Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

NASA Technical Reports Server (NTRS)

Zhang, Xiang (Inventor); Chen, Fanqing Frank (Inventor); Su, Kai-Hang (Inventor); Wei, Qi-Huo (Inventor); Ellman, Jonathan A. (Inventor); Sun, Cheng (Inventor)

2014-01-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

DOEpatents

Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

2014-04-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Roundtable on Urban Living Environment Research (RULER).

PubMed

Vlahov, David; Agarwal, Siddharth Raj; Buckley, Robert M; Caiaffa, Waleska Teixeira; Corvalan, Carlos F; Ezeh, Alex Chika; Finkelstein, Ruth; Friel, Sharon; Harpham, Trudy; Hossain, Maharufa; de Faria Leao, Beatriz; Mboup, Gora; Montgomery, Mark R; Netherland, Julie C; Ompad, Danielle C; Prasad, Amit; Quinn, Andrew T; Rothman, Alexander; Satterthwaite, David E; Stansfield, Sally; Watson, Vanessa J

2011-10-01

For 18 months in 2009-2010, the Rockefeller Foundation provided support to establish the Roundtable on Urban Living Environment Research (RULER). Composed of leading experts in population health measurement from a variety of disciplines, sectors, and continents, RULER met for the purpose of reviewing existing methods of measurement for urban health in the context of recent reports from UN agencies on health inequities in urban settings. The audience for this report was identified as international, national, and local governing bodies; civil society; and donor agencies. The goal of the report was to identify gaps in measurement that must be filled in order to assess and evaluate population health in urban settings, especially in informal settlements (or slums) in low- and middle-income countries. Care must be taken to integrate recommendations with existing platforms (e.g., Health Metrics Network, the Institute for Health Metrics and Evaluation) that could incorporate, mature, and sustain efforts to address these gaps and promote effective data for healthy urban management. RULER noted that these existing platforms focus primarily on health outcomes and systems, mainly at the national level. Although substantial reviews of health outcomes and health service measures had been conducted elsewhere, such reviews covered these in an aggregate and perhaps misleading way. For example, some spatial aspects of health inequities, such as those pointed to in the 2008 report from the WHO's Commission on the Social Determinants of Health, received limited attention. If RULER were to focus on health inequities in the urban environment, access to disaggregated data was a priority. RULER observed that some urban health metrics were already available, if not always appreciated and utilized in ongoing efforts (e.g., census data with granular data on households, water, and sanitation but with little attention paid to the spatial dimensions of these data). Other less obvious elements

Visualizing dopamine released from living cells using a nanoplasmonic probe

NASA Astrophysics Data System (ADS)

Qin, W. W.; Wang, S. P.; Li, J.; Peng, T. H.; Xu, Y.; Wang, K.; Shi, J. Y.; Fan, C. H.; Li, D.

2015-09-01

We report the development of an ultrasensitive nanoplasmonic probe for discriminative detection and imaging of dopamine released from living cells. The sensing mechanism is based on the dopamine-induced seeded-growth of Au nanoparticles (Au NPs) that leads to the shift of the plasmon band. This platform allows for the detection of dopamine with a detection limit down to 0.25 pM within 1 min. This nanoplasmonic assay is further applied to visualize the release of dopamine from living rat pheochromocytoma (PC12) cells under ATP-stimulation with dark-field microscopy (DFM). The DFM results together with real time fluorescence imaging of PC12 cells stained with the Fluo calcium indicator, suggested that ATP stimulated-release of dopamine is concomitant with the Ca2+ influx, and the influx of Ca2+ is through ATP-activated channels instead of the voltage-gated Ca2+ channel (VGC).We report the development of an ultrasensitive nanoplasmonic probe for discriminative detection and imaging of dopamine released from living cells. The sensing mechanism is based on the dopamine-induced seeded-growth of Au nanoparticles (Au NPs) that leads to the shift of the plasmon band. This platform allows for the detection of dopamine with a detection limit down to 0.25 pM within 1 min. This nanoplasmonic assay is further applied to visualize the release of dopamine from living rat pheochromocytoma (PC12) cells under ATP-stimulation with dark-field microscopy (DFM). The DFM results together with real time fluorescence imaging of PC12 cells stained with the Fluo calcium indicator, suggested that ATP stimulated-release of dopamine is concomitant with the Ca2+ influx, and the influx of Ca2+ is through ATP-activated channels instead of the voltage-gated Ca2+ channel (VGC). Electronic supplementary information (ESI) available: Fig. S1-S4 and Table S1. See DOI: 10.1039/c5nr04433b

Nanoplasmonics tuned "click chemistry".

PubMed

Tijunelyte, I; Guenin, E; Lidgi-Guigui, N; Colas, F; Ibrahim, J; Toury, T; Lamy de la Chapelle, M

2016-04-07

Nanoplasmonics is a growing field of optical condensed matter science dedicated to optical phenomena at the nanoscale level in metal systems. Extensive research on noble metallic nanoparticles (NPs) has emerged within the last two decades due to their ability to keep the optical energy concentrated in the vicinity of NPs, in particular, the ability to create optical near-field enhancement followed by heat generation. We have exploited these properties in order to induce a localised "click" reaction in the vicinity of gold nanostructures under unfavourable experimental conditions. We demonstrate that this reaction can be controlled by the plasmonic properties of the nanostructures and we propose two physical mechanisms to interpret the observed plasmonic tuning of the "click" chemistry.

On the convergence and accuracy of the FDTD method for nanoplasmonics.

PubMed

Lesina, Antonino Calà; Vaccari, Alessandro; Berini, Pierre; Ramunno, Lora

2015-04-20

Use of the Finite-Difference Time-Domain (FDTD) method to model nanoplasmonic structures continues to rise - more than 2700 papers have been published in 2014 on FDTD simulations of surface plasmons. However, a comprehensive study on the convergence and accuracy of the method for nanoplasmonic structures has yet to be reported. Although the method may be well-established in other areas of electromagnetics, the peculiarities of nanoplasmonic problems are such that a targeted study on convergence and accuracy is required. The availability of a high-performance computing system (a massively parallel IBM Blue Gene/Q) allows us to do this for the first time. We consider gold and silver at optical wavelengths along with three "standard" nanoplasmonic structures: a metal sphere, a metal dipole antenna and a metal bowtie antenna - for the first structure comparisons with the analytical extinction, scattering, and absorption coefficients based on Mie theory are possible. We consider different ways to set-up the simulation domain, we vary the mesh size to very small dimensions, we compare the simple Drude model with the Drude model augmented with two critical points correction, we compare single-precision to double-precision arithmetic, and we compare two staircase meshing techniques, per-component and uniform. We find that the Drude model with two critical points correction (at least) must be used in general. Double-precision arithmetic is needed to avoid round-off errors if highly converged results are sought. Per-component meshing increases the accuracy when complex geometries are modeled, but the uniform mesh works better for structures completely fillable by the Yee cell (e.g., rectangular structures). Generally, a mesh size of 0.25 nm is required to achieve convergence of results to ∼ 1%. We determine how to optimally setup the simulation domain, and in so doing we find that performing scattering calculations within the near-field does not necessarily produces large

Quantitative Comparison of Protein Adsorption and Conformational Changes on Dielectric-Coated Nanoplasmonic Sensing Arrays.

PubMed

Ferhan, Abdul Rahim; Jackman, Joshua A; Sut, Tun Naw; Cho, Nam-Joon

2018-04-22

Nanoplasmonic sensors are a popular, surface-sensitive measurement tool to investigate biomacromolecular interactions at solid-liquid interfaces, opening the door to a wide range of applications. In addition to high surface sensitivity, nanoplasmonic sensors have versatile surface chemistry options as plasmonic metal nanoparticles can be coated with thin dielectric layers. Within this scope, nanoplasmonic sensors have demonstrated promise for tracking protein adsorption and substrate-induced conformational changes on oxide film-coated arrays, although existing studies have been limited to single substrates. Herein, we investigated human serum albumin (HSA) adsorption onto silica- and titania-coated arrays of plasmonic gold nanodisks by localized surface plasmon resonance (LSPR) measurements and established an analytical framework to compare responses across multiple substrates with different sensitivities. While similar responses were recorded on the two substrates for HSA adsorption under physiologically-relevant ionic strength conditions, distinct substrate-specific behavior was observed at lower ionic strength conditions. With decreasing ionic strength, larger measurement responses occurred for HSA adsorption onto silica surfaces, whereas HSA adsorption onto titania surfaces occurred independently of ionic strength condition. Complementary quartz crystal microbalance-dissipation (QCM-D) measurements were also performed, and the trend in adsorption behavior was similar. Of note, the magnitudes of the ionic strength-dependent LSPR and QCM-D measurement responses varied, and are discussed with respect to the measurement principle and surface sensitivity of each technique. Taken together, our findings demonstrate how the high surface sensitivity of nanoplasmonic sensors can be applied to quantitatively characterize protein adsorption across multiple surfaces, and outline broadly-applicable measurement strategies for biointerfacial science applications.

Highly sensitive dendrimer-based nanoplasmonic biosensor for drug allergy diagnosis.

PubMed

Soler, Maria; Mesa-Antunez, Pablo; Estevez, M-Carmen; Ruiz-Sanchez, Antonio Jesus; Otte, Marinus A; Sepulveda, Borja; Collado, Daniel; Mayorga, Cristobalina; Torres, Maria Jose; Perez-Inestrosa, Ezequiel; Lechuga, Laura M

2015-04-15

A label-free biosensing strategy for amoxicillin (AX) allergy diagnosis based on the combination of novel dendrimer-based conjugates and a recently developed nanoplasmonic sensor technology is reported. Gold nanodisks were functionalized with a custom-designed thiol-ending-polyamido-based dendron (d-BAPAD) peripherally decorated with amoxicilloyl (AXO) groups (d-BAPAD-AXO) in order to detect specific IgE generated in patient's serum against this antibiotic during an allergy outbreak. This innovative strategy, which follows a simple one-step immobilization procedure, shows exceptional results in terms of sensitivity and robustness, leading to a highly-reproducible and long-term stable surface which allows achieving extremely low limits of detection. Moreover, the viability of this biosensor approach to analyze human biological samples has been demonstrated by directly analyzing and quantifying specific anti-AX antibodies in patient's serum without any sample pretreatment. An excellent limit of detection (LoD) of 0.6ng/mL (i.e. 0.25kU/L) has been achieved in the evaluation of clinical samples evidencing the potential of our nanoplasmonic biosensor as an advanced diagnostic tool to quickly identify allergic patients. The results have been compared and validated with a conventional clinical immunofluorescence assay (ImmunoCAP test), confirming an excellent correlation between both techniques. The combination of a novel compact nanoplasmonic platform and a dendrimer-based strategy provides a highly sensitive label free biosensor approach with over two times better detectability than conventional SPR. Both the biosensor device and the carrier structure hold great potential in clinical diagnosis for biomarker analysis in whole serum samples and other human biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Probing the Interaction of Dielectric Nanoparticles with Supported Lipid Membrane Coatings on Nanoplasmonic Arrays

PubMed Central

Ferhan, Abdul Rahim; Ma, Gamaliel Junren; Jackman, Joshua A.; Sut, Tun Naw; Park, Jae Hyeon; Cho, Nam-Joon

2017-01-01

The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays. A key emphasis was placed on controlling membrane functionality by tuning the membrane surface charge vis-à-vis lipid composition. The optical sensing properties of the bare and SLB-coated sensor surfaces were quantitatively compared, and provided an experimental approach to evaluate nanoparticle–membrane interactions across different SLB platforms. While the interaction of negatively-charged silica nanoparticles (SiNPs) with a zwitterionic SLB resulted in monotonic adsorption, a stronger interaction with a positively-charged SLB resulted in adsorption and lipid transfer from the SLB to the SiNP surface, in turn influencing the LSPR measurement responses based on the changing spatial proximity of transferred lipids relative to the sensor surface. Precoating SiNPs with bovine serum albumin (BSA) suppressed lipid transfer, resulting in monotonic adsorption onto both zwitterionic and positively-charged SLBs. Collectively, our findings contribute a quantitative understanding of how supported lipid membrane coatings influence the sensing performance of nanoplasmonic arrays, and demonstrate how the high surface sensitivity of nanoplasmonic sensors is well-suited for detecting the complex interactions between nanoparticles and lipid membranes. PMID:28644423

Designing a multicolor long range nanoscopic ruler for the imaging of heterogeneous tumor cells

NASA Astrophysics Data System (ADS)

Chavva, Suhash Reddy; Viraka Nellore, Bhanu Priya; Pramanik, Avijit; Sinha, Sudarson Sekhar; Jones, Stacy; Ray, Paresh Chandra

2016-07-01

Tumor heterogeneity is one of the biggest challenges in cancer treatment and diagnosis. A multicolor optical ruler is essential to address the heterogeneous tumor cell complexity. Driven by this need, the current article reports the design of a multicolor long range nanoscopic ruler for screening tumor heterogeneity by accurately identifying epithelial cells and cancer stem cells (CSCs) simultaneously. A nanoscopic surface energy transfer (NSET) ruler has been developed using blue fluorescence polymer dots (PDs) and red fluorescence gold cluster dots (GCDs) as multicolor fluorescence donor and plasmonic gold nanoparticle (GNP) acts as an excellent acceptor. Reported experimental results demonstrated that the multicolor nanoscopic ruler's working window is above 35 nm distances, which is more than three times farther than that of Förster resonance energy transfer (FRET) distance limit. Theoretical modeling using Förster dipole-dipole coupling and dipole to nanoparticle surface energy transfer have been used to discuss the possible mechanism for multicolor nanoscopic ruler's long-range capability. Using RNA aptamers that are specific for the target cancer cells, experimental data demonstrate that the nanoscopic ruler can be used for screening epithelial and CSCs simultaneously from a whole blood sample with a detection capability of 10 cells per mL. Experimental data show that the nanoscopic ruler can distinguish targeted cells from non-targeted cells.

21 CFR 886.1790 - Nearpoint ruler.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Nearpoint ruler. 886.1790 Section 886.1790 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL... to which the visual lines are directed when convergence is at its maximum). (b) Classification. Class...

Enhancement of fluorescence using nanoplasmonic and photonic structures

NASA Astrophysics Data System (ADS)

Arya, Akash; Tagore, Amit K.; Dantham, Venkata R.

2018-05-01

Two different nanoplasmonic structures have been synthesized using wet-chemistry method and demonstrated the enhancement of fluorescence of dye molecules. The difficulties associated with the plasmonic enhancement of fluorescence are discussed and to overcome these, an efficient approach has been proposed to enhance the fluorescence of a few molecules with the help of a high quality factor photonic microstructure (whispering gallery mode microresonator). The fabrication details of microresonators and experimental arrangement for enhancing the fluorescence are reported here.

Improving the social and emotional climate of classrooms: a clustered randomized controlled trial testing the RULER Approach.

PubMed

Rivers, Susan E; Brackett, Marc A; Reyes, Maria R; Elbertson, Nicole A; Salovey, Peter

2013-02-01

The RULER Approach ("RULER") is a setting-level, social and emotional learning program that is grounded in theory and evidence. RULER is designed to modify the quality of classroom social interactions so that the climate becomes more supportive, empowering, and engaging. This is accomplished by integrating skill-building lessons and tools so that teachers and students develop their emotional literacy. In a clustered randomized control trial, we tested the hypothesis that RULER improves the social and emotional climate of classrooms. Depending upon condition assignment, 62 schools either integrated RULER into fifth- and sixth-grade English language arts (ELA) classrooms or served as comparison schools, using their standard ELA curriculum only. Multi-level modeling analyses showed that compared to classrooms in comparison schools, classrooms in RULER schools were rated as having higher degrees of warmth and connectedness between teachers and students, more autonomy and leadership among students, and teachers who focused more on students' interests and motivations. These findings suggest that RULER enhances classrooms in ways that can promote positive youth development.

Improving classroom quality with the RULER Approach to Social and Emotional Learning: proximal and distal outcomes.

PubMed

Hagelskamp, Carolin; Brackett, Marc A; Rivers, Susan E; Salovey, Peter

2013-06-01

The RULER Approach to Social and Emotional Learning ("RULER") is designed to improve the quality of classroom interactions through professional development and classroom curricula that infuse emotional literacy instruction into teaching-learning interactions. Its theory of change specifies that RULER first shifts the emotional qualities of classrooms, which are then followed, over time, by improvements in classroom organization and instructional support. A 2-year, cluster randomized controlled trial was conducted to test hypotheses derived from this theory. Sixty-two urban schools either integrated RULER into fifth- and sixth-grade English language arts (ELA) classrooms or served as comparison schools, using their standard ELA curriculum only. Results from multilevel modeling with baseline adjustments and structural equation modeling support RULER's theory of change. Compared to classrooms in comparison schools, classrooms in RULER schools exhibited greater emotional support, better classroom organization, and more instructional support at the end of the second year of program delivery. Improvements in classroom organization and instructional support at the end of Year 2 were partially explained by RULER's impacts on classroom emotional support at the end of Year 1. These findings highlight the important contribution of emotional literacy training and development in creating engaging, empowering, and productive learning environments.

Silicon-based horizontal nanoplasmonic slot waveguides for on-chip integration.

PubMed

Zhu, Shiyang; Liow, T Y; Lo, G Q; Kwong, D L

2011-04-25

Horizontal metal/insulator/Si/insulator/metal nanoplasmonic slot waveguide (PWG), which is inserted in a conventional Si wire waveguide, is fabricated using the standard Si-CMOS technology. A thin insulator between the metal and the Si core plays a key role: it not only increases the propagation distance as the theoretical prediction, but also prevents metal diffusion and/or metal-Si reaction. Cu-PWGs with the Si core width of ~134-21 nm and ~12-nm-thick SiO2 on each side exhibit a relatively low propagation loss of ~0.37-0.63 dB/µm around the telecommunication wavelength of 1550 nm, which is ~2.6 times smaller than the Al-counterparts. A simple tapered coupler can provide an effective coupling between the PWG and the conventional Si wire waveguide. The coupling efficiency as high as ~0.1-0.4 dB per facet is measured. The PWG allows a sharp bending. The pure bending loss of a Cu-PWG direct 90° bend is measured to be ~0.6-1.0 dB. These results indicate the potential for seamless integration of various functional nanoplasmonic devices in existing Si electronic photonic integrated circuits (Si-EPICs).

Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers.

PubMed

Li, Mei-Xing; Xu, Cong-Hui; Zhang, Nan; Qian, Guang-Sheng; Zhao, Wei; Xu, Jing-Juan; Chen, Hong-Yuan

2018-04-24

DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA circuits and nanomachines. In this work, we reported an exploration of the dynamic process of the toehold-mediated strand displacement via core-satellite plasmon rulers at the single-molecule level. Applying plasmon rulers with unlimited lifetime, single-strand displacement triggered by the invader that resulted in stepwise leaving of satellite from the core was continuously monitored by changes of scattering signal for hours. The kinetics of strand displacement in vitro with three different toehold lengths have been investigated. Also, the study revealed the difference in the kinetics of strand displacement between DNA/RNA and DNA/DNA duplexes. For the kinetics study in vivo, influence from the surrounding medium has been evaluated using both phosphate buffer and cell lysate. Applying core-satellite plasmon rulers with high signal/noise ratio, kinetics study in living cells proceeded for the first time, which was not possible by conventional methods with a fluorescent reporter. The plasmon rulers, which are flexible, easily constructed, and robust, have proven to be effective tools in exploring the dynamical behaviors of biochemical reactions in vivo.

Electrotunable nanoplasmonic liquid mirror

NASA Astrophysics Data System (ADS)

Montelongo, Yunuen; Sikdar, Debabrata; Ma, Ye; McIntosh, Alastair J. S.; Velleman, Leonora; Kucernak, Anthony R.; Edel, Joshua B.; Kornyshev, Alexei A.

2017-11-01

Recently, there has been a drive to design and develop fully tunable metamaterials for applications ranging from new classes of sensors to superlenses among others. Although advances have been made, tuning and modulating the optical properties in real time remains a challenge. We report on the first realization of a reversible electrotunable liquid mirror based on voltage-controlled self-assembly/disassembly of 16 nm plasmonic nanoparticles at the interface between two immiscible electrolyte solutions. We show that optical properties such as reflectivity and spectral position of the absorption band can be varied in situ within +/-0.5 V. This observed effect is in excellent agreement with theoretical calculations corresponding to the change in average interparticle spacing. This electrochemical fully tunable nanoplasmonic platform can be switched from a highly reflective `mirror' to a transmissive `window' and back again. This study opens a route towards realization of such platforms in future micro/nanoscale electrochemical cells, enabling the creation of tunable plasmonic metamaterials.

Biotunable Nanoplasmonic Filter on Few-Layer MoS2 for Rapid and Highly Sensitive Cytokine Optoelectronic Immunosensing.

PubMed

Park, Younggeun; Ryu, Byunghoon; Oh, Bo-Ram; Song, Yujing; Liang, Xiaogan; Kurabayashi, Katsuo

2017-06-27

Monitoring of the time-varying immune status of a diseased host often requires rapid and sensitive detection of cytokines. Metallic nanoparticle-based localized surface plasmon resonance (LSPR) biosensors hold promise to meet this clinical need by permitting label-free detection of target biomolecules. These biosensors, however, continue to suffer from relatively low sensitivity as compared to conventional immunoassay methods that involve labeling processes. Their response speeds also need to be further improved to enable rapid cytokine quantification for critical care in a timely manner. In this paper, we report an immunobiosensing device integrating a biotunable nanoplasmonic optical filter and a highly sensitive few-layer molybdenum disulfide (MoS 2 ) photoconductive component, which can serve as a generic device platform to meet the need of rapid cytokine detection with high sensitivity. The nanoplasmonic filter consists of anticytokine antibody-conjugated gold nanoparticles on a SiO 2 thin layer that is placed 170 μm above a few-layer MoS 2 photoconductive flake device. The principle of the biosensor operation is based on tuning the delivery of incident light to the few-layer MoS 2 photoconductive flake thorough the nanoplasmonic filter by means of biomolecular surface binding-induced LSPR shifts. The tuning is dependent on cytokine concentration on the nanoplasmonic filter and optoelectronically detected by the few-layer MoS 2 device. Using the developed optoelectronic biosensor, we have demonstrated label-free detection of IL-1β, a pro-inflammatory cytokine, with a detection limit as low as 250 fg/mL (14 fM), a large dynamic range of 10 6 , and a short assay time of 10 min. The presented biosensing approach could be further developed and generalized for point-of-care diagnosis, wearable bio/chemical sensing, and environmental monitoring.

Colorimetric nanoplasmonic assay to determine purity and titrate extracellular vesicles.

PubMed

Maiolo, Daniele; Paolini, Lucia; Di Noto, Giuseppe; Zendrini, Andrea; Berti, Debora; Bergese, Paolo; Ricotta, Doris

2015-04-21

Extracellular Vesicles (EVs) - cell secreted vesicles that carry rich molecular information of the parental cell and constitute an important mode of intercellular communication - are becoming a primary topic in translational medicine. EVs (that comprise exosomes and microvesicles/microparticles) have a size ranging from 40 nm to 1 μm and share several physicochemical proprieties, including size, density, surface charge, and light interaction, with other nano-objects present in body fluids, such as single and aggregated proteins. This makes separation, titration, and characterization of EVs challenging and time-consuming. Here we present a cost-effective and fast colorimetric assay for probing by eye protein contaminants and determine the concentration of EV preparations, which exploits the synergy between colloidal gold nanoplasmonics, nanoparticle-protein corona, and nanoparticle-membrane interaction. The assay hits a limit of detection of protein contaminants of 5 ng/μL and has a dynamic range of EV concentration ranging from 35 fM to 35 pM, which matches the typical range of EV concentration in body fluids. This work provides the first example of the exploitation of the nanoparticle-protein corona in analytical chemistry.

Label-free nanoplasmonic sensing of tumor-associate autoantibodies for early diagnosis of colorectal cancer.

PubMed

Soler, Maria; Estevez, M-Carmen; Villar-Vazquez, Roi; Casal, J Ignacio; Lechuga, Laura M

2016-08-03

Colorectal cancer is treatable and curable when detected at early stages. However there is a lack of less invasive and more specific screening and diagnosis methods which would facilitate its prompt identification. Blood circulating autoantibodies which are immediately produced by the immune system at tumor appearance have become valuable biomarkers for preclinical diagnosis of cancer. In this work, we present the rapid and label-free detection of colorectal cancer autoantibodies directly in blood serum or plasma using a recently developed nanoplasmonic biosensor. Our nanoplasmonic device offers sensitive and real-time quantification of autoantibodies with excellent selectivity and reproducibility, achieving limits of detection around 1 nM (150-160 ng mL(-1)). A preliminary evaluation of clinical samples of colorectal cancer patients has shown good correlation with ELISA. These results demonstrate the reliability of the nanobiosensor strategy and pave the way towards the achievement of a sensitive diagnostic tool for early detection of colorectal cancer. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent advances in nanoplasmonic biosensors: applications and lab-on-a-chip integration

NASA Astrophysics Data System (ADS)

Lopez, Gerardo A.; Estevez, M.-Carmen; Soler, Maria; Lechuga, Laura M.

2017-01-01

Motivated by the recent progress in the nanofabrication field and the increasing demand for cost-effective, portable, and easy-to-use point-of-care platforms, localized surface plasmon resonance (LSPR) biosensors have been subjected to a great scientific interest in the last few years. The progress observed in the research of this nanoplasmonic technology is remarkable not only from a nanostructure fabrication point of view but also in the complete development and integration of operative devices and their application. The potential benefits that LSPR biosensors can offer, such as sensor miniaturization, multiplexing opportunities, and enhanced performances, have quickly positioned them as an interesting candidate in the design of lab-on-a-chip (LOC) optical biosensor platforms. This review covers specifically the most significant achievements that occurred in recent years towards the integration of this technology in compact devices, with views of obtaining LOC devices. We also discuss the most relevant examples of the use of the nanoplasmonic biosensors for real bioanalytical and clinical applications from assay development and validation to the identification of the implications, requirements, and challenges to be surpassed to achieve fully operative devices.

Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing

NASA Astrophysics Data System (ADS)

Nguyen, Anh H.; Lee, Jong Uk; Sim, Sang Jun

2016-02-01

RNA splicing plays important roles in transcriptome and proteome diversity. Herein, we describe the use of a nanoplasmonic system that unveils RNA folding and assembly during pre-mRNA splicing wherein the quantification of mRNA splice variants is not taken into account. With a couple of SERS-probes and plasmonic probes binding at the boundary sites of exon-2/intron-2 and intron-2/exon-3 of the pre-mature RNA of the β-globin gene, the splicing process brings the probes into the plasmonic bands. For plasmonic probes, a plasmon shift increase of ~29 nm, corresponding to intron removal and exon-2 and exon-3 connection to form the mRNA molecule, is measured by plasmonic coupling. The increased scattering intensity and surface-enhanced Raman scattering (SERS) fingerprinting reveal the clear dynamics of pre-mRNA splicing. Moreover, a time-resolved experiment of individual RNA molecules exhibited a successful splicing and an inhibited splicing event by 33 μM biflavonoid isoginkgetin, a general inhibitor of RNA splicing. The results suggest that the RNA splicing is successfully monitored with the nanoplasmonic system. Thus, this platform can be useful for studying RNA nanotechnology, biomolecular folding, alternative splicing, and maturation of microRNA.

The ruler of inclusion in the process of people learning with visual disability.

PubMed

Mafra, Eliane; Batiz, Eduardo Concepcion; Macedo, Marcelo

2012-01-01

The aim of this project is the development of a pedagogical tool that could address the needs related to the learning process of the blind and could also be used in the pedagogical process of people who are visually impaired. This project also has the objective of showing how the forms of the Ruler of Inclusion were planned in order to facilitate learning while addressing issues related to its safety, practicality and multifunctionality, aspects that are broached in a future work using descriptive, exploratory and phenomenological analyses to verify the understanding of the learning concepts applied to the ruler.

Standard rulers, candles, and clocks from the low-redshift universe.

PubMed

Heavens, Alan; Jimenez, Raul; Verde, Licia

2014-12-12

We measure the length of the baryon acoustic oscillation (BAO) feature, and the expansion rate of the recent Universe, from low-redshift data only, almost model independently. We make only the following minimal assumptions: homogeneity and isotropy, a metric theory of gravity, a smooth expansion history, and the existence of standard candles (supernovæ) and a standard BAO ruler. The rest is determined by the data, which are compilations of recent BAO and type IA supernova results. Making only these assumptions, we find for the first time that the standard ruler has a length of 103.9±2.3h⁻¹ Mpc. The value is a measurement, in contrast to the model-dependent theoretical prediction determined with model parameters set by Planck data (99.3±2.1h⁻¹ Mpc). The latter assumes the cold dark matter model with a cosmological constant, and that the ruler is the sound horizon at radiation drag. Adding passive galaxies as standard clocks or a local Hubble constant measurement allows the absolute BAO scale to be determined (142.8±3.7 Mpc), and in the former case the additional information makes the BAO length determination more precise (101.9±1.9h⁻¹ Mpc). The inverse curvature radius of the Universe is weakly constrained and consistent with zero, independently of the gravity model, provided it is metric. We find the effective number of relativistic species to be N(eff)=3.53±0.32, independent of late-time dark energy or gravity physics.

Enhancing Teacher Effectiveness in Spain: A Pilot Study of the Ruler Approach to Social and Emotional Learning

ERIC Educational Resources Information Center

Castillo, Ruth; Fernández-Berrocal, Pablo; Brackett, Marc A.

2013-01-01

This study examined the effects of an evidence-based social and emotional learning (SEL) program, The RULER Approach to Social and Emotional Learning (RULER), on teacher self reports of engagement, teacher-student interactions, and burnout. Participants were 47 teachers from 19 public schools in Spain who either volunteered for training on RULER…

Wavelength dependent vertical integration of nanoplasmonic circuits utilizing coupled ring resonators

NASA Astrophysics Data System (ADS)

Nielsen, M.; Elezzabi, A. Y.

2013-03-01

To become a competitor to replace CMOS-electronics for next-generation data processing, signal routing, and computing, nanoplasmonic circuits will require an analogue to electrical vias in order to enable vertical connections between device layers. Vertically stacked nanoplasmonic nanoring resonators formed of Ag/Si/Ag gap plasmon waveguides were studied as a novel 3-D coupling scheme that could be monolithically integrated on a silicon platform. The vertically coupled ring resonators were evanescently coupled to 100 nm x 100 nm Ag/Si/Ag input and output waveguides and the whole device was submerged in silicon dioxide. 3-D finite difference time domain simulations were used to examine the transmission spectra of the coupling device with varying device sizes and orientations. By having the signal coupling occur over multiple trips around the resonator, coupling efficiencies as high as 39% at telecommunication wavelengths between adjacent layers were present with planar device areas of only 1.00 μm2. As the vertical signal transfer was based on coupled ring resonators, the signal transfer was inherently wavelength dependent. Changing the device size by varying the radii of the nanorings allowed for tailoring the coupled frequency spectra. The plasmonic resonator based coupling scheme was found to have quality (Q) factors of upwards of 30 at telecommunication wavelengths. By allowing different device layers to operate on different wavelengths, this coupling scheme could to lead to parallel processing in stacked independent device layers.

Sensitive and Selective Plasmon Ruler Nanosensors for Monitoring the Apoptotic Drug Response in Leukemia

PubMed Central

2015-01-01

Caspases are proteases involved in cell death, where caspase-3 is the chief executioner that produces an irreversible cutting event in downstream protein substrates and whose activity is desired in the management of cancer. To determine such activity in clinically relevant samples with high signal-to-noise, plasmon rulers are ideal because they are sensitively affected by their interparticle separation without ambiguity from photobleaching or blinking effects. A plasmon ruler is a noble metal nanoparticle pair, tethered in close proximity to one another via a biomolecule, that acts through dipole–dipole interactions and results in the light scattering to increase exponentially. In contrast, a sharp decrease in intensity is observed when the pair is confronted by a large interparticle distance. To align the mechanism of protease activity with building a sensor that can report a binary signal in the presence or absence of caspase-3, we present a caspase-3 selective plasmon ruler (C3SPR) composed of a pair of Zn0.4Fe2.6O4@SiO2@Au core–shell nanoparticles connected by a caspase-3 cleavage sequence. The dielectric core (Zn0.4Fe2.6O4@SiO2)-shell (Au) geometry provided a brighter scattering intensity versus solid Au nanoparticles, and the magnetic core additionally acted as a purification handle during the plasmon ruler assembly. By monitoring the decrease in light scattering intensity per plasmon ruler, we detected caspase-3 activity at single molecule resolution across a broad dynamic range. This was observed to be as low as 100 fM of recombinant material or 10 ng of total protein from cellular lysate. By thorough analyses of single molecule trajectories, we show caspase-3 activation in a drug-treated chronic myeloid leukemia (K562) cancer system as early as 4 and 8 h with greater sensitivity (2- and 4-fold, respectively) than conventional reagents. This study provides future implications for monitoring caspase-3 as a biomarker and efficacy of drugs. PMID:25166742

Solvent effect on FRET spectroscopic ruler

NASA Astrophysics Data System (ADS)

Qu, Songyuan; Liu, Chuanbo; Liu, Qiong; Wu, Wei; Du, Baoji; Wang, Jin

2018-03-01

A discrepancy has emerged in recent years between single-molecule Förster resonance energy transfer (smFRET) measurements and small angle X-ray scattering (SAXS) or small angle neutron scattering experiments in the study of unfolded or intrinsically disordered proteins in denaturing solutions. Despite significant advances that have been made in identifying various factors which may have contributed to the manifestation of the so-called smFRET-SAXS discrepancy, no consensus has been reached so far on its original source or eventual resolution. In this study, we investigate this problem from the perspective of the solvent effect on FRET spectroscopic ruler (SEFSR), a generic term we use to describe various solvent-dependent factors affecting the accuracy of the FRET experimental method that is known as a "spectroscopic ruler." Some factors belonging to SEFSR, such as direct dye-solvent interaction and labeling configuration, seem to have not received due attention regarding their significance in contributing to the discrepancy. We identify SEFSR by measuring a rigid segment of a double-stranded DNA in various solutions using the smFRET method and evaluate its relative importance in smFRET experiments by measuring segments of a single-stranded DNA and polyethylene glycol (PEG) in solutions. We find that SEFSR can produce non-negligible FRET-inferred interdye distance changes in various solutions, with an intensity following the Hofmeister series in ionic solutions and dependent on labeling configurations. SEFSR is found to be significant in GuHCl and urea solutions, which can fully cover the apparent expansion signal of dye-labeled PEG. Our findings suggest that SEFSR may have played an important role in contributing to the smFRET-SAXS discrepancy.

Large - scale Rectangular Ruler Automated Verification Device

NASA Astrophysics Data System (ADS)

Chen, Hao; Chang, Luping; Xing, Minjian; Xie, Xie

2018-03-01

This paper introduces a large-scale rectangular ruler automated verification device, which consists of photoelectric autocollimator and self-designed mechanical drive car and data automatic acquisition system. The design of mechanical structure part of the device refer to optical axis design, drive part, fixture device and wheel design. The design of control system of the device refer to hardware design and software design, and the hardware mainly uses singlechip system, and the software design is the process of the photoelectric autocollimator and the automatic data acquisition process. This devices can automated achieve vertical measurement data. The reliability of the device is verified by experimental comparison. The conclusion meets the requirement of the right angle test procedure.

The Effects of the "Fraction Ruler" Manipulative for Teaching Computation of Fractions

ERIC Educational Resources Information Center

Schiller, Diane Profita

1977-01-01

Explores the hypothesis that students in the fourth, fifth and sixth grade who were exposed to the "fraction ruler" as a manipulative for exploring basic fraction operations would perform more successfully in addition, subtraction and multiplication problems than students taught fraction operations by the traditional method. (Author/RK)

Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells.

PubMed

Sustarsic, Marko; Kapanidis, Achillefs N

2015-10-01

Single-molecule Förster resonance energy transfer (smFRET) serves as a molecular ruler that is ideally posed to study static and dynamic heterogeneity in living cells. Observing smFRET in cells requires appropriately integrated labeling, internalization and imaging strategies, and significant progress has been made towards that goal. Pioneering studies have demonstrated smFRET detection in both prokaryotic and eukaryotic systems, using both wide-field and confocal microscopies, and have started to answer exciting biological questions. We anticipate that future technical developments will open the door to smFRET for the study of structure, conformational changes and kinetics of biomolecules in living cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiplexed Nanoplasmonic Temporal Profiling of T-Cell Response under Immunomodulatory Agent Exposure

PubMed Central

2016-01-01

Immunomodulatory drugs—agents regulating the immune response—are commonly used for treating immune system disorders and minimizing graft versus host disease in persons receiving organ transplants. At the cellular level, immunosuppressant drugs are used to inhibit pro-inflammatory or tissue-damaging responses of cells. However, few studies have so far precisely characterized the cellular-level effect of immunomodulatory treatment. The primary challenge arises due to the rapid and transient nature of T-cell immune responses to such treatment. T-cell responses involve a highly interactive network of different types of cytokines, which makes precise monitoring of drug-modulated T-cell response difficult. Here, we present a nanoplasmonic biosensing approach to quantitatively characterize cytokine secretion behaviors of T cells with a fine time-resolution (every 10 min) that are altered by an immunosuppressive drug used in the treatment of T-cell-mediated diseases. With a microfluidic platform integrating antibody-conjugated gold nanorod (AuNR) arrays, the technique enables simultaneous multi-time-point measurements of pro-inflammatory (IL-2, IFN-γ, and TNF-α) and anti-inflammatory (IL-10) cytokines secreted by T cells. The integrated nanoplasmonic biosensors achieve precise measurements with low operating sample volume (1 μL), short assay time (∼30 min), heightened sensitivity (∼20–30 pg/mL), and negligible sensor crosstalk. Data obtained from the multicytokine secretion profiles with high practicality resulting from all of these sensing capabilities provide a comprehensive picture of the time-varying cellular functional state during pharmacologic immunosuppression. The capability to monitor cellular functional response demonstrated in this study has great potential to ultimately permit personalized immunomodulatory treatment. PMID:27478873

Direct writing of metal nanostructures: lithographic tools for nanoplasmonics research.

PubMed

Leggett, Graham J

2011-03-22

Continued progress in the fast-growing field of nanoplasmonics will require the development of new methods for the fabrication of metal nanostructures. Optical lithography provides a continually expanding tool box. Two-photon processes, as demonstrated by Shukla et al. (doi: 10.1021/nn103015g), enable the fabrication of gold nanostructures encapsulated in dielectric material in a simple, direct process and offer the prospect of three-dimensional fabrication. At higher resolution, scanning probe techniques enable nanoparticle particle placement by localized oxidation, and near-field sintering of nanoparticulate films enables direct writing of nanowires. Direct laser "printing" of single gold nanoparticles offers a remarkable capability for the controlled fabrication of model structures for fundamental studies, particle-by-particle. Optical methods continue to provide a powerful support for research into metamaterials.

3D chiral nanoplasmonics: fabrication, chiroptic engineering, mechanism, and application in enantioselection (Presentation Recording)

NASA Astrophysics Data System (ADS)

Huang, Zhifeng

2015-09-01

Chirality does naturally exist, and the building blocks of life (e.g. DNA, proteins, peptides and sugars) are usually chiral. Chirality inherently imposes chemical/biological selectivity on functional molecules; hence the discrimination in molecular chirality from an enantiomer to the other mirror image (i.e. enantioselection) has fundamental and application significance. Enantiomers interact with left and right handed circularly polarized light in a different manner with respect to optical extinction; hence, electronic circular dichroism (ECD) has been widely used for enantioselection. However, enantiomers usually have remarkably low ECD intensity, mainly owing to the small electric transition dipole moment induced by molecular sizes compared to the ECD-active wavelength in the UV-visible-near IR region. To enhance ECD magnitude, recently it has being developed 3D chiral nanoplasmonic structures having a helical path, and the dimensions are comparable to the ECD wavelength. However, it is still ambiguous the origin of 3D chiroplasmonics, and there is a lack of studying the interaction of 3D chiroplasmoncs with enantiomers for the application of enantioselection. Herein, we will present a one-step fabrication of 3D silver nanospirals (AgNSs) via low-substrate-temperature glancing angle deposition. AgNSs can be deposited on a wide range of substrates (including transparent and flexible substrates), in an area on the order of cm2. A set of spiral dimensions (such as spiral pitches, number of turns and handedness) have been easily engineered to tune the chiroptic properties, leading to studying the chiroplasmonic principles together with finite element simulation and the LC model. At the end, it will be demonstrated that 3D chiroplasmonics can differentiate molecular chirality of enantiomers with dramatic enhancement in the anisotropy g factor. This study opens a door to sensitively discriminate enantiomer chirality.

TG (Tri-Goniometry) technique: Obtaining perfect angles in Z-plasty planning with a simple ruler.

PubMed

Görgülü, Tahsin; Olgun, Abdulkerim

2016-03-01

The Z-plasty is used frequently in hand surgery to release post-burn scar contractures. Correct angles and equalization of each limb are the most important parts of the Z-plasty technique. A simple ruler is enough for equalization of limb but a goniometer is needed for accuracy and equalization of angles. Classically, angles of 30°, 45°, 60°, 75°, and 90° are used. These angles are important when elongating a contracture line or decreasing tension. Our method uses only trigonometry coefficients and a simple ruler, which is easily obtained and sterilized, enabling surgeons to perform all types of Z-plasty perfectly without measuring angles using a goniometer. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

Laser confocal measurement system for curvature radius of lenses based on grating ruler

NASA Astrophysics Data System (ADS)

Tian, Jiwei; Wang, Yun; Zhou, Nan; Zhao, Weirui; Zhao, Weiqian

2015-02-01

In the modern optical measurement field, the radius of curvature (ROC) is one of the fundamental parameters of optical lens. Its measurement accuracy directly affects the other optical parameters, such as focal length, aberration and so on, which significantly affect the overall performance of the optical system. To meet the demand of measurement instruments for radius of curvature (ROC) with high accuracy in the market, we develop a laser confocal radius measurement system with grating ruler. The system uses the peak point of the confocal intensity curve to precisely identify the cat-eye and confocal positions and then measure the distance between these two positions by using the grating ruler, thereby achieving the high-precision measurement for the ROC. The system has advantages of high focusing sensitivity and anti-environment disturbance ability. And the preliminary theoretical analysis and experiments show that the measuring repeatability can be up to 0.8 um, which can provide an effective way for the accurate measurement of ROC.

Nanoplasmonic-gold-cylinder-array-enhanced terahertz source

NASA Astrophysics Data System (ADS)

Zhiguang, Ao; Jinhai, Sun; He, Cai; Guofeng, Song; Jiakun, Song; Yuzhi, Song; Yun, Xu

2016-12-01

Photoconductive antennas (PCAs) based on nanoplasmonic gratings contact electrodes have been proposed to satisfy the demand for high power, efficiency and responsivity terahertz (THz) sources. Reducing the average photo-generated carrier transport path to the photoconductor contact electrodes was previously considered the dominant mechanism to improve PCAs' power. However, considering the bias in a real device, the electric field between gratings is limited and the role of surface plasmonic resonance (SPR) field enhancement is more important in improving THz radiation. This paper, based on SPR, analyzes the interaction between incident light and substrate in nano cylinder array PCAs and clearly shows that the SPR can enhance the light absorption in the substrate. After the optimization of the structure size, the proposed structure can offer 87% optical transmission into GaAs substrate. Compared with conventional PCAs, the optical transmission into the substrate will increase 5.8 times and the enhancement factor of substrate absorption will reach 13.7 respectively. Project supported by the National Basic Research Program of China (Nos. 2015CB351902, 2015CB932402), the National Key Research Program of China (No. 2011ZX01015-001), and the National Natural Science Foundation of China (No. U143231).

Figure of merit for macrouniformity based on image quality ruler evaluation and machine learning framework

NASA Astrophysics Data System (ADS)

Wang, Weibao; Overall, Gary; Riggs, Travis; Silveston-Keith, Rebecca; Whitney, Julie; Chiu, George; Allebach, Jan P.

2013-01-01

Assessment of macro-uniformity is a capability that is important for the development and manufacture of printer products. Our goal is to develop a metric that will predict macro-uniformity, as judged by human subjects, by scanning and analyzing printed pages. We consider two different machine learning frameworks for the metric: linear regression and the support vector machine. We have implemented the image quality ruler, based on the recommendations of the INCITS W1.1 macro-uniformity team. Using 12 subjects at Purdue University and 20 subjects at Lexmark, evenly balanced with respect to gender, we conducted subjective evaluations with a set of 35 uniform b/w prints from seven different printers with five levels of tint coverage. Our results suggest that the image quality ruler method provides a reliable means to assess macro-uniformity. We then defined and implemented separate features to measure graininess, mottle, large area variation, jitter, and large-scale non-uniformity. The algorithms that we used are largely based on ISO image quality standards. Finally, we used these features computed for a set of test pages and the subjects' image quality ruler assessments of these pages to train the two different predictors - one based on linear regression and the other based on the support vector machine (SVM). Using five-fold cross-validation, we confirmed the efficacy of our predictor.

