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Sample records for molecule programmed death-1

  1. Lack of the programmed death-1 receptor renders host susceptible to enteric microbial infection through impairing the production of the mucosal natural killer cell effector molecules.

    PubMed

    Solaymani-Mohammadi, Shahram; Lakhdari, Omar; Minev, Ivelina; Shenouda, Steve; Frey, Blake F; Billeskov, Rolf; Singer, Steven M; Berzofsky, Jay A; Eckmann, Lars; Kagnoff, Martin F

    2016-03-01

    The programmed death-1 receptor is expressed on a wide range of immune effector cells, including T cells, natural killer T cells, dendritic cells, macrophages, and natural killer cells. In malignancies and chronic viral infections, increased expression of programmed death-1 by T cells is generally associated with a poor prognosis. However, its role in early host microbial defense at the intestinal mucosa is not well understood. We report that programmed death-1 expression is increased on conventional natural killer cells but not on CD4(+), CD8(+) or natural killer T cells, or CD11b(+) or CD11c(+) macrophages or dendritic cells after infection with the mouse pathogen Citrobacter rodentium. Mice genetically deficient in programmed death-1 or treated with anti-programmed death-1 antibody were more susceptible to acute enteric and systemic infection with Citrobacter rodentium. Wild-type but not programmed death-1-deficient mice infected with Citrobacter rodentium showed significantly increased expression of the conventional mucosal NK cell effector molecules granzyme B and perforin. In contrast, natural killer cells from programmed death-1-deficient mice had impaired expression of those mediators. Consistent with programmed death-1 being important for intracellular expression of natural killer cell effector molecules, mice depleted of natural killer cells and perforin-deficient mice manifested increased susceptibility to acute enteric infection with Citrobacter rodentium. Our findings suggest that increased programmed death-1 signaling pathway expression by conventional natural killer cells promotes host protection at the intestinal mucosa during acute infection with a bacterial gut pathogen by enhancing the expression and production of important effectors of natural killer cell function.

  2. Programmed Death-1 and Its Ligand Are Novel Immunotolerant Molecules Expressed on Leukemic B Cells in Chronic Lymphocytic Leukemia

    PubMed Central

    Mertens, Daniel; Tomczak, Waldemar; Wlasiuk, Paulina; Kosior, Kamila; Piechnik, Agnieszka; Bojarska-Junak, Agnieszka; Dmoszynska, Anna; Giannopoulos, Krzysztof

    2012-01-01

    Programmed death-1 (PD-1) is an immunoreceptor predominantly expressed on exhausted T cells, which through an interaction with its ligand (PD-L1), controls peripheral tolerance by limiting effector functions of T lymphocytes. qRT-PCR for PD-1, PD-L1 and their splicing forms as well as flow cytometric assessment of surface expression was performed in a cohort of 58 chronic lymphocytic leukemia (CLL) patients. In functional studies, we assessed the influence of the proliferative response of leukemic B-cells induced by IL-4 and CD40L on PD-1 transcripts and expression on the protein level. The median level of PD-1, but not PD-L1, transcripts in CLL patients was higher in comparison to healthy volunteers (HVs, n = 43, p = 0.0057). We confirmed the presence of PD-1 and PD-L1 on the CLL cell surface, and found the expression of PD-1, but not PD-L1, to be higher among CLL patients in comparison to HVs (47.2% vs. 14.8%, p<0.0001). The Kaplan-Meier curves for the time to progression and overall survival in groups with high and low surface expression of PD-1 and PD-L1 revealed no prognostic value in CLL patients. After stimulation with IL-4 and CD40L, protein expression of PD-1 was significantly increased in samples that responded and up-regulated CD38. PD-1, which is aberrantly expressed both at mRNA and cell surface levels in CLL cells might represent a novel immunotolerant molecule involved in the pathomechanism of the disease, and could provide a novel target for future therapies. PMID:22532845

  3. Antagonizing programmed death-1 and programmed death ligand-1 as a therapeutic approach for gastric cancer

    PubMed Central

    Liu, Xiaojun; Yang, Zhongxia; Latchoumanin, Olivier; Qiao, Liang

    2016-01-01

    Malignant tumor cells are equipped with mechanisms that can help them escape the surveillance by host immune system. Immune checkpoint molecules can transduce coinhibitory signals to immunocompetent cells and exert immunosuppressive roles in antitumor immunity. Programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) are the two important checkpoint molecules with great potential in targeted cancer therapy. Several antibodies targeting PD-1 and PD-L1 have been approved for clinical use. In this review, we focus on the recent development of targeting PD-1 and PD-L1 in gastric cancer (GC) therapy. PMID:27803740

  4. The effect of chemotherapy on programmed cell death 1/programmed cell death 1 ligand axis: some chemotherapeutical drugs may finally work through immune response

    PubMed Central

    Luo, Min; Fu, Liwu

    2016-01-01

    Most tumors are immunogenic which would trigger some immune response. Chemotherapy also has immune potentiating mechanisms of action. But it is unknown whether the immune response is associated with the efficacy of chemotherapy and the development of chemoresistance. Recently, there is a growing interest in immunotherapy, among which the co-inhibitory molecules, programmed cell death 1/programmed cell death 1 ligand (PD-1/PD-L1) leads to immune evasion. Since some reports showed that conventional chemotherapeutics can induce the expression of PD-L1, we try to summarize the effect of chemotherapy on PD-1/PD-L1 axis and some potential molecules relevant to PD-1/PD-L1 in chemoresistance in this review. PMID:26919108

  5. Programmed death-1 & its ligands: promising targets for cancer immunotherapy.

    PubMed

    Shrimali, Rajeev K; Janik, John E; Abu-Eid, Rasha; Mkrtichyan, Mikayel; Khleif, Samir N

    2015-01-01

    Novel strategies for cancer treatment involving blockade of immune inhibitors have shown significant progress toward understanding the molecular mechanism of tumor immune evasion. The preclinical findings and clinical responses associated with programmed death-1 (PD-1) and PD-ligand pathway blockade seem promising, making these targets highly sought for cancer immunotherapy. In fact, the anti-PD-1 antibodies, pembrolizumab and nivolumab, were recently approved by the US FDA for the treatment of unresectable and metastatic melanoma resistant to anticytotoxic T-lymphocyte antigen-4 antibody (ipilimumab) and BRAF inhibitor. Here, we discuss strategies of combining PD-1/PD-ligand interaction inhibitors with other immune checkpoint modulators and standard-of-care therapy to break immune tolerance and induce a potent antitumor activity, which is currently a research area of key scientific pursuit.

  6. Development of amino- and dimethylcarbamate-substituted resorcinol as programmed cell death-1 (PD-1) inhibitor.

    PubMed

    Liu, An; Dong, Lei; Wei, Xiao-Li; Yang, Xiao-Hong; Xiao, Jun-Hai; Liu, Zai-Qun

    2016-06-10

    Blockading the interaction of programmed death-1 (PD-1) protein with its ligands (PD-Ls, such as PD-L1) was proved to be a pathway for suppressing the development of tumors and other degradations of biological species. Thus, finding PD-1 inhibitors situated at the convergence point of drug discovery. In addition to some monoclonal antibodies applied to treat cancers clinically, the screening of organic molecules for hindering the interaction of PD-1 with PD-L1 became an efficient strategy in the development of PD-1 inhibitors. We herein applied resorcinol and 3-hydroxythiophenol as the core to link with N,N-dimethylcarbamate and other alkyl-substituted amines to afford 13 amine-appended phenyl dimethylcarbamates (AAPDs). The test for blockading the combination of PD-1 with PD-L1 revealed that abilities of 13 AAPDs were higher than that of sulfamethizole, a successful PD-1 inhibitor. In particular, large hydrophobic substituents at amine moiety or a nitro at resorcinol skeleton enhanced the inhibitory effect of AAPD even higher than that of sulfamethoxypyridazine, another successful PD-1 inhibitor. The present results may provide valuable information for further investigation on synthetic PD-1 inhibitors. PMID:27063329

  7. Programmed death-1/programmed death-L1 signaling pathway and its blockade in hepatitis C virus immunotherapy

    PubMed Central

    Salem, Mohamed L; El-Badawy, Ahmed

    2015-01-01

    Chronic hepatitis C virus (HCV) infection is a public health issue that often progresses to life-threatening complications, including liver cirrhosis, fibrosis, and hepatocellular carcinoma. Impaired immune responses to HCV are key features of chronic HCV infection. Therefore, intervention strategies usually involve enhancing the immune responses against HCV. Cytotoxic CD8+ T lymphocytes (CTLs) play a critical role in the control of HCV infection. However, their cytolytic function can be impaired by the expression of co-inhibitory molecules. Programmed death-1 (PD-1) receptor and its ligand PD-L1 function in a T cell co-inhibitory pathway, which either blocks the function of CTLs or the differentiation of CD8+ T cells. During chronic HCV infection, the immune inhibitory receptor PD-1 is upregulated on dysfunctional HCV-specific CD8+ T cells. As such, blockade of the PD-1/PD-L1 pathway in these CD8+ T cells might restore their functional capabilities. Indeed, clinical trials using therapies to block this pathway have shown promise in the fostering of anti-HCV immunity. Understanding how chronic HCV infection induces upregulation of PD-1 on HCV specific T cells and how the PD-1/PD-L1 interaction develops HCV specific T cell dysfunction will accelerate the development of an efficacious prophylactic and therapeutic vaccination against chronic HCV infections, which will significantly improve HCV treatments and patient survival. In this review, we discuss the relationship between PD-1 expression and clinical responses and the potential use of PD-1 blockade for anti-HCV therapy. PMID:26483866

  8. Where Do Programmed Death-1 Inhibitors Fit in the Management of Malignant Lymphoma?

    PubMed

    Ansell, Stephen M

    2016-02-01

    Tumor-specific cytotoxic T cells have the capacity to target and eradicate malignant B cells in patients with Hodgkin and non-Hodgkin lymphoma; however, multiple mechanisms, including regulatory T cells, immunosuppressive ligands, and immune exhaustion, suppress an effective antitumor immune response. One mechanism that is used by malignant cells to inhibit the immune response is overexpression of programmed death ligand 1 or 2 (PD-L1 or PD-L2) on the cancer cell surface. These ligands interact with the programmed death-1 (PD-1) receptor expressed on intratumoral T cells and provide an inhibitory signal, thereby suppressing the antitumor immune response. Monoclonal antibodies that block PD-1 signaling prevent T-cell inhibition and promote a T-cell-mediated antilymphoma response. Blocking antibodies that are directed against PD-1 or PD-L1 are currently being tested in patients with lymphoma and have shown remarkable efficacy, particularly in patients with relapsed Hodgkin lymphoma. On the basis of the promising activity of this approach, PD-1 inhibitors are being used as single-agent therapy in patients with relapsed Hodgkin lymphoma, and these inhibitors are also being tested in combination with standard chemotherapy or targeted agents in ongoing clinical trials. PMID:26869644

  9. Nivolumab, an Anti-Programmed Cell Death-1 Antibody, Induces Fulminant Type 1 Diabetes.

    PubMed

    Miyoshi, Yuka; Ogawa, Osamu; Oyama, Yu

    2016-01-01

    Programmed cell death-1 (PD-1), an immunoreceptor, is located on T cells and pro-B cells and interacts with its ligands to inhibit T cell activation and proliferation, thereby promoting immunological self-tolerance. Nivolumab, an anti-PD1 antibody, blocks PD-1 and can restore anticancer immune responses by abrogating PD-1 pathway-mediated T-cell inhibition. Autoimmune adverse events are expected with PD-1 therapy. Fulminant type 1 diabetes is the subtype of type 1 diabetes. The clinical feature is the extremely rapid progression of hyperglycemia and ketoacidosis. Here we describe a 66-year-old woman with advanced melanoma who was treated with nivolumab. After 4 months and six doses of the medicine, the patient was admitted to the hospital with complaints of nausea and vomiting. The laboratory data showed ketonuria, hyperglycemia (531 mg/dl), high anion gap metabolic acidosis, HbA1c (7.3%), and absence of insulin-secreting capacity. These data are compatible with the criteria of fulminant type 1 diabetes. The patient was diagnosed with diabetic ketoacidosis because of fulminant type 1 diabetes. The findings of this case indicated that nivolumab can cause fulminant type 1 diabetes. Diabetic ketoacidosis due to fulminant type 1 diabetes is potentially fatal condition. Thus, diabetic ketoacidosis due to fulminant type 1 diabetes should be considered in the differential diagnosis when patients treated with nivolumab complain of gastrointestinal symptoms. PMID:27297738

  10. Development and Fit-for-Purpose Validation of a Soluble Human Programmed Death-1 Protein Assay.

    PubMed

    Ni, Yan G; Yuan, Xiling; Newitt, John A; Peterson, Jon E; Gleason, Carol R; Haulenbeek, Jonathan; Santockyte, Rasa; Lafont, Virginie; Marsilio, Frank; Neely, Robert J; DeSilva, Binodh; Piccoli, Steven P

    2015-07-01

    Programmed death-1 (PD-1) protein is a co-inhibitory receptor which negatively regulates immune cell activation and permits tumors to evade normal immune defense. Anti-PD-1 antibodies have been shown to restore immune cell activation and effector function-an exciting breakthrough in cancer immunotherapy. Recent reports have documented a soluble form of PD-1 (sPD-1) in the circulation of normal and disease state individuals. A clinical assay to quantify sPD-1 would contribute to the understanding of sPD-1-function and facilitate the development of anti-PD-1 drugs. Here, we report the development and validation of a sPD-1 protein assay. The assay validation followed the framework for full validation of a biotherapeutic pharmacokinetic assay. A purified recombinant human PD-1 protein was characterized extensively and was identified as the assay reference material which mimics the endogenous analyte in structure and function. The lower limit of quantitation (LLOQ) was determined to be 100 pg/mL, with a dynamic range spanning three logs to 10,000 pg/mL. The intra- and inter-assay imprecision were ≤15%, and the assay bias (percent deviation) was ≤10%. Potential matrix effects were investigated in sera from both normal healthy volunteers and selected cancer patients. Bulk-prepared frozen standards and pre-coated Streptavidin plates were used in the assay to ensure consistency in assay performance over time. This assay appears to specifically measure total sPD-1 protein since the human anti-PD-1 antibody, nivolumab, and the endogenous ligands of PD-1 protein, PDL-1 and PDL-2, do not interfere with the assay.

  11. Immunological effects of the anti-programmed death-1 antibody on human peripheral blood mononuclear cells.

    PubMed

    Akiyama, Yasuto; Nonomura, Chizu; Kondou, Ryota; Miyata, Haruo; Ashizawa, Tadashi; Maeda, Chie; Mitsuya, Koichi; Hayashi, Nakamasa; Nakasu, Yoko; Yamaguchi, Ken

    2016-09-01

    Immune checkpoint antibody-mediated blockade has gained attention as a new cancer immunotherapy strategy. Accumulating evidence suggests that this therapy imparts a survival benefit to metastatic melanoma and non-small cell lung cancer patients. A substantial amount of data on immune checkpoint antibodies has been collected from clinical trials; however, the direct effect of the antibodies on human peripheral blood mononuclear cells (PBMCs) has not been exclusively investigated. In this study, we developed an anti-programmed death-1 (PD-1) antibody (with biosimilarity to nivolumab) and examined the effects of the antibody on PBMCs derived from cancer patients. Specifically, we investigated the effects of the anti-PD-1 antibody on proliferation, cytokine production, cytotoxic T lymphocytes (CTL) and regulatory T cells. These investigations yielded several important results. First, the anti-PD-1 antibody had no obvious effect on resting PBMCs; however, high levels of the anti-PD-1 antibody partly stimulated PBMC proliferation when accompanied by an anti-CD3 antibody. Second, the anti-PD-1 antibody restored the growth inhibition of anti-CD3 Ab-stimulated PBMCs mediated by PD-L1. Third, the anti-PD-1 antibody exhibited a moderate inhibitory effect on the induction of myeloid-derived suppressor cells (MDSCs) by anti-CD3 antibody stimulation. Additionally, the presence of the anti-PD-1 antibody promoted antigen-specific CTL induction, which suggests that combining anti-PD-1 antibody and conventional immunotherapy treatments may have beneficial effects. These results indicate that specific cellular immunological mechanisms are partly responsible for the antitumor effect exhibited by the anti-PD-1 antibody against advanced cancers in clinical trials. PMID:27573705

  12. A Monoclonal Antibody Specific for the Programmed Death-1 Homolog Prevents Graft Versus Host Disease in Mouse Models1

    PubMed Central

    Flies, Dallas B; Wang, Shengdian; Xu, Haiying; Chen, Lieping

    2011-01-01

    Upon interaction with B7 homolog 1, Programmed Death-1 transmits a critical co-inhibitory signal to T cells to negatively regulate immune responses. By extensively searching the genomic database with the immunoglobulin variable region of PD-1, we identified a homolog and named it Programmed Death-1 homolog (PD-1H). PD-1H is broadly expressed on the cell surface of hematopoietic cells, and could be further upregulated on CD4+ and CD8+ T cells following activation. We have generated a monoclonal antibody against PD-1H, which strikingly prevents acute graft versus host disease (GVHD) in semi- and fully-allogeneic murine models, leading to full chimerism following treatment. GVHD remains a primary hindrance to successful allogeneic hematopoietic cell transplantation therapy for the treatment of hematologic malignancy. Therefore, manipulation of PD-1H function may provide a new modality for controlling T cell responses to allogeneic tissues in transplant medicine. PMID:21768399

  13. Programmed Death-1 Antibody Blocks Therapeutic Effects of T-Regulatory Cells in Cockroach Antigen-Induced Allergic Asthma

    PubMed Central

    McGee, Halvor S.; Yagita, Hideo; Shao, Zhifei; Agrawal, Devendra K.

    2010-01-01

    We recently reported that the adoptive transfer of T-regulatory cells (Tregs) isolated from lung and spleen tissue of green fluorescent protein–transgenic mice reversed airway hyperresponsiveness and airway inflammation. Because Programmed Death-1 (PD-1) is a pivotal receptor regulating effector T-cell activation by Tregs, we evaluated whether PD-1 is involved in the therapeutic effect of naturally occurring Tregs (NTregs) and inducible Tregs (iTregs) in cockroach (CRA)-sensitized and challenged mice. The CD4+CD25+ NTregs and CD4+CD25− iTregs isolated from the lungs and spleens of BALB/c mice were adoptively transferred into CRA-sensitized and CRA-challenged mice with and without anti–PD-1 antibody (100 μg/mice). The CD4+CD25+ T cells in the lung were phenotyped after adoptive transfer. Concentrations of IL-4, IL-5, IL-10, IFN-γ, and IL-13 in bronchoalveolar lavage fluid (BALF) were measured using ELISA. The NTregs and iTregs from either lung or spleen tissue reversed airway hyperresponsiveness for at least 4 wk. However, the therapeutic effect was blocked by administering the anti–PD-1 antibody. The administration of Tregs-recipient mice with anti–PD-1 antibody significantly decreased cytotoxic T-lymphocyte antigen-4 expression, with low concentrations of Forkhead-winged transcriptional factor box 3 (Foxp3) mRNA transcripts in lung CD4+CD25+ T cells. These mice had substantially higher concentrations of BALF IL-4, IL-5, and IL-13, but significantly decreased levels of BALF IL-10. Adoptive therapy recipients without the anti–PD-1 antibody exhibited high levels of CTLA-4 expression and Foxp3 transcripts in lung CD4+CD25+ T cells, with a significant decrease in BALF IL-4, IL-5, and IL-13 concentrations and a substantial increase in BALF IL-10 concentrations. These data suggest that the reversal of airway hyperresponsiveness and airway inflammation by Tregs is mediated in part by PD-1, because other costimulatory molecules (e.g., inducible costimulatory

  14. Elevated Expression of Programmed Death-1 and Programmed Death Ligand-1 Negatively Regulates Immune Response against Cervical Cancer Cells

    PubMed Central

    Chen, Zhifang; Pang, Nannan; Du, Rong; Zhu, Yuejie; Fan, Lingling; Cai, Donghui

    2016-01-01

    The present study is to measure the expression of programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1), as well as its clinical significance in cervical cancer patients. Our results showed that different T cell subsets in patients with cervical cancer had high expression of PD-1, and DCs had high expression of PD-L1. High expression of PD-1 on Treg cells in cervical cancer patients facilitated the production of TGF-β and IL-10 but inhibited the production of IFN-γ. Cervical cancer elevated the expression of PD-1 and PD-L1 in mRNA level. PD-1 expression in peripheral blood of cervical cancer patients was related with tumor differentiation, lymph node metastasis, and invasiveness. PD-1/PD-L1 pathway inhibited lymphocyte proliferation but enhanced the secretion of IL-10 and TGF-β in vitro. In summary, our findings demonstrate that elevated levels of PD-1/PD-L1, TGF-β, and IL-10 in peripheral blood of cervical cancer patients may negatively regulate immune response against cervical cancer cells and contribute to the progression of cervical cancer. Therefore, PD-1/PD-L1 pathway may become an immunotherapy target in the future. PMID:27721577

  15. Crystal Structure of the Complex Between Programmed Death-1 (PD-1) and its Ligand PD-L2

    SciTech Connect

    Lazar-Molnar,E.; Yan, Q.; Cao, E.; Ramagopal, U.; Nathenson, S.; Almo, S.

