Library Of Blocks Research Articles

Expanding the Reticular Chemistry Building Block Library toward Highly Connected Nets: Ultraporous MOFs Based on 18-Connected Ternary, Trigonal Prismatic Superpolyhedra.

The chemistry of metal-organic frameworks (MOFs) continues to expand rapidly, providing materials with diverse structures and properties. The reticular chemistry approach, where well-defined structural building blocks are combined together to form crystalline open framework solids, has greatly accelerated the discovery of new and important materials. However, its full potential toward the rational design of MOFs relies on the availability of highly connected building blocks because these greatly reduce the number of possible structures. Toward this, building blocks with connectivity greater than 12 are highly desirable but extremely rare. We report here the discovery of novel 18-connected, trigonal prismatic, ternary building blocks (tbb's) and their assembly into unique MOFs, denoted as Fe-tbb-MOF-x (x: 1, 2, 3), with hierarchical micro- and mesoporosity. The remarkable tbb is an 18-c supertrigonal prism, with three points of extension at each corner, consisting of triangular (3-c) and rectangular (4-c) carboxylate-based organic linkers and trigonal prismatic [Fe3(μ3-Ο)(-COO)6]+ clusters. The tbb's are linked together by an 18-c cluster made of 4-c ligands and a crystallographically distinct Fe3(μ3-Ο) trimer, forming overall a 3-D (3,4,4,6,6)-c five nodal net. The hierarchical, highly porous nature of Fe-tbb-MOF-x (x: 1, 2, 3) was confirmed by recording detailed sorption isotherms of Ar, CH4, and CO2 at 87, 112, and 195 K, respectively, revealing an ultrahigh BET area (4263-4847 m2 g-1) and pore volume (1.95-2.29 cm3 g-1). Because of the observed ultrahigh porosities, the H2 and CH4 storage properties of Fe-tbb-MOF-x were investigated, revealing well-balanced high gravimetric and volumetric deliverable capacities for cryoadsorptive H2 storage (11.6 wt %/41.4 g L-1, 77 K/100 bar-160 K/5 bar), as well as CH4 storage at near ambient temperatures (367 mg g-1/160 cm3 STP cm-3, 5-100 bar at 298 K), placing these materials among the top performing MOFs. The present work opens new directions to apply reticular chemistry for the construction of novel MOFs with tunable porosities based on contracted or expanded tbb analogues.

DESIGN AND IMPLEMENTATION OF REAL-TIME NON-LINEAR DYNAMIC SIMULATION OF FIGHTER AIRCRAFT ON MULTICORE PROCESSOR

Simulation is a system to imitate the operation of various kinds of real-world facilities or processes for training, behavior study or entertainment purposes. Some implementation of fighter aircraft simulation is done sequentially using FORTRAN and MATLAB / Simulink. On the other hand, a multicore (parallel) computer system has been in the personal computer environment, so the multicore computing paradigm should be considered. Intel Threading Building Blocks (TBB) library need to be utilized in multicore programming. This paper discusses the design and implementation of real-time nonlinear dynamic simulation of fighter aircraft on multicore processor. The aircraft model used in this study is F16 data. Implementation of the simulation code is written in C++ with Intel TBB, OpenGL, Open Scene Graph, and Open Dynamic Engine library. The testing results of non-linear dynamics simulation of fighter aircraft show that the speedup on an Intel Core 2 Duo processor is 1.1776 x for elevator doublet input (short period), while speedup on an Intel i7 is 1.5405 x for rudder doublet input (dutch roll). Key Words: multicore computing, real-time simulation, nonlinear dynamic, fighter aircraft model

Simulation of CMOS technology microcircuit elements with eco-friendly practices in agro-industrial production

The paper explores contemporary design technologies for CMOS LSIs and examines challenges encountered during the modelling of LSIs at various hierarchical levels within the design process. The analysis underscores the pressing need for developing software tools for fault modelling while minimizing computational expenses. In addition to addressing the technical aspects, this study sheds light on the influence of ecology and agro-industrial practices on the microcircuit modelling process. Emphasis is placed on resource efficiency and mitigating adverse environmental impacts, particularly in the context of agro-industrial production. The paper discusses the requirements for creating and utilizing SF block libraries, aiming at establishing databases facilitating swift identification, environmental monitoring, and evaluation of the ecological footprint resulting from agro-industrial activities. Moreover, the paper presents principles for constructing VLSI CAD centres that navigate the delicate balance between advanced technologies and environmental sustainability. These principles provide a foundation for developing a unified hardware and software complex tailored for designing radio- electronic equipment while taking into consideration the specific needs and challenges of the agricultural sector.