Integrated nanoplasmonic quantum interfaces for room-temperature single-photon sources

NASA Astrophysics Data System (ADS)

Peyskens, Frédéric; Englund, Dirk; Chang, Darrick

2017-12-01

We describe a general analytical framework of a nanoplasmonic cavity-emitter system interacting with a dielectric photonic waveguide. Taking into account emitter quenching and dephasing, our model directly reveals the single-photon extraction efficiency η as well as the indistinguishability I of photons coupled into the waveguide mode. Rather than minimizing the cavity modal volume, our analysis predicts an optimum modal volume to maximize η that balances waveguide coupling and spontaneous emission rate enhancement. Surprisingly, our model predicts that near-unity indistinguishability is possible, but this requires a much smaller modal volume, implying a fundamental performance trade-off between high η and I at room temperature. Finally, we show that maximizing η I requires that the system has to be driven in the weak coupling regime because quenching effects and decreased waveguide coupling drastically reduce η in the strong coupling regime.

Preliminary Findings from RULER Approach in Spanish Teachers' Emotional Intelligence and Work Engagement

ERIC Educational Resources Information Center

Castillo-Gualda, Ruth; García, Valme; Pena, Mario; Galán, Arturo; Brackett, Marc A.

2017-01-01

Introduction: The goal of this study was to assess the effectiveness of a socio-emotional learning program, RULER, on enhancing both the emotional intelligence and work-related outcomes in Spanish teachers. Measures included: Ability emotional intelligence, assessed by the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT) and work-related…

Periodically patterned structures for nanoplasmonic and biomedical applications

NASA Astrophysics Data System (ADS)

Peer, Akshit

Periodically patterned nanostructures have imparted profound impact on diverse scientific disciplines. In physics, chemistry, and materials science, artificially engineered photonic crystals have demonstrated an unprecedented ability to control the propagation of photons through light concentration and diffraction. The field of photonic crystals has led to many technical advances in fabricating periodically patterned nanostructures in dielectric/metallic materials and controlling the light-matter interactions at the nanoscale. In the field of biomaterials, it is of great interest to apply our knowledge base of photonic materials and explore how such periodically patterned structures control diverse biological functions by varying the available surface area, which is a key attribute for surface hydrophobicity, cell growth and drug delivery. Here we describe closely related scientific applications of large-scale periodically patterned polymers and metal nanostructures. The dissertation starts with nanoplasmonics for improving photovoltaic devices, where we design and optimize experimentally realizable light-trapping nanostructures using rigorous scattering matrix simulations for enhancing the performance of organic and perovskite solar cells. The use of periodically patterned plasmonic metal cathode in conjunction with polymer microlens array significantly improves the absorption in solar cells, providing new opportunities for photovoltaic device design. We further show the unprecedented ability of nanoplasmonics to concentrate light at the nanoscale by designing a large-area plasmonic nanocup array with frequency-selective optical transmission. The fabrication of nanostructure is achieved by coating non-uniform gold layer over a submicron periodic nanocup array imprinted on polystyrene using soft lithography. The gold nanocup array shows extraordinary optical transmission at a wavelength close to the structure period. The resonance wavelength for transmission can be

A design of Si-based nanoplasmonic structure as an antenna and reception amplifier for visible light communication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, J. H.; Lin, Z. Y.; Liu, P.

2014-10-21

Visible light communication has been widely investigated due to its larger bandwidth and higher bit rate, and it can combine with the indoor illumination system that makes it more convenient to carry out. Receiving and processing the visible light signal on chip request for nanophotonics devices performing well. However, conventional optical device cannot be used for light-on-chip integration at subwavelength dimensions due to the diffraction limit. Herein, we propose a design of Si-based nanoplasmonic structure as an antenna and reception amplifier for visible light communication based on the interaction between Si nanoparticle and Au nanorod. This device integrates the uniquemore » scattering property of high-refractive index dielectric Si nanoparticles, whose scattering spectrum is dependent on the particle size, with the localized surface plasmon resonance of Au nanorod. We calculated the spectra collected by plane detector and near field distribution of nanostructure, and theoretically demonstrate that the proposed device can act as good receiver, amplifier and superlens during the visible light signal receiving and processing. Besides, unlike some other designs of nanoantenna devices focused less on how to detect the signals, our hybrid nanoantenna can realize the transfer between the scattering source and the detector effectively by Au nanorod waveguides. These findings suggest that the designed nanoplasmonic structure is expected to be used in on-chip nanophotonics as antenna, spectral splitter and demultiplexer for visible light communication.« less

Optimal Golomb Ruler Sequences Generation for Optical WDM Systems: A Novel Parallel Hybrid Multi-objective Bat Algorithm

NASA Astrophysics Data System (ADS)

Bansal, Shonak; Singh, Arun Kumar; Gupta, Neena

2017-02-01

In real-life, multi-objective engineering design problems are very tough and time consuming optimization problems due to their high degree of nonlinearities, complexities and inhomogeneity. Nature-inspired based multi-objective optimization algorithms are now becoming popular for solving multi-objective engineering design problems. This paper proposes original multi-objective Bat algorithm (MOBA) and its extended form, namely, novel parallel hybrid multi-objective Bat algorithm (PHMOBA) to generate shortest length Golomb ruler called optimal Golomb ruler (OGR) sequences at a reasonable computation time. The OGRs found their application in optical wavelength division multiplexing (WDM) systems as channel-allocation algorithm to reduce the four-wave mixing (FWM) crosstalk. The performances of both the proposed algorithms to generate OGRs as optical WDM channel-allocation is compared with other existing classical computing and nature-inspired algorithms, including extended quadratic congruence (EQC), search algorithm (SA), genetic algorithms (GAs), biogeography based optimization (BBO) and big bang-big crunch (BB-BC) optimization algorithms. Simulations conclude that the proposed parallel hybrid multi-objective Bat algorithm works efficiently as compared to original multi-objective Bat algorithm and other existing algorithms to generate OGRs for optical WDM systems. The algorithm PHMOBA to generate OGRs, has higher convergence and success rate than original MOBA. The efficiency improvement of proposed PHMOBA to generate OGRs up to 20-marks, in terms of ruler length and total optical channel bandwidth (TBW) is 100 %, whereas for original MOBA is 85 %. Finally the implications for further research are also discussed.

Three-Dimensional Integration of Black Phosphorus Photodetector with Silicon Photonics and Nanoplasmonics.

PubMed

Chen, Che; Youngblood, Nathan; Peng, Ruoming; Yoo, Daehan; Mohr, Daniel A; Johnson, Timothy W; Oh, Sang-Hyun; Li, Mo

2017-02-08

We demonstrate the integration of a black phosphorus photodetector in a hybrid, three-dimensional architecture of silicon photonics and metallic nanoplasmonics structures. This integration approach combines the advantages of the low propagation loss of silicon waveguides, high-field confinement of a plasmonic nanogap, and the narrow bandgap of black phosphorus to achieve high responsivity for detection of telecom-band, near-infrared light. Benefiting from an ultrashort channel (∼60 nm) and near-field enhancement enabled by the nanogap structure, the photodetector shows an intrinsic responsivity as high as 10 A/W afforded by internal gain mechanisms, and a 3 dB roll-off frequency of 150 MHz. This device demonstrates a promising approach for on-chip integration of three distinctive photonic systems, which, as a generic platform, may lead to future nanophotonic applications for biosensing, nonlinear optics, and optical signal processing.

PagP Crystallized from SDS/Cosolvent Reveals the Route for Phospholipid Access to the Hydrocarbon Ruler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuesta-Seijo, Jose Antonio; Neale, Chris; Khan, M. Adil

2012-02-06

Enzymatic reactions involving bilayer lipids occur in an environment with strict physical and topological constraints. The integral membrane enzyme PagP transfers a palmitoyl group from a phospholipid to lipid A in order to assist Escherichia coli in evading host immune defenses during infection. PagP measures the palmitoyl group with an internal hydrocarbon ruler that is formed in the interior of the eight-stranded antiparallel {beta} barrel. The access and egress of the palmitoyl group is thought to take a lateral route from the bilayer phase to the barrel interior. Molecular dynamics, mutagenesis, and a 1.4 {angstrom} crystal structure of PagP inmore » an SDS/2-methyl-2,4-pentanediol (MPD) cosolvent system reveal that phospholipid access occurs at the crenel present between strands F and G of PagP. In this way, the phospholipid head group can remain exposed to the cell exterior while the lipid acyl chain remains in a predominantly hydrophobic environment as it translocates to the protein interior.« less

Trends and challenges of refractometric nanoplasmonic biosensors: a review.

PubMed

Estevez, M-Carmen; Otte, Marinus A; Sepulveda, Borja; Lechuga, Laura M

2014-01-02

Motivated by potential benefits such as sensor miniaturization, multiplexing opportunities and higher sensitivities, refractometric nanoplasmonic biosensing has profiled itself in a short time span as an interesting alternative to conventional Surface Plasmon Resonance (SPR) biosensors. This latter conventional sensing concept has been subjected during the last decades to strong commercialization, thereby strongly leaning on well-developed thin-film surface chemistry protocols. Not surprisingly, the examples found in literature based on this sensing concept are generally characterized by extensive analytical studies of relevant clinical and diagnostic problems. In contrast, the more novel Localized Surface Plasmon Resonance (LSPR) alternative finds itself in a much earlier, and especially, more fundamental stage of development. Driven by new fabrication methodologies to create nanostructured substrates, published work typically focuses on the novelty of the presented material, its optical properties and its use - generally limited to a proof-of-concept - as a label-free biosensing scheme. Given the different stages of development both SPR and LSPR sensors find themselves in, it becomes apparent that providing a comparative analysis of both concepts is not a trivial task. Nevertheless, in this review we make an effort to provide an overview that illustrates the progress booked in both fields during the last five years. First, we discuss the most relevant advances in SPR biosensing, including interesting analytical applications, together with different strategies that assure improvements in performance, throughput and/or integration. Subsequently, the remaining part of this work focuses on the use of nanoplasmonic sensors for real label-free biosensing applications. First, we discuss the motivation that serves as a driving force behind this research topic, together with a brief summary that comprises the main fabrication methodologies used in this field. Next, the

Fabrication of large area flexible nanoplasmonic templates with flow coating

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Qian; Devetter, Brent M.; Roosendaal, Timothy

Here, we describe the development of a custom-built two-axis flow coater for the deposition of polymeric nanosphere monolayers used in the fabrication of large area nanoplasmonic films. The technique described here has the capability of depositing large areas (up to 7” x 10”) of self-assembled monolayers of polymeric nanospheres onto polyethylene terephthalate (PET) films. Here, three sets of film consisting of different diameter (ranging from 100 to 300 nm) polymeric nanospheres were used to demonstrate the capabilities of this instrument. To improve the surface wettability of the PET substrates during wet-deposition we enhanced the wettability by using a forced airmore » blown-arc plasma treatment system. Both the local microstructure, as confirmed by scanning electron microscopy, describing monolayer and multilayer coverage, and the overall macroscopic uniformity of the resultant nanostructured film were optimized by controlling the relative stage to blade speed and nanosphere concentration. As this is a scalable technique, large area films such as the ones described here, have a variety of crucial emerging applications in areas such as energy, catalysis, and chemical sensing.« less

Efficient design of nanoplasmonic waveguide devices using the space mapping algorithm.

PubMed

Dastmalchi, Pouya; Veronis, Georgios

2013-12-30

We show that the space mapping algorithm, originally developed for microwave circuit optimization, can enable the efficient design of nanoplasmonic waveguide devices which satisfy a set of desired specifications. Space mapping utilizes a physics-based coarse model to approximate a fine model accurately describing a device. Here the fine model is a full-wave finite-difference frequency-domain (FDFD) simulation of the device, while the coarse model is based on transmission line theory. We demonstrate that simply optimizing the transmission line model of the device is not enough to obtain a device which satisfies all the required design specifications. On the other hand, when the iterative space mapping algorithm is used, it converges fast to a design which meets all the specifications. In addition, full-wave FDFD simulations of only a few candidate structures are required before the iterative process is terminated. Use of the space mapping algorithm therefore results in large reductions in the required computation time when compared to any direct optimization method of the fine FDFD model.

Popular Explanations of Physical Phenomena: Broken Ruler, Oxygen in the Air and Water Attracted by Electric Charges

ERIC Educational Resources Information Center

Riveros, Héctor G.

2012-01-01

The inquiry-based approach to learning has proven to be quite effective, since Socrates, but it is difficult to found good questions to induce reasoning. Many sources explain wrongly some experimental results, which can be used as discrepant events. Some use the breaking of a ruler with a newspaper to "show" that the atmospheric pressure…

Reaction time norms as measured by ruler drop method in school-going South Asian children: A cross-sectional study.

PubMed

Aranha, V P; Saxena, S; Moitra, M; Narkeesh, K; Arumugam, N; Samuel, A J

2017-01-01

This study aimed to estimate normative range for reaction time using ruler drop method for school-going South Asian children between 6 and 12 years of age. A cross-sectional study was used to evaluate the reaction time for 204 children. Normal values for each age group were obtained. The results of multiple linear regressions showed a decrease in the reaction time values with age, and a significant change occurring between six and eight years of age. No difference in reaction time was obtained between boys and girls. Ruler drop method is an easy to use test and the results of this study provide a normative data for age groups 6-12 years ranging from 214.2ms to 248.8ms. These values can serve as a reference to screen children with delayed reaction time. Copyright © 2016 Elsevier GmbH. All rights reserved.

Liquid crystal mediated active nano-plasmonic based on the formation of hybrid plasmonic-photonic modes

NASA Astrophysics Data System (ADS)

Mehrzad, Hossein; Mohajerani, Ezeddin

2018-02-01

The present study aims to demonstrate how active hybrid nano-plasmonic modes become excited due to the coupling of localized plasmonic resonance and Fabry-Perot (FP) optical modes. The proposed structure includes an integration of a micro-cavity filled with liquid crystals with high anisotropy and a layer of gold nanoislands (NIs). The optical absorption of NI is controllably discretized to the narrow-width modes, called "hybrid modes (HM)," due to the interplay between FP and plasmonic modes. HM could demonstrate a strongly intensified and diminished absorption, compared to the absorption of the bare gold layer. Based on the active plasmonic experiments, the HM boosted the figure of merit related to activation capability up to 40 times and subsequently experienced impressive spectral shifts, leading to very wavelength-selective changes. The theoretical simulation of the HM is provided to suggest relevant insights into the experimental results.

Three dimensional chiral plasmon rulers based on silver nanorod trimers.

PubMed

Han, Chunrui; Yang, Lechen; Ye, Piao; Parrott, Edward P J; Pickwell-Macpherson, Emma; Tam, Wing Yim

2018-04-16

The symmetry dependences of plasmon excitation modes are studied in 3D silver nanorod trimers. The degenerate plasmon modes split into chiral modes by breaking the inversion and mirror symmetry of the nanorod trimer through translation and/or rotation of the middle rod. With a translation operation, successive evolution of the circular dichroism (CD) spectrum can be achieved through gradual breaking of the inversion symmetry. An additional rotation operation produces even dramatic spectral changes due to breaking a quasi-mirror symmetry resulted from the same angular distance of the middle rod to the top and bottom rods. Especially, pairs of new chiral modes can be excited due to the contact of the middle rod with the top-bottom rod pair. The spectral changes in the simulations, which are also demonstrated experimentally, envision the 3D chiral nanorod trimer system as plasmon ruler for spatial configuration retrieval and dynamic bio-process analysis at the single molecule level.

Self-Referenced Smartphone-Based Nanoplasmonic Imaging Platform for Colorimetric Biochemical Sensing.

PubMed

Wang, Xinhao; Chang, Te-Wei; Lin, Guohong; Gartia, Manas Ranjan; Liu, Gang Logan

2017-01-03

Colorimetric sensors usually suffer due to errors from variation in light source intensity, the type of light source, the Bayer filter algorithm, and the sensitivity of the camera to incoming light. Here, we demonstrate a self-referenced portable smartphone-based plasmonic sensing platform integrated with an internal reference sample along with an image processing method to perform colorimetric sensing. Two sensing principles based on unique nanoplasmonics enabled phenomena from a nanostructured plasmonic sensor, named as nanoLCA (nano Lycurgus cup array), were demonstrated here for colorimetric biochemical sensing: liquid refractive index sensing and optical absorbance enhancement sensing. Refractive indices of colorless liquids were measured by simple smartphone imaging and color analysis. Optical absorbance enhancement in the colorimetric biochemical assay was achieved by matching the plasmon resonance wavelength with the chromophore's absorbance peak wavelength. Such a sensing mechanism improved the limit of detection (LoD) by 100 times in a microplate reader format. Compared with a traditional colorimetric assay such as urine testing strips, a smartphone plasmon enhanced colorimetric sensing system provided 30 times improvement in the LoD. The platform was applied for simulated urine testing to precisely identify the samples with higher protein concentration, which showed potential point-of-care and early detection of kidney disease with the smartphone plasmonic resonance sensing system.

Effects of using multi-vide ruler kit in the acquisition of numeracy skills among PROTIM students

NASA Astrophysics Data System (ADS)

Arumugan, Hemalatha A./P.; Obeng, Sharifah Nasriah Wan; Talib, Corrienna Abdul; Bunyamin, Muhammad Abdul Hadi; Ali, Marlina; Ibrahim, Norhasniza; Zawadzki, Rainer

2017-08-01

One effective way to teach arithmetic more interestingly and make it easier to learn is through the use of instructional materials. These can help students master certain mathematical skills, particularly multiplication and division, often considered difficult amongst primary school pupils. Nevertheless, the insufficiency of appropriate instructional materials causes difficulty in understanding how to use the proper technique or apply the concept, especially in multiplication. With this in mind, this study investigated whether the innovative and creative instructional material designed to assist and enhance numeracy skills, namely the Multi-vide Ruler kit, could increase students' ability in solving multiplication and division questions and whether it affected their interest in solving numeracy problems. Participants in this study included ten PROTIM (Program Tiga M [Three M Program] - membaca [reading], menulis [writing] dan mengira [calculate]) students, 9-10 years old, who had difficulties in reading, writing and arithmetic. In order to get appropriate support for qualitative research, a pre and post-test containing ten basic mathematical operations, was implemented together with the Multi-vide Ruler Kit. The findings of the qualitative case study, with the pre and post-tests, showed significant differences in their achievement and interest in two-digit multiplication and division operations. The results suggest that this approach could improve PROTIM student's ability to solve basic mathematical operations. What was most encouraging was the increase in students' interest in solving numeracy problems.

A 10-A spectroscopic ruler applied to short polyprolines.

PubMed

Sahoo, Harekrushna; Roccatano, Danilo; Hennig, Andreas; Nau, Werner M

2007-08-08

Fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides of the general structure Trp-(Pro)n-Dbo-NH2 (n = 1-6) was investigated by steady-state and time-resolved fluorescence, CD, and NMR spectroscopy as well as by molecular dynamics (MD) simulations (GROMOS96 force field). The Trp/Dbo FRET pair is characterized by a very short Förster radius (R0 ca. 9 A), which allowed distance determinations in such short peptides. Water and propylene glycol were investigated as solvents. The peptides were designed to show an early nucleation of the poly(Pro)II (PPII) secondary helix structure for n > or = 2, which was confirmed by their CD spectra. The shortest peptide (n = 1) adopts preferentially the trans conformation about the Trp-Pro bond, as confirmed by NMR spectra. The FRET efficiencies ranged 2-72% and were found to depend sensitively on the peptide length, i.e., the number of intervening proline residues. The analysis of the FRET data at different levels of theory (assuming either a fixed distance or distance distributions according to a wormlike chain or Gaussian model) afforded donor-acceptor distances between ca. 8 A (n = 1) and ca. 16 A (n = 6) in water, which were found to be similar or slightly higher in propylene glycol. The distances afforded by the Trp/Dbo FRET pair were found to be reasonable in comparison to literature data, expectations from the PPII helix structure, and the results from MD simulations. The persistence lengths for the longer peptides were found to lie at 30-70 A in water and 220 +/- 40 A in propylene glycol, suggesting a more rigid PPII helical structure in propylene glycol. A detailed comparison with literature data on FRET in polyprolines demonstrates that the donor-acceptor distances extracted by FRET are correlated with the Förster radii of the employed FRET pairs. This demonstrates the limitations of using FRET

High-capacity optical long data memory based on enhanced Young's modulus in nanoplasmonic hybrid glass composites.

PubMed

Zhang, Qiming; Xia, Zhilin; Cheng, Yi-Bing; Gu, Min

2018-03-22

Emerging as an inevitable outcome of the big data era, long data are the massive amount of data that captures changes in the real world over a long period of time. In this context, recording and reading the data of a few terabytes in a single storage device repeatedly with a century-long unchanged baseline is in high demand. Here, we demonstrate the concept of optical long data memory with nanoplasmonic hybrid glass composites. Through the sintering-free incorporation of nanorods into the earth abundant hybrid glass composite, Young's modulus is enhanced by one to two orders of magnitude. This discovery, enabling reshaping control of plasmonic nanoparticles of multiple-length allows for continuous multi-level recording and reading with a capacity over 10 terabytes with no appreciable change of the baseline over 600 years, which opens new opportunities for long data memory that affects the past and future.

Visualization of Nanoplasmonic Coupling to Molecular Orbital in Light Emission Induced by Tunneling Electrons.

PubMed

Yu, Arthur; Li, Shaowei; Wang, Hui; Chen, Siyu; Wu, Ruqian; Ho, W

2018-05-09

The coupling between localized plasmon and molecular orbital in the light emission from a metallic nanocavity has been directly detected and imaged with sub-0.1 nm resolution. The light emission intensity was enhanced when the energy difference between the tunneling electrons and the lowest unoccupied molecular orbital (LUMO) of an azulene molecule matches the energy of a plasmon mode of the nanocavity defined by the Ag-tip and Ag (110) substrate of a scanning tunneling microscope (STM). The spatially resolved image of the light emission intensity matches the spatial distribution of the LUMO obtained by scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. Our results highlight the near-field coupling of a molecular orbital to the radiative decay of a plasmonic excitation in a confined nanoscale junction.

Collective coherence in nearest neighbor coupled metamaterials: A metasurface ruler equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Ningning; Zhang, Weili, E-mail: weili.zhang@okstate.edu; Singh, Ranjan, E-mail: ranjans@ntu.edu.sg

The collective coherent interactions in a meta-atom lattice are the key to myriad applications and functionalities offered by metasurfaces. We demonstrate a collective coherent response of the nearest neighbor coupled split-ring resonators whose resonance shift decays exponentially in the strong near-field coupled regime. This occurs due to the dominant magnetic coupling between the nearest neighbors which leads to the decay of the electromagnetic near fields. Based on the size scaling behavior of the different periodicity metasurfaces, we identified a collective coherent metasurface ruler equation. From the coherent behavior, we also show that the near-field coupling in a metasurface lattice existsmore » even when the periodicity exceeds the resonator size. The identification of a universal coherence in metasurfaces and their scaling behavior would enable the design of novel metadevices whose spectral tuning response based on near-field effects could be calibrated across microwave, terahertz, infrared, and the optical parts of the electromagnetic spectrum.« less

Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site.

PubMed

Hatoum-Aslan, Asma; Maniv, Inbal; Marraffini, Luciano A

2011-12-27

Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in Staphylococcus epidermidis. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.

The Interaction Effects of Program Training, Dosage, and Implementation Quality on Targeted Student Outcomes for The RULER Approach to Social and Emotional Learning

ERIC Educational Resources Information Center

Reyes, Maria Regina; Brackett, Marc A.; Rivers, Susan E.; Elbertson, Nicole A.; Salovey, Peter

2012-01-01

This study examined how training, dosage, and implementation quality of a social and emotional learning program, The RULER Approach, were related to students' social and emotional competencies. There were no main effects for any of the variables on student outcomes, but students had more positive outcomes when their teachers (a) attended more…

Merging colloidal nanoplasmonics and surface plasmon resonance spectroscopy for enhanced profiling of multiple myeloma-derived exosomes.

PubMed

Di Noto, Giuseppe; Bugatti, Antonella; Zendrini, Andrea; Mazzoldi, Elena Laura; Montanelli, Alessandro; Caimi, Luigi; Rusnati, Marco; Ricotta, Doris; Bergese, Paolo

2016-03-15

A novel approach for sorting exosomes from multiple myeloma (MM), monoclonal gammopathy of undetermined significance (MGUS) and healthy individuals is presented. The method is based on the combination of colloidal gold nanoplasmonics and surface plasmon resonance (SPR) biosensing and probes distinctive colloidal properties of MM-derived exosomes, such as molar concentration and cell membrane binding preferences. It allowed to discover that MM patients produce about four folds more exosomes than MGUS and healthy individuals. In addition, it showed that among the analyzed exosomes, only the MM-derived ones bind heparin - a structural analog of heparan sulfate proteoglycans known to mediate exosome endocytosis - with an apparent dissociation constant (Kd) equal to about 1 nM, indicating a high affinity binding. This plasmonic method complements the classical biochemical profiling approach to exosomes, expanding the MM biomarker panel and adding biosensors to the toolbox to diagnose MM. It may find applications for other diseases and has wider interest for fundamental and translational research involving exosomes. Copyright © 2015 Elsevier B.V. All rights reserved.

Nanoplasmonic Quantification of Tumor-derived Extracellular Vesicles in Plasma Microsamples for Diagnosis and Treatment Monitoring

PubMed Central

Liang, Kai; Liu, Fei; Fan, Jia; Sun, Dali; Liu, Chang; Lyon, Christopher J.; Bernard, David W.; Li, Yan; Yokoi, Kenji; Katz, Matthew H.; Koay, Eugene J.; Zhao, Zhen; Hu, Ye

2017-01-01

Tumour-derived extracellular vesicles (EVs) are of increasing interest as a resource of diagnostic biomarkers. However, most EV assays require large samples, are time-consuming, low-throughput and costly, and thus impractical for clinical use. Here, we describe a rapid, ultrasensitive and inexpensive nanoplasmon-enhanced scattering (nPES) assay that directly quantifies tumor-derived EVs from as little as 1 μL of plasma. The assay uses the binding of antibody-conjugated gold nanospheres and nanorods to EVs captured by EV-specific antibodies on a sensor chip to produce a local plasmon effect that enhances tumour-derived EV detection sensitivity and specificity. We identified a pancreatic cancer EV biomarker, ephrin type-A receptor 2 (EphA2), and demonstrate that an nPES assay for EphA2-EVs distinguishes pancreatic cancer patients from pancreatitis patients and healthy subjects. EphA2-EVs were also informative in staging tumour progression and in detecting early responses to neoadjuvant therapy, with better performance than a conventional enzyme-linked immunosorbent assay. The nPES assay can be easily refined for clinical use, and readily adapted for diagnosis and monitoring of other conditions with disease-specific EV biomarkers. PMID:28791195

Nanoplasmonically Engineered Interfaces on Amorphous TiO2 for Highly Efficient Photocatalysis in Hydrogen Evolution.

PubMed

Liang, Huijun; Meng, Qiuxia; Wang, Xiaobing; Zhang, Hucheng; Wang, Jianji

2018-04-25

The nanoplasmonic metal-driven photocatalytic activity depends heavily on the spacing between metal nanoparticles (NPs) and semiconductors, and this work shows that ethylene glycol (EG) is an ideal candidate for interface spacer. Controlling the synthetic systems at pH 3, the composite of Ag NPs with EG-stabilized amorphous TiO 2 (Ag/TiO 2 -3) was synthesized by the facile light-induced reduction. It is verified that EG spacers can set up suitable geometric arrangement in the composite: the twin hydroxyls act as stabilizers to bind Ag NPs and TiO 2 together and the nonconductive alkyl chains consisting only of two CH 2 are able to separate the two building blocks completely and also provide the shortest channels for an efficient transfer of radiation energies to reach TiO 2 . Employed as photocatalysts in hydrogen evolution under visible light, amorphous TiO 2 hardly exhibits the catalytic activity due to high defect density, whereas Ag/TiO 2 -3 represents a remarkably high catalytic efficiency. The enhancement mechanism of the reaction rate is proposed by the analysis of the compositional, structural, and optical properties from a series of Ag/TiO 2 composites.

Madness and Rulers: Events in Coorg and London in 1810, as observed by the Hon. Arthur Cole, the resident at Mysore

PubMed Central

Jain, Sanjeev; Sarin, Alok

2015-01-01

What happens if a King becomes mentally ill? Excerpts from the personal papers of Arthur Henry Cole, Resident to the Kingdom of Mysore in 1809, open up fascinating insights into the madness of rulers, in neighboring Coorg and faraway London, and ways in which different societies responded to this. Musings on legal capacity and restrictions imposed on account of insanity, as well as migration and ennui in imperial colonies inevitably follow. PMID:26124533

Call for papers for special issue of Journal of Molecular Spectroscopy focusing on "Frequency-comb spectroscopy"

NASA Astrophysics Data System (ADS)

Foltynowicz, Aleksandra; Picqué, Nathalie; Ye, Jun

2018-05-01

Frequency combs are becoming enabling tools for many applications in science and technology, beyond the original purpose of frequency metrology of simple atoms. The precisely evenly spaced narrow lines of a laser frequency comb inspire intriguing approaches to molecular spectroscopy, designed and implemented by a growing community of scientists. Frequency-comb spectroscopy advances the frontiers of molecular physics across the entire electro-magnetic spectrum. Used as frequency rulers, frequency combs enable absolute frequency measurements and precise line shape studies of molecular transitions, for e.g. tests of fundamental physics and improved determination of fundamental constants. As light sources interrogating the molecular samples, they dramatically improve the resolution, precision, sensitivity and acquisition time of broad spectral-bandwidth spectroscopy and open up new opportunities and applications at the leading edge of molecular spectroscopy and sensing.

The pH ruler: a Java applet for developing interactive exercises on acids and bases.

PubMed

Barrette-Ng, Isabelle H

2011-07-01

In introductory biochemistry courses, it is often a struggle to teach the basic concepts of acid-base chemistry in a manner that is relevant to biological systems. To help students gain a more intuitive and visual understanding of abstract acid-base concepts, a simple graphical construct called the pH ruler Java applet was developed. The applet allows students to visualize the abundance of different protonation states of diprotic and triprotic amino acids at different pH values. Using the applet, the student can drag a widget on a slider bar to change the pH and observe in real time changes in the abundance of different ionization states of this amino acid. This tool provides a means for developing more complex inquiry-based, active-learning exercises to teach more advanced topics of biochemistry, such as protein purification, protein structure and enzyme mechanism.

Theoretical investigation of silicide Schottky barrier detector integrated in horizontal metal-insulator-silicon-insulator-metal nanoplasmonic slot waveguide.

PubMed

Zhu, Shiyang; Lo, G Q; Kwong, D L

2011-08-15

An ultracompact integrated silicide Schottky barrier detector (SBD) is designed and theoretically investigated to electrically detect the surface plasmon polariton (SPP) propagating along horizontal metal-insulator-silicon-insulator-metal nanoplasmonic slot waveguides at the telecommunication wavelength of 1550 nm. An ultrathin silicide layer inserted between the silicon core and the insulator, which can be fabricated precisely using the well-developed self-aligned silicide process, absorbs the SPP power effectively if a suitable silicide is chosen. Moreover, the Schottky barrier height in the silicide-silicon-silicide configuration can be tuned substantially by the external voltage through the Schottky effect owing to the very narrow silicon core. For a TaSi(2) detector with optimized dimensions, numerical simulation predicts responsivity of ~0.07 A/W, speed of ~60 GHz, dark current of ~66 nA at room temperature, and minimum detectable power of ~-29 dBm. The design also suggests that the device's size can be reduced and the overall performances will be further improved if a silicide with smaller permittivity is used. © 2011 Optical Society of America

A Readiness Ruler for Assessing Motivation to Change in People with Eating Disorders.

PubMed

St-Hilaire, Annie; Axelrod, Kaitlyn; Geller, Josie; Mazanek Antunes, Juliana; Steiger, Howard

2017-09-01

We examined the psychometric properties of the Eating Disorder Readiness Ruler a simple self-report instrument designed to enable rapid assessment of readiness to change problematic eating behaviours in people with clinical eating disorders. We administered the ED-RR, the Eating Disorders Examination Questionnaire and a measure of autonomous and controlled motivation for change to 206 individuals receiving outpatient treatment for an eating disorder. A principal axis factoring analysis of the ED-RR yielded a significant two-factor solution (explaining 59% of variance)-one factor pertaining to restriction and body image preoccupation (four items), the other to binge-eating and vomiting symptoms (two items). The ED-RR showed good internal consistency (alpha coefficients for the two factors being .77 and .84 respectively). Furthermore, individuals reporting higher readiness showed higher scores on independent measures of autonomous motivation and greater symptom reductions over time. Results suggest that the ED-RR is a psychometrically sound tool with potential clinical utility. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.

Comparison of Standardized Clinical Evaluation of Wounds Using Ruler Length by Width and Scout Length by Width Measure and Scout Perimeter Trace

PubMed Central

Langemo, Diane; Spahn, James; Spahn, Thomas; Pinnamaneni, V. Chowdry

2015-01-01

ABSTRACT The study objective was to examine precision in wound measurement using a recently Food and Drug Administration-approved Scout (WoundVision, LLC, Indianapolis, Indiana) device to measure wound length (L) and width (W). Wound perimeter and a ruler measurement of L and W were also made. Images of 40 actual patient wounds were measured using the Scout device. All 3 techniques (length, width, perimeter) demonstrated acceptable within and between reader precision; however, the best precision was in wound perimeter measurement. PMID:25679463

Nanoplasmonic biosensor: detection and amplification of dual bio-signatures of circulating tumor DNA.

PubMed

Nguyen, Anh H; Sim, Sang Jun

2015-05-15

Circulating tumor DNA (ctDNA) bearing tumor-specific mutation and methylation are promising biomarkers for noninvasive cancer assessment. However, existing methods for ctDNA detection are restricted to genetic mutations. Recently, nanoplasmonics has emerged as a platform for one-step dual detection with high sensitivity and specificity. Here we present a strategy for ultrasensitive detection of tumor-specific mutations (E542K and E545K) and methylation of ctDNA of PIK3CA gene based on localized surface plasmon resonance (LSPR) and the coupling plasmon mode of gold nanoparticles (AuNPs). Peptide nucleic acids (PNA) is used as a probe to capture and enrich the 69-bp PIK3CA ctDNA. The exposure of PNA-probed AuNPs to 200 fM ctDNA generates LSPR-peak shift of 4.3 nm, corresponding to the primary response. Immunogold colloids are exploited as methylation detectors and plasmon coupling based enhancement for secondary response. LSPR-peak shifted from 4.3 nm to 11.4 nm upon the immunogold colloids binding to two methylcytosines (mCpG), which is an approximately 107% increase, compared to that of the primary response. This enhancement leads to four times (~50 fM) improvement of sensitivity and because of two mCpG sites, ctDNA was detected. These results demonstrate that the sensor can simultaneously detect the hot-spot mutation and epigenetic changes on the ctDNA. Promisingly, other specific-tumor mutants and epigenetic changes can be detected at low concentration with this platform. Copyright © 2014 Elsevier B.V. All rights reserved.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics.

PubMed

Inci, Fatih; Filippini, Chiara; Baday, Murat; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L; Carocci, Margot; Yamamoto, Hidemi S; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R; Singhal, Amit; Yang, Priscilla L; Nibert, Max L; Fichorova, Raina N; Lau, Daryl T-Y; Henrich, Timothy J; Kaye, Kenneth M; Schachter, Steven C; Kuritzkes, Daniel R; Steinmetz, Lars M; Gambhir, Sanjiv S; Davis, Ronald W; Demirci, Utkan

2015-08-11

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

PubMed Central

Inci, Fatih; Filippini, Chiara; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S.; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L.; Carocci, Margot; Yamamoto, Hidemi S.; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R.; Singhal, Amit; Yang, Priscilla L.; Nibert, Max L.; Fichorova, Raina N.; Lau, Daryl T.-Y.; Henrich, Timothy J.; Kaye, Kenneth M.; Schachter, Steven C.; Kuritzkes, Daniel R.; Steinmetz, Lars M.; Gambhir, Sanjiv S.; Davis, Ronald W.; Demirci, Utkan

2015-01-01

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes. PMID:26195743

Ultra-compact structure in intermediate-luminosity radio quasars: building a sample of standard cosmological rulers and improving the dark energy constraints up to z 3

NASA Astrophysics Data System (ADS)

Cao, Shuo; Zheng, Xiaogang; Biesiada, Marek; Qi, Jingzhao; Chen, Yun; Zhu, Zong-Hong

2017-09-01

Context. Ultra-compact structure in radio sources (especially in quasars that can be observed up to very high redshifts), with milliarcsecond angular sizes measured by very-long-baseline interferometry (VLBI), is becoming an important astrophysical tool for probing both cosmology and the physical properties of AGN. Aims: We present a newly compiled data set of 120 milliarcsec. compact radio sources representing intermediate-luminosity quasars covering the redshift range 0.46 < z < 2.76 and check the possibility of using these sources as independent cosmological probes. These quasars observed at 2.29 GHz show negligible dependence on redshifts and intrinsic luminosity, and thus represent a fixed comoving-length of standard ruler. Methods: For a cosmological ruler with intrinsic length lm, the angular size-redshift relation can be written as θ(z) = lm/DA(z, where θ(z) is the angular size at redshift z, and DA(z) is the corresponding angular diameter distance. We use a compilation of angular size and redshift data for ultra-compact radio sources from a well-known VLBI survey, and implement a new cosmology-independent technique to calibrate the linear size of this standard ruler, which is also used to test different cosmological models with and without the flat universe assumption. Results: We determine the linear size of this standard ruler as lm = 11.03 ± 0.25 pc, which is the typical radius at which AGN jets become opaque at the observed frequency ν 2 GHz. Our measurement of this linear size is also consistent with the previous and recent radio observations at other different frequencies. In the framework of flat ΛCDM model, we find a high value of the matter density parameter, Ωm = 0.322+0.244-0.141, and a low value of the Hubble constant, H0 = 67.6+7.8-7.4 km s-1 Mpc-1, which is in excellent agreement with the cosmic microwave background (CMB) anisotropy measurements by Planck. We obtain Ωm = 0.309+0.215-0.151, w = -0.970+0.500-1.730 at 68.3% CL for the

Multiplexed nanoplasmonic biosensor for one-step simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine.

PubMed

Soler, Maria; Belushkin, Alexander; Cavallini, Andrea; Kebbi-Beghdadi, Carole; Greub, Gilbert; Altug, Hatice

2017-08-15

Development of rapid and multiplexed diagnostic tools is a top priority to address the current epidemic problem of sexually transmitted diseases. Here we introduce a novel nanoplasmonic biosensor for simultaneous detection of the two most common bacterial infections: Chlamydia trachomatis and Neisseria gonorrhoeae. Our plasmonic microarray is composed of gold nanohole sensor arrays that exhibit the extraordinary optical transmission (EOT), providing highly sensitive analysis in a label-free configuration. The integration in a microfluidic system and the precise immobilization of specific antibodies on the individual sensor arrays allow for selective detection and quantification of the bacteria in real-time. We achieved outstanding sensitivities for direct immunoassay of urine samples, with a limit of detection of 300 colony forming units (CFU)/mL for C. trachomatis and 1500CFU/mL for N. gonorrhoeae. The multiplexing capability of our biosensor was demonstrated by analyzing different urine samples spiked with either C. trachomatis or N. gonorrhoeae, and also containing both bacteria. We could successfully detect, identify and quantify the levels of the two bacteria in a one-step assay, without the need for DNA extraction or amplification techniques. This work opens up new possibilities for the implementation of point-of-care biosensors that enable fast, simple and efficient diagnosis of sexually transmitted infections. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

High sensitive detection of copper II ions using D-penicillamine-coated gold nanorods based on localized surface plasmon resonance

NASA Astrophysics Data System (ADS)

Hong, Yoochan; Jo, Seongjae; Park, Joohyung; Park, Jinsung; Yang, Jaemoon

2018-05-01

In this paper, we describe the development of a nanoplasmonic biosensor based on the localized surface plasmon resonance (LSPR) effect that enables a sensitive and selective recognition of copper II ions. First, we fabricated the nanoplasmonics as LSPR substrates using gold nanorods (GNR) and the nano-adsorption method. The LSPR sensitivity of the nanoplasmonics was evaluated using various solvents with different refractive indexes. Subsequently, D-penicillamine (DPA)—a chelating agent of copper II ions—was conjugated to the surface of the GNR. The limit of detection (LOD) for the DPA-conjugated nanoplasmonics was 100 pM. Furthermore, selectivity tests were conducted using various divalent cations, and sensitivity tests were conducted on the nanoplasmonics under blood-like environments. Finally, the developed nanoplasmonic biosensor based on GNR shows great potential for the effective recognition of copper II ions, even in human blood conditions.

High sensitive detection of copper II ions using D-penicillamine-coated gold nanorods based on localized surface plasmon resonance.

PubMed

Hong, Yoochan; Jo, Seongjae; Park, Joohyung; Park, Jinsung; Yang, Jaemoon

2018-05-25

In this paper, we describe the development of a nanoplasmonic biosensor based on the localized surface plasmon resonance (LSPR) effect that enables a sensitive and selective recognition of copper II ions. First, we fabricated the nanoplasmonics as LSPR substrates using gold nanorods (GNR) and the nano-adsorption method. The LSPR sensitivity of the nanoplasmonics was evaluated using various solvents with different refractive indexes. Subsequently, D-penicillamine (DPA)-a chelating agent of copper II ions-was conjugated to the surface of the GNR. The limit of detection (LOD) for the DPA-conjugated nanoplasmonics was 100 pM. Furthermore, selectivity tests were conducted using various divalent cations, and sensitivity tests were conducted on the nanoplasmonics under blood-like environments. Finally, the developed nanoplasmonic biosensor based on GNR shows great potential for the effective recognition of copper II ions, even in human blood conditions.

Colorimetric monitoring of nanometer distance changes in DNA-templated plasmon rulers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lermusiaux, Laurent; Bidault, Sebastien

2016-03-01

The nanometer-scale sensitivity of plasmon coupling allows the translation of minute morphological changes in nanostructures into macroscopic optical signals. In particular, single nanostructure scattering spectroscopy provides a direct estimation of interparticle distances in gold nanoparticle (AuNP) dimers linked by a short DNA double-strand [M. P. Busson et al, Nano Lett. 11, 5060 (2011)]. We demonstrate here that this spectroscopic information can be inferred from simple widefield measurements on a calibrated color camera [L. Lermusiaux et al, ACS Nano 9, 978 (2015)]. This allows us to analyze the influence of electrostatic and steric interparticle interactions on the morphology of DNA-templated AuNP groupings. Furthermore, polarization-resolved measurements on a color CCD provide a parallel imaging of AuNP dimer orientations. We apply this spectroscopic characterization to identify dimers featuring two different conformations of the same DNA template. In practice, the biomolecular scaffold contains a hairpin-loop that opens after hybridization to a specific DNA sequence and increases the interparticle distance [L. Lermusiaux et al, ACS Nano 6, 10992 (2012)]. These results open exciting perspectives for the parallel sensing of single specific DNA strands using plasmon rulers. We discuss the limits of this approach in terms of the physicochemical stability and reactivity of these nanostructures and demonstrate the importance of engineering the AuNP surface chemistry, in particular using amphiphilic ligands [L. Lermusiaux and S. Bidault, Small (2015), in press].

Cholesterol affects the interaction between an ionic liquid and phospholipid vesicles. A study by differential scanning calorimetry and nanoplasmonic sensing.

PubMed

Russo, Giacomo; Witos, Joanna; Rantamäki, Antti H; Wiedmer, Susanne K

2017-12-01

The present work aims at studying the interactions between cholesterol-rich phosphatidylcholine-based lipid vesicles and trioctylmethylphosphonium acetate ([P 8881 ][OAc]), a biomass dissolving ionic liquid (IL). The effect of cholesterol was assayed by using differential scanning calorimetry (DSC) and nanoplasmonic sensing (NPS) measurement techniques. Cholesterol-enriched dipalmitoyl-phosphatidylcholine vesicles were exposed to different concentrations of the IL, and the derived membrane perturbation was monitored by DSC. The calorimetric data could suggest that the binding and infiltration of the IL are delayed in the vesicles containing cholesterol. To clarify our findings, NPS was applied to quantitatively follow the resistance of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine incorporating 0, 10, and 50mol% of cholesterol toward the IL exposure over time. The membrane perturbation induced by different concentrations of IL was found to be a concentration dependent process on cholesterol-free lipid vesicles. Moreover, our results showed that lipid depletion in cholesterol-enriched lipid vesicles is inversely proportional to the increasing amount of cholesterol in the vesicles. These findings support that cholesterol-rich lipid bilayers are less susceptible toward membrane disrupting agents as compared to membranes that do not incorporate any sterols. This probably occurs because cholesterol tightens the phospholipid acyl chain packing of the plasma membranes, increasing their resistance and reducing their permeability. Copyright © 2017 Elsevier B.V. All rights reserved.

Hybrid strategies for nanolithography and chemical patterning

NASA Astrophysics Data System (ADS)

Srinivasan, Charan

Remarkable technological advances in photolithography have extended patterning to the sub-50-nm regime. However, because photolithography is a top-down approach, it faces substantial technological and economic challenges in maintaining the downward scaling trends of feature sizes below 30 nm. Concurrently, fundamental research on chemical self-assembly has enabled the path to access molecular length scales. The key to the success of photolithography is its inherent economies of scale, which justify the large capital investment for its implementation. In this thesis research, top-down and bottom-up approaches have been combined synergistically, and these hybrid strategies have been employed in applications that do not have the economies of scale found in semiconductor chip manufacturing. The specific instances of techniques developed here include molecular-ruler lithography and a series of nanoscale chemical patterning methods. Molecular-ruler lithography utilizes self-assembled multilayered films as a sidewall spacer on initial photolithographically patterned gold features (parent) to place a second-generation feature (daughter) in precise proximity to the parent. The parent-daughter separation, which is on the nanometer length scale, is defined by the thickness of the molecular-ruler resist. Analogous to protocols followed in industry to evaluate lithographic performance, electrical test-pad structures were designed to interrogate the nanostructures patterned by molecular-ruler nanolithography, failure modes creating electrical shorts were mapped to each lithographic step, and subsequent lithographic optimization was performed to pattern nanoscale devices with excellent electrical performance. The optimized lithographic processes were applied to generate nanoscale devices such as nanowires and thin-film transistors (TFTs). Metallic nanowires were patterned by depositing a tertiary generation material in the nanogap and surrounding micron-scale regions, and then

Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

PubMed Central

Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

2010-01-01

Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs.

