Using natural language processing techniques to inform research on nanotechnology

Literature in the field of nanotechnology is exponentially increasing with more and more engineered nanomaterials being created, characterized, and tested for performance and safety. With the deluge of published data, there is a need for natural language processing approaches to semi-automate the cataloguing of engineered nanomaterials and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine natural language processing (NLP)-based tools were identified: NanoPort, NanoMapper, TechPerceptor, a Text Mining Framework, a Nanodevice Analyzer, a Clinical Trial Document Classifier, Nanotoxicity Searcher, NanoSifter, and NEIMiner. We conclude with recommendations for sharing NLP-related tools through online repositories to broaden participation in nanoinformatics

Enabling Design and Simulation of Massive Parallel Nanoarchitectures

A common element in emerging nanotechnologies is the increasing complex- ity of the problems to face when attempting the design phase, because issues related to technology, specific application and architecture must be evalu- ated simultaneously. In several cases faced problems are known, but require a fresh re-think on the basis of different constraints not enforced by standard design tools. Among the emerging nanotechnologies, the two-dimensional structures based on nanowire arrays is promising in particular for massively parallel architec- tures. Several studies have been proposed on the exploration of the space of architectural solutions, but only a few derived high-level information from the results of an extended and reliable characterization of low-level structures. The tool we present is of aid in the design of circuits based on nanotech- nologies, here discussed in the specific case of nanowire arrays, as best candi- date for massively parallel architectures. It enables the designer to start from a standard High-level Description Languages (HDL), inherits constraints at physical level and applies them when organizing the physical implementation of the circuit elements and of their connections. It provides a complete simu- lation environment with two levels of refinement. One for DC analysis using a fast engine based on a simple switch level model. The other for obtaining transient performance based on automatic extraction of circuit parasitics, on detailed device (nanowire-FET) information derived by experiments or by existing accurate models, and on spice-level modeling of the nanoarray. Re- sults about the method used for the design and simulation of circuits based on nanowire-FET and nanoarray will be presente

Emerging physical unclonable functions with nanotechnology

Physical unclonable functions (PUFs) are increasingly used for authentication and identification applications as well as the cryptographic key generation. An important feature of a PUF is the reliance on minute random variations in the fabricated hardware to derive a trusted random key. Currently, most PUF designs focus on exploiting process variations intrinsic to the CMOS technology. In recent years, progress in emerging nanoelectronic devices has demonstrated an increase in variation as a consequence of scaling down to the nanoregion. To date, emerging PUFs with nanotechnology have not been fully established, but they are expected to emerge. Initial research in this area aims to provide security primitives for emerging integrated circuits with nanotechnology. In this paper, we review emerging nanotechnology-based PUFs

Advancing nanoelectronic device modeling through peta-scale computing and deployment on nanoHUB

Recent improvements to existing HPC codes NEMO 3-D and OMEN, combined with access to peta-scale computing resources, have enabled realistic device engineering simulations that were previously infeasible. NEMO 3-D can now simulate 1 billion atom systems, and, using 3D spatial decomposition, scale to 32768 cores. Simulation time for the band structure of an experimental P doped Si quantum computing device fell from 40 minutes to I minute. OMEN can perform fully quantum mechanical transport calculations for real-word UTB FETs on 147,456 cores in roughly 5 minutes. Both of these tools power simulation engines on the nanoHUB, giving the community access to previously unavailable research capabilities

Nanotechnology and supramolecular chemistry in controlled release and molecular recognition proceses for biomedical applications"

