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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. 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 .

  4. 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.

  5. 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

  6. 75 FR 28187 - Importation of Tomatoes From Souss-Massa-Draa, Morocco; Technical Amendment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-20

    ... Inspection Service 7 CFR Part 319 RIN 0579-AC77 Importation of Tomatoes From Souss-Massa-Draa, Morocco... consignments of tomatoes from the Souss-Massa-Draa region of Morocco into the United States. However, we incorrectly referred to the national plant protection organization of Morocco as the Moroccan Ministry...

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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).

  18. 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

  19. 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

  20. 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.

  1. Molecular breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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).

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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).

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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).

  1. 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)

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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).

  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. 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.

  10. 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.

  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. 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

  15. 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...

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. [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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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)

  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. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Phylogenetic molecular function annotation

    PubMed Central

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

    2010-01-01

    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. PMID:20664722

  13. 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.

  14. 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.

  15. 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.

  16. [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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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)

  7. 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.

  8. Polypeptides Based Molecular Electronics

    DTIC Science & Technology

    2008-10-06

    can be nanoengineer/ nanoassemble individual building blocks at the molecular level, atom by atom, to form conducting channel towards realization of...properties of the self-assembled interconnects are characterized as well. These peptides can be nanoengineer/ nanoassemble individual building blocks at

  9. 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.

  10. 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.

  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. 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…

  13. 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.

  14. 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).

  15. 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

  16. 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.

  17. [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

  18. 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)

  19. 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.

  20. 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

  1. Molecular processes in comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1988-01-01

    The transition dipole moments of the c 3 Pi u - a 3 Sigma g +, i 3 Pi g - c 3 Pi u, and i 3 Pi g - b 3 Sigma u + transitions of molecular hydrogen were calculated over a wide range of internuclear distances R. Calculations of the emission spectra are nearing completion. Substantial progress was made in the calculation of the absorption coefficient of a colliding pair of hydrogen atoms in the binary encounter approximation. Detailed calculations were performed on the continuum emission arising from the excitation of the a 3 sigma g + state of H2 by the impact of electrons of various energies. Each curve is labelled by the electron energy in electron volts. The strong emission near Lyman alpha is interesting in that it is produced by excitation of molecular hydrogen.

  2. 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

  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. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Molecular Vaccines for Malaria

    DTIC Science & Technology

    2010-01-01

    is a p:micularly elegant example of molecular design applied to a recombi nant prote in , combining rational antigen choice (the vaccine uses a major...ing list of examples concordant with these principles. One is rhe ex istence of cryptic epitopes- normally immunologically silent epitopes rhar when...to divert· the immune response from cryptic epitopes formed by the potential binding site lying within the groove,l7 AMAI illustrates the barrier

  10. 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.

  11. 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

  12. [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.

  13. 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

  14. 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.

  15. Handbook of molecular lasers

    NASA Astrophysics Data System (ADS)

    Cheo, Peter K.

    The technology and applications of molecular lasers (MLs) are examined in chapters contributed by leading experts. Topics addressed include ML emission spectra, CO2 TEA lasers, RF-discharge-excited CO2 lasers, high-energy short-pulse CO2 lasers, high-power electron-beam-controlled CO2 lasers, HF/DF chemical lasers, optically pumped FIR MLs, and transients and instabilities in FIR MLs. Extensive diagrams, drawings, graphs, photographs, and tables of numerical data are provided.

  16. 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.

  17. 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.

  18. 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

  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. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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}.

  9. 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.

  10. 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.

  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. 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

  13. [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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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)

  19. 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.

  20. 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.

  1. 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

  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. 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.

  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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  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 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.

  19. [Molecular genetics of hypercholesterolemia].

    PubMed

    Schwarzová, Lucie

    2016-01-01

    The review focuses on the molecular background of an inborn error of lipid metabolism -familial hypercholesterolemia. FH describes a group of genetic defects resulting in severe elevations of blood cholesterol levels and increased risk of premature coronary heart disease. Most cases are due to the mutations decreasing and/or destroying the function of the LDL receptor (85-90 % of cases), smaller portion of cases is caused by defects in the gene encoding the ligand for LDL receptor - apolipoprotein B-100 (5-10 %). Less than 5 % of cases has gain-of-function station of the PCSK9 gene that increases the rate of degradation of the LDL receptor molecules. Autosomal recessive form of the disease, caused by the mutations in LDLR adaptor protein 1 gene, is extremely rare.Key words: APOB - familial hypercholesterolemia - LDLR - LDLRAP1 - PCSK9.

  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 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

  2. 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.

  3. 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

  4. Molecular Cloning of Adenosinediphosphoribosyl Transferase.

    DTIC Science & Technology

    1987-09-08

    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...Pharmacology and the Cardiovascular Research Institute September 8, 1987 .’, 5.’- "’S ". -f, AFOSR - 85 -0377 PROGRESS REPORT Molecular Cloning of

  5. 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

  6. 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.

  7. 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".

  8. 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.

  9. 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.

  10. 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…

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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)

  16. Classical and molecular genetic mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. 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.

  18. 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)

  19. 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.

  20. 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…

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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}.

  15. 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

  16. 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

  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. Molecular Pharmacology of Phytocannabinoids.

    PubMed

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

    2017-01-01

    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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. [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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Computerized molecular modeling of carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  19. 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.

  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. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. 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.

  7. 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)

  8. 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.

  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. 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 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 has 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.

  11. 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.

  12. [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.

  13. Molecular tools used in agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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....

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  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. 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).

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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

  4. [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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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…

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  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. 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.

  1. 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

  2. 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.

  3. [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.

  4. 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.

  5. 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…

  6. 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.

  7. 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.

  8. 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.

  9. 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)

  10. [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.

  11. 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)

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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…

  18. 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.

  19. 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.

  20. 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…

  1. 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.

  2. 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

  3. 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.

  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. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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)

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Proteomics, nanotechnology and molecular diagnostics.

    PubMed

    Johnson, Christopher J; Zhukovsky, Nikolay; Cass, Anthony E G; Nagy, Judit M

    2008-02-01

    Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.

  3. 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.

  4. Visualization Software for Molecular Assemblies

    PubMed Central

    Goddard, Thomas D; Ferrin, Thomas E

    2007-01-01

    Summary Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments and other molecular assemblies is advancing on many fronts. New developments include molecular representations that offer better control over level of detail, lighting that improves the perception of depth, and two-dimensional projections that simplify data interpretation. Programmable graphics processors offer quality, speed and visual effects not previously possible, while 3D printers, haptic interaction devices, and auto-stereo displays show promise in more naturally engaging our senses. Visualization methods are developed by diverse groups of researchers with differing goals: experimental biologists, database developers, computer scientists, and package developers. We survey recent developments and problems faced by the developer community in bringing innovative visualization methods into widespread use. PMID:17728125

  5. 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.

  6. Hierarchical analysis of molecular spectra

    SciTech Connect

    Davis, M.J.

    1996-03-01

    A novel representation of molecular spectra in terms of hierarchical trees has proven to be an important aid for the study of many significant problems in gas-phase chemical dynamics. Trees are generated from molecular spectra by monitoring the changes that occur in a spectrum as resolution is changed in a continuous manner. A tree defines a genealogy among all lines of a spectrum. This allows for a detailed understanding of the assignment of features of a spectrum that may be difficult to obtain any other way as well as an understanding of intramolecular energy transfer time scales, mechanisms, and pathways. The methodology has been applied to several problems: transition state spectroscopy, intramolecular energy transfer in highly excited molecules, high-resolution overtone spectroscopy, and the nature of the classical-quantum correspondence when there is classical chaos (``quantum chaos``).

  7. Molecular model for chirality phenomena.

    PubMed

    Latinwo, Folarin; Stillinger, Frank H; Debenedetti, Pablo G

    2016-10-21

    Chirality is a hallmark feature for molecular recognition in biology and chemical physics. We present a three-dimensional continuum model for studying chirality phenomena in condensed phases using molecular simulations. Our model system is based upon a simple four-site molecule and incorporates non-trivial kinetic behavior, including the ability to switch chirality or racemize, as well as thermodynamics arising from an energetic preference for specific chiral interactions. In particular, we introduce a chiral renormalization parameter that can locally favor either homochiral or heterochiral configurations. Using this model, we explore a range of chirality-specific phenomena, including the kinetics of chiral inversion, the mechanism of spontaneous chiral symmetry breaking in the liquid, chirally driven liquid-liquid phase separation, and chiral crystal structures.

  8. Molecular Recognition and Ligand Association

    NASA Astrophysics Data System (ADS)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  9. Molecular Imaging of Ovarian Cancer

    PubMed Central

    Sharma, Sai Kiran; Nemieboka, Brandon; Sala, Evis; Lewis, Jason S.; Zeglis, Brian M.

    2016-01-01

    Ovarian cancer is the most lethal gynecologic malignancy and the fifth leading cause of cancer-related death in women. Over the past decade, medical imaging has played an increasingly valuable role in the diagnosis, staging, and treatment planning of the disease. In this “Focus on Molecular Imaging” review, we seek to provide a brief yet informative survey of the current state of the molecular imaging of ovarian cancer. The article is divided into sections according to modality, covering recent advances in the MR, PET, SPECT, ultrasound, and optical imaging of ovarian cancer. Although primary emphasis is given to clinical studies, preclinical investigations that are particularly innovative and promising are discussed as well. Ultimately, we are hopeful that the combination of technologic innovations, novel imaging probes, and further integration of imaging into clinical protocols will lead to significant improvements in the survival rate for ovarian cancer. PMID:27127223

  10. Molecular etiology of idiopathic cardiomyopathy

    PubMed Central

    Arimura, T; Hayashi, T; Kimura, A

    2007-01-01

    Summary Idiopathic cardiomyopathy (ICM) is a primary cardiac disorder associated with abnormalities of ventricular wall thickness, size of ventricular cavity, contraction, relaxation, conduction and rhythm. Over the past two decades, molecular genetic analyses have revealed that mutations in the various genes cause ICM and such information concerning the genetic basis of ICM enables us to speculate the pathogenesis of this heterogeous cardiac disease. This review focuses on the molecular pathogenesis, i.e., genetic abnormalities and functional alterations due to the mutations especially in sarcomere/cytoskeletal components, in three characteristic features of ICM, hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) and restrictive cardiomyopathy (RCM). Understanding the functional abnormalities of the sarcomere/cytoskeletal components, in ICM, has unraveled the function of these components not only as a contractile unit but also as a pivot for transduction of biochemical signals. PMID:18646564

  11. Seebeck effect in molecular junctions.

    PubMed

    Zimbovskaya, Natalya A

    2016-05-11

    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.

  12. 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.

  13. The evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Shu, Frank H.; Lizano, Susana

    1988-01-01

    The problem of the structure and evolution of molecular clouds is reviewed, with particular emphasis given to the relationship with star formation. The basic hypothesis is that magnetic fields are the primary agents for supporting molecular clouds, although damped Alfven waves may play an important role in the direction parallel to the field lines. This picture naturally leads to a conception of 'bimodal star formation'. It is proposed that high-mass stars form from the overall gravitational collapse of a supercritical cloud, whereas low-mass stars form from small individual cores that slowly condense by ambipolar diffusion from a more extended envelope until they pass the brink of graviational instability and begin to collapse dynamically from 'inside-out'. The evidence that the infall stage of protostellar evolution is terminated by the development of a powerful stellar wind is reviewed.

  14. Variational Approach to Molecular Kinetics.

    PubMed

    Nüske, Feliks; Keller, Bettina G; Pérez-Hernández, Guillermo; Mey, Antonia S J S; Noé, Frank

    2014-04-08

    The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous to the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.

  15. 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.

  16. Fluorescence applications in molecular neurobiology

    PubMed Central

    Taraska, Justin W.; Zagotta, William N.

    2012-01-01

    Summary Macromolecules drive the complex behavior of neurons. For example, channels and transporters control the movements of ions across membranes, SNAREs direct the fusion of vesicles at the synapse, and motors move cargo throughout the cell. Understanding the structure, assembly, and conformational movements of these and other neuronal proteins is essential to understanding the brain. Developments in fluorescence have allowed the architecture and dynamics of proteins to be studied in real time and in a cellular context with great accuracy. In this review, we cover classic and recent methods for studying protein structure, assembly, and dynamics with fluorescence. These methods include fluorescence and luminescence resonance energy transfer, single molecule bleaching analysis, intensity measurements, co-localization microscopy, electron transfer, and bi-molecular complementation analysis. We present the principles of these methods, highlight recent work that uses the methods, and discuss a framework for interpreting results as they apply to molecular neurobiology. PMID:20434995

  17. Molecular control of facial morphology

    PubMed Central

    Liu, B.; Rooker, S.M.; Helms, J.A.

    2010-01-01

    We present a developmental perspective on the concept of phylotypic and phenotypic stages of craniofacial development. Within Orders of avians and mammals, a phylotypic period exists when the morphology of the facial prominences is minimally divergent. We postulate that species-specific facial variations arise as a result of subtle shifts in the timing and the duration of molecular pathway activity (e.g., heterochrony), and present evidence demonstrating a critical role for Wnt and FGF signaling in this process. The same molecular pathways that shape the vertebrate face are also implicated in craniofacial deformities, indicating that comparisons between and among animal species may represent a novel method for the identification of human craniofacial disease genes. PMID:19747977

  18. Molecular Mechanisms of Nitroarene Degradation

    DTIC Science & Technology

    2002-09-17

    nitrobenzene with the concomitant formation of catechol . The analogous enzyme system in Pseudomonas JS42 oxidizes 2-nitrotoluene to 3-methylcatechol and...2NTDO) system from Pseudomonas JS42. The enzymes catalyzing the initial oxidations of nitrobenzene and 2-nitrotoluene belong to a family of...color and the native molecular weight (35,000) showed that the active enzyme was a monomer. The N-terminal sequence of the recombinant reductase was

  19. Molecular Science Computing: 2010 Greenbook

    SciTech Connect

    De Jong, Wibe A.; Cowley, David E.; Dunning, Thom H.; Vorpagel, Erich R.

    2010-04-02

    This 2010 Greenbook outlines the science drivers for performing integrated computational environmental molecular research at EMSL and defines the next-generation HPC capabilities that must be developed at the MSC to address this critical research. The EMSL MSC Science Panel used EMSL’s vision and science focus and white papers from current and potential future EMSL scientific user communities to define the scientific direction and resulting HPC resource requirements presented in this 2010 Greenbook.

  20. Controlling proteins through molecular springs.

    PubMed

    Zocchi, Giovanni

    2009-01-01

    We argue that the mechanical control of proteins-the notion of controlling chemical reactions and processes by mechanics-is conceptually interesting. We give a brief review of the main accomplishments so far, leading to our present approach of using DNA molecular springs to exert controlled stresses on proteins. Our focus is on the physical principles that underlie both artificial mechanochemical devices and natural mechanisms of allostery.

  1. Molecular diagnostics and parasitic disease.

    PubMed

    Vasoo, Shawn; Pritt, Bobbi S

    2013-09-01

    Molecular parasitology represents an emerging field in microbiology diagnostics. Although most assays use nonstandardized, laboratory-developed methods, a few commercial systems have recently become available and are slowly being introduced into larger laboratories. In addition, a few methodologies show promise for use in field settings in which parasitic infections are endemic. This article reviews the available techniques and their applications to major parasitic diseases such as malaria, leishmaniasis, and trichomoniasis.

