Game on, science - how video game technology may help biologists tackle visualization challenges

Dy-SheHeRASADe: A representation of the β sheet dynamics through surface descriptors

Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories. Appropriate visualization of MD trajectories is becoming essential to provide an immediate and intuitive understanding of a molecule's dynamics and function. In this study, we implement a novel 3D graphical representation, Dynamical Sheets Helper for RepresentAtion of SurfAce Descriptors (Dy-SheHeRASADe), to visualize the β sheet secondary structures of proteins in the context of molecular dynamics. Dy-SheHeRASADe is developed in UnityMol, an open source molecular viewer and prototyping platform. We considered β sheet fluctuations and hydrogen bond formation during molecular dynamics simulations to characterize the parts of β sheets with large motions or with labile bonds. We propose two visualization modes based on a surface representation of the β sheets calculated according to the positions of the α carbons and the hydrogen bonds between the β strands. The volumetric mode, in which this surface is enclosed in a semi-transparent volume that represents the fluctuation zone of the sheet during dynamics. The heatmap mode, in which the surface is colored according to the amplitude values of the α carbons. In addition, we quantify the β sheet fluctuations by displaying the values of the largest and smallest movements of the β sheets, the surface area of the sheets, and the number of hydrogen bonds.

MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform

Computer-based tools for visualizing and manipulating molecular structures in real-time hold immense potential for accelerating research and improving education, but are only used to a limited extent. This paper explores the possibilities of these powerful techniques and presents a classification of common interactive modeling tasks, such as assembly, deformation, sampling of rare events, along with relevant use cases, especially for the study of membranes and membrane proteins. I introduce MolPlay─a platform that provides a ready-to-use software environment with a curated set of hands-on examples to democratize access to interactive molecular simulations and analyses (IMSA). These research tools allow researchers to visualize, manipulate, and study digital models of molecules in real-time and can be started directly from a small, portable storage device. The portable, self-contained nature of MolPlay enables versatile deployment scenarios ranging from outreach to teaching in computer laboratories to facilitating the distribution of research software. Initial tests at an international workshop have shown that MolPlay appeals to different target groups and lowers the access barriers to IMSA. By consolidating more than a decade of expertise into one accessible platform, MolPlay represents a significant step toward broader adoption of these underutilized but powerful computational techniques in education and research.

From complex data to clear insights: visualizing molecular dynamics trajectories

Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities

The industry's transition from three-dimensional (3D) glasses to virtual reality (VR) headsets has left modelers stranded without hardware supply, since walking around and waving arms in a virtual world is a great experience but also very tiring when doing time-intensive modeling work. We present a novel software implementation that uses a VR headset while sitting at a desk in front of the normal screen, which is beamed into the virtual reality together with keyboard, mouse, and chair using the headset's cameras and an extra tracker attached to the seat-back. Compared to 3D glasses, this yields a comparably relaxing but much more immersive workplace and provides additional possibilities such as taking molecules into one's hands, standing up, and walking or teleporting through the models. This VR functionality has been combined with a molecular graphics engine based on Vulkan, a next-generation cross-platform application programming interface (API) for GPUs and the successor of the widely used Open Graphics Library (OpenGL). It is built into the YASARA Model program, which includes many features like small and large molecule builders, electron densities, partial surfaces, contact analysis, coordinate manipulation, and animations. Interactive tutorials are provided to guide modelers into VR and familiarize them with the molecular modeling features. YASARA Model is available for Linux, Windows, Android, and MacOS (the latter without VR) with an introductory video at www.YASARA.org/vr.

