoC monolithically integrates a quad-core 1.5-GHz ARM Cortex-A53 application processor, dual-core Cortex-R5 real-time processing units, 4,000 FPGA DSP resources, and up to 16 digital-RF transmit and receive paths. Each RF transmit path includes a 14-bit, 6.4-GS/s RF-DAC and a flexible digital up conversion (DUC) chain. The RF receive channels contain 12-bit, 4-gigasamples per second (GS/s) RF-ADCs and a flexible digital down conversion (DDC) chain. All RF paths include a programmable complex digital mixer with numerically controlled oscillator (NCO), digital compensation of RF paths, on-chip RF-clock generation, and a flexible wideband interface to the FPGA fabric. The device is housed in a 40x40-mm, 1,517-pin ball grid array (BGA) package and is manufactured in a 16-nm Fin field-effect transistor (FinFET) process.

Next generation web based live data monitoring for W7-X

The Wendelstein 7-X stellarator experiment by its nature has the need for continuous live data monitoring. New technical and security related requirements make a redesign of the monitoring architecture, originating in the first years of the century, necessary. Besides that, new developments in technologies, user interfaces and generally IT supported work flows, generate new expectations at the system user level, including live remote participation.To answer these upcoming demands, the CoDaC team at Wendelstein 7-X has designed a new architecture for monitoring data management, distribution and observation. As a very flexible user interface, a client web application was developed, utilizing modern technologies like WebSockets and WebGL for high performance live data visualization. A touch friendly interface design offers both broad support for new access tools (like tablets, smart phones, smart TV sets) and a very flexible and intuitive work flow.This paper describes the new MonA-LISA monitoring architecture and gives a short overview over the options provided by the web based monitoring client.

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics.

Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.

Research on Microvibrations Generated by a Control Moment Gyroscope on a Flexible Interface Based on a Dynamic Substructure Method

Microvibrations generated by a control moment gyroscope (CMG) will couple with a flexible spacecraft structure, and this seriously degrades certain point performances of a spacecraft. This study focuses on investigating the coupled microvibrations caused by a CMG on a flexible interface by using a dynamic substructure method (DSM). First, a DSM based on a frequency response function (FRF) is established, and this method is used to simultaneously synthesize multiple substructures with different coordinates irrespective of whether their connection interfaces are rigid or flexible. Second, the bearings and the gimbal servo system are simplified into linear springs, and therefore the CMG model is equivalent to a mass-spring-damping system with eighteen degrees of freedom (DOFs). Third, the established DSM is employed to deduce the FRF matrix of the CMG-flexible interface coupling system that consists of CMG mounted on an aluminum honeycomb sandwich palate (AHSP). Dynamic responses of the coupling system are calculated by the derived FRF matrix. Finally, MATLAB and multibody dynamics simulations are conducted to analyze and validate the dynamic responses of the coupling system obtained by the DSM. The results indicate that the DSM is appropriate to predict the coupled microvibrations of CMG on a flexible interface and exhibits high prediction accuracy and computational efficiency.