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Sample records for baixa massa molecular

  1. Keynote Address: Rev. Mark Massa

    ERIC Educational Resources Information Center

    Massa, Mark S.

    2011-01-01

    Rev. Mark S. Massa, S.J., is the dean and professor of Church history at the School of Theology and Ministry at Boston College. He was invited to give a keynote to begin the third Catholic Higher Education Collaborative Conference (CHEC), cosponsored by Boston College and Fordham University. Fr. Massa's address posed critical questions about…

  2. From Noun to Intensifier: Massa and Massa's in Flemish Varieties of Dutch

    ERIC Educational Resources Information Center

    De Clerck, Bernard; Colleman, Timothy

    2013-01-01

    In this paper a case of synchronic layering is examined in which Dutch "massa" ("mass") and plural "massa's" ("masses") are attested with lexical uses as a collective noun, quantifying uses ("a large quantity of") and intensifying uses ("very")--with plural "massa's" only--in some Flemish varieties of Dutch. Against the background of…

  3. From Noun to Intensifier: Massa and Massa's in Flemish Varieties of Dutch

    ERIC Educational Resources Information Center

    De Clerck, Bernard; Colleman, Timothy

    2013-01-01

    In this paper a case of synchronic layering is examined in which Dutch "massa" ("mass") and plural "massa's" ("masses") are attested with lexical uses as a collective noun, quantifying uses ("a large quantity of") and intensifying uses ("very")--with plural "massa's" only--in some Flemish varieties of Dutch. Against the background of…

  4. Ruptured Massa Intermedia Secondary to Hydrocephalus.

    PubMed

    El Damaty, Ahmed; Langner, Soenke; Schroeder, Henry W S

    2017-01-01

    We report a case of ruptured massa intermedia (MI) as a sequela of hydrocephalus. A single case report is presented describing the sequelae of tumor bed hematoma after a posterior fossa hemangioblastoma resection in which the patient bled 3 days after surgery, resulting in secondary hydrocephalus and subsequently dilatation of the third ventricle, which resulted in rupture of the MI. The patient was managed on emergency basis with an external ventricular drain then endoscopically with a third ventriculostomy and clot extraction. Absent MI is not uncommon in hydrocephalic patients, and it is assumed to be the result of rupture from acute dilatation of the third ventricle. Our case report proves this assumption and documents the presence and absence of the MI before and after developing hydrocephalus. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. A note on a paper by Massa and Pagani.

    NASA Astrophysics Data System (ADS)

    Edgar, S. B.

    1987-11-01

    Massa and Pagani [1] have given a neat refutal to the conjecture [2] that the Riemann tensor is derivable from a tensor potential. Their method consists of assuming such a relationship does exist and examining the resulting integrability conditions; they show that the existence of such a potential will impose nontrivial restrictions on the Riemann tensor and so conclude that, in general, such a potential cannot exist. Although Massa and Pagani posed the problem and interpreted the conclusion in ordinary tensor notation the actual derivation of the crucial constraint equation was carried out in the language of tensor-valued differential forms, and is quite involved. In this note it is shown that the crucial equation can be obtained quite naturally and easily in ordinary tensor notation.

  6. Perda de massa em ventos empoeirados de estrelas supergigantes

    NASA Astrophysics Data System (ADS)

    Vidotto, A. A.; Jatenco-Pereira, V.

    2003-08-01

    Em praticamente todas as regiões do diagrama HR, as estrelas apresentam evidências observacionais de perda de massa. Na literatura, pode-se encontrar trabalhos que tratam tanto do diagnóstico da perda de massa como da construção de modelos que visam explicá-la. O amortecimento de ondas Alfvén tem sido utilizado como mecanismo de aceleração de ventos homogêneos. Entretanto, sabe-se que os envelopes de estrelas frias contêm grãos sólidos e moléculas. Com o intuito de estudar a interação entre as ondas Alfvén e a poeira e a sua conseqüência na aceleração do vento estelar, Falceta-Gonçalves & Jatenco-Pereira (2002) desenvolveram um modelo de perda de massa para estrelas supergigantes. Neste trabalho, apresentamos um estudo do modelo acima proposto para avaliar a dependência da taxa de perda de massa com alguns parâmetros iniciais como, por exemplo, a densidade r0, o campo magnético B0, o comprimento de amortecimento da onda L0, seu fluxo f0, entre outros. Sendo assim, aumentando f0 de 10% a partir de valores de referência, vimos que aumenta consideravelmente, enquanto que um aumento de mesmo valor em r0, B0 e L0 acarreta uma diminuição em .

  7. Efeitos do binarismo não resolvido na determinação da função de massa de aglomerados

    NASA Astrophysics Data System (ADS)

    Kerber, L. O.; Santiago, B. X.

    2003-08-01

    Através de simulações numéricas buscamos quantificar os efeitos que o binarismo não resolvido causa na determinação da função de massa (MF) de aglomerados estelares. Geramos diagramas cor-magnitude (CMDs) artificiais simulando uma população única, caracterizada por estrelas de mesma idade e composição quí mica, com uma fração de binárias não resolvidas e distribuição em massa das estrelas dada por uma MF do tipo lei de potência. A presença de pares de estrelas não resolvidos faz com que a MF obtida da função de luminosidade (LF) tenha a têndencia de ser mais plana do que a MF que gerou o CMD artificial. Propomos um tratamento de correção para tal efeito. Outro efeito relacionado diz respeito ao alargamento do CMD, que apresenta-se como um indicador do número total de estrelas no domí nio de baixas massas (m < 0.6M¤). Todos os resultados acima possuem uma forte dependência com os erros fotométricos e estão baseados na hipótese de que ambas estrelas do par não resolvido são sorteadas de uma mesma MF de forma independente. O objetivo final é aplicarmos o tratamento aqui desenvolvido para implementarmos a análise da nossa amostra de aglomerados ricos da Grande Nuvem de Magalhães.

  8. Thalamic Massa Intermedia Duplication in a Dysmorphic 14 month-old Toddler

    PubMed Central

    Whitehead, Matthew T

    2015-01-01

    The massa intermedia is an inconstant parenchymal band connecting the medial thalami. It may be thickened in various disease processes such as Chiari II malformation or absent in other disease states. However, the massa intermedia may also be absent in up to 30% of normal human brains. To the best of my knowledge, detailed imaging findings of massa intermedia duplication have only been described in a single case report. An additional case of thalamic massa intermedia duplication discovered on a routine brain MR performed for dysmorphic facial features is reported herein. PMID:26622932

  9. Spatial variability in secondary metabolites of the indo-pacific sponge Stylissa massa.

    PubMed

    Rohde, Sven; Gochfeld, Deborah J; Ankisetty, Sridevi; Avula, Bharathi; Schupp, Peter J; Slattery, Marc

    2012-05-01

    Chemical diversity represents a measure of selective pressures acting on genotypic variability. In order to understand patterns of chemical ecology and biodiversity in the environment, it is necessary to enhance our knowledge of chemical diversity within and among species. Many sponges produce variable levels of secondary metabolites in response to diverse biotic and abiotic environmental factors. This study evaluated intra-specific variability in secondary metabolites in the common Indo-Pacific sponge Stylissa massa over various geographic scales, from local to ocean basin. Several major metabolites were quantified in extracts from sponges collected in American Samoa, Pohnpei, Saipan, and at several sites and depths in Guam. Concentrations of several of these metabolites varied geographically across the Pacific basin, with American Samoa and Pohnpei exhibiting the greatest differences, and Guam and Saipan more similar to each other. There were also significant differences in concentrations among different sites and depths within Guam. The crude extract of S. massa exhibited feeding deterrence against the omnivorous pufferfish Canthigaster solandri at natural concentrations, however, none of the isolated compounds was deterrent at the maximum natural concentrations observed, nor were mixtures of these compounds, thus emphasizing the need for bioassay-guided isolation to characterize specific chemical defenses. Antibacterial activity against a panel of ecologically relevant pathogens was minimal. Depth transplants, predator exclusion, and UV protection experiments were performed, but although temporal variability in compound concentrations was observed, there was no evidence that secondary metabolite concentration in S. massa was induced by any of these factors. Although the reasons behind the variability observed in the chemical constituents of S. massa are still in question, all sponges are not created equal from a chemical standpoint, and these studies provide

  10. Modeling the Minho River plume intrusion into the Rias Baixas (NW Iberian Peninsula)

    NASA Astrophysics Data System (ADS)

    Sousa, M. C.; Vaz, N.; Alvarez, I.; Gomez-Gesteira, M.; Dias, J. M.

    2014-08-01

    The Minho River discharge is recognized as particularly important in driving the circulation and hydrography of Rias Baixas, which are highly productive fishery and aquaculture regions extremely sensitive to environmental characteristics. The intrusion of the Minho River plume inside these Rias can reverse the normal circulation pattern and affect the macronutrient concentrations, imposing a control on new production within the estuarine environment. Consequently, detailed knowledge of the propagation of the plume in this zone facilitates largely the management of many exploited and protected local species. Thus, the main purpose of this work is to study the propagation and influence of Minho estuarine plume in Rias Baixas circulation and hydrography through the development and validation of an application of MOHID numerical model including a local coastal nesting configuration fed by Minho River discharge predicted by an estuary model. The nesting configuration and the Minho estuary model were validated and then applied to research the role of the wind and Minho River discharge effects on the circulation reversal. The spring of 1998 was chosen as the validation period for Minho estuarine plume propagation, considering there were field data available for this period confirming the intrusion of the Minho River plume in Rias Baixas and reversing the normal circulation pattern. Predictions replicate accurately the hydrodynamics and thermohaline patterns in Minho estuary and Rias Baixas under these conditions showing that the developed model application reproduces the dynamics of the coupled estuarine-near coastal systems under research. Results showed that a buoyancy intrusion caused by the Minho River reverses the normal estuarine salinity longitudinal gradient and estuarine circulation of the Rias de Vigo and Pontevedra. Moreover, it was found that a continuous moderate Minho River discharge combined with southerly winds is enough to reverse the Rias Baixas

  11. Influence of the Minho River plume on the Rias Baixas (NW of the Iberian Peninsula)

    NASA Astrophysics Data System (ADS)

    Sousa, M. C.; Vaz, N.; Alvarez, I.; Gomez-Gesteira, M.; Dias, J. M.

    2014-11-01

    The buoyancy generated by the Minho estuarine plume can flood the Rias Baixas for long periods, reversing the normal salinity gradients. Thus, the main purpose of this work was to study the propagation of Minho estuarine plume to the Rias Baixas, establishing the wind and river discharge conditions in which this plume affects the circulation and hydrography features of these coastal systems as well as the plume characteristics under the most probable forcing conditions, through the application of the numerical model MOHID. For this purpose, several scenarios with different river discharges and wind were simulated. The numerical results revealed that the Minho estuarine plume responds rapidly to wind variations and is influenced by coastline geometry. Under Minho River discharges higher than 700 m3 s- 1 and weak northward winds (3 m s- 1) the circulation patterns of the Rias de Vigo and Pontevedra are reversed. On the other hand, moderate northward winds (6 m s- 1) combined with Minho River discharges higher than 200 m3 s- 1, 300 m3 s- 1 and 700 m3 s- 1 reverse the circulation pattern of the Rias de Vigo, Pontevedra and Arousa, respectively. Under the same conditions, the water exchange between Rias Baixas was analyzed using a particle-tracking model following the trajectories of particles released close to the Minho River mouth. Over 5 days, under Minho River discharges higher than 2100 m3 s- 1 combined with northward winds of 6 m s- 1, an intense water exchange between Rias was observed. However, only 20% of the particles found in Ria de Pontevedra come directly from the Minho River.

  12. Homogeneity of monthly precipitation series from 1932 to 2010 in the Souss Massa Region-Morocco

    NASA Astrophysics Data System (ADS)

    Abahous, Houria; Ronchail, Josyane; Sifeddine, Abdelfattah; Kenny, Lahcen; Bouchaou, Lhoussaine

    2017-04-01

    Water resources are vulnerable to precipitation fluctuations, especially in arid area such as the Souss-Massa region. Therefore, the analysis and the simulation of the regional rainfall characteristics at decadal scale are of great importance. The availability of long-term time series is often limited by their quality. A network of local meteorological stations recording monthly precipitations from 1932 to 2010 is provided by the Hydraulic basin of Souss Massa Agency. A dataset of 19 selected stations is undergoing an interative process of quality control and homogeneity assessment using ProclimDB/Anclim and Homer softwares. Suspicious monthly data are identified with a combination of criterions. We analyse the standardized precipitation index to better distinguish real climate events from erroneous data in the analyzed series. Statistically significant annual change-points are detected with both absolute and relative methods by using a criterion of validation. The temporal distribution of outliers shows an annual cycle and a decrease of their occurence since the eighties. We also assess the year of 1973 as a change point related to climate in Western High Atlas Mountains stations.

  13. Simulação de ejeções de massa coronal

    NASA Astrophysics Data System (ADS)

    Corsini, M. A.; Silva, A. V. R.

    2003-08-01

    Ejeções de massa coronal (EMC) são bolhas gigantes de gás permeadas por campos magnéticos que são ejetadas do Sol durante um período de várias horas. Caso estas ejeções atinjam a Terra, geralmente, causam uma série de distúrbios às comunicações de longa distância e navegação, além de danos a satélites e transformadores. Portanto, é desejável que sejamos capazes de prever quando estas ejeções atingirão a Terra. Para tanto, é necessário um bom entendimento dos mecanismos causadores das ejeções e, principalmente, de como se dá a propagação das EMC e sua interação com o vento solar que permeia o meio interplanetário. Nesse sentido foi desenvolvido um programa computacional para resolver as equações MHD (Magneto-Hidro-Dinâmica) que regem a evolução das EMC. Primeiramente foram estabelecidas as condições necessárias para descrever o vento solar, no estado estacionário, que permeia todo o meio interplanetário. Num primeiro momento, resolveu-se o sistema de equações para o caso do vento isotérmico, conhecida como a solução de Parker, a fim de testarmos o modelo. Então, foi considerado o caso do vento solar com temperatura variável no meio interplanetário. Este resultado foi utilizado como a base de nosso sistema em seu instante inicial. Posteriormente foram feitas as considerações necessárias para descrever a propagação da Ejeção de Massa Coronal. As EMC foram simuladas como um aumento de densidade e temperatura local na coroa solar. A órbita e a posição da Terra foram incluídas no sistema. Os dados gerados possibilitaram uma análise da evolução da EMC pelo meio interplanetário até encontrar-se com a Terra. Os perfis de densidade e temperatura a 1 Unidade Astronômica são comparados com os dados de satélites reportados na literatura.

  14. Pesticide residues in tomatoes from greenhouses in Souss Massa Valley, Morocco.

    PubMed

    Salghi, R; Luis, G; Rubio, C; Hormatallah, A; Bazzi, L; Gutiérrez, A J; Hardisson, A

    2012-03-01

    Eight pesticide residues in tomato samples collected in the area of Souss Massa Valley (Southern Morocco) were analyzed. The detected residue levels ranged from 0.001 to 0.400 mg kg(-1) for dicofol, from 0.003 to 0.170 mg kg(-1) for procymidone, from 0.001 to 0.250 mg kg(-1) for chlorothalonil, from 0.050 to 0.500 mg kg(-1) for bifenthrin, from 0.001 to 0.010 mg kg(-1) for λ-cyhalothrin, from 0.001 to 0.300 mg kg(-1) for cypermethrin, from 0.010 to 1 mg kg(-1) for deltamethrin and from 0.003 to 1.123 mg kg(-1) for endosulfan. European MRL for endosulfan in tomatoes set in 0.500 mg kg(-1), was exceeded in 8 samples, and MRL for deltamethrin set in 0.300 mg kg(-1) for tomatoes was exceeded in 2 samples.

  15. Massa do gás e das estrelas em aglomerados: eficiência da formação estelar

    NASA Astrophysics Data System (ADS)

    Laganá, T. F.; Lima Neto, G. B.

    2003-08-01

    Os aglomerados de galáxias apresentam um interesse especial para a cosmologia observacional. Eles são as maiores estruturas ligadas pela gravitação no Universo e relaxadas na região central. A comparação entre a massa do gás intra-aglomerado (responsável por ~25% da massa total, inferida a partir de observações em raios-X), a massa contida nas estrelas (i.e., nas galáxias) e a massa total (incluindo a matéria escura não bariônica), nos dá informações importantes sobre os processos de formação e evolução de aglomerados. Por exemplo, a razão entre a massa do gás e a massa total é uma medida da fração de bárions no Universo (razão entre a matéria bariônica e matéria escura) e, utilizando a densidade de bárions predita pela nucleosíntese primordial, podemos deduzir a densidade de matéria escura no Universo (cf. White et al. 1993). O objetivo deste trabalho é obter as razões entre as massas do gás, estelar (contida nas galáxias), e a total (massa dinâmica). As massas do gás e total são obtidas a partir das análises fotométrica e espectroscópica em raios-X enquanto que a massa estelar é obtida pela análise fotométrica das galáxias. Esta análise foi aplicada ao aglomerado Abell 496 observado pelo satélite XMM-Newton. A massa contida nas galáxias foi estimada a partir da função de luminosidade obtida por Durret et al. (2002). Para determinar as massas dinâmica e do gás nos precisamos determinar os perfis radiais de densidade e temperatura. Nós apresentaremos aqui estes resultados e suas implicações na eficiência da formação estelar em Abell 496.

  16. Spongiacidin C, a pyrrole alkaloid from the marine sponge Stylissa massa, functions as a USP7 inhibitor.

    PubMed

    Yamaguchi, Michitaka; Miyazaki, Mitsue; Kodrasov, Matthew P; Rotinsulu, Henki; Losung, Fitje; Mangindaan, Remy E P; de Voogd, Nicole J; Yokosawa, Hideyoshi; Nicholson, Benjamin; Tsukamoto, Sachiko

    2013-07-01

    USP7, a deubiquitylating enzyme hydrolyzing the isopeptide bond at the C-terminus of ubiquitin, is an emerging cancer target. We isolated spongiacidin C from the marine sponge Stylissa massa as the first USP7 inhibitor from a natural source. This compound inhibited USP7 most strongly with an IC50 of 3.8 μM among several USP family members tested. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Impact of agricultural practices on groundwater quality in intensive irrigated area of Chtouka-Massa, Morocco.

    PubMed

    Malki, Mouna; Bouchaou, Lhoussaine; Hirich, Abdelaziz; Ait Brahim, Yassine; Choukr-Allah, Redouane

    2017-01-01

    The Plio-Quaternary aquifer of Chtouka is located in Southwestern of Morocco. The intensive agricultural activity in Chtouka basin requires the mobilization of 94% of fresh water resources for irrigation. This overexploitation, along with the succession of drought years, sea water intrusion and various sources of pollution, affected the quality and availability of groundwater resources. Several sampling campaigns were carried out in different sites of the study area in order to investigate the spatial variation of groundwater quality. The temporal evolution of groundwater level shows that the water table was subjected to a gradual decline during the last decade, indicating an intensive exploitation mainly in irrigated areas. In the Southern part around Belfaa and the irrigated area along Massa River, nitrate concentrations exceed 50mg/L, which is the threshold set by the World Health Organization, while in the northern part around Biougra and Ait Amira, the nitrate concentration is mostly below 50mg/L indicating a relative good groundwater quality. This finding can be explained by the improvement of agricultural practices, particularly the conversion of flood and sprinkler irrigation to drip irrigation (80% of the total irrigated area) in most of the developed farms in this part of the study area. Moreover, the exploitation of groundwater from the deep aquifer, due to the increasing water demand in the region, can also explain the low chemical concentrations since the deep aquifer is not affected by anthropogenic pollutants or marine intrusion. Stable isotopes ((18)O and (2)H) highlight the different origins of groundwater, indicating the complexity of the aquifer system path flows, which is attributable to the intensive exploitation and irrigation water return. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Psychosocial factors and metabolic parameters: is there any association in elderly people? The Massa Lombarda Project

    PubMed Central

    Bove, Marilisa; Carnevali, Lucio; Cicero, Arrigo FG; Grandi, Elisa; Gaddoni, Morena; Noera, Giorgio; Gaddi, Antonio V

    2010-01-01

    Objective Several Studies claim that psychophysical stress and depression contribute significantly to cardiovascular disease (CVD) development. The aim of our research is to discover and analyse a possible relationship between two psychosocial disorders (Depression and Perceived Mental Stress) and traditional cardiovascular risk markers. Methods We selected 106 subjects (M:58, F:48), mean age 79,5 ± 3,8 years old, from The Massa Lombarda Project, an epidemiological study including 7000 north Italian adult subjects. We carried out anamnesis, clinical and blood tests. Then we administered the Perceived Stress Questionnaire (PSQ range-score 0-1) and the Self Rating Depression Scale (SRDS range score 50-70 Z), as validated instruments for depression and stress evaluation, which focus on the individual's subjective perception and emotional response. Statistical descriptive and inferential analysis of data collected were performed. Results The Multiple linear regression analysis showed a negative correlation between PSQ Index score and Uric Acid, LDL-C, BMI, Systolic and Diastolic Blood Pressure values, a positive and statistically significant correlation between PSQ Index score and Triglycerides(P<0.05). We found an inverse relationship between Zung SRDS score and LDL-C, Uric Acid, Glucose, Waist Circumference values, this correlation was significant only for Uric Acid (P<0.01); besides a positive and significant correlation between Zung SRDS and Triglycerides (P<0.05) was observed. Conclusion We suppose that psycho-emotional stress and depression disorder, often diagnosed in elderly people, may influence different metabolic parameters (triglycerides, Uric Acid, BMI) that are involved in the complex process of Metabolic Syndrome. PMID:20635238

  19. Dust deposits in Souss?Massa basin, South-West of Morocco: granulometrical, mineralogical and geochemical characterisation

    NASA Astrophysics Data System (ADS)

    Khiri, F.; Ezaidi, A.; Kabbachi, K.

    2004-08-01

    Samples of dust deposits were periodically collected from July 1, 1997 to January 30, 1999, at Souss-Massa basin, in the South of Morocco. Granulometrical, geochemical and mineralogical characterisations show that quartz, calcite and feldspars dominate the mineral contents of the dust deposit with a minor clay fraction. It indicates the mineralogical composition of dust collected in peri-Saharan regions. The material collected in the summer period is dominated by local dust against a mixture of local and proximal dusts in the winter period.

  20. Unusual circulation patterns of the Rias Baixas induced by Minho freshwater intrusion (NW of the Iberian Peninsula).

    PubMed

    Sousa, Magda Catarina; Mendes, Renato; Alvarez, Ines; Vaz, Nuno; Gomez-Gesteira, Moncho; Dias, João Miguel

    2014-01-01

    The Minho River, situated 30 km south of the Rias Baixas, is the most important freshwater source flowing into the Western Galician coast (NW of the Iberian Peninsula). The buoyancy generated by the Minho estuarine plume can reverse the normal circulation pattern inside the Rias Baixas affecting the exchange between the Rias and the ocean, changing the input of nutrients. Nevertheless, this inversion of the circulation patterns is not a well-monitored phenomenon. The only published results based on in situ data related to the presence of the Minho River plume inside the Rias de Vigo and Pontevedra correspond to an event measured on spring 1998. In this case unexpectedly higher inflow surface current velocities were found at the Ria de Pontevedra, located further away from Minho River. Thus, the main aim of this study is to research the main factors inducing this unusual pattern on the circulation of the Rias de Vigo and Pontevedra. A numerical model implementation of MOHID previously developed, calibrated, and validated for this coastal area was used. Several scenarios were performed in order to explain the individual effect of the Minho River, rivers discharging into each Rias, and estuarine morphology changes. According to the model results, the Minho River discharge is a key factor in the establishment of the negative circulation, while small rivers inside the Rias slightly attenuate this circulation. The negative circulation was stronger in Ria de Pontevedra independently of the distance of this coastal system from the Minho River mouth, showing that morphologic estuarine features are the main factor justifying the different local circulation patterns.

  1. Unusual Circulation Patterns of the Rias Baixas Induced by Minho Freshwater Intrusion (NW of the Iberian Peninsula)

    PubMed Central

    Sousa, Magda Catarina; Mendes, Renato; Alvarez, Ines; Vaz, Nuno; Gomez-Gesteira, Moncho; Dias, João Miguel

    2014-01-01

    The Minho River, situated 30 km south of the Rias Baixas, is the most important freshwater source flowing into the Western Galician coast (NW of the Iberian Peninsula). The buoyancy generated by the Minho estuarine plume can reverse the normal circulation pattern inside the Rias Baixas affecting the exchange between the Rias and the ocean, changing the input of nutrients. Nevertheless, this inversion of the circulation patterns is not a well-monitored phenomenon. The only published results based on in situ data related to the presence of the Minho River plume inside the Rias de Vigo and Pontevedra correspond to an event measured on spring 1998. In this case unexpectedly higher inflow surface current velocities were found at the Ria de Pontevedra, located further away from Minho River. Thus, the main aim of this study is to research the main factors inducing this unusual pattern on the circulation of the Rias de Vigo and Pontevedra. A numerical model implementation of MOHID previously developed, calibrated, and validated for this coastal area was used. Several scenarios were performed in order to explain the individual effect of the Minho River, rivers discharging into each Rias, and estuarine morphology changes. According to the model results, the Minho River discharge is a key factor in the establishment of the negative circulation, while small rivers inside the Rias slightly attenuate this circulation. The negative circulation was stronger in Ria de Pontevedra independently of the distance of this coastal system from the Minho River mouth, showing that morphologic estuarine features are the main factor justifying the different local circulation patterns. PMID:25402444

  2. Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

    DTIC Science & Technology

    2017-05-05

    Materials Science Materials Science and Technology Division L. maSSa Hunter College, City University of New York New York, New York i REPORT...are characterized by many different geometries, which potentially can be optimized with respect to specific materials design criteria, i.e., molecular

  3. Uranium in vegetable foodstuffs: should residents near the Cunha Baixa uranium mine site (Central Northern Portugal) be concerned?

    PubMed

    Neves, M O; Abreu, M M; Figueiredo, V

    2012-04-01

    Large uranium accumulations in vegetable foodstuffs may present risks of human health if they are consumed. The objective of this study was to evaluate the uranium concentrations in different vegetable foodstuffs and grown in agricultural soils, which are then consumed by the residents of the village of Cunha Baixa (Portugal),--located in an former uranium mining area. This study was conducted to address concerns expressed by the local farmers as well as to provide data for uranium-related health risk assessments for the area. Soils, irrigation water and edible tissues of lettuce, potato, green bean, carrot, cabbage, apple and maize (Latuca sativa L., Solanum tuberosum L., Phaseolus vulgaris L., Daucus carota L., Brassica oleracea L., Malus domestica Borkh, Zea mays L., respectively) were sampled and uranium determined. High uranium concentrations were found in some soils (U(total) > 50 mg/kg), in irrigation waters (218 to 1,035 μg/l) and in some vegetable foodstuffs (up to 234, 110, 30, 26, 22, 16 and 1.6 μg/kg fresh weight for lettuce, potato with peel, green bean pods, cabbage, corn, carrot and apple, respectively). However, the results of the toxicity hazard analysis were reassuring the estimated level of uranium exposure through the ingestion of these vegetable foodstuffs was low, suggesting no chemical health risk (hazard quotient <1) to this uranium exposure pathway for a local residents during their lifetime, even for the most sensitive part of the population (child).

  4. On ambiente de binárias de pequena massa em formação: o caso do glóbulo cometário CG30 e IRAS08076-3556

    NASA Astrophysics Data System (ADS)

    Hickel, G. R.; Vilas-Boas, J. W. S.

    2003-08-01

    Neste trabalho, combinamos observações de polarização linear no óptico (banda R), dados no infravermelho distante (IRAS) e observações de transições moleculares em radiofreqüências (CO e espécies isotópicas, HCN e HCO+) para analisar o glóbulo cometário (GC) CG30 (na região da IRAS Vela Shell), que apresenta objetos Herbig-Haro e ejeções de matéria, além de uma fonte pontual IRAS em seu interior. Os objetivos deste estudo são: determinar a eficiência de formação estelar nos glóbulos cometários, através da relação entre a massa total do GC e da massa das estrelas em formação; determinar como o campo magnético influencia na formação de estrelas no interior destes objetos; e analisar as modificações que ejeções de matéria de estrelas em formação causam no gás e no campo magnético dos GCs. Combinando nossos dados com trabalhos já publicados, mostramos que CG30 tem uma eficiência de formação estelar em torno de 3%; que o campo magnético é importante na manutenção da estrutura global do GC e demonstra sinais de torção e compressão; e que a ejeção bipolar de matéria das estrelas do par formam uma ejeção quadripolar, a qual influencia na densidade e temperatura do gás e no grau de polarização dos grãos de poeira associados ao gás do GC.

  5. Application of multiple isotopic and geochemical tracers for investigation of recharge, salinization, and residence time of water in the Souss-Massa aquifer, southwest of Morocco

    USGS Publications Warehouse

    Bouchaou, L.; Michelot, J.L.; Vengosh, A.; Hsissou, Y.; Qurtobi, M.; Gaye, C.B.; Bullen, T.D.; Zuppi, G.M.

    2008-01-01

    Groundwater and surface water in Souss-Massa basin in the west-southern part of Morocco is characterized by a large variation in salinity, up to levels of 37 g L-1. The high salinity coupled with groundwater level decline pose serious problems for current irrigation and domestic water supplies as well as future exploitation. A combined hydrogeologic and isotopic investigation using several chemical and isotopic tracers such as Br/Cl, ??18O, ??2H, 3H, 87Sr/86Sr, ??11B, and 14C was carried out in order to determine the sources of water recharge to the aquifer, the origin of salinity, and the residence time of water. Stable isotope, 3H and 14C data indicate that the high Atlas mountains in the northern margin of the Souss-Massa basin with high rainfall and low ??18O and ??2H values (-6 to -8??? and -36 to -50???) is currently constitute the major source of recharge to the Souss-Massa shallow aquifer, particularly along the eastern part of the basin. Localized stable isotope enrichments offset meteoric isotopic signature and are associated with high nitrate concentrations, which infer water recycling via water agricultural return flows. The 3H and 14C data suggest that the residence time of water in the western part of the basin is in the order of several thousands of years; hence old water is mined, particularly in the coastal areas. The multiple isotope analyses and chemical tracing of groundwater from the basin reveal that seawater intrusion is just one of multiple salinity sources that affect the quality of groundwater in the Souss-Massa aquifer. We differentiate between modern seawater intrusion, salinization by remnants of seawater entrapped in the middle Souss plains, recharge of nitrate-rich agricultural return flow, and dissolution of evaporate rocks (gypsum and halite minerals) along the outcrops of the high Atlas mountains. The data generated in this study provide the framework for a comprehensive management plan in which water exploitation should shift

  6. Participatory Planning for the improvement of water management in uncertain conditions: Case study of the Souss-Massa basin in Morocco

    NASA Astrophysics Data System (ADS)

    Imani, Yasmina; Lahlou, Ouiam; Slimani, Imane; Joyce, Brian

    2016-04-01

    Due to its geographical location and to the natural features of its climate, Morocco is known as a drought prone and water scarce country. However, the country now faces, in the current context of Climate Change, an increasing and alarming water scarcity due to the combined effects of a strong decline of precipitations and a growing pressure on water resources induced by the economic development and demographic growth. Aware of this pressing issue, Morocco implemented a national water strategy based on the decentralization of water management at the river basin level and the establishment of Integrated Water Resources Management master plans for each basin. Unfortunately, these plans often underestimate the impact of uncertainty and this may lead to inefficient and unsustainable water management strategies. In this context, the aim of this study is to develop an innovative approach for robust decision making in uncertain conditions by coupling the WEAP (Water Evaluation and Planning System) model and the "XLRM" robust decision making framework to support the evaluation of management options and promote long-term sustainable integrated water management strategies at the basin level. The Souss-Massa basin, located in the south-western part of the country was retained as a case study because of its strategic importance but also because it now faces, as a consequence of the irrational use of water resources during the last decades significant water resources management challenges mainly due to the overexploitation of ground water resources, the increased of water demand due to the irrigation development, the urban and industrial growth and the expansion of tourism. Thus, in this study, a three step methodology was developed. First, the WEAP model were developed and calibrated for the Souss-Massa basin. In a second step, a XLRM participatory workshop gathering the basin main stakeholders were organized in order to identify the EXogenous factors (key uncertainties

  7. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    2010-07-01

    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 the 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.

  8. Molecular breeding

    USDA-ARS?s Scientific Manuscript database

    Use of molecular and genomic tools to assist selection of parents or progeny has become an integral part of modern cotton breeding. In this chapter, the basic components of molecular cotton breeding are described. These components include: molecular marker development, genetic and physical map const...

  9. Assessment of the health status in the Massa Lombarda cohort: a preliminary description of the program evaluating cardio-cerebro-vascular disease risk factors and quality of life in an elderly population.

    PubMed

    Nascetti, S; Linarello, S; Scurti, M; Grandi, E; Gaddoni, M; Noera, G; Gaddi, A

    2004-01-01

    The Massa Lombarda program (MLP) is the first step of a European multi-center program, promoted and coordinated from Bologna University's Academic Spin off Health Research and Development, which attempts to manage advanced sanitary research in general population. The instant individual definition (IID) study is the first phase of the program concerning the study of risk factors (RF) and early diagnosis of coronary heart disease (CHD), through a new diagnostic technology called myocardial perfusion scoring system (MPS). The study consists of a longitudinal observational epidemiological investigation of adult population (above 25 years of age) resident in Massa Lombarda (Ravenna), with the survey of social and biological parameters. The elderly part of the population (1000 subjects above 75 years) was submitted to a more complex analysis, as part of the study on health status in European aging populations, aimed at revealing the determinants influencing the healthy aging, and at identifying their impact on mortality,cardiovascular and respiratory morbidity, disability and decline of quality of life. Laboratory analyses were aimed at identifying the following factors: (i) Genetic markers related to pro and anti-inflammatory cytokine- codifying genes. (ii) Oxidative stress-involved molecules,and inflammation-involved genes, and more in general genes involved in the brittleness(iii) (ApoE). Appraising the degree of interaction with non-genetic factors, like measurable immunological markers in the peripheral blood, markers of reactions to oxidative stress,evaluation of metabolic parameters. Moreover, old population is expected to answer the questionnaires for evaluation of the dietary habits, physical activity, self-sufficiency,cognitive ability, motor coordination, perceived stress and social relationships.

  10. Molecular Plasmonics.

    PubMed

    Wilson, Andrew J; Willets, Katherine A

    2016-06-12

    In this review, we survey recent advances in the field of molecular plasmonics beyond the traditional sensing modality. Molecular plasmonics is explored in the context of the complex interaction between plasmon resonances and molecules and the ability of molecules to support plasmons self-consistently. First, spectroscopic changes induced by the interaction between molecular and plasmonic resonances are discussed, followed by examples of how tuning molecular properties leads to active molecular plasmonic systems. Next, the role of the position and polarizability of a molecular adsorbate on surface-enhanced Raman scattering signals is examined experimentally and theoretically. Finally, we introduce recent research focused on using molecules as plasmonic materials. Each of these examples is intended to highlight the role of molecules as integral components in coupled molecule-plasmon systems, as well as to show the diversity of applications in molecular plasmonics.

  11. Determinação do extremo de baixa luminosidade da função de luminosidade através de simulações de Monte Carlo

    NASA Astrophysics Data System (ADS)

    Campos, P. E.; Mendes de Oliveira, C.

    2003-08-01

    Neste trabalho apresentamos os principais resultados do estudo da população de galáxias anãs de baixo brilho superficial dos grupos compactos HCG44 e HCG68. A inclinação do extremo de baixa luminosidade a da função de luminosidade desses grupos foi estimado através de simulações de Monte Carlo. O método consistiu em simular galáxias anãs de baixo brilho superficial em imagens reais seguindo uma distribuição de magnitudes dada uma função de Schechter. Foram testados vários modelos com diferentes valores para os parâmetros M* e a da função de Schechter, e para cada um dos modelos foi repetido o mesmo processo de recuperação, seleção e análise usados com as galáxias anãs dos grupos. Os resultados de cada modelo foram então comparados com o observado nos grupos. Nossos resultados indicam que a distribuição de magnitudes (para magnitudes absolutas até MR»-12) observadas nos grupos são compatíveis com uma função de luminosidade de Schechter dada por um M* = -16 e um a entre -1.0 e -1.4, e portanto de acordo com a tendência observada de uma inclinação do extremo de baixa luminosidade da função de luminosidade de grupos mais plana (~1.2, Trentham & Tully 2002, MNRAS, 335, 712) que esperado pelo modelo hierárquico de formação de estruturas CDM (Cold Dark Matter - Matéria Escura Fria).

  12. Molecular pharmacognosy.

    PubMed

    Huang, LuQi; Xiao, PeiGen; Guo, LanPing; Gao, WenYuan

    2010-06-01

    This article analyzes the background and significance of molecular pharmacognosy, including the molecular identification of medicinal raw materials, phylogenetic evolution of medicinal plants and animals, evaluation and preservation of germplasm resources for medicinal plants and animals, etiology of endangerment and protection of endangered medicinal plants and animals, biosynthesis and bioregulation of active components in medicinal plants, and characteristics and the molecular bases of top-geoherbs.

  13. 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

  14. Molecular motors

    NASA Astrophysics Data System (ADS)

    Allemand, Jean François Desbiolles, Pierre

    2015-10-01

    How do we move? More precisely, what are the molecular mechanisms that can explain that our muscles, made of very small components can move at a osopic scale? To answer these questions we must introduce molecular motors. Those motors are proteins, or small protein assemblies that, in our cells, transform chemical energy into mechanical work. Then, like we could do for a oscopic motor, used in a car or in a fan, we are going to study the basic behavior of these molecular machines, present what are their energy sources, calculate their power, their yield. If molecular motors are crucial for our oscopic movements, we are going to see that they are also essential to cellular transport and that considering the activity of some enzymes as molecular motors bring some interesting new insights on their activity.

  15. 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

  16. Molecular Haeckel.

    PubMed

    Elinson, Richard P; Kezmoh, Lorren

    2010-07-01

    More than a century ago, Ernst Haeckel created embryo drawings to illustrate the morphological similarity of vertebrate early embryos. These drawings have been both widely presented and frequently criticized. At the same time that the idea of morphological similarity was recently attacked, there has been a growing realization of molecular similarities in the development of tissues and organs. We have surveyed genes expressed in vertebrate embryos, and we have used them to construct drawings that we call Molecular Haeckels. The Molecular Haeckels emphasize that, based on gene expression, there is a greater similarity among vertebrate embryos than even Haeckel might have imagined. (c) 2010 Wiley-Liss, Inc.

  17. Transfer of U, Al and Mn in the water-soil-plant (Solanum tuberosum L.) system near a former uranium mining area (Cunha Baixa, Portugal) and implications to human health.

    PubMed

    Neves, M O; Figueiredo, V R; Abreu, M M

    2012-02-01

    Knowledge about metals in crops, grown in contaminated soils around mine sites, is limited and concerns about exposure to hazardous elements through the consumption of contaminated foodstuff, are high. In this study a field experiment was carried out in two agricultural soils located near a former uranium mine area (Cunha Baixa, Portugal). The purpose of the study was to assess the effect of irrigation water quality on soil-potato (Solanum tuberosum L.) crop system and to evaluate if the consumption of the crop represents health risk to the local villagers. The soils were divided in two plots: one irrigated with contaminated water (U: 1.03-1.04mg/L; Al: 7.5-8.00mg/L; Mn: 4.52mg/L) and the other with uncontaminated water (U: 14-10μg/L; Al: 17-23μg/L; Mn: 2.4-5.7μg/L). After irrigation and potato growth, only soil characteristics, as salinity and total U and Mn concentrations were significantly different from those measured at the beginning of the experiment. Within the potato plants, elements were mostly translocated and concentrated in the aerial part: stems and leaves (U: 73-87%; Al: 85-96%; Mn: 85-94%), which minimize the risk of contamination of the edible tissue. In potato tubers, the highest average concentrations (121-590μg U/kg; 25-64mg Al/kg; 12-13mg Mn/kg dry weight) were registered at soil plots irrigated with contaminated water. Uranium and Al were mostly concentrated in the potato peel (88-96 and 76-85%, respectively), and Mn (67-78%) in the pulp, which reinforces the importance of removing peel to minimize human exposure. The risk analysis calculated for non-cancer health effects (hazard quotient), related only to the exposure through the consumption of this basic foodstuff, revealed safety for Cunha Baixa village residents (adults and children) even when potato crop was grown on U enriched soils and irrigated with contaminated water. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Molecular printing

    PubMed Central

    Braunschweig, Adam B.; Huo, Fengwei; Mirkin, Chad A.

    2014-01-01

    Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography and soft lithography. Both are characterized by material and substrate flexibility, but dip-pen nanolithography has unlimited pattern design whereas soft lithography has limited pattern flexibility but is low in cost and has high throughput. Advances in DPN tip arrays and inking methods have increased the throughput and enabled applications such as multiplexed arrays. A new approach to molecular printing, polymer-pen lithography, achieves low-cost, high-throughput and pattern flexibility. This Perspective discusses the evolution and future directions of molecular printing. PMID:21378889

  19. Molecular Astrophysics

    NASA Astrophysics Data System (ADS)

    Hartquist, T. W.