Data-Driven Discovery of Organic Electronic Materials Enabled by Hybrid Top-Down/Bottom-Up Design.

The high-throughput exploration and screening of molecules for organic electronics involves either a 'top-down' curation and mining of existing repositories, or a 'bottom-up' assembly of user-defined fragments based on known synthetic templates. Both are time-consuming approaches requiring significant resources to compute electronic properties accurately. Here, 'top-down' is combined with 'bottom-up' through automatic assembly and statistical models, thus providing a platform for the fragment-based discovery of organic electronic materials. This study generates a top-down set of 117K synthesized molecules containing structures, electronic and topological properties and chemical composition, and uses them as building blocks for bottom-up design. A tool is developed to automate the coupling of these building blocks at their C(sp2/sp)-H bonds, providing a fundamental link between the two dataset construction philosophies. Statistical models are trained on this dataset and a subset of resulting top-down/bottom-up compounds, enabling on-the-fly prediction of ground and excited state properties with high accuracy across organic compound space. With access to ab initio-quality optical properties, this bottom-up pipeline may be applied to any materials design campaign using existing compounds as building blocks. To illustrate this, over a million molecules are screened for singlet fission. tThe leading candidates provide insight into the features promoting this multiexciton-generatingprocess.

Mononuclear or Coordination Polymer Complexes? Both Are Possible for 3,6,9-Trioxaundecanedioic Acid

Investigating the driving forces leading to the formation of a specific supramolecular architecture among a wide spectrum of all the possibly obtainable structures is not an easy task. The contemporary literature provides several models for correctly predicting the thermodynamically accessible structures that can originate from a library of building blocks. Definitions are rigid by their very nature, so their application may sometimes require a shift in perspective. In the study presented herein, we describe the crystal structures of three metallo-supramolecular architectures assembled from deprotonated derivatives of 3,6,9-trioxaundecanedioic acid and Mn(II), Co(II) and Zn(II). In the Mn(II) case, the complexation resulted in a complex of a discrete/heptacoordinated nature, whereas the other two structures appeared as helical polymers. To explain such an anomaly, in this work, we describe how the interplay between the flexibility of the ligand spacer and the number of coordinating atoms involved determines the divergent or convergent organisation of the final coordination architecture.

Single-Crystal Three-Dimensional Covalent Organic Framework Constructed from 6-Connected Triangular Prism Node.

The limited structural diversity of three-dimensional covalent organic frameworks (3D COFs) greatly restricts their application exploration. Therefore, there is an urgent need to expand their library of molecular building blocks, such as the development of highly connected (>4 reaction sites) polyhedral nodes. Herein, by precisely controlling the precursor conformation, we rationally designed a new 6-connected triangular prism node derived from the triphenylbenzene molecule and further used it to construct a novel 3D COF (3D-TMTAPB-COF) via imine condensation reaction. Surprisingly, without the addition of competing reagents, 3D-TMTAPB-COF crystallized directly into single crystals of ∼15 μm in size and was determined to adopt a rare 6-fold interpenetrated (Class IIIa interpenetration) acs topology. In addition, 3D-TMTAPB-COF showed a high SF6 adsorption capacity (60.9 cm3 g-1) and good SF6/N2 selectivity (335) at 298 K and 1 bar, superior to those of most crystalline porous materials. This work not only confirms the possibility of growing large-size single-crystal 3D COFs formed with strong covalent bonds by a solvothermal method in the absence of modulators, but also reports a novel triangular prism node for future construction of 3D COFs with interesting applications.