First-principle study of Cu-, Ag-, and Au-decorated Si-doped carbon quantum dots (Si@CQD) for CO2 gas sensing efficacies

CONTEXT

Nanosensor materials for the trapping and sensing of CO₂ gas in the ecosystem were investigated herein to elucidate the adsorption, sensibility, selectivity, conductivity, and reactivity of silicon-doped carbon quantum dot (Si@CQD) decorated with Ag, Au, and Cu metals. The gas was studied in two configurations on its O and C sites. When the metal-decorated Si@CQD interacted with the CO₂ gas on the C adsorption site of the gas, there was a decrease in all the interactions with the lowest energy gap of 1.084 eV observed in CO₂_C_Cu_Si@CQD followed by CO₂_C_Au_Si@CQD which recorded a slightly higher energy gap of 1.094 eV, while CO₂_C_Ag_Si@CQD had an energy gap of 2.109 eV. On the O adsorption sites, a decrease was observed in CO₂_O_Au_Si@CQD which had the least energy gap of 1.140 eV, whereas there was a significant increase after adsorption in CO₂_O_Ag_Si@CQD and CO₂_O_Cu_Si@CQD with calculated ∆E values of 2.942 eV and 3.015 eV respectively. The adsorption energy alongside the basis set supposition error (BSSE) estimation reveals that CO₂_C_Au_Si@CQD, CO₂_C_Ag_Si@CQD, and CO₂_C_Cu_Si@CQD were weakly adsorbed, while chemisorption was present in the CO₂_O_Ag_Si@CQD, CO₂_O_Cu_Si@CQD, and CO₂_O_Au_Si@CQD interactions. Indeed, the adsorption of CO₂ on the different metal-decorated quantum dots affects the Fermi level (E_f) and the work function (Φ) of each of the decorated carbon quantum dots owed to their low E_f values and high ∆Φ% which shows that they can be a prospective work function-based sensor material.

METHODS

Electronic structure theory method based on first-principle density functional theory (DFT) computation at the B3LYP-GD3(BJ)/Def2-SVP level of theory was utilized through the use of the Gaussian 16 and GaussView 6.0.16 software packages. Post-processing computational code such as multi-wavefunction was employed for result analysis and visualization.

Developing virtual and augmented reality applications for science, technology, engineering and math education

The Rhode Island IDeA Network of Biomedical Research Excellence Molecular Informatics Core at the University of Rhode Island Information Technology Services Innovative Learning Technologies developed virtual and augmented reality applications to teach concepts in biomedical science, including pharmacology, medicinal chemistry, cell culture and nanotechnology. The apps were developed as full virtual reality/augmented reality and 3D gaming versions, which do not require virtual reality headsets. Development challenges included creating intuitive user interfaces, text-to-voice functionality, visualization of molecules and implementing complex science concepts. In-app quizzes are used to assess the user's understanding of topics, and user feedback was collected for several apps to improve the experience. The apps were positively reviewed by users and are being implemented into the curriculum at the University of Rhode Island.

Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots

This paper describes the design philosophy for our cloud-based virtual reality (VR) co-creation environment (CCE) for molecular modeling. Using interactive VR simulation can provide enhanced perspectives in molecular modeling for intuitive live demonstration and experimentation in the CCE. Then the use of the CCE can enhance knowledge creation by bringing people together to share and create ideas or knowledge that may not emerge otherwise. Our prototype CCE discussed here, which was developed to demonstrate our design philosophy, has already enabled multiple members to log in and touch virtual molecules running on a cloud server with no noticeable network latency via real-time artificial intelligence techniques. The CCE plays an essential role in the rational design of molecular robot parts, which consist of bio-molecules such as DNA and protein molecules.

A brief history of visualizing membrane systems in molecular dynamics simulations

Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.

Student perceptions toward virtual reality training in dental implant education

Objectives

Both the shortage of professional teaching resources and the expensive dental implant supplies impede the effective training of dental undergraduate in implantology. Virtual reality (VR) technology may provide solutions to solve these problems. This pilot study was implemented to explore the usability and acceptance of a VR application in the training of dental implant among dental students at the Jinan University School of Stomatology.

Methods

We designed and developed a VR system with head-mounted displays (HMDs) to assist dental implant training. Undergraduate dental students were invited to experience a 30-minute "Introduction to dental implants" VR-HMDs training module. A total of 119 dental students participated the training. Firstly, the VR interactive training on dental implant was described, illustrated and practiced. Next, a system usability scale (SUS) survey was used to verify the usability and feasibility of the VR application on training dental students. Finally, the participants were given a questionnaire to provide their perceptions and feedback of the usefulness of the VR application for training dental implant skills.