    2008-01-01

    Programmed death-1 (PD-1) is a member of the CD28/B7 superfamily that delivers negative signals upon interaction with its two ligands, PD-L1 or PD-L2. The high-resolution crystal structure of the complex formed by the complete ectodomains of murine PD-1 and PD-L2 revealed a 1:1 receptor:ligand stoichiometry and displayed a binding interface and overall molecular organization distinct from that observed in the CTLA-4/B7 inhibitory complexes. Furthermore, our structure also provides insights into the association between PD-1 and PD-L1 and highlights differences in the interfaces formed by the two PD-1 ligands (PD-Ls) Mutagenesis studies confirmed the details of the proposed PD-1/PD-L binding interfaces and allowed for the design of a mutant PD-1 receptor with enhanced affinity. These studies define spatial and organizational constraints that control the localization and signaling of PD-1/PD-L complexes within the immunological synapse and provide a basis for manipulating the PD-1 pathways for immunotherapy.

  16. Soluble Programmed Death 1 (PD-1) Is Decreased in Patients With Immune Thrombocytopenia (ITP): Potential Involvement of PD-1 Pathway in ITP Immunopathogenesis.

    PubMed

    Birtas Atesoglu, Elif; Tarkun, Pinar; Demirsoy, Esra Terzi; Geduk, Ayfer; Mehtap, Ozgur; Batman, Adnan; Kaya, Fatih; Cekmen, Mustafa Baki; Gulbas, Zafer; Hacıhanefioglu, Abdullah

    2016-04-01

    Immune thrombocytopenia (ITP) is an autoimmune disease characterized by dysregulation of T cells. Programmed death (PD) 1 and programmed death 1 ligand 1 (PD-L1) are cosignaling molecules, and the major role of the PD-1 pathway is the inhibition of self-reactive T cells and to protect against autoimmune diseases. We measured levels of serum soluble PD 1 (sPD-1) and serum soluble PD-L1 (sPD-L1) in 67 patients with ITP (24 newly diagnosed ITP [ndITP], 43 chronic ITP [cITP]) and 21 healthy controls (HCs). We determined decreased serum sPD-1 levels both in patients with ndITP and in patients with cITP when compared to HC. Moreover, there was a positive correlation between sPD-1 levels and platelet counts. The sPD-L1 levels were decreased in patients with ndITP when compared to patients with cITP. This is the first study investigating PD-1 signaling pathway in ITP. Decreased sPD-1 levels may have a role in ITP pathogenesis as without the inhibitory regulation of PD-1, sustained activation of T cells may cause inflammatory responses which is the case in ITP.

  17. Catching up with solid tumor oncology: what is the evidence for a prognostic role of programmed cell death-ligand 1/programmed cell death-1 expression in B-cell lymphomas?

    PubMed Central

    McClanahan, Fabienne; Sharp, Thomas G.; Gribben, John G.

    2016-01-01

    Therapeutic strategies targeting the programmed cell death-ligand 1/programmed cell death-1 pathway have shown significant responses and good tolerability in solid malignancies. Although preclinical studies suggest that inhibiting programmed cell death-ligand 1/programmed cell death-1 interactions might also be highly effective in hematological malignancies, remarkably few clinical trials have been published. Determining patients who will benefit most from programmed cell death-ligand 1/programmed cell death-1-directed immunotherapy and whether programmed cell death-ligand 1/programmed cell death-1 are adequate prognostic markers becomes an increasingly important clinical question, especially as aberrant programmed cell death-ligand 1/programmed cell death-1 expression are key mediators of impaired anti-tumor immune responses in a range of B-cell lymphomas. Herein, we systematically review the published literature on the expression and prognostic value of programmed cell death-ligand 1/programmed cell death-1 in these patients and identify considerable differences in expression patterns, distribution and numbers of programmed cell death-ligand 1+/programmed cell death-1+cells, both between and within lymphoma subtypes, which is reflected in conflicting findings regarding the prognostic value of programmed cell death-ligand 1+/programmed cell death-1+ cells. This can be partly explained by differences in methodologies (techniques, protocols, cutoff values) and definitions of positivity. Moreover, lymphomagenesis, disease progression, and prognosis appear to be determined not only by the presence, numbers and distribution of specific subtypes of T cells, but also by other cells and additional immune checkpoints. Collectively, our findings indicate that programmed cell death-ligand 1/programmed cell death-1 interactions play an essential role in B-cell lymphoma biology and are of clinical importance, but that the overall outcome is determined by additional components

  18. Expression of programmed death 1 ligand 1 on periodontal tissue cells as a possible protective feedback mechanism against periodontal tissue destruction

    PubMed Central

    ZHANG, JIEHUA; WANG, CHIEH-MEI; ZHANG, PING; WANG, XIAOQIAN; CHEN, JIAO; YANG, JUN; LU, WANLU; ZHOU, WENJIE; YUAN, WENWEN; FENG, YUN

    2016-01-01

    Programmed death 1 ligand 1 (PD-L1) is a negative co-stimulatory molecule in immune responses. Previous reports have indicated that inflammatory cytokines can upregulate the expression of PD-L1 in tumor cells, which in turn suppresses host immune responses. Periodontitis is characterized by persistent inflammation of the periodontium, which is initiated by infection with oral bacteria and results in damage to cells and the matrices of the periodontal connective tissues. In the present study, the expression and function of PD-L1 in periodontal tissue destruction were examined. Periodontal ligament cells (PDLCs) were stimulated by inflammatory cytokines and periodontal pathogens. The expression and function of PD-L1 on the surface of PDLCs was investigated using flow cytometry in vitro. Periodontal disease was induced by the injection of Porphyromonas gingivalis in mouse models. The expression levels of PD-L1 in the periodontal tissues of the mice were analyzed using flow cytometry and immunohistochemistry. PD-L1 was inducibly expressed on the PDLCs by the inflammatory cytokines and periodontal pathogens. The inflammation-induced expression of PD-L1 was shown to cause the apoptosis of activated T lymphocytes and improve the survival of PDLCs. Furthermore, in the mouse model of experimental periodontitis, the expression of PD-L1 in severe cases of periodontitis was significantly lower, compared with that in mild cases. By contrast, no significant differences were observed between the healthy control and severe periodontitis groups. The results of the present study showed that the expression of PD-L1 may inhibit the destruction of periodontal tissues, indicating the involvement of a possible protective feedback mechanism against periodontal infection. PMID:26847035

  19. Mathematics and Molecules: Exploring Connections via Programming.

    ERIC Educational Resources Information Center

    Ploger, Don; Carlock, Margaret

    1996-01-01

    Examines the self-directed activity of two students who learned about molecular structure by writing computer programs. The programs displayed the solution of a mathematics problem, then the programs were extended to represent several classes of organic molecules. Different ways to enhance mathematical connections to chemistry education are…

  20. Programmed Death-1 Ligand 2-Mediated Regulation of the PD-L1 to PD-1 Axis Is Essential for Establishing CD4(+) T Cell Immunity.

    PubMed

    Karunarathne, Deshapriya S; Horne-Debets, Joshua M; Huang, Johnny X; Faleiro, Rebecca; Leow, Chiuan Yee; Amante, Fiona; Watkins, Thomas S; Miles, John J; Dwyer, Patrick J; Stacey, Katryn J; Yarski, Michael; Poh, Chek Meng; Lee, Jason S; Cooper, Matthew A; Rénia, Laurent; Richard, Derek; McCarthy, James S; Sharpe, Arlene H; Wykes, Michelle N

    2016-08-16

    Many pathogens, including Plasmodium spp., exploit the interaction of programmed death-1 (PD-1) with PD-1-ligand-1 (PD-L1) to "deactivate" T cell functions, but the role of PD-L2 remains unclear. We studied malarial infections to understand the contribution of PD-L2 to immunity. Here we have shown that higher PD-L2 expression on blood dendritic cells, from Plasmodium falciparum-infected individuals, correlated with lower parasitemia. Mechanistic studies in mice showed that PD-L2 was indispensable for establishing effective CD4(+) T cell immunity against malaria, because it not only inhibited PD-L1 to PD-1 activity but also increased CD3 and inducible co-stimulator (ICOS) expression on T cells. Importantly, administration of soluble multimeric PD-L2 to mice with lethal malaria was sufficient to dramatically improve immunity and survival. These studies show immuno-regulation by PD-L2, which has the potential to be translated into an effective treatment for malaria and other diseases where T cell immunity is ineffective or short-lived due to PD-1-mediated signaling.

  1. Programmed Death-1 Ligand 2-Mediated Regulation of the PD-L1 to PD-1 Axis Is Essential for Establishing CD4(+) T Cell Immunity.

    PubMed

    Karunarathne, Deshapriya S; Horne-Debets, Joshua M; Huang, Johnny X; Faleiro, Rebecca; Leow, Chiuan Yee; Amante, Fiona; Watkins, Thomas S; Miles, John J; Dwyer, Patrick J; Stacey, Katryn J; Yarski, Michael; Poh, Chek Meng; Lee, Jason S; Cooper, Matthew A; Rénia, Laurent; Richard, Derek; McCarthy, James S; Sharpe, Arlene H; Wykes, Michelle N

    2016-08-16

    Many pathogens, including Plasmodium spp., exploit the interaction of programmed death-1 (PD-1) with PD-1-ligand-1 (PD-L1) to "deactivate" T cell functions, but the role of PD-L2 remains unclear. We studied malarial infections to understand the contribution of PD-L2 to immunity. Here we have shown that higher PD-L2 expression on blood dendritic cells, from Plasmodium falciparum-infected individuals, correlated with lower parasitemia. Mechanistic studies in mice showed that PD-L2 was indispensable for establishing effective CD4(+) T cell immunity against malaria, because it not only inhibited PD-L1 to PD-1 activity but also increased CD3 and inducible co-stimulator (ICOS) expression on T cells. Importantly, administration of soluble multimeric PD-L2 to mice with lethal malaria was sufficient to dramatically improve immunity and survival. These studies show immuno-regulation by PD-L2, which has the potential to be translated into an effective treatment for malaria and other diseases where T cell immunity is ineffective or short-lived due to PD-1-mediated signaling. PMID:27533014

  2. [Increased expressions of programmed death 1 (PD-1) and its ligands in peripheral CD3(+) T cells and CD19(+) B cells in patients with hepatocellular carcinoma].

    PubMed

    Liu, Wei; Chai, Lin; Liang, Junli; Lu, Zhizhong; Yang, Siwei

    2016-09-01

    Objective To investigate the changes of programmed death 1 (PD-1) and ligands, as well as interferon-γ (IFN-γ) in peripheral blood mononuclear cells (PBMCs) of patients with hepatocellular carcinoma (HCC). Methods The peripheral blood was collected from 15 early HCC patients, 13 progressive HCC patients and 12 healthy volunteers. PBMCs was isolated from the peripheral blood. The expressions of PD-1, PD-L1 and PD-L2 in PBMCs were detected by flow cytometry; the serum level of IFN-γ was determined by ELISA; the correlation of PD-1 and IFN-γ was analyzed with Pearson's correlation and One-way ANOVA. Results The expression levels of PD-1, PD-L1 and PD-L2 in CD3(+) T cells and CD19(+) B cells and serum IFN-γ level in progressive HCC patients were significantly higher than those in the healthy group and early HCC patients. The expression levels of PD-1, PD-L1 and PD-L2 in the CD3(+) T cells and CD19(+) B cells of the HCC patients were positively correlated with IFN-γ. Conclusion The expression levels of PD-1, PD-L1 and PD-L2 increase in the PBMCs of HCC patients; PD-1 and PD-L1 are correlated with IFN-γ level. PMID:27609582

  3. Mice lacking Programmed cell death-1 show a role for CD8+ T cells in long-term immunity against blood-stage malaria

    PubMed Central

    Horne-Debets, Joshua M.; Karunarathne, Deshapriya S.; Faleiro, Rebecca J.; Poh, Chek Meng; Renia, Laurent; Wykes, Michelle N.

    2016-01-01

    Even after years of experiencing malaria, caused by infection with Plasmodium species, individuals still have incomplete immunity and develop low-density parasitemia on re-infection. Previous studies using the P. chabaudi (Pch) mouse model to understand the reason for chronic malaria, found that mice with a deletion of programmed cell death-1 (PD-1KO) generate sterile immunity unlike wild type (WT) mice. Here we investigated if the mechanism underlying this defect during acute immunity also impacts on long-term immunity. We infected WT and PD-1KO mice with Pch-malaria and measured protection as well as immune responses against re-infections, 15 or 20 weeks after the original infection had cleared. WT mice showed approximately 1% parasitemia compared to sterile immunity in PD-1KO mice on re-infection. An examination of the mechanisms of immunity behind this long-term protection in PD-1KO mice showed a key role for parasite-specific CD8+ T cells even when CD4+ T cells and B cells responded to re-infection. These studies indicate that long-term CD8+ T cell-meditated protection requires consideration for future malaria vaccine design, as part of a multi-cell type response. PMID:27217330

  4. Coordination programming of photofunctional molecules.

    PubMed

    Sakamoto, Ryota; Kusaka, Shinpei; Hayashi, Mikihiro; Nishikawa, Michihiro; Nishihara, Hiroshi

    2013-04-05

    Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET) initiated by the metal-to-ligand charge transfer (MLCT) transition of the Cu(I) state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinato)zinc(II) complexes. Conventional homoleptic bis(dipyrrinato)zinc(II) complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynyl)fumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

  5. Programmed death-1 is required for systemic self-tolerance in newly generated T cells during the establishment of immune homeostasis.

    PubMed

    Thangavelu, G; Parkman, J C; Ewen, C L; Uwiera, R R E; Baldwin, T A; Anderson, C C

    2011-05-01

    Lymphopenia driven T cell activation is associated with autoimmunity. That lymphopenia does not always lead to autoimmunity suggests that control mechanisms may exist. We assessed the importance of the co-inhibitory receptor programmed death-1 (PD-1) in the control of lymphopenia-driven autoimmunity in newly generated T cells vs. established peripheral T cells and in thymic selection. PD-1 was not required for negative selection in the thymus or for maintenance of self tolerance following transfer of established PD-1⁻/⁻ peripheral T cells to a lymphopenic host. In contrast, PD-1 was essential for systemic self tolerance in newly generated T cells under lymphopenic conditions, as PD-1⁻/⁻ recent thymic emigrants (RTE), generated after transfer of PD-1⁻/⁻ hematopoietic stem cell (HSC) precursors or thymocytes into lymphopenic adult Rag⁻/⁻ recipients, induced a rapidly lethal multi-organ inflammatory disease. Disease could be blocked by using lymph node deficient recipients, indicating that lymphopenia driven PD-1⁻/⁻ T cell activation required access to sufficient lymph node stroma. These data suggested that PD-1⁻/⁻ mice themselves might be substantially protected from autoimmunity because their T cell repertoire is first generated early in life, a period naturally deficient in lymph node stroma. Consistent with this idea, neonatal Rag⁻/⁻ recipients of PD-1⁻/⁻ HSC were resistant to disease. Thus, a critical role of PD-1 resides in the control of RTE in lymphopenia. The data suggest that PD-1 and a paucity of lymphoid stroma cooperate to control autoimmunity in newly generated T cells. Clinical therapies for autoimmune disease employing lymphoablation and hematopoietic stem cell transplantation will need to take into account functional polymorphisms in the PD-1 pathway, if the treatment is to ameliorate rather than exacerbate autoimmunity.

  6. Programmed death-1 expression on HIV-1-specific CD8+ T cells is shaped by epitope specificity, T-cell receptor clonotype usage and antigen load

    PubMed Central

    Kløverpris, Henrik N.; McGregor, Reuben; McLaren, James E.; Ladell, Kristin; Stryhn, Anette; Koofhethile, Catherine; Brener, Jacqui; Chen, Fabian; Riddell, Lynn; Graziano, Luzzi; Klenerman, Paul; Leslie, Alasdair; Buus, Søren; Price, David A.; Goulder, Philip

    2014-01-01

    Objectives: Although CD8+ T cells play a critical role in the control of HIV-1 infection, their antiviral efficacy can be limited by antigenic variation and immune exhaustion. The latter phenomenon is characterized by the upregulation of multiple inhibitory receptors, such as programmed death-1 (PD-1), CD244 and lymphocyte activation gene-3 (LAG-3), which modulate the functional capabilities of CD8+ T cells. Design and methods: Here, we used an array of different human leukocyte antigen (HLA)-B∗15 : 03 and HLA-B∗42 : 01 tetramers to characterize inhibitory receptor expression as a function of differentiation on HIV-1-specific CD8+ T-cell populations (n = 128) spanning 11 different epitope targets. Results: Expression levels of PD-1, but not CD244 or LAG-3, varied substantially across epitope specificities both within and between individuals. Differential expression of PD-1 on T-cell receptor (TCR) clonotypes within individual HIV-1-specific CD8+ T-cell populations was also apparent, independent of clonal dominance hierarchies. Positive correlations were detected between PD-1 expression and plasma viral load, which were reinforced by stratification for epitope sequence stability and dictated by effector memory CD8+ T cells. Conclusion: Collectively, these data suggest that PD-1 expression on HIV-1-specific CD8+ T cells tracks antigen load at the level of epitope specificity and TCR clonotype usage. These findings are important because they provide evidence that PD-1 expression levels are influenced by peptide/HLA class I antigen exposure. PMID:24906112

  7. The Expression of Programmed Death-1 on CD4+ and CD8+ T Lymphocytes in Patients with Type 2 Diabetes and Severe Sepsis

    PubMed Central

    Li, Chunsheng; Shao, Rui

    2016-01-01

    Objective To investigate the expression of Programmed death-1 (PD-1) on T lymphocytes in patients with type 2 diabetes mellitus (T2DM) and severe sepsis, we determined PD-1 expression on CD4+ and CD8+ T lymphocytes of patients with T2DM, severe sepsis, and T2DM combined with severe sepsis. Research Design and Methods This prospective and observational study included 50 healthy controls, 80 cases of T2DM without infection (T2DM group), 88 cases of severe sepsis without T2DM (SS group), and 77 cases of severe sepsis combined with T2DM (SS+T2DM group). Expression of peripheral blood PD-1+ CD4+ T cells and PD-1+ CD8+ T cells were compared between these 4 groups. Then, 28-day survival of the SS and SS+T2DM patients was assessed, and the expression of PD-1 on T cells was also compared between survivors and non-survivors. Results Percentages of PD-1+ CD4+ T cells and PD-1+ CD8+ T cells were higher in the T2DM group than in the healthy control group, and were highest in the SS and SS+T2DM groups. However, the expression of PD-1 on T cells and the mortality showed no significant difference between the SS and SS+T2DM groups. The expression of PD-1 on T cells was higher in non-survivors than survivors, but within the survivor group or non-survivor group, no difference can be detected between those with T2DM and those without T2DM. Conclusion The expression of PD-1 on T cells was increased in both T2DM and severe septic patients, but combining T2DM did not cause a further increase on the PD-1 expression in patients with severe sepsis. PMID:27459386

  8. Programmed death 1 deficiency induces the polarization of macrophages/microglia to the M1 phenotype after spinal cord injury in mice.

    PubMed

    Yao, Anhui; Liu, Fangfang; Chen, Kun; Tang, Liang; Liu, Ling; Zhang, Kun; Yu, Caiyong; Bian, Ganlan; Guo, Hongmin; Zheng, Jingjing; Cheng, Peng; Ju, Gong; Wang, Jian

    2014-07-01

    The inflammatory response following spinal cord injury (SCI) involves the activation of resident microglia and the infiltration of macrophages. Macrophages and microglia can be polarized into the classically activated proinflammatory M1 phenotype or the alternatively activated anti-inflammatory M2 phenotype. Programmed cell death 1 (PD-1) is a critical immune inhibitory receptor involved in innate and adaptive immune responses. However, whether PD-1 is involved in the modulation of macrophage/microglial polarization is unknown. In this study, the mRNA levels of pd1 gradually increased after SCI, and PD-1 protein was found in macrophages/microglia in injured spinal cord sections. PD-1 knockout (KO) mice showed poor locomotor recovery after spinal cord crushing compared with wild-type mice. M1-type macrophages/microglia accumulated in greater numbers in the injured spinal cord of PD-1-KO mice. Under polarized stimulation, induced expression of PD-1 occurred in cultured macrophages and microglia. PD-1 suppressed M1 polarization by reducing the phosphorylation of signal transducer and activator of transcription 1 (STAT1) and promoted M2 polarization by increasing STAT6 phosphorylation. In PD-1-KO mice, the M1 response was enhanced via the activation of STAT1 and nuclear factor-kappa B. Furthermore, PD-1 played various roles in phagocytosis in macrophages and microglia. Therefore, our results suggest that PD-1 signaling plays an important role in the regulation of macrophage/microglial polarization. Thus, deregulated PD-1 signaling may induce the polarization of macrophages/microglia toward the M1 phenotype. Overall, our results provide new insights into the modulatory mechanisms of macrophage/microglial polarization, thereby possibly facilitating the development of new therapies for SCI via the regulation of macrophage/microglial polarization through PD-1 signaling.

  9. Expression of programmed death-1 ligand (PD-L1) in tumor-infiltrating lymphocytes is associated with favorable spinal chordoma prognosis.