Evaluation of Robotic Ankle-Foot Orthosis with Different Actuators Using Simscape Multibody for Foot-Drop Patients

Gait cycle plays a major role in human locomotion. Patients with neuromuscular problems are unable to walk normally. Foot drop causes difficulty in lifting the front part of the foot and affects the dorsiflexion (DF) and plantar flexion (PF) motion of the foot. Patient with foot drop must use ankle braces to achieve a normal gait. The existing ankle-foot orthosis (AFO) has its own limitations, as it does not produce adequate PF motion. To overcome this scenario, a study was conducted to analyse the two-degrees-of-freedom (DOF) motion of a robotic ankle foot orthosis (RAFO) with a spring-based series elastic actuator (SEA) and scissor actuator. The objective of this paper is to evaluate the two DOF of RAFO with two different actuators using simscape multibody. The RAFO with actuators were designed using Solidworks, and simulation was carried out using simscape multibody, to analyse the 2-DOF motion. The dynamic motion analysis was carried out using block libraries, bodies, joints, constraints, revolute joints, sensors and a proportional integral (PI) controller. From the simulation results, the total range of motion (ROM) 40° (PF angle of –25° and DF angle of 15°) is achieved by the proposed RAFO with different actuators. Further, based on the results, the input power consumption of spring-based SEA was found to be less than the scissor actuator. Similarly, torque and output power generation of the scissor actuator was found to be greater than spring-based SEA to achieve the normal human ROM. Hence, the designer can choose a hybrid actuator for foot-drop-disorder applications.

Large-Scale Synthesis of Covalent Organic Frameworks: Challenges and Opportunities.

Connecting organic building blocks by covalent bonds to design porous crystalline networks has led to covalent organic frameworks (COFs), consequently transferring the flexibility of dynamic linkages from discrete architectures to extended structures. By virtue of the library of organic building blocks and the diversity of dynamic linkages and topologies, COFs have emerged as a novel field of organic materials that propose a platform for tailor-made complex structural design. Progress over the past two decades in the design, synthesis, and functional exploration of COFs in diverse applications successively established these frameworks in materials chemistry. The large-scale synthesis of COFs with uniform structures and properties is of profound importance for commercialization and industrial applications; however, this is in its infancy at present. An innovative designing and synthetic approaches have paved novel ways to address future hurdles. This review article highlights the fundamental of COFs, including designing principles, coupling reactions, topologies, structural diversity, synthetic strategies, characterization, growth mechanism, and activation aspects of COFs. Finally, the major challenges and future trends for large-scale COF fabrication are outlined.

FRAGMENTISE: A user-friendly, cross-platform tool to create and analyze comprehensive small-molecule fragment databases.

The ongoing COVID-19 pandemic, and constant demand for new therapies in unmet clinical needs, necessitates strategies to identify drug candidates for rapid clinical deployment. Over the years, fragment-based drug design (FBDD) has emerged as a mainstream lead discovery strategy in academia, biotechnology start-ups, and large pharma. Chemical building block libraries are the fundamental component of virtually any FBDD campaign. Current trends focus on smaller and smarter libraries that offer synthetically amenable starting points for rational lead generation. Therefore, there remains an ever-increasing need for new methods to generate fragment libraries to seed early-stage drug discovery programs. Here, we present FRAGMENTISE-a new user-friendly, cross-platform tool for user-tunable retrosynthetic small-molecule fragmentation. FRAGMENTISE allows for visualization, similarity search, annotation, and in-depth analysis of the fragment databases in the medicinal chemistry context. FRAGMENTISE is available as standalone software for Linux, Windows, and macOS users, with a graphical interface or command-line version.

Scaling superconducting quantum chip with highly integratable quantum building blocks

Designing and fabricating large-scale superconducting quantum chips with increasing number of qubits is a pressing challenge for the quantum computing. Here, we propose a three-dimensional stacked chip architecture comprised with quantum building blocks. In which, two primary types of blocks are the qubit block and the coupling block. They are designed as functional parts that can be utilized within the same footprint across multiple levels of the chip stack in the vertical direction. Common technological problems, such as the sensitivity of capacitors and coupling strengths to fabrication parameters, and dielectric losses from interfaces, can be addressed at the intra-block or block level efficiently. Once a library of standard blocks is designed and verified, they can be selected and arranged into arrays on chips at the placing stage of the design flow for specific quantum applications. Such chip structure and design protocol will reduce the design difficulty, and promote the reuse of standard blocks, thus paving the way for chips for noisy intermediate-scale quantum computing and quantum error correction.