    2005-07-01

    Part I. Molecular Clouds and the Distribution of Molecules in the Milky Way and Other Galaxies: 1. Molecular clouds in the Milky Way P. Friberg and A. Hjalmarson; 2. Molecules in galaxies L. Blitz; Part II. Diffuse Molecular Clouds: 3. Diffuse cloud chemistry E. F. Van Dishoeck; 4. Observations of velocity and density structure in diffuse clouds W. D. Langer; 5. Shock chemistry in diffuse clouds T. W. Hartquist, D. R. Flower and G. Pineau des Forets; Part III. Quiescent Dense Clouds: 6. Chemical modelling of quiescent dense interstellar clouds T. J. Millar; 7. Interstellar grain chemistry V. Buch; 8. Large molecules and small grains in astrophysics S. H. Lepp; Part IV. Studies of Molecular Processes: 9. Molecular photoabsorption processes K. P. Kirby; 10. Interstellar ion chemistry: laboratory studies D. Smith, N. G. Adams and E. E. Ferguson; 11. Theoretical considerations on some collisional processes D. R. Bates; 12. Collisional excitation processes E. Roueff; 13. Neutral reactions at Low and High Temperatures M. M. Graff; Part V. Atomic Species in Dense Clouds: 14. Observations of atomic species in dense clouds G. J. Melnick; 15. Ultraviolet radiation in molecular clouds W. G. Roberge; 16. Cosmic ray induced photodissociation and photoionization of interstellar molecules R. Gredel; 17. Chemistry in the molecular cloud Barnard 5 S. B. Charnley and D. A. Williams; 18. Molecular cloud structure, motions, and evolution P. C. Myers; Part VI. H in Regions of Massive Star Formation: 19. Infrared observations of line emission from molecular hydrogen T. R. Geballe; 20. Shocks in dense molecular clouds D. F. Chernoff and C. F. McKee; 21. Dissociative shocks D. A. Neufeld; 22. Infrared molecular hydrogen emission from interstellar photodissociation regions A. Sternberg; Part VII. Molecules Near Stars and in Stellar Ejecta: 23. Masers J. M. Moran; 24. Chemistry in the circumstellar envelopes around mass-losing red giants M. Jura; 25. Atoms and molecules in supernova 1987a R

  20. [Molecular imaging].

    PubMed

    Turetschek, K; Wunderbaldinger, P

    2002-01-01

    The disclosure of the human genoma, the progress in understanding of diseases on molecular and cellular levels, the discovery of new disease-specific targets, and the development of new medications will revolutionize our understanding of the etiology and the treatment of many disease entities. Radiologists are faced with a paradigm shift from unspecific to specific molecular imaging techniques as well as with enormous speed in the development of new methods and should be enrolled actively in this field of medicine.

  1. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  2. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  3. Molecular gastronomy

    NASA Astrophysics Data System (ADS)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  4. Molecular methods

    SciTech Connect

    1993-12-31

    Chapter 5, describes some of the most important molecular methods used in the study of chromosome structure and function. The methods discussed include fragmentation of DNA, cloning, flow cytometry and chromosome sorting, is situ hybridization, polymerase chain reaction (PCR), and yeast artificial chromosomes (YACs). 18 refs., 3 figs., 1 tab.

  5. Herbal composition Gambigyeongsinhwan (4) from Curcuma longa, Alnus japonica, and Massa Medicata Fermentata inhibits lipid accumulation in 3T3-L1 cells and regulates obesity in Otsuka Long-Evans Tokushima Fatty rats.

    PubMed

    Roh, Jong Sung; Lee, Hyunghee; Woo, Sangee; Yoon, Miso; Kim, Jeongjun; Park, Sun Dong; Shin, Soon Shik; Yoon, Michung

    2015-08-02

    Adipocyte lipid accumulation due to impaired fatty acid oxidation causes adipocyte hypertrophy and adipose tissue increment, leading to obesity. The aim of this study was to determine the antiobesity effects of the herbal composition Gambigyeongsinhwan (4) (GGH(4)) composed of Curcuma longa L. (Zingiberaceae), Alnus japonica (Thunb.) Steud. (Betulaceae), and the fermented traditional Korean medicine Massa Medicata Fermentata. The effects of GGH(4) and the individual components on lipid accumulation in 3T3-L1 adipocytes and body weight gain in Otsuka Long-Evans Tokushima Fatty (OLETF) rats were examined using Oil red O staining, hematoxylin and eosin staining, quantitative real-time PCR, and peroxisome proliferator-activated receptor α (PPARα) transactivation assay. GGH(4), individual components, and an active principle of Curcuma longa curcumin inhibited lipid accumulation and mRNA levels of adipocyte-specific genes (PPARγ, aP2, and C/EBPα) in 3T3-L1 adipocytes compared with control cells. Treatment with GGH(4), the individual components or curcmumin increased mRNA levels of mitochondrial (CPT-1, MCAD, and VLCAD) and peroxisomal (ACOX and thiolase) PPARα target genes. GGH(4) and the individual components also increased PPARα reporter gene expression compared with control cells. These effects were most prominent in GGH(4)-treated cells. However, the PPARα antagonist GW6471 reversed the inhibitory effects of GGH(4) on adipogenesis. An in vivo study showed that GGH(4) decreased body weight gain, adipose tissue mass, and visceral adipocyte size with increasing mRNA levels of adipose tissue PPARα target genes in OLETF rats. These results demonstrate that GGH(4) has an antiobesity effects through the inhibition of adipocyte lipid accumulation, and this process may be mediated in part through adipose PPARα activation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  6. Molecular Rotors

    DTIC Science & Technology

    2006-10-31

    Molecular Dipolar Rotors on Insulating Surfaces," Salamanca , Spain. Trends in Nanotechnology Conference. September 5-9, 2003 [86] Laura I. Clarke, Mary Beth...Horansky at the Trends in Nanotechnology Conference, Salamanca , Spain (September 5-9, 2003). [145] Michl, J. “Unusual Molecules: Artificial Surface...temperature and frequency for difluorophenylene rotor crystal. Figure JP6. Monte Carlo results for the local potential asymmetry at

  7. Molecular Imprinting

    NASA Astrophysics Data System (ADS)

    Dufaud, V.; Bonneviot, L.

    Our senses of smell and taste are able to recognise molecules selectively, to the point where they can even discriminate between different chiral states. This property, called molecular recognition, is essential to all forms of life [1]. It is based on the principle of a specific interaction between a receptor or host and a target molecule, which will be identified among a multitude of others, then selectively adsorbed. If the host is endowed with reactive functions, the attached molecule may be transported or transformed. Enzymes are the archetypal host molecules exploiting the idea of molecular recognition. Their complexation sites comprise a hydrophobic pocket with definite shape within which amino acid residues are located in a precisely defined way. The combined effect of these different characteristics underlies not only the affinity for some specific substrate, but also the transformation of this substrate into the desired product [2]. In fact, the phenomena actually brought into play are much more involved, being made up of an ensemble of physicochemical events that act together in a cooperative way, either simultaneously or sequentially, and in which the molecular processes are difficult to follow in detail.

  8. 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

  9. Molecular Mechanics

    PubMed Central

    Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

  10. Molecular paleontology.

    PubMed

    Marota, I; Rollo, F

    2002-01-01

    Molecular paleontology, i.e., the recovery of DNA from ancient human, animal, and plant remains is an innovative research field that has received progressively more attention from the scientific community since the 1980s. In the last decade, the field was punctuated by claims which aroused great interest but eventually turned out to be fakes--the most famous being the sequence of dinosaur DNA later shown to be of human origin. At present, the discipline is characterized by some certainties and many doubts. We know, for example, that we have reasonable chances to recover authentic DNA from a mammoth carcass, while our chances are negligible (or nonexistent) in the case of a dynastic mummy from Egypt. On the other hand, though we are developing convincing models of DNA decay in bone, we are not yet able to predict whether a certain paleontological or archeological site will yield material amenable to DNA analysis. This article reviews some of the most important and promising investigations using molecular paleontology approaches, such as studies on the conservation of DNA in human bone, the quest for ancient DNA in permafrost-frozen fauna, the Tyrolean iceman, and the Neandertals.

  11. Molecular spintronics.

    PubMed

    Sanvito, Stefano

    2011-06-01

    The electron spin made its debut in the device world only two decades ago but today our ability of detecting the spin state of a moving electron underpins the entire magnetic data storage industry. This technological revolution has been driven by a constant improvement in our understanding on how spins can be injected, manipulated and detected in the solid state, a field which is collectively named Spintronics. Recently a number of pioneering experiments and theoretical works suggest that organic materials can offer similar and perhaps superior performances in making spin-devices than the more conventional inorganic metals and semiconductors. Furthermore they can pave the way for radically new device concepts. This is Molecular Spintronics, a blossoming research area aimed at exploring how the unique properties of the organic world can marry the requirements of spin-devices. Importantly, after a first phase, where most of the research was focussed on exporting the concepts of inorganic spintronics to organic materials, the field has moved to a more mature age, where the exploitation of the unique properties of molecules has begun to emerge. Molecular spintronics now collects a diverse and interdisciplinary community ranging from device physicists to synthetic chemists to surface scientists. In this critical review, I will survey this fascinating, rapidly evolving, field with a particular eye on new directions and opportunities. The main differences and challenges with respect to standard spintronics will be discussed and so will be the potential cross-fertilization with other fields (177 references).

  12. Molecular Plasmonics.

    PubMed

    Lauchner, Adam; Schlather, Andrea E; Manjavacas, Alejandro; Cui, Yao; McClain, Michael J; Stec, Grant J; García de Abajo, F Javier; Nordlander, Peter; Halas, Naomi J

    2015-09-09

    Graphene supports surface plasmons that have been observed to be both electrically and geometrically tunable in the mid- to far-infrared spectral regions. In particular, it has been demonstrated that graphene plasmons can be tuned across a wide spectral range spanning from the mid-infrared to the terahertz. The identification of a general class of plasmonic excitations in systems containing only a few dozen atoms permits us to extend this versatility into the visible and ultraviolet. As appealing as this extension might be for active nanoscale manipulation of visible light, its realization constitutes a formidable technical challenge. We experimentally demonstrate the existence of molecular plasmon resonances in the visible for ionized polycyclic aromatic hydrocarbons (PAHs), which we reversibly switch by adding, then removing, a single electron from the molecule. The charged PAHs display intense absorption in the visible regime with electrical and geometrical tunability analogous to the plasmonic resonances of much larger nanographene systems. Finally, we also use the switchable molecular plasmon in anthracene to demonstrate a proof-of-concept low-voltage electrochromic device.

  13. Molecular Fountain

    NASA Astrophysics Data System (ADS)

    Cheng, Cunfeng; van der Poel, Aernout P. P.; Jansen, Paul; Quintero-Pérez, Marina; Wall, Thomas E.; Ubachs, Wim; Bethlem, Hendrick L.

    2016-12-01

    The resolution of any spectroscopic or interferometric experiment is ultimately limited by the total time a particle is interrogated. Here we demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiments, ammonia molecules are decelerated and cooled using electric fields, launched upwards with a velocity between 1.4 and 1.9 m/s and observed as they fall back under gravity. A combination of quadrupole lenses and bunching elements is used to shape the beam such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of <10 μ K and a longitudinal temperature of <1 μ K ) when the molecules are in free fall, while being strongly focused at the detection region. The molecules are in free fall for up to 266 ms, making it possible, in principle, to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theories.

  14. Determinação da massa de júpiter a partir das órbitas de seus satélites: um experimento didático

    NASA Astrophysics Data System (ADS)

    Schlickmann, M. S.; Saito, R. K.; Becker, D. A.; Rezende, M. F., Jr.; Cid Fernandes, R.

    2003-08-01

    Este trabalho apresenta o roteiro piloto de uma prática observacional em astronomia, junto com os primeiros resultados obtidos nesta fase de implementacão. O projeto, que será executado em duas etapas, visa introduzir noções de Astronomia a alunos do Ensino Médio e iniciantes nos cursos de Física. O experimento consiste em medir as órbitas dos satélites Galileanos e, a partir da análise dos dados coletados, verificar a validade da Lei das órbitas de Kepler, determinando a massa do planeta Júpiter. Em uma primeira etapa, as observações serão feitas utilizando um telescópio Meade LX200 10" e câmera CCD para obter uma seqüência de imagens do planeta, que possibilitará medir o movimento de seus satélites. A segunda etapa terá início a partir do funcionamento do telescópio em modo robótico, com a possibilidade de observações via internet por instituições de ensino. Para o desenvolvimento deste experimento foram inicialmente coletadas várias imagens de Júpiter obtidas com os instrumentos citados acima. Estas imagens serviram como base para confecção dos roteiros para a experiência no nível médio e superior. Os roteiros serão inicialmente apresentados em uma home-page. Nela também se buscará uma contextualização histórica da experiência bem como o estabelecimento de relações com professores e alunos, propostas metodológicas e a disponibilização dos programas computacionais necessários para a utilização "on-line" pelos usuários. O projeto conta com apoio da Fundação VITAE.

  15. Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When

  16. Molecular Biosignatures

    NASA Astrophysics Data System (ADS)

    Summons, Roger E.; Albrecht, Pierre; McDonald, Gene; Moldowan, J. Michael

    2008-03-01

    Life, as we know it, is based on carbon chemistry operating in an aqueous environment. Living organisms process chemicals, make copies of themselves, are autonomous and evolve in concert with the environment. All these characteristics are driven by, and operate through, carbon chemistry. The carbon chemistry of living systems is an exact branch of science and we have detailed knowledge of the basic metabolic and reproductive machinery of living organisms. We can recognise the residual biochemicals long after life has expired and otherwise lost most life-defining features. Carbon chemistry provides a tool for identifying extant and extinct life on Earth and, potentially, throughout the Universe. In recognizing that certain distinctive compounds isolable from living systems had related fossil derivatives, organic geochemists coined the term biological marker compound or biomarker (e.g. Eglinton et al. in Science 145:263-264, 1964) to describe them. In this terminology, biomarkers are metabolites or biochemicals by which we can identify particular kinds of living organisms as well as the molecular fossil derivatives by which we identify defunct counterparts. The terms biomarker and molecular biosignature are synonymous. A defining characteristic of terrestrial life is its metabolic versatility and adaptability and it is reasonable to expect that this is universal. Different physiologies operate for carbon acquisition, the garnering of energy and the storage and processing of information. As well as having a range of metabolisms, organisms build biomass suited to specific physical environments, habitats and their ecological imperatives. This overall ‘metabolic diversity’ manifests itself in an enormous variety of accompanying product molecules (i.e. natural products). The whole field of organic chemistry grew from their study and now provides tools to link metabolism (i.e. physiology) to the occurrence of biomarkers specific to, and diagnostic for, particular kinds

  17. Molecular Spintronics

    NASA Astrophysics Data System (ADS)

    Sanvito, Stefano

    2010-03-01

    In organic molecules and molecular solids the weak spin-orbit and hyperfine interactions result in extremely long spin-lifetimes reaching up to the second mark. However the same are characterized by a generally poor mobility, so that the spin-diffusion lengths are rather short. These peculiar characteristics position organic molecules in a unique space within Spintronics and one should envision applications where the spins are manipulated close to where they are injected [1]. In this contribution I will review the current state of the art of the theory of spin-transport and manipulation in organic molecules. I will start the discussion by presenting a new mechanism, the electrostatic spin crossover effect, for manipulating electrically the magnetic state of a molecules without calling for current-driven spin-transfer torques [2]. This is based on the fact that the different spin states of a molecule Stark-shift differently and it is mostly effective when inversion symmetry is broken. Then I will move to discuss the consequences of such an effect on the transport properties of a molecule presenting two magnetic centers and demonstrate that there exist a critical voltage at which the current becomes temperature-independent [3]. Finally I will present results for spin-transport in Mn12 and demonstrate that the magnetic state of the molecule can be read electrically with a single I-V read-out obtained by using non-magnetic electrodes [4]. [4pt] [1] G. Szulczewski, S. Sanvito and J.M.D. Coey, Nature Materials 8, 693 (2009).[0pt] [2] N. Baadji, M. Piacenza, T. Tugsuz, F. Della Sala, G. Maruccio and S. Sanvito, Nature Materials 8, 813 (2009).[0pt] [3] S.K. Shukla and S. Sanvito, Phys. Rev. B, in press; also at arXiv:0905.1607.[0pt] [4] C.D. Pemmaraju, I. Rungger and S. Sanvito, Phys. Rev. B 80, 104422 (2009).

  18. 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)

  19. 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.

  20. Molecular Outflows: Observed Properties

    NASA Astrophysics Data System (ADS)

    Bally, John; Lane, Adair P.

    Introduction Molecular Outflow Characteristics Recent Developments EHV CO Outflows Luminosity Dependence of Flow Properties and Statistics Optical and Near-IR Observations of Molecular Outflows Outflow Models

  1. On molecular graph comparison.

    PubMed

    Melo, Jenny A; Daza, Edgar

    2011-06-01

    Since the last half of the nineteenth century, molecular graphs have been present in several branches of chemistry. When used for molecular structure representation, they have been compared after mapping the corresponding graphs into mathematical objects. However, direct molecular comparison of molecular graphs is a research field less explored. The goal of this mini-review is to show some distance and similarity coefficients which were proposed to directly compare molecular graphs or which could be useful to do so.

  2. 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.

  3. 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.

  4. Sur l'origine par altération du substratum schisteux de la minéralisation chlorurée des eaux d'une nappe côtière sous climat semi-aride (Chtouka-Massa, Maroc)

    NASA Astrophysics Data System (ADS)

    Krimissa, Samira; Michelot, Jean-Luc; Bouchaou, Lhoussaine; Mudry, Jacques; Hsissou, Youssef

    2004-11-01

    The origin of chloride ions in groundwater from the Chtouka-Massa plain (Morocco) was studied by using chemical and isotopic analyses of water, and petrographic and chemical analyses of rocks. It appears that the schist formation, which forms the basement of the studied aquifer, is the main source of the high Cl - concentrations in groundwater. In these schists, chloride is, for a part, probably contained in biotites, and is released into groundwater through the weathering of these minerals. However, the exceptionally high chloride contents of these schists are difficult to explain if one does not assume that they also contain evaporitic-type minerals. To cite this article: S. Krimissa et al., C. R. Geoscience 336 (2004).

  5. Artificial molecular motors.

    PubMed

    Kassem, Salma; van Leeuwen, Thomas; Lubbe, Anouk S; Wilson, Miriam R; Feringa, Ben L; Leigh, David A

    2017-05-09

    Motor proteins are nature's solution for directing movement at the molecular level. The field of artificial molecular motors takes inspiration from these tiny but powerful machines. Although directional motion on the nanoscale performed by synthetic molecular machines is a relatively new development, significant advances have been made. In this review an overview is given of the principal designs of artificial molecular motors and their modes of operation. Although synthetic molecular motors have also found widespread application as (multistate) switches, we focus on the control of directional movement, both at the molecular scale and at larger magnitudes. We identify some key challenges remaining in the field.

  6. 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...

  7. 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.

  8. Molecular similarity measures.

    PubMed

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2004-01-01

    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 a chemistry space. Although all three concepts molecular similarity, molecular representation, and chemistry 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 is, representations 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.

  9. Workshop on molecular animation.

    PubMed

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

    2010-10-13

    From February 25 to 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.

  10. 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.

  11. 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

  12. Molecular modelling and molecular dynamics of CFTR.

    PubMed

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  13. 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.

  14. 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...

  15. Interstellar molecular clouds.

    PubMed

    Bally, J

    1986-04-11

    The interstellar medium in our galaxy contains matter in a variety of states ranging from hot plasma to cold and dusty molecular gas. The molecular phase consists of giant clouds, which are the largest gravitationally bound objects in the galaxy, the primary reservoir of material for the ongoing birth of new stars, and the medium regulating the evolution of galactic disks.

  16. Molecular biology of development

    SciTech Connect

    Davidson, E.H.; Firtel, R.A.

    1984-01-01

    This book is a compilation of papers presented at a symposium on the molecular biology of development. Topics discussed include: cytoplasmic localizations and pattern formations, gene expression during oogenesis and early development, developmental expression of gene families molecular aspects of plant development and transformation in whole organisms and cells.

  17. 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...

  18. Biological Molecular Machines

    NASA Astrophysics Data System (ADS)

    Kurzyński, Michał

    2007-11-01

    Like small molecules taking part in usual chemical reactions, biological molecular machines perform their functions owing to thermal fluctuations and the only difference consists in more complex and specially organized internal dynamics. It is this dynamics that determines processes of free energy transduction in molecular machines. The case of the actomyosin motor is considered in some detail.

  19. Making molecular machines work.

    PubMed

    Browne, Wesley R; Feringa, Ben L

    2006-10-01

    In this review we chart recent advances in what is at once an old and very new field of endeavour--the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a discussion of design principles used to control linear and rotary motion in such molecular systems, this review will address the advances towards the construction of synthetic machines that can perform useful functions. Approaches taken by several research groups to construct wholly synthetic molecular machines and devices are compared. This will be illustrated with molecular rotors, elevators, valves, transporters, muscles and other motor functions used to develop smart materials. The demonstration of molecular machinery is highlighted through recent examples of systems capable of effecting macroscopic movement through concerted molecular motion. Several approaches to illustrate how molecular motor systems have been used to accomplish work are discussed. We will conclude with prospects for future developments in this exciting field of nanotechnology.

  20. 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

  1. A importância da poeira e ondas de Alfvén na estabilidade de nuvens moleculares anãs

    NASA Astrophysics Data System (ADS)

    Falceta-Gonçalves, D.; de Juli, M. C.; Jatenco-Pereira, V.

    2003-08-01

    Nuvens moleculares anãs se apresentam dinamicamente estáveis, embora possuam massas muito maiores que a massa de Jeans. Por este motivo, a estabilidade destes objetos não pode ser explicada considerando-se apenas a pressão térmica. Campos magnéticos, aproximadamente uniformes e de ~mG, exercem um termo extra de pressão que sustenta a nuvem, mas somente na direção perpendicular às linhas de campo. Para a direção paralela, ondas de Alfvén geradas por turbulências no meio, por exemplo, têm sido utilizadas. Estas, sendo supostamente fracamente amortecidas, poderiam sustentar a nuvem nesta direção. Entretanto, estes meios contêm grandes quantidades de poeira carregada eletricamente. Estes grãos de poeira possuem frequências cíclotron, que podem entrar em ressonância com as ondas. Neste trabalho calculamos os efeitos que o amortecimento cíclotron da poeira teriam na propagação da onda, e consequentemente na estabilidade da nuvem. Considerando um fluxo de ondas, com um dado espectro de frequências, e uma população de grãos de poeira, com distribuição de tamanho observada, foi possível mostrar que o amortecimento é eficiente em uma larga banda de frequências. Neste caso as ondas seriam rapidamente amortecidas gerando pequenas condensações de alta densidade, e não poderiam ser utilizadas para explicar a estabilidade de uma nuvem inteira. Desta forma, rotação e turbulência seriam candidatos alternativos para garantir a estabilidade destes objetos.

  2. Multifunctionality in molecular magnetism.

    PubMed

    Pinkowicz, Dawid; Czarnecki, Bernard; Reczyński, Mateusz; Arczyński, Mirosław

    2015-01-01

    Molecular magnetism draws from the fundamental ideas of structural chemistry and combines them with experimental physics resulting in one of the highest profile current topics, namely molecular materials that exhibit multifunctionality. Recent advances in the design of new generations of multifunctional molecular magnets that retain the functions of the building blocks and exhibit non-trivial magnetic properties at higher temperatures provide promising evidence that they may be useful for the future construction of nanoscale devices. This article is not a complete review but is rather an introduction into thefascinating world of multifunctional solids with magnetism as the leitmotif. We provide a subjective selection and discussion of the most inspiring examples of multifunctional molecular magnets: magnetic sponges, guest-responsive magnets, molecular magnets with ionic conductivity, photomagnets and non-centrosymmetric and chiral magnets.

  3. Molecular imaging in endoscopy

    PubMed Central

    Hoetker, Michael S

    2013-01-01

    Molecular imaging focuses on the molecular signature of cells rather than morphological changes in the tissue. The need for this novel type of imaging arises from the often difficult detection and characterization especially of small and/or premalignant lesions. Molecular imaging specifically visualizes biological properties of a lesion and might thereby be able to close diagnostic gaps, e.g. when differentiating hyperplastic from neoplastic polyps or detecting the margins of intraepithelial neoplastic spread. Additionally, not only the detection and discrimination of lesions could be improved: based on the molecular features identified using molecular imaging, therapy regimens could be adjusted on the day of diagnosis to allow for personalized medicine and optimized care for each individual patient. PMID:24917945

  4. Crystalline molecular flasks.

    PubMed

    Inokuma, Yasuhide; Kawano, Masaki; Fujita, Makoto

    2011-05-01

    A variety of host compounds have been used as molecular-scale reaction vessels, protecting guests from their environment or restricting the space available around them, thus favouring particular reactions. Such molecular 'flasks' can endow guest molecules with reactivities that differ from those in bulk solvents. Here, we extend this concept to crystalline molecular flasks, solid-state crystalline networks with pores within which pseudo-solution-state reactions can take place. As the guest molecules can spontaneously align along the walls and channels of the hosts, structural changes in the substrates can be directly observed by in situ X-ray crystallography during reaction. Recently, this has enabled observation of the molecular structures of transient intermediates and other labile species, in the form of sequential structural snapshots of the chemical transformation. Here, we describe the principles, development and applications of crystalline molecular flasks.

  5. 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.

  6. Molecular gearing systems

    SciTech Connect

    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 that 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.

  7. 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.

  8. 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

  9. Molecular Programming with DNA

    NASA Astrophysics Data System (ADS)

    Winfree, Erik

    2009-05-01

    Information can be stored in molecules and processed by molecular reactions. Molecular information processing is at the heart of all biological systems; might it soon also be at the heart of non-biological synthetic chemical systems? Perhaps yes. One technological approach comes from DNA nanotechnology and DNA computing, where DNA is used as a non-biological informational polymer that can be rationally designed to create a rich class of molecular systems -- for example, DNA molecules that self-assemble precisely, that fold into complex nanoscale objects, that act as mechanical actuators and molecular motors, and that make decisions based on digital and analog logic. I will argue that to fully exploit their design potential, we will need to invent programming languages for specifying the behavior of information-based molecular systems, to create theoretical tools for understanding and analyzing the behavior of molecular programs, to develop compilers that automate the design of molecules with the desired behaviors, and to expand experimental techniques so that the implementation and debugging of complex molecular systems becomes as commonplace and practical as computer programming.

  10. 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

  11. Molecular shape sorting using molecular organic cages.

    PubMed

    Mitra, Tamoghna; Jelfs, Kim E; Schmidtmann, Marc; Ahmed, Adham; Chong, Samantha Y; Adams, Dave J; Cooper, Andrew I

    2013-04-01

    The energy-efficient separation of chemical feedstocks is a major sustainability challenge. Porous extended frameworks such as zeolites or metal-organic frameworks are one potential solution to this problem. Here, we show that organic molecules, rather than frameworks, can separate other organic molecules by size and shape. A molecular organic cage is shown to separate a common aromatic feedstock (mesitylene) from its structural isomer (4-ethyltoluene) with an unprecedented perfect specificity for the latter. This specificity stems from the structure of the intrinsically porous cage molecule, which is itself synthesized from a derivative of mesitylene. In other words, crystalline organic molecules are used to separate other organic molecules. The specificity is defined by the cage structure alone, so this solid-state 'shape sorting' is, uniquely, mirrored for cage molecules in solution. The behaviour can be understood from a combination of atomistic simulations for individual cage molecules and solid-state molecular dynamics simulations.

  12. Potential molecular wires and molecular alligator clips

    NASA Astrophysics Data System (ADS)

    Schumm, Jeffry S.; Pearson, Darren L.; Jones, LeRoy, II; Hara, Ryuichiro; Tour, James M.

    1996-12-01

    The synthesis of oligo(2-ethylphenylene-ethynylene)s, oligo(2-(0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s, and oligo(3-ethylthiophene-ethynylene)s is described via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, octamer and 16-mer of the oligo(3-ethylthiophene-ethynylene)s and oligo(2-0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s. The 16-mers are 100 Å and 128 Å long, respectively. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers versus the random coils of polystyrene. These differences become quite apparent at the octamer stage. The preparation of thiol-protected end groups is described. These may serve as molecular alligator clips for adhesion to gold surfaces. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

  13. [Molecular diagnostics in neuropathology].

    PubMed

    Dietmaier, W; Lorenz, J; Riemenschneider, M J

    2015-03-01

    As in only few other areas of oncology, molecular markers in neurooncology have become an integral part of clinical decision-making. This development is driven by a bustling scientific activity exploring the molecular basis and pathogenesis of human brain tumors. In addition, a high percentage of brain tumor patients are included in clinical studies in which molecular markers are assessed and linked with clinical informativeness. First steps towards more differentiated therapeutic strategies against brain tumors have thus been taken. The implementation in the clinical and diagnostic routine requires a detailed knowledge and a close collaboration between all medical disciplines involved.

  14. Molecularly imprinted membranes.

    PubMed

    Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

    2012-07-19

    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.

  15. 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

  16. Molecular Motors from DNA

    NASA Astrophysics Data System (ADS)

    Turberfield, Andrew

    2013-03-01

    DNA is a wonderful material for nanoscale construction: its self-assembly can be programmed by making use of its information-carrying capability and its hybridization or hydrolysis can be used as to provide energy for synthetic molecular machinery. With DNA it is possible to design and build three-dimensional scaffolds, to attach molecular components to them with sub-nanometre precision-and then to make them move. I shall describe our work on autonomous, biomimetic molecular motors powered by chemical fuels and the use of synthetic molecular machinery to control covalent chemical synthesis. I shall demonstrate bipedal motors whose operation depends on the coordination of the chemomechanical cycles of two separate catalytic centres and burnt bridges motors that can be programmed to navigate networks of tracks. I shall also discuss the use of kinesin motor proteins to power synthetic devices.

  17. [Molecular diagnostics in pathology].

    PubMed

    Stenzinger, A; Penzel, R; Endris, V; Weichert, W

    2013-05-01

    Tissue-based molecular diagnostics is a fast growing diagnostic field, which already complements morphologic classifications in many cases. Pathology based molecular diagnosis is performed almost exclusively on paraffin embedded material and always in conjunction with histopathology. Besides the classic field of tissue based detection of pathogenic organisms such as bacteria, viruses and fungi, molecular diagnostics of tumor tissue is one of the current hot topics in oncology. In this context the detection of predictive molecular biomarkers, such as specific mutations, allows patient stratification for individually tailored treatment strategies and thereby is one of the key components of individualized patient care in oncology. The rapidly growing number of clinically relevant predictive biomarkers together with impressive technical advances, specifically the development of massive parallel sequencing, will modify the care of patients with malignant diseases. Pathology, therefore, has returned in the very center of interdisciplinary patient care.

  18. Are there molecular signatures?

    SciTech Connect

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  19. Atomic & Molecular Interactions

    SciTech Connect

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  20. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  1. Natural Product Molecular Fossils.

    PubMed

    Falk, Heinz; Wolkenstein, Klaus

    2017-01-01

    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.

  2. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  3. The Molecular Model Game

    NASA Astrophysics Data System (ADS)

    Myers, Stephanie A.

    2003-04-01

    The Molecular Model Game is used to review Lewis structures and VSEPR theory. In this game, teams of students compete to complete problems quickly. Variations with other types of problems involving stoichiometry or equilibria are also possible.

  4. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  5. Molecular Machines: Nanoscale gadgets

    NASA Astrophysics Data System (ADS)

    Garcia-Garibay, Miguel A.

    2008-06-01

    Meeting their biological counterparts halfway, artificial molecular machines embedded in liquid crystals, crystalline solids and mesoporous materials are poised to meet the demands of the next generation of functional materials.

  6. THE DARK MOLECULAR GAS

    SciTech Connect

    Wolfire, Mark G.; Hollenbach, David; McKee, Christopher F. E-mail: dhollenbach@seti.or

    2010-06-20

    The mass of molecular gas in an interstellar cloud is often measured using line emission from low rotational levels of CO, which are sensitive to the CO mass, and then scaling to the assumed molecular hydrogen H{sub 2} mass. However, a significant H{sub 2} mass may lie outside the CO region, in the outer regions of the molecular cloud where the gas-phase carbon resides in C or C{sup +}. Here, H{sub 2} self-shields or is shielded by dust from UV photodissociation, whereas CO is photodissociated. This H{sub 2} gas is 'dark' in molecular transitions because of the absence of CO and other trace molecules, and because H{sub 2} emits so weakly at temperatures 10 K molecular component. This component has been indirectly observed through other tracers of mass such as gamma rays produced in cosmic-ray collisions with the gas and far-infrared/submillimeter wavelength dust continuum radiation. In this paper, we theoretically model this dark mass and find that the fraction of the molecular mass in this dark component is remarkably constant ({approx}0.3 for average visual extinction through the cloud A-bar{sub V{approx_equal}}8) and insensitive to the incident ultraviolet radiation field strength, the internal density distribution, and the mass of the molecular cloud as long as A-bar{sub V}, or equivalently, the product of the average hydrogen nucleus column and the metallicity through the cloud, is constant. We also find that the dark mass fraction increases with decreasing A-bar{sub V}, since relatively more molecular H{sub 2} material lies outside the CO region in this case.

  7. Molecular diagnosis of genodermatoses.

    PubMed

    Wessagowit, Vesarat

    2013-01-01

    The progress of molecular genetics helps clinicians to prove or exclude a suspected diagnosis for a vast and yet increasing number of genodermatoses. This leads to precise genetic counselling, prenatal diagnosis and preimplantation genetic haplotyping for many inherited skin conditions. It is also helpful in such occasions as phenocopy, late onset and incomplete penetrance, uniparental disomy, mitochondrial inheritance and pigmentary mosaicism. Molecular methods of two genodermatoses are explained in detail, i.e. genodermatoses with skin fragility and neurofibromatosis type 1.

  8. 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.

  9. Introductory molecular genetics

    SciTech Connect

    Edwards-Moulds, J.

    1986-01-01

    This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.

  10. 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.

  11. Nearby Molecular Hydrogen

    NASA Technical Reports Server (NTRS)

    Lebrun, F.

    1984-01-01

    If the gas-to-dust ratio is sufficiently uniform throughout the local interstellar medium, galaxy counts may provide a useful probe of the large scale structure of the interstellar gas. This idea substantiated by gamma ray observations led to the discovery of nearby molecular cloud complexes. The reddening studies indicate that one of them lies between 80 and 140 pc from the Sun. From CO observations, its molecular mass is estimated to be a few 1000 stellar mass units.

  12. Molecularly Imprinted Ionomers

    DTIC Science & Technology

    2002-04-05

    ion selective electrodes and ion selective optical sensors using a modified version of the molecular imprinting technique. The modification is a...materials may be the means to realize this goal. An additional application of metal ion imprinted polymers is as sensors . The ability to detect a...been shown to have dramatic effects on polymer properties. The benefits of ionic crosslinking on molecular imprinting are two-fold. First, ionic

  13. 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.

  14. PREFACE: Molecular nanomachines

    NASA Astrophysics Data System (ADS)

    Comtet, Geneviève; Dujardin, Gérald

    2006-08-01

    The concept of molecular nanomachines has become a reality in the past few years in organic and supramolecular chemistry, in biochemistry and in atom-scale manipulation with the scanning tunnelling microscope (STM). In chemistry, molecules can be designed and synthesized to have specific electrical, mechanical, optical or reactive properties. In biochemistry, single natural biomolecules can be isolated and activated as nanomachines. In atom-scale manipulation, the STM can be used to power and to control the operation of individual molecules as molecular nanomachines. The fields of chemical synthesis, biomolecular machines and atom-scale manipulations, have each developed as a separate entity. However, mutual integration of these different research fields appears to be a very fruitful approach for the future of molecular nanomachines. This special section of Journal of Physics: Condensed Matter is the follow-up to a meeting held in Les Houches (France) on 17-21 January 2005 on molecular nanomachines. The section aims to contribute to the readers’ understanding by giving a clear overview of the principal issues of molecular nanomachines. We hope that it will facilitate new collaborations between researchers from these different fields, so necessary for the integrated development of molecular nanomachines.

  15. Molecular classification of gliomas.

    PubMed

    Masui, Kenta; Mischel, Paul S; Reifenberger, Guido

    2016-01-01

    The identification of distinct genetic and epigenetic profiles in different types of gliomas has revealed novel diagnostic, prognostic, and predictive molecular biomarkers for refinement of glioma classification and improved prediction of therapy response and outcome. Therefore, the new (2016) World Health Organization (WHO) classification of tumors of the central nervous system breaks with the traditional principle of diagnosis based on histologic criteria only and incorporates molecular markers. This will involve a multilayered approach combining histologic features and molecular information in an "integrated diagnosis". We review the current state of diagnostic molecular markers for gliomas, focusing on isocitrate dehydrogenase 1 or 2 (IDH1/IDH2) gene mutation, α-thalassemia/mental retardation syndrome X-linked (ATRX) gene mutation, 1p/19q co-deletion and telomerase reverse transcriptase (TERT) promoter mutation in adult tumors, as well as v-raf murine sarcoma viral oncogene homolog B1 (BRAF) and H3 histone family 3A (H3F3A) aberrations in pediatric gliomas. We also outline prognostic and predictive molecular markers, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, and discuss the potential clinical relevance of biologic glioblastoma subtypes defined by integration of multiomics data. Commonly used methods for individual marker detection as well as novel large-scale DNA methylation profiling and next-generation sequencing approaches are discussed. Finally, we illustrate how advances in molecular diagnostics affect novel strategies of targeted therapy, thereby raising new challenges and identifying new leads for personalized treatment of glioma patients.

  16. Molecular biology in physiology

    SciTech Connect

    Chien, S.; Gargus, J.J.

    1987-08-01

    The aim of this symposium on molecular biology in physiology was to introduce molecular biology to physiologists who had relatively little exposure to the new developments in this field, so that they can become conversant on this topic and contribute to the advancement of physiology by incorporating molecular biological approaches as a part of their research arsenal. This report is a review of the symposium, which consisted of two four-part sessions. Each session had four papers. After the discussion of the basic concepts, terminology, and methodology used in molecular biology, it was shown how these basic principles have been applied to the study of the genes encoding two membrane proteins that have important transport functions (band 3 and ATPase). The second half of the symposium consisted of papers on the state-of-the-art developments in the application of molecular biology to the studies of the atrial natriuretic factor and renin genes, adenylate cyclase-coupled adrenergic receptors, acetylcholine receptors and sodium channel, and long-term and short-term memories. The ultimate goal is that these examples will provide an impetus for the opening of new frontiers of research in physiology by taking advantage of the tools developed from recent advances in molecular biology.

  17. 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.

  18. 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.

  19. Interstellar molecular clouds

    NASA Astrophysics Data System (ADS)

    Bally, J.

    1986-04-01

    The physical properties of the molecular phase of the interstellar medium are studied with regard to star formation and the structure of the Galaxy. Most observations of molecular clouds are made with single-dish, high-surface precision radio telescopes, with the best resolution attainable at 0.2 to 1 arcmin; the smallest structures that can be resolved are of order 10 to the 17th cm in diameter. It is now believed that: (1) most of the mass of the Galaxy is in the form of giant molecular clouds; (2) the largest clouds and those responsible for most massive star formation are concentrated in spiral arms; (3) the molecular clouds are the sites of perpetual star formation, and are significant in the chemical evolution of the Galaxy; (4) giant molecular clouds determine the evolution of the kinematic properties of galactic disk stars; (5) the total gas content is diminishing with time; and (6) most clouds have supersonic internal motions and do not form stars on a free-fall time scale. It is concluded that though progress has been made, more advanced instruments are needed to inspect the processes operating within stellar nurseries and to study the distribution of the molecular clouds in more distant galaxies. Instruments presently under construction which are designed to meet these ends are presented.

  20. Nanotechnology Review: Molecular Electronics to Molecular Motors

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  1. Nanotechnology Review: Molecular Electronics to Molecular Motors

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  2. Vínculos sobre um modelo de quartessência de Chaplygin usando observações do satélite chandra da fração de massa de gás em aglomerados de galáxias

    NASA Astrophysics Data System (ADS)

    de Souza, R. S.

    2003-08-01

    Observações de Supernovas do tipo Ia mostram que a expansão do Universo está acelerando. Segundo as equações de Einstein uma componente com pressão negativa (energia escura) é necessária para explicar a aceleração cósmica. Além da energia escura é usualmente admitido que no Universo há também uma matéria exótica com pressão zero, que é chamada de matéria escura. Essa componente possui um papel fundamental na formação de estruturas no Universo. Recentemente tem se explorado a possibilidade de que matéria e energia escura poderiam ser unificadas através de uma única componente, que tem sido denominada de quartessência. Um exemplo de fluido com essas características é o Gás de Chaplygin Generalizado, que possui uma equação de estado da forma p = -A/ra. Inicialmente consideramos o caso especial a = 1 (gás de Chaplygin) e vinculamos parâmetros do modelo utilizando observações em raios-X do satélite Chandra da fração de massa de gás em aglomerados de galáxias. Uma comparação dos vínculos obtidos com esse teste com outros testes, tais como supernovas e idade do Universo, mostra que esse teste é bastante restritivo. Exibiremos ainda resultados para o caso em que a curvatura é nula e o parâmetro a está compreendido no intervalo -1 < a 1.

  3. Phylogenetic molecular function annotation

    NASA Astrophysics Data System (ADS)

    Engelhardt, Barbara E.; Jordan, Michael I.; Repo, Susanna T.; Brenner, Steven E.

    2009-07-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called "phylogenomics") is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

  4. 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.