  2. Chemomechanics with Molecular Force Probes

    DTIC Science & Technology

    2010-03-30

    Prescribed by ANSI Std Z39-18 quantified by pressure, and its effect on the reaction rate is governed by the reaction’s volume of acti- vation, ΔV‡ [8...into chemomechanical coupling. Covalent bond rearrange- ments involve large energy changes, making them particularly attractive as the basis of novel...scales related, from the macroscopic force that accounts for large -scale dis- tortion in material in response to an external load down to molecular

  3. Calculation of molecular excitation rates

    NASA Technical Reports Server (NTRS)

    Flynn, George

    1993-01-01

    State-to-state collisional excitation rates for interstellar molecules observed by radio astronomers continue to be required to interpret observed line intensities in terms of local temperatures and densities. A problem of particular interest is collisional excitation of water which is important for modeling the observed interstellar masers. In earlier work supported by a different NASA Grant, excitation of water in collisions with He atoms was studied; after many years of successively more refined calculations that problem now seems to be well understood, and discrepancies with earlier experimental data for related (pressure broadening) phenomena are believed to reflect experimental errors. Because of interstellar abundances, excitation by H2, the dominant interstellar species, is much more important than excitation by He, although it has been argued that rates for excitation by these are similar. Under the current grant theoretical study of this problem has begun which is greatly complicated by the additional degrees of freedom which must be included both in determining the interaction potential and also in the molecular scattering calculation. We have now computed the interaction forces for nearly a thousand molecular geometries and are close to having an acceptable global fit to these points which is necessary for the molecular dynamics calculations. Also, extensive modifications have been made to the molecular scattering code, MOLSCAT. These included coding the rotational basis sets and coupling matrix elements required for collisions of an asymmetric top with a linear rotor. A new method for numerical solution of the coupled equations has been incorporated. Because of the long-ranged nature of the water-hydrogen interaction it is necessary to integrate the equations to rather large intermolecular separations, and the integration methods previously available in MOLSCAT are not ideal for such cases. However, the method used by Alexander in his HIBRIDON code is

  4. Molecular diagnosis: Implications for ophthalmology.

    PubMed

    Rosenbaum, James T; Sibley, Cailin H; Choi, Dongseok; Harrington, Christina A; Planck, Stephen R

    2016-01-01

    The effort to subdivide diseases and to individualize therapies based on characteristics of the patient has been labeled precision medicine. Jameson and Longo define precision medicine as "treatments targeted to the needs of individual patients on the basis of genetic, biomarker, phenotypic or psychosocial characteristics that distinguish a given patient from other patients with similar clinical presentations" (Jameson and Longo, 2015). We illustrate how molecular diagnosis can be applied to orbital inflammatory disease to achieve the goals of precision medicine.

  5. Terahertz Technology and Molecular Interactions

    DTIC Science & Technology

    2010-12-16

    fingerprint, as the concentration of the target gas is increased from zero at some concentration the identification statistics rapidly change from ran...REPORT THz Technology and Molecular Interactions 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The purpose of this project was to explore opportunities...development of compact solid state point sensors for chemical identification with ‘absolute’ specificity, (2) studies of the phenomenology that underlies

  6. Molecular defects in the chondrodysplasias

    SciTech Connect

    Rimoin, D.L.

    1996-05-03

    There has been a recent explosion of knowledge concerning the biochemical and molecular defects in the skeletal dysplasia. Through both the candidate gene approach and positional cloning, specific gene defects that produce the skeletal dysplasia have been identified and may be classified into several general categories: (1) qualitative or quantitative abnormalities in the structural proteins of cartilage; (2) inborn errors of cartilage metabolism; (3) defects in local regulators of cartilage growth; and (4) systemic defects influencing cartilage development. 35 refs., 1 tab.

  7. Molecular Clouds: Observation to Experiment

    SciTech Connect

    Kane, J O; Ryutov, D D; Mizuta, A; Remington, B A; Pound, M W

    2004-05-06

    Our ongoing investigation of how 'Pillars' and other structure form in molecular clouds irradiated by ultraviolet (UV) stars has revealed that the Rayleigh-Taylor instability is strongly suppressed by recombination in the photoevaporated outflow, that clumps and filaments may be key, that the evolution of structure is well-modeled by compressible hydrodynamics, and that directionality of the UV radiation may have significant effects. We discuss a generic, flexible set of laboratory experiments that can address these issues.

  8. Better, Cheaper, Faster Molecular Dynamics

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

  9. Molecular Control of Macromolecular Properties

    NASA Astrophysics Data System (ADS)

    Holcombe, Thomas Wesley, III

    Molecular level control over macromolecules has been at the heart of human advancement, long before Hermann Staudinger coined the term Makromolekule. From the development of primitive pharmaceuticals to the advanced materials that sent Man into outer-space, We have been tinkering with God's paint since our inception. The work described herein primarily involves advances concerning poly-aromatic macromolecules for use in future electronic applications, particularly that of organic photovoltaics. There is a final chapter, however, that gives the reader a taste of how some molecular level changes can be directly visualized with modern microscopy techniques. Chapter 1 provides a very brief introduction to conjugated polymers and molecular level control over macromolecular properties. Chapters 2--4 introduces the concept of polymer substitution as a means by which to control and improve charge generation in organic photovoltaic devices. Chapters 5 and 6 show how these polymers can take on larger, defined structures, yet are still beholden to intrinsic molecular properties---such as regioregularity, a fancy word for the regularity of the position in which two aromatic rings are joined together. Chapter 7 re-examines the role of polymer substitution on photovoltaic performance, this time with an emphasis on homo-polymer packing rather than electron transfer at the donor/acceptor interface. Finally, Chapter 8 visualizes how controlling the environment about a single metal atom can lead directly to a cyclic polyolefin. Individually, these advances do not yield any breakthroughs noticeable to a general audience; collectively, they sit atop a mountain of human knowledge, waiting to provide a stepping stone for the next generation.

  10. An antilock molecular braking system.

    PubMed

    Sun, Wei-Ting; Huang, Shou-Ling; Yao, Hsuan-Hsiao; Chen, I-Chia; Lin, Ying-Chih; Yang, Jye-Shane

    2012-08-17

    A light-driven molecular brake displaying an antilock function is constructed by introducing a nonradiative photoinduced electron transfer (PET) decay channel to compete with the trans (brake-off) → cis (brake-on) photoisomerization. A fast release of the brake can be achieved by deactivating the PET process through addition of protons. The cycle of irradiation-protonation-irradiation-deprotonation conducts the brake function and mimics the antilock braking system (ABS) of vehicles.

  11. Molecular imaging in the eye.

    PubMed

    Eter, Nicole

    2010-11-01

    Molecular imaging plays an increasingly powerful role in elucidating pathophysiological pathways, in advancing drug discovery and in deciphering developmental processes. Multiple modalities, including optical imaging, ultrasound, nuclear imaging, computed tomography and various techniques of MRI are now being used to obtain fundamental new insights at the cellular and molecular level, both in basic research, using animal models and in clinical studies. In permitting unique optical access, the eye is particularly well suited for molecular imaging, for example, transgenic mice in which the fractalkine receptor is rendered intrinsically fluorescent to allow for in vivo monitoring of myeloid immune cells within the retina and choroid by scanning laser ophthalmoscopy (SLO). Retinal cell apoptosis can be assessed by intravitreal injection of fluorescent-labelled annexin 5 in vivo using a similar SLO technique. Intravital microscopy also allows visualisation of CD11c-positive dendritic cells in transgenic mice expressing yellow-fluorescent protein in these immune cells. Adoptive transfer of fluorescent-labelled transgenic T-cells enables visualisation of infiltration by specific T-cells into various eye compartments. On the other hand, functional imaging can be provided by new MR methodologies: deuterium MRI and diffusion MRI analysis techniques permit dynamic studies of water movement in animal eyes. MRI also enables pharmacokinetic studies on ocular drug delivery and detects biomarkers for treatment efficacy in retinopathies. Undoubtedly, these and further molecular imaging techniques currently being developed will have a fundamental impact on experimental and clinical ophthalmology and thus on our understanding of eye disease and development of therapy in general.

  12. Molecular Strategies Against Sulfur Mustard Toxicity

    DTIC Science & Technology

    2010-04-01

    meiosis . Our current understanding of epigenetic regulation of gene expression involves basically two classes of molecular mechanisms: histone...Molecular Strategies Against Sulfur Mustard Toxicity 30 - 4 RTO-MP-HFM-182 meiosis . Our current understanding of epigenetic gene regulation

  13. The Molecular Weight Distribution of Polymer Samples

    ERIC Educational Resources Information Center

    Horta, Arturo; Pastoriza, M. Alejandra

    2007-01-01

    Various methods for the determination of the molecular weight distribution (MWD) of different polymer samples are presented. The study shows that the molecular weight averages and distribution of a polymerization completely depend on the characteristics of the reaction itself.

  14. 14th international symposium on molecular beams

    SciTech Connect

    Not Available

    1992-09-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation & dynamics; and surfaces.

  15. 14th international symposium on molecular beams

    SciTech Connect

    Not Available

    1992-01-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation dynamics; and surfaces.

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

    PubMed

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

    2016-03-01

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

  17. The molecular biology of ilarviruses.

    PubMed

    Pallas, Vicente; Aparicio, Frederic; Herranz, Mari C; Sanchez-Navarro, Jesus A; Scott, Simon W

    2013-01-01

    Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses.

  18. Molecular mechanisms of temperature adaptation

    PubMed Central

    Bagriantsev, Sviatoslav N; Gracheva, Elena O

    2015-01-01

    Thermal perception is a fundamental physiological process pertaining to the vast majority of organisms. In vertebrates, environmental temperature is detected by the primary afferents of the somatosensory neurons in the skin, which express a ‘choir’ of ion channels tuned to detect particular temperatures. Nearly two decades of research have revealed a number of receptor ion channels that mediate the perception of several temperature ranges, but most still remain molecularly orphaned. Yet even within this well-researched realm, most of our knowledge largely pertains to two closely related species of rodents, mice and rats. While these are standard biomedical research models, mice and rats provide a limited perspective to elucidate the general principles that drive somatosensory evolution. In recent years, significant advances have been made in understanding the molecular mechanism of temperature adaptation in evolutionarily distant vertebrates and in organisms with acute thermal sensitivity. These studies have revealed the remarkable versatility of the somatosensory system and highlighted adaptations at the molecular level, which often include changes in biophysical properties of ion channels from the transient receptor potential family. Exploiting non-standard animal models has the potential to provide unexpected insights into general principles of thermosensation and thermoregulation, unachievable using the rodent model alone. PMID:25433072

  19. Fiber sensors for molecular detection

    NASA Astrophysics Data System (ADS)

    Gu, Claire; Yang, Xuan; Zhang, Jin; Newhouse, Rebecca; Cao, Liangcai

    2010-11-01

    The demand on sensors for detecting chemical and biological agents is greater than ever before, including medical, environmental, food safety, military, and security applications. At present, most detection or sensing techniques tend to be either non-molecular specific, bulky, expensive, relatively inaccurate, or unable to provide real time data. Clearly, alternative sensing technologies are urgently needed. Recently, we have been working to develop a compact fiber optic surface enhanced Raman scattering (SERS) sensor system that integrates various novel ideas to achieve compactness, high sensitivity and consistency, molecular specificity, and automatic preliminary identification capabilities. The unique sensor architecture is expected to bring SERS sensors to practical applications due to a combination of 1) novel SERS substrates that provide the high sensitivity and consistency, molecular specificity, and applicability to a wide range of compounds; 2) a unique hollow core optical fiber probe with double SERS substrate structure that provides the compactness, reliability, low cost, and ease of sampling; and 3) an innovative matched spectral filter set that provides automatic preliminary molecule identification. In this paper, we will review the principle of operation and some of the important milestones of fiber SERS sensor development with emphasis on our recent work to integrate photonic crystal fiber SERS probes with a portable Raman spectrometer and to demonstrate a matched spectral filter for molecule identification.

  20. Molecular approach to echinoderm regeneration.

    PubMed

    Thorndyke, M C; Chen, W C; Beesley, P W; Patruno, M

    2001-12-15

    Until very recently echinoderm regeneration research and indeed echinoderm research in general has suffered because of the lack of critical mass. In terms of molecular studies of regeneration, echinoderms in particular have lagged behind other groups in this respect. This is in sharp contrast to the major advances achieved with molecular and genetic techniques in the study of embryonic development in echinoderms. The aim of our studies has been to identify genes involved in the process of regeneration and in particular neural regeneration in different echinoderm species. Our survey included the asteroid Asterias rubens and provided evidence for the expression of Hox gene homologues in regenerating radial nerve cords. Present evidence suggests: 1) ArHox1 expression is maintained in intact radial nerve cord and may be upregulated during regeneration. 2) ArHox1 expression may contribute to the dedifferentiation and/or cell proliferation process during epimorphic regeneration. From the crinoid Antedon bifida, we have been successful in cloning a fragment of a BMP2/4 homologue (AnBMP2/4) and analysing its expression during arm regeneration. Here, we discuss the importance of this family of growth factors in several regulatory spheres, including maintaining the identity of pluripotent blastemal cells or as a classic skeletal morphogenic regulator. There is clearly substantial scope for future echinoderm research in the area of molecular biology and certain aspects are discussed in this review.

  1. Molecular Basis of Symbiotic Promiscuity

    PubMed Central

    Perret, Xavier; Staehelin, Christian; Broughton, William J.

    2000-01-01

    Eukaryotes often form symbioses with microorganisms. Among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. Plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. Of these, symbioses between legumes and rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium) are the most important from an agricultural perspective. Nitrogen-fixing nodules arise when symbiotic rhizobia penetrate their hosts in a strictly controlled and coordinated manner. Molecular codes are exchanged between the symbionts in the rhizosphere to select compatible rhizobia from pathogens. Entry into the plant is restricted to bacteria that have the “keys” to a succession of legume “doors”. Some symbionts intimately associate with many different partners (and are thus promiscuous), while others are more selective and have a narrow host range. For historical reasons, narrow host range has been more intensively investigated than promiscuity. In our view, this has given a false impression of specificity in legume-Rhizobium associations. Rather, we suggest that restricted host ranges are limited to specific niches and represent specialization of widespread and more ancestral promiscuous symbioses. Here we analyze the molecular mechanisms governing symbiotic promiscuity in rhizobia and show that it is controlled by a number of molecular keys. PMID:10704479

  2. Ubiquitin: molecular modeling and simulations.

    PubMed

    Ganoth, Assaf; Tsfadia, Yossi; Wiener, Reuven

    2013-11-01

    The synthesis and destruction of proteins are imperative for maintaining their cellular homeostasis. In the 1970s, Aaron Ciechanover, Avram Hershko, and Irwin Rose discovered that certain proteins are tagged by ubiquitin before degradation, a discovery that awarded them the 2004 Nobel Prize in Chemistry. Compelling data gathered during the last several decades show that ubiquitin plays a vital role not only in protein degradation but also in many cellular functions including DNA repair processes, cell cycle regulation, cell growth, immune system functionality, hormone-mediated signaling in plants, vesicular trafficking pathways, regulation of histone modification and viral budding. Due to the involvement of ubiquitin in such a large number of diverse cellular processes, flaws and impairments in the ubiquitin system were found to be linked to cancer, neurodegenerative diseases, genetic disorders, and immunological disorders. Hence, deciphering the dynamics and complexity of the ubiquitin system is of significant importance. In addition to experimental techniques, computational methodologies have been gaining increasing influence in protein research and are used to uncover the structure, stability, folding, mechanism of action and interactions of proteins. Notably, molecular modeling and molecular dynamics simulations have become powerful tools that bridge the gap between structure and function while providing dynamic insights and illustrating essential mechanistic characteristics. In this study, we present an overview of molecular modeling and simulations of ubiquitin and the ubiquitin system, evaluate the status of the field, and offer our perspective on future progress in this area of research.

  3. The molecular composition of ambers

    USGS Publications Warehouse

    Grimalt, J.O.; Simoneit, B.R.T.; Hatcher, P.G.; Nissenbaum, A.

    1988-01-01

    Bulk (elemental composition, IR, CP/MAS 13C NMR) and molecular (GC-MS) analyses have been performed on a series of ambers and resins derived from different locations (Dominican Republic, Philippines, Canada, Israel, New Zealand, Chile) having diverse botanical affinities (Araucariaceae, Hymenaea) and variable age (from Holocene to Early Cretaceous). No major differences have been observed from the elemental composition and the spectroscopic data; however, the molecular analyses of the solvent extractable fraction show that a specific mixture of components is present in each sample. These are mainly diterpenoid products that in general are also found abundantly in the higher plants from which the ambers and resins originate. Nevertheless, a direct relationship between major terpenoid constituents in fossil resins and precursor plant materials can only be established for the younger samples. Irrespective of the geographical or botanical origin of the ambers and resins, several common age-dependent molecular transformation trends can be recognized: (1) progressive loss of olefinic bonds (especially those located in exocyclic positions), (2) decrease of functionalized products, and (3) increasing proportion of aromatized components. However, even in the samples of older age (Cretaceous) the degree of aromatization is very low when compared with that of other higher-plant related materials such as fossilized woods or low rank coals. This indicates that maturation must involve essentially olefin polymerization processes instead of extensive aromatization. ?? 1988.