    PubMed

    Zou, Ming-Xiang; Peng, An-Bo; Lv, Guo-Hua; Wang, Xiao-Bin; Li, Jing; She, Xiao-Ling; Jiang, Yi

    2016-01-01

    Aberrant expression of programmed death-1 (PD-1) receptor/PD-1 ligand (PD-L1) proteins alters human immunoresponse and promotes tumor development and progression. We assessed the expression status of PD-1 and PD-L1 in spinal chordoma tissue specimens and their association with clinicopathological characteristics of patients. Formalin-fixed paraffin-embedded tumor samples from 54 patients with spinal chordoma were collected for immunohistochemical analysis of PD-1 and PD-L1 expression. The association of the expression levels of PD-1 and PD-L1 with clinicopathological variables and survival data were statistically analyzed. Lymphocyte infiltrates were present in all 54 patient samples. Of 54 samples, 37 (68.5%) had both positive PD-1 and PD-L1 expression in tumor cell membrane. Moreover, 38 (70.4%) and 12 (22.2%) had positive PD-1 and PD-L1 expression in tumor-infiltrating lymphocytes (TILs), respectively. Tumors with positive PD-L1 expression were significantly associated with advanced stages of chordoma (p = 0.041) and TIL infiltration (p = 0.005), and had a borderline association with tumor grade (p = 0.051). However, positive tumor PD-L1 expression was not significantly associated with local recurrence-free survival (LRFS) or overall survival (OS). PD-1 expression in TILs was associated with poor LRFS (χ(2) = 10.051, p = 0.002, log-rank test). Multivariate analysis showed that PD-L1 expression only in TILs was an independent predictor for LRFS (HR = 0.298, 95% CI: 0.098-0.907, p = 0.033), and OS (HR = 0.188, 95% CI: 0.051-0.687, p = 0.011) in spinal chordoma patients. In conclusion, PD-L1 expression in TILs was an independent predictor for both LRFS and OS in spinal chordoma patients. Our findings suggest that the PD-1/PD-L1 pathway may be a novel therapeutic target for the immunotherapy of chordoma.

  10. Expression of programmed death-1 ligand (PD-L1) in tumor-infiltrating lymphocytes is associated with favorable spinal chordoma prognosis

    PubMed Central

    Zou, Ming-Xiang; Peng, An-Bo; Lv, Guo-Hua; Wang, Xiao-Bin; Li, Jing; She, Xiao-Ling; Jiang, Yi

    2016-01-01

    Aberrant expression of programmed death-1 (PD-1) receptor/PD-1 ligand (PD-L1) proteins alters human immunoresponse and promotes tumor development and progression. We assessed the expression status of PD-1 and PD-L1 in spinal chordoma tissue specimens and their association with clinicopathological characteristics of patients. Formalin-fixed paraffin-embedded tumor samples from 54 patients with spinal chordoma were collected for immunohistochemical analysis of PD-1 and PD-L1 expression. The association of the expression levels of PD-1 and PD-L1 with clinicopathological variables and survival data were statistically analyzed. Lymphocyte infiltrates were present in all 54 patient samples. Of 54 samples, 37 (68.5%) had both positive PD-1 and PD-L1 expression in tumor cell membrane. Moreover, 38 (70.4%) and 12 (22.2%) had positive PD-1 and PD-L1 expression in tumor-infiltrating lymphocytes (TILs), respectively. Tumors with positive PD-L1 expression were significantly associated with advanced stages of chordoma (p = 0.041) and TIL infiltration (p = 0.005), and had a borderline association with tumor grade (p = 0.051). However, positive tumor PD-L1 expression was not significantly associated with local recurrence-free survival (LRFS) or overall survival (OS). PD-1 expression in TILs was associated with poor LRFS (χ2 = 10.051, p = 0.002, log-rank test). Multivariate analysis showed that PD-L1 expression only in TILs was an independent predictor for LRFS (HR = 0.298, 95% CI: 0.098-0.907, p = 0.033), and OS (HR = 0.188, 95% CI: 0.051-0.687, p = 0.011) in spinal chordoma patients. In conclusion, PD-L1 expression in TILs was an independent predictor for both LRFS and OS in spinal chordoma patients. Our findings suggest that the PD-1/PD-L1 pathway may be a novel therapeutic target for the immunotherapy of chordoma. PMID:27508049

  11. Programed death-1/programed death-ligand 1 expression in lymph nodes of HIV infected patients: results of a pilot safety study in rhesus macaques using anti–programed death-ligand 1 (Avelumab)

    PubMed Central

    Gill, Amanda L.; Green, Samantha A.; Abdullah, Shahed; Le Saout, Cecile; Pittaluga, Stefania; Chen, Hui; Turnier, Refika; Lifson, Jeffrey; Godin, Steven; Qin, Jing; Sneller, Michael C.; Cuillerot, Jean-Marie; Sabzevari, Helen; Lane, H. Clifford; Catalfamo, Marta

    2016-01-01

    Objective: The programed death-1 (PD1)/programed death-ligand 1 (PD-L1) pathway plays a critical role in balancing immunity and host immunopathology. During chronic HIV/SIV infection, there is persistent immune activation accompanied by accumulation of virus-specific cells with terminally differentiated phenotypes and expression of regulatory receptors such as PD1. These observations led us to hypothesize that the PD1/PD-L1 pathway contributes to the functional dysregulation and ineffective viral control, and its blockade may be a potential immunotherapeutic target. Methods: Lymph node biopsies from HIV-infected patients (n = 23) were studied for expression of PD1 and PD-L1. In addition, we assessed the safety and biological activity of a human anti-PD-L1 antibody (Avelumab) in chronically SIV-infected rhesus macaques. Results: PD-L1 expression was observed in cells with myloid/macrophage morphology in HIV-infected lymph nodes. Administration of anti-PD-L1 was well tolerated, and no changes in body weights, hematologic, or chemistry parameters were observed during the study. Blockade of PD-L1 led to a trend of transient viral control after discontinuation of treatment. Conclusion: Administration of anti-PD-L1 in chronic SIV-infected rhesus macaques was well tolerated. Overall, these data warrant further investigation to assess the efficacy of anti-PD-L1 treatment on viral control in chronic SIV infection as a prelude to such therapy in humans. PMID:27490642

  12. Overall Survival and Long-Term Safety of Nivolumab (Anti–Programmed Death 1 Antibody, BMS-936558, ONO-4538) in Patients With Previously Treated Advanced Non–Small-Cell Lung Cancer

    PubMed Central

    Gettinger, Scott N.; Horn, Leora; Gandhi, Leena; Spigel, David R.; Antonia, Scott J.; Rizvi, Naiyer A.; Powderly, John D.; Heist, Rebecca S.; Carvajal, Richard D.; Jackman, David M.; Sequist, Lecia V.; Smith, David C.; Leming, Philip; Carbone, David P.; Pinder-Schenck, Mary C.; Topalian, Suzanne L.; Hodi, F. Stephen; Sosman, Jeffrey A.; Sznol, Mario; McDermott, David F.; Pardoll, Drew M.; Sankar, Vindira; Ahlers, Christoph M.; Salvati, Mark; Wigginton, Jon M.; Hellmann, Matthew D.; Kollia, Georgia D.; Gupta, Ashok K.; Brahmer, Julie R.

    2015-01-01

    Purpose Programmed death 1 is an immune checkpoint that suppresses antitumor immunity. Nivolumab, a fully human immunoglobulin G4 programmed death 1 immune checkpoint inhibitor antibody, was active and generally well tolerated in patients with advanced solid tumors treated in a phase I trial with expansion cohorts. We report overall survival (OS), response durability, and long-term safety in patients with non–small-cell lung cancer (NSCLC) receiving nivolumab in this trial. Patients and Methods Patients (N = 129) with heavily pretreated advanced NSCLC received nivolumab 1, 3, or 10 mg/kg intravenously once every 2 weeks in 8-week cycles for up to 96 weeks. Tumor burden was assessed by RECIST (version 1.0) after each cycle. Results Median OS across doses was 9.9 months; 1-, 2-, and 3-year OS rates were 42%, 24%, and 18%, respectively, across doses and 56%, 42%, and 27%, respectively, at the 3-mg/kg dose (n = 37) chosen for further clinical development. Among 22 patients (17%) with objective responses, estimated median response duration was 17.0 months. An additional six patients (5%) had unconventional immune-pattern responses. Response rates were similar in squamous and nonsquamous NSCLC. Eighteen responding patients discontinued nivolumab for reasons other than progressive disease; nine (50%) of those had responses lasting > 9 months after their last dose. Grade 3 to 4 treatment-related adverse events occurred in 14% of patients. Three treatment-related deaths (2% of patients) occurred, each associated with pneumonitis. Conclusion Nivolumab monotherapy produced durable responses and encouraging survival rates in patients with heavily pretreated NSCLC. Randomized clinical trials with nivolumab in advanced NSCLC are ongoing. PMID:25897158

  13. Concomitant targeting of programmed death-1 (PD-1) and CD137 improves the efficacy of radiotherapy in a mouse model of human BRAFV600-mutant melanoma.

    PubMed

    Kroon, Paula; Gadiot, Jules; Peeters, Marlies; Gasparini, Alessia; Deken, Marcel A; Yagita, Hideo; Verheij, Marcel; Borst, Jannie; Blank, Christian U; Verbrugge, Inge

    2016-06-01

    T cell checkpoint blockade with antibodies targeting programmed cell death (ligand)-1 (PD-1/PD-L1) and/or cytotoxic T lymphocyte-antigen 4 (CTLA-4) has improved therapy outcome in melanoma patients. However, a considerable proportion of patients does not benefit even from combined α-CTLA-4 and α-PD-1 therapy. We therefore examined to which extent T cell (co)stimulation and/or stereotactic body radiation therapy (SBRT) could further enhance the therapeutic efficacy of T cell checkpoint blockade in a genetically engineered mouse melanoma model that is driven by PTEN-deficiency, and BRAFV600 mutation, as in human, but lacks the sporadic UV-induced mutations. Tumor-bearing mice were treated with different combinations of immunomodulatory antibodies (α-CTLA-4, α-PD-1, α-CD137) or interleukin-2 (IL-2) alone or in combination with SBRT. None of our immunotherapeutic approaches (alone or in combination) had any anti-tumor efficacy, while SBRT alone delayed melanoma outgrowth. However, α-CD137 combined with α-PD-1 antibodies significantly enhanced the anti-tumor effect of SBRT, while the anti-tumor effect of SBRT was not enhanced by interleukin-2, or the combination of α-CTLA-4 and α-PD-1. We conclude that α-CD137 and α-PD-1 antibodies were most effective in enhancing SBRT-induced tumor growth delay in this mouse melanoma model, outperforming the ability of IL-2, or the combination of α-CTLA-4 and α-PD-1 to synergize with SBRT. Given the high mutational load and increased immunogenicity of human melanoma with the same genotype, our findings encourage testing α-CD137 and α-PD-1 alone or in combination with SBRT clinically, particularly in patients refractory to α-CTLA-4 and/or α-PD-1 therapy. PMID:27160390

  14. Programmed death-1 (PD-1)/PD-1 ligand pathway-mediated immune responses against human T-lymphotropic virus type 1 (HTLV-1) in HTLV-1-associated myelopathy/tropical spastic paraparesis and carriers with autoimmune disorders.

    PubMed

    Kozako, Tomohiro; Yoshimitsu, Makoto; Akimoto, Masaki; White, Yohann; Matsushita, Kakushi; Soeda, Shinji; Shimeno, Hiroshi; Kubota, Ryuji; Izumo, Shuji; Arima, Naomichi

    2011-11-01

    Human T-lymphotropic virus-1 (HTLV-1) causes HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T-cell leukemia-lymphoma in individuals with dysfunctional immune responses. In this study, to characterize the HTLV-1-specific cytotoxic T lymphocyte (CTL) populations in asymptomatic HTLV-1 carriers (ACs), HAM/TSP patients, and carriers with autoimmune disorders (CAIDs), we examined the role of programmed death-1 and its ligand (PD-1/PD-L1) in HTLV-1-specific CTL functions using an HTLV-1 Tax/HLA-A*0201 tetramer and an HTLV-1 Tax/HLA-A*2402 tetramer. Interestingly, the percentage of HTLV-1 Tax301-309/HLA-A*2402 tetramer(+)CD8(+) cells expressing PD-1 in ACs was significantly higher than the percentage of HTLV-1 Tax11-19/HLA-A*0201 tetramer(+)CD8(+) cells expressing PD-1. PD-1 expression was significantly downregulated on HTLV-1-specific CTLs in HAM/TSP compared with ACs. PD-L1 expression was observed in a small proportion of unstimulated lymphocytes from ACs and was greater in ACs than in HAM/TSP and CAIDs after short-term culture. Furthermore, CTL degranulation was impaired in HAM/TSP, whereas anti-PD-L1 blockade significantly increased CTL function in ACs. Downregulation of PD-1 on HTLV-1-specific CTLs and loss of PD-L1 expression in HAM/TSP and CAIDs, along with impaired function of HTLV-1-specific CTLs in HAM/TSP, may underlie the apparently dysfunctional immune response against HTLV-1. PMID:21851845

  15. Expression of Programmed Cell Death 1 Ligand 2 (PD-L2) is a Distinguishing Feature of Primary Mediastinal (Thymic) Large B-cell Lymphoma and Associated with PDCD1LG2 Copy Gain

    PubMed Central

    Shi, Min; Roemer, Margaretha GM; Chapuy, Bjoern; Liao, Xiaoyun; Sun, Heather; Pinkus, Geraldine S.; Shipp, Margaret A.; Freeman, Gordon J.; Rodig, Scott J.

    2016-01-01

    Primary mediastinal (thymic) large B-cell lymphoma (PMBL) and diffuse large B-cell lymphoma (DLBCL) are tumors with distinct clinical and molecular characteristics that are difficult to distinguish by histopathological and phenotypic analyses alone. Programmed cell death 1 ligand 2 (PD-L2) is a cell surface protein expressed by activated macrophages and dendritic cells that binds PD-1 on T-cells to inhibit immune responses. Amplification and/or translocations involving chromosome 9p24.1, a region that includes PDCD1LG2 encoding PD-L2, is a common event in PMBL but not DLBCL and suggests that PD-L2 expression might be a distinguishing feature of PMBL. We developed an assay for the immunohistochemical detection of PD-L2 protein in fixed biopsy specimens (PD-L2 IHC) which we applied to a cohort of PMBLs and DLBCLs. For a subset of cases, we correlated the results of PD-L2 IHC with PDCD1LG2 copy number as determined by qPCR. Twenty-three of 32 (72%) PMBLs but only 1 of 37 (3%) DLBCLs were positive by PD-L2 IHC. Among PMBLs with PDCD1LG2 copy number gain, all were positive by PD-L2 IHC. One PMBL without copy number gain was positive by PD-L2 IHC. When expressed in PMBL, PD-L2 was restricted to tumor cells and not detected on intra-tumoral macrophages. We conclude that PD-L2 protein is robustly expressed by the majority of PMBLs but only rare DLBCLs and often associated with PDCD1LG2 copy gain. PD-L2 IHC may serve as a useful ancillary test for distinguishing PMBL from DLBCL and for the rational selection of patients for therapeutic antibodies that inhibit PD-1 signaling. PMID:25025450

  16. Expression of programmed cell death 1 ligand 2 (PD-L2) is a distinguishing feature of primary mediastinal (thymic) large B-cell lymphoma and associated with PDCD1LG2 copy gain.

    PubMed

    Shi, Min; Roemer, Margaretha G M; Chapuy, Bjoern; Liao, Xiaoyun; Sun, Heather; Pinkus, Geraldine S; Shipp, Margaret A; Freeman, Gordon J; Rodig, Scott J

    2014-12-01

    Primary mediastinal (thymic) large B-cell lymphoma (PMBL) and diffuse large B-cell lymphoma (DLBCL) are tumors with distinct clinical and molecular characteristics that are difficult to distinguish by histopathologic and phenotypic analyses alone. Programmed cell death 1 ligand 2 (PD-L2) is a cell surface protein expressed by activated macrophages and dendritic cells that binds PD-1 on T cells to inhibit immune responses. Amplification and/or translocations involving chromosome 9p24.1, a region that includes PDCD1LG2-encoding PD-L2, is a common event in PMBL but not DLBCL and suggests that PD-L2 expression might be a distinguishing feature of PMBL. We developed an assay for the immunohistochemical detection of PD-L2 protein in fixed biopsy specimens (PD-L2 IHC), which we applied to a cohort of PMBLs and DLBCLs. For a subset of cases, we correlated the results of PD-L2 IHC with PDCD1LG2 copy number (CN) as determined by quantitative polymerase chain reaction. Twenty-three of 32 (72%) PMBLs but only 1 of 37 (3%) DLBCLs were positive by PD-L2 IHC. Among PMBLs with PDCD1LG2 CN gain, all were positive by PD-L2 IHC. One PMBL without CN gain was positive by PD-L2 IHC. When expressed in PMBL, PD-L2 was restricted to tumor cells and not detected on intratumoral macrophages. We conclude that PD-L2 protein is robustly expressed by the majority of PMBLs but only rare DLBCLs and often associated with PDCD1LG2 copy gain. PD-L2 IHC may serve as a useful ancillary test for distinguishing PMBL from DLBCL and for the rational selection of patients for therapeutic antibodies that inhibit PD-1 signaling. PMID:25025450

  17. A Randomized, Double-Blind, Placebo-Controlled Assessment of BMS-936558, a Fully Human Monoclonal Antibody to Programmed Death-1 (PD-1), in Patients with Chronic Hepatitis C Virus Infection

    PubMed Central

    Gardiner, David; Lalezari, Jay; Lawitz, Eric; DiMicco, Michael; Ghalib, Rheem; Reddy, K. Rajender; Chang, Kyong-Mi; Sulkowski, Mark; Marro, Steven O’; Anderson, Jeffrey; He, Bing; Kansra, Vikram; McPhee, Fiona; Wind-Rotolo, Megan; Grasela, Dennis; Selby, Mark; Korman, Alan J.; Lowy, Israel

    2013-01-01

    Expression of the programmed death 1 (PD-1) receptor and its ligands are implicated in the T cell exhaustion phenotype which contributes to the persistence of several chronic viral infections, including human hepatitis C virus (HCV). The antiviral potential of BMS-936558 (MDX-1106) – a fully human anti-PD-1 monoclonal immunoglobulin-G4 that blocks ligand binding – was explored in a proof-of-concept, placebo-controlled single-ascending-dose study in patients (N = 54) with chronic HCV infection. Interferon-alfa treatment-experienced patients (n = 42) were randomized 5∶1 to receive a single infusion of BMS-936558 (0.03, 0.1, 0.3, 1.0, 3.0 mg/kg [n = 5 each] or 10 mg/kg [n = 10]) or of placebo (n = 7). An additional 12 HCV treatment-naïve patients were randomized to receive 10 mg/kg BMS-936558 (n = 10) or placebo (n = 2). Patients were followed for 85 days post-dose. Five patients who received BMS-936558 (0.1 [n = 1] or 10 mg/kg) and one placebo patient achieved the primary study endpoint of a reduction in HCV RNA ≥0.5 log10 IU/mL on at least 2 consecutive visits; 3 (10 mg/kg) achieved a >4 log10 reduction. Two patients (10 mg/kg) achieved HCV RNA below the lower limit of quantitation (25 IU/mL), one of whom (a prior null-responder) remained RNA-undetectable 1 year post-study. Transient reductions in CD4+, CD8+ and CD19+ cells, including both naïve and memory CD4+ and CD8+ subsets, were observed at Day 2 without evidence of immune deficit. No clinically relevant changes in immunoglobulin subsets or treatment-related trends in circulating cytokines were noted. BMS-936558 exhibited dose-related exposure increases, with a half-life of 20–24 days. BMS-936558 was mostly well tolerated. One patient (10 mg/kg) experienced an asymptomatic grade 4 ALT elevation coincident with the onset of a 4-log viral load reduction. Six patients exhibited immune-related adverse events of mild-to-moderate intensity, including two cases of

  18. Programmed necrosis in inflammation: Toward identification of the effector molecules.

    PubMed

    Wallach, David; Kang, Tae-Bong; Dillon, Christopher P; Green, Douglas R

    2016-04-01

    Until recently, programmed cell death was conceived of as a single set of molecular pathways. We now know of several distinct sets of death-inducing mechanisms that lead to differing cell-death processes. In one of them--apoptosis--the dying cell affects others minimally. In contrast, programmed necrotic cell death causes release of immunostimulatory intracellular components after cell-membrane rupture. Defining the in vivo relevance of necrotic death is hampered because the molecules initiating it [such as receptor-interacting protein kinase-1 (RIPK1), RIPK3, or caspase-1] also serve other functions. Proteins that participate in late events in two forms of programmed necrosis [mixed lineage kinase domain-like protein (MLKL) in necroptosis and gasdermin-D in pyroptosis] were recently discovered, bringing us closer to identifying molecules that strictly serve in death mediation, thereby providing probes for better assessing its role in inflammation.

  19. DUO: A general program for calculating spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    DUO is a general, user-friendly program for computing rotational, rovibrational and rovibronic spectra of diatomic molecules. DUO solves the Schrödinger equation for the motion of the nuclei not only for the simple case of uncoupled, isolated electronic states (typical for the ground state of closed-shell diatomics) but also for the general case of an arbitrary number and type of couplings between electronic states (typical for open-shell diatomics and excited states). Possible couplings include spin-orbit, angular momenta, spin-rotational and spin-spin. Corrections due to non-adiabatic effects can be accounted for by introducing the relevant couplings using so-called Born-Oppenheimer breakdown curves. DUO requires user-specified potential energy curves and, if relevant, dipole moment, coupling and correction curves. From these it computes energy levels, line positions and line intensities. Several analytic forms plus interpolation and extrapolation options are available for representation of the curves. DUO can refine potential energy and coupling curves to best reproduce reference data such as experimental energy levels or line positions. DUO is provided as a Fortran 2003 program and has been tested under a variety of operating systems.

