Atomic Building Blocks Research Articles

Status and Prospects of Research on Deep Learning-based De Novo Generation of Drug Molecules.

Traditional molecular de novo generation methods, such as evolutionary algorithms, generate new molecules mainly by linking existing atomic building blocks. The challenging issues in these methods include difficulty in synthesis, failure to achieve desired properties, and structural optimization requirements. Advances in deep learning offer new ideas for rational and robust de novo drug design. Deep learning, a branch of machine learning, is more efficient than traditional methods for processing problems, such as speech, image, and translation. This study provides a comprehensive overview of the current state of research in de novo drug design based on deep learning and identifies key areas for further development. Deep learning-based de novo drug design is pivotal in four key dimensions. Molecular databases form the basis for model training, while effective molecular representations impact model performance. Common DL models (GANs, RNNs, VAEs, CNNs, DMs) generate drug molecules with desired properties. The evaluation metrics guide research directions by determining the quality and applicability of generated molecules. This abstract highlights the foundational aspects of DL-based de novo drug design, offering a concise overview of its multifaceted contributions. Consequently, deep learning in de novo molecule generation has attracted more attention from academics and industry. As a result, many deep learning-based de novo molecule generation types have been actively proposed.

Two-dimensional material templates for van der Waals epitaxy, remote epitaxy, and intercalation growth

Epitaxial growth, a crystallographically oriented growth induced by the chemical bonding between crystalline substrate and atomic building blocks, has been a key technique in the thin-film and heterostructure applications of semiconductors. However, the epitaxial growth technique is limited by different lattice mismatch and thermal expansion coefficients of dissimilar crystals. Two-dimensional (2D) materials with dangling bond-free van der Waals surfaces have been used as growth templates for the hetero-integration of highly mismatched materials. Moreover, the ultrathin nature of 2D materials also allows for remote epitaxial growth and confinement growth of quasi-2D materials via intercalation. Here, we review the hetero-dimensional growth on 2D substrates: van der Waals epitaxy (vdWE), quasi vdWE, and intercalation growth. We discuss the growth mechanism and fundamental challenges for vdWE on 2D substrates. We also examine emerging vdWE techniques that use epitaxial liftoff and confinement epitaxial growth in detail. Finally, we give a brief review of radiation effects in 2D materials and contrast the damage induced with their 3D counterparts.

Dissipative discrete time crystals in a pump-modulated Kerr microcavity

Time crystals represent temporal analogues of the spatial self-ordering exhibited by atomic or molecular building blocks of solid-state crystals. The pursuit of discrete time crystals (DTCs) in periodically forced Floquet closed systems has revealed how they can evade thermalization and loss of temporal order. Recently, it has been shown that even with coupling to the ambient and its concomitant noise, some states maintain their time crystalline order, forming dissipative DTCs. Here, we introduce a scheme for the realization and state control of dissipative DTCs hinging on pumping a Kerr optical resonator with a phase-modulated continuous-wave laser. We show the possible symmetry breaking states possess temporal long-range order and analyze the phase noise of the accompanying signature radio frequency (RF) subharmonic. Besides offering a technique for generating high-spectral-purity RF signals, this versatile platform empowers controlled switching between various DTC states through accessible experimental knobs, hence facilitating the future study of DTC phase transitions.

A Data-driven Approach for General Visual Quality Control in a Robotic Workcell

Setting up computer vision quality control tasks in a robot workcell is expensive, time consuming, and often requires expert knowledge. In this work, a highly adaptable approach to mitigate this issue is introduced. First, an ontology of atomic building blocks is defined, where each block represents one computer vision algorithm. Second, these blocks are used to generate a complex graph structure. The generation follows a set of rules, which can be shown to the inexperienced worker as a list of simple questions. Afterwards, this graph can be refined. Finally, the graph is integrated into the robotic assembly sequence, and the visual quality control procedure can be executed. Two industrial use cases show the feasibility of this approach. Thus, this work leverages computer vision aided quality control tasks in robot workcells.

Broadband microwave spectroscopy of semiconductor nanowire-based Cooper-pair transistors

The Cooper-pair transistor (CPT), a small superconducting island enclosed between two Josephson weak links, is the atomic building block of various superconducting quantum circuits. Utilizing gate-tunable semiconductor channels as weak links, the energy scale associated with the Josephson tunneling can be changed with respect to the charging energy of the island, tuning the extent of its charge fluctuations. Here, we directly demonstrate this control by mapping the energy level structure of a CPT made of an indium arsenide nanowire (NW) with a superconducting aluminum shell. We extract the device parameters based on the exhaustive modeling of the quantum dynamics of the phase-biased nanowire CPT and directly measure the even-odd parity occupation ratio as a function of the device temperature, relevant for superconducting and prospective topological qubits.

Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an “on/off”-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system’s π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

On the Possibility of Using the Jellium Model as a Guide To Design Bimetallic Superalkali Cations.