PubMed

Hatoum-Aslan, Asma; Samai, Poulami; Maniv, Inbal; Jiang, Wenyan; Marraffini, Luciano A

2013-09-27

Small RNAs undergo maturation events that precisely determine the length and structure required for their function. CRISPRs (clustered regularly interspaced short palindromic repeats) encode small RNAs (crRNAs) that together with CRISPR-associated (cas) genes constitute a sequence-specific prokaryotic immune system for anti-viral and anti-plasmid defense. crRNAs are subject to multiple processing events during their biogenesis, and little is known about the mechanism of the final maturation step. We show that in the Staphylococcus epidermidis type III CRISPR-Cas system, mature crRNAs are measured in a Cas10·Csm ribonucleoprotein complex to yield discrete lengths that differ by 6-nucleotide increments. We looked for mutants that impact this crRNA size pattern and found that an alanine substitution of a conserved aspartate residue of Csm3 eliminates the 6-nucleotide increments in the length of crRNAs. In vitro, recombinant Csm3 binds RNA molecules at multiple sites, producing gel-shift patterns that suggest that each protein binds 6 nucleotides of substrate. In vivo, changes in the levels of Csm3 modulate the crRNA size distribution without disrupting the 6-nucleotide periodicity. Our data support a model in which multiple Csm3 molecules within the Cas10·Csm complex bind the crRNA with a 6-nucleotide periodicity to function as a ruler that measures the extent of crRNA maturation.

A Ruler Protein in a Complex for Antiviral Defense Determines the Length of Small Interfering CRISPR RNAs

PubMed Central

Hatoum-Aslan, Asma; Samai, Poulami; Maniv, Inbal; Jiang, Wenyan; Marraffini, Luciano A.

2013-01-01

Small RNAs undergo maturation events that precisely determine the length and structure required for their function. CRISPRs (clustered regularly interspaced short palindromic repeats) encode small RNAs (crRNAs) that together with CRISPR-associated (cas) genes constitute a sequence-specific prokaryotic immune system for anti-viral and anti-plasmid defense. crRNAs are subject to multiple processing events during their biogenesis, and little is known about the mechanism of the final maturation step. We show that in the Staphylococcus epidermidis type III CRISPR-Cas system, mature crRNAs are measured in a Cas10·Csm ribonucleoprotein complex to yield discrete lengths that differ by 6-nucleotide increments. We looked for mutants that impact this crRNA size pattern and found that an alanine substitution of a conserved aspartate residue of Csm3 eliminates the 6-nucleotide increments in the length of crRNAs. In vitro, recombinant Csm3 binds RNA molecules at multiple sites, producing gel-shift patterns that suggest that each protein binds 6 nucleotides of substrate. In vivo, changes in the levels of Csm3 modulate the crRNA size distribution without disrupting the 6-nucleotide periodicity. Our data support a model in which multiple Csm3 molecules within the Cas10·Csm complex bind the crRNA with a 6-nucleotide periodicity to function as a ruler that measures the extent of crRNA maturation. PMID:23935102

Development of an optically-based tension-indicating implanted orthopedic screw with a luminescent spectral ruler

NASA Astrophysics Data System (ADS)

Ravikumar, Nakul; Rogalski, Melissa M.; Benza, Donny; Lake, Joshua; Urban, Matthew; Pelham, Hunter; Anker, Jeffrey N.; DesJardins, John D.

2017-03-01

An orthopaedic screw was designed with an optical tension-indicator to non-invasively quantify screw tension and monitor the load sharing between the bone and the implant. The screw both applies load to the bone, and measures this load by reporting the strain on the screw. The screw contains a colorimetric optical encoder that converts axial strain into colorimetric changes visible through the head of the screw, or luminescent spectral changes that are detected through tissue. Screws were tested under cyclic mechanical loading to mimic in-vivo conditions to verify the sensitivity, repeatability, and reproducibility of the sensor. In the absence to tissue, color was measured using a digital camera as a function of axial load on a stainless steel cannulated (hollow) orthopedic screw, modified by adding a passive colorimetric strain gauge through the central hole. The sensor was able to quantify clinically-relevant bone healing strains. The sensor exhibited good repeatability and reproducibility but also displayed hysteresis due to the internal mechanics of the screw. The strain indicator was also modified for measurement through tissue by replacing the reflective colorimetric sensor with a low-background X-ray excited optical luminescence signal. Luminescent spectra were acquired through 6 mm of chicken breast tissue. Overall, this research shows feasibility for a unique device which quantifies the strain on an orthopedic screw. Future research will involve reducing hysteresis by changing the mechanism of strain transduction in the screw, miniaturizing the luminescent strain gauge, monitoring bending as well as tension, using alternative luminescent spectral rulers based upon near infrared fluorescence or upconversion luminescence, and application to monitoring changes in pretension and load sharing during bone healing.

The larynx ruler to measure height and profile of vocal folds: a proof of concept.

PubMed

Desuter, Gauthier; Mertens, Benjamin; Delchambre, Alain; van Lith-Bijl, Julie; van Benthem, Peter Paul; Sjögren, Elisabeth

2017-01-01

Glottic leakage during phonation is a direct consequence of unilateral vocal fold (VF) paralysis. This air leakage can be in the horizontal plane and in the vertical plane. Presently, there is no easily applicable medical device allowing noninvasive, office-based measurement of the relative vertical position of the VFs. The larynx ruler (LR) is a laser-based measuring device that could meet the previously stated need, using a flexible endoscope. This study represents a proof of concept regarding the use of the LR in assessing VF relative positions in the vertical plane. One fresh male human cadaver larynx, free of neurologic and anatomic disease, was explored with the LR system through the operative channel of a flexible gastroenterology video-endoscope. The tip of the video-endoscope was located in the laryngeal vestibule. The right crico-arytenoid joint was posteriorly disarticulated. Tilting of the VF was obtained by pulling or pushing the arytenoid cartilage with a mosquito forceps fixed to the stump of the previously sectioned superior tip of the posterior crico-arytenoid muscle allowing anterior and posterior tilting of the arytenoid cartilage in order to induce an elevation or a depression of the VF process. Ten "push" and ten "pull" sessions were performed. The distance from the tip of the video-endoscope to each illuminated pixel of the laser beam was recorded. The level difference between the left and right VFs was measured for each recording. Data provided by the LR were consistently in accordance with the movements applied on the VFs. The accuracy of 0.2 mm of the LR is compatible with the envisioned applications for the human larynx. The LR system represents a feasible technique to evaluate respective vertical position of VFs in the human larynx. Technical limitations were identified that will require improvements before experimental use on human beings.

Portable SERS sensor for malachite green and other small dye molecules

NASA Astrophysics Data System (ADS)

Qiu, Suyan; Zhao, Fusheng; Li, Jingting; Shih, Wei-Chuan

2017-02-01

Sensitive detection of specific chemicals on site can be extremely powerful in many fields. Owing to its molecular fingerprinting capability, surface-enhanced Raman scattering has been one of the technological contenders. In this paper, we describe the novel use of DNA topological nanostructure on nanoporous gold nanoparticle (NPG-NP) array chip for chemical sensing. NPG-NP features large surface area and high-density plasmonic field enhancement known as "hotspots". Hence, NPG-NP array chip has found many applications in nanoplasmonic sensor development. This technique can provide novel label-free molecular sensing capability and enables high sensitivity and specificity detection using a portable Raman spectrometer.

Plasmon ruler with angstrom length resolution.

PubMed

Hill, Ryan T; Mock, Jack J; Hucknall, Angus; Wolter, Scott D; Jokerst, Nan M; Smith, David R; Chilkoti, Ashutosh

2012-10-23

We demonstrate a plasmon nanoruler using a coupled film nanoparticle (film-NP) format that is well-suited for investigating the sensitivity extremes of plasmonic coupling. Because it is relatively straightforward to functionalize bulk surface plasmon supporting films, such as gold, we are able to precisely control plasmonic gap dimensions by creating ultrathin molecular spacer layers on the gold films, on top of which we immobilize plasmon resonant nanoparticles (NPs). Each immobilized NP becomes coupled to the underlying film and functions as a plasmon nanoruler, exhibiting a distance-dependent resonance red shift in its peak plasmon wavelength as it approaches the film. Due to the uniformity of response from the film-NPs to separation distance, we are able to use extinction and scattering measurements from ensembles of film-NPs to characterize the coupling effect over a series of very short separation distances-ranging from 5 to 20 Å-and combine these measurements with similar data from larger separation distances extending out to 27 nm. We find that the film-NP plasmon nanoruler is extremely sensitive at very short film-NP separation distances, yielding spectral shifts as large as 5 nm for every 1 Å change in separation distance. The film-NP coupling at extremely small spacings is so uniform and reliable that we are able to usefully probe gap dimensions where the classical Drude model of the conducting electrons in the metals is no longer descriptive; for gap sizes smaller than a few nanometers, either quantum or semiclassical models of the carrier response must be employed to predict the observed wavelength shifts. We find that, despite the limitations, large field enhancements and extreme sensitivity persist down to even the smallest gap sizes.

Roadmap on plasmonics

NASA Astrophysics Data System (ADS)

Stockman, Mark I.; Kneipp, Katrin; Bozhevolnyi, Sergey I.; Saha, Soham; Dutta, Aveek; Ndukaife, Justus; Kinsey, Nathaniel; Reddy, Harsha; Guler, Urcan; Shalaev, Vladimir M.; Boltasseva, Alexandra; Gholipour, Behrad; Krishnamoorthy, Harish N. S.; MacDonald, Kevin F.; Soci, Cesare; Zheludev, Nikolay I.; Savinov, Vassili; Singh, Ranjan; Groß, Petra; Lienau, Christoph; Vadai, Michal; Solomon, Michelle L.; Barton, David R., III; Lawrence, Mark; Dionne, Jennifer A.; Boriskina, Svetlana V.; Esteban, Ruben; Aizpurua, Javier; Zhang, Xiang; Yang, Sui; Wang, Danqing; Wang, Weijia; Odom, Teri W.; Accanto, Nicolò; de Roque, Pablo M.; Hancu, Ion M.; Piatkowski, Lukasz; van Hulst, Niek F.; Kling, Matthias F.

2018-04-01

Plasmonics is a rapidly developing field at the boundary of physical optics and condensed matter physics. It studies phenomena induced by and associated with surface plasmons—elementary polar excitations bound to surfaces and interfaces of good nanostructured metals. This Roadmap is written collectively by prominent researchers in the field of plasmonics. It encompasses selected aspects of nanoplasmonics. Among them are fundamental aspects, such as quantum plasmonics based on the quantum-mechanical properties of both the underlying materials and the plasmons themselves (such as their quantum generator, spaser), plasmonics in novel materials, ultrafast (attosecond) nanoplasmonics, etc. Selected applications of nanoplasmonics are also reflected in this Roadmap, in particular, plasmonic waveguiding, practical applications of plasmonics enabled by novel materials, thermo-plasmonics, plasmonic-induced photochemistry and photo-catalysis. This Roadmap is a concise but authoritative overview of modern plasmonics. It will be of interest to a wide audience of both fundamental physicists and chemists, as well as applied scientists and engineers.

Plasmon Ruler with Ångstrom Length Resolution

PubMed Central

Hill, Ryan T.; Mock, Jack J.; Hucknall, Angus; Wolter, Scott D.; Jokerst, Nan M.; Smith, David R.; Chilkoti, Ashutosh

2012-01-01

We demonstrate a plasmon nanoruler using a coupled film-nanoparticle (film-NP) format that is well suited for investigating the sensitivity extremes of plasmonic coupling. Because it is relatively straightforward to functionalize bulk, surface plasmon supporting films such as gold, we are able to precisely control plasmonic gap dimensions by creating ultra-thin molecular spacer layers on the gold films, on top of which we immobilize plasmon resonant nanoparticles (NPs). Each immobilized NP becomes coupled to the underlying film and functions as a plasmon nanoruler, exhibiting a distance-dependent resonance red-shift in its peak plasmon wavelength as it approaches the film. Due to the uniformity of response from the film-NPs to separation distance, we are able to use extinction and scattering measurements from ensembles of film-NPs to characterize the coupling effect over a series of very short separation distances – ranging from 5 – 20 Å – and combine these measurements with similar data from larger separation distances extending out to 27 nm. We find that the film-NP plasmon nanoruler is extremely sensitive at very short film-NP separation distances, yielding spectral shifts as large as 5 nm for every 1 Å change in separation distance. The film-NP coupling at extremely small spacings is so uniform and reliable that we are able to usefully probe gap dimensions where the classical Drude model of the conducting electrons in the metals is no longer descriptive; for gap sizes smaller than a few nanometers, either quantum or semi-classical models of the carrier response must be employed to predict the observed wavelength shifts. We find that, despite the limitations, large field enhancements and extreme sensitivity persist down to even the smallest gap sizes. PMID:22966857

A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET).

PubMed

Lerner, Eitan; Ploetz, Evelyn; Hohlbein, Johannes; Cordes, Thorben; Weiss, Shimon

2016-07-07

Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

The Ruler Protein EscP of the Enteropathogenic Escherichia coli Type III Secretion System Is Involved in Calcium Sensing and Secretion Hierarchy Regulation by Interacting with the Gatekeeper Protein SepL

PubMed Central

Shaulov, Lihi; Gershberg, Jenia; Deng, Wanyin; Finlay, B. Brett

2017-01-01

ABSTRACT The type III secretion system (T3SS) is a multiprotein complex that plays a central role in the virulence of many Gram-negative bacterial pathogens. To ensure that effector proteins are efficiently translocated into the host cell, bacteria must be able to sense their contact with the host cell. In this study, we found that EscP, which was previously shown to function as the ruler protein of the enteropathogenic Escherichia coli T3SS, is also involved in the switch from the secretion of translocator proteins to the secretion of effector proteins. In addition, we demonstrated that EscP can interact with the gatekeeper protein SepL and that the EscP-SepL complex dissociates upon a calcium concentration drop. We suggest a model in which bacterial contact with the host cell is accompanied by a drop in the calcium concentration that causes SepL-EscP complex dissociation and triggers the secretion of effector proteins. PMID:28049143

Giant plasmonic energy and momentum transfer on the nanoscale

NASA Astrophysics Data System (ADS)

Durach, Maxim

We have developed a general theory of the plasmonic enhancement of many-body phenomena resulting in a closed expression for the surface plasmon-dressed Coulomb interaction. It is shown that this interaction has a resonant nature. We have also demonstrated that renormalized interaction is a long-ranged interaction whose intensity is considerably increased compared to bare Coulomb interaction over the entire region near the plasmonic nanostructure. We illustrate this theory by re-deriving the mirror charge potential near a metal sphere as well as the quasistatic potential behind the so-called perfect lens at the surface plasmon (SP) frequency. The dressed interaction for an important example of a metal--dielectric nanoshell is also explicitly calculated and analyzed. The renormalization and plasmonic enhancement of the Coulomb interaction is a universal effect, which affects a wide range of many-body phenomena in the vicinity of metal nanostructures: chemical reactions, scattering between charge carriers, exciton formation, Auger recombination, carrier multiplication, etc. We have described the nanoplasmonic-enhanced Forster resonant energy transfer (FRET) between quantum dots near a metal nanoshell. It is shown that this process is very efficient near high-aspect-ratio nanoshells. We have also obtained a general expression for the force exerted by an electromagnetic field on an extended polarizable object. This expression is applicable to a wide range of situations important for nanotechnology. Most importantly, this result is of fundamental importance for processes involving interaction of nanoplasmonic fields with metal electrons. Using the obtained expression for the force, we have described a giant surface-plasmon-induced drag-effect rectification (SPIDER), which exists under conditions of the extreme nanoplasmonic confinement. Under realistic conditions in nanowires, this giant SPIDER generates rectified THz potential differences up to 10V and extremely strong

State Repression and its Effects on Civil Conflict, Socio-Economic Outcomes, and Leadership Tenure

DTIC Science & Technology

feedback loop: how citizens respond peacefully or violently influences the type of repression rulers employ. How rulers use repression influences how and...whether citizens protest. Moreover, how rulers respond to their citizens may influence leadership duration. Obviously, the relationship among repression...US (and allied) officials may want policy options to influence rulers who are becoming increasingly repressive (as in Turkey and Egypt) or leaders who

Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler.

PubMed

Zhu, Peizhi; Clamme, Jean-Pierre; Deniz, Ashok A

2005-11-01

A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10-30 A range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules.

Fluorescence Quenching by TEMPO: A Sub-30 Å Single-Molecule Ruler

PubMed Central

Zhu, Peizhi; Clamme, Jean-Pierre; Deniz, Ashok A.

2005-01-01

A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10–30 Å range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules. PMID:16199509

Progress on China nuclear data processing code system

NASA Astrophysics Data System (ADS)

Liu, Ping; Wu, Xiaofei; Ge, Zhigang; Li, Songyang; Wu, Haicheng; Wen, Lili; Wang, Wenming; Zhang, Huanyu

2017-09-01

China is developing the nuclear data processing code Ruler, which can be used for producing multi-group cross sections and related quantities from evaluated nuclear data in the ENDF format [1]. The Ruler includes modules for reconstructing cross sections in all energy range, generating Doppler-broadened cross sections for given temperature, producing effective self-shielded cross sections in unresolved energy range, calculating scattering cross sections in thermal energy range, generating group cross sections and matrices, preparing WIMS-D format data files for the reactor physics code WIMS-D [2]. Programming language of the Ruler is Fortran-90. The Ruler is tested for 32-bit computers with Windows-XP and Linux operating systems. The verification of Ruler has been performed by comparison with calculation results obtained by the NJOY99 [3] processing code. The validation of Ruler has been performed by using WIMSD5B code.

DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica

PubMed Central

Wang, Rui; Li, Ming; Gong, Luyao; Hu, Songnian; Xiang, Hua

2016-01-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) acquire new spacers to generate adaptive immunity in prokaryotes. During spacer integration, the leader-preceded repeat is always accurately duplicated, leading to speculations of a repeat-length ruler. Here in Haloarcula hispanica, we demonstrate that the accurate duplication of its 30-bp repeat requires two conserved mid-repeat motifs, AACCC and GTGGG. The AACCC motif was essential and needed to be ∼10 bp downstream from the leader-repeat junction site, where duplication consistently started. Interestingly, repeat duplication terminated sequence-independently and usually with a specific distance from the GTGGG motif, which seemingly served as an anchor site for a molecular ruler. Accordingly, altering the spacing between the two motifs led to an aberrant duplication size (29, 31, 32 or 33 bp). We propose the adaptation complex may recognize these mid-repeat elements to enable measuring the repeat DNA for spacer integration. PMID:27085805

Standard Methodology for Assessment of Range of Motion While Wearing Body Armor

DTIC Science & Technology

2013-09-30

8 Figure 14: Meter stick (with close up...the tester to place against the measurement scale. A variety of rulers, meter sticks (Figure 14), and T square rulers (Figure 15) were used as well...All rulers and meter sticks had cm and mm marks on them. Figure 12: 20 cm block Figure 13: Measuring block Figure 14: Meter stick

Minding the gap: Children's difficulty conceptualizing spatial intervals as linear measurement units.

PubMed

Solomon, Tracy L; Vasilyeva, Marina; Huttenlocher, Janellen; Levine, Susan C

2015-11-01

Understanding measurement units is critical to mathematics and science learning, but it is a topic that American students find difficult. In 3 studies, we investigated the challenges underlying this difficulty in kindergarten and second grade by comparing performance on different versions of a linear measurement task. Children measured crayons that were either aligned or shifted relative to the left edge of either a continuous ruler or a row of discrete units. The alignment (aligned, shifted) and the measuring tool (ruler, discrete units) were crossed to form 4 types of problems. Study 1 showed good performance in both grades on both types of aligned problems as well as on the shifted problems with discrete units. In contrast, performance was at chance on the shifted ruler problems. Study 2 showed that performance on shifted discrete unit problems declined when numbers were placed on the units, particularly for kindergarteners, suggesting that on the shifted ruler problems, the presence of numbers may have contributed to children's difficulty. However, Study 3 showed that the difficulty on the shifted ruler problems persisted even when the numbers were removed from the ruler. Taken together, these findings suggest that there are multiple challenges to understanding measurement, but that a key challenge is conceptualizing the ruler as a set of countable spatial interval units. (c) 2015 APA, all rights reserved).

Preserving π-conjugation in covalently functionalized carbon nanotubes for optoelectronic applications.

PubMed

Setaro, Antonio; Adeli, Mohsen; Glaeske, Mareen; Przyrembel, Daniel; Bisswanger, Timo; Gordeev, Georgy; Maschietto, Federica; Faghani, Abbas; Paulus, Beate; Weinelt, Martin; Arenal, Raul; Haag, Rainer; Reich, Stephanie

2017-01-30

Covalent functionalization tailors carbon nanotubes for a wide range of applications in varying environments. Its strength and stability of attachment come at the price of degrading the carbon nanotubes sp 2 network and destroying the tubes electronic and optoelectronic features. Here we present a non-destructive, covalent, gram-scale functionalization of single-walled carbon nanotubes by a new [2+1] cycloaddition. The reaction rebuilds the extended π-network, thereby retaining the outstanding quantum optoelectronic properties of carbon nanotubes, including bright light emission at high degree of functionalization (1 group per 25 carbon atoms). The conjugation method described here opens the way for advanced tailoring nanotubes as demonstrated for light-triggered reversible doping through photochromic molecular switches and nanoplasmonic gold-nanotube hybrids with enhanced infrared light emission.

EQUALS Investigations: Remote Rulers.

ERIC Educational Resources Information Center

Mayfield, Karen; Whitlow, Robert

EQUALS is a teacher education program that helps elementary and secondary educators acquire methods and materials to attract minority and female students to mathematics. It supports a problem-solving approach to mathematics which has students working in groups, uses active assessment methods, and incorporates a broad mathematics curriculum…

Study on the calibration and optimization of double theodolites baseline

NASA Astrophysics Data System (ADS)

Ma, Jing-yi; Ni, Jin-ping; Wu, Zhi-chao

2018-01-01

For the double theodolites measurement system baseline as the benchmark of the scale of the measurement system and affect the accuracy of the system, this paper puts forward a method for calibration and optimization of the double theodolites baseline. Using double theodolites to measure the known length of the reference ruler, and then reverse the baseline formula. Based on the error propagation law, the analyses show that the baseline error function is an important index to measure the accuracy of the system, and the reference ruler position, posture and so on have an impact on the baseline error. The optimization model is established and the baseline error function is used as the objective function, and optimizes the position and posture of the reference ruler. The simulation results show that the height of the reference ruler has no effect on the baseline error; the posture is not uniform; when the reference ruler is placed at x=500mm and y=1000mm in the measurement space, the baseline error is the smallest. The experimental results show that the experimental results are consistent with the theoretical analyses in the measurement space. In this paper, based on the study of the placement of the reference ruler, for improving the accuracy of the double theodolites measurement system has a reference value.

Patterned self-assembled monolayers for nanoscale lithography and the control of catalytically produced electroosmosis

NASA Astrophysics Data System (ADS)

Subramanian, Shyamala

This thesis explores two applications of self-assembled monolayers (SAMs) (a) for developing novel molecular assembly based nanolithography techniques and (b) for tailoring zeta-potential of surfaces towards achieving directional control of catalytically induced fluid flow. The first half of the thesis develops the process of molecular ruler lithography using sacrificial host structures. This is a novel hybrid nanolithography technique which combines chemical self-assembly with conventional fabrication methods for improving the resolution of existing lithography tools to sub-50 nm. Previous work related to molecular ruler lithography have shown the use of thiol-SAMs, placed one on top of the other like a molecular resist, for scaling down feature sizes. In this thesis various engineering solutions for improving the reproducibility, yield, nanoscale roughness and overall manufacturability of the process are introduced. This is achieved by introducing a sacrificial inert layer underneath the gold parent structure. This bilayer sacrificial host allows for preferential, easy and quick removal of the parent structures, isolates the parent metal from the underlying substrate and improves reproducibility of the lift-off process. Also it opens avenues for fabrication of high aspect ratio features. Also molecular layer vapor deposition method is developed for building the multilayer molecular resist via vapor phase to reduce contaminations and yield issues associated with solution phase deposition. The smallest isolated metal features produced using this process were 40 nm in width. The second half of the thesis describes application of thiol-SAMs to tailor surface properties of gold, specifically the surface charge or zeta potential. Previous work has demonstrated that the direction of movement of fluid in the vicinity of a catalytically active bimetallic junction placed in a solution of dilute hydrogen peroxide depends on the charge of the gold surface. SAMs with

Tamper indicating gold nanocup plasmonic films

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeVetter, Brent M.; Bernacki, Bruce E.; Bennett, Wendy D.

The spectral signature of nanoplasmonic films are both robust and tailorable with optical responses ranging from the visible to the near-infrared. We present the development of flexible, elastomeric nanoplasmonic films consisting of periodic arrays of gold nanocups as tamper indicating films. Gold nanocups have polarization-sensitive optical properties that may be manufactured into films that offer unique advantages for tamper indication. These flexible films can be made quickly and at low-cost using commercially available monodisperse polystyrene nanospheres through self-assembly followed by plasma etching, metal deposition, and lift-off from a sacrificial substrate. Polarization- and angle-dependent optical spectroscopic measurements were performed to characterizemore » the fabricated films. Furthermore, using polarization-sensitive hyperspectral imaging, we demonstrate how these films can be applied to tamper indication and counterfeit resistance applications.« less

Tamper indicating gold nanocup plasmonic films

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeVetter, Brent M.; Bernacki, Bruce E.; Bennett, Wendy D.

2017-02-13

The spectral signature of nanoplasmonic films are both robust and tailorable with optical responses ranging from the visible to the near-infrared. We present the development of flexible, elastomeric nanoplasmonic films consisting of periodic arrays of gold nanocups as tamper indicating films. Gold nanocups have polarization-sensitive optical properties that may be manufactured into films that offer unique advantages for tamper indication. These flexible films can be made quickly and at low-cost using commercially available monodisperse polystyrene nanospheres through self-assembly followed by plasma etching, metal deposition, and lift-off from a sacrificial substrate. Polarization- and angle-dependent optical spectroscopic measurements were performed to characterizemore » the fabricated films. Using polarization-sensitive hyperspectral imaging, we demonstrate how these films can be applied to tamper indication and counterfeit resistance applications.« less

Reconfigurable Nano-Plasmonics Holography

DTIC Science & Technology

2013-04-01

conventional copper interconnects will no longer support increased clock speeds and the industry will enter a new regime of electronic interconnect... flotation ; 2) an in- coupler grating on one side of the beams, also in the top layer and also with the in- sulator removed beneath; 3) an out-coupler slit

Resonance Energy Transfer-Based Molecular Switch Designed Using a Systematic Design Process Based on Monte Carlo Methods and Markov Chains

NASA Astrophysics Data System (ADS)

Rallapalli, Arjun

A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical. In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications. We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the

Rule Systems for Runtime Verification: A Short Tutorial

NASA Astrophysics Data System (ADS)

Barringer, Howard; Havelund, Klaus; Rydeheard, David; Groce, Alex

In this tutorial, we introduce two rule-based systems for on and off-line trace analysis, RuleR and LogScope. RuleR is a conditional rule-based system, which has a simple and easily implemented algorithm for effective runtime verification, and into which one can compile a wide range of temporal logics and other specification formalisms used for runtime verification. Specifications can be parameterized with data, or even with specifications, allowing for temporal logic combinators to be defined. We outline a number of simple syntactic extensions of core RuleR that can lead to further conciseness of specification but still enabling easy and efficient implementation. RuleR is implemented in Java and we will demonstrate its ease of use in monitoring Java programs. LogScope is a derivation of RuleR adding a simple very user-friendly temporal logic. It was developed in Python, specifically for supporting testing of spacecraft flight software for NASA’s next 2011 Mars mission MSL (Mars Science Laboratory). The system has been applied by test engineers to analysis of log files generated by running the flight software. Detailed logging is already part of the system design approach, and hence there is no added instrumentation overhead caused by this approach. While post-mortem log analysis prevents the autonomous reaction to problems possible with traditional runtime verification, it provides a powerful tool for test automation. A new system is being developed that integrates features from both RuleR and LogScope.

Drug convertarule.

PubMed

Brodie, M J; Robson, A; Murray, T

1983-04-09

A convenient pocket ruler has been developed that allows conversion between metric and molar measurements of many of the drugs for which therapeutic monitoring in the circulation is commonly used. The ruler also gives information to the clinician on suggested therapeutic ranges for the incorporated drugs.

Family planning gets a new boost.

PubMed

Ponle, B

1993-01-01

A workshop on family planning was held during 1993 in Ota, Ogun State Nigeria. An active participant was the Emir of Dass, Alhaji Bilyamini Othman, who helped to develop strategies for the implementation of the Family Health Services Project of the Federal Ministry of Health. His commitment to family planning surprised participants, since most pious Muslims are some of the least sympathetic groups. Alhaji Bilyamini is very enthusiastic about family planning and gives the advice that Allah would not like people to have children who could not be fed. Many men come to him for advice and he suggests that the men allow their wives to adopt family planning. Alhaji Bilyamini was educated at Ahmadu Bello University in business administration and currently is a chairman of the advisory committee for the Planned Parenthood Federation of Nigeria in Bauchi State. The involvement of traditional rulers such as Alhaji Bilyamini has been practiced since 1987, when the USAID approached rulers about family planning. Others who have received family planning messages were the Sultan of Sokoto, the Emirs of Kano and Suleija, and the Shehu of Borno, who also have involved their subordinates. The rulers and subordinates who receive training assist in broadcasting the messages to the people. Because of the authoritative position of the rule in the community, a family planning supporter among rulers means the whole community will be convinced. Future plans include involving the rulers through the first phase. Alhaji Bilyamini recommends continued involvement of traditional rulers, because of their success in changing public perceptions. For example, in Bauchi state, condom discussion was considered taboo, and now condoms are advertised on television. Not all emirs have so enthusiastically embraced the family planning idea. An emir in Ogun state turned away visiting family planning experts days before his daughter died while trying at school to abort a pregnancy. Conference participants

Optimal design of nanoplasmonic materials using genetic algorithms as a multiparameter optimization tool.

PubMed

Yelk, Joseph; Sukharev, Maxim; Seideman, Tamar

2008-08-14

An optimal control approach based on multiple parameter genetic algorithms is applied to the design of plasmonic nanoconstructs with predetermined optical properties and functionalities. We first develop nanoscale metallic lenses that focus an incident plane wave onto a prespecified, spatially confined spot. Our results illustrate the mechanism of energy flow through wires and cavities. Next we design a periodic array of silver particles to modify the polarization of an incident, linearly polarized plane wave in a desired fashion while localizing the light in space. The results provide insight into the structural features that determine the birefringence properties of metal nanoparticles and their arrays. Of the variety of potential applications that may be envisioned, we note the design of nanoscale light sources with controllable coherence and polarization properties that could serve for coherent control of molecular, electronic, or electromechanical dynamics in the nanoscale.

An Ancient Inca Tax and Metallurgy in Peru

ERIC Educational Resources Information Center

Journal of Chemical Education, 2007

2007-01-01

The discovery of ancient Inca tax rulers and other metallurgical objects in Peru show that the ancient civilizations of the country smelted metals. The analysis shows that the smelters in Peru switched from the production of copper to silver after a tax was imposed on them by the Inca rulers.

In situ nanoplasmonic probing of enzymatic activity of monolayer-confined glucose oxidase on colloidal nanoparticles.

PubMed

He, Haili; Xu, Xiaolong; Wu, Haoxi; Zhai, Yujuan; Jin, Yongdong

2013-05-07

In situ probing protein-particle interactions and activities of proteins on colloidal nanoparticle (NP) surfaces is a long-standing key challenge in understanding the nanobio interfaces and virtually important for a variety of biological and biomedical applications. The interactions of NPs with proteins, for instance, are known to form NP bioconjugates or protein coronas; protein surface immobilization and molecular layer-by-layer deposition techniques are widely used, but a clear understanding of the confinement effect on protein activity by molecular coating, at the monolayer level, remains poorly understood. We explore here a novel approach, using colloidal plasmonic nanocomplexes coated with glucose oxidase (GOx) as self-sensing nanoprobes for in situ optical probing of surface-confined enzymatic activity, which is at least 1-2 orders of magnitude more sensitive than standard colorimetric assays for detecting GOx activity. We found that enzymatic activity of monolayer-confined GOx on colloidal NPs was significantly enhanced as compared with free GOx (also proved by conformational changes from circular dichroism studies), with a low apparent Michaelis-Menten constant Km of ~0.115 mM and high turnover kcat/Km of ~8394 M(-1)·s(-1); compared with the "anchored-type" suspending GOx, the outmost polyelectrolyte monolayer-protected "sandwiched-type" GOx exhibits significantly improved enzymatic activities toward higher temperatures and wider pH range. This finding is of fundamental important and instructive for safe use of such nanomaterials for bioapplications.

Ptosis assessment spectacles: a new method of measuring lid position and movement in children.

PubMed

Khandwala, Mona; Dey, Sarju; Harcourt, Cassie; Wood, Clive; Jones, Carole A

2011-01-01

Accurate assessment of eyelid position and movement is vital in planning the surgical correction of ptosis. Conventional measurements taken using a millimeter ruler are considered the gold standard, although in young children this can be a difficult procedure. The authors have designed ptosis assessment spectacles with a measuring millimeter scale marked on the center of the lens to facilitate accurate assessment of eyelid position and function in children. The purpose of the study was to assess the accuracy and reproducibility of eyelid measurement using these ptosis assessment spectacles. Fifty-two children aged 2-12 years were recruited in this study. Each child underwent 2 sets of measurements. The first was undertaken by an ophthalmologist in the conventional manner using a ruler, and the second set made with ptosis assessment spectacles. On each occasion the palpebral aperture, skin crease, and levator function were recorded in millimeters. A verbal analog scale was used to assess parent satisfaction with each method. Clinically acceptable reproducibility was shown with the ruler and the spectacles for all measurements: palpebral aperture, skin crease, and levator function. Parents significantly preferred the glasses for measurement, as compared with the ruler (p < 0.05). The spectacles are as accurate as conventional methods of measurement, but are easier to use. Children tolerate these spectacles well, and most parents preferred them to the ruler.

Simplify Uncertainty Analysis with Excel Macros Reflective ePortfolios--ChE Student Perceptions of Learning from Reflective ePortfolio Creation

ERIC Educational Resources Information Center

Davis, Richard A.

2015-01-01

A simple classroom exercise is used to teach students about the law of propagation of uncertainty in experimental measurements and analysis. Students calculate the density of a rectangular wooden block with a hole from several measurements of mass and length using a ruler and scale. The ruler and scale give students experience with estimating…

Nanoscale Reactions In Opto-magneto-electric Systems

NASA Astrophysics Data System (ADS)

Zeng, Zheng

My research is interdisciplinary in the areas of chemistry, physics and biology for better understanding of synergies between nanomaterials and opto-magneto-electric systems aimed at the practical applications in biosensor, energy (energy storage and electrocatalysis), and biomimetics, in particular, the associated electron transfer, light-matter interactions in nanoscale, such as surface plasmon resonance (SPR) (nanoplasmonics), and magnetic field effect on these phenomena with targeted nanomaterials. Specific research thrusts include: (1) investigation of surface plasmon generation from a novel nanoledge structure on thin metal film. The results are used for the nanostructure optimization for a nanofluidic-nanoplasmonic platform that may function as a multiplexed biosensor for protein biomarker detection; (2) examination of magnetic field effect on uniformly deposited metal oxide on electrospun carbon nanofiber (ECNF) scaffold for efficient energy storage (supercapacitor) and electrocatalytic energy conversion (oxygen reduction reduction). (3) magnetic response of cryptochrome 1 (CRY1) in photoinduced heterogeneous electron transfer (PHET).

Optical forces, torques, and force densities calculated at a microscopic level using a self-consistent hydrodynamics method

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-04-01

The calculation of optical force density distribution inside a material is challenging at the nanoscale, where quantum and nonlocal effects emerge and macroscopic parameters such as permittivity become ill-defined. We demonstrate that the microscopic optical force density of nanoplasmonic systems can be defined and calculated using the microscopic fields generated using a self-consistent hydrodynamics model that includes quantum, nonlocal, and retardation effects. We demonstrate this technique by calculating the microscopic optical force density distributions and the optical binding force induced by external light on nanoplasmonic dimers. This approach works even in the limit when the nanoparticles are close enough to each other so that electron tunneling occurs, a regime in which classical electromagnetic approach fails completely. We discover that an uneven distribution of optical force density can lead to a light-induced spinning torque acting on individual particles. The hydrodynamics method offers us an accurate and efficient approach to study optomechanical behavior for plasmonic systems at the nanoscale.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rossi, Tuomas P., E-mail: tuomas.rossi@alumni.aalto.fi; Sakko, Arto; Puska, Martti J.

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate thatmore » the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.« less

Multiresonant layered plasmonic films

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeVetter, Brent M.; Bernacki, Bruce E.; Bennett, Wendy D.

Multi-resonant nanoplasmonic films have numerous applications in areas such as nonlinear optics, sensing, and tamper indication. While techniques such as focused ion beam milling and electron beam lithography can produce high-quality multi-resonant films, these techniques are expensive, serial processes that are difficult to scale at the manufacturing level. Here, we present the fabrication of multi-resonant nanoplasmonic films using a layered stacking technique. Periodically-spaced gold nanocup substrates were fabricated using self-assembled polystyrene nanospheres followed by oxygen plasma etching and metal deposition via magnetron sputter coating. By adjusting etch parameters and initial nanosphere size, it was possible to achieve an optical responsemore » ranging from the visible to the near-infrared. Singly resonant, flexible films were first made by performing peel-off using an adhesive-coated polyolefin film. Through stacking layers of the nanofilm, we demonstrate fabrication of multi-resonant films at a fraction of the cost and effort as compared to top-down lithographic techniques.« less

Periodic nanostructural materials for nanoplasmonics

NASA Astrophysics Data System (ADS)

Choi, Dukhyun

2017-02-01

Nanoscale periodic material design and fabrication are essentially fundamental requirement for basic scientific researches and industrial applications of nanoscience and engineering. Innovative, effective, reproducible, large-area uniform, tunable and robust nanostructure/material syntheses are still challenging. Here, I would like to introduce the novel periodic nanostructural materials particularly with uniformly ordered nanoporous or nanoflower structures, which are fabricated by simple, cost-effective, and high-throughput wet chemical methods. I also report large-area periodic plasmonic nanostructures based on template-based nanolithography. The surface morphology and optical properties are characterized by SEM and UV-vis. spectroscopy. Furthermore, their enhancement factor is evaluated by using SERS signals.

Wafer-scale aluminum nano-plasmonics

NASA Astrophysics Data System (ADS)

George, Matthew C.; Nielson, Stew; Petrova, Rumyana; Frasier, James; Gardner, Eric

2014-09-01

The design, characterization, and optical modeling of aluminum nano-hole arrays are discussed for potential applications in surface plasmon resonance (SPR) sensing, surface-enhanced Raman scattering (SERS), and surface-enhanced fluorescence spectroscopy (SEFS). In addition, recently-commercialized work on narrow-band, cloaked wire grid polarizers composed of nano-stacked metal and dielectric layers patterned over 200 mm diameter wafers for projection display applications is reviewed. The stacked sub-wavelength nanowire grid results in a narrow-band reduction in reflectance by 1-2 orders of magnitude, which can be tuned throughout the visible spectrum for stray light control.

Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins

PubMed Central

Krojer, Tobias; Pangerl, Karen; Kurt, Juliane; Sawa, Justyna; Stingl, Christoph; Mechtler, Karl; Huber, Robert; Ehrmann, Michael; Clausen, Tim

2008-01-01

Aberrant proteins represent an extreme hazard to cells. Therefore, molecular chaperones and proteases have to carry out protein quality control in each cellular compartment. In contrast to the ATP-dependent cytosolic proteases and chaperones, the molecular mechanisms of extracytosolic factors are largely unknown. To address this question, we studied the protease function of DegP, the central housekeeping protein in the bacterial envelope. Our data reveal that DegP processively degrades misfolded proteins into peptides of defined size by employing a molecular ruler comprised of the PDZ1 domain and the proteolytic site. Furthermore, peptide binding to the PDZ domain transforms the resting protease into its active state. This allosteric activation mechanism ensures the regulated and rapid elimination of misfolded proteins upon folding stress. In comparison to the cytosolic proteases, the regulatory features of DegP are established by entirely different mechanisms reflecting the convergent evolution of an extracytosolic housekeeping protease. PMID:18505836

Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper

NASA Astrophysics Data System (ADS)

Heli, B.; Morales-Narváez, E.; Golmohammadi, H.; Ajji, A.; Merkoçi, A.

2016-04-01

The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and

Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen.

PubMed

Subramanian, Sundar Raman; Singam, Ettayapuram Ramaprasad Azhagiya; Berinski, Michael; Subramanian, Venkatesan; Wade, Rebecca C

2016-08-25

Sequence-specific cleavage of collagen by mammalian collagenase plays a pivotal role in cell function. Collagenases are matrix metalloproteinases that cleave the peptide bond at a specific position on fibrillar collagen. The collagenase Hemopexin-like (HPX) domain has been proposed to be responsible for substrate recognition, but the mechanism by which collagenases identify the cleavage site on fibrillar collagen is not clearly understood. In this study, Brownian dynamics simulations coupled with atomic-detail and coarse-grained molecular dynamics simulations were performed to dock matrix metalloproteinase-1 (MMP-1) on a collagen IIIα1 triple helical peptide. We find that the HPX domain recognizes the collagen triple helix at a conserved R-X11-R motif C-terminal to the cleavage site to which the HPX domain of collagen is guided electrostatically. The binding of the HPX domain between the two arginine residues is energetically stabilized by hydrophobic contacts with collagen. From the simulations and analysis of the sequences and structural flexibility of collagen and collagenase, a mechanistic scheme by which MMP-1 can recognize and bind collagen for proteolysis is proposed.

Mode matching in multiresonant plasmonic nanoantennas for enhanced second harmonic generation

NASA Astrophysics Data System (ADS)

Celebrano, Michele; Wu, Xiaofei; Baselli, Milena; Großmann, Swen; Biagioni, Paolo; Locatelli, Andrea; de Angelis, Costantino; Cerullo, Giulio; Osellame, Roberto; Hecht, Bert; Duò, Lamberto; Ciccacci, Franco; Finazzi, Marco

2015-05-01

Boosting nonlinear frequency conversion in extremely confined volumes remains a challenge in nano-optics research, but can enable applications in nanomedicine, photocatalysis and background-free biosensing. To obtain brighter nonlinear nanoscale sources, approaches that enhance the electromagnetic field intensity and counter the lack of phase matching in nanoplasmonic systems are often employed. However, the high degree of symmetry in the crystalline structure of plasmonic materials (metals in particular) and in nanoantenna designs strongly quenches second harmonic generation. Here, we describe doubly-resonant single-crystalline gold nanostructures with no axial symmetry displaying spatial mode overlap at both the excitation and second harmonic wavelengths. The combination of these features allows the attainment of a nonlinear coefficient for second harmonic generation of ˜5 × 10-10 W-1, enabling a second harmonic photon yield higher than 3 × 106 photons per second. Theoretical estimations point toward the use of our nonlinear plasmonic nanoantennas as efficient platforms for label-free molecular sensing.

Self-assembled three-dimensional nanocrown array.

PubMed

Hong, Soongweon; Kang, Taewook; Choi, Dukhyun; Choi, Yeonho; Lee, Luke P

2012-07-24

Although an ordered nanoplasmonic probe array will have a huge impact on light harvesting, selective frequency response (i.e., nanoantenna), and quantitative molecular/cellular imaging, the realization of such an array is still limited by conventional techniques due to the serial processing or resolution limit by light diffraction. Here, we demonstrate a thermodynamically driven, self-assembled three-dimensional nanocrown array that consists of a core and six satellite gold nanoparticles (GNPs). Our ordered nanoprobe array is fabricated over a large area by thermal dewetting of thin gold film on hexagonally ordered porous anodic alumina (PAA). During thermal dewetting, the structural order of the PAA template dictates the periodic arrangement of gold nanoparticles, rendering the array of gold nanocrown. Because of its tunable size (i.e., 50 nm core and 20 nm satellite GNPs), arrangement, and periodicity, the nanocrown array shows multiple optical resonance frequencies at visible wavelengths as well as angle-dependent optical properties.