  4. Clinical applications in molecular imaging.

    PubMed

    Heneweer, Carola; Grimm, Jan

    2011-02-01

    Molecular imaging is aimed at the noninvasive in vivo characterization and measurement of processes at a cellular and molecular level with clinical imaging methods. Contrast agents are constructed to target markers that are specific either for certain diseases or for functional states of specialized tissues. Efforts are currently focused mainly on processes involved in angiogenesis, inflammation, and apoptosis. Cell tracking is performed for diagnostic purposes as well as for monitoring of novel cell therapies. Visualization of these processes would provide more precise information about disease expansion as well as treatment response, and could lead to a more individualized therapy for patients. Many attempts have shown promising results in preclinical studies; however, translation into the clinic remains a challenge. This applies especially to paediatrics because of more stringent safety concerns and the low prevalence of individual diseases. The most promising modalities for clinical translation are nuclear medicine methods (positron emission tomography [PET] and single photon emission CT [SPECT]) due to their high sensitivity, which allows concentrations below biological activity. However, special dose consideration is required for any application of ionizing radiation especially in children. While very little has been published on molecular imaging in a paediatric patient population beyond fluorodeoxyglucose (FDG)-PET and metaiodobenzylguanidine (MIBG) tracers, this review will attempt to discuss approaches that we believe have promise for paediatric imaging. These will include agents that already reached clinical trials as well as preclinical developments with high potential for clinical application.

  5. Surface modification by molecular ions

    SciTech Connect

    Hanley, L.; Schultz, D. G.; Ada, E. T.

    1999-06-10

    There are several advantages in using molecular ions for surface modification. The modification can be confined to the uppermost layer of the surface, the molecular character of the ion can be imparted to the surface, and sputter yields are often higher. These effects are demonstrated by the use of mass selected ion beams incident on well characterized surfaces. Energy transfer is examined by detecting the masses and energies of ions scattered off surfaces and performing molecular dynamics simulations. Surface modification is followed by chemical analysis with x-ray photoelectron spectroscopy and surface mass spectrometry. TRIDYN monte carlo simulations are used to support some of the modification experiments. Energy transfer is examined for Si(CD{sub 3}){sub 3}{sup +} scattered off clean and hexanethiolate covered Au(111). Adsorbate desorption cross sections and substrate damage depths for NH{sub 3}/CO/Ni(111) are compared for 10-1000 eV isobaric atomic and polyatomic ions, Xe{sup +} and SF{sub 5}{sup +}. The surface chemical modification of polystyrene thin films by 10-100 eV SF{sub 5}{sup +} and C{sub 3}F{sub 5}{sup +} ions is also examined.

  6. Scalable Molecular Dynamics with NAMD

    PubMed Central

    Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus

    2008-01-01

    NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654

  7. Molecular approaches to Taenia asiatica.

    PubMed

    Jeon, Hyeong-Kyu; Eom, Keeseon S

    2013-02-01

    Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

  8. Molecular diagnostics of myeloproliferative neoplasms.

    PubMed

    Langabeer, Stephen E; Andrikovics, Hajnalka; Asp, Julia; Bellosillo, Beatriz; Carillo, Serge; Haslam, Karl; Kjaer, Lasse; Lippert, Eric; Mansier, Olivier; Oppliger Leibundgut, Elisabeth; Percy, Melanie J; Porret, Naomi; Palmqvist, Lars; Schwarz, Jiri; McMullin, Mary F; Schnittger, Susanne; Pallisgaard, Niels; Hermouet, Sylvie

    2015-10-01

    Since the discovery of the JAK2 V617F mutation in the majority of the myeloproliferative neoplasms (MPN) of polycythemia vera, essential thrombocythemia and primary myelofibrosis ten years ago, further MPN-specific mutational events, notably in JAK2 exon 12, MPL exon 10 and CALR exon 9 have been identified. These discoveries have been rapidly incorporated into evolving molecular diagnostic algorithms. Whilst many of these mutations appear to have prognostic implications, establishing MPN diagnosis is of immediate clinical importance with selection, implementation and the continual evaluation of the appropriate laboratory methodology to achieve this diagnosis similarly vital. The advantages and limitations of these approaches in identifying and quantitating the common MPN-associated mutations are considered herein with particular regard to their clinical utility. The evolution of molecular diagnostic applications and platforms has occurred in parallel with the discovery of MPN-associated mutations, and it therefore appears likely that emerging technologies such as next-generation sequencing and digital PCR will in the future play an increasing role in the molecular diagnosis of MPN.

  9. Molecular diodes in optical rectennas

    NASA Astrophysics Data System (ADS)

    Duché, David; Palanchoke, Ujwol; Terracciano, Luigi; Dang, Florian-Xuan; Patrone, Lionel; Le Rouzo, Judikael; Balaban, Téodore Silviu; Alfonso, Claude; Charai, Ahmed; Margeat, Olivier; Ackermann, Jorg; Gourgon, Cécile; Simon, Jean-Jacques; Escoubas, Ludovic

    2016-09-01

    The photo conversion efficiencies of the 1st and 2nd generat ion photovoltaic solar cells are limited by the physical phenomena involved during the photo-conversion processes. An upper limit around 30% has been predicted for a monojunction silicon solar cell. In this work, we study 3rd generation solar cells named rectenna which could direct ly convert visible and infrared light into DC current. The rectenna technology is at odds with the actual photovoltaic technologies, since it is not based on the use of semi-conducting materials. We study a rectenna architecture consist ing of plasmonic nano-antennas associated with rectifying self assembled molecular diodes. We first opt imized the geometry of plasmonic nano-antennas using an FDTD method. The optimal antennas are then realized using a nano-imprint process and associated with self assembled molecular diodes in 11- ferrocenyl-undecanethiol. Finally, The I(V) characterist ics in darkness of the rectennas has been carried out using an STM. The molecular diodes exhibit averaged rect ification ratios of 5.

  10. Molecular phylogenetics: testing evolutionary hypotheses.

    PubMed

    Walsh, David A; Sharma, Adrian K

    2009-01-01

    A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.

  11. Molecular collisions coming into focus.

    PubMed

    Onvlee, Jolijn; Vogels, Sjoerd N; von Zastrow, Alexander; Parker, David H; van de Meerakker, Sebastiaan Y T

    2014-08-14

    The Stark deceleration method exploits the concepts of charged particle accelerator physics to produce beams of neutral polar molecules with an almost perfect quantum state purity, a tunable velocity and a narrow velocity distribution. These monochromatic molecular beams offer interesting perspectives for precise studies of molecular scattering processes, in particular when used in conjunction with state-of-the-art laser-based detection techniques such as velocity map imaging. Here, we describe crossed beam scattering experiments in which the Stark deceleration method is combined with the velocity map imaging technique. The narrow velocity spread of Stark-decelerated molecular beams results in scattering images with unprecedented velocity and angular resolution. We demonstrate this by resolving quantum diffraction oscillations in state-to-state inelastic differential scattering cross sections for collisions between NO radicals and rare gas atoms. We describe the future prospects of this "best-of-two-worlds" combination, ranging from scattering studies at low collision energies to bimolecular scattering using two decelerators, and discuss the challenges that lie ahead to achieve these goals.

  12. Astrobiological molecularly imprinted polymer sensors

    NASA Astrophysics Data System (ADS)

    Izenberg, Noam R.; Murrray, George M.; Pilato, Robert S.; Baird, Lance M.; Levin, Scott M.; Van Houten, Kelly A.

    2009-06-01

    The purpose of the Astrobiological MIP Sensor (AMS) Project is to develop reliable, low-cost, low-mass, low-power consumption detection technologies for in situ analysis of biochemical markers, and other indicators of astrobiological importance. To this end, we are investigating the potential role that molecularly imprinted polymers (MIP) could serve in the recognition of pre-biotic and biotic compounds in planetary, astrobiological and geochemical mission profiles. While MIPs are effective molecular recognition tools, a signal transduction method must be developed so that the recognition of analytes can be realized. In the course of this study, surface plasmon resonance (SPR) will be the detection method of the MIP recognition event. In addition, MIP-coated SPR substrates were subjected to vibration, temperature and radiation testing to demonstrate that they could withstand the rigors of space travel. The methods developed in this study require capture of the biomarkers onto the SPR sensor chip, followed by addition of a MIP. It is the binding of the MIP to the SPR bound analyte that amplifies the SPR signal associated with binding of the low molecular weight analyte. The MIPs, developed in this study are water-soluble processable star polymers while the SPR device used was SensíQ™ by Nomatics. Proof-of-principal experiments were first demonstrated using amino biotin.

  13. Molecular Identification of the Schwannomatosis Locus

    DTIC Science & Technology

    2004-07-01

    AD Award Number: DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia M. MacCollin, M.D...COVERED (Leave blank) July 2004 Annual (1 Jul 2003 - 30 Jun 2004) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Molecular Identification of the Schwannomatosis...linkage and loss of heterozygosity analyses. 3. To determine the molecular mechanism of tumor formation in these patients using complementary molecular

  14. Molecular Imaging of the Kidneys

    PubMed Central

    Szabo, Zsolt; Alachkar, Nada; Xia, Jinsong; Mathews, William B.; Rabb, Hamid

    2010-01-01

    Radionuclide imaging of the kidneys with gamma cameras involves the use of labeled molecules seeking functionally critical molecular mechanisms in order to detect the pathophysiology of the diseased kidneys and achieve an early, sensitive and accurate diagnosis. The most recent imaging technology, PET, permits quantitative imaging of the kidney at a spatial resolution appropriate for the organ. H215O, 82RbCl, and [64Cu] ETS are the most important radiopharmaceuticals for measuring renal blood flow. The renin angiotensin system is the most important regulator of renal blood flow; this role is being interrogated by detecting angiotensin receptor subtype AT1R using in vivo PET imaging. Membrane organic anion transporters are important for the function of the tubular epithelium; therefore, Tc-99m MAG3 as well as some novel radiopharmaceuticals such as copper-64 labeled mono oxo-tetraazamacrocyclic ligands have been utilized for molecular renal imaging. Additionally, other radioligands that interact with the organic cation transporters or peptide transporters have developed. Focusing on early detection of kidney injury at the molecular level is an evolving field of great significance. Potential imaging targets are the kidney injury molecule- 1 (KIM-1) that is highly expressed in kidney injury and renal cancer but not in normal kidneys. While pelvic clearance, in addition to parenchymal transport, is an important measure in obstructive nephropathy, techniques that focus on upregulated molecules in response to tissue stress resulted from obstruction will be of great implication. Monocyte chemoattractant protein -1 (MCP-1) is a well-suited molecule in this case. The greatest advances in molecular imaging of the kidneys have been recently achieved in detecting renal cancer. In addition to the ubiquitous [18F]FDG, other radioligands such as [11C]acetate and anti-[18F]FACBC have emerged. Radioimmuno-imaging with [124I]G250 could lead to radioimmunotherapy for renal cancer

  15. Molecular neurobiology in neurology and psychiatry

    SciTech Connect

    Kandel, E.R.

    1987-01-01

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

  16. Novel methods for molecular dynamics simulations.

    PubMed

    Elber, R

    1996-04-01

    In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.

  17. Amorphous Molecular Organic Solids for Gas Adsorption

    SciTech Connect

    Tian, Jian; Thallapally, Praveen K.; Dalgarno, Scott J.; McGrail, B. Peter; Atwood, Jerry L.

    2009-07-06

    We show that molecular organic compounds with large accessible internal cavities, as part of their rigid molecular structure, display exceptional ability for gas storage and separation in the amorphous solid state. This finding suggests for the first time that long-range molecular order is not a prerequisite for organic molecules to be engineered as porous materials

  18. Molecular imprinting in sol-gel matrix.

    PubMed

    Gupta, Radha; Kumar, Ashok

    2008-01-01

    Molecular imprinting is a newly developed methodology which provides molecular assemblies of desired structures and properties and is being increasingly used for several applications such as in separation processes, microreactors, immunoassays and antibody mimics, catalysis, artificial enzymes, biosensor recognition elements and bio- and chemo-sensors. The ambient processing conditions and versatility of the sol-gel process makes sol-gel glassy matrix suitable for molecular imprinting. The progress of sol-gel based molecular imprinted polymers (MIPs) for various applications can be seen from the growing number of publications. The main focus of the review is molecular imprinting in sol-gel matrix and applications of molecular imprinted sol-gel derived materials for the development of sensors. Combining sol-gel process with molecular imprinting enables to procure the sensors with greater sensitivity and selectivity necessary for sensing applications. The merits, problems, challenges and factors affecting molecular imprinting in sol-gel matrix have been discussed. Considerable attention has been drawn on recent developments like use of organically modified silane precursors (ORMOSILS) for the synthesis of hybrid molecular imprinted polymers (HMIPs) and applying surface sol-gel process for molecular imprinting. The development of molecular imprinted sol-gel nanotubes for biochemical separation and bio-imprinting is a new advancement and is under progress. Templated xerogels and molecularly imprinted sol-gel films provide a good platform for various sensor applications.

  19. Molecular Imaging: Current Status and Emerging Strategies

    PubMed Central

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

    2011-01-01

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

  20. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  1. Molecular Simulations of Porphyrins and Heme Proteins

    SciTech Connect

    SHELNUTT,JOHN A.

    2000-01-18

    An overview of the use of classical mechanical molecular simulations of porphyrins, hydroporphyrins, and heme proteins is given. The topics cover molecular mechanics calculations of structures and conformer energies of porphyrins, energies of barriers for interconversion between stable conformers, molecular dynamics of porphyrins and heme proteins, and normal-coordinate structural analysis of experimental and calculated porphyrin structures. Molecular mechanics and dynamics are currently a fertile area of research on porphyrins. In the future, other computational methods such as Monte Carlo simulations, which have yet to be applied to porphyrins, will come into use and open new avenues of research into molecular simulations of porphyrins.

  2. Molecular clips and tweezers hosting neutral guests.

    PubMed

    Hardouin-Lerouge, Marie; Hudhomme, Piétrick; Sallé, Marc

    2011-01-01

    Intense current interest in supramolecular chemistry is devoted to the construction of molecular assemblies displaying controlled molecular motion associated to recognition. On this ground, molecular clips and tweezers have focused an increasing attention. This tutorial review points out the recent advances in the construction of always more sophisticated molecular clips and tweezers, illustrating their remarkably broad structural variety and focusing on their binding ability towards neutral guests. A particular attention is brought to recent findings in dynamic molecular tweezers whose recognition ability can be regulated by external stimuli. Porphyrin-based systems will not be covered here as this very active field has been recently reviewed.

  3. Developing accurate molecular mechanics force fields for conjugated molecular systems.

    PubMed

    Do, Hainam; Troisi, Alessandro

    2015-10-14

    A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.

  4. Molecular complexes in close and far away

    PubMed Central

    Klemperer, William; Vaida, Veronica

    2006-01-01

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

  5. Molecular imaging for personalized cancer care.

    PubMed

    Kircher, Moritz F; Hricak, Hedvig; Larson, Steven M

    2012-04-01

    Molecular imaging is rapidly gaining recognition as a tool with the capacity to improve every facet of cancer care. Molecular imaging in oncology can be defined as in vivo characterization and measurement of the key biomolecules and molecularly based events that are fundamental to the malignant state. This article outlines the basic principles of molecular imaging as applied in oncology with both established and emerging techniques. It provides examples of the advantages that current molecular imaging techniques offer for improving clinical cancer care as well as drug development. It also discusses the importance of molecular imaging for the emerging field of theranostics and offers a vision of how molecular imaging may one day be integrated with other diagnostic techniques to dramatically increase the efficiency and effectiveness of cancer care.

  6. Molecular genetics of Thiobacillus ferrooxidans.

    PubMed Central

    Rawlings, D E; Kusano, T

    1994-01-01

    Thiobacillus ferrooxidans is a gram-negative, highly acidophilic (pH 1.5 to 2.0), autotrophic bacterium that obtains its energy through the oxidation of ferrous iron or reduced inorganic sulfur compounds. It is usually dominant in the mixed bacterial populations that are used industrially for the extraction of metals such as copper and uranium from their ores. More recently, these bacterial consortia have been used for the biooxidation of refractory gold-bearing arsenopyrite ores prior to the recovery of gold by cyanidation. The commercial use of T. ferrooxidans has led to an increasing interest in the genetics and molecular biology of the bacterium. Initial investigations were aimed at determining whether the unique physiology and specialized habitat of T. ferrooxidans had been accompanied by a high degree of genetic drift from other gram-negative bacteria. Early genetic studies were comparative in nature and concerned the isolation of genes such as nifHDK, glnA, and recA, which are widespread among bacteria. From a molecular biology viewpoint, T. ferrooxidans appears to be a typical member of the proteobacteria. In most instances, cloned gene promoters and protein products have been functional in Escherichia coli. Although T. ferrooxidans has proved difficult to transform with DNA, research on indigenous plasmids and the isolation of the T. ferrooxidans merA gene have resulted in the development of a low-efficiency electroporation system for one strain of T. ferrooxidans. The most recent studies have focused on the molecular genetics of the pathways associated with nitrogen metabolism, carbon dioxide fixation, and components of the energy-producing mechanisms. PMID:8177170

  7. Carbon isotope controlled molecular switches

    NASA Astrophysics Data System (ADS)

    Foster, Brian K.