  5. Molecular interaction databases.

    PubMed

    Orchard, Sandra

    2012-05-01

    Molecular interaction databases are playing an ever more important role in our understanding of the biology of the cell. An increasing number of resources exist to provide these data and many of these have adopted the controlled vocabularies and agreed-upon standardised data formats produced by the Molecular Interaction workgroup of the Human Proteome Organization Proteomics Standards Initiative (HUPO PSI-MI). Use of these standards allows each resource to establish PSI Common QUery InterfaCe (PSICQUIC) service, making data from multiple resources available to the user in response to a single query. This cooperation between databases has been taken a stage further, with the establishment of the International Molecular Exchange (IMEx) consortium which aims to maximise the curation power of numerous data resources, and provide the user with a non-redundant, consistently annotated set of interaction data. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. [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.

  7. 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.

  8. 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

  9. [Molecular diagnosis of ADPKD].

    PubMed

    Scolari, Francesco; Savoldi, Gianfranco; Mazza, Cinzia; Izzi, Claudia

    2016-01-01

    Most patients with ADPKD do not need molecular genetic testing. When indicated, Sanger sequencing is the most commonly used technique. When a pathogenic mutation is not identified by Sanger, multiplex ligation-dependent probe amplification analysis (MLPA) should be performed to detect gene rearrangement (insertion or deletion). The next generation sequencing (NGS) techniques can provide high-throughput and comprehensive diagnostic screening at lower cost. Finally, in the future, targeted (TS) or whole exome sequencing (WES) will likely play a role in the molecular diagnostics of ADPKD. Molecular genetic testing is indicated in several conditions: no family history; equivocal/atypical renal imaging; marked discordant disease within family; early and severe PKD; reproductive counseling and pre-implantation genetic diagnosis; related living donor transplantation.

  10. Molecular modeling of peptides.

    PubMed

    Kuczera, Krzysztof

    2015-01-01

    This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.

  11. DNA based molecular motors

    NASA Astrophysics Data System (ADS)

    Michaelis, Jens; Muschielok, Adam; Andrecka, Joanna; Kügel, Wolfgang; Moffitt, Jeffrey R.

    2009-12-01

    Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid-a process that is driven by one of the most powerful molecular motors.

  12. Molecular neuropathology of gliomas.

    PubMed

    Riemenschneider, Markus J; Reifenberger, Guido

    2009-01-01

    Gliomas are the most common primary human brain tumors. They comprise a heterogeneous group of benign and malignant neoplasms that are histologically classified according to the World Health Organization (WHO) classification of tumors of the nervous system. Over the past 20 years the cytogenetic and molecular genetic alterations associated with glioma formation and progression have been intensely studied and genetic profiles as additional aids to the definition of brain tumors have been incorporated in the WHO classification. In fact, first steps have been undertaken in supplementing classical histopathological diagnosis by the use of molecular tests, such as MGMT promoter hypermethylation in glioblastomas or detection of losses of chromosome arms 1p and 19q in oligodendroglial tumors. The tremendous progress that has been made in the use of array-based profiling techniques will likely contribute to a further molecular refinement of glioma classification and lead to the identification of glioma core pathways that can be specifically targeted by more individualized glioma therapies.

  13. 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

  14. 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

  15. Visualizing molecular unidirectional rotation

    NASA Astrophysics Data System (ADS)

    Lin, Kang; Song, Qiying; Gong, Xiaochun; Ji, Qinying; Pan, Haifeng; Ding, Jingxin; Zeng, Heping; Wu, Jian

    2015-07-01

    We directly visualize the spatiotemporal evolution of a unidirectional rotating molecular rotational wave packet. Excited by two time-delayed polarization-skewed ultrashort laser pulses, the cigar- or disk-shaped rotational wave packet is impulsively kicked to unidirectionally rotate as a quantum rotor which afterwards disperses and exhibits field-free revivals. The rich dynamics can be coherently controlled by varying the timing or polarization of the excitation laser pulses. The numerical simulations very well reproduce the experimental observations and intuitively revivify the thoroughgoing evolution of the molecular rotational wave packet of unidirectional spin.

  16. 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

  17. 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.

  18. Open source molecular modeling.

    PubMed

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

    2016-09-01

    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. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Substructured multibody molecular dynamics.

    SciTech Connect

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  20. Molecular tectonics: from simple tectons to complex molecular networks.

    PubMed

    Hosseini, Mir Wais

    2005-04-01

    Molecular networks in the crystalline phase are infinite periodic molecular assemblies formed under self-assembly conditions between self-complementary or complementary tectons. These millimeter-size structures may be regarded as hypermolecules formed by supramolecular synthesis using reversible intertecton interactions. Molecular tectonics, based on molecular recognition events and their iteration, is the approach dealing with design and preparation of molecular networks in the solid state. In this Account, an overview of the rational behind this approach is presented. A variety of molecular networks based on van der Waals interactions and hydrogen and coordination bonding possessing diverse connectivity and topology are discussed.

  1. Photoionization of molecular clusters

    NASA Astrophysics Data System (ADS)

    Andres, R. P.; Calo, J. M.

    1981-12-01

    An experimental apparatus consisting of a novel multiple expansion cluster source coupled with a molecular beam system and photoionization mass spectrometer has been designed and constructed. This apparatus has been thoroughly tested and preliminary measurements of the growth kinetics of water clusters and the photoionization cross section of the water dimer have been carried out.

  2. Making Molecular Borromean Rings

    ERIC Educational Resources Information Center

    Pentecost, Cari D.; Tangchaivang, Nichol; Cantrill, Stuart J.; Chichak, Kelly S.; Peters, Andrea J.; Stoddart, Fraser J.

    2007-01-01

    A procedure that requires seven 4-hour blocks of time to allow undergraduate students to prepare the molecular Borromean rings (BRs) on a gram-scale in 90% yield is described. The experiment would serve as a nice capstone project to culminate any comprehensive organic laboratory course and expose students to fundamental concepts, symmetry point…

  3. 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.

  4. Clickable molecularly imprinted nanoparticles.

    PubMed

    Xu, Changgang; Ye, Lei

    2011-06-07

    Terminal alkynyl and azide groups are introduced on the surface of molecularly imprinted core-shell nanoparticles using precipitation polymerization. These clickable groups enable simple nanoparticle conjugation and surface modification under mild reaction conditions, opening new opportunities for nanoparticle-based assays and chemical sensing.

  5. The molecular universe

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    2013-07-01

    Molecular absorption and emission bands dominate the visible, infrared, and submillimeter spectra of most objects with associated gas. These observations reveal a surprisingly rich array of molecular species and attest to a complex chemistry taking place in the harsh environment of the interstellar medium of galaxies. Molecules are truly everywhere and an important component of interstellar gas. This review surveys molecular observations in the various spectral windows and summarizes the chemical and physical processes involved in the formation and evolution of interstellar molecules. The rich organic inventory of space reflects the multitude of chemical processes involved that, on the one hand, build up molecules an atom at a time and, on the other hand, break down large molecules injected by stars to smaller fragments. Both this bottom-up and the trickle-down chemistry are reviewed. The emphasis is on understanding the characteristics of complex polycyclic aromatic hydrocarbon molecules and fullerenes and their role in chemistry as well as the intricate interaction of gas-phase ion-molecule and neutral-neutral reactions and the chemistry taking place on grain surfaces in dense clouds in setting the organic inventory of regions of star and planet formation and their implications for the chemical history of the Solar System. Many aspects of molecular astrophysics are illustrated with recent observations of the HIFI instrument on the Herschel Space Observatory.

  6. Polypeptides Based Molecular Electronics

    DTIC Science & Technology

    2008-10-06

    Molecular Electronics 4 Figure 3. Dehydration synthesis reaction CHAPTER 2 Review of Literature 2.1 Peptides 2.1.1 Introduction to peptides...Peptides are biomolecules formed from the 20 naturally occurring amino acids. Figure 3 shows dehydration synthesis reaction (known as condensation

  7. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  8. Making Molecular Borromean Rings

    ERIC Educational Resources Information Center

    Pentecost, Cari D.; Tangchaivang, Nichol; Cantrill, Stuart J.; Chichak, Kelly S.; Peters, Andrea J.; Stoddart, Fraser J.

    2007-01-01

    A procedure that requires seven 4-hour blocks of time to allow undergraduate students to prepare the molecular Borromean rings (BRs) on a gram-scale in 90% yield is described. The experiment would serve as a nice capstone project to culminate any comprehensive organic laboratory course and expose students to fundamental concepts, symmetry point…

  9. Reading the Molecular Clock.

    ERIC Educational Resources Information Center

    McKean, Kevin

    1983-01-01

    Suggesting that the evolutionary record may be written in proteins and genes, discusses research in which species are compared by immunology, DNA, and radioimmunoassay. Molecular studies show that DNA from humans and chimps is 98 percent identical, a degree of similarity usually occurring only among animals of the same genus. (JN)

  10. Atomic and Molecular Physics

    NASA Technical Reports Server (NTRS)

    Bhatia, Anand K.

    2005-01-01

    A symposium on atomic and molecular physics was held on November 18, 2005 at Goddard Space Flight Center. There were a number of talks through the day on various topics such as threshold law of ionization, scattering of electrons from atoms and molecules, muonic physics, positron physics, Rydberg states etc. The conference was attended by a number of physicists from all over the world.

  11. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  12. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik R

    2008-01-01

    Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.

  13. Molecular Imaging Without Radiopharmaceuticals?

    PubMed Central

    Gore, John C.; Yankeelov, Thomas E.; Peterson, Todd. E.; Avison, Malcolm J.

    2009-01-01

    The limitations on the sensitivity for detecting small changes in MRI, CT, and ultrasound pulse-echo images are used to estimate the practical requirements for molecular imaging and targeted contrast enhancement for these modalities. These types of imaging are highly unlikely to approach the sensitivity for detecting molecular processes of radionuclear methods, and the prospects for achieving sufficient concentrations of appropriate agents in vivo are poor for several types of applications such as small-molecule targeting of specific receptors. However, using relatively large carrier systems such as particles and liposomes, sufficient concentrations of paramagnetic agents may be delivered to achieve MR-signal changes adequate for detection. The use of higher-resolution MR images will aid the prospects for molecular imaging in small animals. Theoretic considerations also predict that a similar approach, using rather large particles or carriers of materials with a high atomic number, may also be successful for CT, especially with additional developments such as the use of monochromatic x-rays. The prospects of molecular imaging by x-ray imaging may not be as bleak as has been predicted. For ultrasound detection, gas-filled bubbles can provide a sufficient backscattered sound intensity to be detectable at concentrations and sizes not much different from agents designed for these other modalities. PMID:19443583

  14. Reading the Molecular Clock.

    ERIC Educational Resources Information Center

    McKean, Kevin

    1983-01-01

    Suggesting that the evolutionary record may be written in proteins and genes, discusses research in which species are compared by immunology, DNA, and radioimmunoassay. Molecular studies show that DNA from humans and chimps is 98 percent identical, a degree of similarity usually occurring only among animals of the same genus. (JN)

  15. 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.

  16. Molecular ion photofragment spectroscopy

    SciTech Connect

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  17. Molecular fMRI

    PubMed Central

    Bartelle, Benjamin B.; Barandov, Ali

    2016-01-01

    Comprehensive analysis of brain function depends on understanding the dynamics of diverse neural signaling processes over large tissue volumes in intact animals and humans. Most existing approaches to measuring brain signaling suffer from limited tissue penetration, poor resolution, or lack of specificity for well-defined neural events. Here we discuss a new brain activity mapping method that overcomes some of these problems by combining MRI with contrast agents sensitive to neural signaling. The goal of this “molecular fMRI” approach is to permit noninvasive whole-brain neuroimaging with specificity and resolution approaching current optical neuroimaging methods. In this article, we describe the context and need for molecular fMRI as well as the state of the technology today. We explain how major types of MRI probes work and how they can be sensitized to neurobiological processes, such as neurotransmitter release, calcium signaling, and gene expression changes. We comment both on past work in the field and on challenges and promising avenues for future development. SIGNIFICANCE STATEMENT Brain researchers currently have a choice between measuring neural activity using cellular-level recording techniques, such as electrophysiology and optical imaging, or whole-brain imaging methods, such as fMRI. Cellular level methods are precise but only address a small portion of mammalian brains; on the other hand, whole-brain neuroimaging techniques provide very little specificity for neural pathways or signaling components of interest. The molecular fMRI techniques we discuss have particular potential to combine the specificity of cellular-level measurements with the noninvasive whole-brain coverage of fMRI. On the other hand, molecular fMRI is only just getting off the ground. This article aims to offer a snapshot of the status and future prospects for development of molecular fMRI techniques. PMID:27076413

  18. Multimodality Cardiovascular Molecular Imaging Technology

    PubMed Central

    O’Donnell, Matthew; McVeigh, Elliot R.; Strauss, H. William; Tanaka, Atsushi; Bouma, Brett E.; Tearney, Guillermo J.; Guttman, Michael A.; Garcia, Ernest V.

    2010-01-01

    Cardiovascular molecular imaging is a new discipline that integrates scientific advances in both functional imaging and molecular probes to improve our understanding of the molecular basis of the cardiovascular system. These advances are driven by in vivo imaging of molecular processes in animals, usually small animals, and are rapidly moving toward clinical applications. Molecular imaging has the potential to revolutionize the diagnosis and treatment of cardiovascular disease. The 2 key components of all molecular imaging systems are the molecular contrast agents and the imaging system providing spatial and temporal localization of these agents within the body. They must deliver images with the appropriate sensitivity and specificity to drive clinical applications. As work in molecular contrast agents matures and highly sensitive and specific probes are developed, these systems will provide the imaging technologies required for translation into clinical tools. This is the promise of molecular medicine. PMID:20457794

  19. [Molecular abnormalities in lymphomas].

    PubMed

    Delsol, G

    2010-11-01

    Numerous molecular abnormalities have been described in lymphomas. They are of diagnostic and prognostic value and are taken into account for the WHO classification of these tumors. They also shed some light on the underlying molecular mechanisms involved in lymphomas. Overall, four types of molecular abnormalities are involved: mutations, translocations, amplifications and deletions of tumor suppressor genes. Several techniques are available to detect these molecular anomalies: conventional cytogenetic analysis, multicolor FISH, CGH array or gene expression profiling using DNA microarrays. In some lymphomas, genetic abnormalities are responsible for the expression of an abnormal protein (e.g. tyrosine-kinase, transcription factor) detectable by immunohistochemistry. In the present review, molecular abnormalities observed in the most frequent B, T or NK cell lymphomas are discussed. In the broad spectrum of diffuse large B-cell lymphomas microarray analysis shows mostly two subgroups of tumors, one with gene expression signature corresponding to germinal center B-cell-like (GCB: CD10+, BCL6 [B-Cell Lymphoma 6]+, centerine+, MUM1-) and a subgroup expressing an activated B-cell-like signature (ABC: CD10-, BCL6-, centerine-, MUM1+). Among other B-cell lymphomas with well characterized molecular abnormalies are follicular lymphoma (BCL2 deregulation), MALT lymphoma (Mucosa Associated Lymphoid Tissue) [API2-MALT1 (mucosa-associated-lymphoid-tissue-lymphoma-translocation-gene1) fusion protein or deregulation BCL10, MALT1, FOXP1. MALT1 transcription factors], mantle cell lymphoma (cycline D1 [CCND1] overexpression) and Burkitt lymphoma (c-Myc expression). Except for ALK (anaplastic lymphoma kinase)-positive anaplastic large cell lymphoma, well characterized molecular anomalies are rare in lymphomas developed from T or NK cells. Peripheral T cell lymphomas not otherwise specified are a heterogeneous group of tumors with frequent but not recurrent molecular abnormalities

  20. 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)

  1. 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)

  2. Molecular biology of potyviruses.

    PubMed

    Revers, Frédéric; García, Juan Antonio

    2015-01-01

    Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.

  3. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  4. Activating the molecular spinterface

    NASA Astrophysics Data System (ADS)

    Cinchetti, Mirko; Dediu, V. Alek; Hueso, Luis E.

    2017-05-01

    The miniaturization trend in the semiconductor industry has led to the understanding that interfacial properties are crucial for device behaviour. Spintronics has not been alien to this trend, and phenomena such as preferential spin tunnelling, the spin-to-charge conversion due to the Rashba-Edelstein effect and the spin-momentum locking at the surface of topological insulators have arisen mainly from emergent interfacial properties, rather than the bulk of the constituent materials. In this Perspective we explore inorganic/molecular interfaces by looking closely at both sides of the interface. We describe recent developments and discuss the interface as an ideal platform for creating new spin effects. Finally, we outline possible technologies that can be generated thanks to the unique active tunability of molecular spinterfaces.

  5. Managing molecular diversity.

    PubMed

    Perez, Juan J

    2005-02-01

    The present work provides an overview of the different methods used in molecular diversity analysis. Issues like identifying voids in proprietary databases, reducing the number of redundancies present in databases, or designing focused libraries by grouping compounds similar to a template with the aim to fine tune its properties, are potent diversity analysis tools that may be used to optimize molecules based on their properties and specifically, to speed up the process of lead discovery and optimization. The present work describes first methods that are used to describe molecular systems. This is followed by a section devoted to describe different measures of similarity between molecules, to finish with a description of different methods used to select subsets molecules according to the constraints imposed. The final section deals with the validation of these methods, based on different studies available in the literature.

  6. Wholly Synthetic Molecular Machines.

    PubMed

    Cheng, Chuyang; Stoddart, J Fraser

    2016-06-17

    The past quarter of a century has witnessed an increasing engagement on the part of physicists and chemists in the design and synthesis of molecular machines de novo. This minireview traces the development of artificial molecular machines from their prototypes in the form of shuttles and switches to their emergence as motors and pumps where supplies of energy in the form of chemical fuel, electrochemical potential and light activation become a minimum requirement for them to function away from equilibrium. The challenge facing this rapidly growing community of scientists and engineers today is one of putting wholly synthetic molecules to work, both individually and as collections. Here, we highlight some of the recent conceptual and practical advances relating to the operation of wholly synthetic rotary and linear motors. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Molecular psychiatry of zebrafish

    PubMed Central

    Stewart, Adam Michael; Ullmann, Jeremy F.P.; Norton, William H.J.; Brennan, Caroline H.; Parker, Matthew O.; Gerlai, Robert; Kalueff, Allan V.

    2014-01-01

    Due to their well-characterized neural development and high genetic homology to mammals, zebrafish (Danio rerio) have emerged as a powerful model organism in the field of biological psychiatry. Here, we discuss the molecular psychiatry of zebrafish, and its implications for translational neuroscience research and modeling CNS disorders. In particular, we outline recent genetic and technological developments allowing for in-vivo examinations, high-throughput screening and whole-brain analyses in larval and adult zebrafish. We also summarize the application of these molecular techniques to the understanding of neuropsychiatric disease, outlining the potential of zebrafish for modeling complex brain disorders, including attention-deficit/hyperactivity disorder (ADHD), aggression, post-traumatic stress and substance abuse. Critically evaluating the advantages and limitations of larval and adult fish tests, we suggest that zebrafish models become a rapidly emerging new field in modern biological psychiatry research. PMID:25349164

  8. Polyaromatic molecular peanuts

    PubMed Central

    Yazaki, Kohei; Akita, Munetaka; Prusty, Soumyakanta; Chand, Dillip Kumar; Kikuchi, Takashi; Sato, Hiroyasu; Yoshizawa, Michito

    2017-01-01

    Mimicking biological structures such as fruits and seeds using molecules and molecular assemblies is a great synthetic challenge. Here we report peanut-shaped nanostructures comprising two fullerene molecules fully surrounded by a dumbbell-like polyaromatic shell. The shell derives from a molecular double capsule composed of four W-shaped polyaromatic ligands and three metal ions. Mixing the double capsule with various fullerenes (that is, C60, C70 and Sc3N@C80) gives rise to the artificial peanuts with lengths of ∼3 nm in quantitative yields through the release of the single metal ion. The rational use of both metal–ligand coordination bonds and aromatic–aromatic π-stacking interactions as orthogonal chemical glue is essential for the facile preparation of the multicomponent, biomimetic nanoarchitectures. PMID:28656977

  9. Polyaromatic molecular peanuts

    NASA Astrophysics Data System (ADS)

    Yazaki, Kohei; Akita, Munetaka; Prusty, Soumyakanta; Chand, Dillip Kumar; Kikuchi, Takashi; Sato, Hiroyasu; Yoshizawa, Michito

    2017-06-01

    Mimicking biological structures such as fruits and seeds using molecules and molecular assemblies is a great synthetic challenge. Here we report peanut-shaped nanostructures comprising two fullerene molecules fully surrounded by a dumbbell-like polyaromatic shell. The shell derives from a molecular double capsule composed of four W-shaped polyaromatic ligands and three metal ions. Mixing the double capsule with various fullerenes (that is, C60, C70 and Sc3N@C80) gives rise to the artificial peanuts with lengths of ~3 nm in quantitative yields through the release of the single metal ion. The rational use of both metal-ligand coordination bonds and aromatic-aromatic π-stacking interactions as orthogonal chemical glue is essential for the facile preparation of the multicomponent, biomimetic nanoarchitectures.

  10. Polyaromatic molecular peanuts.

    PubMed

    Yazaki, Kohei; Akita, Munetaka; Prusty, Soumyakanta; Chand, Dillip Kumar; Kikuchi, Takashi; Sato, Hiroyasu; Yoshizawa, Michito

    2017-06-28

    Mimicking biological structures such as fruits and seeds using molecules and molecular assemblies is a great synthetic challenge. Here we report peanut-shaped nanostructures comprising two fullerene molecules fully surrounded by a dumbbell-like polyaromatic shell. The shell derives from a molecular double capsule composed of four W-shaped polyaromatic ligands and three metal ions. Mixing the double capsule with various fullerenes (that is, C60, C70 and Sc3N@C80) gives rise to the artificial peanuts with lengths of ∼3 nm in quantitative yields through the release of the single metal ion. The rational use of both metal-ligand coordination bonds and aromatic-aromatic π-stacking interactions as orthogonal chemical glue is essential for the facile preparation of the multicomponent, biomimetic nanoarchitectures.

  11. An Artificial Molecular Transporter

    PubMed Central

    Schäfer, Christian; Ragazzon, Giulio; Colasson, Benoit; La Rosa, Marcello; Silvi, Serena

    2015-01-01

    Abstract The transport of substrates is one of the main tasks of biomolecular machines in living organisms. We report a synthetic small‐molecule system designed to catch, displace, and release molecular cargo in solution under external control. The system consists of a bistable rotaxane that behaves as an acid–base controlled molecular shuttle, whose ring component bears a tether ending with a nitrile group. The latter can be coordinated to a ruthenium complex that acts as the load, and dissociated upon irradiation with visible light. The cargo loading/unloading and ring transfer/return processes are reversible and can be controlled independently. The robust coordination bond ensures that the cargo remains attached to the device while the transport takes place. PMID:27308223

  12. Templated quasicrystalline molecular layers

    NASA Astrophysics Data System (ADS)

    Smerdon, Joe; Young, Kirsty; Lowe, Michael; Hars, Sanger; Yadav, Thakur; Hesp, David; Dhanak, Vinod; Tsai, An-Pang; Sharma, Hem Raj; McGrath, Ronan

    2014-03-01

    Quasicrystals are materials with long range ordering but no periodicity. We report scanning tunneling microscopy (STM) observations of quasicrystalline molecular layers on five-fold quasicrystal surfaces. The molecules adopt positions and orientations on the surface consistent with the quasicrystalline ordering of the substrate. Carbon-60 adsorbs atop sufficiently-separated Fe atoms on icosahedral Al-Cu-Fe to form a unique quasicrystalline lattice whereas further C60 molecules decorate remaining surface Fe atoms in a quasi-degenerate fashion. Pentacene (Pn) adsorbs at tenfold-symmetric points around surface-bisected rhombic triacontahedral clusters in icosahedral Ag-In-Yb. These systems constitute the first demonstrations of quasicrystalline molecular ordering on a template. EPSRC EP/D05253X/1, EP/D071828/1, UK BIS.

  13. An artificial molecular pump

    NASA Astrophysics Data System (ADS)

    Cheng, Chuyang; McGonigal, Paul R.; Schneebeli, Severin T.; Li, Hao; Vermeulen, Nicolaas A.; Ke, Chenfeng; Stoddart, J. Fraser

    2015-06-01

    Carrier proteins consume fuel in order to pump ions or molecules across cell membranes, creating concentration gradients. Their control over diffusion pathways, effected entirely through noncovalent bonding interactions, has inspired chemists to devise artificial systems that mimic their function. Here, we report a wholly artificial compound that acts on small molecules to create a gradient in their local concentration. It does so by using redox energy and precisely organized noncovalent bonding interactions to pump positively charged rings from solution and ensnare them around an oligomethylene chain, as part of a kinetically trapped entanglement. A redox-active viologen unit at the heart of a dumbbell-shaped molecular pump plays a dual role, first attracting and then repelling the rings during redox cycling, thereby enacting a flashing energy ratchet mechanism with a minimalistic design. Our artificial molecular pump performs work repetitively for two cycles of operation and drives rings away from equilibrium toward a higher local concentration.

  14. Molecular diagnosis of onychomycosis.

    PubMed

    Petinataud, D; Berger, S; Contet-Audonneau, N; Machouart, M

    2014-12-01

    Onychomycosis is a frequent cause of nail infections due to dermatophytes. Molds and yeast may also be responsible of these pathologies. Antifungal treatments are frequently given without a mycological diagnosis, partly because of the requisite time for obtaining the biological results. The mycological diagnosis requires a direct microscopic examination and a culture in order to accurately identify the fungal genus and species. Nevertheless, this conventional diagnosis is often time consuming due to the delay of fungal cultures and presents disadvantages that make it not sufficient enough to give a precise and confident response to the clinicians. Therefore additional tests have been developed to help distinguish onychomycosis from other nail disorders. Among them, molecular biology techniques offer modern and rapid tools to improve traditional microbiological diagnosis. In this review, we first present the conventional diagnosis methods for onychomycosis and then we describe the main molecular biology tools and the currently available commercial kits that allow a rapid detection of the pathology.

  15. FORT Molecular Ecology Laboratory

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; Stevens, P.D.

    2011-01-01

    The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.

  16. Molecular opacities for exoplanets.

    PubMed

    Bernath, Peter F

    2014-04-28

    Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy.

  17. Molecular opacities for exoplanets

    PubMed Central

    Bernath, Peter F.

    2014-01-01

    Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy. PMID:24664921

  18. Molecular Biology of Archaebacteria

    DTIC Science & Technology

    1988-03-31

    elucidate at the molecular level some of the features that make archaebacteria unique and distinguish them from eubacteria and eucaryotes. Three types...regulate translation of the mRNA by a mechanism similar to that employed in eubacteria . Thus halophilic archaebacteria retain the same gene order and...possibly also the same regulatory mechanism for controlling ribosomal protein synthesis that is found in eubacteria . Ribosomal protein structure: The

  19. [Hereditary deafness: molecular genetics].

    PubMed

    Hardelin, Jean-Pierre; Denoyelle, Françoise; Levilliers, Jacqueline; Simmler, Marie-Christine; Petit, Christine

    2004-03-01

    This article outlines recent advances in explaining hereditary deafness in molecular terms, focusing on isolated (i.e. nonsyndromic) hearing loss. The number of genes identified (36 to date) is growing rapidly. However, difficulties inherent in genetic linkage analysis, coupled with the possible involvement of environmental causes, have so far prevented the characterization of the main genes causative or predisposing to the late-onset forms of deafness.

  20. Atomic and molecular theory

    SciTech Connect

    Inokuti, Mitio.

    1990-01-01

    The multifaceted role of theoretical physics in understanding the earliest stages of radiation action is discussed. Scientific topics chosen for the present discourse include photoabsorption, electron collisions, and ionic collisions, and electron transport theory, Connections of atomic and molecular physics with condensed-matter physics are also discussed. The present article includes some historical perspective and an outlook for the future. 114 refs., 3 figs.

  1. Primer on molecular genetics

    SciTech Connect

    Not Available

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  2. Communication: Molecular gears.

    PubMed

    Burnell, E Elliott; de Lange, Cornelis A; Meerts, W Leo

    2016-09-07

    The (1)H nuclear magnetic resonance spectrum of hexamethylbenzene orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy. The spectrum contains over 350 000 lines with many overlapping transitions, from which four independent direct dipolar couplings are obtained. The rotations of the six methyl groups appear to be correlated due to mutual steric hindrance. Adjacent methyl groups show counter-rotating or geared motion. Hexamethylbenzene thus behaves as a molecular hexagonal gear.

  3. Linear artificial molecular muscles.

    PubMed

    Liu, Yi; Flood, Amar H; Bonvallet, Paul A; Vignon, Scott A; Northrop, Brian H; Tseng, Hsian-Rong; Jeppesen, Jan O; Huang, Tony J; Brough, Branden; Baller, Marko; Magonov, Sergei; Solares, Santiago D; Goddard, William A; Ho, Chih-Ming; Stoddart, J Fraser

    2005-07-13

    Two switchable, palindromically constituted bistable [3]rotaxanes have been designed and synthesized with a pair of mechanically mobile rings encircling a single dumbbell. These designs are reminiscent of a "molecular muscle" for the purposes of amplifying and harnessing molecular mechanical motions. The location of the two cyclobis(paraquat-p-phenylene) (CBPQT(4+)) rings can be controlled to be on either tetrathiafulvalene (TTF) or naphthalene (NP) stations, either chemically ((1)H NMR spectroscopy) or electrochemically (cyclic voltammetry), such that switching of inter-ring distances from 4.2 to 1.4 nm mimics the contraction and extension of skeletal muscle, albeit on a shorter length scale. Fast scan-rate cyclic voltammetry at low temperatures reveals stepwise oxidations and movements of one-half of the [3]rotaxane and then of the other, a process that appears to be concerted at room temperature. The active form of the bistable [3]rotaxane bears disulfide tethers attached covalently to both of the CBPQT(4+) ring components for the purpose of its self-assembly onto a gold surface. An array of flexible microcantilever beams, each coated on one side with a monolayer of 6 billion of the active bistable [3]rotaxane molecules, undergoes controllable and reversible bending up and down when it is exposed to the synchronous addition of aqueous chemical oxidants and reductants. The beam bending is correlated with flexing of the surface-bound molecular muscles, whereas a monolayer of the dumbbell alone is inactive under the same conditions. This observation supports the hypothesis that the cumulative nanoscale movements within surface-bound "molecular muscles" can be harnessed to perform larger-scale mechanical work.

  4. Functional Molecular Ecological Networks

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  5. Molecular-beam scattering

    SciTech Connect

    Vernon, M.F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N/sub 2/ from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HCl ..-->.. NaCl + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2/sup 2/P/sub 3/2/) and Na(3/sup 2/P/sub 3/2/) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  6. Molecular Vaccines for Malaria

    DTIC Science & Technology

    2010-01-01

    pathogen-associated molecular patterns for cancer immunotherapy. Cancer Gene Ther 200S; 16:310-9. 105. Dempsey PW, Allison ME, Akkaraju S, Goodnow CC ...malaria immunity elicited by recombinant adenovirus. Parasite lmmunol 2000; 22:157-60. 149. Sridhar S, Reyes- Sandoval A, Draper SJ, Moore AC...AT, Koup RA, Roederer M, Bailer RT, 166. Fitzgerald JC, Gao GP, Reyes- Sandoval A, Pavlakis hyperanenuated strain of Listeria monocytogenes. J Enama

  7. 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.

  8. 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.

  9. Molecular dynamics simulations.

    PubMed

    Lindahl, Erik

    2015-01-01

    Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.

  10. Fluorinated benzalkylsilane molecular rectifiers

    NASA Astrophysics Data System (ADS)

    Lamport, Zachary A.; Broadnax, Angela D.; Harrison, David; Barth, Katrina J.; Mendenhall, Lee; Hamilton, Clayton T.; Guthold, Martin; Thonhauser, Timo; Welker, Mark E.; Jurchescu, Oana D.

    2016-11-01

    We report on the synthesis and electrical properties of nine new alkylated silane self-assembled monolayers (SAMs) – (EtO)3Si(CH2)nN = CHPhX where n = 3 or 11 and X = 4-CF3, 3,5-CF3, 3-F-4-CF3, 4-F, or 2,3,4,5,6-F, and explore their rectification behavior in relation to their molecular structure. The electrical properties of the films were examined in a metal/insulator/metal configuration, with a highly-doped silicon bottom contact and a eutectic gallium-indium liquid metal (EGaIn) top contact. The junctions exhibit high yields (>90%), a remarkable resistance to bias stress, and current rectification ratios (R) between 20 and 200 depending on the structure, degree of order, and internal dipole of each molecule. We found that the rectification ratio correlates positively with the strength of the molecular dipole moment and it is reduced with increasing molecular length.

  11. Molecularly Imprinted Biodegradable Nanoparticles.

    PubMed

    Gagliardi, Mariacristina; Bertero, Alice; Bifone, Angelo

    2017-01-10

    Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature. This paper reports the synthesis of a novel molecularly- imprinted nanocarrier, based on poly(lactide-co-glycolide) (PLGA) and acrylic acid, that combines biodegradability and molec- ular recognition properties. A novel three-arm biodegradable cross-linker was synthesized by ring-opening polymerization of glycolide and lactide initiated by glycerol. The resulting macromer was functionalized by introduction of end-functions through reaction with acryloyl chloride. Macromer and acrylic acid were used for the synthesis of narrowly-dispersed nanoparticles by radical polymerization in diluted conditions in the presence of biotin as template molecule. The binding capacity of the imprinted nanoparticles towards biotin and biotinylated bovine serum albumin was twentyfold that of non-imprinted nanoparti- cles. Degradation rates and functional performances were assessed in in vitro tests and cell cultures, demonstrating effective biotin-mediated cell internalization.

  12. Reviewing Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Fernandez Lopez, Manuel

    2017-07-01

    The star formation process involves a wide range of spatial scales, densities and temperatures. Herschel observations of the cold and low density molecular gas extending tens of parsecs, that constitutes the bulk of the molecular clouds of the Milky Way, have shown a network of dense structures in the shape of filaments. These filaments supposedly condense into higher density clumps to form individual stars or stellar clusters. The study of the kinematics of the filaments through single-dish observations suggests the presence of gas flows along the filaments, oscillatory motions due to gravity infall, and the existence of substructure inside filaments that may be threaded by twisted fibers. A few molecular clouds have been mapped with interferometric resolutions bringing more insight into the filament structure. Compression due to large-scale supersonic flows is the preferred mechanism to explain filament formation although the exact nature of the filaments, their origin and evolution are still not well understood. Determining the turbulence drivers behind the origin of the filaments, the relative importance of turbulence, gravity and magnetic fields on regulating the filament structure and evolution, and providing detailed insight on the substructure inside the filaments are among the current open questions in this research area.

  13. Mammalian Molecular Clocks

    PubMed Central

    Kwon, Ilmin; Choe, Han Kyoung; Son, Gi Hoon

    2011-01-01

    As a consequence of the Earth's rotation, almost all organisms experience day and night cycles within a 24-hr period. To adapt and synchronize biological rhythms to external daily cycles, organisms have evolved an internal time-keeping system. In mammals, the master circadian pacemaker residing in the suprachiasmatic nucleus (SCN) of the anterior hypothalamus generates circadian rhythmicity and orchestrates numerous subsidiary local clocks in other regions of the brain and peripheral tissues. Regardless of their locations, these circadian clocks are cell-autonomous and self-sustainable, implicating rhythmic oscillations in a variety of biochemical and metabolic processes. A group of core clock genes provides interlocking molecular feedback loops that drive the circadian rhythm even at the single-cell level. In addition to the core transcription/translation feedback loops, post-translational modifications also contribute to the fine regulation of molecular circadian clocks. In this article, we briefly review the molecular mechanisms and post-translational modifications of mammalian circadian clock regulation. We also discuss the organization of and communication between central and peripheral circadian oscillators of the mammalian circadian clock. PMID:22110358

  14. Molecular biology of hearing

    PubMed Central

    Stöver, Timo; Diensthuber, Marc

    2012-01-01

    The inner ear is our most sensitive sensory organ and can be subdivided into three functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound, which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear houses the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In recent years there has been significant progress in research on the molecular basis of hearing. An increasing number of genes and proteins related to hearing are being identified and characterized. The growing knowledge of these genes contributes not only to greater appreciation of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss. PMID:22558056

  15. Molecular Classification of Medulloblastoma

    PubMed Central

    KIJIMA, Noriyuki; KANEMURA, Yonehiro

    2016-01-01

    Medulloblastoma (MB) is one of the most frequent malignant brain tumors in children. The current standard treatment regimen consists of surgical resection, craniospinal irradiation, and adjuvant chemotherapy. Although these treatments have the potential to increase the survival of 70–80% of patients with MB, they are also associated with serious treatment-induced morbidity. The current risk stratification of MB is based on clinical factors, including age at presentation, metastatic status, and the presence of residual tumor following resection. In addition, recent genomic studies indicate that MB consists of at least four distinct molecular subgroups: WNT, sonic hedgehog (SHH), Group 3, and Group 4. WNT and SHH MBs are characterized by aberrations in the WNT and SHH signaling pathways, respectively. WNT MB has the best prognosis compared to the other MBs, while SHH MB has an intermediate prognosis. The underlying signaling pathways associated with Group 3 and 4 MBs have not been identified. Group 3 MB is frequently associated with metastasis, resulting in a poor prognosis, while Group 4 is sometimes associated with metastasis and has an intermediate prognosis. Group 4 is the most frequent MB and represents 35% of all MBs. These findings suggest that MB is a heterogeneous disease, and that MB subgroups have distinct molecular, demographic, and clinical characteristics. The molecular classification of MBs is redefining the risk stratification of patients with MB, and has the potential to identify new therapeutic strategies for the treatment of MB. PMID:27238212

  16. Fluorinated benzalkylsilane molecular rectifiers

    PubMed Central

    Lamport, Zachary A.; Broadnax, Angela D.; Harrison, David; Barth, Katrina J.; Mendenhall, Lee; Hamilton, Clayton T.; Guthold, Martin; Thonhauser, Timo; Welker, Mark E.; Jurchescu, Oana D.

    2016-01-01

    We report on the synthesis and electrical properties of nine new alkylated silane self-assembled monolayers (SAMs) – (EtO)3Si(CH2)nN = CHPhX where n = 3 or 11 and X = 4-CF3, 3,5-CF3, 3-F-4-CF3, 4-F, or 2,3,4,5,6-F, and explore their rectification behavior in relation to their molecular structure. The electrical properties of the films were examined in a metal/insulator/metal configuration, with a highly-doped silicon bottom contact and a eutectic gallium-indium liquid metal (EGaIn) top contact. The junctions exhibit high yields (>90%), a remarkable resistance to bias stress, and current rectification ratios (R) between 20 and 200 depending on the structure, degree of order, and internal dipole of each molecule. We found that the rectification ratio correlates positively with the strength of the molecular dipole moment and it is reduced with increasing molecular length. PMID:27897250

  17. Thermoelectricity in molecular junctions.

    PubMed

    Reddy, Pramod; Jang, Sung-Yeon; Segalman, Rachel A; Majumdar, Arun

    2007-03-16

    By trapping molecules between two gold electrodes with a temperature difference across them, the junction Seebeck coefficients of 1,4-benzenedithiol (BDT), 4,4'-dibenzenedithiol, and 4,4''-tribenzenedithiol in contact with gold were measured at room temperature to be +8.7 +/- 2.1 microvolts per kelvin (muV/K), +12.9 +/- 2.2 muV/K, and +14.2 +/- 3.2 muV/K, respectively (where the error is the full width half maximum of the statistical distributions). The positive sign unambiguously indicates p-type (hole) conduction in these heterojunctions, whereas the Au Fermi level position for Au-BDT-Au junctions was identified to be 1.2 eV above the highest occupied molecular orbital level of BDT. The ability to study thermoelectricity in molecular junctions provides the opportunity to address these fundamental unanswered questions about their electronic structure and to begin exploring molecular thermoelectric energy conversion.

  18. Molecularly Imprinted Biodegradable Nanoparticles

    NASA Astrophysics Data System (ADS)

    Gagliardi, Mariacristina; Bertero, Alice; Bifone, Angelo

    2017-01-01

    Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature. This paper reports the synthesis of a novel molecularly- imprinted nanocarrier, based on poly(lactide-co-glycolide) (PLGA) and acrylic acid, that combines biodegradability and molec- ular recognition properties. A novel three-arm biodegradable cross-linker was synthesized by ring-opening polymerization of glycolide and lactide initiated by glycerol. The resulting macromer was functionalized by introduction of end-functions through reaction with acryloyl chloride. Macromer and acrylic acid were used for the synthesis of narrowly-dispersed nanoparticles by radical polymerization in diluted conditions in the presence of biotin as template molecule. The binding capacity of the imprinted nanoparticles towards biotin and biotinylated bovine serum albumin was twentyfold that of non-imprinted nanoparti- cles. Degradation rates and functional performances were assessed in in vitro tests and cell cultures, demonstrating effective biotin-mediated cell internalization.

  19. Molecularly Imprinted Biodegradable Nanoparticles

    PubMed Central

    Gagliardi, Mariacristina; Bertero, Alice; Bifone, Angelo

    2017-01-01

    Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature. This paper reports the synthesis of a novel molecularly- imprinted nanocarrier, based on poly(lactide-co-glycolide) (PLGA) and acrylic acid, that combines biodegradability and molec- ular recognition properties. A novel three-arm biodegradable cross-linker was synthesized by ring-opening polymerization of glycolide and lactide initiated by glycerol. The resulting macromer was functionalized by introduction of end-functions through reaction with acryloyl chloride. Macromer and acrylic acid were used for the synthesis of narrowly-dispersed nanoparticles by radical polymerization in diluted conditions in the presence of biotin as template molecule. The binding capacity of the imprinted nanoparticles towards biotin and biotinylated bovine serum albumin was twentyfold that of non-imprinted nanoparti- cles. Degradation rates and functional performances were assessed in in vitro tests and cell cultures, demonstrating effective biotin-mediated cell internalization. PMID:28071745

  20. 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.