Frequency comb transferred by surface plasmon resonance

PubMed Central

Geng, Xiao Tao; Chun, Byung Jae; Seo, Ji Hoon; Seo, Kwanyong; Yoon, Hana; Kim, Dong-Eon; Kim, Young-Jin; Kim, Seungchul

2016-01-01

Frequency combs, millions of narrow-linewidth optical modes referenced to an atomic clock, have shown remarkable potential in time/frequency metrology, atomic/molecular spectroscopy and precision LIDARs. Applications have extended to coherent nonlinear Raman spectroscopy of molecules and quantum metrology for entangled atomic qubits. Frequency combs will create novel possibilities in nano-photonics and plasmonics; however, its interrelation with surface plasmons is unexplored despite the important role that plasmonics plays in nonlinear spectroscopy and quantum optics through the manipulation of light on a subwavelength scale. Here, we demonstrate that a frequency comb can be transformed to a plasmonic comb in plasmonic nanostructures and reverted to the original frequency comb without noticeable degradation of <6.51 × 10−19 in absolute position, 2.92 × 10−19 in stability and 1 Hz in linewidth. The results indicate that the superior performance of a well-defined frequency comb can be applied to nanoplasmonic spectroscopy, quantum metrology and subwavelength photonic circuits. PMID:26898307

Stochastic modeling of stock price process induced from the conjugate heat equation

NASA Astrophysics Data System (ADS)

Paeng, Seong-Hun

2015-02-01

Currency can be considered as a ruler for values of commodities. Then the price is the measured value by the ruler. We can suppose that inflation and variation of exchange rate are caused by variation of the scale of the ruler. In geometry, variation of the scale means that the metric is time-dependent. The conjugate heat equation is the modified heat equation which satisfies the heat conservation law for the time-dependent metric space. We propose a new model of stock prices by using the stochastic process whose transition probability is determined by the kernel of the conjugate heat equation. Our model of stock prices shows how the volatility term is affected by inflation and exchange rate. This model modifies the Black-Scholes equation in light of inflation and exchange rate.

Low-cost, high-sensitivity SERS nano-bio-chip for kinase profiling, drug monitoring and environmental detection: a translational platform technology

NASA Astrophysics Data System (ADS)

Chen, Yi; Liu, Logan

2014-03-01

The interaction of biomolecules and solid-state nanomaterials at the nano-bio interfaces is a long-lasting research topic in nanotechnology. Historically, fundamental problems, such as the electron transfer, energy transfer, and plasmonic interaction at the bio-nano interfaces, have been intensively studied, and revolutionary technologies, such as molecular electronics, peptide chips, nanoplasmonic sensors, have been created. With the combined effort of molecular dynamics simulation and surface-enhanced Raman spectroscopy, we studied the external electric field-induced conformation changes of dodecapeptide probes tethered to a nanostructured metallic surface. Through this study, we demonstrated a reversible manipulation of the biomolecule conformations as well as an in situ eletro-optical detection of the subnanometer conformational changes at the bio-nano interfaces. Based on the proof-of-concept established in this study, we further propose a novel nanophotonic peptide phosphorylation sensor for high-sensitive peptide kinase profiling. We have also demonstrated the same SERS nano-bio-chip can be used for environmental monitoring applications, such as detection of contaminants in drinking water at ultralow concentrates. The fabrication of this nanosensor is based on a single step, lithography-less nanomanufacturing process, which can produce hundreds of these chips in several minutes with nearly 100% yield and uniformity. Therefore, the demonstrated research can be readily translated into industrial mass productions.

The titin A-band rod domain is dispensable for initial thick filament assembly in zebrafish.

PubMed

Myhre, J Layne; Hills, Jordan A; Prill, Kendal; Wohlgemuth, Serene L; Pilgrim, David B

2014-03-01

The sarcomeres of skeletal and cardiac muscle are highly structured protein arrays, consisting of thick and thin filaments aligned precisely to one another and to their surrounding matrix. The contractile mechanisms of sarcomeres are generally well understood, but how the patterning of sarcomeres is initiated during early skeletal muscle and cardiac development remains uncertain. Two of the most widely accepted hypotheses for this process include the "molecular ruler" model, in which the massive protein titin defines the length of the sarcomere and provides a scaffold along which the myosin thick filament is assembled, and the "premyofibril" model, which proposes that thick filament formation does not require titin, but that a "premyofibril" consisting of non-muscle myosin, α-actinin and cytoskeletal actin is used as a template. Each model posits a different order of necessity of the various components, but these have been difficult to test in vivo. Zebrafish motility mutants with developmental defects in sarcomere patterning are useful for the elucidation of such mechanisms, and here we report the analysis of the herzschlag mutant, which shows deficits in both cardiac and skeletal muscle. The herzschlag mutant produces a truncated titin protein, lacking the C-terminal rod domain that is proposed to act as a thick filament scaffold, yet muscle patterning is still initiated, with grossly normal thick and thin filament assembly. Only after embryonic muscle contraction begins is breakdown of sarcomeric myosin patterning observed, consistent with the previously noted role of titin in maintaining the contractile integrity of mature sarcomeres. This conflicts with the "molecular ruler" model of early sarcomere patterning and supports a titin-independent model of thick filament organization during sarcomerogenesis. These findings are also consistent with the symptoms of human titin myopathies that exhibit a late onset, such as tibial muscular dystrophy. Copyright © 2013

Nanoplasmonic generation of ultrashort EUV pulses

NASA Astrophysics Data System (ADS)

Choi, Joonhee; Lee, Dong-Hyub; Han, Seunghwoi; Park, In-Yong; Kim, Seungchul; Kim, Seung-Woo

2012-10-01

Ultrashort extreme-ultraviolet (EUV) light pulses are an important tool for time-resolved pump-probe spectroscopy to investigate the ultrafast dynamics of electrons in atoms and molecules. Among several methods available to generate ultrashort EUV light pulses, the nonlinear frequency upconversion process of high-harmonic generation (HHG) draws attention as it is capable of producing coherent EUV pulses with precise control of burst timing with respect to the driving near-infrared (NIR) femtosecond laser. In this report, we present and discuss our recent experimental data obtained by the plasmon-driven HHG method that generate EUV radiation by means of plasmonic nano-focusing of NIR femtosecond pulses. For experiment, metallic waveguides having a tapered hole of funnel shape inside were fabricated by adopting the focused-ion-beam process on a micro-cantilever substrate. The plasmonic field formed within the funnelwaveguides being coupled with the incident femtosecond pulse permitted intensity enhancement by a factor of ~350, which creates a hot spot of sub-wavelength size with intensities strong enough for HHG. Experimental results showed that with injection of noble gases into the funnel-waveguides, EUV radiation is generated up to wavelengths of 32 nm and 29.6 nm from Ar and Ne gas atoms, respectively. Further, it was observed that lower-order EUV harmonics are cut off in the HHG spectra by the tiny exit aperture of the funnel-waveguide.

Nanoplasmonic Catalysis for Synthetic Fuel Production

DTIC Science & Technology

2010-02-22

understanding of the basic mechanism underlying this enhancement with the ultimate goal of producing synthetic fuels, such as hydrogen , methane and...of producing synthetic fuels, such as hydrogen , methane and methanol using visible illumination. Objectives: - Fabricate arrays of metal...in our energy infrastructure. For photocatalysis , this area is especially exciting because it presents a possible route to direct solar-to-fuel

Curved backgrounds in emergent gravity

NASA Astrophysics Data System (ADS)

Chaurasia, Shikha; Erlich, Joshua; Zhou, Yiyu

2018-06-01

Field theories that are generally covariant but nongravitational at tree level typically give rise to an emergent gravitational interaction whose strength depends on a physical regulator. We consider emergent gravity models in which scalar fields assume the role of clock and rulers, addressing the problem of time in quantum gravity. We discuss the possibility of nontrivial dynamics for clock and ruler fields, and describe some of the consequences of those dynamics for the emergent gravitational theory.

Discovering interesting molecular substructures for molecular classification.

PubMed

Lam, Winnie W M; Chan, Keith C C

2010-06-01

Given a set of molecular structure data preclassified into a number of classes, the molecular classification problem is concerned with the discovering of interesting structural patterns in the data so that "unseen" molecules not originally in the dataset can be accurately classified. To tackle the problem, interesting molecular substructures have to be discovered and this is done typically by first representing molecular structures in molecular graphs, and then, using graph-mining algorithms to discover frequently occurring subgraphs in them. These subgraphs are then used to characterize different classes for molecular classification. While such an approach can be very effective, it should be noted that a substructure that occurs frequently in one class may also does occur in another. The discovering of frequent subgraphs for molecular classification may, therefore, not always be the most effective. In this paper, we propose a novel technique called mining interesting substructures in molecular data for classification (MISMOC) that can discover interesting frequent subgraphs not just for the characterization of a molecular class but also for the distinguishing of it from the others. Using a test statistic, MISMOC screens each frequent subgraph to determine if they are interesting. For those that are interesting, their degrees of interestingness are determined using an information-theoretic measure. When classifying an unseen molecule, its structure is then matched against the interesting subgraphs in each class and a total interestingness measure for the unseen molecule to be classified into a particular class is determined, which is based on the interestingness of each matched subgraphs. The performance of MISMOC is evaluated using both artificial and real datasets, and the results show that it can be an effective approach for molecular classification.

Food kit used by Mercury astronauts

NASA Technical Reports Server (NTRS)

1962-01-01

Food kit used by Mercury astronauts. Some is dehydrated and needs water, other packets are ready to eat. Size is measured relative to a ruler. Included are packets of mushroom soup, orange-grapefruit juice, cocoa beverage, pineapple juice, chicken with gravy, pears, strawberries, beef and vegetables and other assorted food containers (08742-3); mechanism for connecting water dispensor to dehydrated food containers to facilitate rehydration (08744); Group packets of ready to eat space food, with size being measured by a ruler (8745).

JPRS Report, Soviet Union, Political Affairs, Volkogonov’s Political Portrait of Stalin

DTIC Science & Technology

1990-11-09

mind of the Supreme Commander the way the far away Tsaritsyn did, the city that had played an important role in his destiny . It appears that after...chauvinistic stupor, an entire system of spiritual brain- washing, with its hierarchy of fuhrers, and the blind faith in special Aryan destiny . Hitler was...34a lord" and "a ruler." He thought that the real ruler of the world destinies was approaching Berlin from the east. This was the brainchild of the

Hierarchical ultrathin alumina membrane for the fabrication of unique nanodot arrays

NASA Astrophysics Data System (ADS)

Wang, Yuyang; Wang, Yi; Wang, Hailong; Wang, Xinnan; Cong, Ming; Xu, Weiqing; Xu, Shuping

2016-01-01

Ultrathin alumina membranes (UTAMs) as evaporation masks have been a powerful tool for the fabrication of high-density nanodot arrays and have received much attention in magnetic memory devices, photovoltaics, and nanoplasmonics. In this paper, we report the fabrication of a hierarchical ultrathin alumina membrane (HUTAM) with highly ordered submicro/nanoscale channels and its application as an evaporation mask for the realization of unique non-hexagonal nanodot arrays dependent on the geometrical features of the HUTAM. This is the first report of a UTAM with a hierarchical geometry, breaking the stereotype that only limited sets of nanopatterns can be realized using the UTAM method (with typical inter-pore distance of 100 nm). The fabrication of a HUTAM is discussed in detail. An improved, longer wet etching time than previously reported is found to effectively remove the barrier layer and widen the pores of a HUTAM. A growth sustainability issue brought about by pre-patterning is discussed. Spectral comparison was made to distinguish the UTAM nanodots and HUTAM nanodots. Our results can be an inspiration for more sophisticated applications of pre-patterned anodized aluminum oxide in photocatalysis, photovoltaics, and nanoplasmonics.

Instructing cells with programmable peptide DNA hybrids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeman, Ronit; Stephanopoulos, Nicholas; Alvarez, Zaida

The native extracellular matrix is a space in which signals can be displayed dynamically and reversibly, positioned with nanoscale precision, and combined synergistically to control cell function. Here we describe a molecular system that can be programmed to control these three characteristics. In this approach we immobilize peptide-DNA (P-DNA) molecules on a surface through complementary DNA tethers directing cells to adhere and spread reversibly over multiple cycles. The DNA can also serve as a molecular ruler to control the distance-dependent synergy between two peptides. Finally, we use two orthogonal DNA handles to regulate two different bioactive signals, with the abilitymore » to independently up- or downregulate each over time. This enabled us to discover that neural stem cells, derived from the murine spinal cord and organized as neurospheres, can be triggered to migrate out in response to an exogenous signal but then regroup into a neurosphere as the signal is removed.« less

Instructing cells with programmable peptide DNA hybrids

DOE PAGES

Freeman, Ronit; Stephanopoulos, Nicholas; Alvarez, Zaida; ...

2017-07-10

The native extracellular matrix is a space in which signals can be displayed dynamically and reversibly, positioned with nanoscale precision, and combined synergistically to control cell function. Here we describe a molecular system that can be programmed to control these three characteristics. In this approach we immobilize peptide-DNA (P-DNA) molecules on a surface through complementary DNA tethers directing cells to adhere and spread reversibly over multiple cycles. The DNA can also serve as a molecular ruler to control the distance-dependent synergy between two peptides. Finally, we use two orthogonal DNA handles to regulate two different bioactive signals, with the abilitymore » to independently up- or downregulate each over time. This enabled us to discover that neural stem cells, derived from the murine spinal cord and organized as neurospheres, can be triggered to migrate out in response to an exogenous signal but then regroup into a neurosphere as the signal is removed.« less

Instructing cells with programmable peptide DNA hybrids

NASA Astrophysics Data System (ADS)

Freeman, Ronit; Stephanopoulos, Nicholas; Álvarez, Zaida; Lewis, Jacob A.; Sur, Shantanu; Serrano, Chris M.; Boekhoven, Job; Lee, Sungsoo S.; Stupp, Samuel I.

2017-07-01

The native extracellular matrix is a space in which signals can be displayed dynamically and reversibly, positioned with nanoscale precision, and combined synergistically to control cell function. Here we describe a molecular system that can be programmed to control these three characteristics. In this approach we immobilize peptide-DNA (P-DNA) molecules on a surface through complementary DNA tethers directing cells to adhere and spread reversibly over multiple cycles. The DNA can also serve as a molecular ruler to control the distance-dependent synergy between two peptides. Finally, we use two orthogonal DNA handles to regulate two different bioactive signals, with the ability to independently up- or downregulate each over time. This enabled us to discover that neural stem cells, derived from the murine spinal cord and organized as neurospheres, can be triggered to migrate out in response to an exogenous signal but then regroup into a neurosphere as the signal is removed.

Label-Free Optofluidic Nanobiosensor Enables Real-Time Analysis of Single-Cell Cytokine Secretion.

PubMed

Li, Xiaokang; Soler, Maria; Szydzik, Crispin; Khoshmanesh, Khashayar; Schmidt, Julien; Coukos, George; Mitchell, Arnan; Altug, Hatice

2018-06-01

Single-cell analysis of cytokine secretion is essential to understand the heterogeneity of cellular functionalities and develop novel therapies for multiple diseases. Unraveling the dynamic secretion process at single-cell resolution reveals the real-time functional status of individual cells. Fluorescent and colorimetric-based methodologies require tedious molecular labeling that brings inevitable interferences with cell integrity and compromises the temporal resolution. An innovative label-free optofluidic nanoplasmonic biosensor is introduced for single-cell analysis in real time. The nanobiosensor incorporates a novel design of a multifunctional microfluidic system with small volume microchamber and regulation channels for reliable monitoring of cytokine secretion from individual cells for hours. Different interleukin-2 secretion profiles are detected and distinguished from single lymphoma cells. The sensor configuration combined with optical spectroscopic imaging further allows us to determine the spatial single-cell secretion fingerprints in real time. This new biosensor system is anticipated to be a powerful tool to characterize single-cell signaling for basic and clinical research. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular implementation of molecular shift register memories

NASA Technical Reports Server (NTRS)

Beratan, David N. (Inventor); Onuchic, Jose N. (Inventor)

1991-01-01

An electronic shift register memory (20) at the molecular level is described. The memory elements are based on a chain of electron transfer molecules (22) and the information is shifted by photoinduced (26) electron transfer reactions. Thus, multi-step sequences of charge transfer reactions are used to move charge with high efficiency down a molecular chain. The device integrates compositions of the invention onto a VLSI substrate (36), providing an example of a molecular electronic device which may be fabricated. Three energy level schemes, molecular implementation of these schemes, optical excitation strategies, charge amplification strategies, and error correction strategies are described.

Understanding molecular structure from molecular mechanics.

PubMed

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

Estimating Linear Size and Scale: Body Rulers

ERIC Educational Resources Information Center

Jones, Gail; Taylor, Amy; Broadwell, Bethany

2009-01-01

The National Science Education Standards emphasise the use of concepts and skills that cut across the science domains. One of these cross-cutting areas is measurement. Students should know measurement systems, units of measurement, tools and error in measurement as well as the importance of measurement to scientific endeavours. Even though…

Light and redox switchable molecular components for molecular electronics.

PubMed

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

Molecular HIV screening.

PubMed

Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

2013-09-01

Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

A quasi-static continuum model describing interactions between plasmons and non-absorbing biomolecules

NASA Astrophysics Data System (ADS)

Salary, Mohammad Mahdi; Mosallaei, Hossein

2015-06-01

Interactions between the plasmons of noble metal nanoparticles and non-absorbing biomolecules forms the basis of the plasmonic sensors, which have received much attention. Studying these interactions can help to exploit the full potentials of plasmonic sensors in quantification and analysis of biomolecules. Here, a quasi-static continuum model is adopted for this purpose. We present a boundary-element method for computing the optical response of plasmonic particles to the molecular binding events by solving the Poisson equation. The model represents biomolecules with their molecular surfaces, thus accurately accounting for the influence of exact binding conformations as well as structural differences between different proteins on the response of plasmonic nanoparticles. The linear systems arising in the method are solved iteratively with Krylov generalized minimum residual algorithm, and the acceleration is achieved by applying precorrected-Fast Fourier Transformation technique. We apply the developed method to investigate interactions of biotinylated gold nanoparticles (nanosphere and nanorod) with four different types of biotin-binding proteins. The interactions are studied at both ensemble and single-molecule level. Computational results demonstrate the ability of presented model for analyzing realistic nanoparticle-biomolecule configurations. The method can provide comprehensive study for wide variety of applications, including protein structures, monitoring structural and conformational transitions, and quantification of protein concentrations. In addition, it is suitable for design and optimization of the nano-plasmonic sensors.

Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

PubMed

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

Improved sensitivity for W-band Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements with shaped pulses

NASA Astrophysics Data System (ADS)

Bahrenberg, Thorsten; Rosenski, Yael; Carmieli, Raanan; Zibzener, Koby; Qi, Mian; Frydman, Veronica; Godt, Adelheid; Goldfarb, Daniella; Feintuch, Akiva

2017-10-01

Chirp and shaped pulses have been recently shown to be highly advantageous for improving sensitivity in DEER (double electron-electron resonance, also called PELDOR) measurements due to their large excitation bandwidth. The implementation of such pulses for pulse EPR has become feasible due to the availability of arbitrary waveform generators (AWG) with high sampling rates to support pulse shaping for pulses with tens of nanoseconds duration. Here we present a setup for obtaining chirp pulses on our home-built W-band (95 GHz) spectrometer and demonstrate its performance on Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements. We carried out an extensive optimization procedure on two model systems, Gd(III)-PyMTA-spacer-Gd(III)-PyMTA (Gd-PyMTA ruler; zero-field splitting parameter (ZFS) D ∼ 1150 MHz) as well as nitroxide-spacer-nitroxide (nitroxide ruler) to evaluate the applicability of shaped pulses to Gd(III) complexes and nitroxides, which are two important classes of spin labels used in modern DEER/EPR experiments. We applied our findings to ubiquitin, doubly labeled with Gd-DOTA-monoamide (D ∼ 550 MHz) as a model for a system with a small ZFS. Our experiments were focused on the questions (i) what are the best conditions for positioning of the detection frequency, (ii) which pump pulse parameters (bandwidth, positioning in the spectrum, length) yield the best signal-to-noise ratio (SNR) improvements when compared to classical DEER, and (iii) how do the sample's spectral parameters influence the experiment. For the nitroxide ruler, we report an improvement of up to 1.9 in total SNR, while for the Gd-PyMTA ruler the improvement was 3.1-3.4 and for Gd-DOTA-monoamide labeled ubiquitin it was a factor of 1.8. Whereas for the Gd-PyMTA ruler the two setups pump on maximum and observe on maximum gave about the same improvement, for Gd-DOTA-monoamide a significant difference was found. In general the choice of the best set of parameters depends on the D

Molecular Electronic Terms and Molecular Orbital Configurations.

ERIC Educational Resources Information Center

Mazo, R. M.

1990-01-01

Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

Molecular Knots

PubMed Central

Fielden, Stephen D. P.; Woltering, Steffen L.

2017-01-01

Abstract The first synthetic molecular trefoil knot was prepared in the late 1980s. However, it is only in the last few years that more complex small‐molecule knot topologies have been realized through chemical synthesis. The steric restrictions imposed on molecular strands by knotting can impart significant physical and chemical properties, including chirality, strong and selective ion binding, and catalytic activity. As the number and complexity of accessible molecular knot topologies increases, it will become increasingly useful for chemists to adopt the knot terminology employed by other disciplines. Here we give an overview of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry and molecular structure. PMID:28477423

Taking single virus detection and sizing to the limit with molecular sensitivity: the birth of nanoplasmonic-microcavity hybrid sensors

NASA Astrophysics Data System (ADS)

Arnold, S.

2013-03-01

The BioPhotonics community is buzzing at the prospect that ulta-small bio-nanoparticles such as Polio virus and protein can be detected label-free in their native state and sized one at a time. As the awareness that the claim of label-free single protein sensing through the frequency shift of a bare microcavity by A.M. Armani et al in Science in 2007 fades from lack of independent experimental confirmation or a viable physical mechanism to account for the magnitude of the reported wavelength shifts, a new approach has captured the community's interest. It is a product of a marriage between nano-optics and micro-photonics, and is poised to take label-free sensing to the limit.

Molecular Foundry

Science.gov Websites

Molecular Foundry? Research Themes Strategic Plan (PDF) Foundry Careers Foundry Facts Bay Cam Other User Information about current openings at the Molecular Foundry and complete application information is available Scientist, Nanofabrication Facility Molecular Foundry Director Top A U.S. Department of Energy National

Molecular Descriptors

NASA Astrophysics Data System (ADS)

Consonni, Viviana; Todeschini, Roberto

In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

PubMed

Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

2016-03-01

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Engineering molecular machines

NASA Astrophysics Data System (ADS)

Erman, Burak

2016-04-01

Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

Nanoplasmonic lenses for bacteria sorting (Presentation Recording)

NASA Astrophysics Data System (ADS)

Zhu, Xiangchao; Yanik, Ahmet A.

2015-08-01

We demonstrate that patches of two dimensional arrays of circular plasmonic nanoholes patterned on gold-titanium thin film enables subwavelength focusing of visible light in far field region. Efficient coupling of the light with the excited surface plasmon at metal dielectric interface results in strong light transmission. As a result, surface plasmon plays an important role in the far field focusing behavior of the nanohole-aperture patches device. Furthermore, the focal length of the focused beam was found to be predominantly dependent on the overall size of the patch, which is in good agreement with that calculated by Rayleigh-Sommerfield integral formula. The focused light beam can be utilized to separate bio-particles in the dynamic range from 0.1 μm to 1 μm through mainly overcoming the drag force induced by fluid flow. In our proposed model, focused light generated by our plasmonic lenses will push the larger bio-particles in size back to the source of fluid flow and allow the smaller particles to move towards the central aperture of the patch. Such a new kind of plasmonic lenses open up possibility of sorting bacterium-like particles with plasmonic nanolenses, and also represent a promising tool in the field of virology.

Nanoplasmonic Phenomena at Electronic Boundaries in Graphene

DOE PAGES

Fei, Zhe; Ni, Guang -Xin; Jiang, Bor -Yuan; ...

2017-06-30

Here, we review recent discoveries of the intriguing plasmonic phenomena at a variety of electronic boundaries (EBs) in graphene including a line of charges in graphene induced by a carbon nanotube gate, grain boundaries in chemical vapor deposited graphene films, an interface between graphene and moiré patterned graphene, an interface between graphene and bilayer graphene, and others. All these and other EBs cause plasmonic impedance mismatch at the two sides of the boundaries. Manifestations of this effect include plasmonic fringes that stem from plasmon reflections and interference. Quantitative analysis and modeling of these plasmonic fringes uncovered intriguing properties and underlyingmore » physics of the EBs. Potential plasmonic applications associated with these EBs are also briefly discussed.« less

Nanoplasmonic Phenomena at Electronic Boundaries in Graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fei, Zhe; Ni, Guang -Xin; Jiang, Bor -Yuan

Here, we review recent discoveries of the intriguing plasmonic phenomena at a variety of electronic boundaries (EBs) in graphene including a line of charges in graphene induced by a carbon nanotube gate, grain boundaries in chemical vapor deposited graphene films, an interface between graphene and moiré patterned graphene, an interface between graphene and bilayer graphene, and others. All these and other EBs cause plasmonic impedance mismatch at the two sides of the boundaries. Manifestations of this effect include plasmonic fringes that stem from plasmon reflections and interference. Quantitative analysis and modeling of these plasmonic fringes uncovered intriguing properties and underlyingmore » physics of the EBs. Potential plasmonic applications associated with these EBs are also briefly discussed.« less

Molecular similarity measures.

PubMed

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System.

PubMed

Ho, Oanh; Rogne, Per; Edgren, Tomas; Wolf-Watz, Hans; Login, Frédéric H; Wolf-Watz, Magnus

2017-02-24

Many pathogenic Gram-negative bacteria use the type III secretion system (T3SS) to deliver effector proteins into eukaryotic host cells. In Yersinia , the switch to secretion of effector proteins is induced first after intimate contact between the bacterium and its eukaryotic target cell has been established, and the T3SS proteins YscP and YscU play a central role in this process. Here we identify the molecular details of the YscP binding site on YscU by means of nuclear magnetic resonance (NMR) spectroscopy. The binding interface is centered on the C-terminal domain of YscU. Disrupting the YscU-YscP interaction by introducing point mutations at the interaction interface significantly reduced the secretion of effector proteins and HeLa cell cytotoxicity. Interestingly, the binding of YscP to the slowly self-cleaving YscU variant P264A conferred significant protection against autoproteolysis. The YscP-mediated inhibition of YscU autoproteolysis suggests that the cleavage event may act as a timing switch in the regulation of early versus late T3SS substrates. We also show that YscU C binds to the inner rod protein YscI with a dissociation constant ( K d ) of 3.8 μm and with 1:1 stoichiometry. The significant similarity among different members of the YscU, YscP, and YscI families suggests that the protein-protein interactions discussed in this study are also relevant for other T3SS-containing Gram-negative bacteria. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Student Performance in Measuring Distance with Wavelengths in Various Settings

NASA Astrophysics Data System (ADS)

White, Gary

2015-04-01

When physics students are asked to measure the distance between two fixed locations using a pre-defined wavelength as a ruler, there is a surprising failure rate, at least partially due to the fact that the ``ruler'' to be used is not fixed in length (see ``Is a Simple Measurement Task a Roadblock to Student Understanding of Wave Phenomena?,'' by and references therein). I will show some data from introductory classes (algebra- and calculus-based) that replicate this result, and also show some interesting features when comparing a setting involving slinkies with a setting involving surface waves on water.

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

DTIC Science & Technology

2016-06-06

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions In the last five years, the study of ultracold...U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 molecular ion, quantum chemistry, atom ion interaction...Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions Report Title In the last five years, the study of ultracold molecular

The molecular matching problem

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

1993-01-01

Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

A Comparison of Molecular Vibrational Theory to Huckel Molecular Orbital Theory.

ERIC Educational Resources Information Center

Keeports, David

1986-01-01

Compares the similar mathematical problems of molecular vibrational calculations (at any intermediate level of sophistication) and molecular orbital calculations (at the Huckel level). Discusses how the generalizations of Huckel treatment of molecular orbitals apply to vibrational theory. (TW)

Molecular Foundry

Science.gov Websites

Molecular Foundry? Research Themes Strategic Plan (PDF) Foundry Careers Foundry Facts Bay Cam Other User -art instrumentation and expertise. Having merged with the Molecular Foundry in 2014, the facility

Towards molecular electronics with large-area molecular junctions.

PubMed

Akkerman, Hylke B; Blom, Paul W M; de Leeuw, Dago M; de Boer, Bert

2006-05-04

Electronic transport through single molecules has been studied extensively by academic and industrial research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes, break junctions, metallic crossbars and nanopores. For technological applications, molecular tunnel junctions must be reliable, stable and reproducible. The conductance per molecule, however, typically varies by many orders of magnitude. Self-assembled monolayers (SAMs) may offer a promising route to the fabrication of reliable devices, and charge transport through SAMs of alkanethiols within nanopores is well understood, with non-resonant tunnelling dominating the transport mechanism. Unfortunately, electrical shorts in SAMs are often formed upon vapour deposition of the top electrode, which limits the diameter of the nanopore diodes to about 45 nm. Here we demonstrate a method to manufacture molecular junctions with diameters up to 100 microm with high yields (> 95 per cent). The junctions show excellent stability and reproducibility, and the conductance per unit area is similar to that obtained for benchmark nanopore diodes. Our technique involves processing the molecular junctions in the holes of a lithographically patterned photoresist, and then inserting a conducting polymer interlayer between the SAM and the metal top electrode. This simple approach is potentially low-cost and could pave the way for practical molecular electronics.

Residual matrix from different separation techniques impacts exosome biological activity.

PubMed

Paolini, Lucia; Zendrini, Andrea; Di Noto, Giuseppe; Busatto, Sara; Lottini, Elisabetta; Radeghieri, Annalisa; Dossi, Alessandra; Caneschi, Andrea; Ricotta, Doris; Bergese, Paolo

2016-03-24

Exosomes are gaining a prominent role in research due to their intriguing biology and several therapeutic opportunities. However, their accurate purification from body fluids and detailed physicochemical characterization remain open issues. We isolated exosomes from serum of patients with Multiple Myeloma by four of the most popular purification methods and assessed the presence of residual contaminants in the preparations through an ad hoc combination of biochemical and biophysical techniques - including Western Blot, colloidal nanoplasmonics, atomic force microscopy (AFM) and scanning helium ion microscopy (HIM). The preparations obtained by iodixanol and sucrose gradients were highly pure. To the contrary, those achieved with limited processing (serial centrifugation or one step precipitation kit) resulted contaminated by a residual matrix, embedding the exosomes. The contaminated preparations showed lower ability to induce NfkB nuclear translocation in endothelial cells with respect to the pure ones, probably because the matrix prevents the interaction and fusion of the exosomes with the cell membrane. These findings suggest that exosome preparation purity must be carefully assessed since it may interfere with exosome biological activity. Contaminants can be reliably probed only by an integrated characterization approach aimed at both the molecular and the colloidal length scales.

HORIZON RUN 3: TOPOLOGY AS A STANDARD RULER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Speare, Robert; Gott, J. Richard; Kim, Juhan

2015-02-01

We study the physically self-bound cold dark matter halo distribution, which we associate with the massive galaxies within Horizon Run 3, to estimate the accuracy of the determination of the cosmological distance scale measured by the topology analysis. We apply the routine '''Contour 3D''' to the 108 Mock Survey of π steradians out to redshift z = 0.6, which effectively corresponds to the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS) survey, and compare the topology with that of a Gaussian random phase field. We find that given three separate smoothing lengths λ = 15, 21, and 34 h {sup –1} Mpc,more » the least χ{sup 2} fit genus per unit volume (g) yields a 1.7% fractional uncertainty in smoothing length and angular diameter distance to z = 0.6. This is an improvement on former calibrations and presents an error estimate competitive with baryon acoustic oscillation scale techniques. We also present three-dimensional graphics of the Horizon Run 3 spherical mock survey to show a wealth of large-scale structures of the universe that are expected for surveys like BOSS.« less

Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

PubMed

Beckman, Robert; Beverly, Kris; Boukai, Akram; Bunimovich, Yuri; Choi, Jang Wook; DeIonno, Erica; Green, Johnny; Johnston-Halperin, Ezekiel; Luo, Yi; Sheriff, Bonnie; Stoddart, Fraser; Heath, James R

2006-01-01

We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.

Magnetomotive Molecular Nanoprobes

PubMed Central

John, Renu; Boppart, Stephen A.

2012-01-01

Tremendous developments in the field of biomedical imaging in the past two decades have resulted in the transformation of anatomical imaging to molecular-specific imaging. The main approaches towards imaging at a molecular level are the development of high resolution imaging modalities with high penetration depths and increased sensitivity, and the development of molecular probes with high specificity. The development of novel molecular contrast agents and their success in molecular optical imaging modalities have lead to the emergence of molecular optical imaging as a more versatile and capable technique for providing morphological, spatial, and functional information at the molecular level with high sensitivity and precision, compared to other imaging modalities. In this review, we discuss a new class of dynamic contrast agents called magnetomotive molecular nanoprobes for molecular-specific imaging. Magnetomotive agents are superparamagnetic nanoparticles, typically iron-oxide, that are physically displaced by the application of a small modulating external magnetic field. Dynamic phase-sensitive position measurements are performed using any high resolution imaging modality, including optical coherence tomography (OCT), ultrasonography, or magnetic resonance imaging (MRI). The dynamics of the magnetomotive agents can be used to extract the biomechanical tissue properties in which the nanoparticles are bound, and the agents can be used to deliver therapy via magnetomotive displacements to modulate or disrupt cell function, or hyperthermia to kill cells. These agents can be targeted via conjugation to antibodies, and in vivo targeted imaging has been shown in a carcinogen-induced rat mammary tumor model. The iron-oxide nanoparticles also exhibit negative T2 contrast in MRI, and modulations can produce ultrasound imaging contrast for multimodal imaging applications. PMID:21517766

Workshop on Molecular Animation

PubMed Central

Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E.

2011-01-01

Summary February 25–26, 2010, in San Francisco, the Resource for Biocomputing, Visualization and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for: producing high quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories. PMID:20947014

Molecular digital pathology: progress and potential of exchanging molecular data.

PubMed

Roy, Somak; Pfeifer, John D; LaFramboise, William A; Pantanowitz, Liron

2016-09-01

Many of the demands to perform next generation sequencing (NGS) in the clinical laboratory can be resolved using the principles of telepathology. Molecular telepathology can allow facilities to outsource all or a portion of their NGS operation such as cloud computing, bioinformatics pipelines, variant data management, and knowledge curation. Clinical pathology laboratories can electronically share diverse types of molecular data with reference laboratories, technology service providers, and/or regulatory agencies. Exchange of electronic molecular data allows laboratories to perform validation of rare diseases using foreign data, check the accuracy of their test results against benchmarks, and leverage in silico proficiency testing. This review covers the emerging subject of molecular telepathology, describes clinical use cases for the appropriate exchange of molecular data, and highlights key issues such as data integrity, interoperable formats for massive genomic datasets, security, malpractice and emerging regulations involved with this novel practice.

Molecular gearing systems

DOE PAGES

Gakh, Andrei A.; Sachleben, Richard A.; Bryan, Jeff C.

1997-11-01

The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion. Complex synergistic biochemical complexes driven by sophisticated biomechanical processes are quite common. Their biochemical functions are based on the interplay of mechanical and chemical processes, including allosteric effects. In addition, the complexity of this interplay far exceeds thatmore » of typical chemical reactions. Understanding the behavior of artificial molecular devices as well as complex natural molecular biomechanical systems is difficult. Fortunately, the problem can be successfully resolved by direct molecular engineering of simple molecular systems that can mimic desired mechanical or electronic devices. These molecular systems are called technomimetics (the name is derived, by analogy, from biomimetics). Several classes of molecular systems that can mimic mechanical, electronic, or other features of macroscopic devices have been successfully synthesized by conventional chemical methods during the past two decades. In this article we discuss only one class of such model devices: molecular gearing systems.« less

Molecular Population Genetics

PubMed Central

Casillas, Sònia; Barbadilla, Antonio

2017-01-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

Interventional Molecular Imaging.

PubMed

Solomon, Stephen B; Cornelis, Francois

2016-04-01

Although molecular imaging has had a dramatic impact on diagnostic imaging, it has only recently begun to be integrated into interventional procedures. Its significant impact is attributed to its ability to provide noninvasive, physiologic information that supplements conventional morphologic imaging. The four major interventional opportunities for molecular imaging are, first, to provide guidance to localize a target; second, to provide tissue analysis to confirm that the target has been reached; third, to provide in-room, posttherapy assessment; and fourth, to deliver targeted therapeutics. With improved understanding and application of(18)F-FDG, as well as the addition of new molecular probes beyond(18)F-FDG, the future holds significant promise for the expansion of molecular imaging into the realm of interventional procedures. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma.

PubMed

Mariño-Enríquez, Adrián; Bovée, Judith V M G

2016-09-01

Sarcomas are infrequent mesenchymal neoplasms characterized by notable morphological and molecular heterogeneity. Molecular studies in sarcoma provide refinements to morphologic classification, and contribute diagnostic information (frequently), prognostic stratification (rarely) and predict therapeutic response (occasionally). Herein, we summarize the major molecular mechanisms underlying sarcoma pathogenesis and present clinically useful diagnostic, prognostic and predictive molecular markers for sarcoma. Five major molecular alterations are discussed, illustrated with representative sarcoma types, including 1. the presence of chimeric transcription factors, in vascular tumors; 2. abnormal kinase signaling, in gastrointestinal stromal tumor; 3. epigenetic deregulation, in chondrosarcoma, chondroblastoma, and other tumors; 4. deregulated cell survival and proliferation, due to focal copy number alterations, in dedifferentiated liposarcoma; 5. extreme genomic instability, in conventional osteosarcoma as a representative example of sarcomas with highly complex karyotype. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique.

PubMed

Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

2017-04-26

In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed.

Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique

PubMed Central

Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

2017-01-01

In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed. PMID:28445393

Cost-effective flow-through nanohole array-based biosensing platform for the label-free detection of uropathogenic E. coli in real time.

PubMed

Gomez-Cruz, Juan; Nair, Srijit; Manjarrez-Hernandez, Angel; Gavilanes-Parra, Sandra; Ascanio, Gabriel; Escobedo, Carlos

2018-05-30

Rapid, inexpensive and sensitive detection of uropathogenic Escherichia coli (UPEC), a common cause of ascending urinary tract infections (UTIs) including cystitis and pyelonephritis, is critical given the increasing number of cases and its recurrence worldwide. In this paper, we present a label-free nanoplasmonic sensing platform, built with off-the-shelf optical and electronic components, which can detect intact UPEC at concentrations lower than the physiological limit for UTI diagnosis, in real time. The sensing platform consists of a red LED light source, lens assembly, CMOS detector, Raspberry Pi interface in conjugation with a metallic flow-through nanohole array-based sensor. Detection is achieved exploiting nanoplasmonic phenomena from the nanohole arrays through surface plasmon resonance imaging (SPRi) technique. The platform has a bulk sensitivity of 212 pixel intensity unit (PIU)/refractive index unit (RIU), and a resolution in the order of 10 -6 RIU. We demonstrate capture and detection of UPEC with a detection limit of ~100 CFU/ml - a concentration well below the threshold limit for UTI diagnosis in clinical samples. We also demonstrate detection of UPEC in spiked human urine samples for two different concentrations of bacteria. This work is particularly relevant for point-of-care applications, especially for regions around the world where accessibility to medical facilities is heavily dependent upon economy, and availability. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular Population Genetics.

PubMed

Casillas, Sònia; Barbadilla, Antonio

2017-03-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

Spintronics: The molecular way

NASA Astrophysics Data System (ADS)

Cornia, Andrea; Seneor, Pierre

2017-05-01

Molecular spintronics is an interdisciplinary field at the interface between organic spintronics, molecular magnetism, molecular electronics and quantum computing, which is advancing fast and promises large technological payoffs.

A Suggested Molecular Pathology Curriculum for Residents: A Report of the Association for Molecular Pathology.

PubMed

Aisner, Dara L; Berry, Anna; Dawson, D Brian; Hayden, Randall T; Joseph, Loren; Hill, Charles E

2016-03-01

Molecular pathology is an essential element of pathology training. As more molecular tests have become available, there is an increasing need for pathology trainees to receive a strong foundation in molecular pathology. Appointed by the Training and Education Committee of the Association for Molecular Pathology, the Molecular Curriculum Task Force has developed a suggested curriculum in molecular pathology for residents. The foundations of molecular pathology are presented as a series of goals and objectives that residency programs can use to develop their educational programs. As pathologists continue to expand their roles to include regular clinical consultations in the realm of molecular testing, a strong foundation in molecular pathology and genomic medicine has become essential to the practice of pathology. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

PubMed

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

Molecular Weight and Molecular Weight Distributions in Synthetic Polymers.

ERIC Educational Resources Information Center

Ward, Thomas Carl

1981-01-01

Focuses on molecular weight and molecular weight distributions (MWD) and models for predicting MWD in a pedagogical way. In addition, instrumental methods used to characterize MWD are reviewed with emphasis on physical chemistry of each, including end-group determination, osmometry, light scattering, solution viscosity, fractionation, and…

Remote Optical Switch for Localized and Selective Control of Gene Interference

PubMed Central

Lee, Somin Eunice; Liu, Gang Logan; Kim, Franklin; Lee, Luke P.

2009-01-01

Near infrared-absorbing gold nanoplasmonic particles (GNPs) are used as optical switches of gene interference and are remotely controlled using light. We have tuned optical switches to a wavelength where cellular photodamage is minimized. Optical switches are functionalized with double-stranded oligonucleotides. At desired times and at specific intracellular locations, remote optical excitation is used to liberate gene-interfering oligonucleotides. We demonstrate a novel gene-interfering technique offering spatial and temporal control, which is otherwise impossible using conventional gene-interfering techniques. PMID:19128006

Some Stereochemical Principles from Polymers: Molecular Symmetry and Molecular Flexibility

ERIC Educational Resources Information Center

Price, Charles C.

1973-01-01

Discusses the use of the properties of polyethylene, polypropylene, polyisobutylene, and their three epoxides to illustrate the relationships of entropy to molecular properties and the concepts of molecular chirality, geometry, and flexibility. (CC)

Rotating fiber array molecular driver and molecular momentum transfer device constructed therewith

DOEpatents

Milleron, Norman

1983-01-01

A rotating fiber array molecular driver is disclosed which includes a magnetically suspended and rotated central hub to which is attached a plurality of elongated fibers extending radially therefrom. The hub is rotated so as to straighten and axially extend the fibers and to provide the fibers with a tip speed which exceeds the average molecular velocity of fluid molecules entering between the fibers. Molecules colliding with the sides of the rotating fibers are accelerated to the tip speed of the fiber and given a momentum having a directional orientation within a relatively narrow distribution angle at a point radially outward of the hub, which is centered and peaks at the normal to the fiber sides in the direction of fiber rotation. The rotating fiber array may be used with other like fiber arrays or with other stationary structures to form molecular momentum transfer devices such as vacuum pumps, molecular separators, molecular coaters, or molecular reactors.

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

NASA Astrophysics Data System (ADS)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on

Molecular anions.

PubMed

Simons, Jack

2008-07-24

The experimental and theoretical study of molecular anions has undergone explosive growth over the past 40 years. Advances in techniques used to generate anions in appreciable numbers as well as new ion-storage, ion-optics, and laser spectroscopic tools have been key on the experimental front. Theoretical developments on the electronic structure and molecular dynamics fronts now allow one to achieve higher accuracy and to study electronically metastable states, thus bringing theory in close collaboration with experiment in this field. In this article, many of the experimental and theoretical challenges specific to studying molecular anions are discussed. Results from many research groups on several classes of molecular anions are overviewed, and both literature citations and active (in online html and pdf versions) links to numerous contributing scientists' Web sites are provided. Specific focus is made on the following families of anions: dipole-bound, zwitterion-bound, double-Rydberg, multiply charged, metastable, cluster-based, and biological anions. In discussing each kind of anion, emphasis is placed on the structural, energetic, spectroscopic, and chemical-reactivity characteristics that make these anions novel, interesting, and important.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Xiaogang; Biesiada, Marek; Cao, Shuo

A new compilation of 012 angular-size/redshift data for compact radio quasars from very-long-baseline interferometry (VLBI) surveys motivates us to revisit the interaction between dark energy and dark matter with these probes reaching high redshifts z ∼ 3.0. In this paper, we investigate observational constraints on different phenomenological interacting dark energy (IDE) models with the intermediate-luminosity radio quasars acting as individual standard rulers, combined with the newest BAO and CMB observation from Planck results acting as statistical rulers. The results obtained from the MCMC method and other statistical methods including figure of Merit and Information Criteria show that: (1) Compared withmore » the current standard candle data and standard clock data, the intermediate-luminosity radio quasar standard rulers , probing much higher redshifts, could provide comparable constraints on different IDE scenarios. (2) The strong degeneracies between the interaction term and Hubble constant may contribute to alleviate the tension of H {sub 0} between the recent Planck and HST measurements. (3) Concerning the ranking of competing dark energy models, IDE with more free parameters are substantially penalized by the BIC criterion, which agrees very well with the previous results derived from other cosmological probes.« less

Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

PubMed

Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

2016-11-29

The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L

Optical performance and metallic absorption in nanoplasmonic systems.