Tesis por compendioLa presente tesis doctoral, titulada "Nanotecnología y química supramolecular en procesos de liberación controlada y reconocimiento molecular para aplicaciones biomédicas", se centra en dos temas importantes: el reconocimiento molecular y los procesos de liberación controlada. Esta tesis doctoral está estructurada en cuatro capítulos. El primer capítulo introduce el concepto de materiales híbridos orgánicos-inorgánicos funcionalizados con puertas moleculares y sus aplicaciones biomédicas como nanomateriales para dirigir y controlar la liberación controlada de fármacos. Además se introduce una breve descripción sobre sensors colorimétricos basados en la base de la quimica supramolecular, particularmente en los procesos de reconocimiento molecular. En particular, el capítulo 2 describe la preparacion de cinco nanodispositivos que responden a enzimas. Estos materiales híbridos se componen de dos unidades principales: un soporte mesoporoso basado en sílice inorgánica, capaz de encapsular moléculas orgánicas y un compuesto orgánico anclado en la superficie externa del soporte mesoporoso inorgánico que actúa como puerta molecular. Todos los sistemas propuestos utilizan puertas moleculares peptídicas que responden a temperatura o enzimas como estímulo. La segunda parte de esta tesis doctoral se centra en el diseño y desarrollo de un nuevo compuesto químico capaz de detectar monóxido de carbono in vivo. En resumen, para todos los resultados antes mencionados podemos decir que esta tesis doctoral constituye una contribución científica original al desarrollo de la química supramolecular. Sus resultados derivados de los estudios presentados dejan rutas abiertas para continuar el estudio y el desarrollo de nuevos materiales híbridos y sensors químicos más eficientes para aplicaciones biomédicas y terapeuticas.This PhD thesis entitled "Nanotechnology and supramolecular chemistry in controlled release and molecular recognition processes for biomedical applications", is focused on two important subjects: molecular recognition and controlled delivery processes. This PhD thesis is structured in four chapters. The first chapter introduces the concept of organic-inorganic hybrid materials containing switchable "gate-like" ensembles and their biomedical applications as nanomaterials for targeting and control drug delivery. Furthermore, is introduced a short review about chromo-fluorogenic chemosensors based on basic principles of supramolecular chemistry, particulary in molecular recognition processes. In particular, in chapter 2 is focus on the development of enzymatic-driven nanodevices. These hybrid materials are composed of two main units: an inorganic silica based mesoporous scaffold, able to store organic molecules and an organic compound anchored on the external surface of the inorganic mesoporous support than acts as molecular gate. All the systems proposed use peptidic gates that respond to temperature or enzimatic stimulis. The second part of this PhD thesis is focused on the design and development of a new chemical compound capable of detecting carbon monoxide in vivo. In summary, for all the results above mentioned we can say that this PhD thesis constitutes an original scientific contribution to the development of supramolecular chemistry. Its results derived from the studies presented leaves open routes to continue the study and development of new hybrid materials and more efficient chemical sensors with biomedical and therapeutic applications.La present tesi doctoral, titulada "Nanotecnologia i química supramolecular en processos d'alliberament controlat i reconeixement molecular per a aplicacions biomèdiques", es centra en dos temes importants de la química: el reconeixement molecular i els processos d'alliberament controlat. Aquesta tesi doctoral està estructurada en quatre capítols. El primer capítol introdueix el concepte de materials híbrids orgànics-inorgànics funcionalitzats amb portes moleculars i les seves aplicacions biomèdiques com nanomaterials per dirigir i controlar l'alliberament controlat de fàrmacs. A més s'introdueix una breu descripció sobre sensors colorimètrics fonamentats en la base de la química supramolecular, particularment en els processos de reconeixement molecular. En particular, el capítol 2 descriu la preparació de cinc nanodispositius que responen a enzims. Aquests materials híbrids es componen de dues unitats principals: un suport mesoporos basat en sílice inorgànica, capaç d'encapsular molècules orgàniques i un compost orgànic ancorat a la superfície externa del suport mesoporós inorgànic que actua com a porta molecular. La segona part d'aquesta tesi doctoral es centra en el disseny i desenvolupaent d'un nou compost químic capaç de detectar monòxid de carboni in vivo. En resum, per a tots els resultats abans mencionats podem dir que esta tesi doctoral constituïx una contribució científica original al desenvolupament de la química supramolecular. Els seus resultats derivats dels estudis presentats deixen rutes obertes per a continuar l'estudi i el desenvolupament de nous materials hibrids i sensors químics més eficients per a aplicacions biomèdiques i terapeutiques.De La Torre Paredes, C. (2017). Nanotechnology and supramolecular chemistry in controlled release and molecular recognition proceses for biomedical applications" [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/94043TESISCompendi