  20. Elucidating the germination transcriptional program using small molecules.

    PubMed

    Bassel, George W; Fung, Pauline; Chow, Tsz-fung Freeman; Foong, Justin A; Provart, Nicholas J; Cutler, Sean R

    2008-05-01

    The transition from seed to seedling is mediated by germination, a complex process that starts with imbibition and completes with radicle emergence. To gain insight into the transcriptional program mediating germination, previous studies have compared the transcript profiles of dry, dormant, and germinating after-ripened Arabidopsis (Arabidopsis thaliana) seeds. While informative, these approaches did not distinguish the transcriptional responses due to imbibition, shifts in metabolism, or breaking of dormancy from those triggered by the initiation of germination. In this study, three mechanistically distinct small molecules that inhibit Arabidopsis seed germination (methotrexate, 2, 4-dinitrophenol, and cycloheximide) were identified using a small-molecule screen and used to probe the germination transcriptome. Germination-responsive transcripts were defined as those with significantly altered transcript abundance across all inhibitory treatments with respect to control germinating seeds, using data from ATH1 microarrays. This analysis identified numerous germination regulators as germination responsive, including the DELLA proteins GAI, RGA, and RGL3, the abscisic acid-insensitive proteins ABI4, ABI5, ABI8, and FRY1, and the gibberellin receptor GID1A. To help visualize these and other publicly available seed microarray data, we designed a seed mRNA expression browser using the electronic Fluorescent Pictograph platform. An overall decrease in gene expression and a 5-fold greater number of transcripts identified as statistically down-regulated in drug-inhibited seeds point to a role for mRNA degradation or turnover during seed germination. The genes identified in our study as responsive to germination define potential uncharacterized regulators of this process and provide a refined transcriptional signature for germinating Arabidopsis seeds.

  1. HIV-mediated phosphatidylinositol 3-kinase/serine-threonine kinase activation in APCs leads to programmed death-1 ligand upregulation and suppression of HIV-specific CD8 T cells.

    PubMed

    Muthumani, Karuppiah; Shedlock, Devon J; Choo, Daniel K; Fagone, Paolo; Kawalekar, Omkar U; Goodman, Jonathan; Bian, Chaoran B; Ramanathan, Aarti A; Atman, Parikh; Tebas, Pablo; Chattergoon, Michael A; Choo, Andrew Y; Weiner, David B

    2011-09-15

    Recent evidence demonstrates that HIV-1 infection leads to the attenuation of cellular immune responses, which has been correlated with the increased expression of programmed death (PD)-1 on virus-specific CD8(+) T cells. PD-1 is induced upon T cell activation, and its prolonged expression facilitates CD8(+) T cell inhibitory signals when bound to its B7 family ligands, PD-ligand (L)1/2, which are expressed on APCs. Importantly, early reports demonstrated that blockade of the PD-1/PD-L interaction by Abs may help to counter the development of immune exhaustion driven by HIV viral persistence. To better understand the regulation of the PD-1 pathway during HIV infection, we examined the ability of the virus to induce PD-L expression on macrophages and dendritic cells. We found a direct relationship between the infection of APCs and the expression of PD-L1 in which virus-mediated upregulation induced a state of nonresponsiveness in uninfected HIV-specific T cells. Furthermore, this exhaustion phenotype was revitalized by the blockade of PD-L1, after which T cells regained their capacity for proliferation and the secretion of proinflammatory cytokines IFN-γ, IL-2, and IL-12 upon restimulation. In addition, we identify a critical role for the PI3K/serine-threonine kinase signaling pathway in PD-L1 upregulation of APCs by HIV, because inhibition of these intracellular signal transducer enzymes significantly reduced PD-L1 induction by infection. These data identify a novel mechanism by which HIV exploits the immunosuppressive PD-1 pathway and suggest a new role for virus-infected cells in the local corruption of immune responses required for viral suppression.

  2. Enhanced Cytotoxic CD8 T Cell Priming Using Dendritic Cell-Expressing Human Papillomavirus-16 E6/E7-p16INK4 Fusion Protein with Sequenced Anti-Programmed Death-1.

    PubMed

    Garcia-Bates, Tatiana M; Kim, Eun; Concha-Benavente, Fernando; Trivedi, Sumita; Mailliard, Robbie B; Gambotto, Andrea; Ferris, Robert L

    2016-03-15

    The incidence of human papillomavirus (HPV)-related head and neck squamous cell carcinoma has increased in recent decades, though HPV prevention vaccines may reduce this rise in the future. HPV-related cancers express the viral oncoproteins E6 and E7. The latter inactivates the tumor suppressor protein retinoblastoma (Rb), which leads to the overexpression of p16(INK4) protein, providing unique Ags for therapeutic HPV-specific cancer vaccination. We developed potential adenoviral vaccines that express a fusion protein of HPV-16 E6 and E7 (Ad.E6E7) alone or fused with p16 (Ad.E6E7p16) and also encoding an anti-programmed death (PD)-1 Ab. Human monocyte-derived dendritic cells (DC) transduced with Ad.E6E7 or Ad.E6E7p16 with or without Ad.αPD1 were used to activate autologous CD8 CTL in vitro. CTL responses were tested against naturally HPV-infected head and neck squamous cell carcinoma cells using IFN-γ ELISPOT and [(51)Cr]release assay. Surprisingly, stimulation and antitumor activity of CTL were increased after incubation with Ad.E6E7p16-transduced DC (DC.E6E7p16) compared with Ad.E6E7 (DC.E6E7), a result that may be due to an effect of p16 on cyclin-dependent kinase 4 levels and IL-12 secretion by DC. Moreover, the beneficial effect was most prominent when anti-PD-1 was introduced during the second round of stimulation (after initial priming). These data suggest that careful sequencing of Ad.E6E7.p16 with Ad.αPD1 could improve antitumor immunity against HPV-related tumors and that p16 may enhance the immunogenicity of DC, through cyclin-dependent pathways, Th1 cytokine secretion, and by adding a nonviral Ag highly overexpressed in HPV-induced cancers. PMID:26851223

  3. A Computer Program for the Distribution of End-to-End Distances in Polymer Molecules

    ERIC Educational Resources Information Center

    Doorne, William Van; And Others

    1976-01-01

    Describes a Fortran program that illustrates how the end-to-end distances in randomly coiled polymer molecules is affected by varying the number and lengths of chains and the angles between them. (MLH)

  4. Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program.

    PubMed

    Izumi, Hiroshi; Nafie, Laurence A; Dukor, Rina K

    2016-05-01

    Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X-ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E-5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragment mb_3a6c4c of mevastatin () in combination with the SMiles ARbitrary Target Specification (SMARTS) description suggested that a change in the conformation of this fragment may be the driving force for dissociation of mevastatin from its target protein. Chirality 28:370-375, 2016. © 2016 Wiley Periodicals, Inc.

  5. Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria.

    PubMed

    Nievas, Fiorela L; Bogino, Pablo C; Giordano, Walter

    2016-05-01

    Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules. Here, we describe a sequence of experiments designed to expand the understanding and capabilities of biochemistry students using techniques for extraction and identification of QS and QQ signal molecules from peanut rhizospheric soil bacteria, including culturing and manipulation of bacteria under sterile conditions. The program provides students with an opportunity to perform useful assays, draw conclusions from their results, and discuss possible extensions of the study. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:256-262, 2016.

  6. A finite difference Hartree-Fock program for atoms and diatomic molecules

    NASA Astrophysics Data System (ADS)

    Kobus, Jacek

    2013-03-01

    The newest version of the two-dimensional finite difference Hartree-Fock program for atoms and diatomic molecules is presented. This is an updated and extended version of the program published in this journal in 1996. It can be used to obtain reference, Hartree-Fock limit values of total energies and multipole moments for a wide range of diatomic molecules and their ions in order to calibrate existing and develop new basis sets, calculate (hyper)polarizabilities (αzz, βzzz, γzzzz, Az,zz, Bzz,zz) of atoms, homonuclear and heteronuclear diatomic molecules and their ions via the finite field method, perform DFT-type calculations using LDA or B88 exchange functionals and LYP or VWN correlations ones or the self-consistent multiplicative constant method, perform one-particle calculations with (smooth) Coulomb and Krammers-Henneberger potentials and take account of finite nucleus models. The program is easy to install and compile (tarball+configure+make) and can be used to perform calculations within double- or quadruple-precision arithmetic. Catalogue identifier: ADEB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEB_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 171196 No. of bytes in distributed program, including test data, etc.: 9481802 Distribution format: tar.gz Programming language: Fortran 77, C. Computer: any 32- or 64-bit platform. Operating system: Unix/Linux. RAM: Case dependent, from few MB to many GB Classification: 16.1. Catalogue identifier of previous version: ADEB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 98(1996)346 Does the new version supersede the previous version?: Yes Nature of problem: The program finds virtually exact solutions of the Hartree-Fock and density functional theory type equations for atoms, diatomic molecules and their ions

  7. Regulation Effects by Programmed Molecules for Transcription-Based Diagnostic Automata towards Therapeutic Use

    NASA Astrophysics Data System (ADS)

    Hirabayashi, Miki; Ohashi, Hirotada; Kubo, Tai

    We have presented experimental analysis on the controllability of our transcription-based diagnostic biomolecular automata by programmed molecules. Focusing on the noninvasive transcriptome diagnosis by salivary mRNAs, we already proposed the novel concept of diagnostic device using DNA computation. This system consists of the main computational element which has a stem shaped promoter region and a pseudo-loop shaped read-only memory region for transcription regulation through the conformation change caused by the recognition of disease-related biomarkers. We utilize the transcription of malachite green aptamer sequence triggered by the target recognition for observation of detection. This algorithm makes it possible to release RNA-aptamer drugs multiply, different from the digestion-based systems by the restriction enzyme which was proposed previously, for the in-vivo use, however, the controllability of aptamer release is not enough at the previous stage. In this paper, we verified the regulation effect on aptamer transcription by programmed molecules in basic conditions towards the developm! ent of therapeutic automata. These results would bring us one step closer to the realization of new intelligent diagnostic and therapeutic automata based on molecular circuits.

  8. Maternal diet, bioactive molecules, and exercising as reprogramming tools of metabolic programming.

    PubMed

    Mathias, Paulo C F; Elmhiri, Ghada; de Oliveira, Júlio C; Delayre-Orthez, Carine; Barella, Luiz F; Tófolo, Laize P; Fabricio, Gabriel S; Chango, Abalo; Abdennebi-Najar, Latifa

    2014-04-01

    Nutrition and lifestyle, particularly over-nutrition and lack of exercise, promote the progression and pathogenesis of obesity and metabolic diseases. Nutrition is likely the most important environmental factor that modulates the expression of genes involved in metabolic pathways and a variety of phenotypes associated with obesity and diabetes. During pregnancy, diet is a major factor that influences the organ developmental plasticity of the foetus. Experimental evidence shows that nutritional factors, including energy, fatty acids, protein, micronutrients, and folate, affect various aspects of metabolic programming. Different epigenetic mechanisms that are elicited by bioactive factors in early critical developmental ages affect the susceptibility to several diseases in adulthood. The beneficial effects promoted by exercise training are well recognised, and physical exercise may be considered one of the more prominent non-pharmacological tools that can be used to attenuate metabolic programming and to consequently ameliorate the illness provoked by metabolic diseases and reduce the prevalence of obesity, type 2 diabetes, and cardiovascular diseases. Literature on the different outcomes of unbalanced diets and the beneficial effects of some bioactive molecules during gestation and lactation on the metabolic health of offspring, as well as the potential mechanisms underlying these effects, was reviewed. The importance of the combined effects of functional nutrition and exercise as reprogramming tools of metabolic programming is discussed in depth. Finally, this review provides recommendations to healthcare providers that may aid in the control of early programming in an attempt to optimise the health of the mother and child.

  9. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

    NASA Astrophysics Data System (ADS)

    Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

    2012-02-01

    A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input

  10. ATIRS package: A program suite for the rovibrational analysis of infrared spectra of asymmetric top molecules

    NASA Astrophysics Data System (ADS)

    Tasinato, N.; Pietropolli Charmet, A.; Stoppa, P.

    2007-06-01

    Nowadays high-resolution infrared spectra can be recorded quite easily and therefore it has become important to assist the rovibrational analysis, especially the assignment step, that is still fraught with many problems in the presence of perturbation effects. In this article we provide a description of ATIRS, a complete software suite developed for assisting in the rotational investigation of vibrational bands of asymmetric top molecules. This package uses the Pickett's CALPGM suite for fitting transitions and predicting line positions and is composed by three stand-alone applications: (1) Visual Loomis-Wood for the assignment of spectral lines based on Loomis-Wood type diagrams; (2) Visual CALPGM, a new graphical interface to Pickett's programs SPFIT and SPCAT; (3) Visual Spectra Simulator for the simulation of spectra. The graphical interface to the CALPGM suite is developed for asymmetric rotors. The main feature of this application is to avoid the use of the parameter codes that are here replaced employing the well known parameter names or symbols. Highlighting the regular transition sequences, Visual Loomis-Wood assists in the assignment of the spectral lines. It visualizes the description of a transition and the assignment can be simply done by mouse-clicking on the diagram; moreover its display mode feature lets to check the experimental spectrum in which all the assigned lines together with their description are reported. Visual Spectra Simulator provides a simple and functionally application that, using the calculated frequencies and intensities given by SPCAT, simulates the high-resolution infrared spectrum and compare it to the experimental one. ATIRS, freely available to the spectroscopic community, is designed to be easy to use and presents a standard graphical interface; being based on the CALPGM package it can handle forbidden transitions and perturbations among many states.

  11. A computer program for a line-by-line calculation of spectra from diatomic molecules and atoms assuming a Voight line profile

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.; Lyle, G. C.; Whiting, E. E.

    1969-01-01

    Computer program predicts the spectra resulting from electronic transitions of diatomic molecules and atoms in local thermodynamic equilibrium. The program produces a spectrum by accounting for the contribution of each rotational and atomic line considered.

  12. Suppression of the FOXM1 transcriptional program via novel small molecule inhibition

    PubMed Central

    Gormally, Michael V.; Dexheimer, Thomas S.; Marsico, Giovanni; Sanders, Deborah A.; Lowe, Christopher; Matak-Vinkovi, Dijana; Michael, Sam; Jadhav, Ajit; Rai, Ganesha; Maloney, David J.; Simeonov, Anton; Balasubramanian, Shankar

    2014-01-01

    The transcription factor FOXM1 binds to sequence-specific motifs on DNA (C/TAAACA) through its DNA binding domain (DBD), and activates proliferation- and differentiation-associated genes. Aberrant overexpression of FOXM1 is a key feature in oncogenesis and progression of many human cancers. Here — from a high-throughput screen applied to a library of 54,211 small molecules — we identify novel small molecule inhibitors of FOXM1 that block DNA binding. One of the identified compounds: FDI-6 (NCGC00099374) is characterized in depth and is shown to bind directly to FOXM1 protein, to displace FOXM1 from genomic targets in MCF-7 breast cancer cells, and induce concomitant transcriptional down-regulation. Global transcript profiling of MCF-7 cells by RNA-seq shows that FDI-6 specifically down regulates FOXM1-activated genes with FOXM1 occupancy confirmed by ChIP-seq. This small molecule mediated effect is selective for FOXM1-controlled genes with no effect on genes regulated by homologous forkhead family factors. PMID:25387393

  13. Computer program for determining rotational line intensity factors for diatomic molecules

    NASA Technical Reports Server (NTRS)

    Whiting, E. E.

    1973-01-01

    A FORTRAN IV computer program, that provides a new research tool for determining reliable rotational line intensity factors (also known as Honl-London factors), for most electric and magnetic dipole allowed diatomic transitions, is described in detail. This users manual includes instructions for preparing the input data, a program listing, detailed flow charts, and three sample cases. The program is applicable to spin-allowed dipole transitions with either or both states intermediate between Hund's case (a) and Hund's case (b) coupling and to spin-forbidden dipole transitions with either or both states intermediate between Hund's case (c) and Hund's case (b) coupling.

  14. Structure and interactions of the human programmed cell death 1 receptor.

    PubMed

    Cheng, Xiaoxiao; Veverka, Vaclav; Radhakrishnan, Anand; Waters, Lorna C; Muskett, Frederick W; Morgan, Sara H; Huo, Jiandong; Yu, Chao; Evans, Edward J; Leslie, Alasdair J; Griffiths, Meryn; Stubberfield, Colin; Griffin, Robert; Henry, Alistair J; Jansson, Andreas; Ladbury, John E; Ikemizu, Shinji; Carr, Mark D; Davis, Simon J

    2013-04-26

    PD-1, a receptor expressed by T cells, B cells, and monocytes, is a potent regulator of immune responses and a promising therapeutic target. The structure and interactions of human PD-1 are, however, incompletely characterized. We present the solution nuclear magnetic resonance (NMR)-based structure of the human PD-1 extracellular region and detailed analyses of its interactions with its ligands, PD-L1 and PD-L2. PD-1 has typical immunoglobulin superfamily topology but differs at the edge of the GFCC' sheet, which is flexible and completely lacks a C" strand. Changes in PD-1 backbone NMR signals induced by ligand binding suggest that, whereas binding is centered on the GFCC' sheet, PD-1 is engaged by its two ligands differently and in ways incompletely explained by crystal structures of mouse PD-1 · ligand complexes. The affinities of these interactions and that of PD-L1 with the costimulatory protein B7-1, measured using surface plasmon resonance, are significantly weaker than expected. The 3-4-fold greater affinity of PD-L2 versus PD-L1 for human PD-1 is principally due to the 3-fold smaller dissociation rate for PD-L2 binding. Isothermal titration calorimetry revealed that the PD-1/PD-L1 interaction is entropically driven, whereas PD-1/PD-L2 binding has a large enthalpic component. Mathematical simulations based on the biophysical data and quantitative expression data suggest an unexpectedly limited contribution of PD-L2 to PD-1 ligation during interactions of activated T cells with antigen-presenting cells. These findings provide a rigorous structural and biophysical framework for interpreting the important functions of PD-1 and reveal that potent inhibitory signaling can be initiated by weakly interacting receptors.

  15. Theoretical research program to predict the properties of molecules and clusters containing transition metal atoms

    NASA Technical Reports Server (NTRS)

    Walch, S.

    1984-01-01

    The primary focus of this research has been the theoretical study of transition metal (TM) chemistry. A major goal of this work is to provide reliable information about the interaction of H atoms with iron metal. This information is needed to understand the effect of H atoms on the processes of embrittlement and crack propagation in iron. The method in the iron hydrogen studies is the cluster method in which the bulk metal is modelled by a finite number of iron atoms. There are several difficulties in the application of this approach to the hydrogen iron system. First the nature of TM-TM and TM-H bonding for even diatomic molecules was not well understood when these studies were started. Secondly relatively large iron clusters are needed to provide reasonable results.

  16. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  17. Programmed Lab Experiments for Biochemical Investigation of Quorum-Sensing Signal Molecules in Rhizospheric Soil Bacteria

    ERIC Educational Resources Information Center

    Nievas, Fiorela L.; Bogino, Pablo C.; Giordano, Walter

    2016-01-01

    Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences…

  18. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Mielke, Steven L.; Clarkson, Kenneth L.; Truhlar, Donald G.

    2012-08-01

    We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Catalogue identifier: AEMF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon

  19. DVR3D: a program suite for the calculation of rotation-vibration spectra of triatomic molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan; Kostin, Maxim A.; Barletta, Paolo; Harris, Gregory J.; Polyansky, Oleg L.; Ramanlal, Jayesh; Zobov, Nikolai F.