PubMed

Arnold, Matthew D; Blaber, Martin G

2009-03-02

Optical metrics relating to metallic absorption in representative plasmonic systems are surveyed, with a view to developing heuristics for optimizing performance over a range of applications. We use the real part of the permittivity as the independent variable; consider strengths of particle resonances, resolving power of planar lenses, and guiding lengths of planar waveguides; and compare nearly-free-electron metals including Al, Cu, Ag, Au, Li, Na, and K. Whilst the imaginary part of metal permittivity has a strong damping effect, field distribution is equally important and thus factors including geometry, real permittivity and frequency must be considered when selecting a metal. Al performs well at low permittivities (e.g. sphere resonances, superlenses) whereas Au & Ag only perform well at very negative permittivities (shell and rod resonances, LRSPP). The alkali metals perform well overall but present engineering challenges.

Electro-chemical manifestation of nanoplasmonics in fractal media

NASA Astrophysics Data System (ADS)

Baskin, Emmanuel; Iomin, Alexander

2013-06-01

Electrodynamics of composite materials with fractal geometry is studied in the framework of fractional calculus. This consideration establishes a link between fractal geometry of the media and fractional integrodifferentiation. The photoconductivity in the vicinity of the electrode-electrolyte fractal interface is studied. The methods of fractional calculus are employed to obtain an analytical expression for the giant local enhancement of the optical electric field inside the fractal composite structure at the condition of the surface plasmon excitation. This approach makes it possible to explain experimental data on photoconductivity in the nano-electrochemistry.

Quantum Corrections in Nanoplasmonics: Shape, Scale, and Material

NASA Astrophysics Data System (ADS)

Christensen, Thomas; Yan, Wei; Jauho, Antti-Pekka; Soljačić, Marin; Mortensen, N. Asger

2017-04-01

The classical treatment of plasmonics is insufficient at the nanometer-scale due to quantum mechanical surface phenomena. Here, an extension of the classical paradigm is reported which rigorously remedies this deficiency through the incorporation of first-principles surface response functions—the Feibelman d parameters—in general geometries. Several analytical results for the leading-order plasmonic quantum corrections are obtained in a first-principles setting; particularly, a clear separation of the roles of shape, scale, and material is established. The utility of the formalism is illustrated by the derivation of a modified sum rule for complementary structures, a rigorous reformulation of Kreibig's phenomenological damping prescription, and an account of the small-scale resonance shifting of simple and noble metal nanostructures.

Novel nanoplasmonic biosensor integrated in a microfluidic channel

NASA Astrophysics Data System (ADS)

Solis-Tinoco, V.; Sepulveda, B.; Lechuga, L. M.

2015-06-01

An important motivation of the actual biosensor research is to develop a multiplexed sensing platform of high sensitivity fabricated with large-scale and low-cost technologies for applications such as diagnosis and monitoring of diseases, drug discovery and environmental control. Biosensors based on localized plasmon resonance (LSPR) have demonstrated to be a novel and effective platform for quantitative detection of biological and chemical analytes. Here, we describe a novel label-free nanobiosensor consisting of an array of closely spaced, vertical, elastomeric nanopillars capped with plasmonic gold nanodisks in a SU-8 channel. The principle is based on the refractive index sensing using the LSPR of gold nanodisks. The fabrication of the nanobiosensor is based on replica molding technique and gold nanodisks are incorporated on the polymer structures by e-beam evaporation. In this work, we provide the strategies for controlling the silicon nanostructure replication using thermal polymers and photopolymers with different Young's modulus, in order to minimize the common distortions in the process and to obtain a reliable replica of the Si master. The master mold of the biosensor consists of a hexagonal array of silicon nanopillars, whose diameter is ~200 nm, and whose height can range from 250 nm to 1.300 μm, separated 400 nm from the center to center, integrated in a SU-8 microfluidic channel.

Low Dimensional Carbon Materials for Nanooptics and Nanoplasmonics

DTIC Science & Technology

2015-12-11

structure of the 2D glass supported by a graphene window and identified it as a bi-tetrahedral layer of SiO2 only 3 atoms thick. Our atomic resolution...developed can be directly applied to study other 2D materials such as molybdenum disulfide and 2D glasses . Novel properties in these materials open...up new avenues for studying old and new physics including glass phase transition and valley Hall effect. 15. SUBJECT TERMS graphene, bilayer graphene

Molecular Research in Aquaculture

USDA-ARS?s Scientific Manuscript database

Molecular research and biotechnology have long been fields of study with applications useful to aquaculture and other animal sciences. Molecular Research in Aquaculture looks to provide an understanding of molecular research and its applications to the aquaculture industry in a format that allows in...

Enantiomerically enriched, polycrystalline molecular sieves

DOE PAGES

Brand, Stephen K.; Schmidt, Joel E.; Deem, Michael W.; ...

2017-05-01

Zeolite and zeolite-like molecular sieves are being used in a large number of applications such as adsorption and catalysis. Achievement of the long-standing goal of creating a chiral, polycrystalline molecular sieve with bulk enantioenrichment would enable these materials to perform enantioselective functions. Here, we report the synthesis of enantiomerically enriched samples of a molecular sieve. For this study, enantiopure organic structure directing agents are designed with the assistance of computational methods and used to synthesize enantioenriched, polycrystalline molecular sieve samples of either enantiomer. Computational results correctly predicted which enantiomer is obtained, and enantiomeric enrichment is proven by high-resolution transmission electronmore » microscopy. The enantioenriched and racemic samples of the molecular sieves are tested as adsorbents and heterogeneous catalysts. The enantioenriched molecular sieves show enantioselectivity for the ring opening reaction of epoxides and enantioselective adsorption of 2-butanol (the R enantiomer of the molecular sieve shows opposite and approximately equal enantioselectivity compared with the S enantiomer of the molecular sieve, whereas the racemic sample of the molecular sieve shows no enantioselectivity).« less

Enantiomerically enriched, polycrystalline molecular sieves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brand, Stephen K.; Schmidt, Joel E.; Deem, Michael W.

Zeolite and zeolite-like molecular sieves are being used in a large number of applications such as adsorption and catalysis. Achievement of the long-standing goal of creating a chiral, polycrystalline molecular sieve with bulk enantioenrichment would enable these materials to perform enantioselective functions. Here, we report the synthesis of enantiomerically enriched samples of a molecular sieve. For this study, enantiopure organic structure directing agents are designed with the assistance of computational methods and used to synthesize enantioenriched, polycrystalline molecular sieve samples of either enantiomer. Computational results correctly predicted which enantiomer is obtained, and enantiomeric enrichment is proven by high-resolution transmission electronmore » microscopy. The enantioenriched and racemic samples of the molecular sieves are tested as adsorbents and heterogeneous catalysts. The enantioenriched molecular sieves show enantioselectivity for the ring opening reaction of epoxides and enantioselective adsorption of 2-butanol (the R enantiomer of the molecular sieve shows opposite and approximately equal enantioselectivity compared with the S enantiomer of the molecular sieve, whereas the racemic sample of the molecular sieve shows no enantioselectivity).« less

Workshop on Molecular Evolution

NASA Technical Reports Server (NTRS)

Cummings, Michael P.

2004-01-01

Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

Realization of Molecular-Based Transistors.

PubMed

Richter, Shachar; Mentovich, Elad; Elnathan, Roey

2018-06-06

Molecular-based devices are widely considered as significant candidates to play a role in the next generation of "post-complementary metal-oxide-semiconductor" devices. In this context, molecular-based transistors: molecular junctions that can be electrically gated-are of particular interest as they allow new modes of operation. The properties of molecular transistors composed of a single- or multimolecule assemblies, focusing on their practicality as real-world devices, concerning industry demands and its roadmap are compared. Also, the capability of the gate electrode to modulate the molecular transistor characteristics efficiently is addressed, showing that electrical gating can be easily facilitated in single molecular transistors and that gating of transistor composed of molecular assemblies is possible if the device is formed vertically. It is concluded that while the single-molecular transistor exhibits better performance on the lab-scale, its realization faces signifacant challenges when compared to those faced by transistors composed of a multimolecule assembly. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.

PubMed

Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro

2012-11-21

In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.

Group Theoretical Route to Deterministic Weyl Points in Chiral Photonic Lattices.

PubMed

Saba, Matthias; Hamm, Joachim M; Baumberg, Jeremy J; Hess, Ortwin

2017-12-01

Topological phases derived from point degeneracies in photonic band structures show intriguing and unique behavior. Previously identified band degeneracies are based on accidental degeneracies and subject to engineering on a case-by-case basis. Here we show that deterministic pseudo Weyl points with nontrivial topology and hyperconic dispersion exist at the Brillouin zone center of chiral cubic symmetries. This conceivably allows realization of topologically protected frequency isolated surface bands in 3D and n=0 properties as demonstrated for a nanoplasmonic system and a photonic crystal.

Group Theoretical Route to Deterministic Weyl Points in Chiral Photonic Lattices

NASA Astrophysics Data System (ADS)

Saba, Matthias; Hamm, Joachim M.; Baumberg, Jeremy J.; Hess, Ortwin

2017-12-01

Topological phases derived from point degeneracies in photonic band structures show intriguing and unique behavior. Previously identified band degeneracies are based on accidental degeneracies and subject to engineering on a case-by-case basis. Here we show that deterministic pseudo Weyl points with nontrivial topology and hyperconic dispersion exist at the Brillouin zone center of chiral cubic symmetries. This conceivably allows realization of topologically protected frequency isolated surface bands in 3D and n =0 properties as demonstrated for a nanoplasmonic system and a photonic crystal.

Molecular optoelectronics: the interaction of molecular conduction junctions with light.

PubMed

Galperin, Michael; Nitzan, Abraham

2012-07-14

The interaction of light with molecular conduction junctions is attracting growing interest as a challenging experimental and theoretical problem on one hand, and because of its potential application as a characterization and control tool on the other. It stands at the interface between two important fields, molecular electronics and molecular plasmonics and has attracted attention as a challenging scientific problem with potentially important technological consequences. Here we review the present state of the art of this field, focusing on several key phenomena and applications: using light as a switching device, using light to control junction transport in the adiabatic and non-adiabatic regimes, light generation in biased junctions and Raman scattering from such systems. This field has seen remarkable progress in the past decade, and the growing availability of scanning tip configurations that can combine optical and electrical probes suggests that further progress towards the goal of realizing molecular optoelectronics on the nanoscale is imminent.

Analysis of molecular interactions in solid dosage forms; challenge to molecular pharmaceutics.

PubMed

Yamamoto, Keiji; Limwikrant, Waree; Moribe, Kunikazu

2011-01-01

The molecular states of active pharmaceutical ingredients (APIs) in pharmaceutical dosage forms strongly affect the properties and quality of a drug. Various important fundamental physicochemical studies were reviewed from the standpoint of molecular pharmaceutics. Mechanochemical effects were evaluated in mixtures of APIs and pharmaceutical additives. Amorphization, complex formation and nanoparticle formation are observed after grinding process depending on the combination of APIs and pharmaceutical additives. Sealed-heating method and mesoporous materials have been used to investigate drug molecular interactions in dosage forms. Molecular states have been investigated using powder X-ray diffraction, thermal analysis, IR, solid state fluorometry, and NMR. © 2011 Pharmaceutical Society of Japan

On the Relationship between Molecular Hit Rates in High-Throughput Screening and Molecular Descriptors.

PubMed

Hansson, Mari; Pemberton, John; Engkvist, Ola; Feierberg, Isabella; Brive, Lars; Jarvis, Philip; Zander-Balderud, Linda; Chen, Hongming

2014-06-01

High-throughput screening (HTS) is widely used in the pharmaceutical industry to identify novel chemical starting points for drug discovery projects. The current study focuses on the relationship between molecular hit rate in recent in-house HTS and four common molecular descriptors: lipophilicity (ClogP), size (heavy atom count, HEV), fraction of sp(3)-hybridized carbons (Fsp3), and fraction of molecular framework (f(MF)). The molecular hit rate is defined as the fraction of times the molecule has been assigned as active in the HTS campaigns where it has been screened. Beta-binomial statistical models were built to model the molecular hit rate as a function of these descriptors. The advantage of the beta-binomial statistical models is that the correlation between the descriptors is taken into account. Higher degree polynomial terms of the descriptors were also added into the beta-binomial statistic model to improve the model quality. The relative influence of different molecular descriptors on molecular hit rate has been estimated, taking into account that the descriptors are correlated to each other through applying beta-binomial statistical modeling. The results show that ClogP has the largest influence on the molecular hit rate, followed by Fsp3 and HEV. f(MF) has only a minor influence besides its correlation with the other molecular descriptors. © 2013 Society for Laboratory Automation and Screening.

Organic-based molecular switches for molecular electronics.

PubMed

Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

2011-10-05

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.

Molecular toxicity of nanomaterials.

PubMed

Chang, Xue-Ling; Yang, Sheng-Tao; Xing, Gengmei

2014-10-01

With the rapid developments in the fields of nanoscience and nanotechnlogy, more and more nanomaterials and their based consumer products have been used into our daily life. The safety concerns of nanomaterials have been well recognized by the scientific community and the public. Molecular mechanism of interactions between nanomaterials and biosystems is the most essential topic and final core of the biosafety. In the last two decades, nanotoxicology developed very fast and toxicity phenomena of nanomaterials have been reported. To achieve better understanding and detoxication of nanomaterials, thorough studies of nanotoxicity at molecular level are important. The interactions between nanomaterials and biomolecules have been widely investigated as the first step toward the molecular nanotoxicology. The consequences of such interactions have been discussed in the literature. Besides this, the chemical mechanism of nanotoxicology is gaining more attention, which would lead to a better design of nontoxic nanomaterials. In this review, we focus on the molecular nanotoxicology and explore the toxicity of nanomaterials at molecular level. The molecular level studies of nanotoxicology are summarized and the published nanotoxicological data are revisited.

Molecular biomimetics: utilizing nature's molecular ways in practical engineering.

PubMed

Tamerler, Candan; Sarikaya, Mehmet

2007-05-01

In nature, proteins are the machinery that accomplish many functions through their specific recognition and interactions in biological systems from single-celled to multicellular organisms. Biomolecule-material interaction is accomplished via molecular specificity, leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, molecular recognition and, consequently, functions developed through successive cycles of mutation and selection. Using biology as a guide, we can now understand, engineer and control peptide-material interactions and exploit these to tailor novel materials and systems for practical applications. We adapted combinatorial biology protocols to display peptide libraries, either on the cell surface or on phages, to select short peptides specific to a variety of practical materials systems. Following the selection step, we determined the kinetics and stability of peptide binding experimentally to understand the bound peptide structure via modeling and its assembly via atomic force microscopy. The peptides were further engineered to have multiple repeats or their amino acid sequences varied to tailor their function. Both nanoparticles and flat inorganic substrates containing multimaterials patterned at the nano- and microscales were used for self-directed immobilization of molecular constructs. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems with wide ranging applications, from tissue engineering, drug delivery and biosensors, to nanotechnology and bioremediation. Here we give examples of protein-mediated functional materials in biology, peptide selection and engineering with affinity to inorganics, demonstrate potential utilizations in materials science, engineering and medicine, and describe future prospects.

Molecular robots with sensors and intelligence.

PubMed

Hagiya, Masami; Konagaya, Akihiko; Kobayashi, Satoshi; Saito, Hirohide; Murata, Satoshi

2014-06-17

CONSPECTUS: What we can call a molecular robot is a set of molecular devices such as sensors, logic gates, and actuators integrated into a consistent system. The molecular robot is supposed to react autonomously to its environment by receiving molecular signals and making decisions by molecular computation. Building such a system has long been a dream of scientists; however, despite extensive efforts, systems having all three functions (sensing, computation, and actuation) have not been realized yet. This Account introduces an ongoing research project that focuses on the development of molecular robotics funded by MEXT (Ministry of Education, Culture, Sports, Science and Technology, Japan). This 5 year project started in July 2012 and is titled "Development of Molecular Robots Equipped with Sensors and Intelligence". The major issues in the field of molecular robotics all correspond to a feedback (i.e., plan-do-see) cycle of a robotic system. More specifically, these issues are (1) developing molecular sensors capable of handling a wide array of signals, (2) developing amplification methods of signals to drive molecular computing devices, (3) accelerating molecular computing, (4) developing actuators that are controllable by molecular computers, and (5) providing bodies of molecular robots encapsulating the above molecular devices, which implement the conformational changes and locomotion of the robots. In this Account, the latest contributions to the project are reported. There are four research teams in the project that specialize on sensing, intelligence, amoeba-like actuation, and slime-like actuation, respectively. The molecular sensor team is focusing on the development of molecular sensors that can handle a variety of signals. This team is also investigating methods to amplify signals from the molecular sensors. The molecular intelligence team is developing molecular computers and is currently focusing on a new photochemical technology for accelerating DNA

Both “illness and temptation of the enemy”: melancholy, the medieval patient and the writings of King Duarte of Portugal (r. 1433–38)

PubMed Central

McCleery, Iona

2009-01-01

Recent historians have rehabilitated King Duarte of Portugal, previously maligned and neglected, as an astute ruler and philosopher. There is still a tendency, however, to view Duarte as a depressive or a hypochondriac, due to his own description of his melancholy in his advice book, the Loyal Counselor. This paper reassesses Duarte's writings, drawing on key approaches in the history of medicine, such as narrative medicine and the history of the patient. It is important to take Duarte's views on his condition seriously, placing them in the medical and theological contexts of his time and avoiding modern retrospective diagnosis. Duarte's writings can be used to explore the impact of plague, doubt and death on the life of a well-educated and conscientious late-medieval ruler. PMID:21874137

Both "illness and temptation of the enemy": melancholy, the medieval patient and the writings of King Duarte of Portugal (r. 1433-38).

PubMed

McCleery, Iona

2009-06-01

Recent historians have rehabilitated King Duarte of Portugal, previously maligned and neglected, as an astute ruler and philosopher. There is still a tendency, however, to view Duarte as a depressive or a hypochondriac, due to his own description of his melancholy in his advice book, the Loyal Counselor. This paper reassesses Duarte's writings, drawing on key approaches in the history of medicine, such as narrative medicine and the history of the patient. It is important to take Duarte's views on his condition seriously, placing them in the medical and theological contexts of his time and avoiding modern retrospective diagnosis. Duarte's writings can be used to explore the impact of plague, doubt and death on the life of a well-educated and conscientious late-medieval ruler.

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

PubMed Central

Garcia-Garibay, Miguel A.

2005-01-01

Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation. PMID:16046543

Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at

Magnetismo Molecular (Molecular Magentism)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reis, Mario S; Moreira Dos Santos, Antonio F

The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail themore » physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.« less

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Monitoring adsorption of gold nanoparticles on gold nanodisk array using dark-field hyperspectral microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhao, Fusheng; Zenasni, Oussama; Li, Jingting; Shih, Wei-Chuan

2017-02-01

Localized surface plasmon resonance (LSPR) arises from the interaction of light with noble metal nanoparticles, which induces a collective oscillation in the free electrons. The size and shape of the metallic nanostructure significantly impact LSPR frequency and strength. Nanoplasmonic sensor has become a recent research focus due to its significant signal enhancement and robust signal transduction measured by extinction spectroscopy, fluorescence, Raman scattering, and absorption spectroscopy. Dark-field microscopy, in contrast, reports the scattered photons after light-matter interactions. In this case, the nanoparticles can be understood as dipole radiators whose free electrons oscillate in concert. Coupled with spectroscopy, this platform allows the collection of plasmonically scattered spectra from gold nanoparticles. Plasmonic coupling between electron-beam lithography patterned gold nanodisks (AuND) and colloidal gold nanoparticles (AuNP) can change the plasmonic resonance of the original entities, and can be effectively studied by dark-field hyperspectral microscopy. Typically, a pronounced redshift can be observed when plasmonic coupling occurs. When these nano-entities are functionalized with interactive surface moieties, biochemistry and molecular processes can be studied. In this paper, we will present the capability of assessing the process of immobilizing streptavidin-functionalized AuNPs on an array of biotin-terminated AuNDs. By monitoring changes in the LSPR band of AuNDs, we are able to evaluate similar processes in other molecular systems. In addition, plasmon coupling induced scattering intensity variations can be measured by an electron-multiplied charge-coupled device camera for rapid in situ monitoring. This method can potentially be useful in studying dynamic biophysical and biochemical processes in situ.

Molecularly Imprinted Membranes

PubMed Central

Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

2012-01-01

Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

EDITORIAL: Focus on Molecular Electronics FOCUS ON MOLECULAR ELECTRONICS

NASA Astrophysics Data System (ADS)

Scheer, Elke; Reineker, Peter

2008-06-01

The notion 'molecular electronics' has been used more frequently since the 1970s and summarizes a series of physical phenomena and ideas for their application in connection with organic molecules, oligomers, polymers, organic aggregates and solids. The properties studied in this field were connected to optical and electrical phenomena, such as optical absorption, fluorescence, nonlinear optics, energy transport, charge transfer, electrical conductance, and electron and nuclear spin-resonance. The final goal was and is to build devices which can compete or surpass some aspects of inorganic semiconductor devices. For example, on the basis of organic molecules there exist rectifiers, transistors, molecular wires, organic light emitting diodes, elements for photovoltaics, and displays. With respect to applications, one aspect of the organic materials is their broad variability and the lower effort and costs for their processability. The step from microstructures to the investigation of nanostructures is a big challenge also in this field and has lead to what nowadays is called molecular electronics in its narrow sense. In this field the subjects of the studies are often single molecules, e.g. single molecule optical spectroscopy, electrical conductance, i.e. charge transport through a single molecule, the influence of vibrational degrees of freedom, etc. A challenge here is to provide the techniques for addressing in a reproducible way the molecular scale. In another approach small molecular ensembles are studied in order to avoid artefacts from particular contact situations. The recent development of the field is presented in [1-8]. In this Focus Issue we present new results in the field of 'molecular electronics', both in its broad and specialized sense. One of the basic questions is the distribution of the energy levels responsible for optical absorption on the one hand and for the transport of charge on the other. A still unanswered question is whether the Wannier

Localized Chemical Remodeling for Live Cell Imaging of Protein-Specific Glycoform.

PubMed

Hui, Jingjing; Bao, Lei; Li, Siqiao; Zhang, Yi; Feng, Yimei; Ding, Lin; Ju, Huangxian

2017-07-03

Live cell imaging of protein-specific glycoforms is important for the elucidation of glycosylation mechanisms and identification of disease states. The currently used metabolic oligosaccharide engineering (MOE) technology permits routinely global chemical remodeling (GCM) for carbohydrate site of interest, but can exert unnecessary whole-cell scale perturbation and generate unpredictable metabolic efficiency issue. A localized chemical remodeling (LCM) strategy for efficient and reliable access to protein-specific glycoform information is reported. The proof-of-concept protocol developed for MUC1-specific terminal galactose/N-acetylgalactosamine (Gal/GalNAc) combines affinity binding, off-on switchable catalytic activity, and proximity catalysis to create a reactive handle for bioorthogonal labeling and imaging. Noteworthy assay features associated with LCM as compared with MOE include minimum target cell perturbation, short reaction timeframe, effectiveness as a molecular ruler, and quantitative analysis capability. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular transistors based on BDT-type molecular bridges.

PubMed

Wheeler, W D; Dahnovsky, Yu

2008-10-21

In this work we study the effect of electron correlations in molecular transistors with molecular bridges based on 1,4-benzene-dithiol (BDT) and 2-nitro-1,4-benzene-dithiol (nitro-BDT) by using ab initio electron propagator calculations. We find that there is no gate field effect for the BDT based transistor in accordance with the experimental data. After verifying the computational method on the BDT molecule, we consider a transistor with a nitro-BDT molecular bridge. From the electron propagator calculations, we predict strong negative differential resistance at small positive and negative values of source-drain voltages. The explanation of the peak and the minimum in the current is given in terms of the molecular orbital picture and switch-on (-off) properties due to the voltage dependencies of the Dyson poles (ionization potentials). When the current is off, the electronic states on both electrodes are populated resulting in the vanishing tunneling probability due to the Pauli principle. Besides the minimum and the maximum in the I-V characteristics, we find a strong gate field effect in the conductance where the peak at V(sd) = 0.15 eV and E(g) = 4x10(-3) a.u. switches to the minimum at E(g) = -4x10(-3) a.u. A similar behavior is discovered at the negative V(sd). Such a feature can be used for fast current modulation by changing the polarity of a gate field.

Atomic and molecular supernovae

NASA Technical Reports Server (NTRS)

Liu, Weihong

1997-01-01

Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

Noncovalent Molecular Electronics.

PubMed

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

Molecular Adsorber Coating

NASA Technical Reports Server (NTRS)

Straka, Sharon; Peters, Wanda; Hasegawa, Mark; Hedgeland, Randy; Petro, John; Novo-Gradac, Kevin; Wong, Alfred; Triolo, Jack; Miller, Cory

2011-01-01

A document discusses a zeolite-based sprayable molecular adsorber coating that has been developed to alleviate the size and weight issues of current ceramic puck-based technology, while providing a configuration that more projects can use to protect against degradation from outgassed materials within a spacecraft, particularly contamination-sensitive instruments. This coating system demonstrates five times the adsorption capacity of previously developed adsorber coating slurries. The molecular adsorber formulation was developed and refined, and a procedure for spray application was developed. Samples were spray-coated and tested for capacity, thermal optical/radiative properties, coating adhesion, and thermal cycling. Work performed during this study indicates that the molecular adsorber formulation can be applied to aluminum, stainless steel, or other metal substrates that can accept silicate-based coatings. The coating can also function as a thermal- control coating. This adsorber will dramatically reduce the mass and volume restrictions, and is less expensive than the currently used molecular adsorber puck design.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanoparticle–Film Plasmon Ruler Interrogated with Transmission Visible Spectroscopy

PubMed Central

2015-01-01

The widespread use of plasmonic nanorulers (PNRs) in sensing platforms has been plagued by technical challenges associated with the development of methods to fabricate precisely controlled nanostructures with high yield and characterize them with high throughput. We have previously shown that creating PNRs in a nanoparticle–film (NP–film) format enables the fabrication of an extremely large population of uniform PNRs with 100% yield using a self-assembly approach, which facilitates high-throughput PNR characterization using ensemble spectroscopic measurements and eliminates the need for expensive microscopy systems required by many other PNR platforms. We expand upon this prior work herein, showing that the NP–film PNR can be made compatible with aqueous sensing studies by adapting it for use in a transmission localized surface plasmon resonance spectroscopy format, where the coupled NP–film resonance responsible for the PNR signal is directly probed using an extinction measurement from a standard spectrophotometer. We designed slide holders that fit inside standard spectrophotometer cuvettes and position NP–film samples so that the coupled NP–film resonance can be detected in a collinear optical configuration. Once the NP–film PNR samples are cuvette-compatible, it is straightforward to calibrate the PNR in aqueous solution and use it to characterize dynamic, angstrom-scale distance changes resulting from pH-induced swelling of polyelectrolyte (PE) spacer layers as thin as 1 PE layer and also of a self-assembled monolayer of an amine-terminated alkanethiol. This development is an important step toward making PNR sensors more user-friendly and encouraging their widespread use in various sensing schemes. PMID:25541618

Molecular docking.

PubMed

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

Library of molecular associations: curating the complex molecular basis of liver diseases.

PubMed

Buchkremer, Stefan; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, Thorsten; Staib, Frank; Galle, Peter R; Teufel, Andreas

2010-03-20

Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

Piezoelectric sensors based on molecular imprinted polymers for detection of low molecular mass analytes.

PubMed

Uludağ, Yildiz; Piletsky, Sergey A; Turner, Anthony P F; Cooper, Matthew A

2007-11-01

Biomimetic recognition elements employed for the detection of analytes are commonly based on proteinaceous affibodies, immunoglobulins, single-chain and single-domain antibody fragments or aptamers. The alternative supra-molecular approach using a molecularly imprinted polymer now has proven utility in numerous applications ranging from liquid chromatography to bioassays. Despite inherent advantages compared with biochemical/biological recognition (which include robustness, storage endurance and lower costs) there are few contributions that describe quantitative analytical applications of molecularly imprinted polymers for relevant small molecular mass compounds in real-world samples. There is, however, significant literature describing the use of low-power, portable piezoelectric transducers to detect analytes in environmental monitoring and other application areas. Here we review the combination of molecularly imprinted polymers as recognition elements with piezoelectric biosensors for quantitative detection of small molecules. Analytes are classified by type and sample matrix presentation and various molecularly imprinted polymer synthetic fabrication strategies are also reviewed.

Plasmonic Structure Enhanced Exciton Generation at the Interface between the Perovskite Absorber and Copper Nanoparticles

PubMed Central

Lin, Kuen-Feng; Chiang, Chien-Hung; Wu, Chun-Guey

2014-01-01

The refractive index and extinction coefficient of a triiodide perovskite absorber (TPA) were obtained by fitting the transmittance spectra of TPA/PEDOT:PSS/ITO/glass using the transfer matrix method. Cu nanoplasmonic structures were designed to enhance the exciton generation in the TPA and to simultaneously reduce the film thickness of the TPA. Excitons were effectively generated at the interface between TPA and Cu nanoparticles, as observed through the 3D finite-difference time-domain method. The exciton distribution is advantageous for the exciton dissociation and carrier transport. PMID:25295290

A simple molecular orbital treatment of current distributions in quantum transport through molecular junctions

NASA Astrophysics Data System (ADS)

Jhan, Sin-Mu; Jin, Bih-Yaw

2017-11-01

A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes. A few simple molecular junctions consisting of single- and multi-ring conjugated systems are used to demonstrate that local current distributions inside molecular junctions can be decomposed by partial sums of a few leading contributing transition density matrices.

Time-resolved molecular imaging

NASA Astrophysics Data System (ADS)

Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

2016-06-01

Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

Molecular machines open cell membranes

NASA Astrophysics Data System (ADS)

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G.; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B.; Robinson, Jacob T.; Wang, Gufeng; Pal, Robert; Tour, James M.

2017-08-01

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.

Molecular Evolution in Historical Perspective.

PubMed

Suárez-Díaz, Edna

2016-12-01

In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms. These developments sparked important debates between defendants of the molecular and organismic approaches. The most vocal confrontations focused on the relation between primates and humans, and the neutral theory of molecular evolution. By the 1980s and 1990s, the construction of large protein and DNA sequences databases, and the development of computer-based statistical tools, facilitated the coming together of molecular and evolutionary biology. Although in its contemporary form the field of molecular evolution can be traced back to the last five decades, the field has deep roots in twentieth century experimental life sciences. For historians of science, the origins and consolidation of molecular evolution provide a privileged field for the study of scientific debates, the relation between technological advances and scientific knowledge, and the connection between science and broader social concerns.

Molecular machines open cell membranes.

PubMed

García-López, Víctor; Chen, Fang; Nilewski, Lizanne G; Duret, Guillaume; Aliyan, Amir; Kolomeisky, Anatoly B; Robinson, Jacob T; Wang, Gufeng; Pal, Robert; Tour, James M

2017-08-30

Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes. These include using electric and magnetic fields, temperature, ultrasound or light to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation.

Peltier cooling in molecular junctions

NASA Astrophysics Data System (ADS)

Cui, Longji; Miao, Ruijiao; Wang, Kun; Thompson, Dakotah; Zotti, Linda Angela; Cuevas, Juan Carlos; Meyhofer, Edgar; Reddy, Pramod

2018-02-01

The study of thermoelectricity in molecular junctions is of fundamental interest for the development of various technologies including cooling (refrigeration) and heat-to-electricity conversion1-4. Recent experimental progress in probing the thermopower (Seebeck effect) of molecular junctions5-9 has enabled studies of the relationship between thermoelectricity and molecular structure10,11. However, observations of Peltier cooling in molecular junctions—a critical step for establishing molecular-based refrigeration—have remained inaccessible. Here, we report direct experimental observations of Peltier cooling in molecular junctions. By integrating conducting-probe atomic force microscopy12,13 with custom-fabricated picowatt-resolution calorimetric microdevices, we created an experimental platform that enables the unified characterization of electrical, thermoelectric and energy dissipation characteristics of molecular junctions. Using this platform, we studied gold junctions with prototypical molecules (Au-biphenyl-4,4'-dithiol-Au, Au-terphenyl-4,4''-dithiol-Au and Au-4,4'-bipyridine-Au) and revealed the relationship between heating or cooling and charge transmission characteristics. Our experimental conclusions are supported by self-energy-corrected density functional theory calculations. We expect these advances to stimulate studies of both thermal and thermoelectric transport in molecular junctions where the possibility of extraordinarily efficient energy conversion has been theoretically predicted2-4,14.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Assessment of Molecular Modeling & Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materialsmore » modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.« less

Welcome to Molecular Brain

PubMed Central

Mei, Lin; Cho, Kei; Lee, C Justin; Li, Xiao-Jiang; Zhuo, Min; Kaang, Bong-Kiun

2008-01-01

We are delighted to announce the arrival of a brand new journal dedicated to the ever-expanding field of neuroscience. Molecular Brain is a peer-reviewed, open-access online journal that aims at publishing high quality articles as rapidly as possible. The journal will cover a broad spectrum of neuroscience ranging from molecular/cellular to behavioral/cognitive neuroscience and from basic to clinical research. Molecular Brain will publish not only research articles, but also methodology articles, editorials, reviews, and short reports. It will be a premier platform for neuroscientists to exchange their ideas with researchers from around the world to help improve our understanding of the molecular mechanisms of the brain and mind. PMID:18803854

7 CFR 17.8 - Ocean transportation.

Code of Federal Regulations, 2010 CFR

2010-01-01

... transportation accepts the commodity before receipt of an acceptable letter of credit from a bank, the supplier... of princes, rulers or peoples without the fault of the supplier of ocean transportation; wars; public...

Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

NASA Astrophysics Data System (ADS)

Picu, Catalin; Pal, Anirban

Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.

EDITORIAL: Molecular Imaging Technology

NASA Astrophysics Data System (ADS)

Asai, Keisuke; Okamoto, Koji

2006-06-01

'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

Non-linear molecular pattern classification using molecular beacons with multiple targets.

PubMed

Lee, In-Hee; Lee, Seung Hwan; Park, Tai Hyun; Zhang, Byoung-Tak

2013-12-01

In vitro pattern classification has been highlighted as an important future application of DNA computing. Previous work has demonstrated the feasibility of linear classifiers using DNA-based molecular computing. However, complex tasks require non-linear classification capability. Here we design a molecular beacon that can interact with multiple targets and experimentally shows that its fluorescent signals form a complex radial-basis function, enabling it to be used as a building block for non-linear molecular classification in vitro. The proposed method was successfully applied to solving artificial and real-world classification problems: XOR and microRNA expression patterns. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

New concepts for molecular magnets

NASA Astrophysics Data System (ADS)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

PubMed Central

2017-01-01

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. PMID:28637852

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

PubMed

Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

2017-06-28

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

Mapping reversible photoswitching of molecular-resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches.

PubMed

Cho, Duckhyung; Yang, Myungjae; Shin, Narae; Hong, Seunghun

2018-06-07

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular-resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans-to-cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans-to-cis and cis-to-trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general. © 2018 IOP Publishing Ltd.

Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

NASA Astrophysics Data System (ADS)

Wang, Minglang; Wang, Hao; Zhang, Guangping; Wang, Yongfeng; Sanvito, Stefano; Hou, Shimin

2018-05-01

The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, EF, thus hardly affect the transmission around EF; the Au-S interface hybrid states couple with σ-bonds in the molecular backbone forming the conduction channel at EF, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some π-type oxygen orbitals coupling with the Au-S interface hybrid states contribute to the transmission around EF. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols.

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

PubMed

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Molecular beacon sequence design algorithm.

PubMed

Monroe, W Todd; Haselton, Frederick R

2003-01-01

A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

High spectral resolution observations of fluorescent molecular hydrogen in molecular clouds

NASA Technical Reports Server (NTRS)

Burton, Michael G.; Geballe, T. R.; Brand, P. W. J. L.; Moorhouse, A.

1990-01-01

The 1-0 S(1) line of molecular hydrogen has been observed at high spectral resolution in several sources where the emission was suspected of being fluorescent. In NGC 2023, the Orion Bar, and Parsamyan 18, the S(1) line is unresolved, and the line center close to the rest velocity of the ambient molecular cloud. Such behavior is expected for UV-excited line emission. The H2 line widths in molecular clouds thus can serve as diagnostic for shocked and UV-excitation mechanisms. If the lines are broader than several km/s or velocity shifts are observed across a source it is likely that shocks are responsible for the excitation of the gas.

Molecular Imaging: Current Status and Emerging Strategies

PubMed Central

Pysz, Marybeth A.; Gambhir, Sanjiv S.; Willmann, Jürgen K.

2011-01-01

In vivo molecular imaging has a great potential to impact medicine by detecting diseases in early stages (screening), identifying extent of disease, selecting disease- and patient-specific therapeutic treatment (personalized medicine), applying a directed or targeted therapy, and measuring molecular-specific effects of treatment. Current clinical molecular imaging approaches primarily use PET- or SPECT-based techniques. In ongoing preclinical research novel molecular targets of different diseases are identified and, sophisticated and multifunctional contrast agents for imaging these molecular targets are developed along with new technologies and instrumentation for multimodality molecular imaging. Contrast-enhanced molecular ultrasound with molecularly-targeted contrast microbubbles is explored as a clinically translatable molecular imaging strategy for screening, diagnosing, and monitoring diseases at the molecular level. Optical imaging with fluorescent molecular probes and ultrasound imaging with molecularly-targeted microbubbles are attractive strategies since they provide real-time imaging, are relatively inexpensive, produce images with high spatial resolution, and do not involve exposure to ionizing irradiation. Raman spectroscopy/microscopy has emerged as a molecular optical imaging strategy for ultrasensitive detection of multiple biomolecules/biochemicals with both in vivo and ex vivo versatility. Photoacoustic imaging is a hybrid of optical and ultrasound modalities involving optically-excitable molecularly-targeted contrast agents and quantitative detection of resulting oscillatory contrast agent movement with ultrasound. Current preclinical findings and advances in instrumentation such as endoscopes and microcatheters suggest that these molecular imaging modalities have numerous clinical applications and will be translated into clinical use in the near future. PMID:20541650

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

PubMed Central

Liu, Qixin; Cai, Zhiyong

2014-01-01

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Evolutionary molecular medicine.

PubMed

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

PubMed

Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

2012-11-28

Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

[Prospects of molecular breeding in medical plants].

PubMed

Ma, Xiao-Jun; Mo, Chang-Ming

2017-06-01

The molecular-assisted breeding, transgenic breeding and molecular designing breeding are three development directions of plant molecular breeding. Base on these three development directions, this paper summarizes developing status and new tendency of research field of genetic linkage mapping, QTL mapping, association mapping, molecular-assisted selections, pollen-mediated transformations, agrobacterium-mediated transformations, particle gun-mediated transformations, genome editing technologies, whole-genome sequencing, transcriptome sequencing, proteome sequencing and varietal molecular designing. The objective and existing problem of medical plant molecular breeding were discussed the prospect of these three molecular breeding technologies application on medical plant molecular breeding was outlooked. Copyright© by the Chinese Pharmaceutical Association.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces

A concurrent multiscale micromorphic molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Shaofan, E-mail: shaofan@berkeley.edu; Tong, Qi

2015-04-21

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from firstmore » principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.« less

Molecular Force Spectroscopy on Cells

NASA Astrophysics Data System (ADS)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Chirality in molecular collision dynamics

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico

2018-02-01

Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

PubMed

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Listen Up! Noises Can Damage Your Hearing

MedlinePlus

... Shortened Understanding Aphasia Wise Choices It’s a Noisy Planet: Protect Your Hearing Your ears can be your ... the noise (wear earplugs or earmuffs). Links Noisy Planet Noise-Induced Hearing Loss Interactive Sound Ruler AgePage: ...

Molecular chaperones and photoreceptor function

PubMed Central

Kosmaoglou, Maria; Schwarz, Nele; Bett, John S.; Cheetham, Michael E.

2008-01-01

Molecular chaperones facilitate and regulate protein conformational change within cells. This encompasses many fundamental cellular processes: including the correct folding of nascent chains; protein transport and translocation; signal transduction and protein quality control. Chaperones are, therefore, important in several forms of human disease, including neurodegeneration. Within the retina, the highly specialized photoreceptor cell presents a fascinating paradigm to investigate the specialization of molecular chaperone function and reveals unique chaperone requirements essential to photoreceptor function. Mutations in several photoreceptor proteins lead to protein misfolding mediated neurodegeneration. The best characterized of these are mutations in the molecular light sensor, rhodopsin, which cause autosomal dominant retinitis pigmentosa. Rhodopsin biogenesis is likely to require chaperones, while rhodopsin misfolding involves molecular chaperones in quality control and the cellular response to protein aggregation. Furthermore, the specialization of components of the chaperone machinery to photoreceptor specific roles has been revealed by the identification of mutations in molecular chaperones that cause inherited retinal dysfunction and degeneration. These chaperones are involved in several important cellular pathways and further illuminate the essential and diverse roles of molecular chaperones. PMID:18490186

Assessment of Molecular Acoustic Angiography for Combined Microvascular and Molecular Imaging in Preclinical Tumor Models

PubMed Central

Lindsey, Brooks D.; Shelton, Sarah E.; Foster, F. Stuart; Dayton, Paul A.

2017-01-01

Purpose To evaluate a new ultrasound molecular imaging approach in its ability to image a preclinical tumor model and to investigate the capacity to visualize and quantify co-registered microvascular and molecular imaging volumes. Procedures Molecular imaging using the new technique was compared with a conventional ultrasound molecular imaging technique (multi-pulse imaging) by varying the injected microbubble dose and scanning each animal using both techniques. Each of the 14 animals was randomly assigned one of three doses; bolus dose was varied, and the animals were imaged for three consecutive days so that each animal received every dose. A microvascular scan was also acquired for each animal by administering an infusion of non-targeted microbubbles. These scans were paired with co-registered molecular images (VEGFR2-targeted microbubbles), the vessels were segmented, and the spatial relationships between vessels and VEGFR2 targeting locations were analyzed. In 5 animals, an additional scan was performed in which the animal received a bolus of microbubbles targeted to E- and P-selectin. Vessel tortuosity as a function of distance from VEGF and selectin targeting was analyzed in these animals. Results Although resulting differences in image intensity due to varying microbubble dose were not significant between the two lowest doses, superharmonic imaging had significantly higher contrast-to-tissue ratio (CTR) than multi-pulse imaging (mean across all doses: 13.98 dB for molecular acoustic angiography vs. 0.53 dB for multi-pulse imaging; p = 4.9 × 10−10). Analysis of registered microvascular and molecular imaging volumes indicated that vessel tortuosity decreases with increasing distance from both VEGFR2 and selectin targeting sites. Conclusions Molecular acoustic angiography (superharmonic molecular imaging) exhibited a significant increase in CTR at all doses tested due to superior rejection of tissue artifact signals. Due to the high resolution of acoustic

Low Molecular Weight Norbornadiene Derivatives for Molecular Solar‐Thermal Energy Storage

PubMed Central

Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl

2016-01-01

Abstract Molecular solar‐thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193–260 g mol−1) norbornadiene–quadricyclane systems. The molecules feature cyano acceptor and ethynyl‐substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo‐thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396–629 kJ kg−1). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. PMID:27492997

Clustering the Orion B giant molecular cloud based on its molecular emission

PubMed Central

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2017-01-01

Context Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results A clustering analysis based only on the J = 1 – 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes (nH ~ 100 cm−3, ~ 500 cm−3, and > 1000 cm−3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 − 0 line of HCO+ and the N = 1 − 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH ~ 7 × 103 cm−3 ~ 4 × 104 cm−3) for the

Clustering the Orion B giant molecular cloud based on its molecular emission.

PubMed

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional Probability Density Function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. A clustering analysis based only on the J = 1 - 0 lines of three isotopologues of CO proves suffcient to reveal distinct density/column density regimes ( n H ~ 100 cm -3 , ~ 500 cm -3 , and > 1000 cm -3 ), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1 - 0 line of HCO + and the N = 1 - 0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO + and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO + intensity ratio in UV-illuminated regions. Finer distinctions in density classes ( n H ~ 7 × 10 3 cm -3 ~ 4 × 10 4 cm -3 ) for the densest regions are also

Frequency Domain Fluorescent Molecular Tomography and Molecular Probes for Small Animal Imaging

NASA Astrophysics Data System (ADS)

Kujala, Naresh Gandhi

Fluorescent molecular tomography (FMT) is a noninvasive biomedical optical imaging that enables 3-dimensional quantitative determination of fluorochromes distributed in biological tissues. There are three methods for imaging large volume tissues based on different light sources: (a) using a light source of constant intensity, through a continuous or constant wave, (b) using a light source that is intensity modulated with a radio frequency (RF), and (c) using ultrafast pulses in the femtosecond range. In this study, we have developed a frequency domain fluorescent molecular tomographic system based on the heterodyne technique, using a single source and detector pair that can be used for small animal imaging. In our system, the intensity of the laser source is modulated with a RF frequency to produce a diffuse photon density wave in the tissue. The phase of the diffuse photon density wave is measured by comparing the reference signal with the signal from the tissue using a phasemeter. The data acquisition was performed by using a Labview program. The results suggest that we can measure the phase change from the heterogeneous inside tissue. Combined with fiber optics and filter sets, the system can be used to sensitively image the targeted fluorescent molecular probes, allowing the detection of cancer at an early stage. We used the system to detect the tumor-targeting molecular probe Alexa Fluor 680 and Alexa Fluor 750 bombesin peptide conjugates in phantoms as well as mouse tissues. We also developed and evaluated fluorescent Bombesin (BBN) probes to target gastrin-releasing peptide (GRP) receptors for optical molecular imaging. GRP receptors are over-expressed in several types of human cancer cells, including breast, prostate, small cell lung, and pancreatic cancers. BBN is a 14 amino acid peptide that is an analogue to human gastrin-releasing peptide that binds specifically to GRPr receptors. BBN conjugates are significant in cancer detection and therapy. The

Molecular Rotors as Switches

PubMed Central

Xue, Mei; Wang, Kang L.