Custom-tailored DNA origami mechanics for cellular applications

DNA molecules have been used as the building block for the self-assembly of artificial nanostructures. In particular, the DNA origami method has made the design of DNA nanostructures more robust and approachable. Different design approaches have been created and DNA origami has been used in a variety of fields, from plasmonic, to drug delivery, to biology and biophysics. In recent years, DNA nanotechnology has shown very promising uses in studying forces in biological contexts, both by measuring them and applying them. Mechanosensitive systems in biology are widespread and the study of their complex regulation is increasing in importance, and DNA origami has recently been used as a tool to study them. In paper I, we implement an unsupervised software to simulate wireframe DNA origami structures and evaluate their rigidity. After this evaluation, the software produces mutant structures and then the process is started again, iteratively. In this way the software creates an in-silico evolution towards more rigid wireframe DNA origami. The structures are modified following one of two schemes. In the first one, the individual edges are evaluated and then modified by adding or removing individual bases; in the second scheme, the structures have internal supports, and the software can modify the position of these internal supports to create mutants. We show that these two schemes have different results on the rigidity of the structures, with the internal supports-based scheme increasing the rigidity of structures to up to 50%, after several iterations. In paper II, we compare the mechanical characteristics of a lattice-based DNA origami nanostructure and a wireframe DNA origami nanostructure, exploring how the differences between the two affect their interaction with cancer cells. The wireframe structure showed a higher local flexibility when compared to the lattice-based structure. These physical differences play an important role in the interaction between DNA nanostructures and human cancer cells, in particular thanks to the differences in interaction with scavenger receptors. We show that wireframe origamis are more likely to stay on the cell membrane, while the lattice-based origami are more likely to be internalized. This is also reflected in a deeper penetration of the wireframe structures into cell spheroid tissue models. With these observations, we show that the design method should be considered when applying DNA origami for biological applications. In paper III, we aim to expand the design space of wireframe DNA origami, by designing structures with four-helix bundles (4HB) as edges. This is possible thanks to the addition of additional helices to the edge of the wireframe structures, to create 4HB on a square lattice: this results in increased rigidity of the edges. We developed the software for the design of the new type of structures and then we successfully folded a library of five structures, investigating the rigidity of the new type of structures. In addition, we designed a new type of hybrid structures, presenting more rigid 4HB edges and less rigid single helix edges. We think that the development of new ways of designing DNA origami structures can pave the way for the design of nanostructures more suited for specific applications. In paper IV, we design a DNA origami nanoactuator with the aim of pulling on molecular targets. DNA origami is a promising technology in this field because of its high throughput and the relative simplicity when compared with other force spectroscopy techniques. We designed a barrel-like structure with an internal block connected to ssDNA or dsDNA strands, depending on the activation mode of the mechanism. We estimated that the structure can create forces of up to 40 pN, and coarse-grained molecular dynamics simulations in oxDNA and Förster resonance energy transfer experiments confirm the successful activation of the structure. We also demonstrated that the structure, modified with Cy5, cholesterol, and anti-CD3 aptamer, can interact with T cells. We think that DNA origami can become an important tool in the study of mechanosensitive cellular receptors

Air Force Institute of Technology Research Report 2010

This report summarizes the research activities of the Air Force Institute of Technology’s Graduate School of Engineering and Management. It describes research interests and faculty expertise; lists student theses/dissertations; identifies research sponsors and contributions; and outlines the procedures for contacting the school. Included in the report are: faculty publications, conference presentations, consultations, and funded research projects. Research was conducted in the areas of Aeronautical and Astronautical Engineering, Electrical Engineering and Electro-Optics, Computer Engineering and Computer Science, Systems and Engineering Management, Operational Sciences, Mathematics, Statistics and Engineering Physic