Results

The SUS score was 82.00 ± 10.79, indicating a top 10 percentage ranking of the system's usabilitys. The participants' answers to the questionnaire reflected most of them exhibited strong interests in the VR system, with a tendency that the female students were more confident than the male in manipulating the VR system. The participants generally acknowledged the usefulness of VR dental implants, ranking VR value above the traditional laboratory operations, and a preference for using the VR system on learning other skills. They also gave valuable suggestions on VR dental implants for substantial improvement. However, some students were not strongly positive about the VR training in this study, the reason might lie in a more theoretical module was selected for testing, which impacted the students' ratings.

Conclusions

In this study we revealed the feasibility and usability of VR applications on training dental implant among undergraduate dental students. This pilot study showed that the participants benefited from the dental implant VR training by practicing the skills repeatedly. The feedback from student participants affirmed the advantages and their acceptance of the VR application in dental education. Especially, the VR-based technology is highly conducive to clinical operating skills and surgical procedures-focused training in medical education, indicating that the VR system should be combined with the traditional practice approach in improving dental students' practical abilities.

Design - a new way to look at old molecules

We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.

How molecular modelling can better broaden the understanding of glycosylations

Glycosylations are among the most ubiquitous post-translational modifications (PTMs) in proteins, and the effects of their perturbations are seen in various diseases such as cancers, diabetes and arthritis to name a few. Yet they remain one of the most enigmatic aspects of protein structure and function. On the other hand, molecular modelling techniques have been rapidly bridging this knowledge gap since the last decade. In this review, we discuss how these techniques have proven to be indispensable for a better understanding of the role of glycosylations in glycoprotein structure and function.

BlockNet: Beyond reliable spatial Digital Twins to Parallel Metaverse

The development of Digital Twins has enabled them to be widely applied to various fields represented by intelligent manufacturing. A Metaverse, which is parallel to the physical world, needs mature and secure Digital Twins technology in addition to Parallel Intelligence to enable it to evolve autonomously. We propose that Blockchain combined with other areas does not simultaneously require all of the basic elements. We extract the immutable characteristics of Blockchain and propose a secure multidimensional data storage solution called BlockNet that can ensure the security of the digital mapping process of the Internet of Things, thereby improving the data reliability of Digital Twins. Additionally, to address some of the challenges faced by multiscale spatial data processing, we propose a nonmutagenic multidimensional Hash Geocoding method, allowing unique indexing of multidimensional information and avoiding information loss due to data dimensionality reduction while improving the efficiency of information retrieval and facilitating the implementation of the Metaverse through spatial Digital Twins based on these two studies.

Wearable Sensors for Vital Signs Measurement: A Survey

With the outbreak of coronavirus disease-2019 (COVID-19) worldwide, developments in the medical field have aroused concerns within society. As science and technology develop, wearable medical sensors have become the main means of medical data acquisition. To analyze the intelligent development status of wearable medical sensors, the current work classifies and prospects the application status and functions of wireless communication wearable medical sensors, based on human physiological data acquisition in the medical field. By understanding its working principles, data acquisition modes and action modes, the work chiefly analyzes the application of wearable medical sensors in vascular infarction, respiratory intensity, body temperature, blood oxygen concentration, and sleep detection, and reflects the key role of wearable medical sensors in human physiological data acquisition. Further exploration and prospecting are made by investigating the improvement of information security performance of wearable medical sensors, the improvement of biological adaptability and biodegradability of new materials, and the integration of wearable medical sensors and intelligence-assisted rehabilitation. The research expects to provide a reference for the intelligent development of wearable medical sensors and real-time monitoring of human health in the follow-up medical field.