2012-01-01

The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene) monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V) revealed a temperature-dependent negative differential resistance (NDR) associated with the device. The analysis of the device I–V characteristics suggests the source of the

Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Molecular Crystal alphaRDX

DTIC Science & Technology

2013-08-01

potential for HMX / RDX (3, 9). ...................................................................................8 1 1. Purpose This work...6 dispersion and electrostatic interactions. Constants for the SB potential are given in table 1. 8 Table 1. SB potential for HMX / RDX (3, 9...modeling dislocations in the energetic molecular crystal RDX using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

PubMed

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Molecular Typing and Differentiation

EPA Science Inventory

In this chapter, general background and bench protocols are provided for a number of molecular typing techniques in common use today. Methods for the molecular typing and differentiation of microorganisms began to be widely adopted following the development of the polymerase chai...

Distance dependence of the energy transfer rate from a single semiconductor nanostructure to graphene.

PubMed

Federspiel, François; Froehlicher, Guillaume; Nasilowski, Michel; Pedetti, Silvia; Mahmood, Ather; Doudin, Bernard; Park, Serin; Lee, Jeong-O; Halley, David; Dubertret, Benoît; Gilliot, Pierre; Berciaud, Stéphane

2015-02-11

The near-field Coulomb interaction between a nanoemitter and a graphene monolayer results in strong Förster-type resonant energy transfer and subsequent fluorescence quenching. Here, we investigate the distance dependence of the energy transfer rate from individual, (i) zero-dimensional CdSe/CdS nanocrystals and (ii) two-dimensional CdSe/CdS/ZnS nanoplatelets to a graphene monolayer. For increasing distances d, the energy transfer rate from individual nanocrystals to graphene decays as 1/d(4). In contrast, the distance dependence of the energy transfer rate from a two-dimensional nanoplatelet to graphene deviates from a simple power law but is well described by a theoretical model, which considers a thermal distribution of free excitons in a two-dimensional quantum well. Our results show that accurate distance measurements can be performed at the single particle level using graphene-based molecular rulers and that energy transfer allows probing dimensionality effects at the nanoscale.

Stable Molecular Diodes Based on π-π Interactions of the Molecular Frontier Orbitals with Graphene Electrodes.

PubMed

Song, Peng; Guerin, Sarah; Tan, Sherman Jun Rong; Annadata, Harshini Venkata; Yu, Xiaojiang; Scully, Micheál; Han, Ying Mei; Roemer, Max; Loh, Kian Ping; Thompson, Damien; Nijhuis, Christian A

2018-03-01

In molecular electronics, it is important to control the strength of the molecule-electrode interaction to balance the trade-off between electronic coupling strength and broadening of the molecular frontier orbitals: too strong coupling results in severe broadening of the molecular orbitals while the molecular orbitals cannot follow the changes in the Fermi levels under applied bias when the coupling is too weak. Here, a platform based on graphene bottom electrodes to which molecules can bind via π-π interactions is reported. These interactions are strong enough to induce electronic function (rectification) while minimizing broadening of the molecular frontier orbitals. Molecular tunnel junctions are fabricated based on self-assembled monolayers (SAMs) of Fc(CH 2 ) 11 X (Fc = ferrocenyl, X = NH 2 , Br, or H) on graphene bottom electrodes contacted to eutectic alloy of gallium and indium top electrodes. The Fc units interact more strongly with graphene than the X units resulting in SAMs with the Fc at the bottom of the SAM. The molecular diodes perform well with rectification ratios of 30-40, and they are stable against bias stressing under ambient conditions. Thus, tunnel junctions based on graphene with π-π molecule-electrode coupling are promising platforms to fabricate stable and well-performing molecular diodes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancement of photothermal heat generation by metallodielectric nanoplasmonic clusters.

PubMed

Ahmadivand, Arash; Pala, Nezih; Güney, Durdu Ö

2015-06-01

A four-member homogenous quadrumer composed of silver core-shell nanostructures is tailored to enhance photothermal heat generation efficiency in sub-nanosecond time scale. Calculating the plasmonic and photothermal responses of metallic cluster, we show that it is possible to achieve thermal heat flux generation of 64.7 μW.cm^-2 and temperature changes in the range of ΔT = 150 K, using Fano resonant effect. Photothermal heat generation efficiency is even further enhanced by adding carbon nanospheres to the offset gap between particles and obtained thermal heat flux generation of 93.3 μW.cm^-2 and temperature increase of ΔT = 172 K. It is also shown that placement of dielectric spheres gives rise to arise collective magnetic dark plasmon modes that improves the quality of the observed Fano resonances. The presented data attests the superior performance of the proposed metallodielectric structures to utilize in practical tumor and cancer therapies and drug delivery applications.

Aperiodic nanoplasmonic devices for directional colour filtering and sensing.

PubMed

Davis, Matthew S; Zhu, Wenqi; Xu, Ting; Lee, Jay K; Lezec, Henri J; Agrawal, Amit

2017-11-07

Exploiting the wave-nature of light in its simplest form, periodic architectures have enabled a panoply of tunable optical devices with the ability to perform useful functions such as filtering, spectroscopy, and multiplexing. Here, we remove the constraint of structural periodicity to enhance, simultaneously, the performance and functionality of passive plasmonic devices operating at optical frequencies. By using a physically intuitive, first-order interference model of plasmon-light interactions, we demonstrate a simple and efficient route towards designing devices with flexible, multi-spectral optical response, fundamentally not achievable using periodic architectures. Leveraging this approach, we experimentally implement ultra-compact directional light-filters and colour-sorters exhibiting angle- or spectrally-tunable optical responses with high contrast, and low spectral or spatial crosstalk. Expanding the potential of aperiodic systems to implement tailored spectral and angular responses, these results hint at promising applications in solar-energy harvesting, optical signal multiplexing, and integrated sensing.

Wafer-Scale Aluminum Nanoplasmonic Resonators with Optimized Metal Deposition

DTIC Science & Technology

2016-01-04

As observed by others, the location of these plasmonic resonances is accompanied by a sharp change in phase ( Figure 6 C and F).48 17 Figure...bottom of the structure. The reflectance curves (Figure 4) do not show sharp resonances between 300 and 500 nm, but a broader depression in...Letters 2015, 15, 6946-6951. 3. Taguchi, A.; Saito, Y.; Watanabe , K.; Yijian, S.; Kawata, S. Tailoring plasmon resonances in the deep-ultraviolet by size

Nanoplasmonic imaging of latent fingerprints and identification of cocaine.

PubMed

Li, Kun; Qin, Weiwei; Li, Fan; Zhao, Xingchun; Jiang, Bowei; Wang, Kun; Deng, Suhui; Fan, Chunhai; Li, Di

2013-10-25

Search for traces: Aptamer-bound Au nanoparticles (Au NPs) were used to provide high-resolution dark-field microscopy images of latent fingerprints (LFPs) with level 2 and level 3 details. Furthermore, the cocaine-induced aggregation of Au NPs results in a true green-to-red color change of the scattered light, providing a quasi-quantative method to identify cocaine loadings in LFPs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interconnecting wearable devices with nano-biosensing implants through optical wireless communications

NASA Astrophysics Data System (ADS)

Johari, Pedram; Pandey, Honey; Jornet, Josep M.

2018-02-01

Major advancements in the fields of electronics, photonics and wireless communication have enabled the development of compact wearable devices, with applications in diverse domains such as fitness, wellness and medicine. In parallel, nanotechnology is enabling the development of miniature sensors that can detect events at the nanoscale with unprecedented accuracy. On this matter, in vivo implantable Surface Plasmon Resonance (SPR) nanosensors have been proposed to analyze circulating biomarkers in body fluids for the early diagnosis of a myriad of diseases, ranging from cardiovascular disorders to different types of cancer. In light of these results, in this paper, an architecture is proposed to bridge the gap between these two apparently disjoint paradigms, namely, the commercial wearable devices and the advanced nano-biosensing technologies. More specifically, this paper thoroughly assesses the feasibility of the wireless optical intercommunications of an SPR-based nanoplasmonic biochip -implanted subcutaneously in the wrist-, with a nanophotonic wearable smart band which is integrated by an array of nano-lasers and photon-detectors for distributed excitation and measurement of the nanoplasmonic biochip. This is done through a link budget analysis which captures the peculiarities of the intra-body optical channel at (sub) cellular level, the strength of the SPR nanosensor reflection, as well as the capabilities of the nanolasers (emission power, spectrum) and the nano photon-detectors (sensitivity and noise equivalent power). The proposed analysis guides the development of practical communication designs between the wearable devices and nano-biosensing implants, which paves the way through early-stage diagnosis of severe diseases.

The Rolling Release Rulapult

NASA Astrophysics Data System (ADS)

West, Joseph; Ross, Seth; Flesher, James

2011-09-01

The "rulapult" is a low-cost, easy-to-construct, ruler-based catapult for use in the classroom. It is made from durable, inexpensive items that are easy to store. Most of the components can be found with a visit to one or two local stores. A set of 12 complete rulapults can be constructed for less than 150, including the one-time cost of the only tool needed for construction, a single handheld one-hole paper punch. The unit price per rulapult approaches 10.25 as the number of rulapults constructed becomes "large." A rulapult can be constructed by a single middle school student in less than five minutes. Ping-Pong® balls or marshmallows are suggested for use as projectiles as they pose a minimal safety hazard. The range of a typical rulapult when firing a Ping-Pong ball is approximately 4.0 m, just right for classroom or hallway testing. The smaller (1-cm size) marshmallows have a range of about 5.0 m, but due to their "squishy" nature, the range is less consistent from shot to shot. For the rest of the discussion, it is presumed that the projectile is a Ping-Pong ball (the ball). The ball can easily knock over a large Styrofoam™ cup, but despite its impressive range and "knock-down power," the rulers used are "limp" enough that a direct hit to your hand by the ruler will not cause noticeable pain or injury.

75 FR 340 - Approval for Expansion of Subzone 22F, Abbott Molecular, Inc. (Pharmaceutical and Molecular...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Order No. 1654] Approval for Expansion of Subzone 22F, Abbott Molecular, Inc. (Pharmaceutical and Molecular Diagnostic Products), Chicago, IL, Area... manufacturing authority on behalf of Abbott Molecular, Inc., within FTZ 22F in Des Plaines and Elk Grove Village...

Magnetohydrodynamic Models of Molecular Tornadoes

NASA Astrophysics Data System (ADS)

Au, Kelvin; Fiege, Jason D.

2017-07-01

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

Molecular markers in pediatric neuro-oncology.

PubMed

Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao

2012-09-01

Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment.

Molecular markers in pediatric neuro-oncology

PubMed Central

Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao

2012-01-01

Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment. PMID:23095836

A 17 GHz molecular rectifier

PubMed Central

Trasobares, J.; Vuillaume, D.; Théron, D.; Clément, N.

2016-01-01

Molecular electronics originally proposed that small molecules sandwiched between electrodes would accomplish electronic functions and enable ultimate scaling to be reached. However, so far, functional molecular devices have only been demonstrated at low frequency. Here, we demonstrate molecular diodes operating up to 17.8 GHz. Direct current and radio frequency (RF) properties were simultaneously measured on a large array of molecular junctions composed of gold nanocrystal electrodes, ferrocenyl undecanethiol molecules and the tip of an interferometric scanning microwave microscope. The present nanometre-scale molecular diodes offer a current density increase by several orders of magnitude compared with that of micrometre-scale molecular diodes, allowing RF operation. The measured S11 parameters show a diode rectification ratio of 12 dB which is linked to the rectification behaviour of the direct current conductance. From the RF measurements, we extrapolate a cut-off frequency of 520 GHz. A comparison with the silicon RF-Schottky diodes, architecture suggests that the RF-molecular diodes are extremely attractive for scaling and high-frequency operation. PMID:27694833

Natural Product Molecular Fossils.

PubMed

Falk, Heinz; Wolkenstein, Klaus

The natural products synthesized by organisms that were living a long time ago gave rise to their molecular fossils. These can consist of either the original unchanged compounds or they may undergo peripheral transformations in which their skeletons remain intact. In cases when molecular fossils can be traced to their organismic source, they are termed "geological biomarkers".This contribution describes apolar and polar molecular fossils and, in particular biomarkers, along the lines usually followed in organic chemistry textbooks, and points to their bioprecursors when available. Thus, the apolar compounds are divided in linear and branched alkanes followed by alicyclic compounds and aromatic and heterocyclic molecules, and, in particular, the geoporphyrins. The polar molecular fossils contain as functional groups or constituent units ethers, alcohols, phenols, carbonyl groups, flavonoids, quinones, and acids, or are polymers like kerogen, amber, melanin, proteins, or nucleic acids. The final sections discuss the methodology used and the fundamental processes encountered by the biomolecules described, including diagenesis, catagenesis, and metagenesis.

Small business development for molecular diagnostics.

PubMed

Anagostou, Anthanasia; Liotta, Lance A

2012-01-01

Molecular profiling, which is the application of molecular diagnostics technology to tissue and blood -specimens, is an integral element in the new era of molecular medicine and individualized therapy. Molecular diagnostics is a fertile ground for small business development because it can generate products that meet immediate demands in the health-care sector: (a) Detection of disease risk, or early-stage disease, with a higher specificity and sensitivity compared to previous testing methods, and (b) "Companion diagnostics" for stratifying patients to receive a treatment choice optimized to their individual disease. This chapter reviews the promise and challenges of business development in this field. Guidelines are provided for the creation of a business model and the generation of a marketing plan around a candidate molecular diagnostic product. Steps to commercialization are outlined using existing molecular diagnostics companies as learning examples.

Mechanism of molecular recognition on molecular imprinted monolith by capillary electrochromatography.

PubMed

Liu, Zhao-Sheng; Xu, Yan-Li; Yan, Chao; Gao, Ru-Yu

2005-09-16

The recognition mechanism of molecularly imprinted polymer (MIP) in capillary electrochromatography (CEC) is complicated since it possesses a hybrid process, which comprises the features of chromatographic retention, electrophoretic migration and molecular imprinting. For an understanding of the molecular recognition of MIP in CEC, a monolithic MIP in a capillary with 1,1'-binaphthyl-2,2'-diamine (BNA) imprinting was prepared by in situ copolymerization of imprinted molecule, methacrylic acid and ethylene glycol dimethacrylate in porogenic solvent, a mixture of toluene-isooctane. Strong recognition ability and high column performance (theory plates was 43,000 plates/m) of BNA were achieved on this monolithic MIP in CEC mode. In addition, BNA and its structural analogue, 1,1'-bi-2, 2'-naphthol, differing in functional groups, were used as model compounds to study imprinting effect on the resultant BNA-imprinted monolithic column, a reference column without imprinting of BNA and a open capillary. The effects of organic modifier concentration, pH value of buffer, salt concentration of buffer and column temperature on the retention and recognition of two compounds were investigated. The results showed that the molecular recognition on MIP monolith in CEC mode mainly derived from imprinting cavities on BNA-imprinted polymer other than chromatographic retention and electrophoretic migration.

Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.

PubMed

Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper

2016-09-05

Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Microfluidic technology for molecular diagnostics.

PubMed

Robinson, Tom; Dittrich, Petra S

2013-01-01

Molecular diagnostics have helped to improve the lives of millions of patients worldwide by allowing clinicians to diagnose patients earlier as well as providing better ongoing therapies. Point-of-care (POC) testing can bring these laboratory-based techniques to the patient in a home setting or to remote settings in the developing world. However, despite substantial progress in the field, there still remain many challenges. Progress in molecular diagnostics has benefitted greatly from microfluidic technology. This chapter aims to summarise the more recent advances in microfluidic-based molecular diagnostics. Sections include an introduction to microfluidic technology, the challenges of molecular diagnostics, how microfluidic advances are working to solve these issues, some alternative design approaches, and detection within these systems.

How molecular motors work – insights from the molecular machinist's toolbox: the Nobel prize in Chemistry 2016

PubMed Central

Astumian, R. D.

2017-01-01

The Nobel prize in Chemistry for 2016 was awarded to Jean Pierre Sauvage, Sir James Fraser Stoddart, and Bernard (Ben) Feringa for their contributions to the design and synthesis of molecular machines. While this field is still in its infancy, and at present there are no commercial applications, many observers have stressed the tremendous potential of molecular machines to revolutionize technology. However, perhaps the most important result so far accruing from the synthesis of molecular machines is the insight provided into the fundamental mechanisms by which molecular motors, including biological motors such as kinesin, myosin, FoF1 ATPase, and the flagellar motor, function. The ability to “tinker” with separate components of molecular motors allows asking, and answering, specific questions about mechanism, particularly with regard to light driven vs. chemistry driven molecular motors. PMID:28572896

Morphogenesis of Dengue Virus: Molecular Biology and Molecular Organization of Proteins.

DTIC Science & Technology

1981-02-01

envelope and near the virion surface. The divalent cations probably act to stabilize viral envelope proteins, as recently found for feline leukemia ... Virus Sindbis virus (SV) and Semliki Forest Virus (SFV) are arthopod-borne alDhaviruses of the toqavirus family. Both viruses contain a nucleocaosid...AU-AIZ9 b"J MORPHOGENESIS OF DENGUE VIRUS : MOLECULAR BIO0OGY AND MOLECULAR ORGANIZATION OFPROENS(U CALIORNIAUNIV DAVIS DEPT 0F BACTERIOLO0Y J S

Ultra-fast all-optical plasmon induced transparency in a metal–insulator–metal waveguide containing two Kerr nonlinear ring resonators

NASA Astrophysics Data System (ADS)

Nurmohammadi, Tofiq; Abbasian, Karim; Yadipour, Reza

2018-05-01

In this work, an ultra-fast all-optical plasmon induced transparency based on a metal–insulator–metal nanoplasmonic waveguide with two Kerr nonlinear ring resonators is studied. Two-dimensional simulations utilizing the finite-difference time-domain method are used to show an obvious optical bistability and significant switching mechanisms of the signal light by varying the pump-light intensity. The proposed all-optical switching based on plasmon induced transparency demonstrates femtosecond-scale feedback time (90 fs), meaning ultra-fast switching can be achieved. The presented all-optical switch may have potential significant applications in integrated optical circuits.

Molecular Detection of Antimicrobial Resistance

PubMed Central

Fluit, Ad C.; Visser, Maarten R.; Schmitz, Franz-Josef

2001-01-01

The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art. PMID:11585788

Ultrahigh molecular weight aromatic siloxane polymers

NASA Technical Reports Server (NTRS)

Ludwick, L. M.

1982-01-01

The condensation of a diol with a silane in toluene yields a silphenylene-siloxane polymer. The reaction of stiochiometric amounts of the diol and silane produced products with molecular weights in the range 2.0 - 6.0 x 10 to the 5th power. The molecular weight of the product was greatly increased by a multistep technique. The methodology for synthesis of high molecular weight polymers using a two step procedure was refined. Polymers with weight average molecular weights in excess of 1.0 x 10 to the 6th power produced by this method. Two more reactive silanes, bis(pyrrolidinyl)dimethylsilane and bis(gamma butyrolactam)dimethylsilane, are compared with the dimethyleminodimethylsilane in ability to advance the molecular weight of the prepolymer. The polymers produced are characterized by intrinsic viscosity in tetrahydrofuran. Weight and number average molecular weights and polydispersity are determined by gel permeation chromatography.

Stand-off molecular composition analysis

NASA Astrophysics Data System (ADS)

Hughes, Gary B.; Lubin, Philip; Meinhold, Peter; O'Neill, Hugh; Brashears, Travis; Zhang, Qicheng; Griswold, Janelle; Riley, Jordan; Motta, Caio

2015-09-01

Molecular composition of distant stars is explored by observing absorption spectra. The star produces blackbody radiation that passes through the molecular cloud of vaporized material surrounding the star. Characteristic absorption lines are discernible with a spectrometer, and molecular composition is investigated by comparing spectral observations with known material profiles. Most objects in the solar system—asteroids, comets, planets, moons—are too cold to be interrogated in this manner. Molecular clouds around cold objects consist primarily of volatiles, so bulk composition cannot be probed. Additionally, low volatile density does not produce discernible absorption lines in the faint signal generated by low blackbody temperatures. This paper describes a system for probing the molecular composition of cold solar system targets from a distant vantage. The concept utilizes a directed energy beam to melt and vaporize a spot on a distant target, such as from a spacecraft orbiting the object. With sufficient flux (~10 MW/m2), the spot temperature rises rapidly (to ~2 500 K), and evaporation of all materials on the target surface occurs. The melted spot creates a high-temperature blackbody source, and ejected material creates a molecular plume in front of the spot. Bulk composition is investigated by using a spectrometer to view the heated spot through the ejected material. Spatial composition maps could be created by scanning the surface. Applying the beam to a single spot continuously produces a borehole, and shallow sub-surface composition profiling is also possible. Initial simulations of absorption profiles with laser heating show great promise for molecular composition analysis.

Molecular detection of pathogens in water--the pros and cons of molecular techniques.

PubMed

Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

2010-08-01

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

Packet Fragmentation and Reassembly in Molecular Communication.

PubMed

Furubayashi, Taro; Nakano, Tadashi; Eckford, Andrew; Okaie, Yutaka; Yomo, Tetsuya

2016-04-01

This paper describes packet fragmentation and reassembly to achieve reliable molecular communication among bionanomachines. In the molecular communication described in this paper, a sender bionanomachine performs packet fragmentation, dividing a large molecular message into smaller pieces and embedding into smaller molecular packets, so that molecular packets have higher diffusivity to reach the receiver bionanomachine. The receiver bionanomachine then performs packet reassembly to retrieve the original molecular message from a set of molecular packets that it receives. To examine the effect of packet fragmentation and reassembly, we develop analytical models and conduct numerical experiments. Numerical results show that packet fragmentation and reassembly can improve the message delivery performance. Numerical results also indicate that packet fragmentation and reassembly may degrade the performance in the presence of drift in the environment.

A Passion for Science.

ERIC Educational Resources Information Center

Campbell, Nancy

2000-01-01

Explains the process of developing the unit "Building an Aquarium" and introduces four hands-on activities which include teaching students how to read a metric ruler, observing and illustrating an aquatic plant, learning fish anatomy, and learning animal behavior. (YDS)

Test Image by Mars Descent Imager

NASA Image and Video Library

2010-07-19

Ken Edgett, deputy principal investigator for NASA Mars Descent Imager, holds a ruler used as a depth-of-field test target. The instrument took this image inside the Malin Space Science Systems clean room in San Diego, CA, during calibration testing.

Molecular chirality: language, history, and significance.

PubMed

Gal, Joseph

2013-01-01

In this chapter some background material concerning molecular chirality and enantiomerism is presented. First some basic chemical-molecular aspects of chirality are reviewed, after which certain relevant terminology whose use in the literature has been problematic is discussed. Then an overview is provided of some of the early discoveries that laid the foundations of the science of molecular chirality in chemistry and biology, including the discovery of the phenomenon of molecular chirality by L. Pasteur, the proposals for the asymmetric carbon atom by J.H. van 't Hoff and J.A. Lebel, Pasteur's discovery of biological enantioselectivity, the discovery of enantioselectivity at biological receptors by A. Piutti, the studies of enzymatic stereoselectivity by E. Fischer, and the work on enantioselectivity in pharmacology by A. Cushny. Finally, the role of molecular chirality in pharmacotherapy and new-drug development, arguably one of the main driving forces for the current intense interest in the phenomenon of molecular chirality, is discussed.

Molecular-Scale Electronics: From Concept to Function.

PubMed

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Optical/MRI Multimodality Molecular Imaging

NASA Astrophysics Data System (ADS)

Ma, Lixin; Smith, Charles; Yu, Ping

2007-03-01

Multimodality molecular imaging that combines anatomical and functional information has shown promise in development of tumor-targeted pharmaceuticals for cancer detection or therapy. We present a new multimodality imaging technique that combines fluorescence molecular tomography (FMT) and magnetic resonance imaging (MRI) for in vivo molecular imaging of preclinical tumor models. Unlike other optical/MRI systems, the new molecular imaging system uses parallel phase acquisition based on heterodyne principle. The system has a higher accuracy of phase measurements, reduced noise bandwidth, and an efficient modulation of the fluorescence diffuse density waves. Fluorescent Bombesin probes were developed for targeting breast cancer cells and prostate cancer cells. Tissue phantom and small animal experiments were performed for calibration of the imaging system and validation of the targeting probes.

Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

NASA Astrophysics Data System (ADS)

Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

2015-08-01

Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

Molecular Thermometry

PubMed Central

McCabe, Kevin M.; Hernandez, Mark

2010-01-01

Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

Soluble Molecularly Imprinted Nanorods for Homogeneous Molecular Recognition

NASA Astrophysics Data System (ADS)

Liang, Rongning; Wang, Tiantian; Zhang, Huan; Yao, Ruiqing; Qin, Wei

2018-03-01

Nowadays, it is still difficult for molecularly imprinted polymer (MIPs) to achieve homogeneous recognition since they cannot be easily dissolved in organic or aqueous phase. To address this issue, soluble molecularly imprinted nanorods have been synthesized by using soluble polyaniline doped with a functionalized organic protonic acid as the polymer matrix. By employing 1-naphthoic acid as a model, the proposed imprinted nanorods exhibit an excellent solubility and good homogeneous recognition ability. The imprinting factor for the soluble imprinted nanoroads is 6.8. The equilibrium dissociation constant and the apparent maximum number of the proposed imprinted nanorods are 248.5 μM and 22.1 μmol/g, respectively. We believe that such imprinted nanorods may provide an appealing substitute for natural receptors in homogeneous recognition related fields.

Molecular pathology curriculum for medical laboratory scientists: A report of the association for molecular pathology training and education committee.

PubMed

Taylor, Sara; Bennett, Katie M; Deignan, Joshua L; Hendrix, Ericka C; Orton, Susan M; Verma, Shalini; Schutzbank, Ted E

2014-05-01

Molecular diagnostics is a rapidly growing specialty in the clinical laboratory assessment of pathology. Educational programs in medical laboratory science and specialized programs in molecular diagnostics must address the training of clinical scientists in molecular diagnostics, but the educational curriculum for this field is not well defined. Moreover, our understanding of underlying genetic contributions to specific diseases and the technologies used in molecular diagnostics laboratories change rapidly, challenging providers of training programs in molecular diagnostics to keep their curriculum current and relevant. In this article, we provide curriculum recommendations to molecular diagnostics training providers at both the baccalaureate and master's level of education. We base our recommendations on several factors. First, we considered National Accrediting Agency for Clinical Laboratory Sciences guidelines for accreditation of molecular diagnostics programs, because educational programs in clinical laboratory science should obtain its accreditation. Second, the guidelines of several of the best known certifying agencies for clinical laboratory scientists were incorporated into our recommendations. Finally, we relied on feedback from current employers of molecular diagnostics scientists, regarding the skills and knowledge that they believe are essential for clinical scientists who will be performing molecular testing in their laboratories. We have compiled these data into recommendations for a molecular diagnostics curriculum at both the baccalaureate and master's level of education. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Molecular neurobiology in neurology and psychiatry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kandel, E.R.

1987-01-01

This book contains 14 selections. Some of the titles are: An Introduction to Ion Channels; Molecular Neurobiology of the Myelinated Nerve Fiber: Ion-Channel Distributions and Their Implications for Demyelinating Diseases; A Molecular Genetic Approach to Huntington's Disease; and Molecular Features of Cell Adhesion Molecules Involved in Neural Development.

Stereodivergent synthesis with a programmable molecular machine

NASA Astrophysics Data System (ADS)

Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Marcos, Vanesa; Palmer, Leoni I.; Pisano, Simone

2017-09-01

It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism. Here we detail an artificial molecular machine that moves a substrate between different activating sites to achieve different product outcomes from chemical synthesis. This molecular robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addition of a thiol and an alkene to an α,β-unsaturated aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable molecular machines may have significant roles in chemical synthesis and molecular manufacturing.

Computational Design of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Subrahmanyam, Sreenath; Piletsky, Sergey A.

Artificial receptors have been in use for several decades as sensor elements, in affinity separation, and as models for investigation of molecular recognition. Although there have been numerous publications on the use of molecular modeling in characterization of their affinity and selectivity, very few attempts have been made on the application of molecular modeling in computational design of synthetic receptors. This chapter discusses recent successes in the use of computational design for the development of one particular branch of synthetic receptors - molecularly imprinted polymers.

Molecular switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

Molecular contributions to conservation

USGS Publications Warehouse

Haig, Susan M.

1998-01-01

Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

Method of making molecularly doped composite polymer material

DOEpatents

Affinito, John D [Tucson, AZ; Martin, Peter M [Kennewick, WA; Graff, Gordon L [West Richland, WA; Burrows, Paul E [Kennewick, WA; Gross, Mark E. , Sapochak, Linda S.

2005-06-21

A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

Instrumentation in molecular imaging.

PubMed

Wells, R Glenn

2016-12-01

In vivo molecular imaging is a challenging task and no single type of imaging system provides an ideal solution. Nuclear medicine techniques like SPECT and PET provide excellent sensitivity but have poor spatial resolution. Optical imaging has excellent sensitivity and spatial resolution, but light photons interact strongly with tissues and so only small animals and targets near the surface can be accurately visualized. CT and MRI have exquisite spatial resolution, but greatly reduced sensitivity. To overcome the limitations of individual modalities, molecular imaging systems often combine individual cameras together, for example, merging nuclear medicine cameras with CT or MRI to allow the visualization of molecular processes with both high sensitivity and high spatial resolution.

[Molecular techniques in mycology].

PubMed

Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

2008-11-01

An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations.

PubMed

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-14

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

2012-04-01

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.

Clustering the Orion B giant molecular cloud based on its molecular emission

NASA Astrophysics Data System (ADS)

Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

2018-02-01

Context. Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs). Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud. Methods: We use a machine learning clustering method, namely the Meanshift algorithm, to cluster pixels with similar molecular emission, ignoring spatial information. Clusters are defined around each maximum of the multidimensional probability density function (PDF) of the line integrated intensities. Simple radiative transfer models were used to interpret the astrophysical information uncovered by the clustering analysis. Results: A clustering analysis based only on the J = 1-0 lines of three isotopologues of CO proves sufficient to reveal distinct density/column density regimes (nH 100 cm-3, 500 cm-3, and >1000 cm-3), closely related to the usual definitions of diffuse, translucent and high-column-density regions. Adding two UV-sensitive tracers, the J = 1-0 line of HCO+ and the N = 1-0 line of CN, allows us to distinguish two clearly distinct chemical regimes, characteristic of UV-illuminated and UV-shielded gas. The UV-illuminated regime shows overbright HCO+ and CN emission, which we relate to a photochemical enrichment effect. We also find a tail of high CN/HCO+ intensity ratio in UV-illuminated regions. Finer distinctions in density classes (nH 7 × 103 cm-3, 4 × 104 cm-3) for the densest regions are also

The "Collisions Cube" Molecular Dynamics Simulator.

ERIC Educational Resources Information Center

Nash, John J.; Smith, Paul E.

1995-01-01

Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

Molecular Orientation in Two Component Vapor-Deposited Glasses: Effect of Substrate Temperature and Molecular Shape

NASA Astrophysics Data System (ADS)

Powell, Charles; Jiang, Jing; Walters, Diane; Ediger, Mark

Vapor-deposited glasses are widely investigated for use in organic electronics including the emitting layers of OLED devices. These materials, while macroscopically homogenous, have anisotropic packing and molecular orientation. By controlling this orientation, outcoupling efficiency can be increased by aligning the transition dipole moment of the light-emitting molecules parallel to the substrate. Light-emitting molecules are typically dispersed in a host matrix, as such, it is imperative to understand molecular orientation in two-component systems. In this study we examine two-component vapor-deposited films and the orientations of the constituent molecules using spectroscopic ellipsometry, UV-vis and IR spectroscopy. The role of temperature, composition and molecular shape as it effects molecular orientation is examined for mixtures of DSA-Ph in Alq3 and in TPD. Deposition temperature relative to the glass transition temperature of the two-component mixture is the primary controlling factor for molecular orientation. In mixtures of DSA-Ph in Alq3, the linear DSA-Ph has a horizontal orientation at low temperatures and slight vertical orientation maximized at 0.96Tg,mixture, analogous to one-component films.

Molecular dewetting on insulators.

PubMed

Burke, S A; Topple, J M; Grütter, P

2009-10-21

Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C(60) on alkali halides, and the technologically important system of pentacene on SiO(2). These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure.

Transition from direct to inverted charge transport Marcus regions in molecular junctions via molecular orbital gating

NASA Astrophysics Data System (ADS)

Yuan, Li; Wang, Lejia; Garrigues, Alvar R.; Jiang, Li; Annadata, Harshini Venkata; Anguera Antonana, Marta; Barco, Enrique; Nijhuis, Christian A.

2018-04-01

Solid-state molecular tunnel junctions are often assumed to operate in the Landauer regime, which describes essentially activationless coherent tunnelling processes. In solution, on the other hand, charge transfer is described by Marcus theory, which accounts for thermally activated processes. In practice, however, thermally activated transport phenomena are frequently observed also in solid-state molecular junctions but remain poorly understood. Here, we show experimentally the transition from the Marcus to the inverted Marcus region in a solid-state molecular tunnel junction by means of intra-molecular orbital gating that can be tuned via the chemical structure of the molecule and applied bias. In the inverted Marcus region, charge transport is incoherent, yet virtually independent of temperature. Our experimental results fit well to a theoretical model that combines Landauer and Marcus theories and may have implications for the interpretation of temperature-dependent charge transport measurements in molecular junctions.

Molecular imaging in neuroendocrine tumors: molecular uptake mechanisms and clinical results.

PubMed

Koopmans, Klaas P; Neels, Oliver N; Kema, Ido P; Elsinga, Philip H; Links, Thera P; de Vries, Elisabeth G E; Jager, Pieter L

2009-09-01

Neuroendocrine tumors can originate almost everywhere in the body and consist of a great variety of subtypes. This paper focuses on molecular imaging methods using nuclear medicine techniques in neuroendocrine tumors, coupling molecular uptake mechanisms of radiotracers with clinical results. A non-systematic review is presented on receptor based and metabolic imaging methods. Receptor-based imaging covers the molecular backgrounds of somatostatin, vaso-intestinal peptide (VIP), bombesin and cholecystokinin (CCK) receptors and their link with nuclear imaging. Imaging methods based on specific metabolic properties include meta-iodo-benzylguanide (MIBG) and dimercapto-sulphuric acid (DMSA-V) scintigraphy as well as more modern positron emission tomography (PET)-based methods using radio-labeled analogues of amino acids, glucose, dihydroxyphenylalanine (DOPA), dopamine and tryptophan. Diagnostic sensitivities are presented for each imaging method and for each neuroendocrine tumor subtype. Finally, a Forest plot analysis of diagnostic performance is presented for each tumor type in order to provide a comprehensive overview for clinical use.

Molecular size and molecular size distribution affecting traditional balsamic vinegar aging.

PubMed

Falcone, Pasquale Massimiliano; Giudici, Paolo

2008-08-27

A first attempt at a semiquantitative study of molecular weight (MW) and molecular weight distribution (MWD) in cooked grape must and traditional balsamic vinegar (TBV) with increasing well-defined age was performed by high-performance liquid size exclusion chromatography (SEC) using dual detection, that is, differential refractive index (DRI) and absorbance (UV-vis) based detectors. With this aim, MW and MWD, including number- and weight-average MW and polydispersity, were determined with respect to a secondary standard and then analyzed. All investigated vinegar samples were recognized as compositionally and structurally heterogeneous blends of copolymers (melanoidins) spreading over a wide range of molecular sizes: the relative MW ranged from 2 to >2000 kDa. The extent of the polymerization reactions was in agreement with the TBV browning kinetics. MWD parameters varied asymptotically toward either upper or lower limits during aging, reflecting a nonequilibrium status of the balance between polymerization and depolymerization reactions in TBV. MWD parameters were proposed as potential aging markers of TBV.

Molecular complexes in close and far away

PubMed Central

Klemperer, William; Vaida, Veronica

2006-01-01

In this review, gas-phase chemistry of interstellar media and some planetary atmospheres is extended to include molecular complexes. Although the composition, density, and temperature of the environments discussed are very different, molecular complexes have recently been considered as potential contributors to chemistry. The complexes reviewed include strongly bound aggregates of molecules with ions, intermediate-strength hydrogen bonded complexes (primarily hydrates), and weakly bonded van der Waals molecules. In low-density, low-temperature environments characteristic of giant molecular clouds, molecular synthesis, known to involve gas-phase ion-molecule reactions and chemistry at the surface of dust and ice grains is extended here to involve molecular ionic clusters. At the high density and high temperatures found on planetary atmospheres, molecular complexes contribute to both atmospheric chemistry and climate. Using the observational, laboratory, and theoretical database, the role of molecular complexes in close and far away is discussed. PMID:16740667

The merger of electrochemistry and molecular electronics.

PubMed

McCreery, Richard L

2012-02-01

Molecular Electronics has the potential to greatly enhance existing silicon-based microelectronics to realize new functions, higher device density, lower power consumption, and lower cost. Although the investigation of electron transport through single molecules and molecular monolayers in "molecular junctions" is a recent development, many of the relevant concepts and phenomena are derived from electrochemistry, as practiced for the past several decades. The past 10+ years have seen an explosion of research activity directed toward how the structure of molecules affects electron transport in molecular junctions, with the ultimate objective of "rational design" of molecular components with new electronic functions, such as chemical sensing, interactions with light, and low-cost, low-power consumer electronics. In order to achieve these scientifically and commercially important objectives, the factors controlling charge transport in molecules "connected" to conducting contacts must be understood, and methods for massively parallel manufacturing of molecular circuits must be developed. This Personal Account describes the development of reproducible and robust molecular electronic devices, starting with modified electrodes used in electrochemistry and progressing to manufacturable molecular junctions. Although the field faced some early difficulties in reliability and characterization, the pieces are now in place for rapid advances in understanding charge transport at the molecular level. Inherent in the field of Molecular Electronics are many electrochemical concepts, including tunneling, redox exchange, activated electron transfer, and electron coupling between molecules and conducting contacts. Copyright © 2012 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Molecular excitonic seesaws.

PubMed

Wilhelm, Philipp; Schedlbauer, Jakob; Hinderer, Florian; Hennen, Daniel; Höger, Sigurd; Vogelsang, Jan; Lupton, John M

2018-04-17

The breaking of molecular symmetry through photoexcitation is a ubiquitous but rather elusive process, which, for example, controls the microscopic efficiency of light harvesting in molecular aggregates. A molecular excitation within a π-conjugated segment will self-localize due to strong coupling to molecular vibrations, locally changing bond alternation in a process which is fundamentally nondeterministic. Probing such symmetry breaking usually relies on polarization-resolved fluorescence, which is most powerful on the level of single molecules. Here, we explore symmetry breaking by designing a large, asymmetric acceptor-donor-acceptor (A 1 -D-A 2 ) complex 10 nm in length, where excitation energy can flow from the donor, a π-conjugated oligomer, to either one of the two boron-dipyrromethene (bodipy) dye acceptors of different color. Fluorescence correlation spectroscopy (FCS) reveals a nondeterministic switching between the energy-transfer pathways from the oligomer to the two acceptor groups on the submillisecond timescale. We conclude that excitation energy transfer, and light harvesting in general, are fundamentally nondeterministic processes, which can be strongly perturbed by external stimuli. A simple demonstration of the relation between exciton localization within the extended π-system and energy transfer to the endcap is given by considering the selectivity of endcap emission through the polarization of the excitation light in triads with bent oligomer backbones. Bending leads to increased localization so that the molecule acquires bichromophoric characteristics in terms of its fluorescence photon statistics.

String and Sticky Tape Experiments: Refractive Index of Liquids.

ERIC Educational Resources Information Center

Edge, R. D., Ed.

1979-01-01

Describes a simple method of measuring the refractive index of a liquid using a paper cup, a liquid, a pencil, and a ruler. Uses the ratio between the actual depth and the apparent depth of the cup to calculate the refractive index. (GA)

Molecular Electronic Shift Registers

NASA Technical Reports Server (NTRS)

Beratan, David N.; Onuchic, Jose N.

1990-01-01

Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

Measurement Of Molecular Mobilities Of Polymers

NASA Technical Reports Server (NTRS)

Kim, Soon Sam; Tsay, Fun-Dow

1989-01-01

New molecular-probe technique used to measure molecular mobility of polymer. Method based on use of time-resolved electron-spin resonance (ESR) spectroscopy to monitor decay of transient nutation amplitudes from photoexcited triplet states of probe molecules with which polymer is doped. The higher molecular mobility of polymer matrix, the faster nutation amplitudes of the probe molecules decay.

Understanding charge transport in molecular electronics.

PubMed

Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

2003-12-01

For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

ERIC Educational Resources Information Center

Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

2015-01-01

Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in…

Magnetohydrodynamic Models of Molecular Tornadoes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Au, Kelvin; Fiege, Jason D., E-mail: fiege@physics.umanitoba.ca

Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecularmore » tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.« less

Molecular medicine: a path towards a personalized medicine.

PubMed

Miranda, Debora Marques de; Mamede, Marcelo; Souza, Bruno Rezende de; Almeida Barros, Alexandre Guimarães de; Magno, Luiz Alexandre; Alvim-Soares, Antônio; Rosa, Daniela Valadão; Castro, Célio José de; Malloy-Diniz, Leandro; Gomez, Marcus Vinícius; Marco, Luiz Armando De; Correa, Humberto; Romano-Silva, Marco Aurélio

2012-03-01

Psychiatric disorders are among the most common human illnesses; still, the molecular and cellular mechanisms underlying their complex pathophysiology remain to be fully elucidated. Over the past 10 years, our group has been investigating the molecular abnormalities in major signaling pathways involved in psychiatric disorders. Recent evidences obtained by the Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (National Institute of Science and Technology - Molecular Medicine, INCT-MM) and others using behavioral analysis of animal models provided valuable insights into the underlying molecular alterations responsible for many complex neuropsychiatric disorders, suggesting that "defects" in critical intracellular signaling pathways have an important role in regulating neurodevelopment, as well as in pathophysiology and treatment efficacy. Resources from the INCT have allowed us to start doing research in the field of molecular imaging. Molecular imaging is a research discipline that visualizes, characterizes, and quantifies the biologic processes taking place at cellular and molecular levels in humans and other living systems through the results of image within the reality of the physiological environment. In order to recognize targets, molecular imaging applies specific instruments (e.g., PET) that enable visualization and quantification in space and in real-time of signals from molecular imaging agents. The objective of molecular medicine is to individualize treatment and improve patient care. Thus, molecular imaging is an additional tool to achieve our ultimate goal.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Supernova brightening from chameleon-photon mixing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burrage, C.

2008-02-15

Measurements of standard candles and measurements of standard rulers give an inconsistent picture of the history of the universe. This discrepancy can be explained if photon number is not conserved as computations of the luminosity distance must be modified. I show that photon number is not conserved when photons mix with chameleons in the presence of a magnetic field. The strong magnetic fields in a supernova mean that the probability of a photon converting into a chameleon in the interior of the supernova is high, this results in a large flux of chameleons at the surface of the supernova. Chameleonsmore » and photons also mix as a result of the intergalactic magnetic field. These two effects combined cause the image of the supernova to be brightened resulting in a model which fits both observations of standard candles and observations of standard rulers.« less

Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

PubMed

Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

2014-02-25

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Investigating Evolutionary Questions Using Online Molecular Databases.

ERIC Educational Resources Information Center

Puterbaugh, Mary N.; Burleigh, J. Gordon

2001-01-01

Recommends using online molecular databases as teaching tools to illustrate evolutionary questions and concepts while introducing students to public molecular databases. Provides activities in which students make molecular comparisons between species. (YDS)

Emerging molecular phenotypes of asthma

PubMed Central

Ray, Anuradha; Oriss, Timothy B.

2014-01-01

Although asthma has long been considered a heterogeneous disease, attempts to define subgroups of asthma have been limited. In recent years, both clinical and statistical approaches have been utilized to better merge clinical characteristics, biology, and genetics. These combined characteristics have been used to define phenotypes of asthma, the observable characteristics of a patient determined by the interaction of genes and environment. Identification of consistent clinical phenotypes has now been reported across studies. Now the addition of various 'omics and identification of specific molecular pathways have moved the concept of clinical phenotypes toward the concept of molecular phenotypes. The importance of these molecular phenotypes is being confirmed through the integration of molecularly targeted biological therapies. Thus the global term asthma is poised to become obsolete, being replaced by terms that more specifically identify the pathology associated with the disease. PMID:25326577

Molecular nano-arches on silicon

NASA Astrophysics Data System (ADS)

Dobrin, S.

2007-08-01

The formation of molecular nano-arches on the Si(1 1 1)-7 × 7 surface was modeled using density functional theory (DFT). It has been suggested, based on the calculations, that the arches are formed by molecular dimers of chlorobenzene at near-monolayer coverages. Molecules of the dimer are covalently bound to two silicon adatoms and to each other thereby forming a molecular arch on the surface. The structure of the molecular dimer was calculated at the B3LYP/6-31G(d) level of theory. The dimers were found to be stable at room temperature, and to form a near-monolayer coverage, which has been observed in the experiment [X.H. Chen, Q. Kong, J.C. Polanyi, D. Rogers, S. So, Surf. Sci. 340 (1995) 224; Y. Cao, J.F. Deng, G.Q. Xu, J. Chem. Phys. 112 (2000) 4759].