    2004-11-01

    The DVR3D program suite calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules. Potential energy and, where necessary, dipole surfaces must be provided. Expectation values of geometrically defined functions can be calculated, a feature which is particularly useful for fitting potential energy surfaces. The programs use an exact (within the Born-Oppenheimer approximation) Hamiltonian and offer a choice of Jacobi or Radau internal coordinates and several body-fixed axes. Rotationally excited states are treated using an efficient two-step algorithm. The programs uses a Discrete Variable Representation (DVR) based on Gauss-Jacobi and Gauss-Laguerre quadrature for all 3 internal coordinates and thus yields a fully point-wise representation of the wavefunctions. The vibrational step uses successive diagonalisation and truncation which is implemented for a number of possible coordinate orderings. The rotational, expectation value and transition dipole programs exploit the savings offered by performing integrals on a DVR grid. The new version has been rewritten in FORTRAN 90 to exploit the dynamic array allocations and the algorithm for dipole and spectra calculations have been substantially improved. New modules allow the z-axis to be embedded perpendicular to the plane of the molecule and for the calculation of expectation values. Program summaryTitle of the program: DVR3D suite Catalogue number: ADTI Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTI Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Programming language: Fortran 90 No. of lines in distributed program, including test data, etc.: 61 574 No. of bytes in distributed program, including test data, etc.: 972 404 Distribution format: tar.gz New version summaryTitle of program: DVR3DRJZ Catalogue number: ADTB Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTB Program obtainable

  20. Perinatal programming of emotional brain circuits: an integrative view from systems to molecules

    PubMed Central

    Bock, Jörg; Rether, Kathy; Gröger, Nicole; Xie, Lan; Braun, Katharina

    2014-01-01

    Environmental influences such as perinatal stress have been shown to program the developing organism to adapt brain and behavioral functions to cope with daily life challenges. Evidence is now accumulating that the specific and individual effects of early life adversity on the functional development of brain and behavior emerge as a function of the type, intensity, timing and the duration of the adverse environment, and that early life stress (ELS) is a major risk factor for developing behavioral dysfunctions and mental disorders. Results from clinical as well as experimental studies in animal models support the hypothesis that ELS can induce functional “scars” in prefrontal and limbic brain areas, regions that are essential for emotional control, learning and memory functions. On the other hand, the concept of “stress inoculation” is emerging from more recent research, which revealed positive functional adaptations in response to ELS resulting in resilience against stress and other adversities later in life. Moreover, recent studies indicate that early life experiences and the resulting behavioral consequences can be transmitted to the next generation, leading to a transgenerational cycle of adverse or positive adaptations of brain function and behavior. In this review we propose a unifying view of stress vulnerability and resilience by connecting genetic predisposition and programming sensitivity to the context of experience-expectancy and transgenerational epigenetic traits. The adaptive maturation of stress responsive neural and endocrine systems requires environmental challenges to optimize their functions. Repeated environmental challenges can be viewed within the framework of the match/mismatch hypothesis, the outcome, psychopathology or resilience, depends on the respective predisposition and on the context later in life. PMID:24550772

  1. A Hybrid Program for Fitting Rotationally Resolved Spectra of Floppy Molecules with One Large-Amplitude Rotatory Motion and One Large-Amplitude Oscillatory Motion.

    PubMed

    Kleiner, Isabelle; Hougen, Jon T

    2015-10-29

    A new hybrid-model fitting program for methylamine-like molecules has been developed, on the basis of an effective Hamiltonian in which the ammonia-like inversion motion is treated using a tunneling formalism, whereas the internal-rotation motion is treated using an explicit kinetic energy operator and potential energy function. The Hamiltonian in the computer program is set up as a 2 × 2 partitioned matrix, where each diagonal block contains a traditional torsion-rotation Hamiltonian (as in the earlier program BELGI), and the two off-diagonal blocks contain tunneling terms. This hybrid formulation permits the use of the permutation-inversion group G6 (isomorphic to C(3v)) for terms in the two diagonal blocks but requires G12 for terms in the off-diagonal blocks. The first application of the new program is to 2-methylmalonaldehyde. Microwave data for this molecule were previously fit using an all-tunneling Hamiltonian formalism to treat both large-amplitude motions. For 2-methylmalonaldehyde, the hybrid program achieves the same quality of fit as was obtained with the all-tunneling program, but fits with the hybrid program eliminate a large discrepancy between internal rotation barriers in the OH and OD isotopologs of 2-methylmalonaldehyde that arose in fits with the all-tunneling program. This large isotopic shift in internal rotation barrier is thus almost certainly an artifact of the all-tunneling model. Other molecules for application of the hybrid program are mentioned.

  2. Defective Tapetum Cell Death 1 (DTC1) Regulates ROS Levels by Binding to Metallothionein during Tapetum Degeneration.

    PubMed

    Yi, Jakyung; Moon, Sunok; Lee, Yang-Seok; Zhu, Lu; Liang, Wanqi; Zhang, Dabing; Jung, Ki-Hong; An, Gynheung

    2016-03-01

    After meiosis, tapetal cells in the innermost anther wall layer undergo program cell death (PCD)-triggered degradation. This step is essential for microspore development and pollen wall maturation. We identified a key gene, Defective Tapetum Cell Death 1 (DTC1), that controls this degeneration by modulating the dynamics of reactive oxygen species (ROS) during rice male reproduction. Mutants defective in DTC1 exhibit phenotypes of an enlarged tapetum and middle layer with delayed degeneration, causing male sterility. The gene is preferentially expressed in the tapetal cells during early anther development. In dtc1 anthers, expression of genes encoding secretory proteases or lipid transporters is significantly reduced, while transcripts of PCD regulatory genes, e.g. UDT1, TDR1, and EAT1/DTD, are not altered. Moreover, levels of DTC1 transcripts are diminished in udt1, tdr, and eat1 anthers. These results suggest that DTC1 functions downstream of those transcription factor genes and upstream of the genes encoding secretory proteins. DTC1 protein interacts with OsMT2b, a ROS scavenger. Whereas wild-type plants accumulate large amounts of ROS in their anthers at Stage 9 of development, those levels remain low during all stages of development in dtc1 anthers. These findings indicate that DTC1 is a key regulator for tapetum PCD by inhibiting ROS-scavenging activity. PMID:26697896

  3. Defective Tapetum Cell Death 1 (DTC1) Regulates ROS Levels by Binding to Metallothionein during Tapetum Degeneration1[OPEN

    PubMed Central

    Moon, Sunok; Lee, Yang-Seok; Zhu, Lu; Jung, Ki-Hong; An, Gynheung

    2016-01-01

    After meiosis, tapetal cells in the innermost anther wall layer undergo program cell death (PCD)-triggered degradation. This step is essential for microspore development and pollen wall maturation. We identified a key gene, Defective Tapetum Cell Death 1 (DTC1), that controls this degeneration by modulating the dynamics of reactive oxygen species (ROS) during rice male reproduction. Mutants defective in DTC1 exhibit phenotypes of an enlarged tapetum and middle layer with delayed degeneration, causing male sterility. The gene is preferentially expressed in the tapetal cells during early anther development. In dtc1 anthers, expression of genes encoding secretory proteases or lipid transporters is significantly reduced, while transcripts of PCD regulatory genes, e.g. UDT1, TDR1, and EAT1/DTD, are not altered. Moreover, levels of DTC1 transcripts are diminished in udt1, tdr, and eat1 anthers. These results suggest that DTC1 functions downstream of those transcription factor genes and upstream of the genes encoding secretory proteins. DTC1 protein interacts with OsMT2b, a ROS scavenger. Whereas wild-type plants accumulate large amounts of ROS in their anthers at Stage 9 of development, those levels remain low during all stages of development in dtc1 anthers. These findings indicate that DTC1 is a key regulator for tapetum PCD by inhibiting ROS-scavenging activity. PMID:26697896

  4. Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1.

    PubMed

    Brosché, Mikael; Blomster, Tiina; Salojärvi, Jarkko; Cui, Fuqiang; Sipari, Nina; Leppälä, Johanna; Lamminmäki, Airi; Tomai, Gloria; Narayanasamy, Shaman; Reddy, Ramesha A; Keinänen, Markku; Overmyer, Kirk; Kangasjärvi, Jaakko

    2014-02-01

    Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR. PMID:24550736

  5. Transcriptomics and Functional Genomics of ROS-Induced Cell Death Regulation by RADICAL-INDUCED CELL DEATH1

    PubMed Central

    Salojärvi, Jarkko; Cui, Fuqiang; Sipari, Nina; Leppälä, Johanna; Lamminmäki, Airi; Tomai, Gloria; Narayanasamy, Shaman; Reddy, Ramesha A.; Keinänen, Markku; Overmyer, Kirk; Kangasjärvi, Jaakko

    2014-01-01

    Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR. PMID:24550736

  6. Arabidopsis radical-induced cell death1 is involved in UV-B signaling.

    PubMed

    Jiang, Lei; Wang, Yan; Björn, Lars Olof; Li, Shaoshan

    2009-06-01

    The Arabidopsis radical-induced cell death1 (rcd1) mutant is sensitive to ozone fumigation and apoplastic superoxide, but tolerant to methyl viologen. In the present article, we report that the rcd1 mutant is also tolerant to supplementary UV-B radiation. The rcd1-1 mutant exhibits less accumulation of TT dimers, increased hypocotyl growth inhibition and higher accumulation of flavonoids under supplemental UV-B radiation. Moreover, the expression of HY5 (elongated hypocotyl5) is increased in the mutant after UV-B treatment. Gene expression downstream of UV-B signaling reveals that COP1 (constitutively photomorphogenic1)-regulated genes have an elevated expression in rcd1-1 mutant under UV-B radiation, while expression of UVR8 (UV resistance locus 8)-regulated and HY5-independent genes are not changed. Interestingly, the expression of RCD1 genes is not significantly changed by UV-B radiation. Previous study has shown that STO protein is interacting with RCD1 in vitro. Here, we found the mRNA level of STO (salt tolerance) is greatly increased in rcd1-1 mutant after UV-B radiation. However, UV-B-induced HY5 and CHS expression is partially inhibited in sto mutant. Based on the above results, it is deduced that the RCD1, working together with STO, is involved in Arabidopsis UV-B signaling.

  7. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  8. Programmed Death-1 Affects Suppressor of Cytokine Signaling-1 Expression in T Cells During Hepatitis C Infection

    PubMed Central

    Frazier, Ashley D.; Zhang, Chun L.; Ni, Lei; Ma, Cheng J.; Zhang, Ying; Wu, Xiao Y.; Atia, Antwan N.; Yao, Zhi Q.

    2010-01-01

    Abstract Chronic hepatitis C virus (HCV) infection is associated with T-cell exhaustion that is mediated through upregulation of the PD-1 negative regulatory pathway. PD-1 expression is induced by HCV core protein, which also induces upregulation of SOCS-1, a key modulator that controls the Jak/STAT pathway regulating cytokine expression. To determine whether these two negative regulatory pathways are linked during T-cell signaling, SOCS-1 expression was examined by blocking the PD-1 pathway in T cells stimulated with anti-CD3/CD28 in the presence of HCV core protein. T cells isolated from healthy subjects or HCV-infected individuals were treated with anti-PD-1 or anti-PDL-1 antibodies in the presence or absence of HCV core protein, and SOCS-1 gene expression was detected by RT-PCR or immunoblotting, while T-cell functions were assayed by flow cytometric analyses. Both PD-1 and SOCS-1 gene expression were upregulated in healthy T cells exposed to HCV core protein, and blocking the PD-1 pathway downregulated SOCS-1 gene expression in these cells. Additionally, T cells isolated from chronically HCV-infected subjects exhibited increased PD-1 and SOCS-1 expression compared to healthy subjects, and SOCS-1 expression in T cells isolated from HCV-infected subjects was also inhibited by blocking PD-1 signaling; this in turn enhanced the phosphorylation of STAT-1, and improved the impaired T-cell proliferation observed in the setting of HCV infection. These data demonstrate that PD-1 and SOCS-1 are linked in dysregulating T-cell signaling during HCV infection, and their cross-talk may coordinately inhibit T-cell signaling pathways that lead to T-cell exhaustion during chronic viral infection. PMID:20883163

  9. Using Symmetry Group Correlation Tables to Explain why Erham (and Other Programs) cannot BE Used to Analyze Torsional Splittings of Some Molecules

    NASA Astrophysics Data System (ADS)

    Groner, Peter

    2016-06-01

    ERHAM has been used to analyze rotational spectra of many molecules with torsional splitting caused by one or two internal rotors. The gauche form of dimethyl ether-d1 whose equilibrium structure has C1 symmetry is an example of a molecule for which ERHAM could not model additional small splittings resolvable for many transitions, whereas the spectrum of the symmetric (anti, trans) form with a C{_s} equilibrium structure could be analyzed successfully with ERHAM. A more recent example where ERHAM failed is pinacolone CH_3-CO-C(CH_3)_3. In this case, the barriers to internal rotation of the methyl groups within the -C(CH_3)_3 unit are too high to produce observable internal rotation splittings, but the splittings due to the CH_3-CO methyl group could not be modeled correctly with ERHAM nor with any other available program (XIAM, BELGI-Cs, BELGI-C1, RAM36). In the paper, it was speculated that BELGI-Cs-2tops might be able to the job, but arguments against this possibility have also been put forward. The correlation between irreducible representations of groups and their subgroups according to Watson can be used not only to determine the total number of substates (components) to be expected but also to help decide which particular program has a chance for a successful analysis. As it turns out, the number of components of split lines depends on the molecular symmetry at equilibrium in relation to the highest possible symmetry for a given molecular symmetry group. Therefore, for pinacolone, the vibrational ground state is split into 10 torsional substates. P. Groner, J. Mol. Spectrosc. 278 (2012) 52-67. C. Richard et al. A&A 552 (2013), A117. Y. Zhao et al., J. Mol. Spectrosc. 318 (2015) 91-100, with references to all other programs mentioned in the abstract. J. K. G. Watson, Can. J. Physics 43 (1965) 1996-2007.

  10. Comprehensive Analysis of the Therapeutic IgG4 Antibody Pembrolizumab: Hinge Modification Blocks Half Molecule Exchange In Vitro and In Vivo.

    PubMed

    Yang, Xiaoyu; Wang, Fengqiang; Zhang, Ying; Wang, Larry; Antonenko, Svetlana; Zhang, Shuli; Zhang, Yi Wei; Tabrizifard, Mohammad; Ermakov, Grigori; Wiswell, Derek; Beaumont, Maribel; Liu, Liming; Richardson, Daisy; Shameem, Mohammed; Ambrogelly, Alexandre

    2015-12-01

    IgG4 antibodies are evolving as an important class of cancer immunotherapies. However, human IgG4 can undergo Fab arm (half molecule) exchange with other IgG4 molecules in vivo. The hinge modification by a point mutation (S228P) prevents half molecule exchange of IgG4. However, the experimental confirmation is still expected by regulatory agencies. Here, we report for the first time the extensive analysis of half molecule exchange for a hinge-modified therapeutic IgG4 molecule, pembrolizumab (Keytruda) targeting programmed death 1 (PD1) receptor that was approved for advanced melanoma. Studies were performed in buffer or human serum using multiple exchange partners including natalizumab (Tysabri) and human IgG4 pool. Formation of bispecific antibodies was monitored by fluorescence resonance energy transfer, exchange with Fc fragments, mixed mode chromatography, immunoassays, and liquid chromatography-mass spectrometry. The half molecule exchange was also examined in vivo in SCID (severe combined immunodeficiency) mice. Both in vitro and in vivo results indicate that the hinge modification in pembrolizumab prevented half molecule exchange, whereas the unmodified counterpart anti-PD1 wt showed active exchange activity with other IgG4 antibodies or self-exchange activity with its own molecules. Our work, as an example expected for meeting regulatory requirements, contributes to establish without ambiguity that hinge-modified IgG4 antibodies are suitable for biotherapeutic applications.

  11. Dehydroascorbate: a possible surveillance molecule of oxidative stress and programmed cell death in the green alga Chlamydomonas reinhardtii.

    PubMed

    Murik, Omer; Elboher, Ahinoam; Kaplan, Aaron

    2014-04-01

    Chlamydomonas reinhardtii tolerates relatively high H2 O2 levels that induce an array of antioxidant activities. However, rather than rendering the cells more resistant to oxidative stress, the cells become far more sensitive to an additional H2 O2 dose. If H2 O2 is provided 1.5-9 h after an initial dose, it induces programmed cell death (PCD) in the wild-type, but not in the dum1 mutant impaired in the mitochondrial respiratory complex III. This mutant does not exhibit a secondary oxidative burst 4-5 h after the inducing H2 O2 , nor does it activate metacaspase-1 after the second H2 O2 treatment. The intracellular dehydroascorbate level, a product of ascorbate peroxidase, increases under conditions leading to PCD. The addition of dehydroascorbate induces PCD in the wild-type and dum1 cultures, but higher levels are required in dum1 cells, where it is metabolized faster. The application of dehydroascorbate induces the expression of metacaspase-2, which is much stronger than the expression of metacaspase-1. The presence or absence of oxidative stress, in addition to the rise in internal dehydroascorbate, may determine which metacaspase is activated during Chlamydomonas PCD. Cell death is strongly affected by the timing of H2 O2 or dehydroascorbate admission to synchronously grown cultures, suggesting that the cell cycle phase may distinguish cells that perish from those that do not. PMID:24345283

  12. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  13. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  14. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  15. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  16. VASCULAR ASSOCIATED DEATH1, a Novel GRAM Domain–Containing Protein, Is a Regulator of Cell Death and Defense Responses in Vascular Tissues

    PubMed Central

    Lorrain, Séverine; Lin, Baiqing; Auriac, Marie Christine; Kroj, Thomas; Saindrenan, Patrick; Nicole, Michel; Balagué, Claudine; Roby, Dominique

    2004-01-01

    The hypersensitive response (HR) is a programmed cell death that is commonly associated with plant disease resistance. A novel lesion mimic mutant, vad1 (for vascular associated death1), that exhibits light conditional appearance of propagative HR-like lesions along the vascular system was identified. Lesion formation is associated with expression of defense genes, production of high levels of salicylic acid (SA), and increased resistance to virulent and avirulent strains of Pseudomonas syringae pv tomato. Analyses of the progeny from crosses between vad1 plants and either nahG transgenic plants, sid1, nonexpressor of PR1 (npr1), enhanced disease susceptibility1 (eds1), or non-race specific disease resistance1 (ndr1) mutants, revealed the vad1 cell death phenotype to be dependent on SA biosynthesis but NPR1 independent; in addition, both EDS1 and NDR1 are necessary for the proper timing and amplification of cell death as well as for increased resistance to Pseudomonas strains. VAD1 encodes a novel putative membrane-associated protein containing a GRAM domain, a lipid or protein binding signaling domain, and is expressed in response to pathogen infection at the vicinity of the hypersensitive lesions. VAD1 might thus represent a new potential function in cell death control associated with cells in the vicinity of vascular bundles. PMID:15269331

  17. 'Escentric' molecules.

    PubMed

    Schön, Geza

    2008-06-01

    Can a fragrance be revolutionary? In this commentary, the creation of two unusual, extravagant fine fragrances, 'escentric01' and 'molecule01', is described. In response to the fantasy components found in release notes of many recent perfume launches, both center around a single real fragrance raw material, the transparent woody aroma chemical 'Iso E Super' (1+2). The perfume 'escentric01' contains 65% of it, accompanied by Trisamber (3), red pepper, lime oil, incense and musks, while 'molecule01' consists exclusively of 'Iso E Super' (1+2). The elegant woody note lives here its own eccentric life--the revolution starts.

  18. Walking molecules.

    PubMed

    von Delius, Max; Leigh, David A

    2011-07-01

    Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references). PMID:21416072

  19. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  20. Small molecule-directed specification of sclerotome-like chondroprogenitors and induction of a somitic chondrogenesis program from embryonic stem cells.

    PubMed

    Zhao, Jiangang; Li, Songhui; Trilok, Suprita; Tanaka, Makoto; Jokubaitis-Jameson, Vanta; Wang, Bei; Niwa, Hitoshi; Nakayama, Naoki

    2014-10-01

    Pluripotent embryonic stem cells (ESCs) generate rostral paraxial mesoderm-like progeny in 5-6 days of differentiation induced by Wnt3a and Noggin (Nog). We report that canonical Wnt signaling introduced either by forced expression of activated β-catenin, or the small-molecule inhibitor of Gsk3, CHIR99021, satisfied the need for Wnt3a signaling, and that the small-molecule inhibitor of BMP type I receptors, LDN193189, was able to replace Nog. Mesodermal progeny generated using such small molecules were chondrogenic in vitro, and expressed trunk paraxial mesoderm markers such as Tcf15 and Meox1, and somite markers such as Uncx, but failed to express sclerotome markers such as Pax1. Induction of the osteochondrogenically committed sclerotome from somite requires sonic hedgehog and Nog. Consistently, Pax1 and Bapx1 expression was induced when the isolated paraxial mesodermal progeny were treated with SAG1 (a hedgehog receptor agonist) and LDN193189, then Sox9 expression was induced, leading to cartilaginous nodules and particles in the presence of BMP, indicative of chondrogenesis via sclerotome specification. By contrast, treatment with TGFβ also supported chondrogenesis and stimulated Sox9 expression, but failed to induce the expression of Pax1 and Bapx1. On ectopic transplantation to immunocompromised mice, the cartilage particles developed under either condition became similarly mineralized and formed pieces of bone with marrow. Thus, the use of small molecules led to the effective generation from ESCs of paraxial mesodermal progeny, and to their further differentiation in vitro through sclerotome specification into growth plate-like chondrocytes, a mechanism resembling in vivo somitic chondrogenesis that is not recapitulated with TGFβ. PMID:25294938

  1. Programs.

    ERIC Educational Resources Information Center

    Community College Journal, 1996

    1996-01-01

    Includes a collection of eight short articles describing model community college programs. Discusses a literacy program, a mobile computer classroom, a support program for at-risk students, a timber-harvesting program, a multimedia presentation on successful women graduates, a career center, a collaboration with NASA, and an Israeli engineering…

  2. Cell Wall Invertase Promotes Fruit Set under Heat Stress by Suppressing ROS-Independent Cell Death1[OPEN

    PubMed Central

    2016-01-01

    Reduced cell wall invertase (CWIN) activity has been shown to be associated with poor seed and fruit set under abiotic stress. Here, we examined whether genetically increasing native CWIN activity would sustain fruit set under long-term moderate heat stress (LMHS), an important factor limiting crop production, by using transgenic tomato (Solanum lycopersicum) with its CWIN inhibitor gene silenced and focusing on ovaries and fruits at 2 d before and after pollination, respectively. We found that the increase of CWIN activity suppressed LMHS-induced programmed cell death in fruits. Surprisingly, measurement of the contents of H2O2 and malondialdehyde and the activities of a cohort of antioxidant enzymes revealed that the CWIN-mediated inhibition on programmed cell death is exerted in a reactive oxygen species-independent manner. Elevation of CWIN activity sustained Suc import into fruits and increased activities of hexokinase and fructokinase in the ovaries in response to LMHS. Compared to the wild type, the CWIN-elevated transgenic plants exhibited higher transcript levels of heat shock protein genes Hsp90 and Hsp100 in ovaries and HspII17.6 in fruits under LMHS, which corresponded to a lower transcript level of a negative auxin responsive factor IAA9 but a higher expression of the auxin biosynthesis gene ToFZY6 in fruits at 2 d after pollination. Collectively, the data indicate that CWIN enhances fruit set under LMHS through suppression of programmed cell death in a reactive oxygen species-independent manner that could involve enhanced Suc import and catabolism, HSP expression, and auxin response and biosynthesis. PMID:27462084

  3. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  4. Cell-Extrinsic MHC Class I Molecule Engagement Augments Human NK Cell Education Programmed by Cell-Intrinsic MHC Class I.