  1. Molecular basis of alcoholism.

    PubMed

    Most, Dana; Ferguson, Laura; Harris, R Adron

    2014-01-01

    Acute alcohol intoxication causes cellular changes in the brain that last for hours, while chronic alcohol use induces widespread neuroadaptations in the nervous system that can last a lifetime. Chronic alcohol use and the progression into dependence involve the remodeling of synapses caused by changes in gene expression produced by alcohol. The progression of alcohol use, abuse, and dependence can be divided into stages, which include intoxication, withdrawal, and craving. Each stage is associated with specific changes in gene expression, cellular function, brain circuits, and ultimately behavior. What are the molecular mechanisms underlying the transition from recreational use (acute) to dependence (chronic)? What cellular adaptations result in drug memory retention, leading to the persistence of addictive behaviors, even after prolonged drug abstinence? Research into the neurobiology of alcoholism aims to answer these questions. This chapter will describe the molecular adaptations caused by alcohol use and dependence, and will outline key neurochemical participants in alcoholism at the molecular level, which are also potential targets for therapy. © 2014 Elsevier B.V. All rights reserved.

  2. Molecular pathology in transfusion medicine.

    PubMed

    Elkins, Matthew B; Davenport, Robertson D; O'Malley, Barbara A; Bluth, Martin H

    2013-12-01

    This article provides an overview of the application of molecular diagnostic methods to red cell and platelet compatibility testing. The advantages and limitations of molecular methods are evaluated compared with traditional serologic methods. The molecular bases of clinically significant red cell and platelet antigens are presented. Current recommendations for reporting molecular assay results and distinctions between genotype and phenotype are discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. PHOTOPHYSICAL PROCESSES IN MOLECULAR SOLIDS.

    DTIC Science & Technology

    BENZOPHENONES , *MOLECULAR ENERGY LEVELS), (*PHOSPHORESCENCE, BENZOPHENONES ), (*PHOTOCHEMICAL REACTIONS, BENZOPHENONES ), ELECTRON TRANSITIONS, SINGLE CRYSTALS, ULTRAVIOLET SPECTRA, VISIBLE SPECTRA, ACETOPHENONES

  4. Molecular proxies for paleoclimatology

    NASA Astrophysics Data System (ADS)

    Eglinton, Timothy I.; Eglinton, Geoffrey

    2008-10-01

    We summarize the applications of molecular proxies in paleoclimatology. Marine molecular records especially are proving to be of value but certain environmentally persistent compounds can also be measured in lake sediments, loess deposits and ice cores. The fundamentals of this approach are the molecular parameters, the compound abundances and carbon, hydrogen, nitrogen and oxygen isotopic contents which can be derived by the analysis of sediment extracts. These afford proxy measures which can be interpreted in terms of the conditions which control climate and also reflect its operation. We discuss two types of proxy; those of terrigenous and those of aquatic origin, and exemplify their application in the study of marine sediments through the medium of ten case studies based in the Atlantic, Mediterranean and Pacific Oceans, and in Antarctica. The studies are mainly for periods in the present, the Holocene and particularly the last glacial/interglacial, but they also include one study from the Cretaceous. The terrigenous proxies, which are measures of continental vegetation, are based on higher plant leaf wax compounds, i.e. long-chain (circa C 30) hydrocarbons, alcohols and acids. They register the relative contributions of C 3 vs. C 4 type plants to the vegetation in the source areas. The two marine proxies are measures of sea surface temperatures (SST). The longer established one, (U 37K') is based on the relative abundances of C 37 alkenones photosynthesized by unicellular algae, members of the Haptophyta. The newest proxy (TEX 86) is based on C 86 glycerol tetraethers (GDGTs) synthesized in the water column by some of the archaeal microbiota, the Crenarchaeota.

  5. THE CALIFORNIA MOLECULAR CLOUD

    SciTech Connect

    Lada, Charles J.; Lombardi, Marco; Alves, Joao F. E-mail: mlombard@eso.or

    2009-09-20

    We present an analysis of wide-field infrared extinction maps of a region in Perseus just north of the Taurus-Auriga dark cloud complex. From this analysis we have identified a massive, nearby, but previously unrecognized, giant molecular cloud (GMC). Both a uniform foreground star density and measurements of the cloud's velocity field from CO observations indicate that this cloud is likely a coherent structure at a single distance. From comparison of foreground star counts with Galactic models, we derive a distance of 450 +- 23 pc to the cloud. At this distance the cloud extends over roughly 80 pc and has a mass of {approx} 10{sup 5} M{sub sun}, rivaling the Orion (A) molecular cloud as the largest and most massive GMC in the solar neighborhood. Although surprisingly similar in mass and size to the more famous Orion molecular cloud (OMC) the newly recognized cloud displays significantly less star formation activity with more than an order of magnitude fewer young stellar objects than found in the OMC, suggesting that both the level of star formation and perhaps the star formation rate in this cloud are an order of magnitude or more lower than in the OMC. Analysis of extinction maps of both clouds shows that the new cloud contains only 10% the amount of high extinction (A{sub K} > 1.0 mag) material as is found in the OMC. This, in turn, suggests that the level of star formation activity and perhaps the star formation rate in these two clouds may be directly proportional to the total amount of high extinction material and presumably high density gas within them and that there might be a density threshold for star formation on the order of n(H{sub 2}) {approx} a few x 10{sup 4} cm{sup -3}.

  6. VMD: visual molecular dynamics.

    PubMed

    Humphrey, W; Dalke, A; Schulten, K

    1996-02-01

    VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.

  7. Supported Molecular Matrix Electrophoresis.

    PubMed

    Matsuno, Yu-Ki; Kameyama, Akihiko

    2015-01-01

    Mucins are difficult to separate using conventional gel electrophoresis methods such as SDS-PAGE and agarose gel electrophoresis, owing to their large size and heterogeneity. On the other hand, cellulose acetate membrane electrophoresis can separate these molecules, but is not compatible with glycan analysis. Here, we describe a novel membrane electrophoresis technique, termed "supported molecular matrix electrophoresis" (SMME), in which a porous polyvinylidene difluoride (PVDF) membrane filter is used to achieve separation. This description includes the separation, visualization, and glycan analysis of mucins with the SMME technique.

  8. Molecular Mechanisms of Preeclampsia

    PubMed Central

    Hod, Tammy; Cerdeira, Ana Sofia; Karumanchi, S. Ananth

    2015-01-01

    Preeclampsia is a pregnancy-specific disease characterized by new onset hypertension and proteinuria after 20 wk of gestation. It is a leading cause of maternal and fetal morbidity and mortality worldwide. Exciting discoveries in the last decade have contributed to a better understanding of the molecular basis of this disease. Epidemiological, experimental, and therapeutic studies from several laboratories have provided compelling evidence that an antiangiogenic state owing to alterations in circulating angiogenic factors leads to preeclampsia. In this review, we highlight the role of key circulating antiangiogenic factors as pathogenic biomarkers and in the development of novel therapies for preeclampsia. PMID:26292986

  9. [Molecular physiology of aging].

    PubMed

    Khavinson, V Kh; Morozov, V G; Malinin, V V

    2001-01-01

    The article is dedicated to the analysis of the peptide bioregulators role in molecular mechanisms of ageing and age-related pathology development. There has been put forward the concept of peptide regulation of ageing based on the priority data of authors long-term investigations on inhibition of involution processes in organs and tissues developed with age and restoration of specific proteins synthesis in cells under the influence of natural and synthetic peptide bioregulators. The prospects of peptide bioregulators employment in gerontological practice are being discussed in the paper with the purpose of treatment and prevention of age-associated pathology and human longevity increase.

  10. Switchable molecular magnets.

    PubMed

    Sato, Osamu

    2012-01-01

    Various molecular magnetic compounds whose magnetic properties can be controlled by external stimuli have been developed, including electrochemically, photochemically, and chemically tunable bulk magnets as well as a phototunable antiferromagnetic phase of single chain magnet. In addition, we present tunable paramagnetic mononuclear complexes ranging from spin crossover complexes and valence tautomeric complexes to Co complexes in which orbital angular momentum can be switched. Furthermore, we recently developed several switchable clusters and one-dimensional coordination polymers. The switching of magnetic properties can be achieved by modulating metals, ligands, and molecules/ions in the second sphere of the complexes.

  11. Molecular mechanisms of etoposide

    PubMed Central

    Montecucco, Alessandra; Zanetta, Francesca; Biamonti, Giuseppe

    2015-01-01

    Etoposide derives from podophyllotoxin, a toxin found in the American Mayapple. It was first synthesized in 1966 and approved for cancer therapy in 1983 by the U.S. Food and Drug Administration (Hande, 1998[25]). Starting from 1980s several studies demonstrated that etoposide targets DNA topoisomerase II activities thus leading to the production of DNA breaks and eliciting a response that affects several aspects of cell metabolisms. In this review we will focus on molecular mechanisms that account for the biological effect of etoposide. PMID:26600742

  12. Molecular anisotropic magnetoresistance

    NASA Astrophysics Data System (ADS)

    Otte, Fabian; Heinze, Stefan; Mokrousov, Yuriy

    2015-12-01

    Using density functional theory calculations, we demonstrate that the effect of anisotropic magnetoresistance (AMR) can be enhanced by orders of magnitude with respect to conventional bulk ferromagnets in junctions containing molecules sandwiched between ferromagnetic leads. We study ballistic transport in metal-benzene complexes contacted by 3 d transition-metal wires. We show that a gigantic AMR can arise from spin-orbit coupling effects in the leads, drastically enhanced by orbital-symmetry filtering properties of the molecules. We further discuss how this molecular anisotropic magnetoresistance (MAMR) can be tuned by the proper choice of materials and their electronic properties.

  13. Molecular Toxicology of Chromatin

    DTIC Science & Technology

    1992-01-01

    FINAL 01 Jan 89 TO 31 Dec 91 4. ITL ANO SUS Y, L RE %UMAS MOLECULAR TOXICOLOGY OF CHROMATIN AFOSR-89-0231 PE - 61102F AUT PR - 2312 TA - A5 Dr Ernest Kun...Waterbury, CT), 2-mercaptoethanol, NAD+, NADPH, nucleo- tides, sodium tungstate , hydrogen peroxide, Tris and MES buffers from Sigma (St. Louis, MO...ml) with sodium tungstate (5.93 g, in 20 ml H20) for 1.5 h followed by extraction of the green product into ethyl acetate, washing with 0.1 N HCl, and

  14. Switchable molecular magnets

    PubMed Central

    SATO, Osamu

    2012-01-01

    Various molecular magnetic compounds whose magnetic properties can be controlled by external stimuli have been developed, including electrochemically, photochemically, and chemically tunable bulk magnets as well as a phototunable antiferromagnetic phase of single chain magnet. In addition, we present tunable paramagnetic mononuclear complexes ranging from spin crossover complexes and valence tautomeric complexes to Co complexes in which orbital angular momentum can be switched. Furthermore, we recently developed several switchable clusters and one-dimensional coordination polymers. The switching of magnetic properties can be achieved by modulating metals, ligands, and molecules/ions in the second sphere of the complexes. PMID:22728438

  15. Molecular origin of friction

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Zhang, Tao; Hu, Yuanzhong

    2004-01-01

    The wearless friction originating from molecular interactions has been discussed in this paper. We find that the frictional properties are closely related to the structural match of two surfaces in relative motion. For the surfaces with incommensurate structure and week inter-surface interaction, zero static and kinetic friction can be achieved. In a sliding considered as in a quasi-static state, the energy dissipation initiates when interfacial particles move in a discontinuous fashion, which gives rise to a finite kinetic friction. The state of superlubricity is a result of computer simulations, but the prediction will encourage people to look for a technical approach to realizing the state of super low friction.

  16. Molecular Comb Development

    SciTech Connect

    Ferrell, T.L.; Thundat, G.T.; Witkowski, C.E., III

    2007-07-17

    This CRADA was developed to enable ORNL to assist Protein Discovery, Inc. to develop a novel biomolecular separation system based on an ORNL patent application 'Photoelectrochemical Molecular Comb' by Thundat, Ferrell, and Brown. The Molecular Comb concept is based on creating light-induced charge carriers at a semiconductor-liquid interface, which is kept at a potential control such that a depletion layer is formed in the semiconductor. Focusing light from a low-power illumination source creates electron-hole pairs, which get separated in the depletion layer. The light-induced charge carriers reaching the surface attract oppositely charged biomolecules present in the solution. The solution is a buffer solution with very small concentrations of biomolecules. As the focused light is moved across the surface of the semiconductor-liquid interface, the accumulated biomolecules follow the light beam. A thin layer of gel or other similar material on the surface of the semiconductor can act as a sieving medium for separating the biomolecules according to their sizes.

  17. Methods in Molecular Biophysics

    NASA Astrophysics Data System (ADS)

    Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph

    2001-12-01

    Our knowledge of biological macromolecules and their interactions is based on the application of physical methods, ranging from classical thermodynamics to recently developed techniques for the detection and manipulation of single molecules. These methods, which include mass spectrometry, hydrodynamics, microscopy, diffraction and crystallography, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, are complementary; each has its specific advantages and limitations. Organised by method, this textbook provides descriptions and examples of applications for the key physical methods in modern biology. It is an invaluable resource for undergraduate and graduate students of molecular biophysics in science and medical schools, as well as research scientists looking for an introduction to techniques beyond their specialty. As appropriate for this interdisciplinary field, the book includes short asides to explain physics aspects to biologists and biology aspects to physicists. Comprehensive coverage and up-to-date treatment of the latest physical methods in modern biology Each method includes a brief historical introduction, theoretical principles, applications, advantages and limitations, and concludes with a checklist of key ideas Interdisciplinary and accessible to biologists, physicists, and those with medical backgrounds

  18. Molecular control of oogenesis.

    PubMed

    Sánchez, Flor; Smitz, Johan

    2012-12-01

    Oogenesis is a complex process regulated by a vast number of intra- and extra-ovarian factors. Oogonia, which originate from primordial germ cells, proliferate by mitosis and form primary oocytes that arrest at the prophase stage of the first meiotic division until they are fully-grown. Within primary oocytes, synthesis and accumulation of RNAs and proteins throughout oogenesis are essential for oocyte growth and maturation; and moreover, crucial for developing into a viable embryo after fertilization. Oocyte meiotic and developmental competence is gained in a gradual and sequential manner during folliculogenesis and is related to the fact that the oocyte grows in interaction with its companion somatic cells. Communication between oocyte and its surrounding granulosa cells is vital, both for oocyte development and for granulosa cells differentiation. Oocytes depend on differentiated cumulus cells, which provide them with nutrients and regulatory signals needed to promote oocyte nuclear and cytoplasmic maturation and consequently the acquisition of developmental competence.The purpose of this article is to summarize recent knowledge on the molecular aspects of oogenesis and oocyte maturation, and the crucial role of cumulus-cell interactions, highlighting the valuable contribution of experimental evidences obtained in animal models. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.

  19. Quantum molecular master equations

    NASA Astrophysics Data System (ADS)

    Brechet, Sylvain D.; Reuse, Francois A.; Maschke, Klaus; Ansermet, Jean-Philippe

    2016-10-01

    We present the quantum master equations for midsize molecules in the presence of an external magnetic field. The Hamiltonian describing the dynamics of a molecule accounts for the molecular deformation and orientation properties, as well as for the electronic properties. In order to establish the master equations governing the relaxation of free-standing molecules, we have to split the molecule into two weakly interacting parts, a bath and a bathed system. The adequate choice of these systems depends on the specific physical system under consideration. Here we consider a first system consisting of the molecular deformation and orientation properties and the electronic spin properties and a second system composed of the remaining electronic spatial properties. If the characteristic time scale associated with the second system is small with respect to that of the first, the second may be considered as a bath for the first. Assuming that both systems are weakly coupled and initially weakly correlated, we obtain the corresponding master equations. They describe notably the relaxation of magnetic properties of midsize molecules, where the change of the statistical properties of the electronic orbitals is expected to be slow with respect to the evolution time scale of the bathed system.

  20. MOLECULAR VACUUM PUMP

    DOEpatents

    Eckberg, E.E.

    1960-09-27

    A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

  1. Molecular enzymology of lipoxygenases.

    PubMed

    Ivanov, Igor; Heydeck, Dagmar; Hofheinz, Katharina; Roffeis, Jana; O'Donnell, Valerie B; Kuhn, Hartmut; Walther, Matthias

    2010-11-15

    Lipoxygenases (LOXs) are lipid peroxidizing enzymes, implicated in the pathogenesis of inflammatory and hyperproliferative diseases, which represent potential targets for pharmacological intervention. Although soybean LOX1 was discovered more than 60years ago, the structural biology of these enzymes was not studied until the mid 1990s. In 1993 the first crystal structure for a plant LOX was solved and following this protein biochemistry and molecular enzymology became major fields in LOX research. This review focuses on recent developments in molecular enzymology of LOXs and summarizes our current understanding of the structural basis of LOX catalysis. Various hypotheses explaining the reaction specificity of different isoforms are critically reviewed and their pros and cons briefly discussed. Moreover, we summarize the current knowledge of LOX evolution by profiling the existence of LOX-related genomic sequences in the three kingdoms of life. Such sequences are found in eukaryotes and bacteria but not in archaea. Although the biological role of LOXs in lower organisms is far from clear, sequence data suggests that this enzyme family might have evolved shortly after the appearance of atmospheric oxygen on earth.

  2. Molecular Epidemiology of Amebiasis

    PubMed Central

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis. PMID:18571478

  3. Attosecond Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Martin, Fernando

    2015-05-01

    The development of attosecond laser pulses allows one to probe the inner working of atoms, molecules and surfaces on the timescale of the electronic response. In molecules, attosecond pump-probe spectroscopy enables investigations of the prompt charge redistribution and localization that accompany photo-excitation processes, where a molecule is lifted from the ground Born-Oppenheimer potential energy surface to one or more excited surfaces, and where subsequent photochemistry evolves on femto- and attosecond timescales. In this talk I will present a few theoretical examples of realistic molecular attosecond pump-probe experiments in which simple molecules are ionized with a single attosecond pulse (or a train of attosecond pulses) and are subsequently probed by one or several infrared or xuv few-cycle pulses. The evolution of the electronic and nuclear densities in the photo-excited molecule or remaining molecular ions is calculated with attosecond time-resolution and is visualized by varying the delay between the pump and probe pulses. The results of these calculations allow us to explain several experimental observations as well as to guide future experimental efforts to uncover ultrafast electron and nuclear dynamics in molecules.

  4. Towards graphyne molecular electronics.

    PubMed

    Li, Zhihai; Smeu, Manuel; Rives, Arnaud; Maraval, Valérie; Chauvin, Remi; Ratner, Mark A; Borguet, Eric

    2015-02-20

    α-Graphyne, a carbon-expanded version of graphene ('carbo-graphene') that was recently evidenced as an alternative zero-gap semiconductor, remains a theoretical material. Nevertheless, using specific synthesis methods, molecular units of α-graphyne ('carbo-benzene' macrocycles) can be inserted between two anilinyl (4-NH2-C6H4)-anchoring groups that allow these fragments to form molecular junctions between gold electrodes. Here, electrical measurements by the scanning tunnelling microscopy (STM) break junction technique and electron transport calculations are carried out on such a carbo-benzene, providing unprecedented single molecule conductance values: 106 nS through a 1.94-nm N-N distance, essentially 10 times the conductance of a shorter nanographenic hexabenzocoronene analogue. Deleting a C4 edge of the rigid C18 carbo-benzene circuit results in a flexible 'carbo-butadiene' molecule that has a conductance 40 times lower. Furthermore, carbo-benzene junctions exhibit field-effect transistor behaviour when an electrochemical gate potential is applied, opening the way for device applications. All the results are interpreted on the basis of theoretical calculations.

  5. Evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Sevenster, M.

    1993-01-01

    The evolution of interstellar molecular hydrogen was studied, with a special interest for the formation and evolution of molecular clouds and star formation within them, by a two-dimensional hydrodynamical simulation performed on a rectangular grid of physical sizes on the order of 100 pc. It is filled with an initial density of approx. 1 cm(exp -3), except for one cell (approx. 1 pc(exp 2)) at the center of the grid where an accretion core of 1-10(exp 3) solar masses is placed. The grid is co-moving with the gridcenter that is on a circular orbit around the Galactic center and that also is the guiding center of epicyclic approximation of orbits of the matter surrounding it. The initial radial velocity is zero; to account for differential rotation the initial tangential velocity (i.e. the movement around the galactic center) is proportional to the radial distance to the grid center. The rate is comparable to the rotation rate at the Local Standard of Rest. The influence of galactic rotation is noticed by spiral or elliptical forms, but on much longer time scales than self gravitation and cooling processes. Density and temperature are kept constant at the boundaries and no inflow is allowed along the tangential boundaries.

  6. Multiscale reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-12-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

  7. Towards graphyne molecular electronics

    NASA Astrophysics Data System (ADS)

    Li, Zhihai; Smeu, Manuel; Rives, Arnaud; Maraval, Valérie; Chauvin, Remi; Ratner, Mark A.; Borguet, Eric

    2015-02-01

    α-Graphyne, a carbon-expanded version of graphene (‘carbo-graphene’) that was recently evidenced as an alternative zero-gap semiconductor, remains a theoretical material. Nevertheless, using specific synthesis methods, molecular units of α-graphyne (‘carbo-benzene’ macrocycles) can be inserted between two anilinyl (4-NH2-C6H4)-anchoring groups that allow these fragments to form molecular junctions between gold electrodes. Here, electrical measurements by the scanning tunnelling microscopy (STM) break junction technique and electron transport calculations are carried out on such a carbo-benzene, providing unprecedented single molecule conductance values: 106 nS through a 1.94-nm N-N distance, essentially 10 times the conductance of a shorter nanographenic hexabenzocoronene analogue. Deleting a C4 edge of the rigid C18 carbo-benzene circuit results in a flexible ‘carbo-butadiene’ molecule that has a conductance 40 times lower. Furthermore, carbo-benzene junctions exhibit field-effect transistor behaviour when an electrochemical gate potential is applied, opening the way for device applications. All the results are interpreted on the basis of theoretical calculations.

  8. Molecular mechanisms in gliomagenesis.

    PubMed

    Hulleman, Esther; Helin, Kristian

    2005-01-01

    Glioma, and in particular high-grade astrocytoma termed glioblastoma multiforme (GBM), is the most common primary tumor of the brain. Primarily because of its diffuse nature, there is no effective treatment for GBM, and relatively little is known about the processes by which it develops. Therefore, in order to design novel therapies and treatments for GBM, research has recently intensified to identify the cellular and molecular mechanisms leading to GBM formation. Modeling of astrocytomas by genetic manipulation of mice suggests that deregulation of the pathways that control gliogenesis during normal brain development, such as the differentiation of neural stem cells (NSCs) into astrocytes, might contribute to GBM formation. These pathways include growth factor-induced signal transduction routes and processes that control cell cycle progression, such as the p16-CDK4-RB and the ARF-MDM2-p53 pathways. The expression of several of the components of these signaling cascades has been found altered in GBM, and recent data indicate that combinations of mutations in these pathways may contribute to GBM formation, although the exact mechanisms are still to be uncovered. Use of novel techniques including large-scale genomics and proteomics in combination with relevant mouse models will most likely provide novel insights into the molecular mechanisms underlying glioma formation and will hopefully lead to development of treatment modalities for GBM.

  9. Molecular mechanisms in cardiomyopathy.

    PubMed

    Dadson, Keith; Hauck, Ludger; Billia, Filio

    2017-07-01

    Cardiomyopathies represent a heterogeneous group of diseases that negatively affect heart function. Primary cardiomyopathies specifically target the myocardium, and may arise from genetic [hypertrophic cardiomyopathy (HCM), arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D), mitochondrial cardiomyopathy] or genetic and acquired [dilated cardiomyopathy (DCM), restrictive cardiomyopathy (RCM)] etiology. Modern genomics has identified mutations that are common in these populations, while in vitro and in vivo experimentation with these mutations have provided invaluable insight into the molecular mechanisms native to these diseases. For example, increased myosin heavy chain (MHC) binding and ATP utilization lead to the hypercontractile sarcomere in HCM, while abnormal protein-protein interaction and impaired Ca(2+) flux underlie the relaxed sarcomere of DCM. Furthermore, expanded access to genetic testing has facilitated identification of potential risk factors that appear through inheritance and manifest sometimes only in the advanced stages of the disease. In this review, we discuss the genetic and molecular abnormalities unique to and shared between these primary cardiomyopathies and discuss some of the important advances made using more traditional basic science experimentation. © 2017 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  10. The Molecular Atlas Project

    NASA Astrophysics Data System (ADS)

    Silverberg, Jesse; Yin, Peng

    The promise of super-resolution microscopy is a technology to discover new biological mechanisms that occur at smaller length scales then previously observable. However, with higher-resolution, we generally lose the larger spatial context of the image itself. The Molecular Atlas Project (MAP) directly asks how these competing interests between super-resolution imaging and broader spatially contextualized information can be reconciled. MAP enables us to acquire, visualize, explore, and annotate proteomic image data representing 7 orders of magnitude in length ranging from molecular (nm) to tissue (cm) scales. This multi-scale understanding is made possible by combining multiplexed DNA-PAINT, a DNA nanotechnology approach to super-resolution imaging, with ``big-data'' strategies for information management and image visualization. With these innovations combined, MAP enables us to explore cell-specific heterogeneity in ductal carcinoma for every cellin a cm-sized tissue section, analyze organoid growth for advances in high-throughput tissue-on-a-chip technology, and examine individual synapses for connectome mapping over extremely wide areas. Ultimately, MAP is a fundamentally new way to interact with multiscale biophysical data.

  11. Molecular phylogenetics before sequences

    PubMed Central

    Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin

    2014-01-01

    From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today. PMID:24572375

  12. Multiscale reactive molecular dynamics

    PubMed Central

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-01-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062

  13. Photoinduced diffusion molecular transport

    NASA Astrophysics Data System (ADS)

    Rozenbaum, Viktor M.; Dekhtyar, Marina L.; Lin, Sheng Hsien; Trakhtenberg, Leonid I.

    2016-08-01

    We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).

  14. 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.

  15. Assessment of Molecular Modeling & Simulation

    SciTech Connect

    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 materials 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.

  16. Molecular Pathophysiology of Gout.

    PubMed

    Desai, Jyaysi; Steiger, Stefanie; Anders, Hans-Joachim

    2017-08-01

    Three contradictory clinical presentations of gout have puzzled clinicians and basic scientists for some time: first, the crescendo of sterile inflammation in acute gouty arthritis; second, its spontaneous resolution, despite monosodium urate (MSU) crystal persistence in the synovium; and third, immune anergy to MSU crystal masses observed in tophaceous or visceral gout. Here, we provide an update on the molecular pathophysiology of these gout manifestations, namely, how MSU crystals can trigger the auto-amplification loop of necroinflammation underlying the crescendo of acute gouty arthritis. We also discuss new findings, such as how aggregating neutrophil extracellular traps (NETs) might drive the resolution of arthritis and how these structures, together with granuloma formation, might support immune anergy, but yet promote tissue damage and remodeling during tophaceous gout. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. GAS PHASE MOLECULAR DYNAMICS

    SciTech Connect

    SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution, high-sensitivity, laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.

  18. Molecular Dynamics Calculations

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two

  19. Molecular pathogenesis of emphysema

    PubMed Central

    Taraseviciene-Stewart, Laimute; Voelkel, Norbert F.

    2008-01-01

    Emphysema is one manifestation of a group of chronic, obstructive, and frequently progressive destructive lung diseases. Cigarette smoking and air pollution are the main causes of emphysema in humans, and cigarette smoking causes emphysema in rodents. This review examines the concept of a homeostatically active lung structure maintenance program that, when attacked by proteases and oxidants, leads to the loss of alveolar septal cells and airspace enlargement. Inflammatory and noninflammatory mechanisms of disease pathogenesis, as well as the role of the innate and adaptive immune systems, are being explored in genetically altered animals and in exposure models of this disease. These recent scientific advances support a model whereby alveolar destruction resulting from a coalescence of mechanical forces, such as hyperinflation, and more recently recognized cellular and molecular events, including apoptosis, cellular senescence, and failed lung tissue repair, produces the clinically recognized syndrome of emphysema. PMID:18246188

  20. Methods in molecular cardiology

    PubMed Central

    de Theije, C.C.; de Windt, L.J.; Doevendans, P.A.

    2002-01-01

    Sequencing is one the major breakthroughs in molecular cardiology. The development of this technique has made it possible to determine the exact order of the nucleotides in DNA. The exact order is relevant for the formation of proteins, through the genetic code. Sequencing is even more important for the identification of genetic variation and disease-causing mutations. The elucidation of the human genome is based on the continuous improvement of this technique, reducing the cost and increasing efficiency. Initially, complex chemical reactions were performed using isotopes to unravel the base sequence in genes. Nowadays, fluorescent capillary-based techniques are available to determine the genetic information. Here, the historical development of the technique is described. In addition, examples are provided on how sequencing is used in clinical medicine. ImagesFigure 2Figure 3Figure 8Figure 9 PMID:25696079

  1. Molecular biology references.

    PubMed

    2003-05-01

    Many of the units in this manual describe methods and techniques for the cloning, expression, and structural analysis of neural genes and proteins. We assume that users of these protocols have at least some introductory background in recombinant DNA technology (or are working with a collaborator who does); therefore, we have not provided comprehensive coverage of all of these topics, but rather have concentrated on presenting selected techniques that will be of the most interest and use to the general neuroscience laboratory. More comprehensive coverage of these topics can be found in Current Protocols in Molecular Biology (CPMB), which is extensively cross-referenced throughout this manual. These cross-references are summarized in this appendix.

  2. Molecular mechanisms of carcinogenesis

    SciTech Connect

    Hall, E.J.

    1997-03-01

    The possibility that chromosomal changes are responsible for neoplasia was proposed in the early years of this century. A combination of improved cytogenetics and the advent of recombinant technology has settled the issue. As recently as 20 years ago, however, the genetic and molecular basis of familiar predisposition to cancer were a mystery, and it is only in the last few years that light has been shed on a few specific types of malignancies. As the genetic basis of human cancer had been documented, a number of genes have been identified as functioning either as oncogenes which act in a dominant fashion to promote tumor growth when mutated, or as tumor suppressor genes which act in a recessive fashion.

  3. Molecular pathogenesis of emphysema.

    PubMed

    Taraseviciene-Stewart, Laimute; Voelkel, Norbert F

    2008-02-01

    Emphysema is one manifestation of a group of chronic, obstructive, and frequently progressive destructive lung diseases. Cigarette smoking and air pollution are the main causes of emphysema in humans, and cigarette smoking causes emphysema in rodents. This review examines the concept of a homeostatically active lung structure maintenance program that, when attacked by proteases and oxidants, leads to the loss of alveolar septal cells and airspace enlargement. Inflammatory and noninflammatory mechanisms of disease pathogenesis, as well as the role of the innate and adaptive immune systems, are being explored in genetically altered animals and in exposure models of this disease. These recent scientific advances support a model whereby alveolar destruction resulting from a coalescence of mechanical forces, such as hyperinflation, and more recently recognized cellular and molecular events, including apoptosis, cellular senescence, and failed lung tissue repair, produces the clinically recognized syndrome of emphysema.

  4. A Truncated Molecular Star.

    PubMed

    Prusty, Soumyakanta; Yazaki, Kohei; Yoshizawa, Michito; Chand, Dillip Kumar

    2017-09-12

    A pentanuclear coordination complex assembled from any palladium(II) component and non-chelating ligands is hitherto unreported. The pentanuclear complex [Pd5 (L1)5 (L2)5 ](BF4 )10 , 1 reported here was prepared by the spontaneous complexation of [Pd(DMSO)4 ](BF4 )2 with the non-chelating bidentate ligands 1,4-phenylenebis(methylene) diisonicotinate, L1 and 4,4'-bipyridine, L2 in a one-pot method at room temperature. The planar polycyclic complex 1 with outer diameters of ≈3 nm is termed as a "molecular star" owing to its resemblance with a pentagram shape. Interim paths leading to the star were also probed to decipher related dynamics of the system. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. W3 molecular cloud

    SciTech Connect

    Thronson, H.A.,JR.; Lada, C.J.; Hewagama, T.

    1985-10-01

    Extensive J = 1 to 0 (C-12)(O-16) and (C-13)(O-16) observations of the W3 molecular cloud and the surrounding region are presented and discussed. The velocity structure in the region is strongly suggestive of a model of large-scale, externally induced star formation. It is shown that star formation occurred in W3 and the nearby star-forming region W3(OH) after the gas within which they lie was swept up by the expanding W4 ionization front. Two condensations dominate the mass structure of the core of W3, one associated with IRS 4 and the other with IRS 5 and 1. A velocity difference between the two condensations is interpreted as indicating the two sources actually are discrete knots. 31 references.

  6. Molecular biology of atherosclerosis

    PubMed Central

    Mannarino, Elmo; Pirro, Matteo

    2008-01-01

    The traditional view of atherosclerosis as a pathological lipid deposition within the artery wall has been redefined by a more complex concept of an ongoing inflammatory disease. The atherosclerotic process is initiated when cardiovascular risk factors, through a chemical, mechanical or immunological insult, activate and/or injury the endothelium, thus contributing to endothelial dysfunction and fragmentation. This triggers a cascade of inflammatory reactions, in which monocytes, macrophages, T lymphocytes, vascular smooth muscle cells actively participate. Particularly, atherosclerotic lesions have been seen to have increased expression of T helper-1 cells together with increased levels of the T helper-1 related pro-inflammatory cytokines. Along with pro-inflammatory cytokines, other molecular factors involved in atherosclerosis appearance, progression and complication include chemokines, growth factors, vasoactive substances, enzymes, apoptosis signals and many others. Many of these molecular factors are both involved as possible markers of the atherosclerotic disease activity and burden, but may also play a crucial role in the pathogenesis of the disease. In recent years, the discovery of progenitor cells of myeloid origin has offered the prospect of merging the most recent theories on the pathogenesis of atherosclerosis with the evolving concept of a role of these progenitor cells in the repair of the injured vessel wall and the neovascularisation of ischemic tissues. This review summarizes current knowledge about the biology of atherosclerosis with emphasis on the mechanisms of endothelial damage and repair and on the concept that the turnover and replacement of endothelial cells is a major determinant in the maintenance of vascular integrity. PMID:22460847

  7. Molecular Diagnosis for Breast Malignancy

    DTIC Science & Technology

    1997-07-01

    AD GRANT NUMBER DAMD17-94-J-4033 TITLE: Molecular Diagnosis for Breast Malignancy PRINCIPAL INVESTIGATOR: Wen-Tien Chen, Ph.D. CONTRACTING...Biomedical Laboratories. - Signature -^yjgf Wen-Tien Chen, Ph.D. Page 4 Molecular diagnosis for breast malignancy (1) FRONT COVER: (2) SF 298...June 8-9, 1995 (abstract). Chen, W.-T, Goldstein LA, Pineiro-Sänchez M, Howard L, Ghersi G, Salamone M, Flessate D, Yeh Y. 1977. " Molecular Diagnosis for

  8. A tunable dendritic molecular actuator.

    PubMed

    Welch, Paul M

    2005-07-01

    I present an electroresponsive molecular actuator based upon a diblock copolymer of a positively charged dendrimer and a negatively charged linear chain. Brownian dynamics simulations demonstrate the hybrid polyampholyte's ability to apply a force or assume an equilibrium molecular strain tunable with an applied electric field. The free energy as a function of molecular strain at differing electric field strengths, as obtained via the Jarzynski identity, suggests a phase transition in the hybrid.

  9. 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.

  10. Interface-assisted molecular spintronics

    SciTech Connect

    Raman, Karthik V.

    2014-09-15

    Molecular spintronics, a field that utilizes the spin state of organic molecules to develop magneto-electronic devices, has shown an enormous scientific activity for more than a decade. But, in the last couple of years, new insights in understanding the fundamental phenomena of molecular interaction on magnetic surfaces, forming a hybrid interface, are presenting a new pathway for developing the subfield of interface-assisted molecular spintronics. The recent exploration of such hybrid interfaces involving carbon based aromatic molecules shows a significant excitement and promise over the previously studied single molecular magnets. In the above new scenario, hybridization of the molecular orbitals with the spin-polarized bands of the surface creates new interface states with unique electronic and magnetic character. This study opens up a molecular-genome initiative in designing new handles to functionalize the spin dependent electronic properties of the hybrid interface to construct spin-functional tailor-made devices. Through this article, we review this subject by presenting a fundamental understanding of the interface spin-chemistry and spin-physics by taking support of advanced computational and spectroscopy tools to investigate molecular spin responses with demonstration of new interface phenomena. Spin-polarized scanning tunneling spectroscopy is favorably considered to be an important tool to investigate these hybrid interfaces with intra-molecular spatial resolution. Finally, by addressing some of the recent findings, we propose novel device schemes towards building interface tailored molecular spintronic devices for applications in sensor, memory, and quantum computing.

  11. 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.

  12. 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.

  13. Molecular Epidemiology of Foodborne Pathogens

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Brown, Eric; Knabel, Stephen J.

    The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".

  14. Interface-assisted molecular spintronics

    NASA Astrophysics Data System (ADS)

    Raman, Karthik V.

    2014-09-01

    Molecular spintronics, a field that utilizes the spin state of organic molecules to develop magneto-electronic devices, has shown an enormous scientific activity for more than a decade. But, in the last couple of years, new insights in understanding the fundamental phenomena of molecular interaction on magnetic surfaces, forming a hybrid interface, are presenting a new pathway for developing the subfield of interface-assisted molecular spintronics. The recent exploration of such hybrid interfaces involving carbon based aromatic molecules shows a significant excitement and promise over the previously studied single molecular magnets. In the above new scenario, hybridization of the molecular orbitals with the spin-polarized bands of the surface creates new interface states with unique electronic and magnetic character. This study opens up a molecular-genome initiative in designing new handles to functionalize the spin dependent electronic properties of the hybrid interface to construct spin-functional tailor-made devices. Through this article, we review this subject by presenting a fundamental understanding of the interface spin-chemistry and spin-physics by taking support of advanced computational and spectroscopy tools to investigate molecular spin responses with demonstration of new interface phenomena. Spin-polarized scanning tunneling spectroscopy is favorably considered to be an important tool to investigate these hybrid interfaces with intra-molecular spatial resolution. Finally, by addressing some of the recent findings, we propose novel device schemes towards building interface tailored molecular spintronic devices for applications in sensor, memory, and quantum computing.

  15. Molecular characteristics of some commercial high-molecular-weight hyaluronans.

    PubMed

    Soltés, L; Mendichi, R; Lath, D; Mach, M; Bakos, D

    2002-10-01

    Commercially available hyaluronan (HA) samples were investigated by the method of size exclusion chromatography (SEC). The fractions eluted from the SEC column were on-line molecularly characterized by using a multi-angle laser light scattering (MALLS) photometer. Along with the SEC-MALLS technique, the high-molecular-weight HA biopolymers were (off-line) analyzed by capillary viscometry.

  16. 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…

  17. 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…

  18. Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.

    2006-04-01

    Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.

  19. Molecular Processes in Comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1998-01-01

    The research focused on molecular hydrogen and its response to ultraviolet radiation, photoelectron impact excitation and X-ray radiation and on the interpretation of the ultraviolet spectra of the Jupiter dayglow and auroras. A systematic effort was made to obtain reliable rate coefficients for rovibrational energy transfer of H2, particularly in collisions with hydrogen atoms. We carried out elaborate quantum-mechanical calculations of the scattering of H and H2 on what had been characterized as a reliable potential energy surface of the H3 molecular system. These calculations took into account reactive channels and rate coefficients for ortho-para transitions were obtained. Quantal calculations are too complex to be applied to all the possible rovibrational transitions and we turned to a semi-classical method. With it we calculated rate coefficients for transitions, reactive and non-reactive, for all the rovibrational levels. We carried out the calculations for three of the available H3 potential energy surfaces. We discovered an unexpected sensitivity of the rate coefficients for the non-reactive channels to the potential energy surface. This discovery stimulated more thorough investigations of the potential energy surface elsewhere and to the construction of a new surface. We have used it in further semi-classical calculations in work that will shortly be 2 completed and which, together with new quantum-mechanical calculations should comprise a set of reliable rate coefficients that can be used in discussions of H2 on the Jovian planets. We carried out a detailed study of the Jovian ultraviolet dayglow. There has been a long-running argument about the dayglow on Jupiter. There are two sources of excitation: fluorescence and photoelectron impact excitation. It had been argued that a third source "the electron glow" was needed to bring theory and observation into agreement. We believe we have shown conclusively that the third source is unnecessary. We have

  20. HIV Molecular Immunology 2015

    SciTech Connect

    Yusim, Karina; Korber, Bette Tina; Brander, Christian; Barouch, Dan; de Boer, Rob; Haynes, Barton F.; Koup, Richard; Moore, John P.; Walker, Bruce D.; Watkins, David

    2016-04-05

    The scope and purpose of the HIV molecular immunology database: HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2015 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/ content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins

  1. Optically controllable molecular logic circuits

    SciTech Connect

    Nishimura, Takahiro Fujii, Ryo; Ogura, Yusuke; Tanida, Jun

    2015-07-06

    Molecular logic circuits represent a promising technology for observation and manipulation of biological systems at the molecular level. However, the implementation of molecular logic circuits for temporal and programmable operation remains challenging. In this paper, we demonstrate an optically controllable logic circuit that uses fluorescence resonance energy transfer (FRET) for signaling. The FRET-based signaling process is modulated by both molecular and optical inputs. Based on the distance dependence of FRET, the FRET pathways required to execute molecular logic operations are formed on a DNA nanostructure as a circuit based on its molecular inputs. In addition, the FRET pathways on the DNA nanostructure are controlled optically, using photoswitching fluorescent molecules to instruct the execution of the desired operation and the related timings. The behavior of the circuit can thus be controlled using external optical signals. As an example, a molecular logic circuit capable of executing two different logic operations was studied. The circuit contains functional DNAs and a DNA scaffold to construct two FRET routes for executing Input 1 AND Input 2 and Input 1 AND NOT Input 3 operations on molecular inputs. The circuit produced the correct outputs with all possible combinations of the inputs by following the light signals. Moreover, the operation execution timings were controlled based on light irradiation and the circuit responded to time-dependent inputs. The experimental results demonstrate that the circuit changes the output for the required operations following the input of temporal light signals.

