State of the Art of Molecular Visualization in Immersive Virtual Environments

Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head-mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.     

Recent Advances on High-Speed and Holographic Two-Photon Direct Laser Writing

Two-Photon Lithography, thanks to its very high sub-diffraction resolution, has become the lithographic technique par excellence in applications requiring small feature sizes and complex 3D pattering. Despite this, the fabrication times required for extended structures remain much longer than those of other competing techniques (UV mask lithography, nanoimprinting, etc.). Its low throughput prevents its wide adoption in industrial applications. To increase it, over the years different solutions have been proposed, although their usage is difficult to generalize and may be limited depending on the specific application. A promising strategy to further increase the throughput of Two-Photon Lithography, opening a concrete window for its adoption in industry, lies in its combination with holography approaches: in this way it is possible to generate dozens of foci from a single laser beam, thus parallelizing the fabrication of periodic structures, or to engineer the intensity distribution on the writing plane in a complex way, obtaining 3D microstructures with a single exposure. Here, the fundamental concepts behind high-speed Two-Photon Lithography and its combination with holography are discussed, and the literary production of recent years that exploits such techniques is reviewed, and contextualized according to the topic covered.     

Bacteria-Responsive Self-Assembly of Antimicrobial Peptide Nanonets for Trap-and-Kill of Antibiotic-Resistant Strains

Bacterial trapping using nanonets is a ubiquitous immune defense mechanism against infectious microbes. These nanonets can entrap microbial cells, effectively arresting their dissemination and rendering them more vulnerable to locally secreted microbicides. Inspired by this evolutionarily conserved anti-infective strategy, a series of 15 to 16 residue-long synthetic β-hairpin peptides is herein constructed with the ability to self-assemble into nanonets in response to the presence of bacteria, enabling spatiotemporal control over microbial killing. Using amyloid-specific K114 assay and confocal microscopy, the membrane components lipoteichoic acid and lipopolysaccharide are shown to play a major role in determining the amyloid-nucleating capacity as triggered by Gram-positive and Gram-negative bacteria respectively. These nanonets displayed both trapping and killing functionalities, hence offering a direct improvement from the trap-only biomimetics in literature. By substituting a single turn residue of the non-amyloidogenic BTT1 peptide, the nanonet-forming BTT1-3A analog is produced with comparable antimicrobial potency. With the same sequence manipulation approach, BTT2-4A analog modified from BTT2 peptide showed improved antimicrobial potency against colistin-resistant clinical isolates. The peptide nanonets also demonstrated robust stability against proteolytic degradation, and promising in vivo efficacy and biosafety profile. Overall, these bacteria-responsive peptide nanonets are promising clinical anti-infective alternatives for circumventing antibiotic resistance.     

Deterministic Polymorphic Engineering of MoTe2 for Photonic and Optoelectronic Applications

Developing selective and coherent polymorphic crystals at the nanoscale offers a novel strategy for designing integrated architectures for photonic and optoelectronic applications such as metasurfaces, optical gratings, photodetectors, and image sensors. Here, a direct optical writing approach is demonstrated to deterministically create polymorphic 2D materials by locally inducing metallic 1T′-MoTe₂ on the semiconducting 2H-MoTe₂ host layer. In the polymorphic-engineered MoTe₂, 2H- and 1T′- crystalline phases exhibit strong optical contrast from near-infrared to telecom-band ranges (1–1.5 µm), due to the change in the band structure and increase in surface roughness. Sevenfold enhancement of third harmonic generation intensity is realized with conversion efficiency (susceptibility) of ≈1.7 × 10⁻⁷ (1.1 × 10⁻¹⁹ m² V⁻²) and ≈1.7 × 10⁻⁸ (0.3 × 10⁻¹⁹ m² V⁻²) for 1T′ and 2H-MoTe₂, respectively at telecom-band ultrafast pump laser. Lastly, based on polymorphic engineering on MoTe₂, a Schottky photodiode with a high photoresponsivity of 90 AW⁻¹ is demonstrated. This study proposes facile polymorphic engineered structures that will greatly benefit realizing integrated photonics and optoelectronic circuits.     

New approach for optimizing the interpretation and representation of the degree of historical-archaeological evidence in the virtual reconstructions

Virtual Reality - Virtual reconstruction is defined as the visual recovery of a building or object through the creation of a three-dimensional model of the asset to be reconstructed, in a...     

Fuzzy Adaptive Control Law for Trajectory Tracking Based on a Fuzzy Adaptive Neural PID Controller of a Multi-rotor Unmanned Aerial Vehicle

International Journal of Control, Automation and Systems - This article presents a fuzzy adaptive control law (FACL) designed for tracking the trajectory of a low-scale unmanned aerial vehicle...     

Optimal Control of Nonlinear Systems Using Experience Inference Human-Behavior Learning

Safety critical control is often trained in a simulated environment to mitigate risk. Subsequent migration of the biased controller requires further adjustments. In this paper, an experience inference human-behavior learning is proposed to solve the migration problem of optimal controllers applied to real-world nonlinear systems. The approach is inspired in the complementary properties that exhibits the hippocampus, the neocortex, and the striatum learning systems located in the brain. The hippocampus defines a physics informed reference model of the real-world nonlinear system for experience inference and the neocortex is the adaptive dynamic programming (ADP) or reinforcement learning (RL) algorithm that ensures optimal performance of the reference model. This optimal performance is inferred to the real-world nonlinear system by means of an adaptive neocortex/striatum control policy that forces the nonlinear system to behave as the reference model. Stability and convergence of the proposed approach is analyzed using Lyapunov stability theory. Simulation studies are carried out to verify the approach.      

Impact of white-matter mask selection on DTI histogram-based metrics as potential biomarkers in cerebral small vessel disease

Magnetic Resonance Materials in Physics, Biology and Medicine - Histogram-based metrics extracted from diffusion-tensor imaging (DTI) have been suggested as potential biomarkers for cerebral small...     

Multimedia ontology population through semantic analysis and hierarchical deep features extraction techniques

Knowledge and Information Systems - The rapid increase of available data in different complex contexts needs automatic tasks to manage and process contents. Semantic Web technologies represent the...     

Design and implementation of efficient QCA full-adders using fault-tolerant majority gates

The Journal of Supercomputing - CMOS technology is facing physical limitations in scaling the manufacturing process. Therefore, to deepen the development of better designs in a smaller area, it is...