PaPILO: A Parallel Presolving Library for Integer and Linear Optimization with Multiprecision Support

Presolving has become an essential component of modern mixed integer program (MIP) solvers, both in terms of computational performance and numerical robustness. In this paper, we present PaPILO, a new C++ header-only library that provides a large set of presolving routines for MIP and linear programming problems from the literature. The creation of PaPILO was motivated by the current lack of (a) solver-independent implementations that (b) exploit parallel hardware and (c) support multiprecision arithmetic. Traditionally, presolving is designed to be fast. Whenever necessary, its low computational overhead is usually achieved by strict working limits. PaPILO’s parallelization framework aims at reducing the computational overhead also when presolving is executed more aggressively or is applied to large-scale problems. To rule out conflicts between parallel presolve reductions, PaPILO uses a transaction-based design. This helps to avoid both the memory-intensive allocation of multiple copies of the problem and special synchronization between presolvers. Additionally, the use of Intel’s Threading Building Blocks library aids PaPILO in efficiently exploiting recursive parallelism within expensive presolving routines, such as probing, dominated columns, or constraint sparsification. We provide an overview of PaPILO’s capabilities and insights into important design choices. History: Accepted by Ted Ralphs, Area Editor for Software Tools. Funding: This work has been financially supported by Research Campus MODAL, funded by the German Federal Ministry of Education and Research [Grants 05M14ZAM, 05M20ZBM], and the European Union’s Horizon 2020 research and innovation programme under grant agreement No 773897 (plan4res). The content of this paper only reflects the author’s views. The European Commission / Innovation and Networks Executive Agency is not responsible for any use that may be made of the information it contains. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2022.0171 ), as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2022.0171 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .

Transmission line fault analysis using actuating relays and Atmega 328P controller

<span lang="EN-US">Since transmission lines account for 80–86% of power system problems, protecting transmission lines is a critical concern. This research proposes a method to identify and categorize various short circuit defects on transmission lines. Various operational and fault circumstances on the transmission of high voltage lines, including L-L fault, single phase to earth fault, and double line fault, double line Three fault scenarios triple line fault, triple line to ground fault, and triple line are simulated using MATLAB software. These flaws damage the linked devices to the power grid. The main motto of this work is to analyze various kinds of faults and also to detect the type of the fault in transmission line. In order to simulate and evaluate the various faults, a 100 km transmission line model was created. A sim power system block library had a fault block, and the harmonic content of the various faults was studied using the FFT tool, the effect of faults was observed. Based on the analysis, a hardware model is designed to identify the faults in transmission line using actuating relays and Atmega 328P microcontroller and display the fault type and parameters like fault impedance, and distance at which fault occurred.</span>

A data-driven interpretation of the stability of organic molecular crystals.

Due to the subtle balance of intermolecular interactions that govern structure-property relations, predicting the stability of crystal structures formed from molecular building blocks is a highly non-trivial scientific problem. A particularly active and fruitful approach involves classifying the different combinations of interacting chemical moieties, as understanding the relative energetics of different interactions enables the design of molecular crystals and fine-tuning of their stabilities. While this is usually performed based on the empirical observation of the most commonly encountered motifs in known crystal structures, we propose to apply a combination of supervised and unsupervised machine-learning techniques to automate the construction of an extensive library of molecular building blocks. We introduce a structural descriptor tailored to the prediction of the binding (lattice) energy and apply it to a curated dataset of organic crystals, exploiting its atom-centered nature to obtain a data-driven assessment of the contribution of different chemical groups to the lattice energy of the crystal. We then interpret this library using a low-dimensional representation of the structure-energy landscape and discuss selected examples of the insights into crystal engineering that can be extracted from this analysis, providing a complete database to guide the design of molecular materials.