    Single molecules represent one fundamental limit to the downscaling of electronics. As a prototype element for carbon-based nanoscale science and technology, the detailed behavior of carbon monoxide (CO) on the copper surface Cu(111) has been investigated. These investigations span from individual carbon isotope resolution, to single molecules, to compact clusters assembled by molecular manipulation via a homemade scanning tunneling microscope (STM). Sub-nanoscale devices, composed of only a few molecules, which exploit both lone CO properties and molecule-molecule interaction, have been designed and assembled. The devices function as bi-stable switches and can serve as classical bits with densities > 50 Tbits/cm2. Operated in the nuclear mass sensitive regime, each switch can also function as a molecular "centrifuge" capable of identifying the isotope of a single carbon atom in real-time. A model, based on electron-vibron couping and inelastic tunneling, has been developed and explains the dynamic behavior of the switch. The interaction between pairs of switches was also explored and it was found that their behavior ranges from completely independent to strongly coupled. Larger nanostructures, which were composed of many sub-switches organized to leverage the fully coupled interaction, link two spatially separated "bits" on the surface. Such a linked system can set or read a state non-locally, which is equivalent to bidirectional information transfer. The linked system has also exhibited logic functionality. These experiments demonstrate scalable molecular cells for information storage, and for information processing through cellular automata logic schemes.

  8. Molecular modeling of polynucleotide complexes.

    PubMed

    Meneksedag-Erol, Deniz; Tang, Tian; Uludağ, Hasan

    2014-08-01

    Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power

  9. Molecular Outflows: Explosive versus Protostellar

    NASA Astrophysics Data System (ADS)

    Zapata, Luis A.; Schmid-Burgk, Johannes; Rodríguez, Luis F.; Palau, Aina; Loinard, Laurent

    2017-02-01

    With the recent recognition of a second, distinctive class of molecular outflows, namely the explosive ones not directly connected to the accretion–ejection process in star formation, a juxtaposition of the morphological and kinematic properties of both classes is warranted. By applying the same method used in Zapata et al., and using 12CO(J = 2-1) archival data from the Submillimeter Array, we contrast two well-known explosive objects, Orion KL and DR21, to HH 211 and DG Tau B, two flows representative of classical low-mass protostellar outflows. At the moment, there are only two well-established cases of explosive outflows, but with the full availability of ALMA we expect that more examples will be found in the near future. The main results are the largely different spatial distributions of the explosive flows, consisting of numerous narrow straight filament-like ejections with different orientations and in almost an isotropic configuration, the redshifted with respect to the blueshifted components of the flows (maximally separated in protostellar, largely overlapping in explosive outflows), the very-well-defined Hubble flow-like increase of velocity with distance from the origin in the explosive filaments versus the mostly non-organized CO velocity field in protostellar objects, and huge inequalities in mass, momentum, and energy of the two classes, at least for the case of low-mass flows. Finally, all the molecular filaments in the explosive outflows point back to approximately a central position (i.e., the place where its “exciting source” was located), contrary to the bulk of the molecular material within the protostellar outflows.

  10. Toward Molecular Catalysts by Computer

    SciTech Connect

    Raugei, Simone; DuBois, Daniel L.; Rousseau, Roger J.; Chen, Shentan; Ho, Ming-Hsun; Bullock, R. Morris; Dupuis, Michel

    2015-02-17

    Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to predict accurately the required properties and ultimately to design catalysts by computer. In this account we first review how thermodynamic properties such as oxidation-reduction potentials (E0), acidities (pKa), and hydride donor abilities (ΔGH-) form the basis for a systematic design of molecular catalysts for reactions that are critical for a secure energy future (hydrogen evolution and oxidation, oxygen and nitrogen reduction, and carbon dioxide reduction). We highlight how density functional theory allows us to determine and predict these properties within “chemical” accuracy (~ 0.06 eV for redox potentials, ~ 1 pKa unit for pKa values, and ~ 1.5 kcal/mol for hydricities). These quantities determine free energy maps and profiles associated with catalytic cycles, i.e. the relative energies of intermediates, and help us distinguish between desirable and high-energy pathways and mechanisms. Good catalysts have flat profiles that avoid high activation barriers due to low and high energy intermediates. We illustrate how the criterion of a flat energy profile lends itself to the prediction of design points by computer for optimum catalysts. This research was carried out in the Center for Molecular Electro-catalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle.

  11. Circadian molecular clocks and cancer.

    PubMed

    Kelleher, Fergal C; Rao, Aparna; Maguire, Anne

    2014-01-01

    Physiological processes such as the sleep-wake cycle, metabolism and hormone secretion are controlled by a circadian rhythm adapted to 24h day-night periodicity. This circadian synchronisation is in part controlled by ambient light decreasing melatonin secretion by the pineal gland and co-ordinated by the suprachiasmatic nucleus of the hypothalamus. Peripheral cell autonomous circadian clocks controlled by the suprachiasmatic nucleus, the master regulator, exist within every cell of the body and are comprised of at least twelve genes. These include the basic helix-loop-helix/PAS domain containing transcription factors; Clock, BMal1 and Npas2 which activate transcription of the periodic genes (Per1 and Per2) and cryptochrome genes (Cry1 and Cry2). Points of coupling exist between the cellular clock and the cell cycle. Cell cycle genes which are affected by the molecular circadian clock include c-Myc, Wee1, cyclin D and p21. Therefore the rhythm of the circadian clock and cancer are interlinked. Molecular examples exist including activation of Per2 leads to c-myc overexpression and an increased tumor incidence. Mice with mutations in Cryptochrome 1 and 2 are arrhythmic (lack a circadian rhythm) and arrhythmic mice have a faster rate of growth of implanted tumors. Epidemiological finding of relevance include 'The Nurses' Health Study' where it was established that women working rotational night shifts have an increased incidence of breast cancer. Compounds that affect circadian rhythm exist with attendant future therapeutic possibilities. These include casein kinase I inhibitors and a candidate small molecule KL001 that affects the degradation of cryptochrome. Theoretically the cell cycle and malignant disease may be targeted vicariously by selective alteration of the cellular molecular clock.

  12. Molecular films associated with LDEF

    NASA Technical Reports Server (NTRS)

    Crutcher, E. R.; Warner, K. J.

    1992-01-01

    The molecular films deposited on the surface of the Long Duration Exposure Facility (LDEF) originated from the paints and room-temperature-vulcanized (RTV) silicone materials intentionally used on the satellite and not from residual contaminants. The high silicone content of most of the films and the uniformity of the films indicates a homogenization process in the molecular deposition and suggests a chemically most favored composition for the final film. The deposition on interior surfaces and vents indicated multiple bounce trajectories or repeated deposition-reemission cycles. Exterior surface deposits indicated a significant return flux. Ultraviolet light exposure was required to fix the deposited film as is indicated by the distribution of the films on interior surfaces and the thickness of films at the vent locations. Thermal conditions at the time of exposure to ultraviolet light seems to be an important factor in the thickness of the deposit. Sunrise facing (ram direction) surfaces always had the thicker film. These were the coldest surfaces at the time of their exposure to ultraviolet light. The films have a layered structure suggesting cyclic deposition. As many as 34 distinct layers were seen in the films. The cyclic nature of the deposition and the chemical uniformity of the film one layer to the next suggest an early deposition of the films though there is evidence for the deposition of molecular films throughout the nearly six year exposure of the satellite. A final 'spray' of an organic material associated with water soluble salts occurred very late in the mission. This may have been the result of one of the shuttle dump activities.

  13. Virtual Screening Using Molecular Simulations

    PubMed Central

    Yang, Tianyi; Wu, Johnny C.; Yan, Chunli; Wang, Yuanfeng; Luo, Ray; Gonzales, Michael B.; Dalby, Kevin N.; Ren, Pengyu

    2011-01-01

    Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) Surface Area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range 0.56~0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data while the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery. PMID:21491494

  14. Wavelet Analysis for Molecular Dynamics

    DTIC Science & Technology

    2015-06-01

    simulation (and the computational work performed in the process). Slower processes, such as torsions and translations, are usually the more relevant ones. The...is no longer as simple as for H2O, nor are the eigenvalues except 0 simple; for the generalized Amber force field (GAFF), they are 14.7 and...short-range molecular dynamics. J Comput Phys. 1995;117(1):1–19. 9. Sun H, Mumby SJ, Maple JR, Hagler AT. An ab initio CFF93 all-atom force field for

  15. Molecular Diagnosis of Cystic Fibrosis.

    PubMed

    Deignan, Joshua L; Grody, Wayne W

    2016-01-01

    This unit describes a recommended approach to identifying causal genetic variants in an individual suspected of having cystic fibrosis. An introduction to the genetics and clinical presentation of cystic fibrosis is initially presented, followed by a description of the two main strategies used in the molecular diagnosis of cystic fibrosis: (1) an initial targeted variant panel used to detect only the most common cystic fibrosis-causing variants in the CFTR gene, and (2) sequencing of the entire coding region of the CFTR gene to detect additional rare causal CFTR variants. Finally, the unit concludes with a discussion regarding the analytic and clinical validity of these approaches.

  16. Molecular-Beam-Epitaxy Program

    NASA Technical Reports Server (NTRS)

    Sparks, Patricia D.

    1988-01-01

    Molecular Beam Epitaxy (MBE) computer program developed to aid in design of single- and double-junction cascade cells made of silicon. Cascade cell has efficiency 1 or 2 percent higher than single cell, with twice the open-circuit voltage. Input parameters include doping density, diffusion lengths, thicknesses of regions, solar spectrum, absorption coefficients of silicon (data included for 101 wavelengths), and surface recombination velocities. Results include maximum power, short-circuit current, and open-circuit voltage. Program written in FORTRAN IV.

  17. Molecular mechanisms of dendrite morphogenesis

    PubMed Central

    Arikkath, Jyothi

    2012-01-01

    Dendrites are key integrators of synaptic information in neurons and play vital roles in neuronal plasticity. Hence, it is necessary that dendrite arborization is precisely controlled and coordinated with synaptic activity to ensure appropriate functional neural network integrity. In the past several years, it has become increasingly clear that several cell intrinsic and extrinsic mechanisms contribute to dendritic arborization. In this review, we will discuss some of the molecular mechanisms that regulate dendrite morphogenesis, particularly in cortical and hippocampal pyramidal neurons and some of the implications of aberrant dendritic morphology for human disease. Finally, we will discuss the current challenges and future directions in the field. PMID:23293584

  18. Molecular replacement then and now

    SciTech Connect

    Scapin, Giovanna

    2013-11-01

    A brief overview, with examples, of the evolution of molecular-replacement methods and models over the past few years is presented. The ‘phase problem’ in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962 ▶), Acta Cryst.15, 24–31]. The term ‘molecular replacement’ was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972 ▶), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the ‘best’ search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to

  19. Craniosynostoses: Phenotypic/molecular correlations

    SciTech Connect

    Cohen, M.M. Jr.

    1995-04-10

    From the discovery of the first known human homeobox mutation in MSX2 for craniosynostosis of the Boston type by Jams to the recent report of 2 mutations in FGFR2 in Apert syndrome by Wilkie, it is clear that the molecular aspects of syndromes with craniosynostosis are becoming known at a dizzying pace. Four of the syndromes involve mutations in FGFR2. The first to emerge was Crouzon syndrome followed by Jackson-Weiss syndrome, Pfeiffer syndrome, and finally Apert syndrome. Earlier, Muenke showed that Pfeiffer syndrome was heterogeneous, some families having a mutation in FGFR1. 50 refs., 4 tabs.

  20. Molecular basis of mechanosensory transduction

    NASA Astrophysics Data System (ADS)

    Gillespie, Peter G.; Walker, Richard G.

    2001-09-01

    Mechanotransduction - a cell's conversion of a mechanical stimulus into an electrical signal - reveals vital features of an organism's environment. From hair cells and skin mechanoreceptors in vertebrates, to bristle receptors in flies and touch receptors in worms, mechanically sensitive cells are essential in the life of an organism. The scarcity of these cells and the uniqueness of their transduction mechanisms have conspired to slow molecular characterization of the ensembles that carry out mechanotransduction. But recent progress in both invertebrates and vertebrates is beginning to reveal the identities of proteins essential for transduction.

  1. Molecular Mechanisms of Nickel Allergy

    PubMed Central

    Saito, Masako; Arakaki, Rieko; Yamada, Akiko; Tsunematsu, Takaaki; Kudo, Yasusei; Ishimaru, Naozumi

    2016-01-01

    Allergic contact hypersensitivity to metals is a delayed-type allergy. Although various metals are known to produce an allergic reaction, nickel is the most frequent cause of metal allergy. Researchers have attempted to elucidate the mechanisms of metal allergy using animal models and human patients. Here, the immunological and molecular mechanisms of metal allergy are described based on the findings of previous studies, including those that were recently published. In addition, the adsorption and excretion of various metals, in particular nickel, is discussed to further understand the pathogenesis of metal allergy. PMID:26848658

  2. Molecular pathways of angiogenesis inhibition

    SciTech Connect

    Tabruyn, Sebastien P.; Griffioen, Arjan W. . E-mail: aw.griffioen@path.unimaas.nl

    2007-03-30

    A large body of evidence now demonstrates that angiostatic therapy represents a promising way to fight cancer. This research recently resulted in the approval of First angiostatic agent for clinical treatment of cancer. Progress has been achieved in decrypting the cellular signaling in endothelial cells induced by angiostatic agents. These agents predominantly interfere with the molecular pathways involved in migration, proliferation and endothelial cell survival. In the current review, these pathways are discussed. A thorough understanding of the mechanism of action of angiostatic agents is required to develop efficient anti-tumor therapies.

  3. Molecular Diagnosis: Implications for Ophthalmology

    PubMed Central

    Sibley, Cailin H.; Choi, Dongseok; Harrington, Christina A.; Planck, Stephen R.

    2016-01-01

    The effort to subdivide diseases and to individualize therapies based on characteristics of the patient has been labelled precision medicine. Jameson and Longo define precision medicine as “treatments targeted to the needs of individual patients on the basis of genetic, biomarker, phenotypic or psychosocial characteristics that distinguish a given patient from other patients with similar clinical presentations” (Jameson and Longo, 2015). We illustrate how molecular diagnosis can be applied to orbital inflammatory disease to achieve the goals of precision medicine. PMID:26608807

  4. Molecular profiles in foregut oncology.

    PubMed

    Sukharamwala, Prashant; Hennessey, Daniel; Wood, Thomas; Singh, Shelly; Ryan, Carrie; Rosemurgy, Alexander

    2016-12-01

    Oncology is and will continue to evolve resulting from a better understanding of the biology and intrinsic genetic profile of each cancer. Tumor biomarkers and targeted therapies are the new face of precision medicine, so it is essential for all physicians caring for cancer patients to understand and assist patients in understanding the role and importance of such markers and strategies to target them. This review was initiated in an attempt to identify, characterize, and discuss literature supporting clinically relevant molecular markers and interventions. The efficacy of targeting specific markers will be examined with data from clinical trials focusing on treatments for esophageal, gastric, liver, gallbladder, biliary tract, and pancreatic cancers.

  5. The molecular neurobiology of depression

    PubMed Central

    Krishnan, Vaishnav; Nestler, Eric J.

    2009-01-01

    Unravelling the pathophysiology of depression is a unique challenge. Not only are depressive syndromes heterogeneous and their aetiologies diverse, but symptoms such as guilt and suicidality are impossible to reproduce in animal models. Nevertheless, other symptoms have been accurately modelled, and these, together with clinical data, are providing insight into the neurobiology of depression. Recent studies combining behavioural, molecular and electrophysiological techniques reveal that certain aspects of depression result from maladaptive stress-induced neuroplastic changes in specific neural circuits. They also show that understanding the mechanisms of resilience to stress offers a crucial new dimension for the development of fundamentally novel antidepressant treatments. PMID:18923511

  6. [Molecular bases of cancer immunology].