  2. Teaching Molecular 3-D Literacy

    ERIC Educational Resources Information Center

    Richardson, David C.; Richardson, Jane S.

    2002-01-01

    This article describes how the use of interactive molecular graphics makes a unique and important contribution to student learning of biochemistry and molecular biology at any level. These authors developed the concept of the kinemage (from "kinetic image"), a different way of organizing computer graphics that is aimed explicitly at the…

  3. Molecular ecology of aquatic microbes

    SciTech Connect

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  4. 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)

  5. 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.

  6. The Molecular Basis of Evolution.

    ERIC Educational Resources Information Center

    Wilson, Allan C.

    1985-01-01

    Discovery that mutations accumulate at steady rates over time in the genes of all lineages of plants and animals has led to new insights into evolution at the molecular and organismal levels. Discusses molecular evolution, examining deoxyribonuclei acid (DNA) sequences, morphological distances, and codon rate of change. (DH)

  7. The Molecular Basis of Evolution.

    ERIC Educational Resources Information Center

    Wilson, Allan C.

    1985-01-01

    Discovery that mutations accumulate at steady rates over time in the genes of all lineages of plants and animals has led to new insights into evolution at the molecular and organismal levels. Discusses molecular evolution, examining deoxyribonuclei acid (DNA) sequences, morphological distances, and codon rate of change. (DH)

  8. 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.

  9. Computationally Designed Molecularly Imprinted Materials

    NASA Astrophysics Data System (ADS)

    Pavel, Dumitru; Lagowski, Jolanta; Faid, Karim

    2004-03-01

    Molecular dynamics simulations were carried out for different molecular systems in order to predict the binding affinities, binding energies, binding distances and the active site groups between the simulated molecular systems and different bio-ligands (theophylline and its derivatives), which have been designed and minimized using molecular simulation techniques. The first simulated molecular systems consisted of a ligand and functional monomer, such as methacrylic acid and its derivatives. For each pair of molecular systems, (10 monomers with a ligand and 10 monomers without a ligand) a total energy difference was calculated in order to estimate the binding energy between a ligand and the corresponding monomers. The analysis of the simulated functional monomers with ligands indicates that the functional group of monomers interacting with ligands tends to be either COOH or CH2=CH. The distances between the ligand and monomer, in the most stable cases as indicated above, are between 2.0-4.5 Å. The second simulated molecular systems consisted of a ligand and a polymer. The polymers were obtained from monomers that were simulated above. And similar to monomer study, for each pair of molecular systems, (polymer with a ligand and polymer without a ligand) a total energy difference was calculated in order to estimate the binding energy between ligand and the corresponding polymer. The binding distance between the active site of a polymer and a ligand will also be discussed.

  10. Classical and molecular genetic mapping

    USDA-ARS?s Scientific Manuscript database

    A brief history of classical genetic mapping in soybean [Glycine max (L.) Merr.] is described. Detailed descriptions are given of the development of molecular genetic linkage maps based upon various types of DNA markers Like many plant and animal species, the first molecular map of soybean was bas...

  11. 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)

  12. Rigid molecular foams

    SciTech Connect

    Steckle, W.P. Jr.; Mitchell, M.A.; Aspen, P.G.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Organic analogues to inorganic zeolites would be a significant step forward in engineered porous materials and would provide advantages in range, selectivity, tailorability, and processing. Rigid molecular foams or {open_quotes}organic zeolites{close_quotes} would not be crystalline materials and could be tailored over a broader range of pore sizes and volumes. A novel process for preparing hypercrosslinked polymeric foams has been developed via a Friedel-Crafts polycondensation reaction. A series of rigid hypercrosslinked foams have been prepared using simple rigid polyaromatic hydrocarbons including benzene, biphenyl, m-terphenyl, diphenylmethane, and polystyrene, with dichloroxylene (DCX) as the pore size. After drying the foams are robust and rigid. Densities of the resulting foams can range from 0.15 g/cc to 0.75 g/cc. Nitrogen adsorption studies have shown that by judiciously selecting monomers and the crosslinking agent along with the level of crosslinking and the cure time of the resulting gel, the pore size, pore size distribution, and the total surface area of the foam can be tailored. Surface areas range from 160 to 1,200 m{sup 2}/g with pore sizes ranging from 6 {angstrom} to 2,000 {angstrom}.

  13. Reverse Engineering Molecular Hypergraphs

    PubMed Central

    Rahman, Ahsanur; Poirel, Christopher L.; Badger, David J.; Estep, Craig; Murali, T.M.

    2014-01-01

    Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multiway interactions among molecules, which occur very often within cells. Hypergraphs may be better representations for networks having such interactions, since hyperedges can naturally represent relationships among multiple molecules. Here, we propose using hypergraphs to capture the uncertainty inherent in reverse engineering gene-gene networks. Some subsets of nodes may induce highly varying subgraphs across an ensemble of networks inferred by a reverse engineering algorithm. We provide a novel formulation of hyperedges to capture this uncertainty in network topology. We propose a clustering-based approach to discover hyperedges. We show that our approach can recover hyperedges planted in synthetic data sets with high precision and recall, even for moderate amount of noise. We apply our techniques to a data set of pathways inferred from genetic interaction data in S. cerevisiae related to the unfolded protein response. Our approach discovers several hyperedges that capture the uncertain connectivity of genes in relevant protein complexes, suggesting that further experiments may be required to precisely discern their interaction patterns. We also show that these complexes are not discovered by an algorithm that computes frequent and dense subgraphs. PMID:24384702

  14. Designing the molecular future

    NASA Astrophysics Data System (ADS)

    Schneider, Gisbert

    2012-01-01

    Approximately 25 years ago the first computer applications were conceived for the purpose of automated `de novo' drug design, prominent pioneering tools being ALADDIN, CAVEAT, GENOA, and DYLOMMS. Many of these early concepts were enabled by innovative techniques for ligand-receptor interaction modeling like GRID, MCSS, DOCK, and CoMFA, which still provide the theoretical framework for several more recently developed molecular design algorithms. After a first wave of software tools and groundbreaking applications in the 1990s—expressly GROW, GrowMol, LEGEND, and LUDI representing some of the key players—we are currently witnessing a renewed strong interest in this field. Innovative ideas for both receptor and ligand-based drug design have recently been published. We here provide a personal perspective on the evolution of de novo design, highlighting some of the historic achievements as well as possible future developments of this exciting field of research, which combines multiple scientific disciplines and is, like few other areas in chemistry, subject to continuous enthusiastic discussion and compassionate dispute.

  15. A paramagnetic molecular voltmeter

    NASA Astrophysics Data System (ADS)

    Surek, Jack T.; Thomas, David D.

    2008-01-01

    We have developed a general electron paramagnetic resonance (EPR) method to measure electrostatic potential at spin labels on proteins to millivolt accuracy. Electrostatic potential is fundamental to energy-transducing proteins like myosin, because molecular energy storage and retrieval is primarily electrostatic. Quantitative analysis of protein electrostatics demands a site-specific spectroscopic method sensitive to millivolt changes. Previous electrostatic potential studies on macromolecules fell short in sensitivity, accuracy and/or specificity. Our approach uses fast-relaxing charged and neutral paramagnetic relaxation agents (PRAs) to increase nitroxide spin label relaxation rate solely through collisional spin exchange. These PRAs were calibrated in experiments on small nitroxides of known structure and charge to account for differences in their relaxation efficiency. Nitroxide longitudinal ( R1) and transverse ( R2) relaxation rates were separated by applying lineshape analysis to progressive saturation spectra. The ratio of measured R1 increases for each pair of charged and neutral PRAs measures the shift in local PRA concentration due to electrostatic potential. Voltage at the spin label is then calculated using the Boltzmann equation. Measured voltages for two small charged nitroxides agree with Debye-Hückel calculations. Voltage for spin-labeled myosin fragment S1 also agrees with calculation based on the p K shift of the reacted cysteine.

  16. Molecular screening in galactosemia

    SciTech Connect

    Elsas, L.J.; Singh, R.; Fernhoff, P.M.

    1994-09-01

    Classical galactosemia (G/G) is caused by the absence of galactose-1-phosphate uridyl transferase (GALT) activity while the Duarte allele produces partial impairment and a specific biochemical phenotype. Cloning and sequencing of the human GALT gene has enabled the identification of prevalent mutations for both Classical and Duarte alleles. The G allele is caused by a Q188R codon mutation in exon 6 in 70% of a Caucasian population while the D allele is caused by an N134D codon mutation in exon 10. Since the Q188R sequence creates a new Hpa II site and the N314D sequence creates a new Sin I site, it is relatively easy to screen for both mutations by multiplex PCR and restriction digest. Here we describe a method for detection of new mutations producing impaired GALT. Patient DNAs are subjected to SSCP (single strand conformational polymorphism) analysis of their 11 GALT exons. Direct sequencing of the exons targeted by SSCP has revealed many codon changes: IVSC 956 (a splice acceptor site loss), S135L, V151A, E203K, A320T, and Y323D. Two of these codon changes, V151A and S135L, have been confirmed as mutations by finding impaired GALT activity in a yeast expression system. We conclude that molecular screening of GALT DNA will clarify the structural biology of GALT and the pathophysiology of galactosemia.

  17. A Paramagnetic Molecular Voltmeter

    PubMed Central

    Surek, Jack T.; Thomas, David D.

    2008-01-01

    We have developed a general electron paramagnetic resonance (EPR) method to measure electrostatic potential at spin labels on proteins to millivolt accuracy. Electrostatic potential is fundamental to energy-transducing proteins like myosin, because molecular energy storage and retrieval is primarily electrostatic. Quantitative analysis of protein electrostatics demands a site-specific spectroscopic method sensitive to millivolt changes. Previous electrostatic potential studies on macromolecules fell short in sensitivity, accuracy and/or specificity. Our approach uses fast-relaxing charged and neutral paramagnetic relaxation agents (PRAs) to increase nitroxide spin label relaxation rate solely through collisional spin exchange. These PRAs were calibrated in experiments on small nitroxides of known structure and charge to account for differences in their relaxation efficiency. Nitroxide longitudinal (R1) and transverse (R2) relaxation rates were separated by applying lineshape analysis to progressive saturation spectra. The ratio of measured R1 increases for each pair of charged and neutral PRAs measures the shift in local PRA concentration due to electrostatic potential. Voltage at the spin label is then calculated using the Boltzmann equation. Measured voltages for two small charged nitroxides agree with Debye-Hückel calculations. Voltage for spin-labeled myosin fragment S1 also agrees with calculation based on the pK shift of the reacted cysteine. PMID:17964835

  18. Photoacoustic molecular imaging

    NASA Astrophysics Data System (ADS)

    Kiser, William L., Jr.; Reinecke, Daniel; DeGrado, Timothy; Bhattacharyya, Sibaprasad; Kruger, Robert A.

    2007-02-01

    It is well documented that photoacoustic imaging has the capability to differentiate tissue based on the spectral characteristics of tissue in the optical regime. The imaging depth in tissue exceeds standard optical imaging techniques, and systems can be designed to achieve excellent spatial resolution. A natural extension of imaging the intrinsic optical contrast of tissue is to demonstrate the ability of photoacoustic imaging to detect contrast agents based on optically absorbing dyes that exhibit well defined absorption peaks in the infrared. The ultimate goal of this project is to implement molecular imaging, in which Herceptin TM, a monoclonal antibody that is used as a therapeutic agent in breast cancer patients that over express the HER2 gene, is labeled with an IR absorbing dye, and the resulting in vivo bio-distribution is mapped using multi-spectral, infrared stimulation and subsequent photoacoustic detection. To lay the groundwork for this goal and establish system sensitivity, images were collected in tissue mimicking phantoms to determine maximum detection depth and minimum detectable concentration of Indocyanine Green (ICG), a common IR absorbing dye, for a single angle photoacoustic acquisition. A breast mimicking phantom was constructed and spectra were also collected for hemoglobin and methanol. An imaging schema was developed that made it possible to separate the ICG from the other tissue mimicking components in a multiple component phantom. We present the results of these experiments and define the path forward for the detection of dye labeled Herceptin TM in cell cultures and mice models.

  19. A molecular bowl sumanene.

    PubMed

    Amaya, Toru; Hirao, Toshikazu

    2011-10-14

    Nonplanar polyaromatic carbon molecules including fullerenes and carbon nanotubes have been attracting great interest due to their potential as materials, catalysts, etc. In this context, bowl-shaped polyaromatic hydrocarbons (π bowls) are considered to be key materials in the science of nonplanar π-conjugated carbon systems. Among π bowls, we focused on a molecular bowl "sumanene (C(21)H(12))" featuring a C(3v) symmetric structural motif present in fullerenes or carbon nanotube molecules. In this article, we present the research on sumanenes to date, including their synthesis, structural characterization, derivatization, complexation, and their potential uses as electrical materials. The characteristic structural feature of a sumanene depends on three sp(3) hybridized carbon atoms at the benzylic positions. Facile functionalization via selective formation of benzylic anions gives stereoselective substituted compounds, the π-extended derivatives, and the deeper π bowls. Furthermore, the dynamically flexible aspect based on bowl-to-bowl inversion is also described. The crystal with a columnar bowl-in-bowl stacking exhibits a high electron transport ability with anisotropy. Complexation with a cyclopentadienyl iron cation results in the first selective formation of the concave-bound complex as a π-bowl complex. This journal is © The Royal Society of Chemistry 2011

  20. Interstellar protonated molecular species

    NASA Astrophysics Data System (ADS)

    Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Arunan, Elangannan

    2017-08-01

    Majority of the known interstellar cations are protonated species believed to be the natural precursors for their corresponding neutral analogues formed via the dissociative recombination process. The protonation of a neutral species can occur in more than one position on the molecular structure thus resulting in more than one proton binding energy value and different protonated species for the same neutral species. In the present work, ab initio quantum calculations are employed to calculate accurate proton binding energies for over 100 neutral interstellar molecules of which majority of the neutral molecules are protonated in more than one position. From the results, protonated species resulting from a high proton binding energy prefers to remain protonated rather than transferring a proton and returning to its neutral form as compared to its analogue that gives rise to a lower proton binding energy (PBE) from the same neutral species. For two protonated species resulting from the same neutral molecule, the one that results in a higher PBE is more stable as compared to its counterpart that is responsible for the lower PBE for the same neutral species. Here, the most stable species are highlighted for all the systems considered.

  1. Radically enhanced molecular recognition

    NASA Astrophysics Data System (ADS)

    Trabolsi, Ali; Khashab, Niveen; Fahrenbach, Albert C.; Friedman, Douglas C.; Colvin, Michael T.; Cotí, Karla K.; Benítez, Diego; Tkatchouk, Ekaterina; Olsen, John-Carl; Belowich, Matthew E.; Carmielli, Raanan; Khatib, Hussam A.; Goddard, William A.; Wasielewski, Michael R.; Stoddart, J. Fraser

    2010-01-01

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication.

  2. Valved molecular beam skimmer

    NASA Astrophysics Data System (ADS)

    Marceca, Ernesto; Becker, Jörg A.; Hensel, Friedrich

    1997-08-01

    Under routine source conditions, the optimum nozzle-skimmer distance to achieve maximum molecular beam intensities is within the range of a few millimeters. In cases where double skimming is additionally required, the distance between the skimmers should be kept small in order to sample a sufficiently large solid angle of the beam and hence maintain a good enough intensity. These two facts make it normally difficult to isolate the first from the second expansion chamber using a commercial vacuum gate valve due to the lack of remaining space. This note presents the design of a vacuum-tight valve which allows the aperture of a skimmer to be closed by plugging a needle directly against its internal conical wall. The valve can be driven manually or pneumatically from outside the vacuum chamber. The helium conductance of the valve was measured to be better than 1×10-8 mbar×l×s-1 for a helium partial pressure difference of 1 bar.

  3. Reverse engineering molecular hypergraphs.

    PubMed

    Rahman, Ahsanur; Poirel, Christopher L; Badger, David J; Estep, Craig; Murali, T M

    2013-01-01

    Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multiway interactions among molecules, which occur very often within cells. Hypergraphs may be better representations for networks having such interactions, since hyperedges can naturally represent relationships among multiple molecules. Here, we propose using hypergraphs to capture the uncertainty inherent in reverse engineering gene-gene networks. Some subsets of nodes may induce highly varying subgraphs across an ensemble of networks inferred by a reverse engineering algorithm. We provide a novel formulation of hyperedges to capture this uncertainty in network topology. We propose a clustering-based approach to discover hyperedges. We show that our approach can recover hyperedges planted in synthetic data sets with high precision and recall, even for moderate amount of noise. We apply our techniques to a data set of pathways inferred from genetic interaction data in S. cerevisiae related to the unfolded protein response. Our approach discovers several hyperedges that capture the uncertain connectivity of genes in relevant protein complexes, suggesting that further experiments may be required to precisely discern their interaction patterns. We also show that these complexes are not discovered by an algorithm that computes frequent and dense subgraphs.

  4. Molecular phylogeny of Coniochaetales.

    PubMed

    García, Dania; Stchigel, Alberto M; Cano, José; Calduch, Misericordia; Hawksworth, David L; Guarro, Josep

    2006-11-01

    Although the taxonomy of ascomycetes has changed dramatically, generic delimitation within the recently proposed order Coniochaetales has not been resolved. In order to clarify the phylogenetic relationships of genera in the Coniochaetaceae, we performed a molecular study based on the analyses of the sequences of the partial SSU and of the variable domains of the LSU rDNA genes. The phylogenetic trees obtained do not support the monophyly of the genera Coniochaeta, Coniochaetidium, Ephemeroascus, and Poroconiochaeta. A morphological study confirmed that there were not enough differences to distinguish these genera, and the latter three are treated as synonyms of Coniochaeta. The phialidic anamorph proved to be an informative phylogenetic character in Coniochaetales, while that the type of ascomata (cleistothecial or perithecial) and the ornamentation of the ascospore walls were of little taxonomic value at the generic level. The circumscription of the genus Coniochaeta is revised. The genera Coniocessia and Coniolariella are proposed as new within the order Xylariales to accommodate Coniochaeta nodulisporioides, and C. gamsii, respectively. The taxonomic position of Synaptospora and Wallrothiella subiculosa are also discussed.

  5. MDplot: Visualise Molecular Dynamics.

    PubMed

    Margreitter, Christian; Oostenbrink, Chris

    2017-05-10

    The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

  6. Molecular factors in migraine

    PubMed Central

    Kowalska, Marta; Prendecki, Michał; Kozubski, Wojciech; Lianeri, Margarita; Dorszewska, Jolanta

    2016-01-01

    Migraine is a common neurological disorder that affects 11% of adults worldwide. This disease most likely has a neurovascular origin. Migraine with aura (MA) and more common form - migraine without aura (MO) – are the two main clinical subtypes of disease. The exact pathomechanism of migraine is still unknown, but it is thought that both genetic and environmental factors are involved in this pathological process. The first genetic studies of migraine were focused on the rare subtype of MA: familial hemiplegic migraine (FHM). The genes analysed in familial and sporadic migraine are: MTHFR, KCNK18, HCRTR1, SLC6A4, STX1A, GRIA1 and GRIA3. It is possible that migraine is a multifactorial disease with polygenic influence. Recent studies have shown that the pathomechanisms of migraine involves both factors responsible for immune response and oxidative stress such as: cytokines, tyrosine metabolism, homocysteine; and factors associated with pain transmission and emotions e.g.: serotonin, hypocretin-1, calcitonin gene-related peptide, glutamate. The correlations between genetic variants of the HCRTR1 gene, the polymorphism 5-HTTLPR and hypocretin-1, and serotonin were observed. It is known that serotonin inhibits the activity of hypocretin neurons and may affect the appearance of the aura during migraine attack. The understanding of the molecular mechanisms of migraine, including genotype-phenotype correlations, may contribute to finding markers important for the diagnosis and treatment of this disease. PMID:27191890

  7. Cisplatin nephrotoxicity: molecular mechanisms

    PubMed Central

    Hanigan, Marie H.; Devarajan, Prasad

    2007-01-01

    Summary Cisplatin is one of the most widely used chemotherapeutic agents for the treatment of several human malignancies. The efficacy of cisplatin is dose dependent, but the significant risk of nephrotoxicity frequently hinders the use of higher doses to maximize its antineoplastic effects. Several advances in our understanding of the biochemical and molecular mechanisms underlying cisplatin nephrotoxicity have recently emerged, and are reviewed in this article. Evidence is presented for distinct mechanisms of cisplatin toxicity in actively dividing tumor cells versus the normally quiescent renal proximal tubular epithelial cells. The unexpected role of gamma-glutamyl transpeptidase in cisplatin nephrotoxicity is elucidated. Recent studies demonstrating the ability of proximal tubular cells to metabolize cisplatin to a nephrotoxin are reviewed. The evidence for apoptosis as a major mechanism underlying cisplatin-induced renal cell injury is presented, along with the data exploring the role of specific intracellular pathways that may mediate the programmed cell death. The information gleaned from this review may provide critical clues to novel therapeutic interventions aimed at minimizing cisplatin-induced nephrotoxicity while enhancing its antineoplastic efficacy. PMID:18185852

  8. Molecular processes in comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1993-01-01

    Classical trajectory calculations of the cross sections for vibrational and rotational energy exchange in direct and reactive collisions of hydrogen atoms and hydrogen molecules have been carried out. To test the sensitivity, three potential energy surfaces have been used. For the exchange transitions which occur at small internuclear distances, the rate coefficients for the three surfaces agree quite well. For the direct transitions, there are significant differences for the pure rotational transitions from j=0 to 2 and from j=1 to j=3 in which there is no change in vibration. For higher j the differences tend to disappear, suggesting that the rotational angular momentum can couple to the orbital angular momentum to overcome the centrifugal barrier. Complete numerically exact quantum mechanical calculations for the process in which vJ changes have been performed. Dr. M. A'Hearn has provided data on the fluorescent population of the NH rotational and fine-structure levels from which we should be able to predict accurate photodissociation lifetimes. The distribution rate of C2 is being investigated. A review of H3(+) in terrestrial and extraterrestrial environments was prepared for a volume of Advances in Atomic, Molecular and Optical Physics.

  9. Molecular chaperones and neuronal proteostasis.

    PubMed

    Smith, Heather L; Li, Wenwen; Cheetham, Michael E

    2015-04-01

    Protein homeostasis (proteostasis) is essential for maintaining the functionality of the proteome. The disruption of proteostasis, due to genetic mutations or an age-related decline, leads to aberrantly folded proteins that typically lose their function. The accumulation of misfolded and aggregated protein is also cytotoxic and has been implicated in the pathogenesis of neurodegenerative diseases. Neurons have developed an intrinsic protein quality control network, of which molecular chaperones are an essential component. Molecular chaperones function to promote efficient folding and target misfolded proteins for refolding or degradation. Increasing molecular chaperone expression can suppress protein aggregation and toxicity in numerous models of neurodegenerative disease; therefore, molecular chaperones are considered exciting therapeutic targets. Furthermore, mutations in several chaperones cause inherited neurodegenerative diseases. In this review, we focus on the importance of molecular chaperones in neurodegenerative diseases, and discuss the advances in understanding their protective mechanisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Electrostatic interactions in molecular materials

    NASA Astrophysics Data System (ADS)

    Painelli, Anna; Terenziani, Francesca

    2004-03-01

    Non-additive collective behavior appears in molecular materials as a result of intermolecular interactions. We present a model for interacting polar and polarizable molecules that applies to different supramolecular architectures of donor-π-acceptor molecules. We follow a bottom-up modeling strategy: the detailed analysis of spectroscopic data of solvated molecules leads to the definition of a simple two-state model for the molecular units. Classical electrostatic interactions are then introduced to model molecular clusters. The molecular properties are strickingly affected by supramolecular interactions, as demonstrated by spectroscopic studies. Brand new phenomena, like phase transitions and multielectron transfer, with no counterpart at the molecular level are observed as direct consequences of electrostatic intermolecular interactions.

  11. Molecular chaperones and neuronal proteostasis

    PubMed Central

    Smith, Heather L.; Li, Wenwen; Cheetham, Michael E.

    2015-01-01

    Protein homeostasis (proteostasis) is essential for maintaining the functionality of the proteome. The disruption of proteostasis, due to genetic mutations or an age-related decline, leads to aberrantly folded proteins that typically lose their function. The accumulation of misfolded and aggregated protein is also cytotoxic and has been implicated in the pathogenesis of neurodegenerative diseases. Neurons have developed an intrinsic protein quality control network, of which molecular chaperones are an essential component. Molecular chaperones function to promote efficient folding and target misfolded proteins for refolding or degradation. Increasing molecular chaperone expression can suppress protein aggregation and toxicity in numerous models of neurodegenerative disease; therefore, molecular chaperones are considered exciting therapeutic targets. Furthermore, mutations in several chaperones cause inherited neurodegenerative diseases. In this review, we focus on the importance of molecular chaperones in neurodegenerative diseases, and discuss the advances in understanding their protective mechanisms. PMID:25770416

  12. Recent patents on molecular cytogenetics.

    PubMed

    Iourov, Ivan Y; Vorsanova, Svetlana G; Yurov, Yuri B

    2008-01-01

    The questions surrounding patenting of DNA sequences encoding specific proteins are relatively well reviewed in the available literature. However, neither applications nor molecular cytogenetic techniques, which use these sequences as a probe, have been reviewed in the light of the patenting. Furthermore, the patenting of the use of numerous probes, which are produced on different types of repetitive genome elements (i.e. satellite DNA or telomeric DNA sequences) and those generated by chromosome microdissection has not been reviewed. Molecular cytogenetic techniques are one of the most applied in current bioscience (as to June 2007, over 40,000 papers in browseable scientific databases mention one or several molecular cytogenetic techniques). Therefore, reviewing recent patents in this field is of general interest for numerous researchers in different areas of biology and medicine. Here, we address world-wide patents on DNA sequences used as molecular cytogenetic probes and molecular cytogenetic techniques to define current state and perspectives of this biomedical direction.

  13. Molecular imaging in Alzheimer's disease.

    PubMed

    Lascola, Christopher

    2005-11-01

    Molecular imaging represents a new term for a long-standing quest to image cellular and molecular processes in vivo. The development of a successful molecular imaging approach starts with a well-defined diagnostic question best answered using in vivo imaging. A selective target for a particular disease state is then identified and a biocompatible probe selective for that target is developed. Many of the challenges of finding selective disease targets and probes that bind selectively to those targets in vivo are evident in the 25-year history of molecular imaging in Alzheimer's disease. This article provides a brief overview of molecular imaging in Alzheimer's disease and its potential for early diagnosis and treatment development.

  14. Molecular force spectroscopy on cells.

    PubMed

    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.

  15. 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.

  16. Floating orbital molecular dynamics simulations.

    PubMed

    Perlt, Eva; Brüssel, Marc; Kirchner, Barbara

    2014-04-21

    We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated.

  17. HIV Molecular Immunology 2014

    SciTech Connect

    Yusim, Karina; Korber, Bette Tina Marie; Barouch, Dan; Koup, Richard; de Boer, Rob; Moore, John P.; Brander, Christian; Haynes, Barton F.; Walker, Bruce D.

    2015-02-03

    HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

  18. Nanoparticles for molecular imaging.

    PubMed

    Sheng, Yang; Liao, Lun De; Thakor, Nitish V; Tan, Mei Chee

    2014-10-01

    Imaging techniques have been instrumental in the visualization of fundamental biological processes, identification and diagnosis of diseased states and the development of structure-function relationships at the cellular, tissue and anatomical levels. Together with the advancements made in imaging techniques, complementary chemical compounds, also known as imaging probes or contrast agents, are developed to improve the visibility of the image by enhancing sensitivity, and for the identification and quantitation of specific molecular species or structures. Extensive studies have been conducted to explore the use of inorganic nanoparticles which exhibit magnetic and optical properties unique to the nano regime so as to enhance the signals sensitivity for magnetic resonance and fluorescent imaging. These physical properties are tailored by controlling the size, shape and surface properties of nanoparticles. In addition, surface modification of nanoparticles is often required to improve its stability, compatibility and functionality. Surfactants, surface-active agents, have been used to engineer the surface characteristics of nanoparticles to improved particle stability and functionality. Surfactants enhance nanoparticle stability through the reduction of surface energy, and by acting as a barrier to agglomeration through either steric hindrance or repulsive electrostatic forces. Coupling of nanoparticles with biomolecules such as antibodies or tumor targeting peptides are enabled by the presence of functional groups (e.g., carboxyl or amine groups) on surfactants. This paper provides an overview of the chemistry underlying the synthesis and surface modification of nanomaterials together with a discussion on how the physical properties (e.g., magnetic, absorption and luminescent) can be controlled. The applications of these nanoparticles for magnetic resonance, fluorescent and photoacoustic imaging techniques that do not rely on ionizing radiation are also covered in

  19. Mechanochemistry of Molecular Motors

    NASA Astrophysics Data System (ADS)

    Bryant, Zev

    2008-03-01

    Molecular motors lie at the heart of biological processes from DNA replication to vesicle transport. We seek to understand the physical mechanisms by which these nanoscale machines convert chemical energy into mechanical work. I will overview our ongoing use of single molecule tracking and manipulation techniques to observe and perturb substeps in the mechanochemical cycles of individual motors, before concentrating on our recent efforts to dissect the structural basis of a ``reverse gear'' in myosin VI. The basic actomyosin motor has been embellished, altered, and re-used many times through the evolution of diverse members of the myosin superfamily. Class VI myosins are highly specialized (-) end directed motors involved in a growing list of functions in animal cells, including endocytosis, cell migration, and maintenance of stereociliar membrane tension. How does myosin VI achieve reverse directionality, despite sharing extensive sequence and structural conservation with (+) end directed myosins? We generated a series of truncated myosin VI constructs and characterized the size and direction of the power stroke for each construct using dual-labeled gliding filament assays and optical trapping. Motors truncated near the end of the converter domain generate (+) end directed motion, whereas longer constructs move toward the (-) end, confirming the importance of a class-specific insert that redirects the lever arm. Our quantitative results suggest a surprising model in which the lever arm rotates ˜180^o during the power stroke. We are currently studying the behavior of engineered myosin VI constructs with artificial lever arms, in order to further challenge and refine our power stroke model.

  20. Molecular imaging in atherosclerosis.

    PubMed

    Glaudemans, Andor W J M; Slart, Riemer H J A; Bozzao, Alessandro; Bonanno, Elena; Arca, Marcello; Dierckx, Rudi A J O; Signore, Alberto

    2010-12-01

    Atherosclerosis is the major cause of cardiovascular disease, which still has the leading position in morbidity and mortality in the Western world. Many risk factors and pathobiological processes are acting together in the development of atherosclerosis. This leads to different remodelling stages (positive and negative) which are both associated with plaque physiology and clinical presentation. The different remodelling stages of atherosclerosis are explained with their clinical relevance. Recent advances in basic science have established that atherosclerosis is not only a lipid storage disease, but that also inflammation has a fundamental role in all stages of the disease. The molecular events leading to atherosclerosis will be extensively reviewed and described. Further on in this review different modalities and their role in the different stages of atherosclerosis will be discussed. Non-nuclear invasive imaging techniques (intravascular ultrasound, intravascular MRI, intracoronary angioscopy and intravascular optical coherence tomography) and non-nuclear non-invasive imaging techniques (ultrasound with Doppler flow, electron-bean computed tomography, coronary computed tomography angiography, MRI and coronary artery MR angiography) will be reviewed. After that we focus on nuclear imaging techniques for detecting atherosclerotic plaques, divided into three groups: atherosclerotic lesion components, inflammation and thrombosis. This emerging area of nuclear imaging techniques can provide measures of biological activity of atherosclerotic plaques, thereby improving the prediction of clinical events. As we will see in the future perspectives, at present, there is no special tracer that can be called the diagnostic tool to diagnose prospective stroke or infarction in patients. Nevertheless, we expect such a tracer to be developed in the next few years and maybe, theoretically, it could even be used for targeted therapy (in the form of a beta-emitter) to combat

  1. Molecular Pharmacology of Phytocannabinoids.

    PubMed

    Turner, Sarah E; Williams, Claire M; Iversen, Leslie; Whalley, Benjamin J

    Cannabis sativa has been used for recreational, therapeutic and other uses for thousands of years. The plant contains more than 120 C21 terpenophenolic constituents named phytocannabinoids. The Δ(9)-tetrahydrocannabinol type class of phytocannabinoids comprises the largest proportion of the phytocannabinoid content. Δ(9)-tetrahydrocannabinol was first discovered in 1971. This led to the discovery of the endocannabinoid system in mammals, including the cannabinoid receptors CB1 and CB2. Δ(9)-Tetrahydrocannabinol exerts its well-known psychotropic effects through the CB1 receptor but this effect of Δ(9)-tetrahydrocannabinol has limited the use of cannabis medicinally, despite the therapeutic benefits of this phytocannabinoid. This has driven research into other targets outside the endocannabinoid system and has also driven research into the other non-psychotropic phytocannabinoids present in cannabis. This chapter presents an overview of the molecular pharmacology of the seven most thoroughly investigated phytocannabinoids, namely Δ(9)-tetrahydrocannabinol, Δ(9)-tetrahydrocannabivarin, cannabinol, cannabidiol, cannabidivarin, cannabigerol, and cannabichromene. The targets of these phytocannabinoids are defined both within the endocannabinoid system and beyond. The pharmacological effect of each individual phytocannabinoid is important in the overall therapeutic and recreational effect of cannabis and slight structural differences can elicit diverse and competing physiological effects. The proportion of each phytocannabinoid can be influenced by various factors such as growing conditions and extraction methods. It is therefore important to investigate the pharmacology of these seven phytocannabinoids further, and characterise the large number of other phytocannabinoids in order to better understand their contributions to the therapeutic and recreational effects claimed for the whole cannabis plant and its extracts.

  2. Diffractive molecular-orbital tomography

    NASA Astrophysics Data System (ADS)

    Zhai, Chunyang; Zhu, Xiaosong; Lan, Pengfei; Wang, Feng; He, Lixin; Shi, Wenjing; Li, Yang; Li, Min; Zhang, Qingbin; Lu, Peixiang

    2017-03-01

    High-order-harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular-orbital tomography and to probe the electronic dynamics with attosecond-Ångström resolutions. Molecular-orbital tomography requires both the amplitude and phase of the high-order harmonics. Yet the measurement of phases requires sophisticated techniques and represents formidable challenges at present. Here we report a scheme, called diffractive molecular-orbital tomography, to retrieve the molecular orbital solely from the amplitude of high-order harmonics without measuring any phase information. We have applied this method to image the molecular orbitals of N2, CO2, and C2H2 . The retrieved orbital is further improved by taking account the correction of Coulomb potential. The diffractive molecular-orbital tomography scheme, removing the roadblock of phase measurement, significantly simplifies the molecular-orbital tomography procedure and paves an efficient and robust way to the imaging of more complex molecules.

  3. 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.

  4. Advances in multimodal molecular imaging.

    PubMed

    Auletta, Luigi; Gramanzini, Matteo; Gargiulo, Sara; Albanese, Sandra; Salvatore, Marco; Greco, Adelaide

    2017-03-01

    Preclinical molecular imaging is an emerging field. Improving the ability of scientists to study the molecular basis of human pathology in animals is of the utmost importance for future advances in all fields of human medicine. Moreover, the possibility of developing new imaging techniques or of implementing old ones adapted to the clinic is a significant area. Cardiology, neurology, immunology and oncology have all been studied with preclinical molecular imaging. The functional techniques of photoacoustic imaging (PAI), fluorescence molecular tomography (FMT), positron emission tomography (PET), and single photon emission computed tomography (SPECT) in association with each other or with the anatomic reference provided by computed tomography (CT) as well as with anatomic and functional information provided by magnetic resonance (MR) have all been proficiently applied to animal models of human disease. All the above-mentioned imaging techniques have shown their ability to explore the molecular mechanisms involved in animal models of disease. The clinical translatability of most of the techniques motivates the ongoing study of their possible fields of application. The ability to combine two or more techniques allows obtaining as much information as possible on the molecular processes involved in pathologies, reducing the number of animals necessary in each experiment. Merging molecular probes compatible with various imaging technique will further expand the capability to achieve the best results.

  5. 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.

  6. Molecularly sensitive optical coherence tomography.

    PubMed

    Bredfeldt, Jeremy S; Vinegoni, Claudio; Marks, Daniel L; Boppart, Stephen A

    2005-03-01

    Molecular contrast in optical coherence tomography (OCT) is demonstrated by use of coherent anti-Stokes Raman scattering (CARS) for molecular sensitivity. Femtosecond laser pulses are focused into a sample by use of a low-numerical-aperture lens to generate CARS photons, and the backreflected CARS signal is interferometrically measured. With the chemical selectivity provided by CARS and the advanced imaging capabilities of OCT, this technique may be useful for molecular contrast imaging in biological tissues. CARS can be generated and interferometrically measured over at least 600 microm of the depth of field of a low-numerical-aperture objective.

  7. 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.

  8. Thermopower measurements in molecular junctions.

    PubMed

    Rincón-García, Laura; Evangeli, Charalambos; Rubio-Bollinger, Gabino; Agraït, Nicolás

    2016-08-07

    The measurement of thermopower in molecular junctions offers complementary information to conductance measurements and is becoming essential for the understanding of transport processes at the nanoscale. In this review, we discuss the recent advances in the study of the thermoelectric properties of molecular junctions. After presenting the theoretical background for thermoelectricity at the nanoscale, we review the experimental techniques for measuring the thermopower in these systems and discuss the main results. Finally, we consider the challenges in the application of molecular junctions in viable thermoelectric devices.

  9. [Molecular diagnosis of melanocytic tumors].

    PubMed

    Bauer, J

    2016-01-01

    Melanoma therapy has undergone a paradigm shift. Classic chemotherapies with poor treatment responses have been replaced by modern immune checkpoint blockades and targeted therapies with excellent responses. The latter require precise diagnosis of mutations in the melanoma genome as molecular targets for the small molecules. The diagnosis of melanomas has also been supplemented by molecular techniques. Differential diagnosis of melanoma and melanoma simulators such as atypical Spitz nevi can be supported by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). Here we review the indications and methods for molecular diagnosis of melanocytic tumors.

  10. Photoelectron photoion molecular beam spectroscopy

    SciTech Connect

    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.

  11. 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

  12. Introduction to Accelerated Molecular Dynamics

    SciTech Connect

    Perez, Danny

    2012-07-10

    Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

  13. Interference-based molecular transistors

    PubMed Central

    Li, Ying; Mol, Jan A.; Benjamin, Simon C.; Briggs, G. Andrew D.

    2016-01-01

    Molecular transistors have the potential for switching with lower gate voltages than conventional field-effect transistors. We have calculated the performance of a single-molecule device in which there is interference between electron transport through the highest occupied molecular orbital and the lowest unoccupied molecular orbital of a single molecule. Quantum interference results in a subthreshold slope that is independent of temperature. For realistic parameters the change in gate potential required for a change in source-drain current of two decades is 20 mV, which is a factor of six smaller than the theoretical limit for a metal-oxide-semiconductor field-effect transistor. PMID:27646692

  14. Metrological Issues in Molecular Radiotherapy

    NASA Astrophysics Data System (ADS)

    D'Arienzo, Marco; Capogni, Marco; Smyth, Vere; Cox, Maurice; Johansson, Lena; Solc, Jaroslav; Bobin, Christophe; Rabus, Hans; Joulaeizadeh, Leila

    2014-08-01

    The therapeutic effect from molecular radiation therapy (MRT), on both tumour and normal tissue, is determined by the radiation absorbed dose. Recent research indicates that as a consequence of biological variation across patients the absorbed dose can vary, for the same administered activity, by as much as two orders of magnitude. The international collaborative EURAMET-EMRP project "Metrology for molecular radiotherapy (MetroMRT)" is addressing this problem. The overall aim of the project is to develop methods of calibrating and verifying clinical dosimetry in MRT. In the present paper an overview of the metrological issues in molecular radiotherapy is provided.

  15. 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.

  16. Molecular tools for chemical biotechnology

    PubMed Central

    Galanie, Stephanie; Siddiqui, Michael S.; Smolke, Christina D.

