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

Predicting the Mechanical Properties of Nanocomposites Reinforced with 1-D, 2-D and 3-D Nanomaterials

Materials with features at the nanoscale can provide unique mechanical properties and increased functionality when included as part of a nanocomposite. This dissertation utilizes computational methods at multiple scales, including molecular dynamics (MD) and density functional theory (DFT), and the coupled atomistic and discrete dislocation multiscale method (CADD), to predict the mechanical properties of nanocomposites possessing nanomaterials that are either 1-D (carbyne chains), 2-D (graphene sheets), or 3-D (Al/amorphous-Si core-shell nanorod). The MD method is used to model Ni-graphene nanocomposites. The strength of a Ni-graphene nanocomposite is found to improve by increasing the gap between the graphene sheet and a crack embedded in the Ni matrix. Ni-graphene nanocomposites also show substantially greater strength than pure Ni, depending on the loading direction and crack orientation relative to the graphene sheet. Moreover, polycrystalline graphene may serve as a better reinforce in Ni-graphene nanocomposites due to its improved interfacial shear stress with the Ni matrix compared to pristine graphene. This work develops a patchwork quilt method for generating polycrystalline graphene sheets for use in MD models. Carbyne-based nanocomposites are modeled from first principles using DFT. This research finds that carbyne can only serve as an effective reinforcement in Ni-based nanocomposites when it is dielectrically screened from the Ni matrix, otherwise the carbyne structure is lost. When graphene is used as a dielectric screen, the local stiffness of the nanocomposite improves with the number of carbyne chains present. Specific stiffness is introduced as an alternative to elastic stiffness for characterizing low-dimensional materials because it is not dependent on volume when derived using an energy vs. strain relation. A two-material formulation of CADD is developed to model Al/a-Si core-shell nanorods under indentation/retraction. The structural deformation behavior is found to be dependent on the geometry of both core and shell. When present, the a-Si shell protects the Al core by delocalizing forces produced by the indenter. It is also found that substrate deformation becomes important for core-shell structures with sufficiently small cores. This work can help guide experimental and computational work related to the discussed 1-D, 2-D and 3-D nanomaterials and aid in future nanocomposite design

The Boston University Photonics Center annual report 2015-2016

This repository item contains an annual report that summarizes activities of the Boston University Photonics Center in the 2015-2016 academic year. The report provides quantitative and descriptive information regarding photonics programs in education, interdisciplinary research, business innovation, and technology development. The Boston University Photonics Center (BUPC) is an interdisciplinary hub for education, research, scholarship, innovation, and technology development associated with practical uses of light.This has been a good year for the Photonics Center. In the following pages, you will see that this year the Center’s faculty received prodigious honors and awards, generated more than 100 notable scholarly publications in the leading journals in our field, and attracted $18.9M in new research grants/contracts. Faculty and staff also expanded their efforts in education and training, and cooperated in supporting National Science Foundation sponsored Sites for Research Experiences for Undergraduates and for Research Experiences for Teachers. As a community, we emphasized the theme of “Frontiers in Plasmonics as Enabling Science in Photonics and Beyond” at our annual symposium, hosted by Bjoern Reinhard. We continued to support the National Photonics Initiative, and contributed as a cooperating site in the American Institute for Manufacturing Integrated Photonics (AIM Photonics) which began this year as a new photonics-themed node in the National Network of Manufacturing Institutes. Highlights of our research achievements for the year include an ambitious new DoD-sponsored grant for Development of Less Toxic Treatment Strategies for Metastatic and Drug Resistant Breast Cancer Using Noninvasive Optical Monitoring led by Professor Darren Roblyer, continued support of our NIH-sponsored, Center for Innovation in Point of Care Technologies for the Future of Cancer Care led by Professor Cathy Klapperich, and an exciting confluence of new grant awards in the area of Neurophotonics led by Professors Christopher Gabel, Timothy Gardner, Xue Han, Jerome Mertz, Siddharth Ramachandran, Jason Ritt, and John White. Neurophotonics is fast becoming a leading area of strength of the Photonics Center. The Industry/University Collaborative Research Center, which has become the centerpiece of our translational biophotonics program, continues to focus onadvancing the health care and medical device industries, and has entered its sixth year of operation with a strong record of achievement and with the support of an enthusiastic industrial membership base