    PubMed

    Barrera-Rodríguez, R; Peralta-Zaragoza, O; Madrid-Marina, V

    1995-01-01

    The immune system is a tight network of different types of cells and molecules. The coordinated action of these elements mounts a precise immune response against tumor cells. However, these cells present several escape mechanisms, leading to tumor progression. This paper shows several cellular and molecular events involved in the regulation of the immune response against tumor cells. The interaction of several molecules such as MHC, TcR, adhesins, tumor antigens and cytokines are discussed, as well as the most recent knowledge about escape mechanisms and immunotherapy.

  7. Maternal Effects in Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Wilke, Claus O.

    2002-02-01

    We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The dependency on the parental genotypes cancels from the mean fitness, but not from the individual sequence concentrations. For finite populations, the position of the error threshold is very sensitive to the influence from parent genotypes. In addition to biological applications, our model is important for understanding the dynamics of self-replicating computer programs.

  8. Molecular charmonium. A new spectroscopy?

    NASA Astrophysics Data System (ADS)

    Fernandez, F.; Ortega, P. G.; Entem, D. R.

    2014-07-01

    Using a constituent quark model, we study the mass and decay channels of meson meson and meson baryon structures in the charm sector. We show that the X(3872) and the X(3940) resonances can be described as mixed charmonium-molecular states with JPC = 1++, whereas the X(3915) and the Y(3940) can be assigned to similar mixed states with JPC = 0++. In the baryon spectrum we identify the Λc+(2940) as a D*N molecule with (I)JP = (0)3/2- and the recently reported Xc(3250) as a D*Δ resonance with (I)JP = (2)1/2-.

  9. Molecular factors of catalytic selectivity.

    PubMed

    Somorjai, Gabor A; Park, Jeong Y

    2008-01-01

    Selectivity--the production of one molecule out of many other thermodynamically feasible product molecules--is the key concept in developing clean processes that do not produce by-products (green chemistry). Small differences in the potential-energy barriers of single reaction steps control which reaction channel is more likely to yield the desired product molecule (selectivity), while the overall activation energy of the reaction controls the turnover rates (activity). Recent studies have demonstrated that tailoring parameters at the atomic or molecular level--such as the surface structures of active sites--gives turnover rates and reaction selectivities that depend on the nanoparticle size and shape. Here, we highlight seven molecular components that influence the selectivity of heterogeneous catalyst reactions on single-crystal model surfaces and colloid nanoparticles: surface structure, adsorbate-induced restructuring, adsorbate mobility, reaction intermediates, surface composition, charge transport, and oxidation states. We show the importance of the single factors by means of examples and describe in situ analyses that permit their roles in surface reactions to be investigated.

  10. Molecular Photovoltaics in Nanoscale Dimension

    PubMed Central

    Burtman, Vladimir; Zelichonok, Alexander; Pakoulev, Andrei V.

    2011-01-01

    This review focuses on the intrinsic charge transport in organic photovoltaic (PVC) devices and field-effect transistors (SAM-OFETs) fabricated by vapor phase molecular self-assembly (VP-SAM) method. The dynamics of charge transport are determined and used to clarify a transport mechanism. The 1,4,5,8-naphthalene-tetracarboxylic diphenylimide (NTCDI) SAM devices provide a useful tool to study the fundamentals of polaronic transport at organic surfaces and to discuss the performance of organic photovoltaic devices in nanoscale. Time-resolved photovoltaic studies allow us to separate the charge annihilation kinetics in the conductive NTCDI channel from the overall charge kinetic in a SAM-OFET device. It has been demonstrated that tuning of the type of conductivity in NTCDI SAM-OFET devices is possible by changing Si substrate doping. Our study of the polaron charge transfer in organic materials proposes that a cation-radical exchange (redox) mechanism is the major transport mechanism in the studied SAM-PVC devices. The role and contribution of the transport through delocalized states of redox active surface molecular aggregates of NTCDI are exposed and investigated. This example of technological development is used to highlight the significance of future technological development of nanotechnologies and to appreciate a structure-property paradigm in organic nanostructures. PMID:21339983

  11. Molecular Components of Catalytic Selectivity

    SciTech Connect

    Somorjai, Gabor A.; Park, Jeong Y.

    2008-07-02

    Selectivity, that is, to produce one molecule out of many other thermodynamically feasible product molecules, is the key concept to develop 'clean manufacturing' processes that do not produce byproducts (green chemistry). Small differences in potential energy barriers for elementary reaction steps control which reaction channel is more likely to yield the desired product molecule (selectivity), instead of the overall activation energy for the reaction that controls turnover rates (activity). Recent studies have demonstrated the atomic- or molecular-level tailoring of parameters such as the surface structures of active sites that give rise to nanoparticle size and shape dependence of turnover rates and reaction selectivities. Here, we highlight seven molecular components that influence reaction selectivities. These include: surface structure, adsorbate-induced restructuring, adsorbate mobility, reaction intermediates, surface composition, charge transport, and oxidation states for model metal single crystal and colloid nanoparticle catalysts. We show examples of their functioning and describe in-situ instruments that permit us to investigate their roles in surface reactions.

  12. Molecular ingredients of heterogeneous catalysis

    SciTech Connect

    Somorjai, G.A.

    1982-06-01

    The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described.

  13. Molecular dynamics of interface rupture

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  14. Molecular Photovoltaics and Artificial Sight

    NASA Astrophysics Data System (ADS)

    Greenbaum, Elias

    2005-03-01

    The goal of this project is insertion of purified Photosystem I (PSI) reaction centers or other photoactive agents into retinal cells where they will restore photoreceptor function to people who suffer from age-related macular degeneration (AMD) or retinitis pigmentosa (RP), diseases that are the leading causes of blindness world-wide. Although the neural ``wiring'' from eye to brain is intact, these patients lack photoreceptor activity. It is the ultimate goal of this project to restore photoreceptor activity to these patients using PSI as the optical trigger. In principle, the approach should work. PSI is a robust integral membrane molecular photovoltaic device. Depending on orientation, it can depolarize or hyperpolarize the cell membrane with sufficient voltage to trigger an action potential. The first objective of this work, reported here, is to impart photoreceptor activity to mammalian cells using the previously determined molecular photovoltaic properties of isolated Photosystem I reaction centers. Incubation of WERI-Rb-1 retinoblastoma cells with functional PSI reaction centers that were isolated from spinach leaves and reconstituted into proteoliposomes resulted in a light-induced PSI-dependent increase in intracellular Ca^2+. The increase, due to Ca^2+ uptake, was dependent on the presence of extracellular Ca^2+ ions.

  15. Molecular mobility in glassy dispersions

    NASA Astrophysics Data System (ADS)

    Mehta, Mehak; McKenna, Gregory B.; Suryanarayanan, Raj

    2016-05-01

    Dielectric spectroscopy was used to characterize the structural relaxation in pharmaceutical dispersions containing nifedipine (NIF) and either poly(vinyl) pyrrolidone (PVP) or hydroxypropyl methylcellulose acetate succinate (HPMCAS). The shape of the dielectric response (permittivity versus log time) curve was observed to be independent of temperature. Thus, for the pure NIF as well as the dispersions, the validity of the time-temperature superposition principle was established. Furthermore, though the shape of the full dielectric response varied with polymer concentration, the regime related to the α- or structural relaxation was found to superimpose for the dispersions, though not with the response of the NIF itself. Hence, there is a limited time-temperature-concentration superposition for these systems as well. Therefore, in this polymer concentration range, calculation of long relaxation times in these glass-forming systems becomes possible. We found that strong drug-polymer hydrogen bonding interactions improved the physical stability (i.e., delayed crystallization) by reducing the molecular mobility. The strength of hydrogen bonding, structural relaxation time, and crystallization followed the order: NIF-PV P>NIF-HPMCAS>NIF. With an increase in polymer concentration, the relaxation times were longer indicating a decrease in molecular mobility. The temperature dependence of relaxation time, in other words fragility, was independent of polymer concentration. This is the first application of the superposition principle to characterize structural relaxation in glassy pharmaceutical dispersions.

  16. Automated Illustration of Molecular Flexibility.

    PubMed

    Bryden, A; Phillips, George N; Gleicher, M

    2012-01-01

    In this paper, we present an approach to creating illustrations of molecular flexibility using normal mode analysis (NMA). The output of NMA is a collection of points corresponding to the locations of atoms and associated motion vectors, where a vector for each point is known. Our approach abstracts the complex object and its motion by grouping the points, models the motion of each group as an affine velocity, and depicts the motion of each group by automatically choosing glyphs such as arrows. Affine exponentials allow the extrapolation of nonlinear effects such as near rotations and spirals from the linear velocities. Our approach automatically groups points by finding sets of neighboring points whose motions fit the motion model. The geometry and motion models for each group are used to determine glyphs that depict the motion, with various aspects of the motion mapped to each glyph. We evaluated the utility of our system in real work done by structural biologists both by utilizing it in our own structural biology work and quantitatively measuring its usefulness on a set of known protein conformation changes. Additionally, in order to allow ourselves and our collaborators to effectively use our techniques we integrated our system with commonly used tools for molecular visualization.

  17. [Molecular biology methods in immunohematology].

    PubMed

    Tournamille, C

    2013-05-01

    The molecular basis of almost all antigens of the 33 blood group systems are known. These knowledge and the advent of the PCR technology have allowed the DNA-based genotyping in order to predict the presence or absence of a blood group antigen on the cell membrane of red blood cells. DNA genotyping is required in cases where red blood cells patient cannot be used for serological typing either after a recent transfusion or because of the presence of autoantibodies on the red blood cells. Numerous DNA assays are available to detect any nucleotide polymorphism on the genes encoding blood group antigens. The technologies have improved to answer quickly to any case of transfusion emergency and to limit the risk of DNA contamination in a molecular diagnostic laboratory. Some technologies are ready for high-throughput blood group genotyping. They will be used in the future to obtain a fully typed blood group card of each donor but also to detect blood donors with rare phenotypes to register them to the Banque Nationale de Sang de Phénotype Rare (BNSPR).

  18. Molecular Nanotechnology and Space Settlement

    NASA Technical Reports Server (NTRS)

    Globus, Al; Saini, Subhash (Technical Monitor)

    1998-01-01

    Atomically precise manipulation of matter is becoming increasingly common in laboratories around the world. As this control moves into aerospace systems, huge improvements in computers, high-strength materials, and other systems are expected. For example, studies suggest that it may be possible to build: 10(exp 18) MIPS computers, 10(exp 15) bytes/sq cm write once memory, $153-412/kg-of-cargo single- stage-to-orbit launch vehicles and active materials which sense their environment and react intelligently. All of NASA's enterprises should benefit significantly from molecular nanotechnology. Although the time may be measured in decades and the precise path to molecular nanotechnology is unclear, all paths (diamondoid, fullerene, self-assembly, biomolecular, etc.) will require very substantial computation. This talk will discuss fullerene nanotechnology and early work on hypothetical active materials consisting of large numbers of identical machines. The speaker will also discuss aerospace applications, particularly missions leading to widespread space settlement (e.g., small near-Earth - object retrieval). It is interesting to note that control of the tiny - individual atoms and molecules - may lead to colonization of the huge -first the solar system, then the galaxy.

  19. Tectonic blocks and molecular clocks

    PubMed Central

    2016-01-01

    Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325840

  20. Fragmentation in filamentary molecular clouds

    NASA Astrophysics Data System (ADS)

    Contreras, Yanett; Garay, Guido; Rathborne, Jill M.; Sanhueza, Patricio

    2016-02-01

    Recent surveys of dust continuum emission at sub-mm wavelengths have shown that filamentary molecular clouds are ubiquitous along the Galactic plane. These structures are inhomogeneous, with overdensities that are sometimes associated with infrared emission and active of star formation. To investigate the connection between filaments and star formation, requires an understanding of the processes that lead to the fragmentation of filaments and a determination of the physical properties of the overdensities (clumps). In this paper, we present a multiwavelength study of five filamentary molecular clouds, containing several clumps in different evolutionary stages of star formation. We analyse the fragmentation of the filaments and derive the physical properties of their clumps. We find that the clumps in all filaments have a characteristic spacing consistent with the prediction of the `sausage' instability theory, regardless of the complex morphology of the filaments or their evolutionary stage. We also find that most clumps have sufficient mass and density to form high-mass stars, supporting the idea that high-mass stars and clusters form within filaments.

  1. Herschel and the Molecular Universe

    NASA Technical Reports Server (NTRS)

    Tielens, A. G. G. M.; Helmich, F. P.

    2006-01-01

    Over the next decade, space-based missions will open up the universe to high spatial and spectral resolution studies at infrared and submillimeter wavelengths. This will allow us to study, in much greater detail, the composition and the origin and evolution of molecules in space. Moreover, molecular transitions in these spectral ranges provide a sensitive probe of the dynamics and the physical and chemical conditions in a wide range of objects at scales ranging from budding planetary systems to galactic and extragalactic sizes. Hence, these missions provide us with the tools to study key astrophysical and astrochemical processes involved in the formation and evolution of planets, stars, and galaxies. These new missions can be expected to lead to the detection of many thousands of new spectral features. Identification, analysis and interpretation of these features in terms of the physical and chemical characteristics of the astronomical sources will require detailed astronomical modeling tools supported by laboratory measurements and theoretical studies of chemical reactions and collisional excitation rates on species of astrophysical relevance. These data will have to be made easily accessible to the scientific community through web-based data archives. In this paper, we will review the Herschel mission and its expected impact on our understanding of the molecular universe.

  2. Molecular signatures of vaccine adjuvants.

    PubMed

    Olafsdottir, Thorunn; Lindqvist, Madelene; Harandi, Ali M

    2015-09-29

    Mass vaccination has saved millions of human lives and improved the quality of life in both developing and developed countries. The emergence of new pathogens and inadequate protection conferred by some of the existing vaccines such as vaccines for tuberculosis, influenza and pertussis especially in certain age groups have resulted in a move from empirically developed vaccines toward more pathogen tailored and rationally engineered vaccines. A deeper understanding of the interaction of innate and adaptive immunity at molecular level enables the development of vaccines that selectively target certain type of immune responses without excessive reactogenicity. Adjuvants constitute an imperative element of modern vaccines. Although a variety of candidate adjuvants have been evaluated in the past few decades, only a limited number of vaccine adjuvants are currently available for human use. A better understanding of the mode of action of adjuvants is pivotal to harness the potential of existing and new adjuvants in shaping a desired immune response. Recent advancement in systems biology powered by the emerging cutting edge omics technology has led to the identification of molecular signatures rapidly induced after vaccination in the blood that correlate and predict a later protective immune response or vaccine safety. This can pave ways to prospectively determine the potency and safety of vaccines and adjuvants. This review is intended to highlight the importance of big data analysis in advancing our understanding of the mechanisms of actions of adjuvants to inform rational development of future human vaccines.

  3. Exciton dispersion in molecular solids.

    PubMed

    Cudazzo, Pierluigi; Sottile, Francesco; Rubio, Angel; Gatti, Matteo

    2015-03-25

    The investigation of the exciton dispersion (i.e. the exciton energy dependence as a function of the momentum carried by the electron-hole pair) is a powerful approach to identify the exciton character, ranging from the strongly localised Frenkel to the delocalised Wannier-Mott limiting cases. We illustrate this possibility at the example of four prototypical molecular solids (picene, pentacene, tetracene and coronene) on the basis of the parameter-free solution of the many-body Bethe-Salpeter equation. We discuss the mixing between Frenkel and charge-transfer excitons and the origin of their Davydov splitting in the framework of many-body perturbation theory and establish a link with model approaches based on molecular states. Finally, we show how the interplay between the electronic band dispersion and the exchange electron-hole interaction plays a fundamental role in setting the nature of the exciton. This analysis has a general validity holding also for other systems in which the electron wavefunctions are strongly localized, as in strongly correlated insulators.

  4. Exciton dispersion in molecular solids

    NASA Astrophysics Data System (ADS)

    Cudazzo, Pierluigi; Sottile, Francesco; Rubio, Angel; Gatti, Matteo

    2015-03-01

    The investigation of the exciton dispersion (i.e. the exciton energy dependence as a function of the momentum carried by the electron-hole pair) is a powerful approach to identify the exciton character, ranging from the strongly localised Frenkel to the delocalised Wannier-Mott limiting cases. We illustrate this possibility at the example of four prototypical molecular solids (picene, pentacene, tetracene and coronene) on the basis of the parameter-free solution of the many-body Bethe-Salpeter equation. We discuss the mixing between Frenkel and charge-transfer excitons and the origin of their Davydov splitting in the framework of many-body perturbation theory and establish a link with model approaches based on molecular states. Finally, we show how the interplay between the electronic band dispersion and the exchange electron-hole interaction plays a fundamental role in setting the nature of the exciton. This analysis has a general validity holding also for other systems in which the electron wavefunctions are strongly localized, as in strongly correlated insulators.