The potential application of the jellium model as guidance in the rational design of bimetallic superalkali cations is examined under gradient-corrected density functional theory for the first time. By using Li, Mg, and Al as atomic building blocks, a series of bimetallic cationic clusters with 2, 8, 20, and 40 valence electrons are obtained and investigated. As the corresponding neutral clusters tend to lose one valence electron to achieve closed-shell states in the jellium model, these studied cations exhibit much lower vertical electron affinities (EAvert , 3.42-4.95 eV) than the ionization energies (IEs) of alkali metal atoms, indicating their superalkali identities. The high stability of these cationic clusters is guaranteed by their considerable HOMO-LUMO gaps and binding energies per atom. Moreover, the feasibility of using the designed superalkalis as efficient reductants to activate CO2 and N2 molecules and as stable building blocks to assemble ionic superatom compounds is explored. Therefore, this study may provide an effective method for obtaining various metallic superatoms with extensive applications on the basis of the simple jellium rule.

Variability in the Syntax of Idioms

Given that the meaning of idioms is not predictable from the literal meaning of their parts, we can broadly define idioms as expressions with a non-compositional interpretation. Since language is a compositional system, this characteristic of idioms might suggest that they are atomic building blocks of language with no internal syntax. However, that turns out not to be the case. This paper explores the syntax of English verbal idioms and their degree of compositionality. Idioms do have an internal syntactic structure that is actually variable to an extent and, despite being superficially similar, different idioms exhibit different syntactic properties. The topics discussed include the variability of determiners in idioms, the subcategorisation of idioms based on their relative compositionality into two groups that behave differently with respect to their syntactic flexibility, and the identification of grammatical categories that are obligatory components of certain idioms but not others.

Exploring Biological Motion Regularities of Human Actions

The ability to detect potentially interacting agents in the surrounding environment is acknowledged to be one of the first perceptual tasks developed by humans, supported by the ability to recognise biological motion. The precocity of this ability suggests that it might be based on rather simple motion properties, and it can be interpreted as an atomic building block of more complex perception tasks typical of interacting scenarios, as the understanding of non-verbal communication cues based on motion or the anticipation of others’ action goals. In this article, we propose a novel perspective for video analysis, bridging cognitive science and machine vision, which leverages the use of computational models of the perceptual primitives that are at the basis of biological motion perception in humans. Our work offers different contributions. In a first part, we propose an empirical formulation for the Two-Thirds Power Law , a well-known invariant law of human movement, and thoroughly discuss its readability in experimental settings of increasing complexity. In particular, we consider unconstrained video analysis scenarios, where, to the best of our knowledge, the invariant law has not found application so far. The achievements of this analysis pave the way for the second part of the work, in which we propose and evaluate a general representation scheme for biological motion characterisation to discriminate biological movements with respect to non-biological dynamic events in video sequences. The method is proposed as the first layer of a more complex architecture for behaviour analysis and human-machine interaction, providing in particular a new way to approach the problem of human action understanding.

A Transformation Framework Proposal for Managers in Business Innovation and Business Transformation Projects-An Information System's Atomic Architecture Vision

Abstract A fundamental architecture element in transforming a traditional business environment and its business information system into an innovative automated and lean business platform is the role of the information system's building vision; that should be crafted in an applicable framework. This framework should include easy to integrate patterns. The proposed just-in-time framework can change the information system's architecture and its implementation outcomes. The atomic information system architecture's role and applied the patterns are of crucial importance for the implementation phase of the complex business transformation projects; where these patterns can be adapted in a just-in-time manner, using atomic building blocks1,2,26. There is also a need to govern (or control) the atomic information system architecture's patterns for business transformation projects; unfortunately an adaptable atomic information system architecture pattern for such projects is inexistent. An atomic information system architecture pattern can be also used in the enterprise's production activities which comes after the finalization of the implementation phase of business transformation project (business transformation project), to control and govern the resultant business system. The atomic information system architecture's pattern main component is the atomic building block that manages the implementation of autonomous business service transactions. In this article the author presents a set of atomic information system architecture recommendations in the form of reusable patterns to promote an optimal information system's architecture.

A Transformation Framework Proposal for Managers in Business Innovation and Business Transformation Projects-intelligent Atomic Building Block Architecture

Today's dynamic global economy forces business companies to struggle for survival; where such companies must be competitive and loosely interconnected in a wide networked business market. It is not a secret that a solid business environment that wants to insure its sustainable business future must adapt itself to frequent business transformation processes, to adapt to such a situation a building block based solution is proposed to support the business transformation project. Such a building block strategy for frequent business transformation changes is translated in a set of recommendations that support the company's business resources in order to optimize the companies’ various business and information technology resources. Unfortunately, most of business transformation projects fail, because of the very difficult business transformation project's “decoupled and technical” implementation or re-engineering phase. The author recommend a re-engineering phase that is based on atomic building blocks architecture; where the business transformation manager must have the right skills to model and prototype the most important Atomic Business Blocks, in order to insure the successes of business transformation projects. It is recommended to apply the adequate atomic business architecture and the needed modeling concepts. Such concepts are based on a one to one mapping pattern that is in turn based on enterprise architecture standards. Business transformation projects should apply an Atomic Business Blocks driven implementation phase that will help the implementation capability of the business transformation project; such an approach needs a specific a set of integration, modeling and prototyping skills 1,2,3 .

