Vivern a virtual environment for multiscale visualization and modeling of DNA nanostructures

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.Fil: Kutak, David. Masaryk University; República ChecaFil: Selzer, Matias Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingenieria de la Computacion. Laboratorio de Investigación y Desarrollo en Visualización yComputación Gráfica; ArgentinaFil: Byska, Jan. Masaryk University; República ChecaFil: Ganuza, María Luján. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingenieria de la Computacion. Laboratorio de Investigación y Desarrollo en Visualización yComputación Gráfica; ArgentinaFil: Barisic, Ivan. Austrian Institute of Technology; AustriaFil: Kozlikova, Barbora. Masaryk University; República ChecaFil: Miao, Haichao. Austrian Institute of Technology; Austri

Sign Gradient Descent Algorithms for Kinetostatic Protein Folding

This paper proposes a sign gradient descent (SGD) algorithm for predicting the three-dimensional folded protein molecule structures under the kinetostatic compliance method (KCM). In the KCM framework, which can be used to simulate the range of motion of peptide-based nanorobots/nanomachines, protein molecules are modeled as a large number of rigid nano-linkages that form a kinematic mechanism under motion constraints imposed by chemical bonds while folding under the kinetostatic effect of nonlinear interatomic force fields. In a departure from the conventional successive kinetostatic fold compliance framework, the proposed SGD-based iterative algorithm in this paper results in convergence to the local minima of the free energy of protein molecules corresponding to their final folded conformations in a faster and more robust manner. KCMbased folding dynamics simulations of the backbone chains of protein molecules demonstrate the effectiveness of the proposed algorithm.Comment: 6 pages, Accepted in 2023 International Conference on Manipulation, Automation and Robotics at Small Scales (MARSS 2023

Nanoinformatics: a new area of research in nanomedicine

pre-printAbstract: Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and -omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Design, Actuation, and Functionalization of Untethered Soft Magnetic Robots with Life-Like Motions: A Review

Soft robots have demonstrated superior flexibility and functionality than conventional rigid robots. These versatile devices can respond to a wide range of external stimuli (including light, magnetic field, heat, electric field, etc.), and can perform sophisticated tasks. Notably, soft magnetic robots exhibit unparalleled advantages among numerous soft robots (such as untethered control, rapid response, and high safety), and have made remarkable progress in small-scale manipulation tasks and biomedical applications. Despite the promising potential, soft magnetic robots are still in their infancy and require significant advancements in terms of fabrication, design principles, and functional development to be viable for real-world applications. Recent progress shows that bionics can serve as an effective tool for developing soft robots. In light of this, the review is presented with two main goals: (i) exploring how innovative bioinspired strategies can revolutionize the design and actuation of soft magnetic robots to realize various life-like motions; (ii) examining how these bionic systems could benefit practical applications in small-scale solid/liquid manipulation and therapeutic/diagnostic-related biomedical fields

Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

What Really is `Molecule' in Molecular Communications? The Quest for Physics of Particle-based Information Carriers

Molecular communication, as implied by its name, uses molecules as information carriers for communication between objects. It has an advantage over traditional electromagnetic-wave-based communication in that molecule-based systems could be biocompatible, operable in challenging environments, and energetically undemanding. Consequently, they are envisioned to have a broad range of applications, such as in the Internet of Bio-nano Things, targeted drug delivery, and agricultural monitoring. Despite the rapid development of the field, with an increasing number of theoretical models and experimental testbeds established by researchers, a fundamental aspect of the field has often been sidelined, namely, the nature of the molecule in molecular communication. The potential information molecules could exhibit a wide range of properties, making them require drastically different treatments when being modeled and experimented upon. Therefore, in this paper, we delve into the intricacies of commonly used information molecules, examining their fundamental physical characteristics, associated communication systems, and potential applications in a more realistic manner, focusing on the influence of their own properties. Through this comprehensive survey, we aim to offer a novel yet essential perspective on molecular communication, thereby bridging the current gap between theoretical research and real-world applications

Human Brain/Cloud Interface

The Internet comprises a decentralized global system that serves humanity’s collective effort to generate, process, and store data, most of which is handled by the rapidly expanding cloud. A stable, secure, real-time system may allow for interfacing the cloud with the human brain. One promising strategy for enabling such a system, denoted here as a “human brain/cloud interface” (“B/CI”), would be based on technologies referred to here as “neuralnanorobotics.” Future neuralnanorobotics technologies are anticipated to facilitate accurate diagnoses and eventual cures for the ∼400 conditions that affect the human brain. Neuralnanorobotics may also enable a B/CI with controlled connectivity between neural activity and external data storage and processing, via the direct monitoring of the brain’s ∼86 × 109 neurons and ∼2 × 1014 synapses. Subsequent to navigating the human vasculature, three species of neuralnanorobots (endoneurobots, gliabots, and synaptobots) could traverse the blood–brain barrier (BBB), enter the brain parenchyma, ingress into individual human brain cells, and autoposition themselves at the axon initial segments of neurons (endoneurobots), within glial cells (gliabots), and in intimate proximity to synapses (synaptobots). They would then wirelessly transmit up to ∼6 × 1016 bits per second of synaptically processed and encoded human–brain electrical information via auxiliary nanorobotic fiber optics (30 cm3) with the capacity to handle up to 1018 bits/sec and provide rapid data transfer to a cloud based supercomputer for real-time brain-state monitoring and data extraction. A neuralnanorobotically enabled human B/CI might serve as a personalized conduit, allowing persons to obtain direct, instantaneous access to virtually any facet of cumulative human knowledge. Other anticipated applications include myriad opportunities to improve education, intelligence, entertainment, traveling, and other interactive experiences. A specialized application might be the capacity to engage in fully immersive experiential/sensory experiences, including what is referred to here as “transparent shadowing” (TS). Through TS, individuals might experience episodic segments of the lives of other willing participants (locally or remote) to, hopefully, encourage and inspire improved understanding and tolerance among all members of the human family