  5. Targeted Molecular Therapies for SBMA.

    PubMed

    Rinaldi, Carlo; Malik, Bilal; Greensmith, Linda

    2016-03-01

    Spinal and bulbar muscular atrophy (SBMA) is a late-onset neuromuscular disease caused by a polyglutamine expansion in the androgen receptor gene which results in progressive spinal and bulbar motor neuron degeneration, and muscle atrophy. Although the causative genetic defect is known, until recently, the molecular pathogenesis of the disease was unclear, resulting in few, if any, targets for therapy development. However, over the past decade, our understanding of the pathomechanisms that play a role in SBMA has increased dramatically, and several of these pathways and mechanisms have now been investigated as possible therapeutic targets. In this review, we discuss some of the key pathomechanisms implicated in SBMA and describe some of the therapeutic strategies that have been tested in SBMA to date, which fall into four main categories: (i) gene silencing; (ii) protein quality control and/or increased protein degradation; (iii) androgen deprivation; and (iv) modulation of AR function. Finally, it is also now clear that in addition to a greater understanding of the molecular mechanisms that underlie disease, the development of an effective disease modifying therapy for SBMA will require the coordinated, collaborative effort of research teams with diverse areas of expertise, clinicians, pharmaceutical companies as well as patient groups.

  6. Antagonistic coevolution accelerates molecular evolution

    PubMed Central

    Paterson, Steve; Vogwill, Tom; Buckling, Angus; Benmayor, Rebecca; Spiers, Andrew J.; Thomson, Nicholas R.; Quail, Mike; Smith, Frances; Walker, Danielle; Libberton, Ben; Fenton, Andrew; Hall, Neil; Brockhurst, Michael A.

    2013-01-01

    The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation1–3. Although the divergence observed at some host-resistance4–6 and parasite-infectivity7–9 genes is consistent with this, the long time periods typically required to study coevolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Φ2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species. PMID:20182425

  7. Iridates from the molecular side

    NASA Astrophysics Data System (ADS)

    Pedersen, Kasper S.; Bendix, Jesper; Tressaud, Alain; Durand, Etienne; Weihe, Høgni; Salman, Zaher; Morsing, Thorbjørn J.; Woodruff, Daniel N.; Lan, Yanhua; Wernsdorfer, Wolfgang; Mathonière, Corine; Piligkos, Stergios; Klokishner, Sophia I.; Ostrovsky, Serghei; Ollefs, Katharina; Wilhelm, Fabrice; Rogalev, Andrei; Clérac, Rodolphe

    2016-07-01

    New exotic phenomena have recently been discovered in oxides of paramagnetic Ir4+ ions, widely known as `iridates'. Their remarkable properties originate from concerted effects of the crystal field, magnetic interactions and strong spin-orbit coupling, characteristic of 5d metal ions. Despite numerous experimental reports, the electronic structure of these materials is still challenging to elucidate, and not attainable in the isolated, but chemically inaccessible, [IrO6]8- species (the simplest molecular analogue of the elementary {IrO6}8- fragment present in all iridates). Here, we introduce an alternative approach to circumvent this problem by substituting the oxide ions in [IrO6]8- by isoelectronic fluorides to form the fluorido-iridate: [IrF6]2-. This molecular species has the same electronic ground state as the {IrO6}8- fragment, and thus emerges as an ideal model for iridates. These results may open perspectives for using fluorido-iridates as building-blocks for electronic and magnetic quantum materials synthesized by soft chemistry routes.

  8. Carbon Nanotube Based Molecular Electronics

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1998-01-01

    Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

  9. Molecular mobility in glassy dispersions.

    PubMed

    Mehta, Mehak; McKenna, Gregory B; Suryanarayanan, Raj

    2016-05-28

    Dielectric spectroscopy was used to characterize the structural relaxation in pharmaceutical dispersions containing nifedipine (NIF) and either poly(vinyl) pyrrolidone (PVP) or hydroxypropyl methylcellulose acetate succinate (HPMCAS). The shape of the dielectric response (permittivity versus log time) curve was observed to be independent of temperature. Thus, for the pure NIF as well as the dispersions, the validity of the time-temperature superposition principle was established. Furthermore, though the shape of the full dielectric response varied with polymer concentration, the regime related to the α- or structural relaxation was found to superimpose for the dispersions, though not with the response of the NIF itself. Hence, there is a limited time-temperature-concentration superposition for these systems as well. Therefore, in this polymer concentration range, calculation of long relaxation times in these glass-forming systems becomes possible. We found that strong drug-polymer hydrogen bonding interactions improved the physical stability (i.e., delayed crystallization) by reducing the molecular mobility. The strength of hydrogen bonding, structural relaxation time, and crystallization followed the order: NIF-PV P>NIF-HPMCAS>NIF. With an increase in polymer concentration, the relaxation times were longer indicating a decrease in molecular mobility. The temperature dependence of relaxation time, in other words fragility, was independent of polymer concentration. This is the first application of the superposition principle to characterize structural relaxation in glassy pharmaceutical dispersions.

  10. Molecular mobility in glassy dispersions

    SciTech Connect

    Mehta, Mehak; McKenna, Gregory B.; Suryanarayanan, Raj

    2016-05-27

    Dielectric spectroscopy was used to characterize the structural relaxation in pharmaceutical dispersions containing nifedipine (NIF) and either poly(vinyl) pyrrolidone (PVP) or hydroxypropyl methylcellulose acetate succinate (HPMCAS). The shape of the dielectric response (permittivity versus log time) curve was observed to be independent of temperature. Thus, for the pure NIF as well as the dispersions, the validity of the time-temperature superposition principle was established. Furthermore, though the shape of the full dielectric response varied with polymer concentration, the regime related to the α- or structural relaxation was found to superimpose for the dispersions, though not with the response of the NIF itself. Hence, there is a limited time-temperature-concentration superposition for these systems as well. Therefore, in this polymer concentration range, calculation of long relaxation times in these glass-forming systems becomes possible. We found that strong drug-polymer hydrogen bonding interactions improved the physical stability (i.e., delayed crystallization) by reducing the molecular mobility. The strength of hydrogen bonding, structural relaxation time, and crystallization followed the order: NIF$-$PV P>NIF$-$HPMCAS>NIF. With an increase in polymer concentration, the relaxation times were longer indicating a decrease in molecular mobility. The temperature dependence of relaxation time, in other words fragility, was independent of polymer concentration. This is the first application of the superposition principle to characterize structural relaxation in glassy pharmaceutical dispersions.

  11. Molecular phylogeny of Arthrotardigrada (Tardigrada).

    PubMed

    Jørgensen, Aslak; Faurby, Søren; Hansen, Jesper G; Møbjerg, Nadja; Kristensen, Reinhardt M

    2010-03-01

    Tardigrades are microscopic ecdysozoans with a worldwide distribution covering marine, limnic and terrestrial habitats. They are regarded as a neglected phylum with regard to studies of their phylogeny. During the last decade molecular data have been included in the investigation of tardigrades. However, the marine arthrotardigrades are still poorly sampled due to their relative rarity, difficult identification and minute size even for tardigrades. In the present study, we have sampled various arthrotardigrades and sequenced the 18S and partial 28S ribosomal subunits. The phylogenetic analyses based on Bayesian inference and maximum parsimony inferred Heterotardigrada (Arthrotardigrada+Echiniscoidea) and Eutardigrada to be monophyletic. Arthrotardigrada was inferred to be paraphyletic as the monophyletic Echiniscoidea is included within the arthrotardigrades. The phylogenetic positions of Stygarctidae and Batillipedidae are poorly resolved with low branch support. The Halechiniscidae is inferred to be polyphyletic as the currently recognized Styraconyxinae is not part of the family. Archechiniscus is the sister-group to the Halechiniscidae and Orzeliscus is placed as one of the basal halechiniscids. The phylogeny of the included eutardigrade taxa resembles the current molecular phylogenies. The genetic diversity within Arthrotardigrada is much larger (18S 15.1-26.5%, 28S 7.2-20.7%) than within Eutardigrada (18S 1.0-12.6%, 28S 1.3-8.2%). This can be explained by higher substitution rates in the arthrotardigrades or by a much younger evolutionary age of the sampled eutardigrades.

  12. Molecular Typing of Borrelia burgdorferi.

    PubMed

    Wang, Guiqing; Liveris, Dionysios; Mukherjee, Priyanka; Jungnick, Sabrina; Margos, Gabriele; Schwartz, Ira

    2014-08-01

    Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens.

  13. Multipose binding in molecular docking.

    PubMed

    Atkovska, Kalina; Samsonov, Sergey A; Paszkowski-Rogacz, Maciej; Pisabarro, M Teresa

    2014-02-14

    Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

  14. Molecular Organization of Vomeronasal Chemoreception

    PubMed Central

    Isogai, Yoh; Si, Sheng; Pont-Lezica, Lorena; Tan, Taralyn; Kapoor, Vikrant; Murthy, Venkatesh N.; Dulac, Catherine

    2011-01-01

    The vomeronasal organ (VNO) plays a key role in mediating the social and defensive responses of many terrestrial vertebrates to species- and sex-specific chemosignals1. Over 250 putative pheromone receptors have been identified in the mouse VNO2,3, but the nature of the signals detected by individual VNO receptors has not yet been elucidated. In order to gain insight into the molecular logic of VNO detection leading to mating, aggression, or defensive responses, we sought to uncover the response profiles of individual vomeronasal receptors to a wide range of animal cues. We describe here the repertoire of ethological and physiological stimuli detected by a large number of individual vomeronasal receptors, and define a global map of vomeronasal signal detection. We demonstrate that the two classes of vomeronasal receptors V1Rs and V2Rs use fundamentally different strategies to encode chemosensory information, and that distinct receptor subfamilies have evolved towards the specific recognition of certain animal groups or chemical structures. The association of large subsets of vomeronasal receptors with cognate, ethologically and physiologically relevant stimuli establishes the molecular foundation of vomeronasal information coding, and opens new avenues for further investigating the neural mechanisms underlying behavior specificity. PMID:21937988

  15. Iridates from the molecular side

    PubMed Central

    Pedersen, Kasper S.; Bendix, Jesper; Tressaud, Alain; Durand, Etienne; Weihe, Høgni; Salman, Zaher; Morsing, Thorbjørn J; Woodruff, Daniel N.; Lan, Yanhua; Wernsdorfer, Wolfgang; Mathonière, Corine; Piligkos, Stergios; Klokishner, Sophia I.; Ostrovsky, Serghei; Ollefs, Katharina; Wilhelm, Fabrice; Rogalev, Andrei; Clérac, Rodolphe

    2016-01-01

    New exotic phenomena have recently been discovered in oxides of paramagnetic Ir4+ ions, widely known as ‘iridates'. Their remarkable properties originate from concerted effects of the crystal field, magnetic interactions and strong spin-orbit coupling, characteristic of 5d metal ions. Despite numerous experimental reports, the electronic structure of these materials is still challenging to elucidate, and not attainable in the isolated, but chemically inaccessible, [IrO6]8– species (the simplest molecular analogue of the elementary {IrO6}8− fragment present in all iridates). Here, we introduce an alternative approach to circumvent this problem by substituting the oxide ions in [IrO6]8− by isoelectronic fluorides to form the fluorido-iridate: [IrF6]2−. This molecular species has the same electronic ground state as the {IrO6}8− fragment, and thus emerges as an ideal model for iridates. These results may open perspectives for using fluorido-iridates as building-blocks for electronic and magnetic quantum materials synthesized by soft chemistry routes. PMID:27435800

  16. Mimicking Temperature Through Molecular Machines

    NASA Astrophysics Data System (ADS)

    Smith, David; Käs, Josef

    2003-03-01

    All eukaryotic cells depend on mechanisms of self-assembly of protein filaments to form a cytoskeleton within the cell. The need for motility and reaction by cells to stimuli additionally requires the existence of pathways which serve to restructure and disassemble cytoskeletal structures. Temperature-driven increases in disorder are the most physically fundamental method for breaking down complex structures, yet would play a destructive role in cellular dynamics. A similar situation is seen on the genetic level with the unfolding of DNA strands for replication and cell division - while temperature-driven unfolding of the strands stands as the most simple pathway, molecular machinery are present to perform the same function without heat-induced damage to the cell (Lodish et al, 2000). We report experimental evidence of a similar mechanism functioning on actin cytoskeletal dynamics, involving collections of the actin-specific molecular motor Myosin II. While crosslink-driven bundling self-assembles complex actomyosin structures (including bundles, asters, and large aggregates) in the near-chemical-equilibrum state, an activation of the motors causes a rapid disassembly of all structures. Such a mechanism is not only harmless to cell function, but occurs on a very rapid timescale which is favorable for quick cytoskeletal dynamics.

  17. Abstract models of molecular walkers

    NASA Astrophysics Data System (ADS)

    Semenov, Oleg

    Recent advances in single-molecule chemistry have led to designs for artificial multi-pedal walkers that follow tracks of chemicals. The walkers, called molecular spiders, consist of a rigid chemically inert body and several flexible enzymatic legs. The legs can reversibly bind to chemical substrates on a surface, and through their enzymatic action convert them to products. We study abstract models of molecular spiders to evaluate how efficiently they can perform two tasks: molecular transport of cargo over tracks and search for targets on finite surfaces. For the single-spider model our simulations show a transient behavior wherein certain spiders move superdiffusively over significant distances and times. This gives the spiders potential as a faster-than-diffusion transport mechanism. However, analysis shows that single-spider motion eventually decays into an ordinary diffusive motion, owing to the ever increasing size of the region of products. Inspired by cooperative behavior of natural molecular walkers, we propose a symmetric exclusion process (SEP) model for multiple walkers interacting as they move over a one-dimensional lattice. We show that when walkers are sequentially released from the origin, the collective effect is to prevent the leading walkers from moving too far backwards. Hence, there is an effective outward pressure on the leading walkers that keeps them moving superdiffusively for longer times. Despite this improvement the leading spider eventually slows down and moves diffusively, similarly to a single spider. The slowdown happens because all spiders behind the leading spiders never encounter substrates, and thus they are never biased. They cannot keep up with leading spiders, and cannot put enough pressure on them. Next, we investigate search properties of a single and multiple spiders moving over one- and two-dimensional surfaces with various absorbing and reflecting boundaries. For the single-spider model we evaluate by how much the

  18. The merger of electrochemistry and molecular electronics.

    PubMed

    McCreery, Richard L

    2012-02-01

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

  19. Molecular clumps in the W51 giant molecular cloud

    NASA Astrophysics Data System (ADS)

    Parsons, H.; Thompson, M. A.; Clark, J. S.; Chrysostomou, A.

    2012-08-01

    In this paper, we present a catalogue of dense molecular clumps located within the W51 giant molecular cloud (GMC). This work is based on Heterodyne Array Receiver Programme 13CO J = 3-2 observations of the W51 GMC and uses the automated CLUMPFIND algorithm to decompose the region into a total of 1575 clumps of which 1130 are associated with the W51 GMC. We clearly see the distinct structures of the W51 complex and the high-velocity stream previously reported. We find the clumps have characteristic diameters of 1.4 pc, excitation temperatures of 12 K, densities of 5.6 × 1021 cm-2, surface densities 0.02 g cm-2 and masses of 90 M⊙. We find a total mass of dense clumps within the GMC of 1.5 × 105 M⊙, with only 1 per cent of the clumps detected by number and 4 per cent by mass found to be supercritical. We find a clump-forming efficiency of 14 ± 1 per cent for the W51 GMC and a supercritical clump-forming efficiency of 0.5-0.5+2.3 per cent. Looking at the clump mass distribution, we find it is described by a single power law with a slope of α=2.4-0.1+0.2 above ˜100 M⊙. By comparing locations of supercritical clumps and young clusters, we see that any future star formation is likely to be located away from the currently active W51A region.