    2013-01-01

    Biotechnological production of high value chemical products increasingly involves engineering in vivo multi-enzyme pathways and host metabolism. Recent approaches to these engineering objectives have made use of molecular tools to advance de novo pathway identification, tunable enzyme expression, and rapid pathway construction. Molecular tools also enable optimization of single enzymes and entire genomes through diversity generation and screening, whole cell analytics, and synthetic metabolic control networks. In this review, we focus on advanced molecular tools and their applications to engineered pathways in host organisms, highlighting the degree to which each tool is generalizable. PMID:23528237

  17. Molecular Hydrodynamics from Memory Kernels

    NASA Astrophysics Data System (ADS)

    Lesnicki, Dominika; Vuilleumier, Rodolphe; Carof, Antoine; Rotenberg, Benjamin

    2016-04-01

    The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as t-3 /2 . We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, which is at odds with incompressible hydrodynamics predictions. Lastly, we discuss the various contributions to the friction, the associated time scales, and the crossover between the molecular and hydrodynamic regimes upon increasing the solute radius.

  18. Molecular Simulations in Astrobiology

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

    2000-01-01

    One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides

  19. Exercises in molecular computing.

    PubMed

    Stojanovic, Milan N; Stefanovic, Darko; Rudchenko, Sergei

    2014-06-17

    CONSPECTUS: The successes of electronic digital logic have transformed every aspect of human life over the last half-century. The word "computer" now signifies a ubiquitous electronic device, rather than a human occupation. Yet evidently humans, large assemblies of molecules, can compute, and it has been a thrilling challenge to develop smaller, simpler, synthetic assemblies of molecules that can do useful computation. When we say that molecules compute, what we usually mean is that such molecules respond to certain inputs, for example, the presence or absence of other molecules, in a precisely defined but potentially complex fashion. The simplest way for a chemist to think about computing molecules is as sensors that can integrate the presence or absence of multiple analytes into a change in a single reporting property. Here we review several forms of molecular computing developed in our laboratories. When we began our work, combinatorial approaches to using DNA for computing were used to search for solutions to constraint satisfaction problems. We chose to work instead on logic circuits, building bottom-up from units based on catalytic nucleic acids, focusing on DNA secondary structures in the design of individual circuit elements, and reserving the combinatorial opportunities of DNA for the representation of multiple signals propagating in a large circuit. Such circuit design directly corresponds to the intuition about sensors transforming the detection of analytes into reporting properties. While this approach was unusual at the time, it has been adopted since by other groups working on biomolecular computing with different nucleic acid chemistries. We created logic gates by modularly combining deoxyribozymes (DNA-based enzymes cleaving or combining other oligonucleotides), in the role of reporting elements, with stem-loops as input detection elements. For instance, a deoxyribozyme that normally exhibits an oligonucleotide substrate recognition region is

  20. Molecularly doped metals.

    PubMed

    Avnir, David

    2014-02-18

    The many millions of organic, inorganic, and bioorganic molecules represent a very rich library of chemical, biological, and physical properties that do not show up among the approximately 100 metals. The ability to imbue metals with any of these molecular properties would open up tremendous potential for the development of new materials. In addition to their traditional features and their traditional applications, metals would have new traits, which would merge their classical virtues such as conductivity and catalytic activity with the diverse properties of these molecules. In this Account, we describe a new materials methodology, which enables, for the first time, the incorporation and entrapment of small organic molecules, polymers, and biomolecules within metals. These new materials are denoted dopant@metal. The creation of dopant@metal yields new properties that are more than or different from the sum of the individual properties of the two components. So far we have developed methods for the doping of silver, copper, gold, iron, palladium, platinum, and some of their alloys, as well as Hg-Ag amalgams. We have successfully altered classical metal properties (such as conductivity), induced unorthodox properties (such as rendering a metal acidic or basic), used metals as heterogeneous matrices for homogeneous catalysts, and formed new metallic catalysts such as metals doped with organometallic complexes. In addition, we have created materials that straddle the border between polymers and metals, we have entrapped enzymes to form bioactive metals, we have induced chirality within metals, we have made corrosion-resistant iron, we formed efficient biocidal materials, and we demonstrated a new concept for batteries. We have developed a variety of methods for synthesizing dopant@metals including aqueous homogeneous and heterogeneous reductions of the metal cations, reductions in DMF, electrochemical entrapments, thermal decompositions of zerovalent metal carbonyls

  1. Exercises in Molecular Computing

    PubMed Central

    2014-01-01

    Conspectus The successes of electronic digital logic have transformed every aspect of human life over the last half-century. The word “computer” now signifies a ubiquitous electronic device, rather than a human occupation. Yet evidently humans, large assemblies of molecules, can compute, and it has been a thrilling challenge to develop smaller, simpler, synthetic assemblies of molecules that can do useful computation. When we say that molecules compute, what we usually mean is that such molecules respond to certain inputs, for example, the presence or absence of other molecules, in a precisely defined but potentially complex fashion. The simplest way for a chemist to think about computing molecules is as sensors that can integrate the presence or absence of multiple analytes into a change in a single reporting property. Here we review several forms of molecular computing developed in our laboratories. When we began our work, combinatorial approaches to using DNA for computing were used to search for solutions to constraint satisfaction problems. We chose to work instead on logic circuits, building bottom-up from units based on catalytic nucleic acids, focusing on DNA secondary structures in the design of individual circuit elements, and reserving the combinatorial opportunities of DNA for the representation of multiple signals propagating in a large circuit. Such circuit design directly corresponds to the intuition about sensors transforming the detection of analytes into reporting properties. While this approach was unusual at the time, it has been adopted since by other groups working on biomolecular computing with different nucleic acid chemistries. We created logic gates by modularly combining deoxyribozymes (DNA-based enzymes cleaving or combining other oligonucleotides), in the role of reporting elements, with stem–loops as input detection elements. For instance, a deoxyribozyme that normally exhibits an oligonucleotide substrate recognition region is

  2. Molecular Simulations in Astrobiology

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

    2000-01-01

    One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides

  3. 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)

  4. Molecular signatures in the transport properties of molecular wire junctions: what makes a junction "molecular"?

    PubMed

    Troisi, Alessandro; Ratner, Mark A

    2006-02-01

    The simplest component of molecular electronics consists of a single-molecule transport junction: a molecule sandwiched between source and drain electrodes, with or without a third gate electrode. In this Concept article, we focus on how molecules control transport in metal-electrode molecular junctions, and where the molecular signatures are to be found. In the situation where the molecule is relatively short and the gap between injection energy and molecular eigenstates is large, transport occurs largely by elastic tunneling, stochastic switching is common, and the vibronic signature can be found using inelastic electron tunneling spectroscopy (IETS). As the energy gaps for injection become smaller, one begins to see stronger molecular signatures - these include Franck-Condon-like structures in the current/voltage characteristic and strong vibronic interactions, which can lead to hopping behavior at the polaron limit. Conformational changes induced by the strong electric field lead to another strong manifestation of the molecular nature of the junction. We overview some of this mechanistic landscape, focusing on significant effects of switching (both stochastic and controlled by the electric field) and of molecular vibronic coupling.

  5. Molecular Mechanism of Water Evaporation.

    PubMed

    Nagata, Yuki; Usui, Kota; Bonn, Mischa

    2015-12-04

    Evaporation is the process by which water changes from a liquid to a gas or vapor, and is a key step in Earth's water cycle. At the molecular level, evaporation requires breaking at least one very strong intermolecular bond between two water molecules at the interface. Despite the importance of this process the molecular mechanism by which an evaporating water molecule gains sufficient energy to escape from the surface has remained elusive. Here, we show, using molecular dynamics simulations at the water-air interface with polarizable classical force field models, that the high kinetic energy of the evaporated water molecule is enabled by a well-timed making and breaking of hydrogen bonds involving at least three water molecules at the interface, the recoil of which allows one of the molecules to escape. The evaporation of water is thus enabled by concerted, ultrafast hydrogen-bond dynamics of interfacial water, and follows one specific molecular pathway.

  6. Computer representation of molecular surfaces

    SciTech Connect

    Max, N.L.

    1981-07-06

    This review article surveys recent work on computer representation of molecular surfaces. Several different algorithms are discussed for producing vector or raster drawings of space-filling models formed as the union of spheres. Other smoother surfaces are also considered.

  7. Molecular tools used in agriculture

    USDA-ARS?s Scientific Manuscript database

    A summary of molecular tools used for research in agriculture were presented. Examples of DNA sequencing, library preparation, use of fingerprinting for pathogens and plant crops, high throughput sequencing, whole-genome amplification, reporter genes, and other methods....

  8. Molecular imaging with engineered physiology

    PubMed Central

    Desai, Mitul; Slusarczyk, Adrian L.; Chapin, Ashley; Barch, Mariya; Jasanoff, Alan

    2016-01-01

    In vivo imaging techniques are powerful tools for evaluating biological systems. Relating image signals to precise molecular phenomena can be challenging, however, due to limitations of the existing optical, magnetic and radioactive imaging probe mechanisms. Here we demonstrate a concept for molecular imaging which bypasses the need for conventional imaging agents by perturbing the endogenous multimodal contrast provided by the vasculature. Variants of the calcitonin gene-related peptide artificially activate vasodilation pathways in rat brain and induce contrast changes that are readily measured by optical and magnetic resonance imaging. CGRP-based agents induce effects at nanomolar concentrations in deep tissue and can be engineered into switchable analyte-dependent forms and genetically encoded reporters suitable for molecular imaging or cell tracking. Such artificially engineered physiological changes, therefore, provide a highly versatile means for sensitive analysis of molecular events in living organisms. PMID:27910951

  9. 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).

  10. Catalysts Encapsulated in Molecular Machines.

    PubMed

    Pan, Tiezheng; Liu, Junqiu

    2016-06-17

    Smart catalysts offer the control of chemical processes and sequences of transformations, and catalysts with unique catalytic behavior can afford chiral products or promote successive polymerization. To meet advanced demands, the key to constructing smart catalysts is to incorporate traditional catalytic functional groups with trigger-induced factors. Molecular machines with dynamic properties and particular topological structures have typical stimulus-responsive features. In recent years, scientists have made efforts to utilize molecular machines (molecular switches, rotaxanes, motors, etc.) as scaffolds to develop smart catalysts. This Minireview focuses on the achievements of developing catalysts encapsulated in molecular machines and their remarkable specialties. This strategy is believed to provide more potential applications in switchable reactions, asymmetric synthesis, and processive catalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Molecular Advancements in Forensic Odontology.

    PubMed

    Babu Rs, A; Rose, D

    2015-05-11

    Forensic odontology explores the field of human identification through dental tissues in cases where there is the destruction of body tissues in criminal investigations and mass disasters. Forensic odontology involves dentists participating in legal and criminal issues. Parameters such as age and gender identification are important in identifying the person or persons. Over the last two decades, the molecular aspect of forensic sciences has increased, and these molecular techniques now provide a novel approach to forensic odontology. Molecular advancements in science like DNA analysis have extended the range of forensic dentistry, as teeth possess the character of resistance toward physical or chemical aggressions. Teeth provide the abundant space for DNA, and hence teeth represent an excellent source of genomic DNA. The present paper focusses on molecular advancements in the field of forensic odontology.

  12. Molecular dermatology comes of age.

    PubMed

    Has, Cristina; Sitaru, Cassian

    2013-01-01

    Groundbreaking advances on the molecular and cellular physiological and physiopathological skin processes, including the complete sequencing of the genome of several species and the increased availability of gene-modified organisms, paved the way to firmly establishing molecular approaches and methods in experimental, translational, and clinical dermatology. As a result, newly developed experimental ex vivo assays and animal models prove exquisite tools for addressing fundamental physiological cutaneous processes and pathogenic mechanisms of skin diseases. A plethora of new findings that were generated using these experimental tools serve as a strong basis for intense translational research efforts aiming at developing new, specific, and sensitive diagnostic tests and efficient "personalized" therapies with less side-effects. Consequently, a broad array of molecular diagnostic tests and therapies for a wide spectrum of skin diseases ranging from genodermatoses through skin neoplasms, allergy, inflammatory and autoimmune diseases, are already routinely used in the clinical dermatology practice. This article highlights several major developments in molecular experimental and clinical dermatology.

  13. 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.

  14. [Molecular monitoring of myeloid leukemia].

    PubMed

    Kiss, Richárd; Király, Attila Péter; Gaál-Weisinger, Júlia; Marosvári, Dóra; Gángó, Péter Ambrus; Demeter, Judit; Bödör, Csaba

    2017-03-08

    The last fifteen years brought a revolution both in treatment and diagnostics of chronic myeloid leukemia. Nowadays, the main method for monitoring of the disease is molecular monitoring with real-time PCR technology which can indicate treatment modification. With the development of the international scale and inter-laboratory standardization the residual tumor mass can be measured accurately and the results are comparable between the different laboratories. By the growing experience in the field of molecular responses we can now accurately predict treatment outcome early on with the so called early molecular response and BCR-ABL1 kinetics, allowing the selection of the best TKI with the treatment-free remission representing real option of the near future. Nevertheless, further advancements can be expected, including the workflow automatization and detection of even deeper molecular responses.

  15. Molecular Aggregation in Disodium Cromoglycate

    NASA Astrophysics Data System (ADS)

    Singh, Gautam; Agra-Kooijman, D.; Collings, P. J.; Kumar, Satyendra

    2012-02-01

    Details of molecular aggregation in the mesophases of the anti-asthmatic drug disodium cromoglycate (DSCG) have been studied using x-ray synchrotron scattering. The results show two reflections, one at wide angles corresponding to π-π stacking (3.32 å) of molecules, and the other at small angles which is perpendicular to the direction of molecular stacking and corresponds to the distance between the molecular aggregates. The latter varies from 35 - 41 å in the nematic (N) phase and 27 -- 32 å in the columnar (M) phase. The temperature evolution of the stack height, positional order correlations in the lateral direction, and orientation order parameter were determined in the N, M, and biphasic regions. The structure of the N and M phases and the nature of the molecular aggregation, together with their dependence on temperature and concentration, will be presented.

  16. Biological and biomimetic molecular machines.

    PubMed

    Huang, Tony J; Juluri, Bala K

    2008-02-01

    The evolution of life facilitates the creation of biological molecular machines. In these so-called 'nanomachines,' nature elegantly shows that when precisely organized and assembled, simple molecular mechanical components can link motions efficiently from the nanometer scale to the macroscopic world, and achieve complex functions such as powering skeletal muscles, synthesizing ATP and producing DNA/RNA. Inspired by nature, researchers are creating artifical molecular machines with tailored structures and properties, with the aim of realizing man-made active nanosystems that operate with the same efficiency and complexity as biological nanomachines. It is anticipated that in the not-too-distant future, unique applications of biological and biomimetic molecular machines will emerge in areas such as biochemical instrumentation and nanomedicine.

  17. Molecular imaging with engineered physiology.

    PubMed

    Desai, Mitul; Slusarczyk, Adrian L; Chapin, Ashley; Barch, Mariya; Jasanoff, Alan

    2016-12-02

    In vivo imaging techniques are powerful tools for evaluating biological systems. Relating image signals to precise molecular phenomena can be challenging, however, due to limitations of the existing optical, magnetic and radioactive imaging probe mechanisms. Here we demonstrate a concept for molecular imaging which bypasses the need for conventional imaging agents by perturbing the endogenous multimodal contrast provided by the vasculature. Variants of the calcitonin gene-related peptide artificially activate vasodilation pathways in rat brain and induce contrast changes that are readily measured by optical and magnetic resonance imaging. CGRP-based agents induce effects at nanomolar concentrations in deep tissue and can be engineered into switchable analyte-dependent forms and genetically encoded reporters suitable for molecular imaging or cell tracking. Such artificially engineered physiological changes, therefore, provide a highly versatile means for sensitive analysis of molecular events in living organisms.

  18. Molecular similarity and property similarity.

    PubMed

    Barbosa, Frédérique; Horvath, Dragos

    2004-01-01

    This paper reviews the main efforts undertaken up to date in order to understand, rationalize and apply the similarity principle (similar compounds=>similar properties) as a computational tool in modern drug discovery. The best suited mathematical expression of this classical working hypothesis of medicinal chemistry needs to be carefully chosen (out of the virtually infinite possible implementations in terms of molecular descriptors and molecular similarity metrics), in order to achieve an optimal validation of the hypothesis that molecules that are neighbors in the Structural Space will also display similar properties. This overview will show why no single "absolute" measure of molecular similarity can be conceived, and why molecular similarity scores should be considered tunable tools that need to be adapted to each problem to solve.

  19. Molecular Profiling of Endometrial Malignancies

    PubMed Central

    Samarnthai, Norasate; Hall, Kevin; Yeh, I-Tien

    2010-01-01

    Molecular profiling of endometrial neoplasms reveals genetic changes in endometrial carcinomas that support the dualistic model, in which type I carcinomas are estrogen-dependent, low grade lesions and type II carcinomas are nonestrogen dependent and high grade. The molecular changes in type I endometrial carcinomas include mutations in PTEN, PIK3CA, KRAS, and β-catenin, along with microsatellite instability, whereas type II endometrial carcinomas are characterized by genetic alterations in p53, HER2/neu, p16, and E-cadherin. For endometrial neoplasms with a malignant mesenchymal component, C-MYC mutations and loss of heterozygosity are frequently seen in carcinosarcomas, and a fusion gene, JAZF1/JJAZ1, is distinctive for endometrial stromal sarcoma. In addition, p53 mutations may play an important role in tumorigenesis of undifferentiated endometrial sarcoma. These molecular changes can help in the diagnosis of endometrial neoplasms, as well as form the basis of molecular targeted therapy. PMID:20368795

  20. Molecular imaging applications for immunology.

    PubMed

    Hildebrandt, Isabel Junie; Gambhir, Sanjiv Sam

    2004-05-01

    The use of multimodality molecular imaging has recently facilitated the study of molecular and cellular events in living subjects in a noninvasive and repetitive manner to improve the diagnostic capability of traditional assays. The noninvasive imaging modalities utilized for both small animal and human imaging include positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound, and computed tomography (CT). Techniques specific to small-animal imaging include bioluminescent imaging (BIm) and fluorescent imaging (FIm). Molecular imaging permits the study of events within cells, the examination of cell trafficking patterns that relate to inflammatory diseases and metastases, and the ability to rapidly screen new drug treatments for distribution and effectiveness. In this paper, we will review the current field of molecular imaging assays (especially those utilizing PET and BIm modalities) and examine how they might impact animal models and human disease in the field of clinical immunology.

  1. Computerized molecular modeling of carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Computerized molecular modleing continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studi...

  2. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  3. 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

  4. Visualization of Molecular Orbitals: Formaldehyde

    ERIC Educational Resources Information Center

    Olcott, Richard J.

    1972-01-01

    Describes a computer program that plots a solid" representation of molecular orbital charge density which can be used to analyze wave functions of molecules. Illustrated with diagrams for formaldehyde. (AL)

  5. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  6. Molecular Mechanism of Water Evaporation

    NASA Astrophysics Data System (ADS)

    Nagata, Yuki; Usui, Kota; Bonn, Mischa

    2015-12-01

    Evaporation is the process by which water changes from a liquid to a gas or vapor, and is a key step in Earth's water cycle. At the molecular level, evaporation requires breaking at least one very strong intermolecular bond between two water molecules at the interface. Despite the importance of this process the molecular mechanism by which an evaporating water molecule gains sufficient energy to escape from the surface has remained elusive. Here, we show, using molecular dynamics simulations at the water-air interface with polarizable classical force field models, that the high kinetic energy of the evaporated water molecule is enabled by a well-timed making and breaking of hydrogen bonds involving at least three water molecules at the interface, the recoil of which allows one of the molecules to escape. The evaporation of water is thus enabled by concerted, ultrafast hydrogen-bond dynamics of interfacial water, and follows one specific molecular pathway.

  7. Molecular Sieve Regeneration System (MSRS)

    SciTech Connect

    Nasise, J.E.; Anderson, J.L. ); Naruse, Y. )

    1992-01-01

    A Molecular Sieve Regeneration System (MSRS) was added to the existing Tritium Waste Treatment system (TWT) within the Tritium Systems Test Assembly (TSTA) at Los Alamos National Laboratory. The Department of Energy (DOE) no longer allows inventory by difference'' for radioactive wastes that are to be buried. The MSRS was designed and built to comply with this requirement. Within the TWT, water is generated by the catalytic conversion of hydrogen isotopes and removed by molecular sieve trapping prior to release to the environment. Molecular sieve regeneration is required to remove the trapped water and to rejuvenate the beds. The MSRS permits the collection and direct tritium assay of regenerated tritiated water from molecular sieve beds. This paper describes the MSRS in detail and how it is interfaced with the TWT.

  8. Molecular Sieve Regeneration System (MSRS)

    SciTech Connect

    Nasise, J.E.; Anderson, J.L.; Naruse, Y.

    1992-03-01

    A Molecular Sieve Regeneration System (MSRS) was added to the existing Tritium Waste Treatment system (TWT) within the Tritium Systems Test Assembly (TSTA) at Los Alamos National Laboratory. The Department of Energy (DOE) no longer allows ``inventory by difference`` for radioactive wastes that are to be buried. The MSRS was designed and built to comply with this requirement. Within the TWT, water is generated by the catalytic conversion of hydrogen isotopes and removed by molecular sieve trapping prior to release to the environment. Molecular sieve regeneration is required to remove the trapped water and to rejuvenate the beds. The MSRS permits the collection and direct tritium assay of regenerated tritiated water from molecular sieve beds. This paper describes the MSRS in detail and how it is interfaced with the TWT.

  9. Visualization of Molecular Orbitals: Formaldehyde

    ERIC Educational Resources Information Center

    Olcott, Richard J.

    1972-01-01

    Describes a computer program that plots a solid" representation of molecular orbital charge density which can be used to analyze wave functions of molecules. Illustrated with diagrams for formaldehyde. (AL)

  10. Molecularly imprinted materials: synthesis, properties, applications

    NASA Astrophysics Data System (ADS)

    Lisichkin, Georgii V.; Krutyakov, Yu A.

    2006-10-01

    This review is devoted to the method of molecular imprinting. The physicochemical fundamentals and mechanisms of covalent and non-covalent molecular imprinting aimed at the development of organic polymeric sorbents capable of molecular recognition are considered. Attention is focused on the preparation of molecular imprints on mineral supports. The mechanisms of molecular recognition in adsorption are discussed. Application fields of materials with molecular imprints are briefly surveyed.

  11. Molecular machinery built from DNA

    NASA Astrophysics Data System (ADS)

    Bath, Jonathan; Turberfield, Andrew J.

    2013-03-01

    DNA can be used as both construction material and fuel for molecular motors. Systems of motors and tracks can be constructed and movement of the motor along the track can be directly observed. The path that a taken by a motor as it navigates a network of tracks can be programmed by instructions that are added externally or carried by the motor itself. Such systems might be used as part molecular assembly lines that can be dynamically reconfigured in response to changing demands.

  12. Molecular dynamics with quantum fluctuations

    SciTech Connect

    Georgescu, Ionut; Mandelshtam, Vladimir A.

    2010-09-01

    A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short-time limit and is computationally very efficient.

  13. Chopped molecular beam multiplexing system

    NASA Technical Reports Server (NTRS)

    Adams, Billy R. (Inventor)

    1986-01-01

    The integration of a chopped molecular beam mass spectrometer with a time multiplexing system is described. The chopping of the molecular beam is synchronized with the time intervals by a phase detector and a synchronous motor. Arithmetic means are generated for phase shifting the chopper with respect to the multiplexer. A four channel amplifier provides the capacity to independently vary the baseline and amplitude in each channel of the multiplexing system.

  14. Molecular basis of lymphokine action

    SciTech Connect

    Webb, D.R. ); Pierce, C.W. ); Cohen, S. )

    1987-01-01

    This book contains over 30 selections. Some of the titles are: Regulation of IL2 and related genes at the mRNA level; Molecular biology of Interleukin-3; Isolation and characterization of mouse and human cDNA clones encoding IL-4 and IgA-Enhancing Factor/Esoinophil CSF (IL-5); Molecular cloning and characterization of the human gene for Interleukin-3 (IL-3); and Soluble immune response suppressor (SIRS) mediated inhibition of cell division.

  15. Atomic and Molecular Databases, VAMDC

    NASA Astrophysics Data System (ADS)

    Dubernet, M. L.; Zwölf, C. M.; Moreau, N.; Ba, Y. A.

    2016-10-01

    The VAMDC Consortium is a worldwide consortium which federates Atomic and Molecular databases through an e-science infrastructure and a political organisation. About 90% of the inter-connected databases handle data that are used for the interpretation of spectra and for the modeling of media of many fields of astrophysics. This paper presents how the VAMDC Consortium is organised in order to publish atomic and molecular data for astrophysics.

  16. Molecular dynamics simulation of pyridine

    NASA Astrophysics Data System (ADS)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

  17. Molecular Spiders in One Dimension

    PubMed Central

    Antal, Tibor; Krapivsky, P. L.; Mallick, Kirone

    2008-01-01

    Molecular spiders are synthetic bio-molecular systems which have “legs” made of short single-stranded segments of DNA. Spiders move on a surface covered with single-stranded DNA segments complementary to legs. Different mappings are established between various models of spiders and simple exclusion processes. For spiders with simple gait and varying number of legs we compute the diffusion coefficient; when the hopping is biased we also compute their velocity. PMID:19079565

  18. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  19. Data warehousing in molecular biology.

    PubMed

    Schönbach, C; Kowalski-Saunders, P; Brusic, V

    2000-05-01

    In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

  20. Chemical engineering of molecular qubits.

    PubMed

    Wedge, C J; Timco, G A; Spielberg, E T; George, R E; Tuna, F; Rigby, S; McInnes, E J L; Winpenny, R E P; Blundell, S J; Ardavan, A

    2012-03-09

    We show that the electron spin phase memory time, the most important property of a molecular nanomagnet from the perspective of quantum information processing, can be improved dramatically by chemically engineering the molecular structure to optimize the environment of the spin. We vary systematically each structural component of the class of antiferromagnetic Cr(7)Ni rings to identify the sources of decoherence. The optimal structure exhibits a phase memory time exceeding 15  μs.

  1. 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

  2. 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

  3. [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.

  4. Molecular Simulations in Astrobiology

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.; Vincenzi, Donald L. (Technical Monitor)

    2001-01-01

    One of the main goals of astrobiology is to understand the origin of cellular life. In the absence of any record of the earliest ancestors of contemporary cells, protocells, the most direct way to test our understanding of their characteristics is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs of molecules that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing and storing energy, and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following, questions about these proteins: (1) How do small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides aggregate to form membrane-spannin(y structures (e.g., channels)? (3) By what mechanisms do such aggregates perform their functions? The simulations are performed using the molecular dynamics (MD) method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated directly in real space while long-range forces are evaluated in reciprocal space, usually using a particle-mesh algorithm which is of order O(NlnN). Currently, a time step of 2 femtoseconds is typically used, thereby making studies of problems occurring on multi-nanosecond time scales (10(exp 6) - 10(exp 8) time steps) accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude. Such an extension requires both algorithmic improvements and codes scalable to a large number of parallel

  5. Molecular Beam Epitaxy of

    NASA Astrophysics Data System (ADS)

    Hsieh, Kuan Hsiung

    Ga(,0.48)In(,0.52)As recently emerges as a promising material for high speed applications. It also has a direct bandgap with gap energy suitable for optical applications. It is the purpose of this thesis to grow high quality Ga(,0.47)In(,0.53)As, lattice-matched Al(,0.48)In(,0.52)As and heterojunction structures by molecular beam epitaxy technique for applications in the areas of modulation-doped high mobility devices and internal photoemission Schottky diodes for infrared detection. Single crystal Al metal deposition on GaInAs by MBE is also studied for its electrical properties. Mobility enhancement has been demonstrated in modulation-doped structures at low temperatures. Very high mobilities were obtained: 10,900 cm('2)/Vs at room temperature, 55,500 cm('2)/Vs at 77K and 70,200 cm('2)/Vs at 10K with corresponding two-dimensional electron gas densities greater than 1 x 10('12) l/cm('2). The quality of Ga(,0.47)In(,0.53)As and the parallel conduction in this material are the limiting factors in its mobility. A new ohmic contact phenomenon has been observed in the MBE single crystal Al metal on Ga(,0.47)In(,0.53)AS samples. Its contact resistivity is measured to be as small as 1 x 10('-6) (OMEGA)-cm('2). The Fermi-level pinning near the conduction band edge might be caused by the interface defects. A planar doping technique has been employed to enhance the built-in barrier height to a value of about 0.5 eV in the single crystal Al on n-p('+)-n-Ga(,0.47)In(,0.52)As structures. This novel quasi-Schottky diode also shows a forward ideal factor of 1.03. As for optical detectors, four kinds of diodes were made for internal photoemission studies: Au Schottky on Ga(,0.47)In(,0.53)As in the wavelength range of 1.9 (mu)m to 2.5 (mu)m, Au Schottky on Al(,0.48)In(,0.52)As in 1.1 (mu)m to 2.0 (mu)m range, single crystal Al on (Al(,0.8)Ga(,0.2))(,0.48)In(,0.52)As with improved quantum yields and lastly a Ga(,0.47)In(,0.53)As/Al(,0.48)In(,0.52)As heterojunction with a measured

  6. Molecular Simulations in Astrobiology

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.; Vincenzi, Donald L. (Technical Monitor)

    2001-01-01

    One of the main goals of astrobiology is to understand the origin of cellular life. In the absence of any record of the earliest ancestors of contemporary cells, protocells, the most direct way to test our understanding of their characteristics is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs of molecules that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing and storing energy, and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following, questions about these proteins: (1) How do small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides aggregate to form membrane-spannin(y structures (e.g., channels)? (3) By what mechanisms do such aggregates perform their functions? The simulations are performed using the molecular dynamics (MD) method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated directly in real space while long-range forces are evaluated in reciprocal space, usually using a particle-mesh algorithm which is of order O(NlnN). Currently, a time step of 2 femtoseconds is typically used, thereby making studies of problems occurring on multi-nanosecond time scales (10(exp 6) - 10(exp 8) time steps) accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude. Such an extension requires both algorithmic improvements and codes scalable to a large number of parallel

  7. Design and Development of Molecular Imaging Probes

    PubMed Central

    Chen, Kai; Chen, Xiaoyuan

    2013-01-01

    Molecular imaging, the visualization, characterization and measurement of biological processes at the cellular, subcellular level, or even molecular level in living subjects, has rapidly gained importance in the dawning era of personalized medicine. Molecular imaging takes advantage of the traditional diagnostic imaging techniques and introduces molecular imaging probes to determine the expression of indicative molecular markers at different stages of diseases and disorders. As a key component of molecular imaging, molecular imaging probe must be able to specifically reach the target of interest in vivo while retaining long enough to be detected. A desirable molecular imaging probe with clinical translation potential is expected to have unique characteristics. Therefore, design and development of molecular imaging probe is frequently a challenging endeavor for medicinal chemists. This review summarizes the general principles of molecular imaging probe design and some fundamental strategies of molecular imaging probe development with a number of illustrative examples. PMID:20388106

  8. Temperature Evolution of Molecular Clouds in the Central Molecular Zone

    NASA Astrophysics Data System (ADS)

    Krieger, Nico; Ott, Jürgen; Walter, Fabian; Kruijssen, J. M. Diederik; Beuther, Henrik

    2017-01-01

    We infer the absolute time dependence of kinematic gas temperature along a proposed orbit of molecular clouds in the Central Molecular Zone (CMZ) of the Galactic Center (GC). Ammonia gas temperature maps are one of the results of the ``Survey of Water and Ammonia in the Galactic Center'' (SWAG, PI: J. Ott); the dynamical model of molecular clouds in the CMZ was taken from Kruijssen et al. (2015). We find that gas temperatures increase as a function of time in both regimes before and after the cloud passes pericenter on its orbit in the GC potential. This is consistent with the recent proposal that pericenter passage triggers gravitational collapse. Other investigated quantities (line width, column density, opacity) show no strong sign of time dependence but are likely dominated by cloud-to-cloud variations.

  9. Molecular Tracers of Turbulent Shocks in Giant Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Pon, Andy; Johnstone, D. I.; Kaufman, M. J.

    2013-01-01

    Molecular clouds exhibit large linewidths, which are usually interpreted as being due to supersonic turbulence. This turbulence plays a key role in many theories of star formation, as it is believed to help support and fragment molecular clouds. Current numerical MHD simulations show that the turbulent energy of a molecular cloud dissipates on the order of a crossing time, but do not explicitly follow how this energy is released. We have run models of C-type shocks, based on Kaufman & Neufeld (1996), propagating into gas with densities near 1000 cm3 at velocities of a few km/s, appropriate for the ambient conditions inside of a molecular cloud, to determine which species and transitions dominate the cooling and radiative energy release associated with the dissipation of turbulent energy in shocks within molecular clouds. Combining these shock models and estimates for the rate of turbulent energy dissipation (Basu & Murali 2001), we produce synthetic CO spectra and predict those line emissions that will be observable with current and upcoming observational facilities, such as Herschel, SOFIA, ALMA, and CCAT. We compare our synthetic shock spectra to the photodissociation region (PDR) models of Kaufman et al. (1999) and show that mid-J CO lines (e.g., CO J = 7 to 6) from molecular clouds illuminated by standard interstellar radiation fields are dominated by emission from shocked gas. We also present Herschel observations of these shock tracing lines. References: Basu, S. & Murali, C. 2001, ApJ, 551, 743 Kaufman, M. J. & Neufeld, D. A. 1996, ApJ, 456, 250 Kaufman, M. J., Wolfire, M. G., Hollenbach, D. J., & Luhman, M. L. 1999, ApJ, 527, 795

  10. Molecular abundances in the Sagittarius A molecular cloud

    NASA Technical Reports Server (NTRS)

    Minh, Y. C.; Irvine, W. M.; Friberg, P.

    1992-01-01

    We have obtained column densities for HCO(+), HCO, HCS(+), C3H2, HC5N, SiO, OCS, HCOOH, CH3CH2OH, and CH3CCH toward Sgr A. The fractional abundance of SiO relative to molecular hydrogen in Sgr A is comparable to that for the Orion plateau, about 10 exp-7 to 10 exp -8, which may be a typical value for hot clouds. The abundances of HCO, CH3CH2OH, and CH3CCH all appear to be enhanced relative to other molecular clouds such as Sgr B2.

  11. Molecular abundances in the Sagittarius A molecular cloud.

    PubMed

    Minh, Y C; Irvine, W M; Friberg, P

    1992-01-01

    We have obtained column densities for HCO+, HCO, HCS+, C3H2, HC5N, SiO, OCS, HCOOH, CH3CH2OH, and CH3CCH toward Sgr A. The fractional abundance of SiO relative to molecular hydrogen in Sgr A is comparable to that for the Orion plateau, approximately 10(-7)-10(-8), which may be a typical value for hot clouds. The abundances of HCO, CH3CH2OH and CH3CCH all appear to be enhanced relative to other molecular clouds such as Sgr B2.

  12. Molecular outflows in the Monoceros OB1 molecular cloud

    NASA Technical Reports Server (NTRS)

    Margulis, Michael; Lada, Charles J.; Snell, Ronald L.

    1988-01-01

    Observations of J = 1-0 emission from CO in nine suspected molecular outflows in the Monoceros OB1 molecular cloud are presented. It is found that, if the five sources which are confirmed to be outflows conserve momentum as they evolve, they will sweep up at least 0.6 percent of the mass of the entire cloud before coming into pressure equilibrium with the ambient gas. This number indicates that it should take at most 160 episodes of similar outflow activity in order to sweep up the bulk of the Mon OB1 cloud to highly supersonic speeds.

  13. Molecular diagnostics: Molecular Med Tri-Con 2013.

    PubMed

    Klein, Roger D

    2013-07-01

    The 20th annual Molecular Med Tri-Con conference, sponsored by Cambridge Health Institute (MA, USA), consisted of over 250 presentations within five parallel 'channels': 'Diagnostics, Therapeutics, Clinical, Informatics and Cancer', along with five preliminary symposia, 15 short courses, a plenary keynote session entitled 'Personalized Oncology - Fulfilling the Promise for Today's Patients' and a keynote panel entitled, 'Emerging Technologies and Industry Perspectives'. Over 3000 individuals from academia, clinical laboratories and industry were in attendance. This article will focus on the Keynote Session of 'Molecular Diagnostics' track within the Diagnostics Channel.

  14. 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.

  15. Molecular modeling of inelastic electron transport in molecular junctions

    NASA Astrophysics Data System (ADS)

    Jiang, Jun; Kula, Mathias; Luo, Yi

    2008-09-01

    A quantum chemical approach for the modeling of inelastic electron tunneling spectroscopy of molecular junctions based on scattering theory is presented. Within a harmonic approximation, the proposed method allows us to calculate the electron-vibration coupling strength analytically, which makes it applicable to many different systems. The calculated inelastic electron transport spectra are often in very good agreement with their experimental counterparts, allowing the revelation of detailed information about molecular conformations inside the junction, molecule-metal contact structures, and intermolecular interaction that is largely inaccessible experimentally.

  16. 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

  17. Nucleic acid based molecular devices.

    PubMed

    Krishnan, Yamuna; Simmel, Friedrich C

    2011-03-28

    In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Molecular subtyping of prostate cancer.

    PubMed

    Kaffenberger, Samuel D; Barbieri, Christopher E

    2016-05-01

    The recent publication of The Cancer Genome Atlas molecular taxonomy of primary prostate cancer highlights the increased understanding of the genomic basis of human prostate cancer, but also emphasizes the complexity and heterogeneity of prostate cancer. Seven molecular subclasses have been defined on the basis of early genomic alterations, which are largely mutually exclusive. We review the recent advances in the genomic understanding of human prostate cancer, with focus on molecular subclassification. Broadly, prostate cancer can be classified based upon whether specific genomic rearrangements, such as the Transmembrane Protease, Serine 2-ETS-related gene fusion occur or whether specific alterations such as Speckle-type POZ protein and forkhead box A1 mutations occur. The molecular drivers remain to be identified in a further quarter of human prostate cancers. Depending upon the molecular subclassification and the coincident genomic alterations, specific clinical insights can be gained from this information, including associations with pathologic factors, race, and prognosis, as well as the possibility for future precision therapies.

  19. OH+ in Diffuse Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Federman, Steven R.; Porras, A. J.; Welty, D. E.; Ritchey, A. M.

    2013-06-01

    We are conducting a comprehensive survey of absorption from diffuse molecular clouds from archival UVES/VLT data. Here we focus on OH+ and OH results, which indicate these molecules prefer different environments. The dominant absorption feature in OH+ arises from a main component seen in CH+, while OH absorption follows CN absorption. This distinction provides useful constraints on OH chemistry in diffuse molecular clouds. Since CH+ detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH+ as well, confirming OH+ and H2O+ observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for high enough density and molecular fraction before detectable amounts of OH are seen. Thus, while OH+ leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds.

  20. Cooperative behavior of molecular motors.

    PubMed

    Vermeulen, Karen C; Stienen, Ger J M; Schmid, Christoph F

    2002-01-01

    Both experimental evidence and theoretical models for collective effects in the working mechanism of molecular motors are reviewed at three different levels, namely: (i) interaction between the two heads of double-headed motors, particularly in processive motors like kinesin, myosin V and myosin VI, (ii) cooperative regulation of muscle thin filaments by accessory proteins and the Ca2+ level, and (iii) collective dynamic effects stemming from the mechanical coupling of molecular motors within macroscopic structures such as muscle thick filaments or axonemes. We aim to bridge the gap between structural information at the molecular level and physiological data with accompanying specific models on the one hand, and general stochastic physical models for the action of molecular motors on the other hand. An underlying assumption is that while, ultimately, the function of molecular motors will be explainable by a quantitative description of specific intramolecular dynamics and intermolecular interactions, for some coarse grained larger scale dynamic features it will be sufficient and illuminating to construct physical models that are simplified to the bare essentials.

  1. Molecular wires, switches and memories

    NASA Astrophysics Data System (ADS)

    Chen, Jia

    Molecular electronics, an emerging field, makes it possible to build individual molecules capable of performing functions identical or analogous to present- day conductors, switches, or memories. These individual molecules, with a nano-meter scale characteristic length, can be designed and chemically synthesized with specific atoms, geometries and charge distribution. This thesis focuses on the design, and measurements of molecular wires, and related strategically engineered structures-molecular switches and memories. The experimental system relies on a thermodynamically driven self-assembling process to attach molecules onto substrate surfaces without intervention from outside. The following topics will be discussed: directed nanoscale manipulation of self-assembled molecules using scanning tunneling microscope; investigation on through-bond transport of nanoscale symmetric metal/conjugated self- assembled monolayers (SAM)/metal junctions, where non- Ohmic thermionic emission was observed to be the dominant process, with isocyanide-Pd contacts showing the lowest thermionic barrier of 0.22 eV; the first realization of robust and large reversible switching behavior in an electronic device that utilizes molecules containing redox centers as the active component, exhibiting negative differential resistance (NDR) and large on-off peak-to-valley ratio (PVR); observation of erasable storage of higher conductivity states in these redox- center containing molecular devices, and demonstration of a two-terminal electronically programmable and erasable molecular memory cell with long bit retention time.

  2. 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.

  3. Modeling Molecular Dynamics from Simulations

    SciTech Connect

    Hinrichs, Nina Singhal

    2009-01-28

    Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

  4. Molecular diagnosis in lung diseases.

    PubMed

    Calabrese, Fiorella; Lunardi, Francesca; Popper, Helmut

    2015-01-01

    The development of different molecular biology techniques in the past decade has led to an explosion of new research in molecular pathology with consequent important applications to diagnosis, prognosis, and therapeutics, as well as a clearer concept of the disease pathogenesis. Many methods used in molecular pathology are now validated and used in several areas of pathological diagnosis, particularly on infectious and neoplastic diseases. The spectrum of infectious diseases, especially lung infective diseases, is now broadening and modifying, thus the pathologist is increasingly involved in the diagnosis of these pathologies. The precise tissue characterization of lung infections has an important impact on specific therapeutic treatment. Increased knowledge of significant alterations in lung cancer has led today to a better understanding of the pathogenic substrate underlying the development, progression and metastasis of neoplastic processes. Molecular tests are now routinely performed in different lung tumors allowing a more precise patient stratification in terms of prognosis and therapy. This review focuses on molecular pathology of the principal infective lung diseases and tumors.