Advanced Machine-Learning Methods for Brain-Computer Interfacing

The brain-computer interface (BCI) connects the brain and the external world through an information transmission channel by interpreting the physiological information of the brain during thinking activities. The effective classification of electroencephalogram (EEG) signals is the key to improving the performance of the system. To improve the classification accuracy of EEG signals in the BCI system, the transfer learning algorithm and the improved Common Spatial Pattern (CSP) algorithm are combined to construct a data classification model. Finally, the effectiveness of the proposed algorithm is verified. The results show that in actual and imagined movements, the accuracy of the left- and right-hand movements at different speeds is higher than when the speeds are the same. The proposed Adaptive Composite Common Spatial Pattern (ACCSP) and Self Adaptive Common Spatial Pattern (SACSP) algorithms have good classification effects on 5 subjects, with an average classification accuracy rate of 83.58 percent, which is an increase of 6.96 percent compared with traditional algorithms. When the training sample size is 10, the classification accuracy of the ACCSP algorithm is higher than that of the traditional CSP algorithm. The improved CSP algorithm combined with transfer learning embodies a good classification effect in both ACCSP and SACSP. Especially, the performance of SACSP mode is better. Combining the improved CSP algorithm proposed with the CSP-based transfer learning algorithm can improve the classification accuracy of the BCI classifier.

Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide

Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.

Effects of changes in glycan composition on glycoprotein dynamics: example of N-glycans on insulin receptor

Glycosylation is among the most common post-translational modifications in proteins, although it is observed in only about 10% of all the protein structures in protein data bank (PDB). Modifications of sugar composition in glycoproteins profoundly impact the overall physiology of the organism. One such example is the development of insulin resistance, which has been attributed to the removal of sialic acid residues from N-glycans of insulin receptor (IR) from various experimental studies. How such modifications affect the glycan-glycoprotein dynamics, and ultimately their function is not clearly understood to date. In this study, we performed molecular dynamics simulations of glycans in different environments. We studied the effects of removal of sialic acid on the glycan, as well as on the dynamics of leucine-rich repeat L1 domain of the IR ectodomain. We observed perturbations in L1 domain dynamics as a result of the removal of sialic acid. The perturbations include an increase in the flexibility of insulin-binding residues, which may affect insulin binding with IR. These changes are accompanied by perturbations in glycan-protein interactions and perturbation of long-range allosteric dynamics. Our observations will further aid in understanding the role of sugars in maintaining homeostasis and how changes in glycan composition may lead to perturbations in homeostasis, ultimately leading to conditions such as insulin resistance.

UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments

Motivated by the current COVID-19 pandemic, which has spurred a substantial flow of structural data, the use of molecular-visualization experiences to make these data sets accessible to a broad audience is described. Using a variety of technology vectors related to the cloud, 3D and virtual reality gear, how to share curated visualizations of structural biology, modeling and/or bioinformatics data sets for interactive and collaborative exploration is examined. FAIR is discussed as an overarching principle for sharing such visualizations. Four initial example scenes related to recent COVID-19 structural data are provided, together with a ready-to-use (and share) implementation in the UnityMol software.

An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19

The era of the explosion of immersive technologies has bumped head-on with the coronavirus disease 2019 (COVID-19) global pandemic caused by the severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2). The proper understanding of the three-dimensional structures that compose the virus, as well as of those involved in the infection process and in treatments, is expected to contribute to the advance of fundamental and applied research against this pandemic, including basic molecular biology studies and drug design. Virtual reality (VR) is a powerful technology to visualize the biomolecular structures that are currently being identified for SARS-CoV-2 infection, opening possibilities to significant advances in the understanding of the disease-associate mechanisms and thus to boost new therapies and treatments. The present availability of VR for a large variety of practical applications together with the increasingly easiness, quality and economic access of this technology is transforming the way we interact with digital information. Here, we review the software implementations currently available for VR visualization of SARS-CoV-2 molecular structures, covering a range of virtual environments: CAVEs, desktop software, and cell phone applications, all of them combined with head-mounted devices like cardboards, Oculus Rift or the HTC Vive. We aim to impulse and facilitate the use of these emerging technologies in research against COVID-19 trying to increase the knowledge and thus minimizing risks before placing huge amounts of money for the development of potential treatments.