    PubMed

    Boudreau, Jeanette E; Liu, Xiao-Rong; Zhao, Zeguo; Zhang, Aaron; Shultz, Leonard D; Greiner, Dale L; Dupont, Bo; Hsu, Katharine C

    2016-08-16

    The effector potential of NK cells is counterbalanced by their sensitivity to inhibition by "self" MHC class I molecules in a process called "education." In humans, interactions between inhibitory killer immunoglobulin-like receptors (KIR) and human MHC (HLA) mediate NK cell education. In HLA-B(∗)27:05(+) transgenic mice and in patients undergoing HLA-mismatched hematopoietic cell transplantation (HCT), NK cells derived from human CD34(+) stem cells were educated by HLA from both donor hematopoietic cells and host stromal cells. Furthermore, mature human KIR3DL1(+) NK cells gained reactivity after adoptive transfer to HLA-B(∗)27:05(+) mice or bone marrow chimeric mice where HLA-B(∗)27:05 was restricted to either the hematopoietic or stromal compartment. Silencing of HLA in primary NK cells diminished NK cell reactivity, while acquisition of HLA from neighboring cells increased NK cell reactivity. Altogether, these findings reveal roles for cell-extrinsic HLA in driving NK cell reactivity upward, and cell-intrinsic HLA in maintaining NK cell education.

  5. Singlet Oxygen-Induced Membrane Disruption and Serpin-Protease Balance in Vacuolar-Driven Cell Death1[OPEN

    PubMed Central

    Carmieli, Raanan; Mor, Avishai; Fluhr, Robert

    2016-01-01

    Singlet oxygen plays a role in cellular stress either by providing direct toxicity or through signaling to initiate death programs. It was therefore of interest to examine cell death, as occurs in Arabidopsis, due to differentially localized singlet oxygen photosensitizers. The photosensitizers rose bengal (RB) and acridine orange (AO) were localized to the plasmalemma and vacuole, respectively. Their photoactivation led to cell death as measured by ion leakage. Cell death could be inhibited by the singlet oxygen scavenger histidine in treatments with AO but not with RB. In the case of AO treatment, the vacuolar membrane was observed to disintegrate. Concomitantly, a complex was formed between a vacuolar cell-death protease, RESPONSIVE TO DESSICATION-21 and its cognate cytoplasmic protease inhibitor ATSERPIN1. In the case of RB treatment, the tonoplast remained intact and no complex was formed. Over-expression of AtSerpin1 repressed cell death, only under AO photodynamic treatment. Interestingly, acute water stress showed accumulation of singlet oxygen as determined by fluorescence of Singlet Oxygen Sensor Green, by electron paramagnetic resonance spectroscopy and the induction of singlet oxygen marker genes. Cell death by acute water stress was inhibited by the singlet oxygen scavenger histidine and was accompanied by vacuolar collapse and the appearance of serpin-protease complex. Over-expression of AtSerpin1 also attenuated cell death under this mode of cell stress. Thus, acute water stress damage shows parallels to vacuole-mediated cell death where the generation of singlet oxygen may play a role. PMID:26884487

  6. The entropies of adsorbed molecules.

    PubMed

    Campbell, Charles T; Sellers, Jason R V

    2012-10-31

    Adsorbed molecules are involved in many reactions on solid surface that are of great technological importance. As such, there has been tremendous effort worldwide to learn how to predict reaction rates and equilibrium constants for reactions involving adsorbed molecules. Theoretical calculation of both the rate and equilibrium constants for such reactions requires knowing the entropy and enthalpy of the adsorbed molecule. While much effort has been devoted to measuring and calculating the enthalpies of well-defined adsorbates, few measurements of the entropies of adsorbates have been reported. We present here a new way to determine the standard entropies of adsorbed molecules (S(ad)(0)) on single crystal surfaces from temperature programmed desorption data, prove its accuracy by comparison to entropies measured by equilibrium methods, and apply it to published data to extract new entropies. Most importantly, when combined with reported entropies, we find that at high coverage, they linearly track the entropy of the gas-phase molecule at the same temperature (T), such that S(ad)(0)(T) = 0.70 S(gas)(0)(T) - 3.3R (R = the gas constant), with a standard deviation of only 2R over a range of 50R. These entropies, which are ~2/3 of the gas, are huge compared to most theoretical predictions. This result can be extended to reliably predict prefactors in the Arrhenius rate constant for surface reactions involving such species, as proven here for desorption. PMID:23033909

  7. Conserved water molecules in bacterial serine hydroxymethyltransferases.

    PubMed

    Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

    2015-10-01

    Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments.

  8. Evaluation of Costimulatory Molecules in Peripheral Blood Lymphocytes of Canine Patients with Histiocytic Sarcoma

    PubMed Central

    Tagawa, Michihito; Maekawa, Naoya; Konnai, Satoru; Takagi, Satoshi

    2016-01-01

    Histiocytic sarcoma is a rapidly progressive and fatal neoplastic disease in dogs. It is unclear whether costimulatory molecules, including CD28, cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4), and programmed death-1 (PD-1), are expressed on peripheral blood lymphocytes (PBLs) of canine patients with histiocytic sarcoma. The objective of this study was to evaluate the expression of CD28, CTLA-4, and PD-1 molecules on PBLs of patients with histiocytic sarcoma, patients with other tumors, and healthy controls. Twenty-six dogs were included in the study, with eight, ten, and eight dogs in the histiocytic sarcoma, other tumor, and healthy control groups, respectively. PBLs and serum were prospectively obtained from patients diagnosed histopathologically with histiocytic sarcoma, other tumors and healthy controls. The surface expression of CTLA-4, CD28, and PD-1 on T lymphocytes was examined using flow cytometric analysis. Serum samples were frozen at −30°C until serum interferon-γ (IFN-γ) was measured by enzyme-linked immunosorbent assay. The expression level of CTLA-4 on CD4+ lymphocytes was significantly higher in the histiocytic sarcoma group than in the control group. The expression of CTLA-4 on CD8+ lymphocytes was significantly higher in the histiocytic sarcoma group than in the other two groups. In addition, the expression of PD-1 on CD8+ lymphocytes was significantly higher in the histiocytic sarcoma group than in the control group. However, no significant differences in CD28 expressions and serum IFN-γ levels were observed. The present results provided evidence showing that the expression levels of CTLA-4 on both CD4+ and CD8+ lymphocytes and PD-1 on CD8+ lymphocytes in peripheral blood obtained from dogs with histiocytic sarcoma were upregulated. The overexpressions of CTLA 4 and PD-1 suggested that antitumor immunity may be suppressed in dogs with histiocytic sarcoma. PMID:26901565

  9. [Endothelial cell adhesion molecules].

    PubMed

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  10. Final Report: Cooling Molecules with Laser Light

    SciTech Connect

    Di Rosa, Michael D.

    2012-05-08

    Certain diatomic molecules are disposed to laser cooling in the way successfully applied to certain atoms and that ushered in a revolution in ultracold atomic physics, an identification first made at Los Alamos and which took root during this program. Despite their manipulation into numerous achievements, atoms are nonetheless mundane denizens of the quantum world. Molecules, on the other hand, with their internal degrees of freedom and rich dynamical interplay, provide considerably more complexity. Two main goals of this program were to demonstrate the feasibility of laser-cooling molecules to the same temperatures as laser-cooled atoms and introduce a means for collecting laser-cooled molecules into dense ensembles, a foundational start of studies and applications of ultracold matter without equivalence in atomic systems.

  11. Parallel Molecular Dynamics Program for Molecules

    SciTech Connect

    Plimpton, Steve

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  12. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  13. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  14. Molecular cloning and responsive expression to injury stimulus of a defender against cell death 1 (DAD1) gene from bay scallops Argopecten irradians.

    PubMed

    Zhu, Ling; Song, Linsheng; Zhang, Huan; Zhao, Jianmin; Li, Chenghua; Xu, Wei

    2008-06-01

    Apoptosis is an active process of cell death, which is an integral part of growth and development in multicellular organisms. The defender against cell death 1 (DAD1), the regulatory protein to inhibit the apoptosis process, was first cloned from the bay scallop Argopecten irradians by randomly sequencing a whole tissue cDNA library and rapid amplification of cDNA end (RACE). The full-length cDNA of the A. irradians DAD1 was 607 bp, consist of a 5'-terminal untranslated region (UTR) of 63 bp, a 3'-terminal UTR of 205 bp with a canonical polyadenylation signal sequence AATAAA and a poly (A) tail, and an open reading frame of 339 bp. The deduced amino acid sequence of the A. irradians DAD1 showed 75.5% identity to Araneus ventricosus, 74.5% to Drosophila melanogaster, and 73.6% to Homo sapiens, Sus scrofa, Mesocricetus auratus, Rattus norvegicus and Mus musculus. Excluding the Saccharomyces cerevisiae DAD1 homologue, all animal DAD1 including A. irradians DAD1 homologue formed a subgroup and all plant DAD1 proteins formed another subgroup in the phylogenetic analysis. The A. irradians DAD1 was expressed in all examined tissues including adductor muscle, mantle, gills, digestive gland, gonad and hemolymph, suggesting that A. irradians DAD1 is expressed in most body tissues. Furthermore, the mRNA expression levels of A. irradians DAD1 gene of hemolymph were particularly high after injury, suggesting that the gene is responsive to injury stimuli. PMID:17294251

  15. Chemical Recycling of Molecules in Cometary Comae

    NASA Astrophysics Data System (ADS)

    Boice, Daniel C.; Kawakita, Hideyo; Shinnaka, Yoshiharu; Kobayashi, Hitomi

    2015-08-01

    Modeling is essential to understand the important physical and chemical processes that occur in cometary comae, especially the relationship between native and sibling molecules, such as, HCN and CN. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms observed in comets. The effects of photoelectrons that react via impacts are important to the overall ionization in the inner coma. We have found that many molecules undergo protonation reactions with primarily water, followed by electron recombination resulting in the original molecules in a vibrationally excited state. These excited molecules spontaneously emit photons back to the ground state. We identify this series of reactions as chemical “recycling.” We discuss the importance of this mechanism for HCN, NH3, and water in comets. We also identify other relevant processes in the collision-dominated, inner coma of a comet within a global modeling framework to better understand observations and in situ measurements of cometary species, especially relationships between native and sibling molecules for the Rosetta Mission to Comet 67P/Churyumov-Gerasimenko.Acknowledgements: We appreciate support from the NSF Planetary Astronomy Program under Grant No. 0908529. This program is partially supported by the MEXT Supported Program for the Strategic Research Foundation at Private Universities, 2014-2018.

  16. Linking ultracold polar molecules.

    PubMed

    Avdeenkov, A V; Bohn, John L

    2003-01-31

    We predict that pairs of polar molecules can be weakly bound together in an ultracold environment, provided that a dc electric field is present. The field that links the molecules together also strongly influences the basic properties of the resulting dimer, such as its binding energy and predissociation lifetime. Because of their long-range character, these dimers will be useful in disentangling cold collision dynamics of polar molecules. As an example, we estimate the microwave photoassociation yield for OH-OH cold collisions.

  17. Chlorophyll breakdown: Pheophorbide a oxygenase is a Rieske-type iron–sulfur protein, encoded by the accelerated cell death 1 gene

    PubMed Central

    Pružinská, Adriana; Tanner, Gaby; Anders, Iwona; Roca, Maria; Hörtensteiner, Stefan

    2003-01-01

    Chlorophyll (chl) breakdown during senescence is an integral part of plant development and leads to the accumulation of colorless catabolites. The loss of green pigment is due to an oxygenolytic opening of the porphyrin macrocycle of pheophorbide (pheide) a followed by a reduction to yield a fluorescent chl catabolite. This step is comprised of the interaction of two enzymes, pheide a oxygenase (PaO) and red chl catabolite reductase. PaO activity is found only during senescence, hence PaO seems to be a key regulator of chl catabolism. Whereas red chl catabolite reductase has been cloned, the nature of PaO has remained elusive. Here we report on the identification of the PaO gene of Arabidopsis thaliana (AtPaO). AtPaO is a Rieske-type iron–sulfur cluster-containing enzyme that is identical to Arabidopsis accelerated cell death 1 and homologous to lethal leaf spot 1 (LLS1) of maize. Biochemical properties of recombinant AtPaO were identical to PaO isolated from a natural source. Production of fluorescent chl catabolite-1 required ferredoxin as an electron source and both substrates, pheide a and molecular oxygen. By using a maize lls1 mutant, the in vivo function of PaO, i.e., degradation of pheide a during senescence, could be confirmed. Thus, lls1 leaves stayed green during dark incubation and accumulated pheide a that caused a light-dependent lesion mimic phenotype. Whereas proteins were degraded similarly in wild type and lls1, a chl-binding protein was selectively retained in the mutant. PaO expression correlated positively with senescence, but the enzyme appeared to be post-translationally regulated as well. PMID:14657372

  18. Chlorophyll breakdown: pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene.

    PubMed

    Pruzinská, Adriana; Tanner, Gaby; Anders, Iwona; Roca, Maria; Hörtensteiner, Stefan

    2003-12-01

    Chlorophyll (chl) breakdown during senescence is an integral part of plant development and leads to the accumulation of colorless catabolites. The loss of green pigment is due to an oxygenolytic opening of the porphyrin macrocycle of pheophorbide (pheide) a followed by a reduction to yield a fluorescent chl catabolite. This step is comprised of the interaction of two enzymes, pheide a oxygenase (PaO) and red chl catabolite reductase. PaO activity is found only during senescence, hence PaO seems to be a key regulator of chl catabolism. Whereas red chl catabolite reductase has been cloned, the nature of PaO has remained elusive. Here we report on the identification of the PaO gene of Arabidopsis thaliana (AtPaO). AtPaO is a Rieske-type iron-sulfur cluster-containing enzyme that is identical to Arabidopsis accelerated cell death 1 and homologous to lethal leaf spot 1 (LLS1) of maize. Biochemical properties of recombinant AtPaO were identical to PaO isolated from a natural source. Production of fluorescent chl catabolite-1 required ferredoxin as an electron source and both substrates, pheide a and molecular oxygen. By using a maize lls1 mutant, the in vivo function of PaO, i.e., degradation of pheide a during senescence, could be confirmed. Thus, lls1 leaves stayed green during dark incubation and accumulated pheide a that caused a light-dependent lesion mimic phenotype. Whereas proteins were degraded similarly in wild type and lls1, a chl-binding protein was selectively retained in the mutant. PaO expression correlated positively with senescence, but the enzyme appeared to be post-translationally regulated as well.

  19. Interlocked molecules: Aqueous assembly

    NASA Astrophysics Data System (ADS)

    Bai, Linyi; Zhao, Yanli

    2015-12-01

    The quantitative self-assembly of mechanically interlocked molecules in water, instead of organic solvents, opens up the possibility of such systems being used in a biological context where their functions can be interfaced with biomolecular systems.

  20. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  1. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  2. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  3. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  4. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  5. Single Molecule Manipulation

    NASA Astrophysics Data System (ADS)

    Kiang, Ching-Hwa

    2011-10-01

    Single-molecule manipulation studies open a door for a close-up investigation of complex biological interactions at the molecular level. In these studies, single biomolecules are pulled while their force response is being monitored. The process is often nonequilibrium, and interpretation of the results has been challenging. We used the atomic force microscope to pull proteins and DNA, and determined the equilibrium properties of the molecules using the recently derived nonequilibrium work theorem. I will present applications of the technique in areas ranging from fundamental biological problems such as DNA mechanics, to complex medical processes such as the mechanical activation of von Willebrand Factor, a key protein in blood coagulation.

  6. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  7. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  8. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  9. Halley's polymeric organic molecules

    NASA Technical Reports Server (NTRS)

    Huebner, W. F.; Boice, D. C.; Korth, A.

    1989-01-01

    The detection of polymeric organic compounds in the mass spectrum of Comet Halley obtained with the Positive Ion Cluster Composition analyzer on Giotto are examined. It is found that, in addition to polyoxymethylene, other polymers and complex molecules may exist in the comet. It is suggested that polymerized hydrogen cyanide may be a source for the observed CN and NH2 jets.

  10. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  11. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  12. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  13. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-09-17

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  14. The role of B7 family molecules in hematologic malignancy

    PubMed Central

    Greaves, Paul

    2013-01-01

    The B7 family consists of structurally related, cell-surface proteins that regulate immune responses by delivering costimulatory or coinhibitory signals through their ligands. Eight family members have been identified to date including CD80 (B7-1), CD86 (B7-2), CD274 (programmed cell death-1 ligand [PD-L1]), CD273 (programmed cell death-2 ligand [PD-L2]), CD275 (inducible costimulator ligand [ICOS-L]), CD276 (B7-H3), B7-H4, and B7-H6. B7 ligands are expressed on both lymphoid and nonlymphoid tissues. The importance of the B7 family in regulating immune responses is clear from their demonstrated role in the development of immunodeficiency and autoimmune diseases. Manipulation of the signals delivered by B7 ligands shows great potential in the treatment of cancers including leukemias and lymphomas and in regulating allogeneic T-cell responses after stem cell transplantation. PMID:23223433

  15. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  16. A toy model for a diatomic molecule

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-08-01

    We introduce a toy model for a diatomic molecule which is based on coupling electronic and nuclear spins to a rigid rotor. Despite its simplicity, the model can be used scientifically to analyze and understand complex molecular hyperfine spectra. In addition, the model has educational value as a number of fundamental symmetries and conservation laws of the molecule can be studied. Because of its simple structure, the model can be readily implemented as a computer program with comparatively short computing times on the order of a few seconds.

  17. Computer Modelling of Biological Molecules: Free Resources on the Internet.

    ERIC Educational Resources Information Center

    Millar, Neil

    1996-01-01

    Describes a three-dimensional computer modeling system for biological molecules which is suitable for sixth-form teaching. Consists of the modeling program "RasMol" together with structure files of proteins, DNA, and small biological molecules. Describes how the whole system can be downloaded from various sites on the Internet. (Author/JRH)

  18. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  19. Cometary Parent Molecules

    NASA Astrophysics Data System (ADS)

    Feldman, Paul

    1990-12-01

    We propose to use HRS observations of a suitable target-of-opportunity comet to study two outstanding problems related to the composition of the volatile component of the cometary nucleus. These problems concern two species, CO and S2, which have been observed in the cometary coma and identified as "parent" molecules sublimating directly from the nucleus. Both of these molecules have their principal fluorescent emissions in the vaccuum ultraviolet. The high spectral resolution will allow the determination of the rotational temperature of CO, which is diagnostic of the source temperature and the excitation mechanism of the observed emission. The determination of the abundance of both CO and S2 in the primarily water ice of the nucleus can serve to constrain current models of comet formation in the primordial solar nebula.

  20. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  1. Calculating Henry’s Constants of Charged Molecules Using SPARC

    EPA Science Inventory

    SPARC Performs Automated Reasoning in Chemistry is a computer program designed to model physical and chemical properties of molecules solely based on thier chemical structure. SPARC uses a toolbox of mechanistic perturbation models to model intermolecular interactions. SPARC has ...

  2. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  3. Molecules in crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Mark A.

    2013-04-01

    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  4. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  5. Advancing Biological Understanding and Therapeutics Discovery with Small Molecule Probes

    PubMed Central

    Schreiber, Stuart L.; Kotz, Joanne D.; Li, Min; Aubé, Jeffrey; Austin, Christopher P.; Reed, John C.; Rosen, Hugh; White, E. Lucile; Sklar, Larry A.; Lindsley, Craig W.; Alexander, Benjamin R.; Bittker, Joshua A.; Clemons, Paul A.; de Souza, Andrea; Foley, Michael A.; Palmer, Michelle; Shamji, Alykhan F.; Wawer, Mathias J.; McManus, Owen; Wu, Meng; Zou, Beiyan; Yu, Haibo; Golden, Jennifer E.; Schoenen, Frank J.; Simeonov, Anton; Jadhav, Ajit; Jackson, Michael R.; Pinkerton, Anthony B.; Chung, Thomas D.Y.; Griffin, Patrick R.; Cravatt, Benjamin F.; Hodder, Peter S.; Roush, William R.; Roberts, Edward; Chung, Dong-Hoon; Jonsson, Colleen B.; Noah, James W.; Severson, William E.; Ananthan, Subramaniam; Edwards, Bruce; Oprea, Tudor I.; Conn, P. Jeffrey; Hopkins, Corey R.; Wood, Michael R.; Stauffer, Shaun R.; Emmitte, Kyle A.