Carbon Nanotube-Coated Scaffolds for Tissue Engineering Applications

Carbon Nanotubes (CNTs) have beneficial properties for cell scaffolding, which has translated into effective growth of bone, muscle, and cardiac cells. However, loose carbon nanotubes can cause in vivo toxicity. To reduce this risk, our team has developed biomimetic scaffolds with multiscale hierarchy where carpet-like CNT arrays are covalently bonded to larger biocompatible substrates. In this study, we have tested such scaffolds in two distinct types of biomedical applications involving glioblastoma and keratinocyte cells. The growth of glioblastoma (GBM) cells on our CNT-coated biomimetic scaffolds was evaluated to check their suitability as a potential chemotherapy-loaded implant for GBM patient treatment. We utilized CNT carpets on flat carbon fiber cloths and porous carbon foams and identified differing effects on cell growth by altering the surface features, such as hydrophilicity. Synthesized CNT-coating is naturally superhydrophobic and prevents GBM cell growth initially, but over time cell proliferation increases to normal levels. When the CNT surface was modified to be hydrophilic, GBM cells followed a normal growth curve. These findings support the feasibility of developing a CNT-coated chemotherapy-loaded implant for post-surgical resection in GBM patients. Keratinocyte cell growth on CNT-coated carbon fiber cloth was investigated to assess its compatibility as a skin graft material for wound healing applications. Due to its covalently linked structure, biocompatibility, functionalizable topological features, and extensive surface area, CNTs could provide a suitable surface for skin cell proliferation. CNTs can also provide directionality, which can be important for supporting scaffolds used in wound healing applications. This project aimed to determine whether the use of CNTs attached to carbon scaffolds are capable of sustaining keratinocyte growth for future development of novel skin graft development. Studies demonstrated biocompatibility for keratinocyte growth as shown by cell proliferation, cell migration, and cytotoxicity analysis. Moreover, the CNT-coated scaffolds provided cytoprotection against environmental stressors such as Ultraviolet-B rays. We also found that keratinocyte cell growth can be tailored through the length of CNT coating and wettability control. These results point to the benefits of designing CNT-coated scaffolds for strategic wound healing applications. These results strongly support the future potential of these bio-mimetic scaffolds in tissue engineering

ScaleTrotter: Illustrative Visual Travels Across Negative Scales

We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data

Photothermal and photodynamic therapy of tumors with plasmonic nanoparticles: challenges and prospects

Cancer remains one of the leading causes of death in the world. For a number of neo-plasms, the efficiency of conventional chemo-and radiation therapies is insufficient because of drug resistance and marked toxicity. Plasmonic photothermal therapy (PPT) using local hyperthermia induced by gold nanoparticles (AuNPs) has recently been extensively explored in tumor treatment. However, despite attractive promises, the current PPT status is limited by laboratory experiments, academic papers, and only a few preclinical studies. Unfortunately, most nanoformulations still share a similar fate: great laboratory promises and fair preclinical trials. This review discusses the current challenges and prospects of plasmonic nanomedicine based on PPT and photodynamic therapy (PDT). We start with consideration of the fundamental principles underlying plasmonic properties of AuNPs to tune their plasmon resonance for the desired NIR-I, NIR-2, and SWIR optical windows. The basic principles for simulation of optical cross-sections and plasmonic heating under CW and pulsed irradiation are discussed. Then, we consider the state-of-the-art methods for wet chemical synthesis of the most popular PPPT AuNPs such as silica/gold nanoshells, Au nanostars, nanorods, and nanocages. The photothermal efficiencies of these nanoparticles are compared, and their applications to current nanomedicine are shortly discussed. In a separate section, we discuss the fabrication of gold and other nanoparticles by the pulsed laser ablation in liquid method. The second part of the review is devoted to our recent experimental results on laser-activated interaction of AuNPs with tumor and healthy tissues and current achievements of other research groups in this application area. The unresolved issues of PPT are the significant accumulation of AuNPs in the organs of the mononuclear phagocyte system, causing potential toxic effects of nanoparticles, and the possibility of tumor recurrence due to the presence of survived tumor cells. The prospective ways of solving these problems are discussed, including developing combined antitumor therapy based on combined PPT and PDT. In the conclusion section, we summarize the most urgent needs of current PPT-based nanomedicine