Game-Like 3D Visualisation of Air Quality Data

The data produced by sensor networks for urban air quality monitoring is becoming a valuable asset for informed health-aware human activity planning. However, in order to properly explore and exploit these data, citizens need intuitive and effective ways of interacting with it. This paper presents CityOnStats, a visualisation tool developed to provide users, mainly adults and young adults, with a game-like 3D environment populated with air quality sensing data, as an alternative to the traditionally passive visualisation techniques. CityOnStats provides several visual cues of pollution presence with the purpose of meeting each user’s preferences. Usability tests with a sample of 30 participants have shown the value of air quality 3D game-based visualisation and have provided empirical support for which visual cues are most adequate for the task at hand.

ProteinVR: Web-based molecular visualization in virtual reality

Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/.

Proteins are microscopic machines that help maintain, defend, and regulate cells. Properly understanding the three-dimensional structures of these machines–as well as the small molecules that interact with them–can advance scientific fields ranging from basic molecular biology to drug discovery. Virtual reality (VR) is a powerful tool for studying protein structures. But many current systems for viewing molecules in VR, though effective, have challenging usability limitations. We have created a new web application called ProteinVR that overcomes these challenges. ProteinVR enables VR molecular visualization in users’ browsers, without requiring them to install a separate program or plugin. It runs on a broad range of desktop, laptop, and mobile devices. For users without VR headsets, ProteinVR leverages mobile-device orientation sensors or video-game-style keyboard navigation to provide an immersive experience. We release ProteinVR as open-source software and have posted a working version at http://durrantlab.com/pvr/.

Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol

N-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of N-glycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions.

Assessment of swimming behavior of the Pacific oyster D-larvae (Crassostrea gigas) following exposure to model pollutants

This study describes an image analysis method that has been used to analyze the swimming behavior of native oyster D-larvae (Crassostrea gigas) from the Arcachon Bay (SW, France). In a second time, this study evaluated the impact of copper and S-metolachlor pollutants on D-larvae swimming activity and the possible relationship between developmental malformations and abnormal swimming behavior. Analyses in wild and cultivated oyster D-larvae were investigated during two breeding-seasons (2014 and 2015) at different sampling sites and dates. In controlled conditions, the average speed of larvae was 144 μm s^-1 and the maximum speed was 297 μm s^-1 while the trajectory is mainly rectilinear. In the presence of environmental concentration of copper or S-metolachlor, no significant difference in maximum or average larval speed was observed compared to the control condition but the percentage of circular trajectory increased significantly while the rectilinear swimming larvae significantly declined. The current study demonstrates that rectilinear trajectories are positively correlated to normal larvae while larvae with shell anomalies are positively correlated to circular trajectories. This abnormal behavior could affect the survival and spread of larvae, and consequently, the recruitment and colonization of new habitats.

Using Photogrammetry to Create a Realistic 3D Anatomy Learning Aid with Unity Game Engine

Learning and processing complex 3D structures can be challenging for students, particularly if relying on 2D images or if there is limited access to the study material. This applies to many fields including anatomy, where students report difficulty visualising complex structures such as the nervous system. We aimed to address this by creating a realistic model of part of the nervous system-the sympathetic nervous system which is known for the 'fight or flight' response. Photogrammetry was chosen to create a 3D digital model of a dissection of the sympathetic nervous system. The 3D model was then incorporated into an interactive learning aid that allowed users to manipulate the model and provided relevant text information and labels. Evaluation of the learning aid by students (n = 7) was positive with 71.4% strongly agreeing that using this application improved their understanding of the anatomy. The majority of students (85.7%) also agreed or strongly agreed that this application provided them with a view of the sympathetic nervous system that they had not seen before. Photogrammetry is a relatively simple and inexpensive method to create realistic 3D digital models that can promote self-directed learning and a greater understanding of complex structures.

Large-Scale Analysis of Visualization Options in a Citizen Science Game

Visualization is a valuable tool in problem solving, especially for citizen science games. In this study, we analyze data from 36,351 unique players of the citizen science game Foldit over a period of 5 years to understand how their choice of visualization options are affected by expertise and problem type. We identified clusters of visualization options, and found differences in how experts and novices view puzzles and that experts differentially change their views based on puzzle type. These results can inform new design approaches to help both novice and expert players visualize novel problems, develop expertise, and problem solve.