  20. Molecular design and QSARs/QSPRs with molecular descriptors family.

    PubMed

    Bolboacă, Sorana D; Jäntschi, Lorentz; Diudea, Mircea V

    2013-06-01

    The aim of the present paper is to present the methodology of the molecular descriptors family (MDF) as an integrative tool in molecular modeling and its abilities as a multivariate QSAR/QSPR modeling tool. An algorithm for extracting useful information from the topological and geometrical representation of chemical compounds was developed and integrated to calculate MDF members. The MDF methodology was implemented and the software is available online (http://l.academicdirect.org/Chemistry/SARs/MDF_SARs/). This integrative tool was developed in order to maximize performance, functionality, efficiency and portability. The MDF methodology is able to provide reliable and valid multiple linear regression models. Furthermore, in many cases, the MDF models were better than the published results in the literature in terms of correlation coefficients (statistically significant Steiger's Z test at a significance level of 5%) and/or in terms of values of information criteria and Kubinyi function. The MDF methodology developed and implemented as a platform for investigating and characterizing quantitative relationships between the chemical structure and the activity/property of active compounds was used on more than 50 study cases. In almost all cases, the methodology allowed obtaining of QSAR/QSPR models improved in explanatory power of structure-activity and structure-property relationships. The algorithms applied in the computation of geometric and topological descriptors (useful in modeling physicochemical or biological properties of molecules) and those used in searching for reliable and valid multiple linear regression models certain enrich the pool of low-cost low-time drug design tools.

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

    PubMed

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

    2016-03-01

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

  2. Molecular imaging with theranostic nanoparticles.

    PubMed

    Jokerst, Jesse V; Gambhir, Sanjiv S

    2011-10-18

    Nanoparticles (NPs) offer diagnostic and therapeutic capabilities not available with small molecules or microscale tools. As the field of molecular imaging has emerged from the blending of molecular biology with medical imaging, NP imaging is increasingly common for both therapeutic and diagnostic applications. The term theranostic describes technology with concurrent and complementary diagnostic and therapeutic capabilities. Although NPs have been FDA-approved for clinical use as transport vehicles for nearly 15 years, full translation of their theranostic potential is incomplete. However, NPs have shown remarkable success in the areas of drug delivery and magnetic resonance imaging. Emerging applications include image-guided resection, optical/photoacoustic imaging in vivo, contrast-enhanced ultrasound, and thermoablative therapy. Diagnosis with NPs in molecular imaging involves the correlation of the signal with a phenotype. The location and intensity of NP signals emanating from a living subject indicate the disease area's size, stage, and biochemical signature. Therapy with NPs uses the image for resection or delivery of a small molecule or RNA therapeutic. Ablation of the affected area is also possible via heat or radioactivity. The ideal theranostic NP includes several features: (1) it selectively and rapidly accumulates in diseased tissue; (2) it reports biochemical and morphological characteristics of the area; (3) it delivers an effective therapeutic; and (4) it is safe and biodegrades with nontoxic byproducts. Such a system contains a central imaging core surrounded by small molecule therapeutics. The system targets via ligands such as IgG and is protected from immune scavengers by a cloak of protective polymer. Although no NP has achieved all of the above criteria, many NPs possess one or more of these features. While the most clinically translatable NPs have been used in the field of magnetic resonance imaging, other types in development are quickly

  3. Molecular Signaling in Muscle Plasticity

    NASA Technical Reports Server (NTRS)

    Epstein, Henry F.

    1999-01-01

    Extended spaceflight under microgravity conditions leads to significant atrophy of weight-bearing muscles. Atrophy and hypertrophy are the extreme outcomes of the high degree of plasticity exhibited by skeletal muscle. Stimuli which control muscle plasticity include neuronal, hormonal, nutritional, and mechanical inputs. The mechanical stimulus for muscle is directly related to the work or exercise against a load performed. Little or no work is performed by weight-bearing muscles under microgravity conditions. A major hypothesis is that focal adhesion kinase (FAK) which is associated with integrin at the adherens junctions and costa meres of all skeletal muscles is an integral part of the major mechanism for molecular signaling upon mechanical stimulation in all muscle fibers. Additionally, we propose that myotonic protein kinase (DMPK) and dystrophin (DYSTR) also participate in distinct mechanically stimulated molecular signaling pathways that are most critical in type I and type II muscle fibers, respectively. To test these hypotheses, we will use the paradigms of hindlimb unloading and overloading in mice as models for microgravity conditions and a potential exercise countermeasure, respectively, in mice. We expect that FAK loss-of-function will impair hypertrophy and enhance atrophy in all skeletal muscle fibers whereas DYSTR and DMPK loss-of-function will have similar but more selective effects on Type IT and Type I fibers, respectively. Gene expression will be monitored by muscle-specific creatine kinase M promoter-reporter construct activity and specific MRNA and protein accumulation in the soleus (type I primarily) and plantaris (type 11 primarily) muscles. With these paradigms and assays, the following Specific Project Aims will be tested in genetically altered mice: 1) identify the roles of DYSTR and its pathway; 2) evaluate the roles of the DMPK and its pathway; 3) characterize the roles of FAK and its pathway and 4) genetically analyze the mechanisms

  4. Molecular chirality: language, history, and significance.

    PubMed

    Gal, Joseph

    2013-01-01

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

  5. Establishing molecular microbiology facilities in developing countries.

    PubMed

    Ahmed, Salman S; Alp, Emine; Ulu-Kilic, Aysegul; Doganay, Mehmet

    2015-01-01

    Microbiology laboratories play an important role in epidemiology and infection control programs. Within microbiology laboratories, molecular microbiology techniques have revolutionized the identification and surveillance of infectious diseases. The combination of excellent sensitivity, specificity, low contamination levels and speed has made molecular techniques appealing methods for the diagnosis of many infectious diseases. In a well-equipped microbiology laboratory, the facility designated for molecular techniques remains indiscrete. However, in most developing countries, poor infrastructure and laboratory mismanagement have precipitated hazardous consequences. The establishment of a molecular microbiology facility within a microbiology laboratory remains fragmented. A high-quality laboratory should include both conventional microbiology methods and molecular microbiology techniques for exceptional performance. Furthermore, it should include appropriate laboratory administration, a well-designed facility, laboratory procedure standardization, a waste management system, a code of practice, equipment installation and laboratory personnel training. This manuscript lays out fundamental issues that need to be addressed when establishing a molecular microbiology facility in developing countries.

  6. Introduction to methods in molecular cardiology.

    PubMed

    Sun, Zhongjie

    2005-01-01

    Molecular cardiology is a new area of cardiovascular medicine that aims to apply molecular biological techniques for the mechanistic investigation, diagnosis, prevention, and treatment of cardiovascular disease. As an emerging discipline, it has changed our conceptual thinking of cardiovascular development, disease etiology, and pathophysiology. Although molecular cardiology is still at a very early stage, it has opened a promising avenue for understanding and controlling cardiovascular disease. With the rapid development and application of molecular biological techniques, scientists and clinicians are closer to curing heart diseases that were thought to be incurable 20 yr ago. There clearly is a need for a more thorough understanding of the molecular mechanisms of cardiovascular diseases to promote the advancement of cell and gene therapy for heart diseases. This chapter briefly reviews state-of-the-art techniques in the area of molecular cardiology.

  7. Small business development for molecular diagnostics.

    PubMed

    Anagostou, Anthanasia; Liotta, Lance A

    2012-01-01

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

  8. Effect of molecular weight on polyphenylquinoxaline properties

    NASA Technical Reports Server (NTRS)

    Jensen, Brian J.

    1991-01-01

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

  9. Molecular pharmacognosy: a new borderline discipline.

    PubMed

    Huang, Lu-Qi; Yuan, Yuan; Cui, Guang-Hong; Dai, Zhu-Bo; Xiao, Pei-Gen

    2009-11-01

    Pharmacognosy has developed rapidly in recent years and now represents a highly interdisciplinary science. At the boundary between pharmacognosy and molecular biology, molecular pharmacognosy has developed as a new borderline discipline. Using the method and technology of molecular biology, molecular pharmacognosy focuses on resolving a wide range of challenging problems, such as distinguishing herbal and animal drug populations by molecular marker assay, conserving and utilizing wild resources on the basis of knowledge of genetic diversity, investigating the mechanism of active compound accumulation and obtaining new resources with higher quality through genetic engineering. Recent research results show that molecular pharmacognosy has extended the scope of pharmacognostical science and plays an important role in the safe and efficient usage of crude drugs.

  10. Molecular mechanisms of cryptococcal meningitis.

    PubMed

    Liu, Tong-Bao; Perlin, David S; Xue, Chaoyang

    2012-01-01

    Fungal meningitis is a serious disease caused by a fungal infection of the central nervous system (CNS) mostly in individuals with immune system deficiencies. Fungal meningitis is often fatal without proper treatment, and the mortality rate remains unacceptably high even with antifungal drug interventions. Currently, cryptococcal meningitis is the most common fungal meningitis in HIV-1/AIDS, and its disease mechanism has been extensively studied. The key steps for fungi to infect brain and cause meningitis after establishment of local infection are the dissemination of fungal cells to the bloodstream and invasion through the blood brain barrier to reach the CNS. In this review, we use cryptococcal CNS infection as an example to describe the current molecular understanding of fungal meningitis, including the establishment of the infection, dissemination, and brain invasion. Host and microbial factors that contribute to these infection steps are also discussed.

  11. Fluorescence applications in molecular neurobiology.

    PubMed

    Taraska, Justin W; Zagotta, William N

    2010-04-29

    Macromolecules drive the complex behavior of neurons. For example, channels and transporters control the movements of ions across membranes, SNAREs direct the fusion of vesicles at the synapse, and motors move cargo throughout the cell. Understanding the structure, assembly, and conformational movements of these and other neuronal proteins is essential to understanding the brain. Developments in fluorescence have allowed the architecture and dynamics of proteins to be studied in real time and in a cellular context with great accuracy. In this review, we cover classic and recent methods for studying protein structure, assembly, and dynamics with fluorescence. These methods include fluorescence and luminescence resonance energy transfer, single-molecule bleaching analysis, intensity measurements, colocalization microscopy, electron transfer, and bimolecular complementation analysis. We present the principles of these methods, highlight recent work that uses the methods, and discuss a framework for interpreting results as they apply to molecular neurobiology.

  12. Theoretical studies of molecular collisions

    NASA Technical Reports Server (NTRS)

    Kouri, Donald J.

    1991-01-01

    The following subject areas are covered: (1) total integral reactive cross sections and vibrationally resolved reaction probabilities for F + H2 = HF + H; (2) a theoretical study of inelastic O + N2 collisions; (3) body frame close coupling wave packet approach to gas phase atom-rigit rotor inelastic collisions; (4) wave packet study of gas phase atom-rigit motor scattering; (5) the application of optical potentials for reactive scattering; (6) time dependent, three dimensional body frame quantal wave packet treatment of the H + H2 exchange reaction; (7) a time dependent wave packet approach to atom-diatom reactive collision probabilities; (8) time dependent wave packet for the complete determination of s-matrix elements for reactive molecular collisions in three dimensions; (9) a comparison of three time dependent wave packet methods for calculating electron-atom elastic scattering cross sections; and (10) a numerically exact full wave packet approach to molecule-surface scattering.

  13. Photoelectron spectroscopy of molecular clusters

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Pitts, Jonathan; Zheng, Chaowen; Knee, Joseph L.

    1995-09-01

    High resolution photoelectron spectroscopy is applied to the study of molecular clusters. The primary species studied are fluorene-Arn complexes. Spectroscopy of the neutral S1 state has been performed on clusters as large as n equals 30. In order to study the photoelectron spectra of the clusters size selectively mass analyzed threshold ionization (MATI) is used which is a mass resolved version of the ZEKE technique. MATI spectroscopy has been applied to clusters up to n equals 5. The spectral shifts in the S1 origin and ion threshold are used as a measure of the relative stability of the different clusters. Using previous experimental and theoretical work on related clusters the structures of the clusters are inferred from the observed spectral shifts. In some cases multiple conformations of a particular cluster size are identified.

  14. Molecular neurobiology of Drosophila taste.

    PubMed

    Freeman, Erica Gene; Dahanukar, Anupama

    2015-10-01

    Drosophila is a powerful model in which to study the molecular and cellular basis of taste coding. Flies sense tastants via populations of taste neurons that are activated by compounds of distinct categories. The past few years have borne witness to studies that define the properties of taste neurons, identifying functionally distinct classes of sweet and bitter taste neurons that express unique subsets of gustatory receptor (Gr) genes, as well as water, salt, and pheromone sensing neurons that express members of the pickpocket (ppk) or ionotropic receptor (Ir) families. There has also been significant progress in terms of understanding how tastant information is processed and conveyed to higher brain centers, and modulated by prior dietary experience or starvation.

  15. Molecular mechanisms of antibiotic resistance.

    PubMed

    Wright, Gerard D

    2011-04-14

    Over the past decade, resistance to antibiotics has emerged as a crisis of global proportion. Microbes resistant to many and even all clinically approved antibiotics are increasingly common and easily spread across continents. At the same time there are fewer new antibiotic drugs coming to market. We are reaching a point where we are no longer able to confidently treat a growing number of bacterial infections. The molecular mechanisms of drug resistance provide the essential knowledge on new drug development and clinical use. These mechanisms include enzyme catalyzed antibiotic modifications, bypass of antibiotic targets and active efflux of drugs from the cell. Understanding the chemical rationale and underpinnings of resistance is an essential component of our response to this clinical challenge.

  16. Molecular and polymeric ceramic precursors

    SciTech Connect

    Sneddon, L.G.

    1991-08-01

    The development of new methods for the production of complex materials is one of the most important problems in modern solid state chemistry and materials science. This project is attempting to apply the synthetic principles which have evolved inorganic and organometallic chemistry to the production of technologically important non-oxide ceramics, such as boron nitride, boron carbide and metal borides. Our recent work has now resulted in the production of new polymer systems, including poly(B-vinylborazine), polyvinylpentaborane and polyborazylene, that have proven to be high yield precursors to boron-based ceramic materials. Current work is now directed toward the synthesis of new types of molecular and polymeric boron-containing species and on exploration of the solid state properties of the ceramics that have been produced in these studies.

  17. Molecular Motion and Confined Polymers

    NASA Astrophysics Data System (ADS)

    Dobrynin, Andrey V.; Jeon, Junhwan

    2004-03-01

    Microorganisms such as myxobacteria, cyanobacteria, and flexibacteria move by gliding. The gliding has been described by two quite different mechanisms: social (S) motility and adventurous (A) motility. Though retraction of type 4-pili provides the force for the S motility, extrusion of slime, which may be associated with the A motility, is not well known. Nozzle-like structures recently found in cyanobacteria can support the A motility. However, complete understaning A motility is still lacking. To describe the A motility, we use molecular dynamics simulations of a polymer growing inside a cylindrically shaped tube with one end capped. Confined polymers provide a driving force for a tube motion as if a rocket flew with emitting gas. It is seen from the mean-squared displacement of a tube that its motion is ballistic under constant applied force.

  18. Molecular regulation of fruit ripening

    PubMed Central

    Osorio, Sonia; Scossa, Federico; Fernie, Alisdair R.

    2013-01-01

    Fruit ripening is a highly coordinated developmental process that coincides with seed maturation. The ripening process is regulated by thousands of genes that control progressive softening and/or lignification of pericarp layers, accumulation of sugars, acids, pigments, and release of volatiles. Key to crop improvement is a deeper understanding of the processes underlying fruit ripening. In tomato, mutations blocking the transition to ripe fruits have provided insights into the role of ethylene and its associated molecular networks involved in the control of ripening. However, the role of other plant hormones is still poorly understood. In this review, we describe how plant hormones, transcription factors, and epigenetic changes are intimately related to provide a tight control of the ripening process. Recent findings from comparative genomics and system biology approaches are discussed. PMID:23785378

  19. Molecular regulation of lumen morphogenesis.

    PubMed

    Datta, Anirban; Bryant, David M; Mostov, Keith E

    2011-02-08

    The asymmetric polarization of cells allows specialized functions to be performed at discrete subcellular locales. Spatiotemporal coordination of polarization between groups of cells allowed the evolution of metazoa. For instance, coordinated apical-basal polarization of epithelial and endothelial cells allows transport of nutrients and metabolites across cell barriers and tissue microenvironments. The defining feature of such tissues is the presence of a central, interconnected luminal network. Although tubular networks are present in seemingly different organ systems, such as the kidney, lung, and blood vessels, common underlying principles govern their formation. Recent studies using in vivo and in vitro models of lumen formation have shed new light on the molecular networks regulating this fundamental process. We here discuss progress in understanding common design principles underpinning de novo lumen formation and expansion.