Rad-hard RISC-V SoC and ASIP ecosystems studies for high-energy physics applications

The increase in complexity and size of modern ASIC designs in the HEP community and the use of advanced semiconductor fabrication processes raises the need for a shift toward a more abstract design methodology, that takes advantage of modularity and programmability to achieve a faster turnaround time both for design and verification. This contribution will present two complementary approaches, one using a RISC-V based System-on-Chip (SoC) and the other based on Application-Specific Instruction set Processors (ASIP). The SoC uses the PicoRV32 open-source RISC-V core and a rad-hard version of the AMBA APB bus to connect peripherals and is primarily geared towards control and monitoring applications. This solution is a demonstrator of what can become a more complete fully radiation-tolerant SoC platform with a standardized interconnect and an IP block library, to serve as the starting point for future ASIC designs. The ASIP based approach targets more the design of data path elements and the use in data processing applications. The presented approach makes use of a commercial ASIP Designer EDA tool to demonstrate an integrated workflow to define, benchmark and optimize an ASIP for a specific use case, starting from a general-purpose processor.

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations.

We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools.

The BioExcel Building Blocks (BioBB) library offers a broad collection of wrappers on top of common biomolecular simulation and bioinformatics tools. The possibility to access the library remotely and programmatically increases its usability, allowing individual and sporadic executions and enabling remote workflows. BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, voiding the need for tool installation. All the information related to the BioBB REST API endpoints is accessible from https://mmb.irbbarcelona.org/biobb-api/. Links to extended documentation, including OpenAPI endpoints specification and examples, Read-The-Docs documentation and a complete workflow tutorial can be found in the Supplementary Table S1. Supplementary data are available at Bioinformatics online.

PID Controller tuning by Virtual Commissioning - a step to Industry 4.0

This paper deals with the validation of the concept of using virtual commissioning of the low-level industrial control systems to adjust PID controller settings. General hardware configurations and logical layers of the experimental setups, which were used during the experiments, are shown and described in details. It is shown how to determine the controller settings using pre-tuning and fine-tuning functionality, available in standard Siemens® Function Blocks Library, that have been launched in virtual commissioning environment. Comparison of the results is a basis to answer the question if the modern virtual commissioning tools currently used in industry have sufficient accuracy to be used as a master tool for the initial PID controller tuning. It is also important to know whether these systems are suitable for use as Industry 4.0 tools, as the simulation is one of its most important part. The first section in your paper

A functional block decomposition method for automatic op-amp design

This paper presents a method to decompose an op-amp into its functional blocks. The method is able to recognize functional blocks on a high level of abstraction, such as loads or amplification stages, which have a large set of possible structural implementations. The paper presents a hierarchical library of functional blocks. With increasing hierarchy levels, the structural representation of the functional blocks becomes more variable while its function emerges. We use the hierarchical order to automatically compute the functional decomposition of an op-amp given as a flat netlist. Experimental results illustrate the method. The functional block decomposition enables a comprehensive formalization of design knowledge for computer-aided design of op-amps. An overview is given how the method is applicable to circuit sizing and structural synthesis of op-amps.

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

AbstractWe introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. The concept is implemented and demonstrated with the BioExcel Building Blocks library (BioBB), a collection of tool wrappers in the field of computational biomolecular simulation. Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow, built using this library and run with 5 different Workflow Manager Systems (WfMS). We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research (CWFR) in order to improve widespread adoption and reuse of computational methods across workflow language barriers.

Comparison of Methods to Select Candidates for High-Density Genotyping; Practical Observations in a Cattle Breeding Program

Imputation can be used to obtain a large number of high-density genotypes at the cost of procuring low-density panels. Accurate imputation requires a well-formed reference population of high-density genotypes to enable statistical inference. Five methods were compared using commercial Wagyu genotype data to identify individuals to produce a “well-formed” reference population. Two methods utilised a relationship matrix (MCG and MCA), two of which utilised a haplotype block library (AHAP2 and IWS), and the last selected high influential sires with greater than 10 progeny (PROG). The efficacy of the methods was assessed based on the total proportion of genetic variance accounted for and the number of haplotypes captured, as well as practical considerations in implementing these methods. Concordance was high between the MCG and MCA and between AHAP2 and IWS but was low between these groupings. PROG-selected animals were most similar to MCA. MCG accounted for the greatest proportion of genetic variance in the population (35%, while the other methods accounted for approximately 30%) and the greatest number of unique haplotypes when a frequency threshold was applied. MCG was also relatively simple to implement, although modifications need to be made to account for DNA availability when running over a whole population. Of the methods compared, MCG is the recommended starting point for an ongoing sequencing project.