A compact microstrip rat-race coupler constituted by nonuniform transmission lines

In this work, a step-by-step development of a compact microstrip rat-race coupler (RRC) has been presented and discussed. A high degree of miniaturization has been obtained by substituting six quarter-wavelength uniform atomic building blocks of a RRC by their nonuniform counterparts. The miniaturization procedure has been real- ized in three progressive steps: (i) the first layout solution of a miniatur- ized RRC has been acquired using an accurate mathematical model of a nonuniform transmission line (NUTL); (ii) the second layout solution has been obtained by a manual refinement and electro-magnetic (EM) fine-tuning of the NUTL geometry aimed at the utilization of the interior of the RRC in a highly efficient manner; (iii) the final layout, occupying only 8.5% estate area in comparison to a conventional RRC, is the result of the EM optimization. The experimental results confirm the theo- retical predictions, proving the vital usefulness of the approach. V C 2014

Atomic Structure of the Anatase TiO2(001) Surface

Understanding the structure of well-defined anatase TiO2 surfaces is critical for deciphering site-specific thermal and photoreaction mechanisms on anatase TiO2. Using ultrahigh vacuum scanning tunneling microscopy (STM), we have studied the atomic structure of anatase TiO2(001) epitaxial thin films grown by oxygen plasma assisted molecular beam epitaxy. Bright rows of the (1×4) reconstructed surface are resolved as three types of features with different sizes. High-resolution STM images taken from the same area at different bias voltages show that these individual features are originated from combinations of two basic atomic building blocks. We propose a modified added molecule model for the anatase TiO2(001) surface structure.

Little Things With Big Effects

Error diagnosis in ICALL typically analyzes learner input in an attempt to abstract and identify indicators of the learner's (mis)conceptions of linguistic properties. For written input, this process usually starts with the identification of tokens that will serve as the atomic building blocks of the analysis. In this paper, we discuss the consequences of mismatches between the learner's perception of a given token and the system's interpretation of its linguistic properties. Based on our analysis of the interaction of beginning learners of Portuguese with the ICALL system TAGARELA, we discuss why tokenization and the interpretation of accented characters deserve particular attention in a system used by language learners. On the computational side, we argue that the mismatches arising in such cases can be addressed in a general way by building ICALL systems on an annotation-based natural language processing architecture which monotonically enriches the representation of learner input.

New approach to a fast and accurate design of microwave circuits with complex topologies

A robust simulation-driven design methodology of microwave circuits with complex topologies has been presented. The general method elaborated is suitable for a wide class of N-port unconventional microwave circuits constructed as a deviation from classic design solutions. The key idea of the approach proposed lies in an iterative redesign of a conventional circuit by a sequential modification and optimisation of its atomic building blocks. The speed and accuracy of the method presented has been acquired by solving a number of simple optimisation problems through surrogate-based optimisation (SBO) techniques, which offer a satisfactory approximation of the optimal design solution. Two exemplary designs have been supplied to verify the method introduced. An abbreviated wideband quarter-wave impedance matching transformer and a miniaturised hybrid branch–line coupler have been developed. Diminished dimensions of the circuits under construction have been achieved by means of compact microstrip resonant cells. As an SBO engine, an implicit space mapping technique has been utilised. The final results have been acquired in only a fraction of time that is necessary for a direct electromagnetic (EM) optimisation to generate competitive results. An experimental validation of the method proving its high utility has been provided.

FUNCTIONAL APPROXIMATION IN MULTISCALE COMPLEX SYSTEMS

One common approach for exploring, approximating and estimating complex system dynamics refers to models based on elementary or atomic building block components of easier interpretation and efficient computation. We adopt a combination of wavelets, greedy approximation and subspace techniques to investigate complex systems such as speculative financial markets. These systems are endowed with multiscale and non-stationary dynamics that we aim to artificially learn by using functional approximation and optimization theory. We show that volatility dynamics are embedded in a sequence of nested informative scales and thus a multiscale estimation approach is indicated to deal with them.

Atomic nature of reconstructed Si(110).

Using scanning tunneling microscopy (STM) we have measured constant-current topographies of reconstructed Si(110). While low-energy-electron diffraction (LEED) showed a 4\ifmmode\times\else\texttimes\fi{}5 pattern with dominant 2\ifmmode\times\else\texttimes\fi{}1 contributions, in STM a 2\ifmmode\times\else\texttimes\fi{}5 periodicity of atomic building blocks is observed. These building blocks are arranged in the form of chains along [\ifmmode\bar\else\textasciimacron\fi{}110]-like directions and show a tendency to pairing, which accounts for the 4\ifmmode\times\else\texttimes\fi{}5 LEED results. The 2\ifmmode\times\else\texttimes\fi{}1 reconstruction, which was previously ascribed to a high-temperature phase of Si(110), is explained by a reduction of chain length caused by the generation of defects with increasing temperature.