  20. Molecular biology of epilepsy genes.

    PubMed

    Williams, Charles A; Battaglia, Agatino

    2013-06-01

    Multifactorial inheritance is the most important model accounting for the genetic behavior of the common epilepsies. Important to this model is the concept that many cumulative or synergistic risk genes ultimately lead to a threshold effect. Sophisticated molecular testing indicates that the common epilepsies are very polygenic without evidence of any single gene having even a mild-to-modest risk effect. However, enrichment of copy number variants in cohorts of individuals with epilepsy indicates that certain structural changes in the genome can confer significant risk for epilepsy. The mechanisms whereby copy number variants confer this effect are not yet known. The study of epilepsy due to single gene defects however has helped clarify certain seizure mechanisms. For example, discoveries using animal models of SCN1A or ARX mutations implicate a predominant role for interneurons due to disturbed GABAergic function. It is hoped that future genetic and neurobiological studies will provide better insight into how multiple genes contribute to the common epilepsies.

  1. Non-Equilibrium Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Ciccotti, Giovanni; Kapral, Raymond; Sergi, Alessandro

    Statistical mechanics provides a well-established link between microscopic equilibrium states and thermodynamics. If one considers systems out of equilibrium, the link between microscopic dynamical properties and non-equilibrium macroscopic states is more difficult to establish [1,2]. For systems lying near equilibrium, linear response theory provides a route to derive linear macroscopic laws and the microscopic expressions for the transport properties that enter the constitutive relations. If the system is displaced far from equilibrium, no fully general theory exists to treat such systems. By restricting consideration to a class of non-equilibrium states which arise from perturbations (linear or non-linear) of an equilibrium state, methods can be developed to treat non-equilibrium states. Furthermore, non-equilibrium molecular dynamics (NEMD) simulation methods can be devised to provide estimates for the transport properties of these systems.

  2. [Molecular diagnosis of autoimmune dermatoses].

    PubMed

    Hoffmann, K; Hertl, M; Sitaru, C

    2016-01-01

    Bullous autoimmune diseases are organ-specific disorders characterized by an autoantibody-mediated blistering of skin and mucous membranes. The detection of tissue-bound and serum autoantibodies is prerequisite for the diagnosis of autoimmune blistering diseases. The individual entities of this group may be difficult to differentiate on clinical grounds alone. An accurate diagnosis is however important for prognosis and therapy. A preliminary diagnostic step includes direct and indirect immunofluorescence microscopy, which provide information about the binding pattern and isotype of autoantibodies and allow the diagnosis of the autoimmune blistering disease. Subsequent characterization of the molecular specificity of autoantibodies is necessary for the exact classification of autoimmune bullous dermatoses. The quantitative measurement of autoantibodies against structural proteins of the skin may be often used to assess disease severity at follow-up.

  3. Elasticity of crystalline molecular explosives

    DOE PAGES

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; ...

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, andmore » an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.« less

  4. Anticancer Molecular Mechanisms of Resveratrol

    PubMed Central

    Varoni, Elena M.; Lo Faro, Alfredo Fabrizio; Sharifi-Rad, Javad; Iriti, Marcello

    2016-01-01

    Resveratrol is a pleiotropic phytochemical belonging to the stilbene family. Though it is only significantly present in grape products, a huge amount of preclinical studies investigated its anticancer properties in a plethora of cellular and animal models. Molecular mechanisms of resveratrol involved signaling pathways related to extracellular growth factors and receptor tyrosine kinases; formation of multiprotein complexes and cell metabolism; cell proliferation and genome instability; cytoplasmic tyrosine kinase signaling (cytokine, integrin, and developmental pathways); signal transduction by the transforming growth factor-β super-family; apoptosis and inflammation; and immune surveillance and hormone signaling. Resveratrol also showed a promising role to counteract multidrug resistance: in adjuvant therapy, associated with 5-fluoruracyl and cisplatin, resveratrol had additive and/or synergistic effects increasing the chemosensitization of cancer cells. Resveratrol, by acting on diverse mechanisms simultaneously, has been emphasized as a promising, multi-target, anticancer agent, relevant in both cancer prevention and treatment. PMID:27148534

  5. Thermodynamics of adaptive molecular resolution

    NASA Astrophysics Data System (ADS)

    Delgado-Buscalioni, R.

    2016-11-01

    A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U(1)-U(0). The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al., J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as `real' thermodynamic variables. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  6. Molecular Mechanisms of Bone Metastasis.

    PubMed

    Weidle, Ulrich H; Birzele, Fabian; Kollmorgen, Gwendlyn; Rüger, Rüdiger

    2016-01-01

    Metastasis of breast and prostate cancer as well as multiple myeloma to the bones represents a significant medical problem. We herein discuss the molecular basis of the creation of pre-metastatic niches, the process of bone metastasis and the phenomenon of tumor dormancy in the bone marrow as well as its regulation. We describe the identification and validation of genes mediating bone metastasis by use of pre-clinical models of bone metastasis. Additionally, we discuss the role of small integrin binding N-linked glycoproteins (SIBLINGS), the chemokine/chemokine receptor CXCL12/CXCR4 pathway and the role of micro RNAs (miRNAs) as mediators of bone metastasis. Finally, we summarize clinical achievements for the treatment of bone metastases.

  7. Huntington Disease: Molecular Diagnostics Approach.

    PubMed

    Bastepe, Murat; Xin, Winnie

    2015-10-06

    Huntington disease (HD) is caused by expansion of a CAG trinucleotide repeat in the first exon of the Huntingtin (HTT) gene. Molecular testing of Huntington disease for diagnostic confirmation and disease prediction requires detection of the CAG repeat expansion. There are three main types of HD genetic testing: (1) diagnostic testing to confirm or rule out disease, (2) presymptomatic testing to determine whether an at-risk individual inherited the expanded allele, and (3) prenatal testing to determine whether the fetus has inherited the expanded allele. This unit includes protocols that describe the complementary use of polymerase chain reactions (PCR) and Southern blot hybridization to accurately measure the CAG trinucleotide repeat size and interpret the test results. In addition, an indirect linkage analysis that does not reveal the unwanted parental HD status in a prenatal testing will also be discussed.

  8. Molecular Simulation of Reverse Micelles

    NASA Astrophysics Data System (ADS)

    Chowdhary, Janamejaya; Ladanyi, Branka

    2009-03-01

    Reverse micelles (RM) are surfactant assemblies containing a nanosized water pool dissolved in a hydrophobic solvent. Understanding their properties is crucial for insight into the effect of confinement on aqueous structure, dynamics as well as physical processes associated with solutes in confinement. We perform molecular dynamics simulations for the RM formed by the surfactant Aerosol-OT (AOT) in isooctane (2,2,4-trimethyl pentane) in order to study the effect of reverse micelle size on the aqueous phase. The structure of the RM is quantified in terms of the radial and pair density distributions. Dynamics are studied in terms of the mean squared displacements and various orientational time correlation functions in different parts of the RM so as to understand the effect of proximity to the interface on aqueous dynamics. Shape fluctuations of the RM are also analyzed.

  9. Molecular Mechanisms of Synaptic Specificity

    PubMed Central

    Margeta, Milica A.; Shen, Kang

    2011-01-01

    Synapses are specialized junctions that mediate information flow between neurons and their targets. A striking feature of the nervous system is the specificity of its synaptic connections: an individual neuron will form synapses only with a small subset of available presynaptic and postsynaptic partners. Synaptic specificity has been classically thought to arise from homophilic or heterophilic interactions between adhesive molecules acting across the synaptic cleft. Over the past decade, many new mechanisms giving rise to synaptic specificity have been identified. Synapses can be specified by secreted molecules that promote or inhibit synaptogenesis, and their source can be a neighboring guidepost cell, not just presynaptic and postsynaptic neurons. Furthermore, lineage, fate, and timing of development can also play critical roles in shaping neural circuits. Future work utilizing large-scale screens will aim to elucidate the full scope of cellular mechanisms and molecular players that can give rise to synaptic specificity. PMID:19969086

  10. Computational methods for molecular docking

    SciTech Connect

    Klebe, G.; Lengauer, T.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.

  11. Molecular-sized fluorescent nanodiamonds

    NASA Astrophysics Data System (ADS)

    Vlasov, Igor I.; Shiryaev, Andrey A.; Rendler, Torsten; Steinert, Steffen; Lee, Sang-Yun; Antonov, Denis; Vörös, Márton; Jelezko, Fedor; Fisenko, Anatolii V.; Semjonova, Lubov F.; Biskupek, Johannes; Kaiser, Ute; Lebedev, Oleg I.; Sildos, Ilmo; Hemmer, Philip. R.; Konov, Vitaly I.; Gali, Adam; Wrachtrup, Jörg

    2014-01-01

    Doping of carbon nanoparticles with impurity atoms is central to their application. However, doping has proven elusive for very small carbon nanoparticles because of their limited availability and a lack of fundamental understanding of impurity stability in such nanostructures. Here, we show that isolated diamond nanoparticles as small as 1.6 nm, comprising only ~400 carbon atoms, are capable of housing stable photoluminescent colour centres, namely the silicon vacancy (SiV). Surprisingly, fluorescence from SiVs is stable over time, and few or only single colour centres are found per nanocrystal. We also observe size-dependent SiV emission supported by quantum-chemical simulation of SiV energy levels in small nanodiamonds. Our work opens the way to investigating the physics and chemistry of molecular-sized cubic carbon clusters and promises the application of ultrasmall non-perturbative fluorescent nanoparticles as markers in microscopy and sensing.

  12. Elasticity of crystalline molecular explosives

    SciTech Connect

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, and an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.

  13. Molecular Spectroscopy of Living Systems

    NASA Astrophysics Data System (ADS)

    Cheng, Ji-Xin

    2016-06-01

    Molecular spectroscopy has been a powerful tool in the study of molecules in gas phase, condensed phase, and at interfaces. The transition from in vitro spectroscopy to spectroscopic imaging of living systems is opening new opportunities to reveal cellular machinery and to enable molecule-based diagnosis (Science 2015, 350: 1054). Such a transition involves more than a simple combination of spectrometry and microscopy. In this presentation, I will discuss the most recent efforts that have pushed the physical limits of spectroscopic imaging in terms of spectral acquisition speed, detection sensitivity, spatial resolution and imaging depth. I will further highlight significant applications in functional analysis of single cells and in label-free detection of diseases.

  14. Molecular characteristics versus biological activity

    USGS Publications Warehouse

    Applegate, Vernon C.; Smith, Manning A.; Willeford, Bennett R.

    1967-01-01

    The molecular characteristics of mononitrophenols containing halogens not only play a key role in their biological activity but provide a novel example of selective toxicity among vertebrate animals. It has been reported that efforts to control the parasitic sea lamprey in the Great Lakes are directed at present to the applications of a selective toxicant to streams inhabited by lamprey larvae. Since 1961, the larvicide that has been used almost exclusively in the control program has been 3-trifluoromethyl-4-nitrophenol (TFM). However, this is only one of about 15 closely related compounds, all halogen-containing mononitrophenols, that display a selectively toxic action upon lampreys. Although not all of the halogenated mononitrophenols are selectively toxic to lampreys (in fact, fewer than half of those tested), no other group of related compounds has displayed any useful larvicidal activity except for the substituted nitrosalicylanilides.

  15. Next-generation molecular diagnostics.

    PubMed

    Aldape, Kenneth; Pfister, Stefan M

    2016-01-01

    The classification of brain tumors is based on the time-honored tradition of histologic examination, coupled with clinicopathologic correlation, and is based on the fundamental importance of microscopic morphologic interpretation. Supplementation by immunohistochemical markers is of substantial value to distinguish related entities and to confirm morphologic impressions. The use of techniques such as fluorescent in situ hybridization (FISH) is also critical in specific situations. However, with these practices, it is clear that the use of state-of-the-art molecular techniques has great promise to add to classification to (1) reduce the subjectivity inherent in interobserver discordance, particularly with specific entities; and (2) elucidate the biologic diversity of entities that are not resolvable by routine methods. In this chapter, we discuss these possibilities, focusing on several tumor types affecting the central nervous system, including diffuse glioma and ependymoma.

  16. Molecular aggregation of humic substances

    USGS Publications Warehouse

    Wershaw, R. L.

    1999-01-01

    Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

  17. Toward molecular catalysts by computer.

    PubMed

    Raugei, Simone; DuBois, Daniel L; Rousseau, Roger; Chen, Shentan; Ho, Ming-Hsun; Bullock, R Morris; Dupuis, Michel

    2015-02-17

    CONSPECTUS: Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to design catalysts by computer. In this Account, we first review how thermodynamic properties such as redox potentials (E°), acidity constants (pKa), and hydride donor abilities (ΔGH(-)) form the basis for a framework for the systematic design of molecular catalysts for reactions that are critical for a secure energy future. We illustrate this for hydrogen evolution and oxidation, oxygen reduction, and CO conversion, and we give references to other instances where it has been successfully applied. The framework is amenable to quantum-chemical calculations and conducive to predictions by computer. We review how density functional theory allows the determination and prediction of these thermodynamic properties within an accuracy relevant to experimentalists (∼0.06 eV for redox potentials, ∼1 pKa unit for pKa values, and 1-2 kcal/mol for hydricities). Computation yielded correlations among thermodynamic properties as they reflect the electron population in the d shell of the metal center, thus substantiating empirical correlations used by experimentalists. These correlations point to the key role of redox potentials and other properties (pKa of the parent aminium for the proton-relay-based catalysts designed in our laboratory) that are easily accessible experimentally or computationally in reducing the parameter space for design. These properties suffice to fully determine free energies maps and profiles associated with catalytic cycles, i.e., the relative energies of intermediates. Their prediction puts us in a position to distinguish a priori between desirable and undesirable pathways and mechanisms. Efficient catalysts have flat free energy profiles that avoid high activation barriers due to low- and high

  18. On factorization of molecular wavefunctions

    NASA Astrophysics Data System (ADS)

    Jecko, Thierry; Sutcliffe, Brian T.; Woolley, R. Guy

    2015-11-01

    Recently there has been a renewed interest in the chemical physics literature of factorization of the position representation eigenfunctions Φ of the molecular Schrödinger equation as originally proposed by Hunter in the 1970s. The idea is to represent Φ in the form φχ where χ is purely a function of the nuclear coordinates, while φ must depend on both electron and nuclear position variables in the problem. This is a generalization of the approximate factorization originally proposed by Born and Oppenheimer, the hope being that an ‘exact’ representation of Φ can be achieved in this form with φ and χ interpretable as ‘electronic’ and ‘nuclear’ wavefunctions respectively. We offer a mathematical analysis of these proposals that identifies ambiguities stemming mainly from the singularities in the Coulomb potential energy.

  19. Molecular neurobiology of Drosophila taste

    PubMed Central

    Freeman, Erica Gene; Dahanukar, Anupama

    2015-01-01

    Drosophila is a powerful model in which to study the molecular and cellular basis of taste coding. Flies sense tastants via populations of taste neurons that are activated by compounds of distinct categories. The past few years have borne witness to studies that define the properties of taste neurons, identifying functionally distinct classes of sweet and bitter taste neurons that express unique subsets of gustatory receptor (Gr) genes, as well as water, salt, and pheromone sensing neurons that express members of the pickpocket (ppk) or ionotropic receptor (Ir) families. There has also been significant progress in terms of understanding how tastant information is processed and conveyed to higher brain centers, and modulated by prior dietary experience or starvation. PMID:26102453

  20. Molecular physiology of mammalian glucokinase.

    PubMed

    Iynedjian, P B

    2009-01-01

    The glucokinase (GCK) gene was one of the first candidate genes to be identified as a human "diabetes gene". Subsequently, important advances were made in understanding the impact of GCK in the regulation of glucose metabolism. Structure elucidation by crystallography provided insight into the kinetic properties of GCK. Protein interaction partners of GCK were discovered. Gene expression studies revealed new facets of the tissue distribution of GCK, including in the brain, and its regulation by insulin in the liver. Metabolic control analysis coupled to gene overexpression and knockout experiments highlighted the unique impact of GCK as a regulator of glucose metabolism. Human GCK mutants were studied biochemically to understand disease mechanisms. Drug development programs identified small molecule activators of GCK as potential antidiabetics. These advances are summarized here, with the aim of offering an integrated view of the role of GCK in the molecular physiology and medicine of glucose homeostasis.