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

Quality Characteristics Analysis and Remaining Shelf Life Prediction of Fresh Tibetan Tricholoma matsutake under Modified Atmosphere Packaging in Cold Chain

Tricholoma matsutake (T. matsutake) growing in Tibet is very popular for its high economic and medicinal value, but fresh T. matsutake has an extremely short shelf life. The shelf life of T. matsutake is complex, influenced by product characteristics, surrounding environmental conditions, and spoilage development. The objective of this work was to study the quality characteristics of fresh T. matsutake during its shelf life period in modified atmosphere packaging (MAP) conditions and establish its remaining shelf life prediction models in a cold chain. In this study, we measured and analyzed quality indicators of fresh T. matsutake, including hardness (cap, stipe), color, odor of sensory characteristics, pH, soluble solids content (SSC), and moisture content (MC) of physical and chemical characteristics under the temperature condition of 4 °C and relative humidity (RH) of 90%. The sensory evaluation results showed that the odor indicator in sensory characteristics was more sensitive to the freshness of T. matsutake. The changes of pH, SSC, and MC were divided into three periods to analyze the physiological changes of T. matsutake. The cap spread process could affect the changes of pH, SSC, and MC in period S₁, and they changed gradually in period S₂. In the period S₃, they changed complicatedly because of deterioration. The remaining shelf life prediction model of T. matsutake was established by the back propagation (BP) neural network method to quantify the relationship between the quality indicators and the remaining shelf life. The shelf life characteristics are complex, which were optimized by correlation analysis. Significant benefits of this work are anticipated on the transportation and preservation of fresh T. matsutake to the market and the reduction of its losses in the postharvest chain.

Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching

We present here an interdisciplinary workshop on the subject of biomolecules offered to undergraduate and high school students with the aim of boosting their interest toward all areas of science contributing to the study of life. The workshop involves mathematics, physics, chemistry, computer science and biology. Based on our own areas of research, molecular modelling is chosen as the central axis as it involves all disciplines. To provide a strong biological motivation for the study of the dynamics of biomolecules, the theme of the workshop is the origin of life. All sessions are built around active pedagogy, including games, and a final poster presentation.

Study of Commodity VR for Computational Material Sciences

Recent advancements in virtual reality (VR) devices and software environments make it possible to easily incorporate this technology for many applications, including computational materials science. For studying three-dimensional (3D) structure models and related chemical information, we focused on using a commodity VR device (VIVE) and an authoring tool (Unity). To visualize 3D chemical structures, disturbances like judder due to dropped frames should be eliminated from the VR experience to improve simulations. We propose a simple evaluation method that is straightforward for the nonexpert or novice VR user. We examine the major visualization representations including ball, ball and stick, and isosurface systems. For systematic benchmark measurements, a pendulum from the VR device was used to generate periodic oscillatory motion during measurements of a time series in frames per second (fps). For VIVE with a refresh rate of 90 Hz, judder occurred when less than 90 fps. We demonstrated the system size limitations for the results of molecular dynamics simulations of phase separation of ABA block copolymers and experimental observations of filler morphologies in rubber.

DXR: A Toolkit for Building Immersive Data Visualizations

This paper presents DXR, a toolkit for building immersive data visualizations based on the Unity development platform. Over the past years, immersive data visualizations in augmented and virtual reality (AR, VR) have been emerging as a promising medium for data sense-making beyond the desktop. However, creating immersive visualizations remains challenging, and often require complex low-level programming and tedious manual encoding of data attributes to geometric and visual properties. These can hinder the iterative idea-to-prototype process, especially for developers without experience in 3D graphics, AR, and VR programming. With DXR, developers can efficiently specify visualization designs using a concise declarative visualization grammar inspired by Vega-Lite. DXR further provides a GUI for easy and quick edits and previews of visualization designs in-situ, i.e., while immersed in the virtual world. DXR also provides reusable templates and customizable graphical marks, enabling unique and engaging visualizations. We demonstrate the flexibility of DXR through several examples spanning a wide range of applications.