    2015-01-01

    Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery. PMID:26046436

  6. Melatonin: a multitasking molecule.

    PubMed

    Reiter, Russel J; Tan, Dun-Xian; Fuentes-Broto, Lorena

    2010-01-01

    Melatonin (N-acetyl-5-methoxytryptamine) has revealed itself as an ubiquitously distributed and functionally diverse molecule. The mechanisms that control its synthesis within the pineal gland have been well characterized and the retinal and biological clock processes that modulate the circadian production of melatonin in the pineal gland are rapidly being unravelled. A feature that characterizes melatonin is the variety of mechanisms it employs to modulate the physiology and molecular biology of cells. While many of these actions are mediated by well-characterized, G-protein coupled melatonin receptors in cellular membranes, other actions of the indole seem to involve its interaction with orphan nuclear receptors and with molecules, for example calmodulin, in the cytosol. Additionally, by virtue of its ability to detoxify free radicals and related oxygen derivatives, melatonin influences the molecular physiology of cells via receptor-independent means. These uncommonly complex processes often make it difficult to determine specifically how melatonin functions to exert its obvious actions. What is apparent, however, is that the actions of melatonin contribute to improved cellular and organismal physiology. In view of this and its virtual absence of toxicity, melatonin may well find applications in both human and veterinary medicine.

  7. Molecules Best Paper Award 2013.

    PubMed

    McPhee, Derek J

    2013-02-05

    Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.

  8. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?

  9. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  10. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another? PMID:17328425

  11. The Submillimeter-wave Rotational Spectra of Interstellar Molecules

    NASA Technical Reports Server (NTRS)

    Herbst, Eric; DeLucia, Frank C.; Butler, R. A. H.; Winnewisser, M.; Winnewisser, G.; Fuchs, U.; Groner, P.; Sastry, K. V. L. N.

    2002-01-01

    We discuss past and recent progress in our long-term laboratory program concerning the submillimeter-wave rotational spectroscopy of known and likely interstellar molecules, especially those associated with regions of high-mass star formation. Our program on the use of spectroscopy to study rotationally inelastic collisions of interstellar interest is also briefly mentioned.

  12. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOEpatents

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  13. Electron-excited molecule interactions

    SciTech Connect

    Christophorou, L.G. Tennessee Univ., Knoxville, TN . Dept. of Physics)

    1991-01-01

    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10{sup 6} to 10{sup 7} times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs.

  14. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  15. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  16. Single molecule tracking

    DOEpatents

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  17. Electrochromic Graphene Molecules

    DOE PAGESBeta

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  18. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  19. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole–dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  20. The Chloroplastic Protein THF1 Interacts with the Coiled-Coil Domain of the Disease Resistance Protein N′ and Regulates Light-Dependent Cell Death1[OPEN

    PubMed Central

    Sekine, Ken-Taro; Wallon, Thérèse; Sugiwaka, Yuji; Kobayashi, Kappei

    2016-01-01

    One branch of plant immunity is mediated through nucleotide-binding/Leu-rich repeat (NB-LRR) family proteins that recognize specific effectors encoded by pathogens. Members of the I2-like family constitute a well-conserved subgroup of NB-LRRs from Solanaceae possessing a coiled-coil (CC) domain at their N termini. We show here that the CC domains of several I2-like proteins are able to induce a hypersensitive response (HR), a form of programmed cell death associated with disease resistance. Using yeast two-hybrid screens, we identified the chloroplastic protein Thylakoid Formation1 (THF1) as an interacting partner for several I2-like CC domains. Co-immunoprecipitations and bimolecular fluorescence complementation assays confirmed that THF1 and I2-like CC domains interact in planta and that these interactions take place in the cytosol. Several HR-inducing I2-like CC domains have a negative effect on the accumulation of THF1, suggesting that the latter is destabilized by active CC domains. To confirm this model, we investigated N′, which recognizes the coat protein of most Tobamoviruses, as a prototypical member of the I2-like family. Transient expression and gene silencing data indicated that THF1 functions as a negative regulator of cell death and that activation of full-length N′ results in the destabilization of THF1. Consistent with the known function of THF1 in maintaining chloroplast homeostasis, we show that the HR induced by N′ is light-dependent. Together, our results define, to our knowledge, novel molecular mechanisms linking light and chloroplasts to the induction of cell death by a subgroup of NB-LRR proteins. PMID:26951433

  1. Aromatic molecules as spintronic devices

    SciTech Connect

    Ojeda, J. H.; Orellana, P. A.; Laroze, D.

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  2. Electrochromic Graphene Molecules

    SciTech Connect

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  3. Featured Molecules: Sucrose and Vanillin

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-04-01

    The WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  4. Proregenerative Properties of ECM Molecules

    PubMed Central

    Plantman, Stefan

    2013-01-01

    After traumatic injuries to the nervous system, regrowing axons encounter a complex microenvironment where mechanisms that promote regeneration compete with inhibitory processes. Sprouting and axonal regrowth are key components of functional recovery but are often counteracted by inhibitory molecules. This review covers extracellular matrix molecules that support neuron axonal outgrowth. PMID:24195084

  5. Micro-Kelvin cold molecules.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-10-01

    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  6. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  7. Random mutagenesis of the nucleotide-binding domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1), a downstream signalling nucleotide-binding, leucine-rich repeat (NB-LRR) protein, identifies gain-of-function mutations in the nucleotide-binding pocket.

    PubMed

    Sueldo, Daniela J; Shimels, Mahdere; Spiridon, Laurentiu N; Caldararu, Octav; Petrescu, Andrei-Jose; Joosten, Matthieu H A J; Tameling, Wladimir I L

    2015-10-01

    Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB-LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death. NRC1 (NB-LRR Required for HR-Associated Cell Death-1) is a tomato (Solanum lycopersicum) NB-LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae. To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide-binding domain and screened them for the ability to induce an elicitor-independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain-of-function mutants, with 10 of them caused by a single amino acid substitution. All substitutions are located in or very close to highly conserved motifs within the nucleotide-binding domain, suggesting modulation of the signalling activity of NRC1. Three-dimensional modelling of the nucleotide-binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain-of-function mutations in NRC1 and provides insight into how the activity of this NB-LRR is regulated.

  8. Associative Electron Stimulated Desorption of Neutral CO Molecules

    NASA Astrophysics Data System (ADS)

    Šutara, F.; Matolín, V.

    2001-11-01

    The Electron Stimulated Desorption (ESD) of neutral CO molecules was studied on polycrystalline Ni surface. Combined ESD and temperature programmed desorption (TPD) measurements were used to observe the variations of neutral ESD yield in dependence on CO coverage, containing direct information about the cross section for ESD of neutral CO molecules in relation to various CO adsorption states. The results show evidence of ESD of neutral CO molecules from dissociative adsorption states. The cross section for this associative ESD process is relatively high in comparison with the CO ESD cross section for molecular CO adsorption.

  9. Enzyme molecules in solitary confinement.

    PubMed

    Liebherr, Raphaela B; Gorris, Hans H

    2014-09-12

    Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  10. Molecule-hugging graphene nanopores.

    PubMed

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A; Branton, Daniel

    2013-07-23

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule's outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤ 0.6 nm along the length of the molecule. PMID:23836648

  11. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  12. Molecules within molecules: Recognition through self-assembly

    PubMed Central

    Hof, Fraser; Rebek, Julius

    2002-01-01

    Synthetic molecular receptors that completely surround their target molecules can be created through the use of noncovalent interactions. These molecular capsules selectively sequester guest molecules from the influence of bulk solvent and other molecules on the basis of size, shape, and chemical complementarity. This reversible isolation spawns unique behavior within the confines of the host; the catalysis of chemical reactions and the stabilization of reactive species are possible outcomes that have been recently demonstrated. Compartmentalization of reagents can also have a dramatic effect on reactions that take place outside of the capsule, producing nonlinear kinetics in relatively simple reaction systems. PMID:11880604

  13. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  14. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  15. Nonsequential double ionization of molecules

    SciTech Connect

    Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Zakrzewski, Jakub; Eckhardt, Bruno

    2005-03-01

    Double ionization of diatomic molecules by short linearly polarized laser pulses is analyzed. We consider the final stage of the ionization process, that is the decay of a highly excited two electron molecule, which is formed after rescattering. The saddles of the effective adiabatic potential energy close to which simultaneous escape of electrons takes place are identified. Numerical simulations of the ionization of molecules show that the process can be dominated by either sequential or nonsequential events. In order to increase the ratio of nonsequential to sequential ionizations very short laser pulses should be applied.

  16. Quantum transport through aromatic molecules

    SciTech Connect

    Ojeda, J. H.; Rey-González, R. R.; Laroze, D.

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  17. Organic heterocyclic molecules become superalkalis.

    PubMed

    Reddy, G Naaresh; Giri, Santanab

    2016-09-21

    An organic molecule which behaves like a superalkali has been designed from an aromatic heterocyclic molecule, pyrrole. Using first-principles calculation and a systematic two-step approach, we can have superalkali molecules with a low ionization energy, even lower than that of Cs. Couple cluster (CCSD) calculation reveals that a new heterocycle, C3N2(CH3)5 derived from a well-known aromatic heterocycle, pyrrole (C4H5N) has an ionization energy close to 3.0 eV. A molecular dynamics calculation on C3N2(CH3)5 reveals that the structure is dynamically stable. PMID:27530344

  18. Ab initio calculations of the photoionization of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Lefebvre-Brion, Helene; Raşeev, Georges

    2003-01-01

    A review is presented of the calculation of photoionization spectra, particularly in the spectral range where electron autoionization of diatomic molecules takes place. In addition to some interesting results obtained over years that compare favourably with experiment, the emphasis here is put on the relation between the methods developed for the calculation of observables associated with the continuum energy spectrum of the electrons and the Alchemy system of programs. This system of programs serves as a basis for initial and intermediate calculations. The examples presented show that diatomic molecules not only in gas phase but also oriented in space or physisorbed at surfaces may be studied readily.

  19. Laboratory spectroscopy of astrophysically interesting molecules

    SciTech Connect

    Davis, S.P.

    1987-11-01

    A systematic program on the laboratory analyses of selected molecular spectra, started in 1958, continues to the present day. The program has included tabulations of molecular spectra, analyses, calculations of molecular parameters, measurements of radiative lifetimes, and determinations of transition strengths. Work has been completed or is in progress on the spectra of ArH(+), CN, C/sub 2/, CS, CaCl, CaH, FeH, HgH, HgD, InI, OH, SH, Si/sub 2/, SiC/sub 2/, TiCl, TiO, TiO(+), ZrCl, ZrO, and ZrS. Molecules under consideration for future work are AlH, NH, SiH, TiH, NO, VO, CS, SiS, YS, CaOH, H/sub 2/O, HCN, C/sub 2/H/sub 2/, and C/sub 3/. 15 references.

  20. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  1. Moving Molecules and Mothball Madness.

    ERIC Educational Resources Information Center

    Strain, John

    1993-01-01

    Describes concrete demonstrations on the states of matter. In the first demonstration, students represent molecules; and, in the second demonstration, moth balls are heated to produce a change of state. (PR)

  2. Molecule-hugging graphene nanopores

    PubMed Central

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel

    2013-01-01

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule. PMID:23836648

  3. Cobalt single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Yang, En-Che; Hendrickson, David N.; Wernsdorfer, Wolfgang; Nakano, Motohiro; Zakharov, Lev N.; Sommer, Roger D.; Rheingold, Arnold L.; Ledezma-Gairaud, Marisol; Christou, George

    2002-05-01

    A cobalt molecule that functions as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atom ions at the corners of a cube. Variable-field and variable-temperature magnetization data have been analyzed to establish that the molecule has a S=6 ground state with considerable negative magnetoanisotropy. Single-ion zero-field interactions (DSz2) at each cobalt ion are the origin of the negative magnetoanisotropy. A single crystal of the compound was studied by means of a micro-superconducting quantum interference device magnetometer in the range of 0.040-1.0 K. Hysteresis was found in the magnetization versus magnetic field response of this single crystal.

  4. Surface chemistry of deuterated molecules

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    1983-03-01

    The chemical composition of grain mantles is calculated in order to determine the concentration of deuterated molecules relative to their hydrogenated counterparts in grain mantles. The computation takes into account reactions involving deuterium in the gas phase and on grain surfaces. The results show that the abundance of deuterium molecules in grain mantles is much higher than expected on the basis of the cosmic abundance ratio of D to H. HDCO has a relatively high abundance in grain mantles as compared to other deuterated molecules, due to the fact that H abstraction from HDCO has a lower activation barrier than D abstraction. The infrared characteristics of the calculated grain mantles are discussed and observational tests of the model calcultions are suggested. The contribution of grain surface chemistry to the concentration of molecules in the gas phase is briefly considered.

  5. Traversing the polymorphic landscape through tuning molecule-molecule, molecule-substrate and molecule-solvent interactions

    NASA Astrophysics Data System (ADS)

    Purdum, Geoffrey; Gessner, Thomas; Weitz, R. Thomas; Loo, Yueh-Lin

    As subtle changes in the crystalline packing motif of molecular semiconductors can have a large impact on charge transport, a thorough understanding of the accessibility of polymorphs in thin films is needed. Using a series of core-chlorinated naphthalene tetracarboxylic diimides, we demonstrate that the choice of the alkyl substituents at the imide functionalities, as well as the choice of substrate and post-deposition processing conditions, tune the relative strengths of molecule-molecule, molecule-substrate and molecule-solvent interactions, providing a handle over polymorphic selection. We access the triclinic polymorph of NTCDI-CH2C3F7 in thermally evaporated thin films; solvent-vapor annealing induces a reversible transformation to its monoclinic polymorph. The addition of a fluoromethylene group in the alkyl substituent increases molecule-molecule interactions and, accordingly, improves the stability of its triclinic polymorph; this derivative does not undergo a polymorphic transformation with any of the post-deposition conditions we have explored.

  6. Formation and dissociation of dust molecules in dusty plasma

    NASA Astrophysics Data System (ADS)

    Yan, Jia; Feng, Fan; Liu, Fucheng; Dong, Lifang; He, Yafeng

    2016-09-01

    Dust molecules are observed in a dusty plasma experiment. By using measurements with high spatial resolution, the formation and dissociation of the dust molecules are studied. The ion cloud in the wake of an upper dust grain attracts the lower dust grain nearby. When the interparticle distance between the upper dust grain and the lower one is less than a critical value, the two dust grains would form a dust molecule. The upper dust grain always leads the lower one as they travel. When the interparticle distance between them is larger than the critical value, the dust molecule would dissociate. Project supported by the National Natural Science Foundation of China (Grant Nos. 11205044 and 11405042), the Natural Science Foundation of Hebei Province, China (Grant Nos. A2011201006 and A2012201015), the Research Foundation of Education Bureau of Hebei Province, China (Grant No. Y2012009), the Program for Young Principal Investigators of Hebei Province, China, and the Midwest Universities Comprehensive Strength Promotion Project, China.

  7. Temperature dependence of charge transport in conjugated single molecule junctions

    NASA Astrophysics Data System (ADS)

    Huisman, Eek; Kamenetska, Masha; Venkataraman, Latha

    2011-03-01

    Over the last decade, the break junction technique using a scanning tunneling microscope geometry has proven to be an important tool to understand electron transport through single molecule junctions. Here, we use this technique to probe transport through junctions at temperatures ranging from 5K to 300K. We study three amine-terminated (-NH2) conjugated molecules: a benzene, a biphenyl and a terphenyl derivative. We find that amine groups bind selectively to undercoordinate gold atoms gold all the way down to 5K, yielding single molecule junctions with well-defined conductances. Furthermore, we find that the conductance of a single molecule junction increases with temperature and we present a mechanism for this temperature dependent transport result. Funded by a Rubicon Grant from The Netherlands Organisation for Scientific Research (NWO) and the NSEC program of NSF under grant # CHE-0641523.

  8. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules.

  9. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jose, K V Jovan; Beckett, Daniel; Raghavachari, Krishnan

    2015-09-01

    We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules.

  10. Measuring an antibody affinity distribution molecule by molecule.

    PubMed

    Temirov, Jamshid P; Bradbury, Andrew R M; Werner, James H

    2008-11-15

    Single molecule fluorescence microscopy was used to observe the binding and unbinding of hapten decorated quantum dots to individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  11. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  12. Spectroscopic modeling of water molecule

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.

    2013-12-01

    This research is devoted to the vibrational spectroscopy inverse problem solution that gives a possibility to design a molecule and make conclusions about its geometry. The valence angle finding based on the usage of inverse spectral vibrational spectroscopy problem is a well-known task. 3N-matrix method was chosen to solve the proposed task. The usage of this method permits to make no assumptions about the molecule force field, besides it can be applied to molecules of matter in liquid state. Anharmonicity constants assessment is an important part of the valence angle finding. The reduction to zero vibrations is necessary because used matrix analytical expression were found in the harmonic approach. In order to find the single-valued inverse spectral problem of vibrational spectroscopy solution a shape parameter characterizing "mixing" of ω1 and ω2 vibrations forms must be found. The minimum of such a function Υ called a divergence parameter was found. This function characterizes method's accuracy. The valence angle assessment was reduced to the divergence parameter minimization. The β value concerning divergence parameter minimum was interpreted as the desired valence angle. The proposed method was applied for water molecule in liquid state: β = (88,8 ±1,7)° . The found angle fits the water molecule nearest surrounding tetrahedral model including hydrogen bond curvature in the first approximation.

  13. Electronic Transport in Organic Molecules

    NASA Astrophysics Data System (ADS)

    Tian, W.; Samanta, M. P.; Henderson, J. I.; Kubiak, C. P.; Datta, S.

    1996-03-01

    A systematic theoretical study of the conductance of a class of organic molecules connected between two gold cantact pads will be presented. This class of molecules consists of oligomers of benzene rings linked at their para-positions and terminated with suitable ligand end groups designed to bond to gold substrates. Such molecules are currently being investigated experimentally for use as interconnectors in nanoscale electronic devices (J.Guay et al, J.Am.Chem.Soc., 115,1869, (1993); M.Dorogi et al, Phys. Rev. B52,9071,(1995); D.B.Janes et al, Superlatt. and Microstruc., in press). Analytical and numerical results will be presented illustrating effects of Metal Induced Gap States (MIGS), end group atoms, geometric and molecular structure on the measured conductance.

  14. Room temperature single molecule microscopes

    SciTech Connect

    Ambrose, W.P.; Goodwin, P.M.; Enderlein, G.; Semin, D.J.; Keller, R.A.

    1997-12-31

    We have developed three capabilities to image the locations of and interrogate immobilized single fluorescent molecules: near-field scanning optical, confocal scanning optical, and wide-field epi-fluorescence microscopy. Each microscopy has its own advantages. Near-field illumination can beat the diffraction limit. Confocal microscopy has high brightness and temporal resolution. Wide-field has the quickest (parallel) imaging capability. With confocal microscopy, we have verified that single fluorescent spots in our images are due to single molecules by observing photon antibunching. Using all three microscopies, we have observed that xanthene molecules dispersed on dry silica curiously exhibit intensity fluctuations on millisecond to minute time scales. We are exploring the connection between the intensity fluctuations and fluctuations in individual photophysical parameters. The fluorescence lifetimes of Rhodamine 6G on silica fluctuate. The complex nature of the intensity and lifetime fluctuations is consistent with a mechanism that perturbs more than one photophysical parameter.

  15. Formation of Ultracold Polar Molecules

    NASA Astrophysics Data System (ADS)

    Taylor-Juarros, E.; Côté, R.; Kirby, K.

    2002-05-01

    A variety of experimental techniques have been employed to create a number of ultracold molecules, including CaH, Na_2, K_2, Cs_2, Rb2 and CO. Novel effects are predicted to occur in samples of ultracold polar molecules.(L. Santos et al.), Phys. Rev. Lett. 85, 1791 (2000). We present calculations of the formation rate of ultracold hydrides (LiH, NaH, KH, RbH, and CsH), using the most accurate molecular potentials and dipole moments available. We show that these polar molecules can be produced in selected vibrational and rotational states by stimulated radiative association in a mixture of ultracold hydrogen and alkali metal atoms. We study the properties of these atomic mixtures as well as those of the hydrides, and explore the effect of shape resonances on the formation rates. [2ex] *Supported by NSF

  16. Proton affinities of hydrated molecules

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes

    2016-09-01

    Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

  17. Interstellar molecules and dense clouds.

    NASA Technical Reports Server (NTRS)

    Rank, D. M.; Townes, C. H.; Welch, W. J.

    1971-01-01

    Current knowledge of the interstellar medium is discussed on the basis of recent published studies. The subjects considered include optical identification of interstellar molecules, radio molecular lines, interstellar clouds, isotopic abundances, formation and disappearance of interstellar molecules, and interstellar probing techniques. Diagrams are plotted for the distribution of galactic sources exhibiting molecular lines, for hydrogen molecule, hydrogen atom and electron abundances due to ionization, for the densities, velocities and temperature of NH3 in the direction of Sagitarius B2, for the lower rotational energy levels of H2CO, and for temporal spectral variations in masing H2O clouds of the radio source W49. Future applications of the maser and of molecular microscopy in this field are visualized.