  5. Molecular therapeutics in prostate cancer.

    PubMed

    Nicholson, B; Theodorescu, D

    2003-01-01

    The purpose of this review is to provide information on the molecular basis of prostate cancer biology and to identify some of the targets for therapy, and highlight some potential strategies for molecular treatment. Here we give a synopsis of what we have learned regarding molecular biology of cancer in general and the directions research might take in the future in order to impact prostate cancer specifically. This work is certainly not encyclopedic in nature and we apologize in advance to colleagues whose work we were no able to include. Hope lies in learning to utilize some of these molecular workings for better prevention, diagnosis, and treatment of the most common solid organ cancer in men. Prostate cancer is a formidable disease and at current rates of diagnosis will affect one-in-six men living in the United States (Greenlee et al., 2000) Many of these men are diagnosed at an early stage of the disease and can be effectively treated by surgery or radiation. However, a significant fraction of men are diagnosed with later stage disease or progress despite early curative therapeutic attempts. Unfortunately, many of these men succumb to prostate cancer, as management options are limited and not always successful. Through an understanding of the molecular processes that occur in the development and progression of prostate cancer, novel therapies will arise that will provide longer survival, better quality of life, and a chance for cure in men afflicted with this disease.

  6. Molecular imprinting: perspectives and applications.

    PubMed

    Chen, Lingxin; Wang, Xiaoyan; Lu, Wenhui; Wu, Xiaqing; Li, Jinhua

    2016-04-21

    Molecular imprinting technology (MIT), often described as a method of making a molecular lock to match a molecular key, is a technique for the creation of molecularly imprinted polymers (MIPs) with tailor-made binding sites complementary to the template molecules in shape, size and functional groups. Owing to their unique features of structure predictability, recognition specificity and application universality, MIPs have found a wide range of applications in various fields. Herein, we propose to comprehensively review the recent advances in molecular imprinting including versatile perspectives and applications, concerning novel preparation technologies and strategies of MIT, and highlight the applications of MIPs. The fundamentals of MIPs involving essential elements, preparation procedures and characterization methods are briefly outlined. Smart MIT for MIPs is especially highlighted including ingenious MIT (surface imprinting, nanoimprinting, etc.), special strategies of MIT (dummy imprinting, segment imprinting, etc.) and stimuli-responsive MIT (single/dual/multi-responsive technology). By virtue of smart MIT, new formatted MIPs gain popularity for versatile applications, including sample pretreatment/chromatographic separation (solid phase extraction, monolithic column chromatography, etc.) and chemical/biological sensing (electrochemical sensing, fluorescence sensing, etc.). Finally, we propose the remaining challenges and future perspectives to accelerate the development of MIT, and to utilize it for further developing versatile MIPs with a wide range of applications (650 references).

  7. Fabrication and Characterization of Molecular Electronic Devices.

    PubMed

    Kim, Youngsang; Song, Hyunwook

    2015-02-01

    The concept of molecular electronic devices is utilizing single molecules or molecular monolayers as active electronic components. Rapid advances in technology have enabled us to engineer molecular electronic devices with diverse functionalities. This review article emphasizes on experimental aspects of electronic devices made with single molecules or molecular monolayers, with a primary focus on the characterization and manipulation of charge transport.

  8. Human molecular embryogenesis: an overview.

    PubMed

    Oligny, L L

    2001-01-01

    Molecular embryology is a rapidly evolving field of great complexity. This overview is primarily for the newcomer to this field, in an attempt to demystify the processes by which a human single-celled zygote eventually forms an embryo. Although all embryonic cells share the same genetic information, they differentiate according to the basic plan dictated not only by multiple families of transcription factors to silence some genes and activate others but also through DNA methylation, histone acetylation, and heterochromatinization. Regional expression of various transcription factors causes embryos to establish primary embryonic axes. Once the basic body plan is established, the region-specific diversity becomes progressively finer, and each cell eventually develops a "molecular address" characterized by the expression of specific genes. The overview is divided into two main parts: embryonic cell growth and morphogenesis. At the present time, more is known about the details of molecular regulation of the embryonic growth than about morphogenesis.

  9. Laser Ablation Molecular Isotopic Spectrometry

    NASA Astrophysics Data System (ADS)

    Russo, Richard E.; Bol'shakov, Alexander A.; Mao, Xianglei; McKay, Christopher P.; Perry, Dale L.; Sorkhabi, Osman

    2011-02-01

    A new method of performing optical isotopic analysis of condensed samples in ambient air and at ambient pressure has been developed: Laser Ablation Molecular Isotopic Spectrometry (LAMIS). The technique uses radiative transitions from molecular species either directly vaporized from a sample or formed by associative mechanisms of atoms or ions in a laser ablation plume. This method is an advanced modification of a known atomic emission technique called laser-induced breakdown spectroscopy (LIBS). The new method — LAMIS — can determine not only chemical composition but also isotopic ratios of elements in the sample. Isotopic measurements are enabled by significantly larger isotopic shifts found in molecular spectra relative to atomic spectra. Analysis can be performed from a distance and in real time. No sample preparation or pre-treatment is required. Detection of the isotopes of hydrogen, boron, carbon, and oxygen are discussed to illustrate the technique.

  10. Molecular diagnostics of neurodegenerative disorders.

    PubMed

    Agrawal, Megha; Biswas, Abhijit

    2015-01-01

    Molecular diagnostics provide a powerful method to detect and diagnose various neurological diseases such as Alzheimer's and Parkinson's disease. The confirmation of such diagnosis allows early detection and subsequent medical counseling that help specific patients to undergo clinically important drug trials. This provides a medical pathway to have better insight of neurogenesis and eventual cure of the neurodegenerative diseases. In this short review, we present recent advances in molecular diagnostics especially biomarkers and imaging spectroscopy for neurological diseases. We describe advances made in Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD), and finally present a perspective on the future directions to provide a framework for further developments and refinements of molecular diagnostics to combat neurodegenerative disorders.

  11. Slow Molecular Recognition by RNA.

    PubMed

    Gleitsman, Kristin R; Sengupta, Raghuvir N; Herschlag, Daniel

    2017-09-28

    Molecular recognition is central to biological processes, function, and specificity. Proteins associate with ligands with maximal rates that match the theoretical limit set by the rate of diffusional collision and with a wide range of observed values. As less is known about RNA association, we compiled association rate constants for all RNA/ligand complexes that we could find in the literature. Like proteins, RNAs exhibit a wide range of association rate constants. However, the fastest RNA association rates are considerably slower than those of the fastest protein associations and fall well below the diffusional limit. The apparently general observation of slow association with RNAs has implications for evolution and for modern-day biology. Our compilation highlights a quantitative molecular property that can contribute to biological understanding and underscores our limited physical understanding of molecular recognition events. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  12. Molecular imaging in cancer treatment

    PubMed Central

    Michalski, Mark H.

    2010-01-01

    The success of cancer therapy can be difficult to predict, as its efficacy is often predicated upon characteristics of the cancer, treatment, and individual that are not fully understood or are difficult to ascertain. Monitoring the response of disease to treatment is therefore essential and has traditionally been characterized by changes in tumor volume. However, in many instances, this singular measure is insufficient for predicting treatment effects on patient survival. Molecular imaging allows repeated in vivo measurement of many critical molecular features of neoplasm, such as metabolism, proliferation, angiogenesis, hypoxia, and apoptosis, which can be employed for monitoring therapeutic response. In this review, we examine the current methods for evaluating response to treatment and provide an overview of emerging PET molecular imaging methods that will help guide future cancer therapies. PMID:20661557

  13. [Molecular targets in colon cancer].

    PubMed

    Borner, M M

    2006-04-01

    Colorectal cancer is the second leading cause of cancer death in Switzerland. The nihilism that dominated the treatment of these patients for decades has been replaced by a measure of enthusiasm, given recent therapeutic advances. New anticancer drugs such as irinotecan and oxaliplatin have changed the standard chemotherapy treatment of metastatic colorectal cancer. However, the real hype has come from molecular targeted therapy. Identification of cellular processes characteristic of colon cancer has permitted therapeutic targeting with favorable therapeutic index. Inhibition of the epidermal growth factor receptor in the clinic has provided proof of principle that interruption of signal transduction cascades in patients has therapeutic potential. Angiogenesis, especially the vascular endothelial growth factor pathway, has been proven to be another highly successful molecular target. In this article, we will review molecular targets, which are under active clinical investigation in colon cancer.

  14. Molecular Pathogenesis of Hepatocellular Carcinoma

    PubMed Central

    Ho, Daniel Wai-Hung; Lo, Regina Cheuk-Lam; Chan, Lo-Kong; Ng, Irene Oi-Lin

    2016-01-01

    The pathogenesis of hepatocellular carcinoma (HCC) is a multistep process involving the progressive accumulation of molecular alterations pinpointing different molecular and cellular events. The next-generation sequencing technology is facilitating the global and systematic evaluation of molecular landscapes in HCC. There is emerging evidence supporting the importance of cancer metabolism and tumor microenvironment in providing a favorable and supportive niche to expedite HCC development. Moreover, recent studies have identified distinct surface markers of cancer stem cell (CSC) in HCC, and they also put forward the profound involvement of altered signaling pathways and epigenetic modifications in CSCs, in addition to the concomitant drug resistance and metastasis. Taken together, multiple key genetic and non-genetic factors, as well as liver CSCs, result in the development and progression of HCC. PMID:27781201

  15. Molecular biomimetics: nanotechnology through biology

    NASA Astrophysics Data System (ADS)

    Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K.-Y.; Schulten, Klaus; Baneyx, François

    2003-09-01

    Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

  16. Molecular recognition of bilayer vesicles.

    PubMed

    Voskuhl, Jens; Ravoo, Bart Jan

    2009-02-01

    Vesicles have been a versatile topic of research in chemistry ever since the discovery that, besides phospholipids, synthetic amphiphiles can also form molecular bilayers enclosing a small aqueous compartment. Non-covalent interactions of receptors and ligands or hosts and guests at vesicle surfaces resemble recognition processes at biological membranes, including cell recognition, adhesion and fusion. Molecular recognition at membranes is often mediated by a multivalent instead of a monovalent interaction. This tutorial review describes the basics as well as the latest developments in biomimetic supramolecular chemistry of bilayer vesicles. We describe how molecular recognition can mediate the interaction between vesicles, and how the biomimetic supramolecular chemistry of vesicles furthers our understanding of biological membranes.

  17. Molecular Modeling of Thermosetting Polymers

    NASA Astrophysics Data System (ADS)

    Patnaik, Soumya; Varshney, Vikas; Farmer, Barry

    2008-03-01

    In this work we present molecular modeling of thermosetting polymers with special emphasis on building atomistic models. Different approaches to building highly cross-linked polymer networks starting from un-crosslinked systems are discussed. A multi-step procedure for relaxing the molecular topology during crosslinking was proposed which allows for minimizing the increase in the residual internal stresses with increasing degree of crosslinking. This methodology was applied to epoxy based thermosets and several materials properties such as density, Young's modulus, glass transition temperature, thermal expansion coefficient and volume shrinkage during curing were calculated and found to be in good agreement with experimental results. Along with the materials properties, the simulations also highlighted the distribution of molecular weight build up and inception of gel point during the network formation.

  18. Physical conditions in molecular clouds

    NASA Technical Reports Server (NTRS)

    Evans, Neal J., II

    1989-01-01

    Recent developments have complicated the picture of the physical conditions in molecular clouds. The discoveries of widespread emission from high-J lines of CD and 12-micron IRAS emission have revealed the presence of considerably hotter gas and dust near the surfaces of molecular clouds. These components can complicate interpretation of the bulk of the cloud gas. Commonly assumed relations between column density or mean density and cloud size are called into question by conflicting results and by consideration of selection effects. Analysis of density and density structure through molecular excitation has shown that very high densities exist in star formation regions, but unresolved structure and possible chemical effects complicate the interpretation. High resolution far-IR and submillimeter observations offer a complementary approach and are beginning to test theoretical predictions of density gradients in clouds.

  19. Energy Ordering of Molecular Orbitals

    PubMed Central

    2016-01-01

    Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations. PMID:27935313

  20. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, E.

    1996-04-09

    A method and apparatus are disclosed for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular sieve. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve. 2 figs.

  1. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, Eliel

    1996-01-01

    A method and apparatus for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve.

  2. Molecular SPECT Imaging: An Overview

    PubMed Central

    Khalil, Magdy M.; Tremoleda, Jordi L.; Bayomy, Tamer B.; Gsell, Willy

    2011-01-01

    Molecular imaging has witnessed a tremendous change over the last decade. Growing interest and emphasis are placed on this specialized technology represented by developing new scanners, pharmaceutical drugs, diagnostic agents, new therapeutic regimens, and ultimately, significant improvement of patient health care. Single photon emission computed tomography (SPECT) and positron emission tomography (PET) have their signature on paving the way to molecular diagnostics and personalized medicine. The former will be the topic of the current paper where the authors address the current position of the molecular SPECT imaging among other imaging techniques, describing strengths and weaknesses, differences between SPECT and PET, and focusing on different SPECT designs and detection systems. Radiopharmaceutical compounds of clinical as well-preclinical interest have also been reviewed. Moreover, the last section covers several application, of μSPECT imaging in many areas of disease detection and diagnosis. PMID:21603240

  3. Molecular biology of nuclear autoantigens.

    PubMed

    Saitta, M R; Keene, J D

    1992-05-01

    This article provides a historical overview of the application of molecular and immunologic techniques to the analysis of autoantigenic structure and function, as well as to autoantibody recognition of protein and nucleic acid autoantigens. Examples presented here illustrate the role of autoantibodies as tools in the elucidation of the autoimmune components of cellular ribonucleoproteins. In turn, the subsequent molecular dissection of autoantigenic ribonucleoproteins has advanced understanding of autoantibody specificities. The nature of autoantibodies reactive with various proteins and nucleic acids will be the subject of the following articles in this issue. Taken together, these studies of antibody-antigen interactions that arise during the autoimmune response have revealed novel mechanisms of molecular recognition within the RNP autoantigens. These findings are of general importance for understanding basic cellular processes and have contributed to our knowledge of the underlying mechanisms of immunoregulatory abnormalities that arise in autoimmune diseases.

  4. Molecular spectroscopic analyses of gelatin.

    PubMed

    Ibrahim, Medhat; Mahmoud, Abdel Aziz; Osman, Osama; Abd el-Aal, Mohamed; Eid, May

    2011-10-15

    The molecular structure of gelatin was studied using Fourier transform infrared spectroscopy FTIR. The spectrum is subjected to deconvolution in order to elucidate the constituents of the molecular structure. B3LYP/6-31g** was used to study 13 amino acids then the scaled spectrum was compared to those of protein in order to describe the contribution of each amino acid into protein structure. A special interest was paid to the NH and C=O region. The reactivity of each amino acid was studied in terms of some important physical parameters like total dipole moment and HOMO/LUMO which describe the interaction of amino acid with their surrounding molecules. Results indicated that B3LYP/6-31g** model is a suitable and precise method for studying molecular structure of protein. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Physical conditions in molecular clouds

    NASA Technical Reports Server (NTRS)

    Evans, Neal J., II

    1989-01-01

    Recent developments have complicated the picture of the physical conditions in molecular clouds. The discoveries of widespread emission from high-J lines of CD and 12-micron IRAS emission have revealed the presence of considerably hotter gas and dust near the surfaces of molecular clouds. These components can complicate interpretation of the bulk of the cloud gas. Commonly assumed relations between column density or mean density and cloud size are called into question by conflicting results and by consideration of selection effects. Analysis of density and density structure through molecular excitation has shown that very high densities exist in star formation regions, but unresolved structure and possible chemical effects complicate the interpretation. High resolution far-IR and submillimeter observations offer a complementary approach and are beginning to test theoretical predictions of density gradients in clouds.

  6. Molecular morphology of cyanobacterial phycobilisomes

    SciTech Connect

    Siegelman, H.W.; Kycia, J.H.

    1982-09-01

    Phycobilisomes were isolated from several cyanobacteria following cell lysis with Triton X-100. They were purified by phosphate precipitation and hydrophobic-interaction chromatography. Their phycobiliprotein compositions were quantitatively determined by application of sets of simultaneous absorbance equations to gel chromatographic separations of the chromoproteins. Phycobilisomes purified from several cyanobacteria had characteristic elution times on agarose gel chromatography. Combining electron microscope observations of phycobilisome structure, phycobiliprotein composition, and agarose gel chromatography estimates of molecular weight permitted the calculation of many details of phycobilisome molecular structure. Complementary chromatic adaptation resulted in a change of phycobilisome composition and structure. The polypeptide compositions of phycobilisomes were examined by sodium dodecyl sulfate-agarose gel chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The phycobilisomes were composed of phycobilipeptides derived from the constituent phycobiliproteins. Higher molecular-weight phycobilipeptide aggregates were also observed. The dominant forces responsible for the maintenance of phycobilisome structure are concluded to be hydropohobic interactions.

  7. [Molecular karyotyping of eukaryotic microorganisms].

    PubMed

    Nasonova, E S

    2012-01-01

    In many fungi and protists small size and weak morphological differentiation of chromosomes embarrass the study of karyotypes using microscopical tools. Molecular karyotyping based on the fractionation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) provides an alternative approach to the analysis of chromosomal sets in such organisms. To assign the bands observed in PFGE gel to the individual chromosomes the following methods of chromosome identification are applied: densitometric analysis of the bands; Southern hybridization with chromosome- and telomere-specific probes, which often is combined with comparative karyotyping of a series of strains with pronounced size polymorphism of chromosomes; comparison of the patterns of restriction fragments of chromosomal DNAs fractioned by KARD 2-D PFGE; comparison with the strains with well-studied interchromosomal rearrangements. Besides estimation of the number and the size of chromosomes, molecular karyotyping allows assessment of haploid genome size and ploidy level, study of genome dynamics, identification of chromosomal rearrangements and associated chromosomal polymorphism. The analysis of karyotype and dynamics of the genomes is important for the study of intra- and interspecial variability, investigation of the chromosome evolution in closely related species and elaboration of the models of speciation. The comparison of molecular karyotypes among isolates of different origin is of great practical importance for clinical diagnostics and for agricultural microbiology. In this review we discuss: 1) the methods of karyotyping and their application to the analysis of chromosomal sets in eukaryotic microorganisms; 2) the specificity of the methods used for extraction and fractionation of intact chromosomal DNAs; 3) the reasons for difficulties in interpretation of molecular karyotypes and the ways of their overcoming; 4) fields of application of molecular karyotyping; 5) the definition of

  8. Oleuropein: Molecular Dynamics and Computation.

    PubMed

    Gentile, Luigi; Uccella, Nicola A; Sivakumar, Ganapathy

    2017-09-11

    Olive oil and table olive biophenols have been shown to significantly enrich the hedonic-sensory and nutritional quality of the Mediterranean diet. Oleuropein is one of the predominate biophenols in green olives and leaves, which not only has noteworthy free-radical quenching activity but also putatively reduces the incidence of various cancers. Clinical trials suggest that the consumption of extra virgin olive oil reduces the risk of several degenerative diseases. The oleuropein-based bioactives in olive oil could reduce tumor necrosis factor α, interleukin-1β and nitric oxide. Therefore, olive bioactives quality should be preserved and even improved due to their disease-fighting properties. Understanding the molecular dynamics of oleuropein is crucial to increase olive oil and table olive quality. The objective of this review is to provide the molecular dynamics and computational mapping of oleuropein. It is a biophenol-secoiridoid expressing different functionalities such as two π-bonds, two esters, two acetals, one catechol, and four hexose hydroxyls within 540 mw. The molecular bond sequential breaking mechanisms were analyzed through unimolecular reactions under electron spray ionization, collision activated dissociations, and fast atom bombardment mass spectrometry. The oleuropein solvent-free reactivity is leading to glucose loss and bioactive aglycone-dialdehydes via secoiridoid ring opening. Oleuropein electron distribution revealed that the free-radical non-polar processes occur from its highest occupied molecular orbital, while the lowest unoccupied molecular orbital is clearly devoted to nucleophilic and base site reactivity. This molecular dynamics and computational mapping of oleuropein could contribute to the engineering of olive-based biomedicine and/or functional food. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. 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.

  10. 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

  11. Molecular modeling of heterogeneous catalysis

    NASA Astrophysics Data System (ADS)

    Gislason, Jason Joseph

    A novel method for modeling heterogeneous catalysis was developed to further facilitate the understanding of catalytic reactor mechanisms. The method employs molecular dynamics simulations, statistical mechanical, and Unity Bond Index - Quadratic Exponential Potential (UBI-QEP) calculations to calculate the rate constants for reactions on metal surfaces. The primary difficulty of molecular dynamics simulations on metal surfaces has been the lack of reliable reactive potential energy surfaces. We have overcome this through the development of the Normalized Bond Index - Reactive Potential Function (NBI-RPF), which can accurately describe the reaction of adsorbates on metal surfaces. The first calculations of rate constants for a reaction on a metal surface using molecular dynamics simulations are presented. This method is applied to the determination of the mechanism for selective hydrogenation of acetylene in an ethylene rich flow. It was determined that the selectivity for acetylene hydrogenation is attributable to the higher reactivity of acetylene versus ethylene with respect to hydrogenation by molecular hydrogen. It was shown that hydrogen transfer from the carbonaceous layer to acetylene or ethylene is insignificant in the hydrogenation process. Molecular dynamics simulations and molecular mechanics calculations were used to determine the diffusion rate constants for dimethylnaphthalene isomers is mordenite. 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene were found to have similar diffusion rate constants. Grand canonical Monte Carlo calculations were performed on the competitive adsorption of 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in type X zeolites exchanged individually with barium, calcium, potassium, and rubidium ions, calcium exchanged MCM-22, and hydrogen form mordenite (MOR), X zeolite, Y zeolite, hypBEB, ZSM- 12, and MCM-22. These calculations showed that barium exchanged X zeolite was the most selective toward 2

  12. Molecular Endotyping of Pulmonary Fibrosis.

    PubMed

    Goodwin, Amanda T; Jenkins, Gisli

    2016-01-01

    Idiopathic pulmonary fibrosis (IPF) is a devastating and incurable progressive fibrotic lung condition associated with a significant disease burden. In recent years there has been an exponential increase in the number of preclinical and clinical studies performed in IPF. IPF is defined according to rigid diagnostic criteria; hence, a significant subset of patients with unclassifiable disease has been excluded from these studies. The traditional diagnostic classification of all progressive fibrotic lung diseases uses specific clinical, radiological, and histopathological features to define each condition. However, the considerable heterogeneity within each form of pulmonary fibrosis has raised the possibility of distinct pathophysiological mechanisms culminating in a common phenotype. Thus, the classification of fibrotic lung diseases according to the driving molecular mechanisms rather than specific user-defined histopathological and radiological features could improve several aspects of clinical care. Discoveries from basic science research have defined multiple complex molecular pathways involved in the pathogenesis of pulmonary fibrosis that may provide markers for the molecular endotyping of this disease. In addition, these molecular pathways have revealed potential therapeutic targets. Reclassifying progressive fibrotic lung diseases according to molecular endotypes may allow for more accurate assessment of prognosis and individualized treatment. Furthermore, recent developments that have been applied to a narrow group of patients with IPF may be applicable to those with other progressive fibrotic lung diseases. This review presents the latest developments from translational research in this area and explains how molecular endotyping could revolutionize the diagnosis, stratification, and treatment of pulmonary fibrosis.

  13. Molecular Modeling of Estrogen Receptor Using Molecular Operating Environment

    ERIC Educational Resources Information Center

    Roy, Urmi; Luck, Linda A.

    2007-01-01

    Molecular modeling is pervasive in the pharmaceutical industry that employs many of our students from Biology, Chemistry and the interdisciplinary majors. To expose our students to this important aspect of their education we have incorporated a set of tutorials in our Biochemistry class. The present article describes one of our tutorials where…

  14. Molecular Modeling of Estrogen Receptor Using Molecular Operating Environment

    ERIC Educational Resources Information Center

    Roy, Urmi; Luck, Linda A.

    2007-01-01

    Molecular modeling is pervasive in the pharmaceutical industry that employs many of our students from Biology, Chemistry and the interdisciplinary majors. To expose our students to this important aspect of their education we have incorporated a set of tutorials in our Biochemistry class. The present article describes one of our tutorials where…

  15. Molecular weight and molecular weight distribution of kraft lignins

    SciTech Connect

    Schmidl, W.; Dong, D.; Fricke, A.L. )

    1990-01-01

    Kraft lignins are the lignin degradation products from kraft pulping. They are complex, heterogeneous polymers with some polar character. The molecular weight of kraft lignins greatly affect the physical properties of black liquors, and are of primary importance in separation from black liquor and in evaluating potential uses. Several purified kraft lignins from slash pine were analyzed for number average molecular weight by vapor pressure osmometry (VPO), for weight average molecular weight by low angle laser light scattering (LALLS), and for the molecular weight distribution by high temperature size exclusion chromatography (SEC). The lignins were run in tetrahydrofuran (THF), N,N-dimethyl formamide (DMF), DMF with 0.1M LiBr, and pyridine at conditions above the Theta temperature. Experimental methods are discussed. The results show that VPO may be used to determine M[sub n] for kraft lignins if the purity of the lignins and the identity of the impurities are known. LALLS can be used to determine M[sub w] for kraft lignins if measurements are made at or above the Theta temperature of the lignin-solvent pair. SEC should be used at temperatures at, or above, the Theta temperature of the lignin-solvent pair. Size separation is highly dependent on the solvent used, and DMF is a much better solvent than THF for high temperature SEC. Future work using moment resolution procedures to derive an accurate calibration curve are also discussed.

  16. MOLECULAR TRACERS OF TURBULENT SHOCKS IN GIANT MOLECULAR CLOUDS

    SciTech Connect

    Pon, A.; Johnstone, D.; Kaufman, M. J. E-mail: Douglas.Johnstone@nrc-cnrc.gc.ca

    2012-03-20

    Giant molecular clouds contain supersonic turbulence and simulations of magnetohydrodynamic turbulence show that these supersonic motions decay in roughly a crossing time, which is less than the estimated lifetimes of molecular clouds. Such a situation requires a significant release of energy. We run models of C-type shocks propagating into gas with densities around 10{sup 3} cm{sup -3} at velocities of a few km s{sup -1}, appropriate for the ambient conditions inside of a molecular cloud, to determine which species and transitions dominate the cooling and radiative energy release associated with shock cooling of turbulent molecular clouds. We find that these shocks dissipate their energy primarily through CO rotational transitions and by compressing pre-existing magnetic fields. We present model spectra for these shocks, and by combining these models with estimates for the rate of turbulent energy dissipation, we show that shock emission should dominate over emission from unshocked gas for mid to high rotational transitions (J > 5) of CO. We also find that the turbulent energy dissipation rate is roughly equivalent to the cosmic-ray heating rate and that the ambipolar diffusion heating rate may be significant, especially in shocked gas.

  17. Studies on molecular recognition of thymidines with molecularly imprinted polymers

    NASA Astrophysics Data System (ADS)

    Chen, Zhen-He; Luo, Ai-Qin; Sun, Li-Quan

    2009-07-01

    Molecularly imprinted polymers (MIPs) with excellent molecular recognition ability have been used in chemical sensors, chromatographic separation and biochemical analyses. Thymidine is an important part of DNA for biomolecular recognition and the intermediate of many medicines. The polymers imprinted with the template of thymidine and 5'-Otosylthymidine have been prepared, using a non-proton solvent, acetonitrile as the porogen. Direct imprinting with thymidine could not form strong molecular interaction sites in this system. Relative MIPs were obtained by bulk polymerization and their adsorption capacities were investigated. The adsorption capacities of MIP (P2) and nonimprinted polymer (P20) for thymidine are 0.120 mg•g-1and 0.103 mg•g-1, respectively. The imprinting factor is 1.17. As 5'-O-tosylthymidine is more soluble than thymidine moiety in acetonitrile and give rise to more sites of molecular recognition. The results demonstrated that the imprinted polymers were able to bind and recognize thymidine moderately in acetonitrile. MIPs imprinted with 5'-O-tosylthymidine like nature enzymes displayed some recognition ability to its analogues. The insoluble derivatives in the non-proton solvent can be an effective template to prepare efficient imprinting recognition sites.

  18. Water in dense molecular clouds

    NASA Technical Reports Server (NTRS)

    Wannier, P. G.; Kuiper, T. B. H.; Frerking, M. A.; Gulkis, S.; Pickett, H. M.; Wilson, W. J.; Pagani, L.; Lecacheux, A.; Encrenaz, P.

    1991-01-01

    The G.P. Kuiper Airborne Observatory (KAO) was used to make initial observations of the half-millimeter ground-state transition of water in seven giant molecular clouds and in two late-type stars. No significant detections were made, and the resulting upper limits are significantly below those expected from other, indirect observations and from several theoretical models. The implied interstellar H2O/CO abundance is less than 0.003 in the cores of three giant molecular clouds. This value is less than expected from cloud chemistry models and also than estimates based on HDO and H3O(+) observations.

  19. Molecular Motors and Stochastic Models

    NASA Astrophysics Data System (ADS)

    Lipowsky, Reinhard

    The behavior of single molecular motors such as kinesin or myosin V, which move on linear filaments, involves a nontrivial coupling between the biochemical motor cycle and the stochastic movement. This coupling can be studied in the framework of nonuniform ratchet models which are characterized by spatially localized transition rates between the different internal states of the motor. These models can be classified according to their functional relationships between the motor velocity and the concentration of the fuel molecules. The simplest such relationship applies to two subclasses of models for dimeric kinesin and agrees with experimental observations on this molecular motor.

  20. Water in dense molecular clouds

    NASA Technical Reports Server (NTRS)

    Wannier, P. G.; Kuiper, T. B. H.; Frerking, M. A.; Gulkis, S.; Pickett, H. M.; Wilson, W. J.; Pagani, L.; Lecacheux, A.; Encrenaz, P.

    1991-01-01

    The G.P. Kuiper Airborne Observatory (KAO) was used to make initial observations of the half-millimeter ground-state transition of water in seven giant molecular clouds and in two late-type stars. No significant detections were made, and the resulting upper limits are significantly below those expected from other, indirect observations and from several theoretical models. The implied interstellar H2O/CO abundance is less than 0.003 in the cores of three giant molecular clouds. This value is less than expected from cloud chemistry models and also than estimates based on HDO and H3O(+) observations.

  1. Molecular pathophysiology of cerebral edema

    PubMed Central

    Gerzanich, Volodymyr; Simard, J Marc

    2015-01-01

    Advancements in molecular biology have led to a greater understanding of the individual proteins responsible for generating cerebral edema. In large part, the study of cerebral edema is the study of maladaptive ion transport. Following acute CNS injury, cells of the neurovascular unit, particularly brain endothelial cells and astrocytes, undergo a program of pre- and post-transcriptional changes in the activity of ion channels and transporters. These changes can result in maladaptive ion transport and the generation of abnormal osmotic forces that, ultimately, manifest as cerebral edema. This review discusses past models and current knowledge regarding the molecular and cellular pathophysiology of cerebral edema. PMID:26661240

  2. Molecular Biomarkers of Knee Pathology.

    PubMed

    Cuellar, Vanessa; Strauss, Eric

    2017-01-01

    The identification of biomarkers has become increasingly important in our fundamental understanding of the molecular basis for disease and subsequently in the advancement of modern medicine. Biomarkers have been identified in a plethora of normal and pathologic conditions and are most often found in blood, tissue, or synovial fluid. Orthopaedic research has more recently focused on biomarkers of cartilage and joint diseases, with an emphasis on understanding the molecular underpinnings of their pathophysiology. This article focuses on the biomarkers identified to date in several select knee pathologies and how further research can contribute to new diagnostic tools and targeted therapeutics.

  3. Nanogap structures for molecular nanoelectronics.

    PubMed

    Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

    2012-02-09

    This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

  4. Molecular pathophysiology of cerebral edema.

    PubMed

    Stokum, Jesse A; Gerzanich, Volodymyr; Simard, J Marc

    2016-03-01

    Advancements in molecular biology have led to a greater understanding of the individual proteins responsible for generating cerebral edema. In large part, the study of cerebral edema is the study of maladaptive ion transport. Following acute CNS injury, cells of the neurovascular unit, particularly brain endothelial cells and astrocytes, undergo a program of pre- and post-transcriptional changes in the activity of ion channels and transporters. These changes can result in maladaptive ion transport and the generation of abnormal osmotic forces that, ultimately, manifest as cerebral edema. This review discusses past models and current knowledge regarding the molecular and cellular pathophysiology of cerebral edema.

  5. Model Pores of Molecular Dimension

    PubMed Central

    Quinn, J. A.; Anderson, J. L.; Ho, W. S.; Petzny, W. J.

    1972-01-01

    Extremely uniform pores of near molecular dimension can be formed by the irradiation-etching technique first demonstrated by Price and Walker. The technique has now been developed to the stage where it can be used to fabricate model membranes for examining the various steric, hydrodynamic, and electrodynamic phenomena encountered in transport through molecular-size pores. Methods for preparing and characterizing membranes with pores as small as 25 A (radius) are described in this paper. Results on pore size determination via Knudsen gas flow and electrolyte conduction are compared. Pore wall modification by monolayer deposition is also discussed. PMID:4339801

  6. Charge exchange molecular ion source

    DOEpatents

    Vella, Michael C.

    2003-06-03

    Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

  7. Molecular catalytic coal liquid conversion

    SciTech Connect

    Stock, L.M.; Yang, Shiyong

    1995-12-31

    This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

  8. Cardiotoxicity of Molecularly Targeted Agents

    PubMed Central

    Hedhli, Nadia; Russell, Kerry S

    2011-01-01

    Cardiac toxicity of molecularly targeted cancer agents is increasingly recognized as a significant side effect of chemotherapy. These new potent therapies may not only affect the survival of cancer cells, but have the potential to adversely impact normal cardiac and vascular function. Unraveling the mechanisms by which these therapies affect the heart and vasculature is crucial for improving drug design and finding alternative therapies to protect patients predisposed to cardiovascular disease. In this review, we summarize the classification and side effects of currently approved molecularly targeted chemotherapeutics. PMID:22758623

  9. Molecular Diagnostic Testing for Aspergillus

    PubMed Central

    Powers-Fletcher, Margaret V.

    2016-01-01

    The direct detection of Aspergillus nucleic acid in clinical specimens has the potential to improve the diagnosis of aspergillosis by offering more rapid and sensitive identification of invasive infections than is possible with traditional techniques, such as culture or histopathology. Molecular tests for Aspergillus have been limited historically by lack of standardization and variable sensitivities and specificities. Recent efforts have been directed at addressing these limitations and optimizing assay performance using a variety of specimen types. This review provides a summary of standardization efforts and outlines the complexities of molecular testing for Aspergillus in clinical mycology. PMID:27487954

  10. Molecular radiotheranostics for neuroendocrine tumours.

    PubMed

    Navalkissoor, Shaunak; Flux, Glenn; Bomanji, Jamshed

    2017-10-01

    This article discusses the important role of nuclear medicine imaging and therapy in the management of neuroendocrine tumours (NETs). Somatostatin receptor scintigraphy has a high impact on patient management versus conventional imaging. Molecular radiotherapy is an important part of the management of patients with NETs. Selection of patients for molecular radiotherapy in NETs is based on uptake on their radionuclide imaging study. The imaging agent has the same mechanism of uptake as the therapeutic agent. Thus, the imaging study preselects patients that are likely to concentrate radiation within their tumours. © Royal College of Physicians 2017. All rights reserved.

  11. Molecular mechanisms of neurite extension.

    PubMed Central

    Valtorta, F; Leoni, C

    1999-01-01

    The extension of neurites is a major task of developing neurons, requiring a significant metabolic effort to sustain the increase in molecular synthesis necessary for plasma membrane expansion. In addition, neurite extension involves changes in the subsets of expressed proteins and reorganization of the cytomatrix. These phenomena are driven by environmental cues which activate signal transduction processes as well as by the intrinsic genetic program of the cell. The present review summarizes some of the most recent progress made in the elucidation of the molecular mechanisms underlying these processes. PMID:10212488

  12. Molecular Mechanisms of Neuronal Responsivity.

    DTIC Science & Technology

    1987-07-10

    O-A187 061 MOLECULAR MECHANISMS OF NEURONAL RESPONSIVITY(U) / VERMONT UNIV BURLINGTON COIL OF MEDICINE V EHRLICH 7 UwKL7RS1S1 IS1 JUL 87 RFOSR-TR-87...The grant was awarded to support the organization of a scientific conference entitled: "Molecular Mechanisms of Neuronal Responsivity." This...from the University of New York, on: "Synaptic Transmission and Neuronal Integration." It should be mentioned that this presentation emerged as a most

  13. Nanogap structures for molecular nanoelectronics

    PubMed Central

    2012-01-01

    This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

  14. Molecular Aggregates in Cryogenic Solutions.

    DTIC Science & Technology

    1981-07-07

    of aggregates from solutions of monomers. Rapid deposition into a precooled sample cell is required to generate an aggregate solution. Such a solution...U AU-A11b 490 COLORAO0 STATE UNIV FORT COLLINS DEPT OF CHEMISTRY F/G 20/8 MOLECULAR AGGREGATES IN CRYOGENIC SOLUTIONS.CU) JUL 81 M W SCHAUER- J LEE...MOLECULAR AGGREGATES IN CRYOGENIC SOLUTIONS by M.W. Schauer, J. Lee, and E.R. Bernstein Prepared for Publication in The Journal of Chemical Physics

  15. Molecular Cloning of Adenosinediphosphoribosyl Transferase.

    DTIC Science & Technology

    1987-09-08

    AD-RIB5 458 NOLECULNA CLONING OF AOENOSINEDXPNOSPHORIBOSyL 1/1 TRNSFERASEMU CAILIFORNIA UNIV SRN FRANCISCO E KUN US SEP 8? WFOSR-TR-87-0982 SWFOSR-B5...ACCESSION NO.D,. 03261102F 2312 A~5 11. TITLE (include Securqt Classification) 0 Molecular Cloning of Adenosinediphosphoribosyl Transferase 12. PERSONAL...I’:- AFOSR.Tlt. 8 7 - 0 9 8,2 0IL * pi AFOSR- 85 -0377 PROGRESS REPORT Molecular Cloning of Adenosinediphosphoribosyl Transferase 5." Period of

  16. [MOLECULAR ASPECTS OF BRUCELLA PERSISTENCE].

    PubMed

    Kulakov Yu K

    2016-01-01

    Brucellosis is a dangerous zoonotic disease of animals and humans caused by bacteria of the genus Brucella, which are able to survive, multiply, and persist in host cells. The review is devoted to the Brucella species persistence connected to the molecular mechanisms of escape from innate and adaptive immunity of the host and active interaction of effector proteins of the type IV secretion system with the host's signaling pathways. Understanding of the molecular mechanisms used by Brucella for the intracellular persistence in the host organism can allow us to develop new and effective means for the prevention and treatment of chronic brucellosis infection.

  17. Electrostatics at the molecular level

    NASA Astrophysics Data System (ADS)

    Zürcher, Ulrich

    2017-01-01

    In molecular systems, positive and negative charges are separated, making them ideal systems to examine electrostatic interactions. The attractive force between positive and negative charges is balanced by repulsive ‘forces’ that are quantum-mechanical in origin. We introduce an ‘effective’ potential energy that captures the repulsion; it allows us to obtain fairly accurate estimates of the bonding properties of molecular systems. We use units (e.g., kcal mol-1 for energy) that emphasize the relevance of electrostatics to macroscopic behavior.

  18. The Molecular Basis of Development.

    ERIC Educational Resources Information Center

    Gehring, Walter J.

    1985-01-01

    Basic architecture of embryo development appears to be under homeobox control (a short stretch of DNA). Outlines research on this genetic segment in fruit flies which led to identification of this control on the embryo's spatial organization. Indicates that molecular mechanisms underlying development may be much more universal than previously…

  19. Small Molecular as SIRT Modulators.

    PubMed

    Yao, Lei; Xu, Xiangming; Chen, Kai

    2016-06-19

    Sirtuins are class III histone deacetylases, they involve in many important biological functions. Small molecules that can modulate sirtuin activity have been shown to have potential for treating many human diseases. In the article, recent development of small molecular as SIRT modulators has been reviewed.

  20. Sarcoidosis, cancer and molecular mimicry.

    PubMed

    Tchernev, G; Wollina, U

    2013-01-01

    Molecular mimicry seems to be the most important factor for the heterogeneous clinical presentation and the immunopathogenesis of sarcoidosis. Molecular mimicry may occur as a result of altered activity of oncogenes. This can lead to crossed-type mediated body reactions targeting structurally similar sections or regions from the tissue homeostasis. Available data suggest that structural analogy between tissue and foreign or de novo-appearing peptides is not always reliable. Nevertheless, lack of amino acid identity between the tissue and the de novo-generated tumour antigens does not exclude the phenomenon of molecular mimicry as the major generator of sarcoidosis. There is growing evidence of the mimicry phenomena, caused not only by the similarity between the amino acids but also between the elements which connect segments in the immunological cascade and which may also be affected by external factors. Molecular mimicry may occur between two identified peptides having similar antigenic surfaces (transitory or not), in the absence of a primary homology in amino acid sequence. As far as tumour antigens are concerned, a structural analogy to the de novo-appearing tumour antigens is more likely than transitory imitation resulting from the additional interference of other physical forces. Further research should be performed to confirm, or reject, the transitory imitation thesis or hypothesis.