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires

Conceptual Considerations in Molecular Science

ERIC Educational Resources Information Center

Sawyer, Donald T.

2005-01-01

There are significant misconceptions within the chemical community and molecular science, particularly in the undergraduate curriculum and the associated textbooks. Some of the misconceptions are described, which give poor basis to understand molecular bonding and structure, and reaction mechanisms.

Molecular studies of achondroplasia

PubMed Central

Nahar, Risha; Saxena, Renu; Kohli, Sudha; Puri, Ratna; Verma, Ishwar Chandra

2009-01-01

Background: Achondroplasia (ACH) is the most frequent form of short-limbed dwarfism, caused by mutations in the FGFR3 gene. It follows an autosomal dominant inheritance, though most cases are sporadic. The molecular techniques are the only available methods to confirm the diagnosis of a skeletal dysplasia. Clinical and radiological features are only suggestive and not confirmatory. The present study was conducted to find out how often the clinical diagnosis of achondroplasia is verified on molecular studies. Materials and Methods: From 1998 through 2007, we carried out molecular analysis for the two common mutations in the FGFR3 gene in 130 cases clinically suspected to have ACH. Results: A diagnostic mutation was identified in 53 (40.8%) cases. The common mutation (1138G>A) was present in 50 (94.7%) of the positive cases, while the rare 1138 G>C substitution was found in three (5.3%). Conclusion: This study shows that confirmation of clinical diagnosis of ACH by molecular genetic testing is essential to distinguish it from other skeletal dysplasias, to plan therapeutic options, and to offer genetic counseling. Management (medical and surgical) in patients confirmed to have ACH, is briefly discussed. PMID:19838370

Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics.

PubMed

Nagata, Yuki; Ohto, Tatsuhiko; Backus, Ellen H G; Bonn, Mischa

2016-04-28

Understanding aqueous interfaces at the molecular level is not only fundamentally important, but also highly relevant for a variety of disciplines. For instance, electrode-water interfaces are relevant for electrochemistry, as are mineral-water interfaces for geochemistry and air-water interfaces for environmental chemistry; water-lipid interfaces constitute the boundaries of the cell membrane, and are thus relevant for biochemistry. One of the major challenges in these fields is to link macroscopic properties such as interfacial reactivity, solubility, and permeability as well as macroscopic thermodynamic and spectroscopic observables to the structure, structural changes, and dynamics of molecules at these interfaces. Simulations, by themselves, or in conjunction with appropriate experiments, can provide such molecular-level insights into aqueous interfaces. In this contribution, we review the current state-of-the-art of three levels of molecular dynamics (MD) simulation: ab initio, force field, and coarse-grained. We discuss the advantages, the potential, and the limitations of each approach for studying aqueous interfaces, by assessing computations of the sum-frequency generation spectra and surface tension. The comparison of experimental and simulation data provides information on the challenges of future MD simulations, such as improving the force field models and the van der Waals corrections in ab initio MD simulations. Once good agreement between experimental observables and simulation can be established, the simulation can be used to provide insights into the processes at a level of detail that is generally inaccessible to experiments. As an example we discuss the mechanism of the evaporation of water. We finish by presenting an outlook outlining four future challenges for molecular dynamics simulations of aqueous interfacial systems.

Nonlinear vibrational excitations in molecular crystals molecular mechanics calculations

NASA Astrophysics Data System (ADS)

Pumilia, P.; Abbate, S.; Baldini, G.; Ferro, D. R.; Tubino, R.

1992-03-01

The coupling constant for vibrational solitons χ has been examined in a molecular mechanics model for acetanilide (ACN) molecular crystal. According to A.C. Scott, solitons can form and propagate in solid acetanilide over a threshold energy value. This can be regarded as a structural model for the spines of hydrogen bond chains stabilizing the α helical structure of proteins. A one dimensional hydrogen bond chain of ACN has been built, for which we have found that, even though experimental parameters are correctly predicted, the excessive rigidity of the isolated chain prevents the formation of a localized distortion around the excitation. Yet, C=O coupling value with softer lattice modes could be rather high, allowing self-trapping to take place.

Effect of molecular weight on polymer processability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karg, R.F.

1983-01-01

Differences in rheological behavior due to the polymer molecular weight and molecular weight distribution have been shown with the MPT. SBR polymers having high molecular weight fractions develop higher stress relaxation time values due to the higher degree of polymer entanglements. Tests conducted at increasing temperatures show the diminishing influence of the polymer entanglements upon stress relaxation time. EPDM polymers show stress relaxation time and head pressure behavior which correlates with mill processability. As anticipated, compounded stock of EPDM have broad molecular weight distribution has higher stress relaxation time values than EPDM compounds with narrow molecular weight distribution.

Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

Molecular Biology of Archaebacteria.

DTIC Science & Technology

1988-03-31

Security Classification) Molecular Biology of Archaebacteria .. d. 12. PERSONAL AUTHOR(S) Patrick P. Dennis * 13a. TYPE OF REPORT 13b. TIME COVERED 14...Escherichia coli Research Objectives i) to characterize the principles of gene organization and regulation of gene expression in archaebacteria ; (ii) to...biophysical and molecular terms some of the mechanisms that allow archaebacteria to inhabit extreme environments. Progress - Year I A’ Ribosomal protein

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P < .01); (2) The ATR-Ft/VMS molecular technique was able to detect the processing induced CHO molecular structure changes; (3) Induced CHO molecular structure spectral features are significantly correlated (P < .05) to CHO subfractions, CHO biodegradation and biodigestion and could be applied to potentially predict CHO biodegradation (R2 = 0.87, RSD = 0.74, P < .01) and intestinal digestible undegraded CHO (R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

PubMed

Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

2014-12-01

In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds.

Synthesis of one-dimensional metal-containing insulated molecular wire with versatile properties directed toward molecular electronics materials.

PubMed

Masai, Hiroshi; Terao, Jun; Seki, Shu; Nakashima, Shigeto; Kiguchi, Manabu; Okoshi, Kento; Fujihara, Tetsuaki; Tsuji, Yasushi

2014-02-05

We report, herein, the design, synthesis, and properties of new materials directed toward molecular electronics. A transition metal-containing insulated molecular wire was synthesized through the coordination polymerization of a Ru(II) porphyrin with an insulated bridging ligand of well-defined structure. The wire displayed not only high linearity and rigidity, but also high intramolecular charge mobility. Owing to the unique properties of the coordination bond, the interconversion between the monomer and polymer states was realized under a carbon monoxide atmosphere or UV irradiation. The results demonstrated a high potential of the metal-containing insulated molecular wire for applications in molecular electronics.

Cognitive Complexity of the Medical Record Is a Risk Factor for Major Adverse Events

PubMed Central

Roberson, David; Connell, Michael; Dillis, Shay; Gauvreau, Kimberlee; Gore, Rebecca; Heagerty, Elaina; Jenkins, Kathy; Ma, Lin; Maurer, Amy; Stephenson, Jessica; Schwartz, Margot

2014-01-01

Context: Patients in tertiary care hospitals are more complex than in the past, but the implications of this are poorly understood because “patient complexity” has been difficult to quantify. Objective: We developed a tool, the Complexity Ruler, to quantify the amount of data (as bits) in the patient’s medical record. We designated the amount of data in the medical record as the cognitive complexity of the medical record (CCMR). We hypothesized that CCMR is a useful surrogate for true patient complexity and that higher CCMR correlates with risk of major adverse events. Design: The Complexity Ruler was validated by comparing the measured CCMR with physician rankings of patient complexity on specific inpatient services. It was tested in a case-control model of all patients with major adverse events at a tertiary care pediatric hospital from 2005 to 2006. Main Outcome Measures: The main outcome measure was an externally reported major adverse event. We measured CCMR for 24 hours before the event, and we estimated lifetime CCMR. Results: Above empirically derived cutoffs, 24-hour and lifetime CCMR were risk factors for major adverse events (odds ratios, 5.3 and 6.5, respectively). In a multivariate analysis, CCMR alone was essentially as predictive of risk as a model that started with 30-plus clinical factors. Conclusions: CCMR correlates with physician assessment of complexity and risk of adverse events. We hypothesize that increased CCMR increases the risk of physician cognitive overload. An automated version of the Complexity Ruler could allow identification of at-risk patients in real time. PMID:24626065

Cognitive complexity of the medical record is a risk factor for major adverse events.

PubMed

Roberson, David; Connell, Michael; Dillis, Shay; Gauvreau, Kimberlee; Gore, Rebecca; Heagerty, Elaina; Jenkins, Kathy; Ma, Lin; Maurer, Amy; Stephenson, Jessica; Schwartz, Margot

2014-01-01

Patients in tertiary care hospitals are more complex than in the past, but the implications of this are poorly understood as "patient complexity" has been difficult to quantify. We developed a tool, the Complexity Ruler, to quantify the amount of data (as bits) in the patient’s medical record. We designated the amount of data in the medical record as the cognitive complexity of the medical record (CCMR). We hypothesized that CCMR is a useful surrogate for true patient complexity and that higher CCMR correlates with risk of major adverse events. The Complexity Ruler was validated by comparing the measured CCMR with physician rankings of patient complexity on specific inpatient services. It was tested in a case-control model of all patients with major adverse events at a tertiary care pediatric hospital from 2005 to 2006. The main outcome measure was an externally reported major adverse event. We measured CCMR for 24 hours before the event, and we estimated lifetime CCMR. Above empirically derived cutoffs, 24-hour and lifetime CCMR were risk factors for major adverse events (odds ratios, 5.3 and 6.5, respectively). In a multivariate analysis, CCMR alone was essentially as predictive of risk as a model that started with 30-plus clinical factors. CCMR correlates with physician assessment of complexity and risk of adverse events. We hypothesize that increased CCMR increases the risk of physician cognitive overload. An automated version of the Complexity Ruler could allow identification of at-risk patients in real time.

Exploring the relative reactivities of the hydroxyl groups of monosaccharides by molecular modeling and molecular mechanics

NASA Astrophysics Data System (ADS)

Box, V. G. S.; Evans-Lora, T.

2000-01-01

The molecular modeling program STR3DI.EXE, and its molecular mechanics module, QVBMM, were used to simulate, and evaluate, the stereo-electronic effects in the mono-alkoxides of the 4,6- O-ethylideneglycopyranosides of allose, mannose, galactose and glucose. This study has confirmed the ability of these molecular modeling tools to predict the regiochemistry and reactivity of these sugar derivatives, and holds considerable implications for unraveling the chemistry of the rare monosaccharides.

Phase behavior of Langmuir monolayers with ionic molecular heads: Molecular simulations

NASA Astrophysics Data System (ADS)

González-Castro, Carlos A.; Ramírez-Santiago, Guillermo

2015-03-01

We carried out Monte Carlo simulations in the N ,Π,T ensemble of a Langmuir monolayer coarse-grained molecular model. Considering that the hydrophilic groups can be ionized by modulating acid-base interactions, here we study the phase behavior of a model that incorporates the short-range steric and long-range ionic interactions. The simulations were carried out in the reduced temperature range 0.1 ≤T*<4.0 , where there is a competition of these interactions. Different order parameters were calculated and analyzed for several values of the reduced surface pressure in the interval, 1 ≤Π*≤40. For most of the surface pressures two directions of molecular tilt were found: (i) towards the nearest neighbor (NN) at low temperatures, T*<0.7, and most of the values of Π* and (ii) towards next-nearest neighbors (NNN) in the temperature interval 0.7 ≤T*<1.1 for Π*<25. We also found the coexistence of the NN and NNN at intermediate temperatures and Π*>25 . A low-temperature reentrant disorder-order-disorder transition in the positions of the molecular heads and in the collective tilt of the tails was found for all the surface pressure values. It was also found that the molecular tails arranged forming "rotating patterns" in the temperature interval, 0.5 molecular heads carry an ion in qualitative agreement with experimental observations of fatty acid monolayers with ionic head groups. Two surface pressure versus area per molecule isotherms were also calculated. At low temperatures near the LC-NN ↔ LC-NNN transitions and at higher temperatures close to the LE ↔ LC transitions. From these isotherms the monolayer's area compression modulus was obtained and its variation ranges in the LE and LC phases were

Modeling Complex Workflow in Molecular Diagnostics

PubMed Central

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

Molecular ferroelectrics: where electronics meet biology.

PubMed

Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

2013-12-28

In the last several years, we have witnessed significant advances in molecular ferroelectrics, with the ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by an overview of the fundamentals of ferroelectricity. The latest developments in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also described.

Molecular ferroelectrics: where electronics meet biology

PubMed Central

Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

2013-01-01

In the last several years, we have witnessed significant advances in molecular ferroelectrics, with ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by overview on the fundamentals of ferroelectricity. Latest development in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also noted. PMID:24018952

Molecular replication

NASA Technical Reports Server (NTRS)

Orgel, Leslie E.

1992-01-01

Recent experiments demonstrating nonenzymatic replication in molecular systems are reviewed. The difficulties facing nonenzymatic replication are discussed along with specificity, fidelity, and mutation in nonenzymatic replication. The prospects for research in this area are considered.

Interfacial Molecular Packing Determines Exciton Dynamics in Molecular Heterostructures: The Case of Pentacene-Perfluoropentacene.

PubMed

Rinn, Andre; Breuer, Tobias; Wiegand, Julia; Beck, Michael; Hübner, Jens; Döring, Robin C; Oestreich, Michael; Heimbrodt, Wolfram; Witte, Gregor; Chatterjee, Sangam

2017-12-06

The great majority of electronic and optoelectronic devices depend on interfaces between p-type and n-type semiconductors. Finding matching donor-acceptor systems in molecular semiconductors remains a challenging endeavor because structurally compatible molecules may not necessarily be suitable with respect to their optical and electronic properties, and the large exciton binding energy in these materials may favor bound electron-hole pairs rather than free carriers or charge transfer at an interface. Regardless, interfacial charge-transfer exciton states are commonly considered as an intermediate step to achieve exciton dissociation. The formation efficiency and decay dynamics of such states will strongly depend on the molecular makeup of the interface, especially the relative alignment of donor and acceptor molecules. Structurally well-defined pentacene-perfluoropentacene heterostructures of different molecular orientations are virtually ideal model systems to study the interrelation between molecular packing motifs at the interface and their electronic properties. Comparing the emission dynamics of the heterosystems and the corresponding unitary films enables accurate assignment of every observable emission signal in the heterosystems. These heterosystems feature two characteristic interface-specific luminescence channels at around 1.4 and 1.5 eV that are not observed in the unitary samples. Their emission strength strongly depends on the molecular alignment of the respective donor and acceptor molecules, emphasizing the importance of structural control for device construction.

Molecular testing practices and perceptions among dermatopathologists.

PubMed

Torre, Kristin; Jhorar, Preeti; Wu, Rong; Pfeifer, John; Elaba, Zendee; Murphy, Michael

2018-06-01

We evaluated how dermatopathologists are employing molecular testing in the setting of neoplastic skin diseases, and assessed their opinions of the broader role and utility of molecular technologies in clinical practice. A 15-question online survey was sent to Fellows of the American Society of Dermatopathology in April 2017. One hundred and thirty-six dermatopathologists completed the survey (response rate = 16%). A majority (94%) of respondents reported experience with one or more molecular testing strategies. Sixty-two percent of dermatopathologists order 12 or more molecular tests per year, while 5% of respondents order 2 or fewer assays per year. More frequent utilization of molecular testing is associated with relevant instruction during residency training (P = .009), primary board certification in pathology (P = .008), academic medical center affiliation (P = <.0001), higher volume clinical practice (P = .0004), presence of on-site clinical molecular pathology/cytogenetics laboratory (P = .007), and greater physician confidence incorporating test results into histopathological assessments (P = <.0001). Wider adoption of molecular testing in dermatopathology may be limited by factors such as physician training, test costs/insurance coverage, logistical issues and lack of evidence-based clinical practice guidelines. Dermatopathologists have concerns regarding clinical validity/utility and inappropriate/overuse of some molecular tests. The importance of longitudinal education in molecular technologies and their applications for trainee and practicing physicians is highlighted. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Topology of molecular interaction networks.

PubMed

Winterbach, Wynand; Van Mieghem, Piet; Reinders, Marcel; Wang, Huijuan; de Ridder, Dick

2013-09-16

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.

Topology of molecular interaction networks

PubMed Central

2013-01-01

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks. Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs. Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes. Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

Molecular pathology and age estimation.

PubMed

Meissner, Christoph; Ritz-Timme, Stefanie

2010-12-15

Over the course of our lifetime a stochastic process leads to gradual alterations of biomolecules on the molecular level, a process that is called ageing. Important changes are observed on the DNA-level as well as on the protein level and are the cause and/or consequence of our 'molecular clock', influenced by genetic as well as environmental parameters. These alterations on the molecular level may aid in forensic medicine to estimate the age of a living person, a dead body or even skeletal remains for identification purposes. Four such important alterations have become the focus of molecular age estimation in the forensic community over the last two decades. The age-dependent accumulation of the 4977bp deletion of mitochondrial DNA and the attrition of telomeres along with ageing are two important processes at the DNA-level. Among a variety of protein alterations, the racemisation of aspartic acid and advanced glycation endproducs have already been tested for forensic applications. At the moment the racemisation of aspartic acid represents the pinnacle of molecular age estimation for three reasons: an excellent standardization of sampling and methods, an evaluation of different variables in many published studies and highest accuracy of results. The three other mentioned alterations often lack standardized procedures, published data are sparse and often have the character of pilot studies. Nevertheless it is important to evaluate molecular methods for their suitability in forensic age estimation, because supplementary methods will help to extend and refine accuracy and reliability of such estimates. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Molecular Pathology Informatics.

PubMed

Roy, Somak

2015-06-01

Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing. Copyright © 2015 Elsevier Inc. All rights reserved.

The Global-Market Doctrine: A Study in Fundamentalist Theology. The Iconoclast.

ERIC Educational Resources Information Center

McMurty, John

1997-01-01

Presents an interesting metaphorical critique of the current enthusiasm for the global market and the free market system. Delineates 10 defining principles of a fundamentalist theological doctrine and then suggests replacing the term "global market" with "Supreme Ruler." Criticizes free market capitalism as being occasionally…

Secondary Mathematics Education in the Soviet Union, an Individual Study Project.

DTIC Science & Technology

1982-05-14

Pythagoras and other well-known congruence theorems on angles and triangles. Concepts of set theory are developed in relation to the topics studied. Grades 6...geometry (areas, volumes, etc.). Geometric topics include: use of the ruler, protractor, and compasses in geometric constructions; Theorem of

Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

NASA Astrophysics Data System (ADS)

Chen, Kai; Leong, Eunice Sok Ping; Rukavina, Michael; Nagao, Tadaaki; Liu, Yan Jun; Zheng, Yuebing

2015-06-01

Molecular plasmonics explores and exploits the molecule-plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP). Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional) of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.

Phase Behavior of Binary Blends of High Molecular Weight Diblock Copolymers with a Low Molecular Weight Triblock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mickiewicz, Rafal A.; Ntoukas, Eleftherios; Avgeropoulos, Apostolos

2009-08-26

Binary blends of four different high molecular weight poly(styrene-b-isoprene) (SI) diblock copolymers with a lower molecular weight poly(styrene-b-isoprene-b-styrene) (SIS) triblock copolymer were prepared, and their morphology was characterized by transmission electron microscopy and ultra-small-angle X-ray scattering. All the neat block copolymers have nearly symmetric composition and exhibit the lamellar morphology. The SI diblock copolymers had number-average molecular weights, Mn, in the range 4.4 x 10{sup 5}--1.3 x 10{sup 6} g/mol and volume fractions of poly(styrene), {Phi}{sub PS}, in the range 0.43--0.49, and the SIS triblock had a molecular weight of Mn 6.2 x 10{sup 4} g/mol with {Phi}{sub PS} =more » 0.41. The high molecular weight diblock copolymers are very strongly segregating, with interaction parameter values, {chi}N, in the range 470--1410. A morphological phase diagram in the parameter space of molecular weight ratio (R = M{sub n}{sup diblock}/1/2M{sub n}{sup triblock}) and blend composition was constructed, with R values in the range between 14 and 43, which are higher than previously reported. The phase diagram revealed a large miscibility gap for the blends, with macrophase separation into two distinct types of microphase-separated domains for weight fractions of SI, w{sub SI} < 0.9, implying virtually no solubility of the much higher molecular weight diblocks in the lower molecular weight triblock. For certain blend compositions, above R 30, morphological transitions from the lamellar to cylindrical and bicontinuous structures were also observed.« less

Using molecular recognition of beta-cyclodextrin to determine molecular weights of low-molecular-weight explosives by MALDI-TOF mass spectrometry.

PubMed

Zhang, Min; Shi, Zhen; Bai, Yinjuan; Gao, Yong; Hu, Rongzu; Zhao, Fenqi

2006-02-01

This study presents a novel method for determining the molecular weights of low molecular weight (MW) energetic compounds through their complexes of beta-cyclodextrin (beta-CD) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in a mass range of 500 to 1700 Da, avoiding matrix interference. The MWs of one composite explosive composed of 2,6-DNT, TNT, and RDX, one propellant with unknown components, and 14 single-compound explosives (RDX, HMX, 3,4-DNT, 2,6-DNT, 2,5-DNT, 2,4,6-TNT, TNAZ, DNI, BTTN, NG, TO, NTO, NP, and 662) were measured. The molecular recognition and inclusion behavior of beta-CD to energetic materials (EMs) were investigated. The results show that (1) the established method is sensitive, simple, accurate, and suitable for determining the MWs of low-MW single-compound explosives and energetic components in composite explosives and propellants; and (2) beta-CD has good inclusion and modular recognition abilities to the above EMs.

Molecular classification of gastric cancer.

PubMed

Chia, N-Y; Tan, P

2016-05-01

Gastric cancer (GC), a heterogeneous disease characterized by epidemiologic and histopathologic differences across countries, is a leading cause of cancer-related death. Treatment of GC patients is currently suboptimal due to patients being commonly treated in a uniform fashion irrespective of disease subtype. With the advent of next-generation sequencing and other genomic technologies, GCs are now being investigated in great detail at the molecular level. High-throughput technologies now allow a comprehensive study of genomic and epigenomic alterations associated with GC. Gene mutations, chromosomal aberrations, differential gene expression and epigenetic alterations are some of the genetic/epigenetic influences on GC pathogenesis. In addition, integrative analyses of molecular profiling data have led to the identification of key dysregulated pathways and importantly, the establishment of GC molecular classifiers. Recently, The Cancer Genome Atlas (TCGA) network proposed a four subtype classification scheme for GC based on the underlying tumor molecular biology of each subtype. This landmark study, together with other studies, has expanded our understanding on the characteristics of GC at the molecular level. Such knowledge may improve the medical management of GC in the future. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Molecular Biology of Lung Cancer

PubMed Central

Nana-Sinkam, Serge Patrick

2013-01-01

Based on recent bench and clinical research, the treatment of lung cancer has been refined, with treatments allocated according to histology and specific molecular features. For example, targeting mutations such as epidermal growth factor receptor (EGFR) with tyrosine kinase inhibitors has been particularly successful as a treatment modality, demonstrating response rates in selected patients with adenocarcinoma tumors harboring EGFR mutations that are significantly higher than those for conventional chemotherapy. However, the development of new targeted therapies is, in part, highly dependent on an improved understanding of the molecular underpinnings of tumor initiation and progression, knowledge of the role of molecular aberrations in disease progression, and the development of highly reproducible platforms for high-throughput biomarker discovery and testing. In this article, we review clinically relevant research directed toward understanding the biology of lung cancer. The clinical purposes of this research are (1) to identify susceptibility variants and field molecular alterations that will promote the early detection of tumors and (2) to identify tumor molecular alterations that serve as therapeutic targets, prognostic biomarkers, or predictors of tumor response. We focus on research developments in the understanding of lung cancer somatic DNA mutations, chromosomal aberrations, epigenetics, and the tumor microenvironment, and how they can advance diagnostics and therapeutics. PMID:23649444

Molecular diagnostics for human leptospirosis.

PubMed

Waggoner, Jesse J; Pinsky, Benjamin A

2016-10-01

The definitive diagnosis of leptospirosis, which results from infection with spirochetes of the genus Leptospira, currently relies on the use of culture, serological testing (microscopic agglutination testing), and molecular detection. The purpose of this review is to describe new molecular diagnostics for Leptospira and discuss advancements in the use of available methods. Efforts have been focused on improving the clinical sensitivity of Leptospira detection using molecular methods. In this review, we describe a reoptimized pathogenic species-specific real-time PCR (targeting lipL32) that has demonstrated improved sensitivity, findings by two groups that real-time reverse-transcription PCR assays targeting the 16S rrs gene can improve detection, and two new loop-mediated amplification techniques. Quantitation of leptospiremia, detection in different specimen types, and the complementary roles played by molecular detection and microscopic agglutination testing will be discussed. Finally, a protocol for Leptospira strain subtyping using variable number tandem repeat targets and high-resolution melting will be described. Molecular diagnostics have an established role for the diagnosis of leptospirosis and provide an actionable diagnosis in the acute setting. The use of real-time reverse-transcription PCR for testing serum/plasma and cerebrospinal fluid, when available, may improve the detection of Leptospira without decreasing clinical specificity.

Molecular approaches to solar energy conversion: the energetic cost of charge separation from molecular-excited states.

PubMed

Durrant, James R

2013-08-13

This review starts with a brief overview of the technological potential of molecular-based solar cell technologies. It then goes on to focus on the core scientific challenge associated with using molecular light-absorbing materials for solar energy conversion, namely the separation of short-lived, molecular-excited states into sufficiently long-lived, energetic, separated charges capable of generating an external photocurrent. Comparisons are made between different molecular-based solar cell technologies, with particular focus on the function of dye-sensitized photoelectrochemical solar cells as well as parallels with the function of photosynthetic reaction centres. The core theme of this review is that generating charge carriers with sufficient lifetime and a high quantum yield from molecular-excited states comes at a significant energetic cost-such that the energy stored in these charge-separated states is typically substantially less than the energy of the initially generated excited state. The role of this energetic loss in limiting the efficiency of solar energy conversion by such devices is emphasized, and strategies to minimize this energy loss are compared and contrasted.

Molecular implementation of simple logic programs.

PubMed

Ran, Tom; Kaplan, Shai; Shapiro, Ehud

2009-10-01

Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications. Biomolecular implementations of finite automata and logic gates have already been developed. Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) <-- Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision. A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.

Terahertz molecular resonance of cancer DNA.

PubMed

Cheon, Hwayeong; Yang, Hee-Jin; Lee, Sang-Hun; Kim, Young A; Son, Joo-Hiuk

2016-11-15

Carcinogenesis involves the chemical and structural alteration of biomolecules in cells. Aberrant methylation of DNA is a well-known carcinogenic mechanism and a common chemical modification of DNA. Terahertz waves can directly observe changes in DNA because the characteristic energies lie in the same frequency region. In addition, terahertz energy levels are not high enough to damage DNA by ionization. Here, we present terahertz molecular resonance fingerprints of DNA methylation in cancer DNA. Methylated cytidine, a nucleoside, has terahertz characteristic energies that give rise to the molecular resonance of methylation in DNA. Molecular resonance is monitored in aqueous solutions of genomic DNA from cancer cell lines using a terahertz time-domain spectroscopic technique. Resonance signals can be quantified to identify the types of cancer cells with a certain degree of DNA methylation. These measurements reveal the existence of molecular resonance fingerprints of cancer DNAs in the terahertz region, which can be utilized for the early diagnosis of cancer cells at the molecular level.

Terahertz molecular resonance of cancer DNA

NASA Astrophysics Data System (ADS)

Cheon, Hwayeong; Yang, Hee-Jin; Lee, Sang-Hun; Kim, Young A.; Son, Joo-Hiuk

2016-11-01

Carcinogenesis involves the chemical and structural alteration of biomolecules in cells. Aberrant methylation of DNA is a well-known carcinogenic mechanism and a common chemical modification of DNA. Terahertz waves can directly observe changes in DNA because the characteristic energies lie in the same frequency region. In addition, terahertz energy levels are not high enough to damage DNA by ionization. Here, we present terahertz molecular resonance fingerprints of DNA methylation in cancer DNA. Methylated cytidine, a nucleoside, has terahertz characteristic energies that give rise to the molecular resonance of methylation in DNA. Molecular resonance is monitored in aqueous solutions of genomic DNA from cancer cell lines using a terahertz time-domain spectroscopic technique. Resonance signals can be quantified to identify the types of cancer cells with a certain degree of DNA methylation. These measurements reveal the existence of molecular resonance fingerprints of cancer DNAs in the terahertz region, which can be utilized for the early diagnosis of cancer cells at the molecular level.

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

PubMed Central

Keskin, O.; Bahar, I.; Badretdinov, A. Y.; Ptitsyn, O. B.; Jernigan, R. L.

1998-01-01

Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study, the interfacial regions of protein-protein complexes are examined to extract inter-molecular inter-residue potentials, using the same statistical methods as those previously adopted for intra-molecular residue pairs. Two sets of energy parameters are derived, corresponding to solvent-mediation and "average residue" mediation. The former set is shown to be highly correlated (correlation coefficient 0.89) with that previously obtained for inter-residue interactions within single chain monomers, while the latter exhibits a weaker correlation (0.69) with its intra-molecular counterpart. In addition to the close similarity of intra- and inter-molecular solvent-mediated potentials, they are shown to be significantly more residue-specific and thereby discriminative compared to the residue-mediated ones, indicating that solvent-mediation plays a major role in controlling the effective inter-residue interactions, either at interfaces, or within single monomers. Based on this observation, a reduced set of energy parameters comprising 20 one-body and 3 two-body terms is proposed (as opposed to the 20 x 20 tables of inter-residue potentials), which reproduces the conventional 20 x 20 tables with a correlation coefficient of 0.99. PMID:9865952

Effect of molecular weight on polyphenylquinoxaline properties

NASA Technical Reports Server (NTRS)

Jensen, Brian J.

1991-01-01

A series of polyphenyl quinoxalines with different molecular weight and end-groups were prepared by varying monomer stoichiometry. Thus, 4,4'-oxydibenzil and 3,3'-diaminobenzidine were reacted in a 50/50 mixture of m-cresol and xylenes. Reaction concentration, temperature, and stir rate were studied and found to have an effect on polymer properties. Number and weight average molecular weights were determined and correlated well with viscosity data. Glass transition temperatures were determined and found to vary with molecular weight and end-groups. Mechanical properties of films from polymers with different molecular weights were essentially identical at room temperature but showed significant differences at 232 C. Diamine terminated polymers were found to be much less thermooxidatively stable than benzil terminated polymers when aged at 316 C even though dynamic thermogravimetric analysis revealed only slight differences. Lower molecular weight polymers exhibited better processability than higher molecular weight polymers.

Molecular imaging of photodynamic therapy

NASA Astrophysics Data System (ADS)

Chang, Sung K.; Errabelli, Divya; Rizvi, Imran; Solban, Nicolas; O'Riordan, Katherine; Hasan, Tayyaba

2006-02-01

Recent advances in light sources, detectors and other optical imaging technologies coupled with the development of novel optical contrast agents have enabled real-time, high resolution, in vivo monitoring of molecular targets. Noninvasive monitoring of molecular targets is particularly relevant to photodynamic therapy (PDT), including the delivery of photosensitizer in the treatment site and monitoring of molecular and physiological changes following treatment. Our lab has developed optical imaging technologies to investigate these various aspects of photodynamic therapy (PDT). We used a laser scanning confocal microscope to monitor the pharmacokinetics of various photosensitizers in in vitro as well as ex vivo samples, and developed an intravital fluorescence microscope to monitor photosensitizer delivery in vivo in small animals. A molecular specific contrast agent that targets the vascular endothelial growth factor (VEGF) was developed to monitor the changes in the protein expression following PDT. We were then able to study the physiological changes due to post-treatment VEGF upregulation by quantifying vascular permeability with in vivo imaging.

Apparatus for molecular weight separation

DOEpatents

Smith, Richard D.; Liu, Chuanliang

2001-01-01

The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations (0-2.5 mM NH4OAc) of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, (4) conducting a two-stage separation or (5) any combination of (1), (2), (3) and (4).

Molecular graph convolutions: moving beyond fingerprints

NASA Astrophysics Data System (ADS)

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-08-01

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph—atoms, bonds, distances, etc.—which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Ferrocene-containing non-interlocked molecular machines.

PubMed

Scottwell, Synøve Ø; Crowley, James D

2016-02-11

Ferrocene is the prototypical organometallic sandwich complex and despite over 60 years passing since the discovery and elucidation of ferrocene's structure, research into ferrocene-containing compounds continues to grow as potential new applications in catalysis, biology and the material sciences are found. Ferrocene is chemically robust and readily functionalized which enables its facile incorporation into more complex molecular systems. This coupled with ferrocene's reversible redox properties and ability function as a "molecular ball bearing" has led to the use of ferrocene as a component in wide range of interlocked and non-interlocked synthetic molecular machine systems. This review will focus on the exploitation of ferrocene (and related sandwich complexes) for the development of non-interlocked synthetic molecular machines.

Molecular graph convolutions: moving beyond fingerprints.

PubMed

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-08-01

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph-atoms, bonds, distances, etc.-which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Applications of Molecular Imaging

PubMed Central

Galbán, Craig; Galbán, Stefanie; Van Dort, Marcian; Luker, Gary D.; Bhojani, Mahaveer S.; Rehemtualla, Alnawaz; Ross, Brian D.

2015-01-01

Today molecular imaging technologies play a central role in clinical oncology. The use of imaging techniques in early cancer detection, treatment response and new therapy development is steadily growing and has already significantly impacted clinical management of cancer. In this chapter we will overview three different molecular imaging technologies used for the understanding of disease biomarkers, drug development, or monitoring therapeutic outcome. They are (1) optical imaging (bioluminescence and fluorescence imaging) (2) magnetic resonance imaging (MRI), and (3) nuclear imaging (e.g, single photon emission computed tomography (SPECT) and positron emission tomography (PET)). We will review the use of molecular reporters of biological processes (e.g. apoptosis and protein kinase activity) for high throughput drug screening and new cancer therapies, diffusion MRI as a biomarker for early treatment response and PET and SPECT radioligands in oncology. PMID:21075334

Stueckelberg and Molecular Physics

NASA Astrophysics Data System (ADS)

Lacki, Jan

The first period of E. C. G. Stueckelberg's scientific career was marked by important contributions he made to molecular physics.1 After publishing his thesis in 1927 in Basel [1] Stueckelberg joined the prestigious Palmer Physical Laboratory in Princeton where he worked under the guidance of Karl Taylor Compton, brother of Arthur Holly Compton. Stueckelberg owed this position devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3 to a recommendation by A. Sommerfeld.2 In this stimulating environment, he devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3

Molecular theory of smectic ordering in liquid crystals with nanoscale segregation of different molecular fragments

NASA Astrophysics Data System (ADS)

Gorkunov, M. V.; Osipov, M. A.; Kapernaum, N.; Nonnenmacher, D.; Giesselmann, F.

2011-11-01

A molecular statistical theory of the smectic A phase is developed taking into account specific interactions between different molecular fragments which enables one to describe different microscopic scenario of the transition into the smectic phase. The effects of nanoscale segregation are described using molecular models with different combinations of attractive and repulsive sites. These models have been used to calculate numerically coefficients in the mean filed potential as functions of molecular model parameters and the period of the smectic structure. The same coefficients are calculated also for a conventional smectic with standard Gay-Berne interaction potential which does not promote the segregation. The free energy is minimized numerically to calculate the order parameters of the smectic A phases and to study the nature of the smectic transition in both systems. It has been found that in conventional materials the smectic order can be stabilized only when the orientational order is sufficiently high, In contrast, in materials with nanosegregation the smectic order develops mainly in the form of the orientational-translational wave while the nematic order parameter remains relatively small. Microscopic mechanisms of smectic ordering in both systems are discussed in detail, and the results for smectic order parameters are compared with experimental data for materials of various molecular structure.

Goals and objectives for molecular pathology education in residency programs. The Association for Molecular Pathology Training and Education Committee.

PubMed

1999-11-01

Increasing knowledge of the molecular basis of disease and advances in technology for analyzing nucleic acids and gene products are changing pathology practice. The explosion of information regarding inherited susceptibility to disease is an important aspect of this transformation. Pathology residency programs are incorporating molecular pathology education into their curricula to prepare newly trained pathologists for the future, yet little guidance has been available regarding the important components of molecular pathology training. We present general goals for pathology training programs for molecular pathology education. These include recommendations to pathology residents for the acquisition of both basic knowledge in human genetics and molecular biology and specific skills relevant to microbiology, molecular oncology, genetics, histocompatibility, and identity determination. The importance of residents gaining facility in integrating data gained via nucleic acid based-technology with other laboratory and clinical information available in the care of patients is emphasized.

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2005-07-01

AD Award Number: DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia M. MacCollin, M.D...NUMBER Molecular Identification of the Schwannomatosis Locus 5b. GRANT NUMBER DAMD17-03-1-0445 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...can be found on next page. 15. SUBJECT TERMS schwannomatosis , tumor suppressor gene, NF2, molecular genetics 16. SECURITY CLASSIFICATION OF: 17

Molecular mechanisms of cryoprotection in aqueous proline: light scattering and molecular dynamics simulations.

PubMed

Troitzsch, R Z; Vass, H; Hossack, W J; Martyna, G J; Crain, J

2008-04-10

Free proline amino acid is a natural cryoprotectant expressed by numerous organisms under low-temperature stress. Previous reports have suggested that complex assemblies underlie its functional properties. We investigate here aqueous proline solutions as a function of temperature using combinations of Raman spectroscopy, Rayleigh-Brillouin light scattering, and molecular dynamics simulations with the view to revealing the molecular origins of the mixtures' functionality as a cryoprotectant. The evolution of the Brillouin frequency shifts and line widths with temperature shows that, above a critical proline concentration, the water-like dynamics is suppressed and viscoelastic behavior emerges: Here, the Landau-Placzek ratio also shows a temperature-independent maximum arising from concentration fluctuations. Molecular dynamics simulations reveal that the water-water correlations in the mixtures depend much more weakly on temperature than does bulk water. By contrast, the water OH Raman bands exhibit strong red-shifts on cooling similar to those seen in ices; however, no evidence of ice lattice phonons is observed in the low-frequency spectrum. We attribute this primarily to enhanced proline-water hydrogen bonding. In general, the picture that emerges is that aqueous proline is a heterogeneous mixture on molecular length scales (characterized by significant concentration fluctuations rather than well-defined aggregates). Simulations reveal that proline also appears to suppress the normal dependence of water structure on temperature and preserves the ambient-temperature correlations even in very cold solutions. The water structure in cold proline solutions therefore appears to be similar to that at a higher effective temperature. This, coupled with the emergence of glassy dynamics offers a molecular explanation for the functional properties of proline as a cryoprotectant without the need to invoke previously proposed complex aggregates.

Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

PubMed

Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

2015-06-01

Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.

Architectonics: Design of Molecular Architecture for Functional Applications.

PubMed

Avinash, M B; Govindaraju, Thimmaiah

2018-02-20

The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing

Variable expression of molecular markers in juvenile nasopharyngeal angiofibroma.

PubMed

Mishra, A; Pandey, A; Mishra, S C

2017-09-01

Molecular categorisation may explain the wide variation in the clinical characteristics of juvenile nasopharyngeal angiofibroma. Variations in molecular markers in juvenile nasopharyngeal angiofibroma in an Indian population were investigated and compared with global reports. Variable molecular marker expression was demonstrated at the regional and global levels. A wide variation in molecular characteristics is evident. Molecular data have been reported for only 11 countries, indicating a clear geographical bias. Only 58 markers have been studied, and most are yet to be validated. Research into the molecular epidemiology of juvenile nasopharyngeal angiofibroma is still in its infancy. Although the molecular variation is not well understood, data obtained so far have prompted important research questions. Hence, multicentre collaborative molecular studies are needed to establish the aetiopathogenesis and establish molecular surrogates for clinical characteristics.

a Molecular Fountain

NASA Astrophysics Data System (ADS)

Cheng, Cunfeng; van der Poel, Aernout P. P.; Ubachs, Wim; Bethlem, Hendrick

2017-06-01

The resolution of any spectroscopic experiment is limited by the coherent interaction time between the probe radiation and the particle that is being studied. The introduction of cooling techniques for atoms and ions has resulted in a dramatic increase of interaction times and accuracy, it is hoped that molecular cooling techniques will lead to a similar increase. Here we demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiment, beams of ammonia molecules are decelerated, trapped and cooled using inhomogeneous electric fields and subsequently launched. Using a combination of quadrupole lenses and buncher elements, the beam is shaped such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of less than 10μK and a longitudinal temperature of less than 1μK) while the molecules are in free fall, but strongly focused at the detection region. The molecules are in free fall for up to 266 milliseconds, making it possible, in principle, to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theories.

Ultrathin inorganic molecular nanowire based on polyoxometalates

PubMed Central

Zhang, Zhenxin; Murayama, Toru; Sadakane, Masahiro; Ariga, Hiroko; Yasuda, Nobuhiro; Sakaguchi, Norihito; Asakura, Kiyotaka; Ueda, Wataru

2015-01-01

The development of metal oxide-based molecular wires is important for fundamental research and potential practical applications. However, examples of these materials are rare. Here we report an all-inorganic transition metal oxide molecular wire prepared by disassembly of larger crystals. The wires are comprised of molybdenum(VI) with either tellurium(IV) or selenium(IV): {(NH4)2[XMo6O21]}n (X=tellurium(IV) or selenium(IV)). The ultrathin molecular nanowires with widths of 1.2 nm grow to micrometre-scale crystals and are characterized by single-crystal X-ray analysis, Rietveld analysis, scanning electron microscopy, X-ray photoelectron spectroscopy, ultraviolet–visible spectroscopy, thermal analysis and elemental analysis. The crystals can be disassembled into individual molecular wires through cation exchange and subsequent ultrasound treatment, as visualized by atomic force microscopy and transmission electron microscopy. The ultrathin molecular wire-based material exhibits high activity as an acid catalyst, and the band gap of the molecular wire-based crystal is tunable by heat treatment. PMID:26139011

NASA Applications of Molecular Nanotechnology

NASA Technical Reports Server (NTRS)

Globus, Al; Bailey, David; Han, Jie; Jaffe, Richard; Levit, Creon; Merkle, Ralph; Srivastava, Deepak

1998-01-01

Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.

Niobate-based octahedral molecular sieves

DOEpatents

Nenoff, Tina M.; Nyman, May D.

2006-10-17

Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

Niobate-based octahedral molecular sieves

DOEpatents

Nenoff, Tina M.; Nyman, May D.

2003-07-22

Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

Conformational Transitions in Molecular Systems

NASA Astrophysics Data System (ADS)

Bachmann, M.; Janke, W.

2008-11-01

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

Photoelectron photoion molecular beam spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trevor, D.J.

1980-12-01

The use of supersonic molecular beams in photoionization mass spectroscopy and photoelectron spectroscopy to assist in the understanding of photoexcitation in the vacuum ultraviolet is described. Rotational relaxation and condensation due to supersonic expansion were shown to offer new possibilities for molecular photoionization studies. Molecular beam photoionization mass spectroscopy has been extended above 21 eV photon energy by the use of Stanford Synchrotron Radiation Laboratory (SSRL) facilities. Design considerations are discussed that have advanced the state-of-the-art in high resolution vuv photoelectron spectroscopy. To extend gas-phase studies to 160 eV photon energy, a windowless vuv-xuv beam line design is proposed.

Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

NASA Astrophysics Data System (ADS)

Yu, Peiqiang; Damiran, Daalkhaijav

2011-06-01

Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques

NASA Astrophysics Data System (ADS)

Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M.; Prates, Luciana L.; Yu, Peiqiang

2017-08-01

The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions.

Teaching Molecular Biology with Microcomputers.

ERIC Educational Resources Information Center

Reiss, Rebecca; Jameson, David

1984-01-01

Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

Plasmon resonance imaging apparatus having nano-lycurgus-cup arrays and methods of use

DOEpatents

Liu, Gang Logan; Gartia, Manas Ranjan; Hsiao, Austin Yin Kyai

2016-10-11

Apparatus and methods are disclosed that are configured to permit nanoplasmonic spectroscopy sensing in the form of colorimetric sensing. An example apparatus involves: (a) an array layer having a top surface and a bottom surface, wherein a plurality of nanoholes are defined in the top surface of the array layer, wherein the plurality of nanoholes each have at least one sidewall surface and a bottom surface, (b) a thin metal film disposed on the top surface of the array layer and on the bottom surface of each of the plurality of nanoholes, and (c) a plurality of nanoparticles disposed on the at least one sidewall surface of the plurality of nanoholes.

Manipulation of metal-dielectric core-shell particles in optical fields

NASA Astrophysics Data System (ADS)

Chvátal, Lukáš; Šiler, Martin; Zemánek, Pavel

2014-12-01

Metal-dielectric core-shell particles represent promising tools in nanoplasmonics. In combination with optical tweezers they can be manipulated in a contactless way through fluid and their plasmonic properties can be used to probe or modify the local environment. We perform a numerical parametric study to find the particle geometry and material parameters under which such particle can be stably confined in optical tweezers. We use the theory based on Mie scattering in the focal field of an ideal water immersion objective of numerical aperture NA=1.2. For very thin metal layers we find that strong trapping on the optical axis can be achieved.