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.

Visualization of Biomedical Data

The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.

Molecular Visualization on the Holodeck

Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching schoolchildren about biomolecules that are the machinery of life. Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. Investigations over three decades have produced an extensive literature evaluating the potential of VR in research and education. Consumer VR headsets are now affordable to researchers and educators, allowing direct tests of whether the technology is valuable in these areas. We survey here advantages and disadvantages of VR for molecular biology in the context of affordable and dramatically more powerful VR and graphics hardware than has been available in the past.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m² display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.

Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly

The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables. Based on the Unity3D game and physics engines, along with rigid body dynamics, we propose a virtual sandbox to model large biological molecules as dynamic chains of rigid bodies interacting together to gain insight into ECM components behaviour in the mesoscopic range. We have preliminary results showing how parameters such as fibre flexibility or the nature and number of interactions between molecules can induce different structures in the basement membrane. Using the Unity3D game engine and virtual reality headset coupled with haptic controllers, we immerse the user inside the corresponding simulation. Untrained users are able to navigate a complex virtual sandbox crowded with large biomolecules models in a matter of seconds.

Storage, visualization, and navigation of 3D genomics data

The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art computing technology, as well as the solutions adopted by the platforms currently available.

Towards the SMART workflow system for computational spectroscopy

Is it possible to convert highly specialized research in the field of computational spectroscopy into robust and user-friendly aids to experiments and industrial applications?

Instant Construction and Visualization of Crowded Biological Environments

We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.

Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions

Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.

Multi-scale simulations of biological systems using the OPEP coarse-grained model

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

Old model organisms and new behavioral end-points: Swimming alteration as an ecotoxicological response

Behavioral responses of aquatic organisms have received much less attention than developmental or reproductive ones due to the scarce presence of user-friendly tools for their acquisition. The technological development of data acquisition systems for quantifying behavior in the aquatic environment and the increase of studies on the understanding the relationship between the behavior of aquatic organisms and the physiological/ecological activities have generated renewed interest in using behavioral responses also in marine ecotoxicology. Recent reviews on freshwater environment show that behavioral end-points are comparatively fast and sensitive, and warrant further attention as tools for assessing the toxicological effects of environmental contaminants. In this mini-review, we perform a systematic analysis of the most recent works that have used marine invertebrate swimming alteration as behavioral end-point in ecotoxicological studies by assessing the differences between behavioral and acute responses in a wide range of species, in order to compare their sensitivity.

Design process and preliminary psychometric study of a video game to detect cognitive impairment in senior adults

INTRODUCTION

Assessment of episodic memory has been traditionally used to evaluate potential cognitive impairments in senior adults. Typically, episodic memory evaluation is based on personal interviews and pen-and-paper tests. This article presents the design, development and a preliminary validation of a novel digital game to assess episodic memory intended to overcome the limitations of traditional methods, such as the cost of its administration, its intrusive character, the lack of early detection capabilities, the lack of ecological validity, the learning effect and the existence of confounding factors.

MATERIALS AND METHODS

Our proposal is based on the gamification of the California Verbal Learning Test (CVLT) and it has been designed to comply with the psychometric characteristics of reliability and validity. Two qualitative focus groups and a first pilot experiment were carried out to validate the proposal.

RESULTS

A more ecological, non-intrusive and better administrable tool to perform cognitive assessment was developed. Initial evidence from the focus groups and pilot experiment confirmed the developed game's usability and offered promising results insofar its psychometric validity is concerned. Moreover, the potential of this game for the cognitive classification of senior adults was confirmed, and administration time is dramatically reduced with respect to pen-and-paper tests.

LIMITATIONS

Additional research is needed to improve the resolution of the game for the identification of specific cognitive impairments, as well as to achieve a complete validation of the psychometric properties of the digital game.

CONCLUSION

Initial evidence show that serious games can be used as an instrument to assess the cognitive status of senior adults, and even to predict the onset of mild cognitive impairments or Alzheimer's disease.

What Can Human-Guided Simulations Bring to RNA Folding?

Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.