  1. Space station molecular sieve development

    NASA Technical Reports Server (NTRS)

    Chang, C.; Rousseau, J.

    1986-01-01

    An essential function of a space environmental control system is the removal of carbon dioxide (CO2) from the atmosphere to control the partial pressure of this gas at levels lower than 3 mm Hg. The use of regenerable solid adsorbents for this purpose was demonstrated effectively during the Skylab mission. Earlier sorbent systems used zeolite molecular sieves. The carbon molecular sieve is a hydrophobic adsorbent with excellent potential for space station application. Although carbon molecular sieves were synthesized and investigated, these sieves were designed to simulate the sieving properties of 5A zeolite and for O2/N2 separation. This program was designed to develop hydrophobic carbon molecular sieves for CO2 removal from a space station crew environment. It is a first phase effort involved in sorbent material development and in demonstrating the utility of such a material for CO2 removal on space stations. The sieve must incorporate the following requirements: it must be hydrophobic; it must have high dynamic capacity for carbon dioxide at the low partial pressure of the space station atmosphere; and it must be chemiclly stable and will not generate contaminants.

  2. Circadian rhythms and molecular noise

    NASA Astrophysics Data System (ADS)

    Gonze, Didier; Goldbeter, Albert

    2006-06-01

    Circadian rhythms, characterized by a period of about 24h, are the most widespread biological rhythms generated autonomously at the molecular level. The core molecular mechanism responsible for circadian oscillations relies on the negative regulation exerted by a protein on the expression of its own gene. Deterministic models account for the occurrence of autonomous circadian oscillations, for their entrainment by light-dark cycles, and for their phase shifting by light pulses. Stochastic versions of these models take into consideration the molecular fluctuations that arise when the number of molecules involved in the regulatory mechanism is low. Numerical simulations of the stochastic models show that robust circadian oscillations can already occur with a limited number of mRNA and protein molecules, in the range of a few tens and hundreds, respectively. Various factors affect the robustness of circadian oscillations with respect to molecular noise. Besides an increase in the number of molecules, entrainment by light-dark cycles, and cooperativity in repression enhance robustness, whereas the proximity of a bifurcation point leads to less robust oscillations. Another parameter that appears to be crucial for the coherence of circadian rhythms is the binding/unbinding rate of the inhibitory protein to the promoter of the clock gene. Intercellular coupling further increases the robustness of circadian oscillations.

  3. A Molecular Basis of Cancer.

    ERIC Educational Resources Information Center

    Weinberg, Robert A.

    1983-01-01

    Discusses the molecular basis of cancer, focusing on genetics of the disease. Indicates that human cancers are initiated by oncogenes (altered versions of normal genes) and that in one case the critical alteration is a single point mutation that changes one amino acid in the protein encoded by the gene. (JN)

  4. Molecular dynamics of silicon indentation

    NASA Astrophysics Data System (ADS)

    Kallman, J. S.; Hoover, W. G.; Hoover, C. G.; de Groot, A. J.; Lee, S. M.; Wooten, F.

    1993-04-01

    We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.

  5. OH+ in Diffuse Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Porras, A. J.; Federman, S. R.; Welty, D. E.; Ritchey, A. M.

    2014-01-01

    Near ultraviolet observations of OH+ and OH in diffuse molecular clouds reveal a preference for different environments. The dominant absorption feature in OH+ arises from a main component seen in CH+ (that with the highest CH+/CH column density ratio), while OH follows CN absorption. This distinction provides new constraints on OH chemistry in these clouds. Since CH+ detections favor low-density gas with small fractions of molecular hydrogen, this must be true for OH+ as well, confirming OH+ and H2O+ observations with the Herschel Space Telescope. Our observed correspondence indicates that the cosmic ray ionization rate derived from these measurements pertains to mainly atomic gas. The association of OH absorption with gas rich in CN is attributed to the need for a high enough density and molecular fraction before detectable amounts are seen. Thus, while OH+ leads to OH production, chemical arguments suggest that their abundances are controlled by different sets of conditions and that they coexist with different sets of observed species. Of particular note is that non-thermal chemistry appears to play a limited role in the synthesis of OH in diffuse molecular clouds.

  6. Scaffolding Learning from Molecular Visualizations

    ERIC Educational Resources Information Center

    Chang, Hsin-Yi; Linn, Marcia C.

    2013-01-01

    Powerful online visualizations can make unobservable scientific phenomena visible and improve student understanding. Instead, they often confuse or mislead students. To clarify the impact of molecular visualizations for middle school students we explored three design variations implemented in a Web-based Inquiry Science Environment (WISE) unit on…

  7. Molecular diagnosis of familial hypercholesterolaemia.

    PubMed

    Graham, Colin A; Latten, Mark J; Hart, Padraig J

    2017-08-01

    Familial hypercholesterolaemia is a hereditary disorder of lipoprotein metabolism which causes a lifelong increase in LDL-C levels resulting in premature coronary heart disease. The present review looks at some of the recent literature on how molecular methods can be used to assist in the definitive diagnosis of familial hypercholesterolaemia in a range of patient groups. Several recent studies have shown that the prevalence of clinical familial hypercholesterolaemia is higher than previously thought at 1/200 to 1/300, and that 2-5% of patients presenting with early myocardial infarction can be found to have a familial hypercholesterolaemia mutation. The present review then examines different approaches to molecular testing for familial hypercholesterolaemia including point mutation panels versus next-generation sequencing gene panels, and the range of genes tested by some of those panels. Finally, we review the recent evidence for polygenic hypercholesterolaemia within clinically defined familial hypercholesterolaemia patient populations. To identify patients with familial hypercholesterolaemia within clinically selected patient groups efficiently, a clinical scoring system should be combined with a molecular testing approach for mutations and for polygenic LDL-C single-nucleotide polymorphisms. Alternatively, a population screening methodology may be appropriate, using mutation testing at an early age before significant atherosclerosis has begun. The precise molecular testing method chosen may depend on the clinical presentation of the patient, and/or the population from which they arise.

  8. Molecular Networks in Drug Discovery

    PubMed Central

    Morrow, John Kenneth; Tian, Longzhang; Zhang, Shuxing

    2013-01-01

    Despite the dramatic increase of global spending on drug discovery and development, the approval rate for new drugs is declining, due chiefly to toxicity and undesirable side effects. Simultaneously, the growth of available biomedical data in the post-genomic era has provided fresh insight into the nature of redundant and compensatory drug-target pathways. This stagnation in drug approval can be overcome by the novel concept of polypharmacology, which is built on the fundamental concept that drugs modulate multiple targets. Polypharmacology can be studied with molecular networks which integrate multidisciplinary concepts including cheminformatics, bioinformatics, and systems biology. In silico techniques such as structure and ligand-based approaches can be employed to study molecular networks and reduce costs by predicting adverse drug reactions and toxicity in the early stage of drug development. By amalgamating strides in this informatics-driven era, designing polypharmacological drugs with molecular network technology exemplifies the next generation of therapeutics with less off-target properties and toxicity. In this review, we will first describe the challenges in drug discovery, and showcase successes using multi-target drugs toward diseases such as cancer and mood disorders. We will then focus on recent development of in silico polypharmacology predictions. Finally, our technologies in molecular network analysis will be presented. PMID:20932236

  9. 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

  10. Molecular clouds without detectable CO

    NASA Astrophysics Data System (ADS)

    Blitz, Leo; Bazell, David; Desert, F. Xavier

    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 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

  11. Measurement Frontiers in Molecular Biology

    NASA Astrophysics Data System (ADS)

    Laderman, Stephen

    2009-03-01

    Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

  12. Molecular outflows in starburst nuclei

    NASA Astrophysics Data System (ADS)

    Roy, Arpita; Nath, Biman B.; Sharma, Prateek; Shchekinov, Yuri

    2016-12-01

    Recent observations have detected molecular outflows in a few nearby starburst nuclei. We discuss the physical processes at work in such an environment in order to outline a scenario that can explain the observed parameters of the phenomenon, such as the molecular mass, speed and size of the outflows. We show that outflows triggered by OB associations, with NOB ≥ 105 (corresponding to a star formation rate (SFR)≥1 M⊙ yr-1 in the nuclear region), in a stratified disc with mid-plane density n0 ˜ 200-1000 cm-3 and scaleheight z0 ≥ 200(n0/102 cm-3)-3/5 pc, can form molecules in a cool dense and expanding shell. The associated molecular mass is ≥107 M⊙ at a distance of a few hundred pc, with a speed of several tens of km s-1. We show that an SFR surface density of 10 ≤ ΣSFR ≤ 50 M⊙ yr-1 kpc-2 favours the production of molecular outflows, consistent with observed values.

  13. Metastable innershell molecular state (MIMS)

    NASA Astrophysics Data System (ADS)

    Bae, Young K.

    2008-07-01

    We propose that the existence of Metastable innershell molecular state (MIMS) was experimentally discovered by Bae et al. in hypervelocity ( v>100 km/s) impact of nanoparticles. The decay of MIMS resulted in the observed intense soft x-rays in the range of 75-100 eV in agreement with Winterberg's recent prediction.

  14. [Molecular mechanisms of bone calcification].

    PubMed

    Hoshi, Kazuto; Ozawa, Hidehiro

    2003-04-01

    Bone matrix consists mainly of hydroxyapatite and organics. The latter include various substances which interact with minerals. Osteoblasts secrete these organic substances and control crystal formation and growth of hydroxyapatite. The authors discuss the molecular mechanisms of calcification by focusing on the mineral/organic interaction.

  15. Molecular Epidemiology of Glanders, Pakistan

    PubMed Central

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O’Neill, Matthew; DeShazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera

    2009-01-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines. PMID:19961695

  16. Molecular Size and Raoult's Law.

    ERIC Educational Resources Information Center

    Kovac, Jeffrey

    1985-01-01

    The concept of an ideal solution is ordinarily introduced in freshman chemistry by means of Raoult's Law, which states that the vapor pressure of a volatile component of a solution is proportional to its mole fraction. The relationship of this law to molecular size is discussed. (JN)

  17. [Molecular diagnostics in endocrine diseases].

    PubMed

    Berg, Jens P; Bjerknes, Robert

    2005-11-03

    Molecular diagnostic techniques provide an unsurpassed opportunity to understand the pathophysiological basis of endocrine disorders. Diseases have been associated with mutations in almost every gene known to have a role in either the production or secretion of a hormone or the mediators of hormone signalling. Even though most of these mutations are rare and account for only a small fraction of endocrine diseases, molecular diagnostics offers a valuable tool for the clinician in these cases. The most common endocrine disorders such as autoimmune thyroiditis, type 2 diabetes mellitus, osteoporosis, growth disorders, and obesity have all major genetic components, but these are mostly unknown. In this review the clinical implications of molecular diagnostics are illustrated for some endocrine diseases: congenital adrenal hyperplasia, congenital hypothyroidism, thyroid hormone resistance, familial hypocalciuric hypercalcaemia, growth hormone deficiency and resistance, and monogenic obesity. Improved diagnostic specificity has direct implications for treatment and follow up in these syndromes. Molecular diagnostics in endocrine tumours and diabetes are presented in two other articles in this series.

  18. Molecular Gas in the Outskirts

    NASA Astrophysics Data System (ADS)

    Watson, Linda C.; Koda, Jin

    The outskirts of galaxies offer extreme environments where we can test our understanding of the formation, evolution and destruction of molecules and their relationship with star formation and galaxy evolution. We review the basic equations that are used in normal environments to estimate physical parameters like the molecular gas mass from CO line emission and dust continuum emission. Then we discuss how those estimates may be affected when applied to the outskirts, where the average gas density, metallicity, stellar radiation field and temperature may be lower. We focus on observations of molecular gas in the outskirts of the Milky Way, extragalactic disk galaxies, early-type galaxies, groups and clusters. The scientific results show the versatility of molecular gas, as it has been used to trace Milky Way spiral arms out to a galactocentric radius of 15 kpc, to study star formation in extended ultraviolet disk galaxies, to probe galaxy interactions in polar-ring S0 galaxies and to investigate ram pressure stripping in clusters. Throughout the chapter, we highlight the physical stimuli that accelerate the formation of molecular gas, including internal processes such as spiral arm compression and external processes such as interactions.

  19. Molecular Ecology of Drinking Water

    EPA Science Inventory

    The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

  20. Molecular Foundry, Berkeley, California (Revised)

    SciTech Connect

    Carlisle, N.

    2008-03-01

    This case study provides information on the Molecular Foundry, which incorporates Labs21 principles in its design and construction. The design includes many of the strategies researched at Lawrence Berkeley Laboratory for energy efficient cleanroom and data centers. The result is an energy efficient high-performing sustainable laboratory.

  1. Molecular signatures of major depression.

    PubMed

    Cai, Na; Chang, Simon; Li, Yihan; Li, Qibin; Hu, Jingchu; Liang, Jieqin; Song, Li; Kretzschmar, Warren; Gan, Xiangchao; Nicod, Jerome; Rivera, Margarita; Deng, Hong; Du, Bo; Li, Keqing; Sang, Wenhu; Gao, Jingfang; Gao, Shugui; Ha, Baowei; Ho, Hung-Yao; Hu, Chunmei; Hu, Jian; Hu, Zhenfei; Huang, Guoping; Jiang, Guoqing; Jiang, Tao; Jin, Wei; Li, Gongying; Li, Kan; Li, Yi; Li, Yingrui; Li, Youhui; Lin, Yu-Ting; Liu, Lanfen; Liu, Tiebang; Liu, Ying; Liu, Yuan; Lu, Yao; Lv, Luxian; Meng, Huaqing; Qian, Puyi; Sang, Hong; Shen, Jianhua; Shi, Jianguo; Sun, Jing; Tao, Ming; Wang, Gang; Wang, Guangbiao; Wang, Jian; Wang, Linmao; Wang, Xueyi; Wang, Xumei; Yang, Huanming; Yang, Lijun; Yin, Ye; Zhang, Jinbei; Zhang, Kerang; Sun, Ning; Zhang, Wei; Zhang, Xiuqing; Zhang, Zhen; Zhong, Hui; Breen, Gerome; Wang, Jun; Marchini, Jonathan; Chen, Yiping; Xu, Qi; Xu, Xun; Mott, Richard; Huang, Guo-Jen; Kendler, Kenneth; Flint, Jonathan

    2015-05-04

    Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual's somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10(-42), odds ratio 1.33 [95% confidence interval [CI] = 1.29-1.37]) and telomere length (p = 2.84 × 10(-14), odds ratio 0.85 [95% CI = 0.81-0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease.

  2. Molecular Ecology of Drinking Water

    EPA Science Inventory

    The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

  3. Fluctuation Relations for Molecular Motors

    NASA Astrophysics Data System (ADS)

    Lacoste, David; Mallick, Kirone

    This review is focused on the application of specific fluctuation relations, such as the Gallavotti-Cohen relation, to ratchet models of a molecular motor. A special emphasis is placed on two-state models such as the flashing ratchet model. We derive the Gallavotti-Cohen fluctuation relation for these models and we discuss some of its implications.

  4. Theoretical Studies of Molecular Spectra

    NASA Technical Reports Server (NTRS)

    McKay, Christopher (Technical Monitor); Freedman, Richard S.

    2002-01-01

    This summary describes the research activities of the principal investigator during the reporting period. The research includes spectroscopy, management of molecular databases, and generation of spectral line profiles and opacity data. The spectroscopy research includes oxygen broadening of nitric oxide (NO), analysis of CO2 spectra, analysis of HNO3 spectra, and analysis of CO spectra.

  5. Instructional Technology and Molecular Visualization

    ERIC Educational Resources Information Center

    Appling, Jeffrey R.; Peake, Lisa C.

    2004-01-01

    The effect of intervening use of molecular visualization software was tested on 73 first-year general chemistry students. Pretests and posttests included both traditional multiple-choice questions and model-building activities. Overall students improved after working with the software, although students performed less well on the model-building…

  6. [Quality control in molecular microbiology].

    PubMed

    Orta Mira, Nieves; Guna Serrano, María Remedio; Gimeno Cardona, Concepción; Pérez, José L

    2008-07-01

    The term quality assurance (QA) refers to the quality control activities related to analytical procedures performed in the clinical microbiology laboratory. QA should include both external and internal quality assessment. Application of quality control tools in molecular microbiology assays is crucial to ensure the accuracy of results and appropriate patient management. External quality control is used for laboratory intercomparisons, detection of random and systematic errors, evaluation of the suitability of some reagents or commercial diagnostic kits, and continuing education. The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology includes quality control procedures for molecular microbiology, as well as specific programs for quantitative determination of the viral load of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV), two highly important molecular markers in clinical settings due to their prognostic value and utility as a treatment guide. Internal quality control allows random and systematic errors to be detected through the inclusion of quality control samples in the assays performed in the laboratory, equipment monitoring, and audit. Evaluation of all molecular microbiology assays before their inclusion in the daily routine work of the laboratory is of utmost importance.

  7. The Molecular Basis of Development.

    ERIC Educational Resources Information Center

    Gehring, Walter J.

    1985-01-01

    Basic architecture of embryo development appears to be under homeobox control (a short stretch of DNA). Outlines research on this genetic segment in fruit flies which led to identification of this control on the embryo's spatial organization. Indicates that molecular mechanisms underlying development may be much more universal than previously…

  8. Molecular Signatures of Major Depression

    PubMed Central

    Cai, Na; Chang, Simon; Li, Yihan; Li, Qibin; Hu, Jingchu; Liang, Jieqin; Song, Li; Kretzschmar, Warren; Gan, Xiangchao; Nicod, Jerome; Rivera, Margarita; Deng, Hong; Du, Bo; Li, Keqing; Sang, Wenhu; Gao, Jingfang; Gao, Shugui; Ha, Baowei; Ho, Hung-Yao; Hu, Chunmei; Hu, Jian; Hu, Zhenfei; Huang, Guoping; Jiang, Guoqing; Jiang, Tao; Jin, Wei; Li, Gongying; Li, Kan; Li, Yi; Li, Yingrui; Li, Youhui; Lin, Yu-Ting; Liu, Lanfen; Liu, Tiebang; Liu, Ying; Liu, Yuan; Lu, Yao; Lv, Luxian; Meng, Huaqing; Qian, Puyi; Sang, Hong; Shen, Jianhua; Shi, Jianguo; Sun, Jing; Tao, Ming; Wang, Gang; Wang, Guangbiao; Wang, Jian; Wang, Linmao; Wang, Xueyi; Wang, Xumei; Yang, Huanming; Yang, Lijun; Yin, Ye; Zhang, Jinbei; Zhang, Kerang; Sun, Ning; Zhang, Wei; Zhang, Xiuqing; Zhang, Zhen; Zhong, Hui; Breen, Gerome; Wang, Jun; Marchini, Jonathan; Chen, Yiping; Xu, Qi; Xu, Xun; Mott, Richard; Huang, Guo-Jen; Kendler, Kenneth; Flint, Jonathan

    2015-01-01

    Summary Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual’s somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10−42, odds ratio 1.33 [95% confidence interval [CI] = 1.29–1.37]) and telomere length (p = 2.84 × 10−14, odds ratio 0.85 [95% CI = 0.81–0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease. PMID:25913401

  9. Thermoelectric efficiency of molecular junctions.

    PubMed

    Perroni, C A; Ninno, D; Cataudella, V

    2016-09-21

    Focus of the review is on experimental set-ups and theoretical proposals aimed to enhance thermoelectric performances of molecular junctions. In addition to charge conductance, the thermoelectric parameter commonly measured in these systems is the thermopower, which is typically rather low. We review recent experimental outcomes relative to several junction configurations used to optimize the thermopower. On the other hand, theoretical calculations provide estimations of all the thermoelectric parameters in the linear and non-linear regime, in particular of the thermoelectric figure of merit and efficiency, completing our knowledge of molecular thermoelectricity. For this reason, the review will mainly focus on theoretical studies analyzing the role of not only electronic, but also of the vibrational degrees of freedom. Theoretical results about thermoelectric phenomena in the coherent regime are reviewed focusing on interference effects which play a significant role in enhancing the figure of merit. Moreover, we review theoretical studies including the effects of molecular many-body interactions, such as electron-vibration couplings, which typically tend to reduce the efficiency. Since a fine tuning of many parameters and coupling strengths is required to optimize the thermoelectric conversion in molecular junctions, new theoretically proposed set-ups are discussed in the conclusions.

  10. Molecular mobility on graphene nanoroads

    PubMed Central

    Jafary-Zadeh, Mehdi; Zhang, Yong-Wei

    2015-01-01

    We study molecular mobility on a graphene nanoroad (GNRD), a pristine graphene strip embedded in between two hydrogenated graphene domains serving as a nanoscale pathway for transporting admolecules. Our molecular dynamics simulations using a prototype physisorbed C60 admolecule demonstrate that the proposed GNRD is able to confine the diffusive motion of the admolecule within the nanoroad up to a certain temperature, depending on its width and edge type. Within the confinement regime, the width and edge-type of the GNRD also play an important role in the molecular motion. Specifically, when the GNRD width is narrower than the admolecule diameter, the admolecule performs one-dimensional hopping motion along the nanoroad. When the GNRD width is larger than the admolecule diameter, the admolecule moves only along one of its edges at low temperatures, and shuffle between two edges at high temperatures. We further show the admolecule motion on the zigzag-edged GRND is faster than that on the armchair-edged GRND with the same width and at the same temperature. These results can be well explained by analysing the potential energy surfaces of the systems. Since such hydrogenated graphene nanostructures have been experimentally realized, our results provide a valuable reference for constructing molecular conveyor circuits. PMID:26242303

  11. Alligator clips to molecular dimensions

    NASA Astrophysics Data System (ADS)

    Prokopuk, Nicholas; Son, Kyung-Ah

    2008-09-01

    Techniques for fabricating nanospaced electrodes suitable for studying electron tunneling through metal-molecule-metal junctions are described. In one approach, top contacts are deposited/placed on a self-assembled monolayer or Langmuir-Blodgett film resting on a conducting substrate, the bottom contact. The molecular component serves as a permanent spacer that controls and limits the electrode separations. The top contact can be a thermally deposited metal film, liquid mercury drop, scanning probe tip, metallic wire or particle. Introduction of the top contact can greatly affect the electrical conductance of the intervening molecular film by chemical reaction, exerting pressure, or simply migrating through the organic layer. Alternatively, vacant nanogaps can be fabricated and the molecular component subsequently inserted. Strategies for constructing vacant nanogaps include mechanical break junction, electromigration, shadow mask lithography, focused ion beam deposition, chemical and electrochemical plating techniques, electron-beam lithography, and molecular and atomic rulers. The size of the nanogaps must be small enough to allow the molecule to connect both leads and large enough to keep the molecules in a relaxed and undistorted state. A significant advantage of using vacant nanogaps in the construction of metal-molecule-metal devices is that the junction can be characterized with and without the molecule in place. Any electrical artifacts introduced by the electrode fabrication process are more easily deconvoluted from the intrinsic properties of the molecule.

  12. Scaffolding Learning from Molecular Visualizations

    ERIC Educational Resources Information Center

    Chang, Hsin-Yi; Linn, Marcia C.

    2013-01-01

    Powerful online visualizations can make unobservable scientific phenomena visible and improve student understanding. Instead, they often confuse or mislead students. To clarify the impact of molecular visualizations for middle school students we explored three design variations implemented in a Web-based Inquiry Science Environment (WISE) unit on…

  13. A Molecular Basis of Cancer.

    ERIC Educational Resources Information Center

    Weinberg, Robert A.

    1983-01-01

    Discusses the molecular basis of cancer, focusing on genetics of the disease. Indicates that human cancers are initiated by oncogenes (altered versions of normal genes) and that in one case the critical alteration is a single point mutation that changes one amino acid in the protein encoded by the gene. (JN)

  14. Cancer Stratification by Molecular Imaging

    PubMed Central

    Weber, Justus; Haberkorn, Uwe; Mier, Walter

    2015-01-01

    The lack of specificity of traditional cytotoxic drugs has triggered the development of anticancer agents that selectively address specific molecular targets. An intrinsic property of these specialized drugs is their limited applicability for specific patient subgroups. Consequently, the generation of information about tumor characteristics is the key to exploit the potential of these drugs. Currently, cancer stratification relies on three approaches: Gene expression analysis and cancer proteomics, immunohistochemistry and molecular imaging. In order to enable the precise localization of functionally expressed targets, molecular imaging combines highly selective biomarkers and intense signal sources. Thus, cancer stratification and localization are performed simultaneously. Many cancer types are characterized by altered receptor expression, such as somatostatin receptors, folate receptors or Her2 (human epidermal growth factor receptor 2). Similar correlations are also known for a multitude of transporters, such as glucose transporters, amino acid transporters or hNIS (human sodium iodide symporter), as well as cell specific proteins, such as the prostate specific membrane antigen, integrins, and CD20. This review provides a comprehensive description of the methods, targets and agents used in molecular imaging, to outline their application for cancer stratification. Emphasis is placed on radiotracers which are used to identify altered expression patterns of cancer associated markers. PMID:25749472

  15. Papillomaviruses: Molecular and clinical aspects

    SciTech Connect

    Howley, P.M.; Broker, T.R.

    1985-01-01

    This book contains nine sections, each consisting of several papers. The section headings are : Papillomaviruses and Human Genital Tract Diseases;Papillomaviruses and Human Cutaneous Diseases, Papillomaviruses and Human Oral and Laryngeal Diseases;Therapeutic Approaches to Papillomavirus Infections;Animal Papillomaviruses;Molecular Biology;Transcription, Replication, and Genome Organization;Epithelial Cell Culture;Papillomavirus Transformation;and Viral Vectors.

  16. Rotaxane-based molecular muscles.

    PubMed

    Bruns, Carson J; Stoddart, J Fraser

    2014-07-15

    CONSPECTUS: More than two decades of investigating the chemistry of bistable mechanically interlocked molecules (MIMs), such as rotaxanes and catenanes, has led to the advent of numerous molecular switches that express controlled translational or circumrotational movement on the nanoscale. Directed motion at this scale is an essential feature of many biomolecular assemblies known as molecular machines, which carry out essential life-sustaining functions of the cell. It follows that the use of bistable MIMs as artificial molecular machines (AMMs) has been long anticipated. This objective is rarely achieved, however, because of challenges associated with coupling the directed motions of mechanical switches with other systems on which they can perform work. A natural source of inspiration for designing AMMs is muscle tissue, since it is a material that relies on the hierarchical organization of molecular machines (myosin) and filaments (actin) to produce the force and motion that underpin locomotion, circulation, digestion, and many other essential life processes in humans and other animals. Muscle is characterized at both microscopic and macroscopic length scales by its ability to generate forces that vary the distance between two points at the expense of chemical energy. Artificial muscles that mimic this ability are highly sought for applications involving the transduction of mechanical energy. Rotaxane-based molecular switches are excellent candidates for artificial muscles because their architectures intrinsically possess movable filamentous molecular components. In this Account, we describe (i) the different types of rotaxane "molecular muscle" architectures that express contractile and extensile motion, (ii) the molecular recognition motifs and corresponding stimuli that have been used to actuate them, and (iii) the progress made on integrating and scaling up these motions for potential applications. We identify three types of rotaxane muscles, namely, "daisy

  17. Ultrasonic attenuation in molecular crystals

    NASA Astrophysics Data System (ADS)

    Perrin, Bernard

    1981-11-01

    It is now well established from an experimental point of view that, concerning the ultrasonic attenuation, molecular crystals exhibit a specific behavior among dielectric crystals. This fact suggests the presence of a relaxation process. Liebermann, who has introduced this field, has proposed a way to analyze this problem and in particular has given an expression for the ultrasonic absorption coefficient in terms of a relaxation time and some thermodynamic quantities. In contrast to Liebermann's approach, a solid-state viewpoint is presented here, and it is shown that this ultrasonic relaxation can be taken into account in the framework of Akhieser's theory. A general expression of the ultrasonic absorption coefficient is calculated in terms of the phonon collision operator using the Boltzmann-equation approach of Woodruff and Ehrenreich. The collision-time approximation widely used in dielectric crystals fails in molecular crystals for which the presence of slow relaxation times in the collision operator prevents the thermalization of the whole set of phonons and gives rise to an ultrasonic relaxation. Thus a more suitable approximation is suggested here, which leads to a new expression of the ultrasonic attenuation valid in molecular crystals. Different forms of this expression are discussed, and comparison with Liebermann's expression used in most of the previous papers shows that the present treatment takes better account of the anisotropy of the solid state. The fit of experimental results obtained for some ionic-molecular crystals also shows that the expression derived here gives better agreement than does Liebermann's. Finally, it is shown that in the framework of the present treatment and under rather general conditions, the anisotropy affects primarily the magnitude of the ultrasonic absorption due to the molecular relaxation, but it does not affect its frequency dependence.

  18. Molecular Testing for Gastrointestinal Cancer

    PubMed Central

    Lee, Hye Seung; Kim, Woo Ho; Kwak, Yoonjin; Koh, Jiwon; Bae, Jeong Mo; Kim, Kyoung-Mee; Chang, Mee Soo; Han, Hye Seung; Kim, Joon Mee; Kim, Hwal Woong; Chang, Hee Kyung; Choi, Young Hee; Park, Ji Y.; Gu, Mi Jin; Lhee, Min Jin; Kim, Jung Yeon; Kim, Hee Sung; Cho, Mee-Yon

    2017-01-01

    With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2–4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus–positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians. PMID:28219002

  19. Molecular Testing for Gastrointestinal Cancer.

    PubMed

    Lee, Hye Seung; Kim, Woo Ho; Kwak, Yoonjin; Koh, Jiwon; Bae, Jeong Mo; Kim, Kyoung-Mee; Chang, Mee Soo; Han, Hye Seung; Kim, Joon Mee; Kim, Hwal Woong; Chang, Hee Kyung; Choi, Young Hee; Park, Ji Y; Gu, Mi Jin; Lhee, Min Jin; Kim, Jung Yeon; Kim, Hee Sung; Cho, Mee-Yon

    2017-03-01

    With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2-4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus-positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians.

  20. Light-driven artificial molecular machines

    NASA Astrophysics Data System (ADS)

    Zheng, Yue Bing; Hao, Qingzhen; Yang, Ying-Wei; Kiraly, Brian; Chiang, I.-Kao; Huang, Tony Jun

    2010-08-01

    Artificial molecular machines represent a growing field of nanoscience and nanotechnology. Stimulated by chemical reagents, electricity, or light, artificial molecular machines exhibit precisely controlled motion at the molecular level; with this ability molecular machines have the potential to make significant impacts in numerous engineering applications. Compared with molecular machines powered by chemical or electrical energy, light-driven molecular machines have several advantages: light can be switched much faster, work without producing chemical waste, and be used for dual purposes-inducing (writing) as well as detecting (reading) molecular motions. The following issues are significant for light-driven artificial molecular machines in the following aspects: their chemical structures, motion mechanisms, assembly and characterization on solid-state surfaces. Applications in different fields of nanotechnology such as molecular electronics, nano-electro-mechanical systems (NEMS), nanophotonics, and nanomedicine are envisaged.

  1. 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

  2. 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)

  3. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.

    PubMed

    Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G

    2016-04-12

    Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.

  4. 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.

  5. Electronics using hybrid-molecular and mono-molecular devices.

    PubMed

    Joachim, C; Gimzewski, J K; Aviram, A

    2000-11-30

    The semiconductor industry has seen a remarkable miniaturization trend, driven by many scientific and technological innovations. But if this trend is to continue, and provide ever faster and cheaper computers, the size of microelectronic circuit components will soon need to reach the scale of atoms or molecules--a goal that will require conceptually new device structures. The idea that a few molecules, or even a single molecule, could be embedded between electrodes and perform the basic functions of digital electronics--rectification, amplification and storage--was first put forward in the mid-1970s. The concept is now realized for individual components, but the economic fabrication of complete circuits at the molecular level remains challenging because of the difficulty of connecting molecules to one another. A possible solution to this problem is 'mono-molecular' electronics, in which a single molecule will integrate the elementary functions and interconnections required for computation.

  6. Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems.

    PubMed

    Nebgen, Ben; Prezhdo, Oleg V

    2016-09-15

    A method for efficiently simulating nonadiabatic molecular dynamics (NAMD) of nanoscale and condensed phase systems is developed and tested. The electronic structure, including force and nonadiabatic coupling, are obtained with the fragment molecular orbital (FMO) approximation, which provides significant computational savings by splitting the system into fragments and computing electronic properties of each fragment subject to the external field due to other all other fragments. The efficiency of the developed technique is demonstrated by studying the effect of explicit solvent molecules on excited state relaxation in the Fe(CO)4 complex. The relaxation in the gas phase occurs on a 50 fs time scale, which is in excellent agreement with previously recorded femtosecond pump-probe spectroscopy. Adding a solvation shell of ethanol molecules to the simulation results in an increase in the excited state lifetime to 100 fs, in agreement with recent femtosecond X-ray spectroscopy measurements.

  7. 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.

  8. Available Instruments for Analyzing Molecular Dynamics Trajectories

    PubMed Central

    Likhachev, I. V.; Balabaev, N. K.; Galzitskaya, O. V.

    2016-01-01

    Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964

  9. Propagation Modeling and Analysis of Molecular Motors in Molecular Communication.

    PubMed

    Chahibi, Youssef; Akyildiz, Ian F; Balasingham, Ilangko

    2016-10-24

    Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell. Motor proteins, such as kinesin and dynein, are able to travel along these tracks directionally, carrying with them large molecules that would otherwise be unreliably transported across the cytoplasm using free diffusion. Molecular communication has been previously proposed for the design and study of MMNs. However, the topological aspects of MMNs, including the effects of branches, have been ignored in the existing studies. In this paper, a physical end-to-end model for MMNs is developed, considering the location of the transmitter node, the network topology, and the receiver nodes. The end-to-end gain and group delay are considered as the performance measures, and analytical expressions for them are derived. The analytical model is validated by Monte-Carlo simulations and the performance of MMNs is analyzed numerically. It is shown that, depending on their nature and position, MMN nodes create impedance effects that are critical for the overall performance. This model could be applied to assist the design of artificial MMNs and to study cargo transport in neurofilaments to elucidate brain diseases related to microtubule jamming.

  10. Propagation Modeling and Analysis of Molecular Motors in Molecular Communication.

    PubMed

    Chahibi, Youssef; Akyildiz, Ian F; Balasingham, Ilangko

    2016-12-01

    Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell. Motor proteins, such as kinesin and dynein, are able to travel along these tracks directionally, carrying with them large molecules that would otherwise be unreliably transported across the cytoplasm using free diffusion. Molecular communication has been previously proposed for the design and study of MMNs. However, the topological aspects of MMNs, including the effects of branches, have been ignored in the existing studies. In this paper, a physical end-to-end model for MMNs is developed, considering the location of the transmitter node, the network topology, and the receiver nodes. The end-to-end gain and group delay are considered as the performance measures, and analytical expressions for them are derived. The analytical model is validated by Monte-Carlo simulations and the performance of MMNs is analyzed numerically. It is shown that, depending on their nature and position, MMN nodes create impedance effects that are critical for the overall performance. This model could be applied to assist the design of artificial MMNs and to study cargo transport in neurofilaments to elucidate brain diseases related to microtubule jamming.

  11. Epitaxial nucleation and growth of molecular films

    NASA Astrophysics Data System (ADS)

    Hooks, Daniel Edwin

    2000-10-01

    The last decade has witnessed an increased emphasis on the design and use of molecular-based materials, commonly in thin film form, as components in electronic devices, sensors, displays, and logic elements. The growing interest in films based on molecular components, rather than their more traditional inorganic counterparts, stems largely from the premise that collective optical and electronic properties can be systematically manipulated through molecular design. Many of these properties depend strongly upon film structure and orientation with respect to the substrate upon which they are deposited. This relationship mandates careful attention to the interface between the primary molecular overlayer and the substrate. Further advances in molecular films and multilayer composites based on molecular films require improved understanding of the role of epitaxy in molecular organization as well as the nucleation events that precede film formation. Determination of critical nucleus dimensions and elucidation of the factors that govern critical size are particularly important for fabricating nanoscale molecular features and controlling domain defects in contiguous molecular films. This thesis describes an examination of the role of epitaxy in the growth of molecular films, including a hierarchical classification and grammar of molecular epitaxy, an atomic force microscopy (AFM) investigation of the intercalation of molecular components into multilayer organic-inorganic composites, and an AFM investigation of the nucleation of molecular films.

  12. 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

  13. Molecular-specific urokinase antibodies

    NASA Technical Reports Server (NTRS)

    Atassi, M. Zouhair (Inventor); Morrison, Dennis R. (Inventor)

    2009-01-01

    Antibodies have been developed against the different molecular forms of urokinase using synthetic peptides as immunogens. The peptides were synthesized specifically to represent those regions of the urokinase molecules which are exposed in the three-dimensional configuration of the molecule and are uniquely homologous to urokinase. Antibodies are directed against the lysine 158-isoleucine 159 peptide bond which is cleaved during activation from the single-chain (ScuPA) form to the bioactive double chain (54 KDa and 33 KDa) forms of urokinase and against the lysine 135 lysine 136 bond that is cleaved in the process of removing the alpha-chain from the 54 KDa form to produce the 33 KDa form of urokinase. These antibodies enable the direct measurement of the different molecular forms of urokinase from small samples of conditioned medium harvested from cell cultures.

  14. A molecular dawn for biogeochemistry

    USGS Publications Warehouse

    Zak, D.R.; Blackwood, C.B.; Waldrop, M.P.

    2006-01-01

    Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. ?? 2006 Elsevier Ltd. All rights reserved.

  15. Seebeck effect in molecular junctions

    NASA Astrophysics Data System (ADS)

    Zimbovskaya, Natalya A.

    2016-05-01

    Advances in the fabrication and characterization of nanoscale systems presently allow for a better understanding of their thermoelectric properties. As is known, the building blocks of thermoelectricity are the Peltier and Seebeck effects. In the present work we review results of theoretical studies of the Seebeck effect in single-molecule junctions and similar systems. The behavior of thermovoltage and thermopower in these systems is controlled by several factors including the geometry of molecular bridges, the characteristics of contacts between the bridge and the electrodes, the strength of the Coulomb interactions between electrons on the bridge, and of electron-phonon interactions. We describe the impact of these factors on the thermopower. Also, we discuss a nonlinear Seebeck effect in molecular junctions.

  16. Molecular approaches to allergen standardization.

    PubMed

    Chapman, Martin D; Briza, Peter

    2012-10-01

    Molecular approaches to allergen standardization include the development of purified natural or recombinant allergen standards whose structural and allergenic properties have been validated, in tandem with certified immunoassays for allergen measurement. Purified allergens can be used individually or incorporated into multiple allergen standards. Multicenter international collaborative studies are required to validate candidate allergen standards and immunoassays, as a prelude to being approved by regulatory agencies. Mass spectrometry is a sophisticated and powerful proteomics tool that is being developed for allergen analysis. Recent results using pollen allergens show that mass spectrometry can identify and measure specific allergens in a complex mixture and can provide precise information of the variability of natural allergen extracts. In future, the combined use of immunoassays and mass spectrometry will provide complete standardization of allergenic products. Molecular standardization will form the basis of new allergy diagnostics and therapeutics, as well as assessment of environmental exposure, and will improve the quality of treatment options for allergic patients.

  17. Carbon Nanotubes: Molecular Electronic Components

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1997-01-01

    The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

  18. Molecular biology of gastric cancer.

    PubMed

    Cervantes, A; Rodríguez Braun, E; Pérez Fidalgo, A; Chirivella González, I

    2007-04-01

    Despite its decreasing incidence overall, gastric cancer is still a challenging disease. Therapy is based mainly upon surgical resection when the tumour remains localised in the stomach. Conventional chemotherapy may play a role in treating micrometastatic disease and is effective as palliative therapy for recurrent or advanced disease. However, the knowledge of molecular pathways implicated in gastric cancer pathogenesis is still in its infancy and the contribution of molecular biology to the development of new targeted therapies in gastric cancer is far behind other more common cancers such as breast, colon or lung. This review will focus first on the difference of two well defined types of gastric cancer: intestinal and diffuse. A discussion of the cell of origin of gastric cancer with some intriguing data implicating bone marrow derived cells will follow, and a comprehensive review of different genetic alterations detected in gastric cancer, underlining those that may have clinical, therapeutic or prognostic implications.

  19. Molecular Diagnostic Tests for Microsporidia

    PubMed Central

    Ghosh, Kaya; Weiss, Louis M.

    2009-01-01

    The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans. PMID:19657457

  20. Molecular beam mass spectrometer development

    NASA Technical Reports Server (NTRS)

    Brock, F. J.; Hueser, J. E.

    1976-01-01

    An analytical model, based on the kinetics theory of a drifting Maxwellian gas is used to determine the nonequilibrium molecular density distribution within a hemispherical shell open aft with its axis parallel to its velocity. The concept of a molecular shield in terrestrial orbit above 200 km is also analyzed using the kinetic theory of a drifting Maxwellian gas. Data are presented for the components of the gas density within the shield due to the free stream atmosphere, outgassing from the shield and enclosed experiments, and atmospheric gas scattered off a shield orbiter system. A description is given of a FORTRAN program for computating the three dimensional transition flow regime past the space shuttle orbiter that employs the Monte Carlo simulation method to model real flow by some thousands of simulated molecules.