Adjoint sensitivity analysis of plasmonic structures using the FDTD method.

PubMed

Zhang, Yu; Ahmed, Osman S; Bakr, Mohamed H

2014-05-15

We present an adjoint variable method for estimating the sensitivities of arbitrary responses with respect to the parameters of dispersive discontinuities in nanoplasmonic devices. Our theory is formulated in terms of the electric field components at the vicinity of perturbed discontinuities. The adjoint sensitivities are computed using at most one extra finite-difference time-domain (FDTD) simulation regardless of the number of parameters. Our approach is illustrated through the sensitivity analysis of an add-drop coupler consisting of a square ring resonator between two parallel waveguides. The computed adjoint sensitivities of the scattering parameters are compared with those obtained using the accurate but computationally expensive central finite difference approach.

Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

PubMed Central

2017-01-01

Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition

Critical Dialogues about the Reading Process with In-Service Teachers and Children

ERIC Educational Resources Information Center

Kim, Koomi; Liwanag, Maria Perpetua; Henderson, Violet; Duckett, Peter

2014-01-01

This article investigates how teacher educators and teachers collaborate via dialogic interactions to support the development of elementary students' reading strategies. By implementing comprehension-centered reading tools such as the Burke reading interview and strategy rulers in partnership with in-service teachers, we are able to sustain…

Molecular evolution and the latitudinal biodiversity gradient.

PubMed

Dowle, E J; Morgan-Richards, M; Trewick, S A

2013-06-01

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Optical Molecular Imaging for Diagnosing Intestinal Diseases

PubMed Central

Kim, Sang-Yeob

2013-01-01

Real-time visualization of the molecular signature of cells can be achieved with advanced targeted imaging techniques using molecular probes and fluorescence endoscopy. This molecular optical imaging in gastrointestinal endoscopy is promising for improving the detection of neoplastic lesions, their characterization for patient stratification, and the assessment of their response to molecular targeted therapy and radiotherapy. In inflammatory bowel disease, this method can be used to detect dysplasia in the presence of background inflammation and to visualize inflammatory molecular targets for assessing disease severity and prognosis. Several preclinical and clinical trials have applied this method in endoscopy; however, this field has just started to evolve. Hence, many problems have yet to be solved to enable the clinical application of this novel method. PMID:24340254

Molecular clouds and galactic spiral structure

NASA Technical Reports Server (NTRS)

Dame, T. M.

1984-01-01

Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

Molecular graph convolutions: moving beyond fingerprints

PubMed Central

Kearnes, Steven; McCloskey, Kevin; Berndl, Marc; Pande, Vijay; Riley, Patrick

2016-01-01

Molecular “fingerprints” encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph—atoms, bonds, distances, etc.—which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement. PMID:27558503

Human papillomavirus molecular biology.

PubMed

Harden, Mallory E; Munger, Karl

Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Boolean logic tree of graphene-based chemical system for molecular computation and intelligent molecular search query.

PubMed

Huang, Wei Tao; Luo, Hong Qun; Li, Nian Bing

2014-05-06

The most serious, and yet unsolved, problem of constructing molecular computing devices consists in connecting all of these molecular events into a usable device. This report demonstrates the use of Boolean logic tree for analyzing the chemical event network based on graphene, organic dye, thrombin aptamer, and Fenton reaction, organizing and connecting these basic chemical events. And this chemical event network can be utilized to implement fluorescent combinatorial logic (including basic logic gates and complex integrated logic circuits) and fuzzy logic computing. On the basis of the Boolean logic tree analysis and logic computing, these basic chemical events can be considered as programmable "words" and chemical interactions as "syntax" logic rules to construct molecular search engine for performing intelligent molecular search query. Our approach is helpful in developing the advanced logic program based on molecules for application in biosensing, nanotechnology, and drug delivery.

Reliability and validity of the AutoCAD software method in lumbar lordosis measurement

PubMed Central

Letafatkar, Amir; Amirsasan, Ramin; Abdolvahabi, Zahra; Hadadnezhad, Malihe

2011-01-01

Objective The aim of this study was to determine the reliability and validity of the AutoCAD software method in lumbar lordosis measurement. Methods Fifty healthy volunteers with a mean age of 23 ± 1.80 years were enrolled. A lumbar lateral radiograph was taken on all participants, and the lordosis was measured according to the Cobb method. Afterward, the lumbar lordosis degree was measured via AutoCAD software and flexible ruler methods. The current study is accomplished in 2 parts: intratester and intertester evaluations of reliability as well as the validity of the flexible ruler and software methods. Results Based on the intraclass correlation coefficient, AutoCAD's reliability and validity in measuring lumbar lordosis were 0.984 and 0.962, respectively. Conclusions AutoCAD showed to be a reliable and valid method to measure lordosis. It is suggested that this method may replace those that are costly and involve health risks, such as radiography, in evaluating lumbar lordosis. PMID:22654681

Reliability and validity of the AutoCAD software method in lumbar lordosis measurement.

PubMed

Letafatkar, Amir; Amirsasan, Ramin; Abdolvahabi, Zahra; Hadadnezhad, Malihe

2011-12-01

The aim of this study was to determine the reliability and validity of the AutoCAD software method in lumbar lordosis measurement. Fifty healthy volunteers with a mean age of 23 ± 1.80 years were enrolled. A lumbar lateral radiograph was taken on all participants, and the lordosis was measured according to the Cobb method. Afterward, the lumbar lordosis degree was measured via AutoCAD software and flexible ruler methods. The current study is accomplished in 2 parts: intratester and intertester evaluations of reliability as well as the validity of the flexible ruler and software methods. Based on the intraclass correlation coefficient, AutoCAD's reliability and validity in measuring lumbar lordosis were 0.984 and 0.962, respectively. AutoCAD showed to be a reliable and valid method to measure lordosis. It is suggested that this method may replace those that are costly and involve health risks, such as radiography, in evaluating lumbar lordosis.

Asteroid Exploration with Autonomic Systems

NASA Technical Reports Server (NTRS)

Truszkowski, Walt; Rash, James; Rouff, Christopher; Hinchey, Mike

2004-01-01

NASA is studying advanced technologies for a future robotic exploration mission to the asteroid belt. The prospective ANTS (Autonomous Nano Technology Swarm) mission comprises autonomous agents including worker agents (small spacecra3) designed to cooperate in asteroid exploration under the overall authoriq of at least one ruler agent (a larger spacecraft) whose goal is to cause science data to be returned to Earth. The ANTS team (ruler plus workers and messenger agents), but not necessarily any individual on the team, will exhibit behaviors that qualify it as an autonomic system, where an autonomic system is defined as a system that self-reconfigures, self-optimizes, self-heals, and self-protects. Autonomic system concepts lead naturally to realistic, scalable architectures rich in capabilities and behaviors. In-depth consideration of a major mission like ANTS in terms of autonomic systems brings new insights into alternative definitions of autonomic behavior. This paper gives an overview of the ANTS mission and discusses the autonomic properties of the mission.

Molecular Volumes and the Stokes-Einstein Equation

ERIC Educational Resources Information Center

Edward, John T.

1970-01-01

Examines the limitations of the Stokes-Einstein equation as it applies to small solute molecules. Discusses molecular volume determinations by atomic increments, molecular models, molar volumes of solids and liquids, and molal volumes. Presents an empirical correction factor for the equation which applies to molecular radii as small as 2 angstrom…

Molecular motors interacting with their own tracks

NASA Astrophysics Data System (ADS)

Artyomov, Max N.; Morozov, Alexander Yu.; Kolomeisky, Anatoly B.

2008-04-01

Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state “burnt-bridge” models. Molecular motors are viewed as diffusing particles that can asymmetrically break or rebuild periodically distributed weak links when passing over them. Our explicit calculations of dynamic properties show that coupling the transport of the unbiased molecular motor with the bridge-burning mechanism leads to a directed motion that lowers fluctuations and produces a dynamic transition in the limit of low concentration of weak links. Interaction between the backward biased molecular motor and the bridge-burning mechanism yields a complex dynamic behavior. For the reversible dissociation the backward motion of the molecular motor is slowed down. There is a change in the direction of the molecular motor’s motion for some range of parameters. The molecular motor also experiences nonmonotonic fluctuations due to the action of two opposing mechanisms: the reduced activity after the burned sites and locking of large fluctuations. Large spatial fluctuations are observed when two mechanisms are comparable. The properties of the molecular motor are different for the irreversible burning of bridges where the velocity and fluctuations are suppressed for some concentration range, and the dynamic transition is also observed. Dynamics of the system is discussed in terms of the effective driving forces and transitions between different diffusional regimes.

Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips

NASA Astrophysics Data System (ADS)

Alaparthi, Madhubabu

In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion. Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.. Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH2Cl2, CH3CN, DMF, and MeOH, through dual pi...H-C T

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

PubMed

Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

2016-09-13

We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

Molecular imaging of Alzheimer disease pathology.

PubMed

Kantarci, K

2014-06-01

Development of molecular imaging agents for fibrillar β-amyloid positron-emission tomography during the past decade has brought molecular imaging of Alzheimer disease pathology into the spotlight. Large cohort studies with longitudinal follow-up in cognitively normal individuals and patients with mild cognitive impairment and Alzheimer disease indicate that β-amyloid deposition can be detected many years before the onset of symptoms with molecular imaging, and its progression can be followed longitudinally. The utility of β-amyloid PET in the differential diagnosis of Alzheimer disease is greatest when there is no pathologic overlap between 2 dementia syndromes, such as in frontotemporal lobar degeneration and Alzheimer disease. However β-amyloid PET alone may be insufficient in distinguishing dementia syndromes that commonly have overlapping β-amyloid pathology, such as dementia with Lewy bodies and vascular dementia, which represent the 2 most common dementia pathologies after Alzheimer disease. The role of molecular imaging in Alzheimer disease clinical trials is growing rapidly, especially in an era when preventive interventions are designed to eradicate the pathology targeted by molecular imaging agents. © 2014 by American Journal of Neuroradiology.

Molecular approaches for classifying endometrial carcinoma.

PubMed

Piulats, Josep M; Guerra, Esther; Gil-Martín, Marta; Roman-Canal, Berta; Gatius, Sonia; Sanz-Pamplona, Rebeca; Velasco, Ana; Vidal, August; Matias-Guiu, Xavier

2017-04-01

Endometrial carcinoma is the most common cancer of the female genital tract. This review article discusses the usefulness of molecular techniques to classify endometrial carcinoma. Any proposal for molecular classification of neoplasms should integrate morphological features of the tumors. For that reason, we start with the current histological classification of endometrial carcinoma, by discussing the correlation between genotype and phenotype, and the most significant recent improvements. Then, we comment on some of the possible flaws of this classification, by discussing also the value of molecular pathology in improving them, including interobserver variation in pathologic interpretation of high grade tumors. Third, we discuss the importance of applying TCGA molecular approach to clinical practice. We also comment on the impact of intratumor heterogeneity in classification, and finally, we will discuss briefly, the usefulness of TCGA classification in tailoring immunotherapy in endometrial cancer patients. We suggest combining pathologic classification and the surrogate TCGA molecular classification for high-grade endometrial carcinomas, as an option to improve assessment of prognosis. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System*

PubMed Central

Ho, Oanh; Rogne, Per; Edgren, Tomas; Wolf-Watz, Hans; Login, Frédéric H.; Wolf-Watz, Magnus

2017-01-01

Many pathogenic Gram-negative bacteria use the type III secretion system (T3SS) to deliver effector proteins into eukaryotic host cells. In Yersinia, the switch to secretion of effector proteins is induced first after intimate contact between the bacterium and its eukaryotic target cell has been established, and the T3SS proteins YscP and YscU play a central role in this process. Here we identify the molecular details of the YscP binding site on YscU by means of nuclear magnetic resonance (NMR) spectroscopy. The binding interface is centered on the C-terminal domain of YscU. Disrupting the YscU-YscP interaction by introducing point mutations at the interaction interface significantly reduced the secretion of effector proteins and HeLa cell cytotoxicity. Interestingly, the binding of YscP to the slowly self-cleaving YscU variant P264A conferred significant protection against autoproteolysis. The YscP-mediated inhibition of YscU autoproteolysis suggests that the cleavage event may act as a timing switch in the regulation of early versus late T3SS substrates. We also show that YscUC binds to the inner rod protein YscI with a dissociation constant (Kd) of 3.8 μm and with 1:1 stoichiometry. The significant similarity among different members of the YscU, YscP, and YscI families suggests that the protein-protein interactions discussed in this study are also relevant for other T3SS-containing Gram-negative bacteria. PMID:28039361

Light-operated machines based on threaded molecular structures.

PubMed

Credi, Alberto; Silvi, Serena; Venturi, Margherita

2014-01-01

Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

[Advance in molecular biology of Dendrobium (Orchidaceae)].

PubMed

Li, Qing; Li, Biao; Guo, Shun-Xing

2016-08-01

With the development of molecular biology, the process in molecular biology research of Dendrobium is going fast. Not only did it provide new ways to identify Dendrobium quickly, reveal the genetic diversity and relationship of Dendrobium, but also lay the vital foundation for explaining the mechanism of Dendrobium growth and metabolism. The present paper reviews the recent process in molecular biology research of Dendrobium from three aspects, including molecular identification, genetic diversity and functional genes. And this review will facilitate the development of this research area and Dendrobium. Copyright© by the Chinese Pharmaceutical Association.

Star formation in evolving molecular clouds

NASA Astrophysics Data System (ADS)

Völschow, M.; Banerjee, R.; Körtgen, B.

2017-09-01

Molecular clouds are the principle stellar nurseries of our universe; they thus remain a focus of both observational and theoretical studies. From observations, some of the key properties of molecular clouds are well known but many questions regarding their evolution and star formation activity remain open. While numerical simulations feature a large number and complexity of involved physical processes, this plethora of effects may hide the fundamentals that determine the evolution of molecular clouds and enable the formation of stars. Purely analytical models, on the other hand, tend to suffer from rough approximations or a lack of completeness, limiting their predictive power. In this paper, we present a model that incorporates central concepts of astrophysics as well as reliable results from recent simulations of molecular clouds and their evolutionary paths. Based on that, we construct a self-consistent semi-analytical framework that describes the formation, evolution, and star formation activity of molecular clouds, including a number of feedback effects to account for the complex processes inside those objects. The final equation system is solved numerically but at much lower computational expense than, for example, hydrodynamical descriptions of comparable systems. The model presented in this paper agrees well with a broad range of observational results, showing that molecular cloud evolution can be understood as an interplay between accretion, global collapse, star formation, and stellar feedback.

Molecular diagnosis and immunotherapy.

PubMed

Sastre, Joaquín; Sastre-Ibañez, Marina

2016-12-01

To describe recent insights into how molecular diagnosis can improve indication and selection of suitable allergens for specific immunotherapy and increase the safety of this therapy. As specific allergen immunotherapy targets specific allergens, identification of the disease-eliciting allergen is a prerequisite for accurate prescription of treatment. In areas of complex sensitization to aeroallergens or in cases of hymenoptera venom allergy, the use of molecular diagnosis has demonstrated that it may lead to a change in indication and selection of allergens for immunotherapy in a large proportion of patients when compared with diagnosis based on skin prick testing and/or specific IgE determination with commercial extracts. These changes in immunotherapy prescription aided by molecular diagnosis have been demonstrated to be cost-effective in some scenarios. Certain patterns of sensitization to grass or olive pollen and bee allergens may identify patients with higher risk of adverse reaction during immunotherapy. Molecular diagnosis, when used with other tools and patients' clinical records, can help clinicians better to select the most appropriate patients and allergens for specific immunotherapy and, in some cases, predict the risk of adverse reactions. The pattern of sensitization to allergens could potentially predict the efficacy of allergen immunotherapy provided that these immunotherapy products contain a sufficient amount of these allergens. Nevertheless, multiplex assay remains a third-level approach, not to be used as screening method in current practice.

Multidisciplinary molecular diagnostics: the 9th European meeting on molecular diagnostics.

PubMed

Loonen, Anne J M; Schuurman, Rob; van den Brule, Adriaan J C

2016-01-01

This report presents a summary of the 9th European Meeting on Molecular Diagnostics held in Noordwijk, The Netherlands, 14-16 October 2015. This 3-day conference covered many relevant topics in the field of molecular diagnostics in humans, including infectious disease, oncology, outbreak management, population-based cancer screening, standardization and quality control, chronic diseases and pharmacogenetics. Beyond these different areas, shared values are new technologies and novel technical and clinical applications. Approximately 450 participants, the majority coming from European countries, attended the meeting. Besides high quality scientific presentations, more than 35 diagnostic companies presented their latest innovations, altogether in an informal and inspiring scientific ambience.

Molecular replacement: tricks and treats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abergel, Chantal, E-mail: chantal.abergel@igs.cnrs-mrs.fr

2013-11-01

To be successful, molecular replacement relies on the quality of the model and of the crystallographic data. Some tricks that could be applied to the models or to the crystal to increase the success rate of MR are discussed here. Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ∼80 000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ∼70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% ofmore » the total structure and the C{sub α} r.m.s.d. between the core model and the structure to be solved must be less than 2 Å. Here, an approach originally implemented in the CaspR server (http://www.igs.cnrs-mrs.fr/Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with ≥30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples.« less

Forensic molecular pathology of violent deaths.

PubMed

Maeda, Hitoshi; Zhu, Bao-li; Ishikawa, Takaki; Michiue, Tomomi

2010-12-15

In forensic pathology, while classical morphology remains a core procedure to investigate deaths, a spectrum of ancillary procedures has been developed and incorporated to detail the pathology. Among them, postmortem biochemistry is important to investigate the systemic pathophysiological changes involved in the dying process that cannot be detected by morphology. In addition, recent advances in molecular biology have provided a procedure to investigate genetic bases of diseases that might present with sudden death, which is called 'molecular autopsy'. Meanwhile, the practical application of RNA analyses to postmortem investigation has not been accepted due to rapid decay after death; however, recent experimental and practical studies using real-time reverse transcription-PCR have suggested that the relative quantification of mRNA transcripts can be applied in molecular pathology for postmortem investigation of deaths, which may be called 'advanced molecular autopsy'. In a broad sense, forensic molecular pathology implies applied medical sciences to investigate the genetic basis of diseases, and the pathophysiology of diseases and traumas leading to death at a biological molecular level in the context of forensic pathology. The possible applications include analyses of local pathology, including tissue injury, ischemia/hypoxia and inflammation at the site of insult or specific tissue damage from intoxication, systemic responses to violence or environmental hazards, disorders due to intoxication, and systemic pathophysiology of fatal process involving major life-support organs. A review of previous studies suggests that systematic postmortem quantitative analysis of mRNA transcripts can be established from multi-faceted aspects of molecular biology and incorporated into death investigations in forensic pathology, to support and reinforce morphological evidence. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Confinement of Aggregation-Induced Emission Molecular Rotors in Ultrathin Two-Dimensional Porous Organic Nanosheets for Enhanced Molecular Recognition.

PubMed

Dong, Jinqiao; Li, Xu; Zhang, Kang; Di Yuan, Yi; Wang, Yuxiang; Zhai, Linzhi; Liu, Guoliang; Yuan, Daqiang; Jiang, Jianwen; Zhao, Dan

2018-03-21

Despite the rapid development of molecular rotors over the past decade, it still remains a huge challenge to understand their confined behavior in ultrathin two-dimensional (2D) nanomaterials for molecular recognition. Here, we report an all-carbon, 2D π-conjugated aromatic polymer, named NUS-25, containing flexible tetraphenylethylene (TPE) units as aggregation-induced emission (AIE) molecular rotors. NUS-25 bulk powder can be easily exfoliated into micrometer-sized lamellar freestanding nanosheets with a thickness of 2-5 nm. The dynamic behavior of the TPE rotors is partially restricted through noncovalent interactions in the ultrathin 2D nanosheets, which is proved by comparative experimental studies including AIE characteristics, size-selective molecular recognition, and theoretical calculations of rotary energy barrier. Because of the partially restricted TPE rotors, NUS-25 nanosheets are highly fluorescent. This property allows NUS-25 nanosheets to be used as a chemical sensor for the specific detection of acenaphthylene among a series of polycyclic aromatic hydrocarbons (PAHs) via fluorescent quenching mechanism. Further investigations show that NUS-25 nanosheets have much higher sensitivity and selectivity than their stacked bulk powder and other similar polymers containing dynamic TPE rotors. The highly efficient molecular recognition can be attributed to the photoinduced electron transfer (PET) from NUS-25 nanosheets to acenaphthylene, which is investigated by time-resolved photoluminescence measurements (TRPL), excitation and emission spectra, and density functional theory (DFT) calculations. Our findings demonstrate that confinement of AIE molecular rotors in 2D nanomaterials can enhance the molecular recognition. We anticipate that the material design strategy demonstrated in this study will inspire the development of other ultrathin 2D nanomaterials equipped with smart molecular machines for various applications.

Observation of molecular level behavior in molecular electronic junction device

NASA Astrophysics Data System (ADS)

Maitani, Masato

In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs

Molecular clouds without detectable CO

NASA Technical Reports Server (NTRS)

Blitz, Leo; Bazell, David; Desert, F. Xavier

1990-01-01

The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to ben an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is then only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase

Molecular clouds without detectable CO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blitz, L.; Bazell, D.; Desert, F.X.

1990-03-01

The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to be an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is thenmore » only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase 18 refs.« less

Molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-02-20

Quinoa starch has very small granules with unique properties. However, the molecular structure of quinoa starch remains largely unknown. In this study, composition and amylopectin molecular structure of 9 quinoa starch samples were characterised by chromatographic techniques. In particular, the amylopectin internal molecular structure, represented by φ, β-limit dextrins (LDs), was explored. Great variations in the composition and molecular structures were recorded among samples. Compared with other amylopectins, quinoa amylopectin showed a high ratio of short chain to long chains (mean:14.6) and a high percentage of fingerprint A-chains (A fp ) (mean:10.4%). The average chain length, external chain length, and internal chain length of quinoa amylopectin were 16.6, 10.6, and 5.00 glucosyl residues, respectively. Pearson correlation and principal component analysis revealed some inherent correlations among structural parameters and a similarity of different samples. Overall, quinoa amylopectins are structurally similar to that from starches with A-type polymorph such as oat and amaranth starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

NGC 3503 and its molecular environment

NASA Astrophysics Data System (ADS)

Duronea, N. U.; Vasquez, J.; Cappa, C. E.; Corti, M.; Arnal, E. M.

2012-01-01

Aims: We present a study of the molecular gas and interstellar dust distribution in the environs of the Hii region NGC 3503 associated with the open cluster Pis 17 with the aim of investigating the spatial distribution of the molecular gas linked to the nebula and achieving a better understanding of the interaction of the nebula and Pis 17 with their molecular environment. Methods: We based our study on 12CO(1-0) observations of a region of ~0.6° in size obtained with the 4-m NANTEN telescope, unpublished radio continuum data at 4800 and 8640 MHz obtained with the ATCA telescope, radio continuum data at 843 MHz obtained from SUMSS, and available IRAS, MSX, IRAC-GLIMPSE, and MIPSGAL images. Results: We found a molecular cloud (Component 1) having a mean velocity of -24.7 km s-1 ,compatible with the velocity of the ionized gas, which is associated with the nebula and its surroundings. Adopting a distance of 2.9 ± 0.4 kpc, the total molecular mass yields (7.6 ± 2.1) × 103M⊙ and density yields 400 ± 240 cm-3. The radio continuum data confirm the existence of an electron density gradient in NGC 3503. The IR emission shows a PDR bordering the higher density regions of the nebula. The spatial distribution of the CO emission shows that the nebula coincides with a molecular clump, and the strongest CO emission peak is located close to the higher electron density region. The more negative velocities of the molecular gas (about -27 km s-1), are coincident with NGC 3503. Candidate young stellar objects (YSOs) were detected toward the Hii region, suggesting that embedded star formation may be occurring in the neighborhood of the nebula. The clear electron density gradient, along with the spatial distribution of the molecular gas and PAHs in the region indicates that NGC 3503 is a blister-type Hii region that has probably undergone a champagne phase.

Molecular Classification and Correlates in Colorectal Cancer

PubMed Central

Ogino, Shuji; Goel, Ajay

2008-01-01

Molecular classification of colorectal cancer is evolving. As our understanding of colorectal carcinogenesis improves, we are incorporating new knowledge into the classification system. In particular, global genomic status [microsatellite instability (MSI) status and chromosomal instability (CIN) status] and epigenomic status [CpG island methylator phenotype (CIMP) status] play a significant role in determining clinical, pathological and biological characteristics of colorectal cancer. In this review, we discuss molecular classification and molecular correlates based on MSI status and CIMP status in colorectal cancer. Studying molecular correlates is important in cancer research because it can 1) provide clues to pathogenesis, 2) propose or support the existence of a new molecular subtype, 3) alert investigators to be aware of potential confounding factors in association studies, and 4) suggest surrogate markers in clinical or research settings. PMID:18165277

The First Molecular Phylogeny of Strepsiptera (Insecta) Reveals an Early Burst of Molecular Evolution Correlated with the Transition to Endoparasitism

PubMed Central

McMahon, Dino P.; Hayward, Alexander; Kathirithamby, Jeyaraney

2011-01-01

A comprehensive model of evolution requires an understanding of the relationship between selection at the molecular and phenotypic level. We investigate this in Strepsiptera, an order of endoparasitic insects whose evolutionary biology is poorly studied. We present the first molecular phylogeny of Strepsiptera, and use this as a framework to investigate the association between parasitism and molecular evolution. We find evidence of a significant burst in the rate of molecular evolution in the early history of Strepsiptera. The evolution of morphological traits linked to parasitism is significantly correlated with the pattern in molecular rate. The correlated burst in genotypic-phenotypic evolution precedes the main phase of strepsipteran diversification, which is characterised by the return to a low and even molecular rate, and a period of relative morphological stability. These findings suggest that the transition to endoparasitism led to relaxation of selective constraint in the strepsipteran genome. Our results indicate that a parasitic lifestyle can affect the rate of molecular evolution, although other causal life-history traits correlated with parasitism may also play an important role. PMID:21738621

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

PubMed Central

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

PubMed

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

Chemical evolution of molecular clouds

NASA Technical Reports Server (NTRS)

Prasad, Sheo S.; Tarafdar, Sankar P.; Villere, Karen R.; Huntress, Wesley T., Jr.

1987-01-01

The principles behind the coupled chemical-dynamical evolution of molecular clouds are described. Particular attention is given to current problems involving the simplest species (i.e., C. CO, O2, and H2) in quiescent clouds. The results of a comparison made between the molecular abundances in the Orion ridge and the hot core (Blake, 1986) are presented.

Molecular sled sequences are common in mammalian proteins.

PubMed

Xiong, Kan; Blainey, Paul C

2016-03-18

Recent work revealed a new class of molecular machines called molecular sleds, which are small basic molecules that bind and slide along DNA with the ability to carry cargo along DNA. Here, we performed biochemical and single-molecule flow stretching assays to investigate the basis of sliding activity in molecular sleds. In particular, we identified the functional core of pVIc, the first molecular sled characterized; peptide functional groups that control sliding activity; and propose a model for the sliding activity of molecular sleds. We also observed widespread DNA binding and sliding activity among basic polypeptide sequences that implicate mammalian nuclear localization sequences and many cell penetrating peptides as molecular sleds. These basic protein motifs exhibit weak but physiologically relevant sequence-nonspecific DNA affinity. Our findings indicate that many mammalian proteins contain molecular sled sequences and suggest the possibility that substantial undiscovered sliding activity exists among nuclear mammalian proteins. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

NASA Astrophysics Data System (ADS)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-01

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

PubMed

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-07

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

Molecular vibrational energy flow

NASA Astrophysics Data System (ADS)

Gruebele, M.; Bigwood, R.

This article reviews some recent work in molecular vibrational energy flow (IVR), with emphasis on our own computational and experimental studies. We consider the problem in various representations, and use these to develop a family of simple models which combine specific molecular properties (e.g. size, vibrational frequencies) with statistical properties of the potential energy surface and wavefunctions. This marriage of molecular detail and statistical simplification captures trends of IVR mechanisms and survival probabilities beyond the abilities of purely statistical models or the computational limitations of full ab initio approaches. Of particular interest is IVR in the intermediate time regime, where heavy-atom skeletal modes take over the IVR process from hydrogenic motions even upon X H bond excitation. Experiments and calculations on prototype heavy-atom systems show that intermediate time IVR differs in many aspects from the early stages of hydrogenic mode IVR. As a result, IVR can be coherently frozen, with potential applications to selective chemistry.

Molecular Diagnosis of Tuberculosis.

PubMed

Nurwidya, Fariz; Handayani, Diah; Burhan, Erlina; Yunus, Faisal

2018-01-01

Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.

Preface - From molecules to molecular materials, biological molecular systems and nanostructures: A collection of contributions presented at the XIIIth International Conference on Molecular Spectroscopy

NASA Astrophysics Data System (ADS)

Ratajczak, Henryk; Drozd, Marek; Fausto, Rui

2016-12-01

This volume contains a series of selected contributions presented at the XIIIth International Conference on Molecular Spectroscopy (ICMS): "From Molecules to Molecular Materials, Biological Molecular Systems and Nanostructures" held in Wrocław, Poland, 9-12 September 2015, under the auspices of the Mayor of Wrocław and the European Academy of Sciences, Arts and Humanities. Wrocław was chosen not accidentally as venue for the conference. With more than a thousand years of history, Wrocław is the location of one of the oldest universities in Central Europe. Being a place where education and science play major roles in the daily life of its inhabitants, Wrocław is also a privileged center for spectroscopy in Poland.

Molecularly Imprinted Intelligent Scaffolds for Tissue Engineering Applications.

PubMed

Neves, Mariana I; Wechsler, Marissa E; Gomes, Manuela E; Reis, Rui L; Granja, Pedro L; Peppas, Nicholas A

2017-02-01

The development of molecularly imprinted polymers (MIPs) using biocompatible production methods enables the possibility to further exploit this technology for biomedical applications. Tissue engineering (TE) approaches use the knowledge of the wound healing process to design scaffolds capable of modulating cell behavior and promote tissue regeneration. Biomacromolecules bear great interest for TE, together with the established recognition of the extracellular matrix, as an important source of signals to cells, both promoting cell-cell and cell-matrix interactions during the healing process. This review focuses on exploring the potential of protein molecular imprinting to create bioactive scaffolds with molecular recognition for TE applications based on the most recent approaches in the field of molecular imprinting of macromolecules. Considerations regarding essential components of molecular imprinting technology will be addressed for TE purposes. Molecular imprinting of biocompatible hydrogels, namely based on natural polymers, is also reviewed here. Hydrogel scaffolds with molecular memory show great promise for regenerative therapies. The first molecular imprinting studies analyzing cell adhesion report promising results with potential applications for cell culture systems, or biomaterials for implantation with the capability for cell recruitment by selectively adsorbing desired molecules.

Development and Testing of Molecular Adsorber Coatings

NASA Technical Reports Server (NTRS)

Abraham, Nithin; Hasegawa, Mark; Straka, Sharon

2012-01-01

The effect of on-orbit molecular contamination has the potential to degrade the performance of spaceflight hardware and diminish the lifetime of the spacecraft. For example, sensitive surfaces, such as optical surfaces, electronics, detectors, and thermal control surfaces, are vulnerable to the damaging effects of contamination from outgassed materials. The current solution to protect these surfaces is through the use of zeolite coated ceramic adsorber pucks. However, these pucks and its additional complex mounting hardware requirements result in several disadvantages, such as size, weight, and cost related concerns, that impact the spacecraft design and the integration and test schedule. As a result, a new innovative molecular adsorber coating was developed as a sprayable alternative to mitigate the risk of on-orbit molecular contamination. In this study, the formulation for molecular adsorber coatings was optimized using various binders, pigment treatment methods, binder to pigment ratios, thicknesses, and spray application techniques. The formulations that passed coating adhesion and vacuum thermal cycling tests were further tested for its adsorptive capacity. Accelerated molecular capacitance tests were performed in an innovatively designed multi-unit system containing idealized contaminant sources. This novel system significantly increased the productivity of the testing phase for the various formulations that were developed. Work performed during the development and testing phases has demonstrated successful application of molecular adsorber coatings onto metallic substrates, as well as, very promising results for the adhesion performance and the molecular capacitance of the coating. Continued testing will assist in the qualification of molecular adsorber coatings for use on future contamination sensitive spaceflight missions.

Advancing the education in molecular diagnostics: the IFCC-Initiative "Clinical Molecular Biology Curriculum" (C-CMBC); a ten-year experience.

PubMed

Lianidou, Evi; Ahmad-Nejad, Parviz; Ferreira-Gonzalez, Andrea; Izuhara, Kenji; Cremonesi, Laura; Schroeder, Maria-Eugenia; Richter, Karin; Ferrari, Maurizio; Neumaier, Michael

2014-09-25

Molecular techniques are becoming commonplace in the diagnostic laboratory. Their applications influence all major phases of laboratory medicine including predisposition/genetic risk, primary diagnosis, therapy stratification and prognosis. Readily available laboratory hardware and wetware (i.e. consumables and reagents) foster rapid dissemination to countries that are just establishing molecular testing programs. Appropriate skill levels extending beyond the technical procedure are required for analytical and diagnostic proficiency that is mandatory in molecular genetic testing. An international committee (C-CMBC) of the International Federation for Clinical Chemistry (IFCC) was established to disseminate skills in molecular genetic testing in member countries embarking on the respective techniques. We report the ten-year experience with different teaching and workshop formats for beginners in molecular diagnostics. Copyright © 2014 Elsevier B.V. All rights reserved.

Determinations of molecular weight and molecular weight distribution of high polymers by the rheological properties

NASA Technical Reports Server (NTRS)

Huang, J. Y.; Hou, T. H.; Tiwari, S. N.

1989-01-01

Several methods are reviewed by which the molecular weight (MW) and the molecular weight distribution (MWD) of polymeric material were determined from the rheological properties. A poly(arylene ether) polymer with six different molecular weights was used in this investigation. Experimentally measured MW and MWD were conducted by GPC/LALLS (gel permeation chromatography/low angle laser light scattering), and the rheological properties of the melts were measured by a Rheometric System Four rheometer. It was found that qualitative information of the MW and MWD of these polymers could be derived from the viscoelastic properties, with the methods proposed by Zeichner and Patel, and by Dormier et al., by shifting the master curves of the dynamic storage modulus, G', and the loss modulus, G'', along the frequency axis. Efforts were also made to calculate quantitative profiles of MW and MWD for these polymers from their rheological properties. The technique recently proposed by Wu was evaluated. It was found that satisfactory results could only be obtained for polymers with single modal distribution in the molecular weight.

Molecular Nanotechnology and Designs of Future

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

Reviewing the status of current approaches and future projections, as already published in the scientific journals and books, the talk will summarize the direction in which computational and experimental molecular nanotechnologies are progressing. Examples of nanotechnological approach to the concepts of design and simulation of atomically precise materials in a variety of interdisciplinary areas will be presented. The concepts of hypothetical molecular machines and assemblers as explained in Drexler's and Merckle's already published work and Han et. al's WWW distributed molecular gears will be explained.

A Hadoop-based Molecular Docking System

NASA Astrophysics Data System (ADS)

Dong, Yueli; Guo, Quan; Sun, Bin

2017-10-01

Molecular docking always faces the challenge of managing tens of TB datasets. It is necessary to improve the efficiency of the storage and docking. We proposed the molecular docking platform based on Hadoop for virtual screening, it provides the preprocessing of ligand datasets and the analysis function of the docking results. A molecular cloud database that supports mass data management is constructed. Through this platform, the docking time is reduced, the data storage is efficient, and the management of the ligand datasets is convenient.

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

Carbon Isotope Chemistry in Molecular Clouds

NASA Technical Reports Server (NTRS)

Robertson, Amy N.; Willacy, Karen

2012-01-01

Few details of carbon isotope chemistry are known, especially the chemical processes that occur in astronomical environments like molecular clouds. Observational evidence shows that the C-12/C-13 abundance ratios vary due to the location of the C-13 atom within the molecular structure. The different abundances are a result of the diverse formation pathways that can occur. Modeling can be used to explore the production pathways of carbon molecules in an effort to understand and explain the chemical evolution of molecular clouds.

Molecular pathogenesis and mechanisms of thyroid cancer

PubMed Central

Xing, Mingzhao

2013-01-01

Thyroid cancer is a common endocrine malignancy. There has been exciting progress in understanding its molecular pathogenesis in recent years, as best exemplified by the elucidation of the fundamental role of several major signalling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these pathways, such as mutation, gene copy-number gain and aberrant gene methylation. Many of these molecular alterations represent novel diagnostic and prognostic molecular markers and therapeutic targets for thyroid cancer, which provide unprecedented opportunities for further research and clinical development of novel treatment strategies for this cancer. PMID:23429735

Molecular science for drug development and biomedicine.

PubMed

Zhong, Wei-Zhu; Zhou, Shu-Feng

2014-11-04

With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of "Molecular Science for Drug Development and Biomedicine", in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine.[...].

At the Origins of a Russian National Consciousness: Eighteenth Century Roots and Napoleonic Wars.

ERIC Educational Resources Information Center

Raeff, Marc

1991-01-01

Discusses influences on the development of Russian nationalism. Describes the development of an intelligentsia and its relationship with both peasants and rulers. Addresses the influence of French and German political and religious thinkers. Emphasizes that the Napoleonic wars provided both a Russian patriotic bond and exposure of Russia's elite…

A Comparison of the Concurrent and Predictive Validity of Three Measures of Readiness to Change Alcohol Use in a Clinical Sample of Adolescents

ERIC Educational Resources Information Center

Maisto, Stephen A.; Krenek, Marketa; Chung, Tammy; Martin, Christopher S.; Clark, Duncan; Cornelius, Jack

2011-01-01

The authors compared 3 measures of readiness to change alcohol use commonly used in clinical research and practice with adolescents: the Readiness Ruler, the SOCRATES (subscales of Recognition and Taking Steps), and a Staging Algorithm. The analysis sample consisted of 161 male and female adolescents presenting for intensive outpatient…

Advanced Metacrystal Media for Aerospace Applications

DTIC Science & Technology

2014-09-14

role of the surface C. Ciracì, E. Poutrina, M. Scalora , D. R. Smith Physical Review B 86, 115451 (2012) Plasmon ruler with Angstrom length...Poutrina, M. Scalora D. R. Smith Physical Review B 85, 201403(R) (2012) Enhancement of four-wave mixing processes by nanoparticle arrays coupled to

Making and Recording Observations: When Done Well, Observations Can Serve as Evidence When Engaging in Science Practices

ERIC Educational Resources Information Center

Arias, Anna Maria; Davis, Elizabeth A.

2016-01-01

Making and recording scientific observations is a fundamental activity of the scientific community. Scientists use their senses and tools (e.g., magnifying glasses, rulers, colored pencils) to make records of the phenomena (e.g., light energy, ecosystems) they are investigating. These observations often serve as evidence in the scientific…

Hadamard Transform Time-of-Flight Mass Spectrometry

DTIC Science & Technology

2010-01-26

mass range of the experiment. For pulsed ionization techniques including laser-based methods such as MALDI(Tanaka, Waki et al. 1988), SELDI(Hutchens...18101. Stryer, L. (1978). "Fluorescence Energy Transfer as a Spectroscopic Ruler." Annual Review of Biochemistry 47(n: 819-846. Tanaka, K., H. Waki , et

Cosmos and Rulership: The Function of Olmec-Style Symbols in Formative Period Mesoamerica.

ERIC Educational Resources Information Center

Reilly, F. Kent III

1990-01-01

States that iconographic investigations of Olmec style art works have produced convincing evidence that rulership during the Early and Middle Formative Period of Mesoamerican prehistory was publicly legitimized by a visual charter. Shows that the charter's naturally derived symbols functioned within a system which stressed the human ruler's access…

"Time" in China.

ERIC Educational Resources Information Center

Weland, James E.

1982-01-01

Discusses how the Chinese have recorded their history by dynasties, the length of time any one imperial clan could retain its hold on the Dragon Throne. Dynastic histories were used to instruct rulers in the ways ethical problems of government had been dealt with in the past. (AM)

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

NASA Astrophysics Data System (ADS)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

Masses, luminosities and dynamics of galactic molecular clouds

NASA Technical Reports Server (NTRS)

Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.

1987-01-01

Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.

Agent-Based Modeling in Molecular Systems Biology.

PubMed

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-07-01

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

2010-06-01

Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

Molecular subgroups of medulloblastoma

PubMed Central

Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

2014-01-01

Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

Circumstellar radio molecular lines

NASA Technical Reports Server (NTRS)

NGUYEN-QUANG-RIEU

1987-01-01

Radio molecular lines appear to be useful probes into the stellar environment. Silicon oxide masers provide information on the physical conditions in the immediate vicinity of the stellar photosphere. Valuable information on the physics operating in the envelope of IRC + 10216 was recently obtained by high sensitivity observations and detailed theoretical analyses. Infrared speckle interferometry in the molecular lines and in the continuum is helpful in the investigation of the inner region of the envelope. These techniques are discussed in terms of late-type star mass loss.

Molecular Imprinting of Macromolecules for Sensor Applications.

PubMed

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-04-19

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

Molecular Imprinting of Macromolecules for Sensor Applications

PubMed Central

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-01-01

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting. PMID:28422082

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

PubMed

Shin, Jaeho; Gu, Kyungyeol; Yang, Seunghoon; Lee, Chul-Ho; Lee, Takhee; Jang, Yun Hee; Wang, Gunuk

2018-06-25

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( F L ) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the F L dependence (i.e., F L -dependent and F L -independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the F L ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( F vdW ) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

Molecular perspectives in differentiated thyroid cancer.

PubMed

Buffet, C; Groussin, L

2015-02-01

Progress in understanding the molecular genetics of thyroid cancer in the last 20 years has accelerated recently with the advent of high-throughput sequencing technologies known as Next-Generation Sequencing. Besides classical molecular abnormalities involving the MAPK (Mitogen Activated Protein Kinase) and PI3K (PhosphoInositide 3-Kinase) pathways that play a key role in follicular-derived thyroid tumorigenesis, new molecular abnormalities have been discovered. The major advances in recent years have been the discovery of new somatic driver gene point mutations (such as RASAL1 [RAS protein activator Like 1] mutations in follicular cancer) and/or mutations that have prognostic value (such as TERT [Telomerase reverse transcriptase] promoter mutations); new chromosomal rearrangements, usually having close connection with exposure to ionizing radiation (such as ALK [Anaplastic Lymphoma Kinase] rearrangements); and deregulation of some gene or microRNA expression representing a molecular signature. Progress made in understanding the molecular mechanisms of thyroid cancer offers new perspectives for the diagnosis of the benign or malignant status of a thyroid nodule, to refine prognosis and offer new perspectives of targeted therapy for radioiodine-refractory cancers. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Silane and Germane Molecular Electronics.

PubMed

Su, Timothy A; Li, Haixing; Klausen, Rebekka S; Kim, Nathaniel T; Neupane, Madhav; Leighton, James L; Steigerwald, Michael L; Venkataraman, Latha; Nuckolls, Colin

2017-04-18

This Account provides an overview of our recent efforts to uncover the fundamental charge transport properties of Si-Si and Ge-Ge single bonds and introduce useful functions into group 14 molecular wires. We utilize the tools of chemical synthesis and a scanning tunneling microscopy-based break-junction technique to study the mechanism of charge transport in these molecular systems. We evaluated the fundamental ability of silicon, germanium, and carbon molecular wires to transport charge by comparing conductances within families of well-defined structures, the members of which differ only in the number of Si (or Ge or C) atoms in the wire. For each family, this procedure yielded a length-dependent conductance decay parameter, β. Comparison of the different β values demonstrates that Si-Si and Ge-Ge σ bonds are more conductive than the analogous C-C σ bonds. These molecular trends mirror what is seen in the bulk. The conductance decay of Si and Ge-based wires is similar in magnitude to those from π-based molecular wires such as paraphenylenes However, the chemistry of the linkers that attach the molecular wires to the electrodes has a large influence on the resulting β value. For example, Si- and Ge-based wires of many different lengths connected with a methyl-thiomethyl linker give β values of 0.36-0.39 Å -1 , whereas Si- and Ge-based wires connected with aryl-thiomethyl groups give drastically different β values for short and long wires. This observation inspired us to study molecular wires that are composed of both π- and σ-orbitals. The sequence and composition of group 14 atoms in the σ chain modulates the electronic coupling between the π end-groups and dictates the molecular conductance. The conductance behavior originates from the coupling between the subunits, which can be understood by considering periodic trends such as bond length, polarizability, and bond polarity. We found that the same periodic trends determine the electric field

Molecular plant breeding: methodology and achievements.

PubMed

Varshney, Rajeev K; Hoisington, Dave A; Nayak, Spurthi N; Graner, Andreas

2009-01-01

The progress made in DNA marker technology has been remarkable and exciting in recent years. DNA markers have proved valuable tools in various analyses in plant breeding, for example, early generation selection, enrichment of complex F(1)s, choice of donor parent in backcrossing, recovery of recurrent parent genotype in backcrossing, linkage block analysis and selection. Other main areas of applications of molecular markers in plant breeding include germplasm characterization/fingerprinting, determining seed purity, systematic sampling of germplasm, and phylogenetic analysis. Molecular markers, thus, have proved powerful tools in replacing the bioassays and there are now many examples available to show the efficacy of such markers. We have illustrated some basic concepts and methodology of applying molecular markers for enhancing the selection efficiency in plant breeding. Some successful examples of product developments of molecular breeding have also been presented.