  18. Phase structure of soliton molecules

    NASA Astrophysics Data System (ADS)

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Böhm, M.; Mitschke, F.

    2007-06-01

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E -fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  19. Phase structure of soliton molecules

    SciTech Connect

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Boehm, M.; Mitschke, F.

    2007-06-15

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E-fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  20. Orbital molecules in electronic materials

    SciTech Connect

    Attfield, J. Paul

    2015-04-01

    Orbital molecules are made up of coupled orbital states on several metal ions within an orbitally ordered (and sometimes also charge-ordered) solid such as a transition metal oxide. Spin-singlet dimers are known in many materials, but recent discoveries of more exotic species such as 18-electron heptamers in AlV{sub 2}O{sub 4} and magnetic 3-atom trimerons in magnetite (Fe{sub 3}O{sub 4}) have shown that orbital molecules constitute a general new class of quantum electronic states in solids.

  1. Extracellular movement of signaling molecules

    PubMed Central

    Müller, Patrick; Schier, Alexander F.

    2011-01-01

    Extracellular signaling molecules have crucial roles in development and homeostasis, and their incorrect deployment can lead to developmental defects and disease states. Signaling molecules are released from sending cells, travel to target cells and act over length scales of several orders of magnitude, from morphogen-mediated patterning of small developmental fields to hormonal signaling throughout the organism. We discuss how signals are modified and assembled for transport, which routes they take to reach their targets and how their range is affected by mobility and stability. PMID:21763615

  2. Extracellular movement of signaling molecules.

    PubMed

    Müller, Patrick; Schier, Alexander F

    2011-07-19

    Extracellular signaling molecules have crucial roles in development and homeostasis, and their incorrect deployment can lead to developmental defects and disease states. Signaling molecules are released from sending cells, travel to target cells, and act over length scales of several orders of magnitude, from morphogen-mediated patterning of small developmental fields to hormonal signaling throughout the organism. We discuss how signals are modified and assembled for transport, which routes they take to reach their targets, and how their range is affected by mobility and stability.

  3. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  4. Slow beams of massive molecules

    NASA Astrophysics Data System (ADS)

    Deachapunya, S.; Fagan, P. J.; Major, A. G.; Reiger, E.; Ritsch, H.; Stefanov, A.; Ulbricht, H.; Arndt, M.

    2008-02-01

    Slow beams of neutral molecules are of great interest for a wide range of applications, from cold chemistry through precision measurements to tests of the foundations of quantum mechanics. We report on the quantitative observation of thermal beams of perfluorinated macromolecules with masses up to 6000 amu, reaching velocities down to 11 m/s. Such slow, heavy and neutral molecular beams are of importance for a new class of experiments in matter-wave interferometry and we also discuss the requirements for further manipulation and cooling schemes with molecules in this unprecedented mass range.

  5. Are solar UV-B- and UV-A-dependent gene expression and metabolite accumulation in Arabidopsis mediated by the stress response regulator RADICAL-INDUCED CELL DEATH1?

    PubMed

    Morales, Luis O; Brosché, Mikael; Vainonen, Julia P; Sipari, Nina; Lindfors, Anders V; Strid, Åke; Aphalo, Pedro J

    2015-05-01

    Wavelengths in the ultraviolet (UV) region of the solar spectrum, UV-B (280-315 nm) and UV-A (315-400 nm), are key environmental signals modifying several aspects of plant physiology. Despite significant advances in the understanding of plant responses to UV-B and the identification of signalling components involved, there is limited information on the molecular mechanisms that control UV-B signalling in plants under natural sunlight. Here, we aimed to corroborate the previous suggested role for RADICAL-INDUCED CELL DEATH1 (RCD1) in UV-B signalling under full spectrum sunlight. Wild-type Arabidopsis thaliana and the rcd1-1 mutant were used in an experimental design outdoors where UV-B and UV-A irradiances were manipulated using plastic films, and gene expression, PYRIDOXINE BIOSYNTHESIS1 (PDX1) accumulation and metabolite profiles were analysed in the leaves. At the level of transcription, RCD1 was not directly involved in the solar UV-B regulation of genes with functions in UV acclimation, hormone signalling and stress-related markers. Furthermore, RCD1 had no role on PDX1 accumulation but modulated the UV-B induction of flavonoid accumulation in leaves of Arabidopsis exposed to solar UV. We conclude that RCD1 does not play an active role in UV-B signalling but rather modulates UV-B responses under full spectrum sunlight.

  6. Monitoring Molecules: Insights and Progress

    PubMed Central

    2015-01-01

    In August, 2014, neuroscientists and physical scientists gathered together on the campus of the University of California, Los Angeles to discuss how to monitor molecules in neuroscience. This field has seen significant growth since its inception in the 1970s. Here, the advances in this field are documented, including its advance into understanding the actions that specific neurotransmitters mediate during behavior. PMID:25514501

  7. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  8. Ultrafast dynamics of single molecules.

    PubMed

    Brinks, Daan; Hildner, Richard; van Dijk, Erik M H P; Stefani, Fernando D; Nieder, Jana B; Hernando, Jordi; van Hulst, Niek F

    2014-04-21

    The detection of individual molecules has found widespread application in molecular biology, photochemistry, polymer chemistry, quantum optics and super-resolution microscopy. Tracking of an individual molecule in time has allowed identifying discrete molecular photodynamic steps, action of molecular motors, protein folding, diffusion, etc. down to the picosecond level. However, methods to study the ultrafast electronic and vibrational molecular dynamics at the level of individual molecules have emerged only recently. In this review we present several examples of femtosecond single molecule spectroscopy. Starting with basic pump-probe spectroscopy in a confocal detection scheme, we move towards deterministic coherent control approaches using pulse shapers and ultra-broad band laser systems. We present the detection of both electronic and vibrational femtosecond dynamics of individual fluorophores at room temperature, showing electronic (de)coherence, vibrational wavepacket interference and quantum control. Finally, two colour phase shaping applied to photosynthetic light-harvesting complexes is presented, which allows investigation of the persistent coherence in photosynthetic complexes under physiological conditions at the level of individual complexes. PMID:24473271

  9. Nonlinear Optical Properties of Molecules.

    NASA Astrophysics Data System (ADS)

    Elliott, Daniel Scott

    The measurement of the hyperpolarizabilities of atoms and molecules serves as a test of molecular wave function computational techniques. In this thesis, hyperpolarizabilities for the three processes dc electric-field induced second -harmonic generation, third-harmonic generation and intensity -dependent refractive index are determined. Measurements are performed on gases so that intermolecular interactions can be neglected. We have measured the third-order polarizability of the conjugated molecules ethylene, 1,3-butadiene, 1,3,5 -hexatriene, and benzene with the technique of dc electric -field induced second-harmonic generation. These experiments were motivated by recent theoretical results which indicated that the hyperpolarizabilities of two of these molecules were negative. Had this proven to be true, it would have been the first such case for a nonresonant hyperpolarizability. Our results for benzene are in good agreement with previous measurements made on benzene in the liquid phase, lending added confidence to the use of local field factors needed for that work. We also report results for the hyperpolarizabilities of chlorodifluoromethane. The third-order polarizability is in reasonable agreement with estimates by the bond additivity approximation. An examination of the electronic dispersion of and vibrational contributions to the third-order polarizability for various processes is presented. New data for the third -harmonic polarizability for the fluorinated methanes and sulfur hexafluoride is included. Currently, ab initio calculations of molecular hyperpolarizabilities do not include any consideration of vibrational motion of the molecule. Our estimates indicate that the vibrational contributions are very important in the case of the Kerr effect. This is an important matter of principle, and should be further investigated. We have also devised an interferometric technique for the measurement of the intensity-dependent dispersion in the refractive index

  10. Pair Tunneling through Single Molecules

    NASA Astrophysics Data System (ADS)

    Raikh, Mikhail

    2007-03-01

    Coupling to molecular vibrations induces a polaronic shift, and can lead to a negative charging energy, U. For negative U, the occupation of the ground state of the molecule is even. In this situation, virtual pair transitions between the molecule and the leads can dominate electron transport. At low temperature, T, these transitions give rise to the charge-Kondo effect [1]. We developed the electron transport theory through the negative-U molecule [2] at relatively high T, when the Kondo correlations are suppressed. Two physical ingredients distinguish our theory from the transport through a superconducting grain coupled to the normal leads [3]: (i) in parallel with sequential pair-tunneling processes, single-particle cotunneling processes take place; (ii) the electron pair on the molecule can be created (or annihilated) by two electrons tunneling in from (or out to) opposite leads. We found that, even within the rate-equation description, the behavior of differential conductance through the negative-U molecule as function of the gate voltage is quite peculiar: the height of the peak near the degeneracy point is independent of temperature, while its width is proportional to T. This is in contrast to the ordinary Coulomb-blockade conductance peak, whose integral strength is T-independent. At finite source-drain bias, V>>T, the width of the conductance peak is ˜V, whereas the conventional Coulomb-blockade peak at finite V splits into two sharp peaks at detunings V/2, and -V/2. Possible applications to the gate-controlled current rectification and switching will be discussed. [1] A. Taraphder and P. Coleman, Phys. Rev. Lett. 66, 2814 (1991). [2] J. Koch, M. E. Raikh, and F. von Oppen, Phys. Rev. Lett. 96, 056803 (2006). [3] F. W. J. Hekking, L. I. Glazman, K. A. Matveev, and R. I. Shekhter, Phys. Rev. Lett. 70, 4138 (1993).

  11. Size selective hydrophobic adsorbent for organic molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K. (Inventor); Hickey, Gregory S. (Inventor)

    1997-01-01

    The present invention relates to an adsorbent formed by the pyrolysis of a hydrophobic silica with a pore size greater than 5 .ANG., such as SILICALITE.TM., with a molecular sieving polymer precursor such as polyfurfuryl alcohol, polyacrylonitrile, polyvinylidene chloride, phenol-formaldehyde resin, polyvinylidene difluoride and mixtures thereof. Polyfurfuryl alcohol is the most preferred. The adsorbent produced by the pyrolysis has a silicon to carbon mole ratio of between about 10:1 and 1:3, and preferably about 2:1 to 1:2, most preferably 1:1. The pyrolysis is performed as a ramped temperature program between about 100.degree. and 800.degree. C., and preferably between about 100.degree. and 600.degree. C. The present invention also relates to a method for selectively adsorbing organic molecules having a molecular size (mean molecular diameter) of between about 3 and 6 .ANG. comprising contacting a vapor containing the small organic molecules to be adsorbed with the adsorbent composition of the present invention.

  12. Small Molecule Bax Agonists for Cancer Therapy

    PubMed Central

    Xin, Meiguo; Li, Rui; Xie, Maohua; Park, Dongkyoo; Owonikoko, Taofeek K.; Sica, Gabriel L.; Corsino, Patrick E.; Zhou, Jia; Ding, Chunyong; White, Mark A.; Magis, Andrew T.; Ramalingam, Suresh S.; Curran, Walter J.; Khuri, Fadlo R.; Deng, Xingming

    2014-01-01

    Bax, a central death regulator, is required at the decisional stage of apoptosis. We recently identified serine 184 (S184) of Bax as a critical functional switch controlling its proapoptotic activity. Here, we employed the structural pocket around S184 as a docking site to screen the NCI library of small molecules using the UCSF-DOCK program suite. Three compounds, small molecule Bax agonists SMBA1, SMBA2 and SMBA3, induce conformational changes in Bax by blocking S184 phosphorylation, facilitating Bax insertion into mitochondrial membranes and forming Bax oligomers. The latter leads to cytochrome c release and apoptosis in human lung cancer cells, which occurs in a Bax- but not Bak-dependent fashion. SMBA1 potently suppresses lung tumor growth via apoptosis by selectively activating Bax in vivo without significant normal tissue toxicity. Development of Bax agonists as a new class of anti-cancer drugs offers a strategy for the treatment of lung cancer and other Bax-expressing malignancies. PMID:25230299

  13. Localized atomic orbitals for atoms in molecules. III. Polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Aufderheide, Keith H.; Chung-Phillips, Alice

    1982-02-01

    Using a previously described method, localized atomic orbitals (LAOs) for atoms in molecules are constructed for the atoms C, N, O, and F in the polyatomic molecules CH4, NH3, OH2, CH3CH3, CH3NH2, CH3OH, CH3F, CH2CH2, C6H6, CO2, and CHCH. As in our prior studies, LAOs partition into sets of core, lone pair, and bonding orbitals. Ordinarily, both core and lone pair LAOs are doubly occupied and bonding is described principally as the interaction of bonding LAOs on adjacent, bonded atoms. Angles between valence LAOs on a given atom continue to vary in a manner reminiscent of trends common to simple valence shell electron pair repulsion theory. Of special interest are the systems CO2, C6H6, and CH3F: The peculiarities germane to these molecules are discussed fully in the text. Finally, certain properties (orbital populations, intra-atomic orbital angles, etc.) of groups (-CH3, -NH2, -OH, etc.) common to several systems studied show a remarkable transferability.

  14. VISTA is an immune checkpoint molecule for human T cells.

    PubMed

    Lines, J Louise; Pantazi, Eirini; Mak, Justin; Sempere, Lorenzo F; Wang, Li; O'Connell, Samuel; Ceeraz, Sabrina; Suriawinata, Arief A; Yan, Shaofeng; Ernstoff, Marc S; Noelle, Randolph

    2014-04-01

    V-domain Ig suppressor of T cell activation (VISTA) is a potent negative regulator of T-cell function that is expressed on hematopoietic cells. VISTA levels are heightened within the tumor microenvironment, in which its blockade can enhance antitumor immune responses in mice. In humans, blockade of the related programmed cell death 1 (PD-1) pathway has shown great potential in clinical immunotherapy trials. Here, we report the structure of human VISTA and examine its function in lymphocyte negative regulation in cancer. VISTA is expressed predominantly within the hematopoietic compartment with highest expression within the myeloid lineage. VISTA-Ig suppressed proliferation of T cells but not B cells and blunted the production of T-cell cytokines and activation markers. Our results establish VISTA as a negative checkpoint regulator that suppresses T-cell activation, induces Foxp3 expression, and is highly expressed within the tumor microenvironment. By analogy to PD-1 and PD-L1 blockade, VISTA blockade may offer an immunotherapeutic strategy for human cancer.

  15. Quantum Monte Carlo for vibrating molecules

    SciTech Connect

    Brown, W.R. |

    1996-08-01

    Quantum Monte Carlo (QMC) has successfully computed the total electronic energies of atoms and molecules. The main goal of this work is to use correlation function quantum Monte Carlo (CFQMC) to compute the vibrational state energies of molecules given a potential energy surface (PES). In CFQMC, an ensemble of random walkers simulate the diffusion and branching processes of the imaginary-time time dependent Schroedinger equation in order to evaluate the matrix elements. The program QMCVIB was written to perform multi-state VMC and CFQMC calculations and employed for several calculations of the H{sub 2}O and C{sub 3} vibrational states, using 7 PES`s, 3 trial wavefunction forms, two methods of non-linear basis function parameter optimization, and on both serial and parallel computers. In order to construct accurate trial wavefunctions different wavefunctions forms were required for H{sub 2}O and C{sub 3}. In order to construct accurate trial wavefunctions for C{sub 3}, the non-linear parameters were optimized with respect to the sum of the energies of several low-lying vibrational states. In order to stabilize the statistical error estimates for C{sub 3} the Monte Carlo data was collected into blocks. Accurate vibrational state energies were computed using both serial and parallel QMCVIB programs. Comparison of vibrational state energies computed from the three C{sub 3} PES`s suggested that a non-linear equilibrium geometry PES is the most accurate and that discrete potential representations may be used to conveniently determine vibrational state energies.

  16. Structure factors for tunneling ionization rates of diatomic molecules

    SciTech Connect

    Saito, Ryoichi; Tolstikhin, Oleg I.; Madsen, Lars Bojer; Morishita, Toru

    2015-05-15

    Within the leading-order, single-active-electron, and frozen-nuclei approximation of the weak-field asymptotic theory, the rate of tunneling ionization of a molecule in an external static uniform electric field is determined by the structure factor for the highest occupied molecular orbital. We present the results of systematic calculations of structure factors for 40 homonuclear and heteronuclear diatomic molecules by the Hartree–Fock method using a numerical grid-based approach implemented in the program X2DHF.

  17. Validating and understanding ring conformations using small molecule crystallographic data.

    PubMed

    Cottrell, Simon J; Olsson, Tjelvar S G; Taylor, Robin; Cole, Jason C; Liebeschuetz, John W

    2012-04-23

    Understanding the conformational preferences of ring structures is fundamental to structure-based drug design. Although the Cambridge Structural Database (CSD) provides information on the preferred conformations of small molecules, analyzing this data can be very time-consuming. In order to overcome this hurdle, tools have been developed for quickly extracting geometrical preferences from the CSD. Here we describe how the program Mogul has been extended to analyze and compare ring conformations, using a library derived from over 900 000 ring fragments in the CSD. We illustrate how these can be used to understand the conformational preferences of molecules in a crystal lattice and bound to proteins. PMID:22372622

  18. Atoms and Molecules. Physical Science in Action[TM]. Schlessinger Science Library. [Videotape].

    ERIC Educational Resources Information Center

    2000

    There are more than 20 million known substances in the universe, and they are all made of the same basic ingredients--atoms and molecules. In this fun and engaging program, kids will learn about the three main subatomic particles--protons, neutrons and electrons--as well as the forces that keep atoms and molecules together. They'll discover how…

  19. Optical highlighter molecules in neurobiology.

    PubMed

    Datta, Sandeep Robert; Patterson, George H

    2012-02-01

    The development of advanced optical methods has played a key role in propelling progress in neurobiology. Genetically-encoded fluorescent molecules found in nature have enabled labeling of individual neurons to study their physiology and anatomy. Here we discuss the recent use of both native and synthetic optical highlighter proteins to address key problems in neurobiology, including questions relevant to synaptic function, neuroanatomy, and the organization of neural circuits.

  20. Vertically coupled dipolar exciton molecules

    NASA Astrophysics Data System (ADS)

    Cohen, Kobi; Khodas, Maxim; Laikhtman, Boris; Santos, Paulo V.; Rapaport, Ronen

    2016-06-01

    While the interaction potential between two dipoles residing in a single plane is repulsive, in a system of two vertically adjacent layers of dipoles it changes from repulsive interaction in the long range to attractive interaction in the short range. Here we show that for dipolar excitons in semiconductor heterostructures, such a potential may give rise to bound states if two such excitons are excited in two separate layers, leading to the formation of vertically coupled dipolar exciton molecules. Our calculations prove the existence of such bound states and predict their binding energy as a function of the layers separation as well as their thermal distributions. We show that these molecules should be observed in realistic systems such as semiconductor coupled quantum well structures and the more recent van der Waals bound heterostructures. Formation of such molecules can lead to new effects such as a collective dipolar drag between layers and new forms of multiparticle correlations, as well as to the study of dipolar molecular dynamics in a controlled system.

  1. Simple molecules as complex systems.

    PubMed

    Furtenbacher, Tibor; Arendás, Péter; Mellau, Georg; Császár, Attila G

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H2(16)O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an "ultra-small-world" property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra.

  2. Simple molecules as complex systems

    PubMed Central

    Furtenbacher, Tibor; Árendás, Péter; Mellau, Georg; Császár, Attila G.

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H216O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an “ultra-small-world” property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  3. Tuberculosis Therapy Modifies the Cytokine Profile, Maturation State, and Expression of Inhibitory Molecules on Mycobacterium tuberculosis-Specific CD4+ T-Cells

    PubMed Central

    Saharia, Kapil K.; Petrovas, Constantinos; Ferrando-Martinez, Sara; Leal, Manuel; Luque, Rafael; Ive, Prudence; Luetkemeyer, Anne; Havlir, Diane; Koup, Richard A.

    2016-01-01

    Background Little is known about the expression of inhibitory molecules cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed-death-1 (PD-1) on Mycobacterium tuberculosis (Mtb)-specific CD4 T-cells and how their expression is impacted by TB treatment. Methods Cryopreserved PBMCs from HIV-TB co-infected and TB mono-infected patients with untreated and treated tuberculosis (TB) disease were stimulated for six hours with PPD and stained. Using polychromatic flow cytometry, we characterized the differentiation state, cytokine profile, and inhibitory molecule expression on PPD-specific CD4 T-cells. Results In our HIV-TB co-infected cohort, TB treatment increased the proportion of PPD-specific CD4 T-cells co-producing IFN-γ+IL-2+TNF-α+ and IFN-γ+IL-2+ (p = 0.0004 and p = 0.0002, respectively) while decreasing the proportion of PPD-specific CD4 T-cells co-producing IFN-γ+MIP1-β+TNF-α+ and IFN-γ+MIP1-β+. The proportion of PPD-specific CD4 T-cells expressing an effector memory phenotype decreased (63.6% vs 51.6%, p = 0.0015) while the proportion expressing a central memory phenotype increased (7.8% vs. 21.7%, p = 0.001) following TB treatment. TB treatment reduced the proportion of PPD-specific CD4 T-cells expressing CTLA-4 (72.4% vs. 44.3%, p = 0.0005) and PD-1 (34.5% vs. 29.2%, p = 0.03). Similar trends were noted in our TB mono-infected cohort. Conclusion TB treatment alters the functional profile of Mtb-specific CD4 T-cells reflecting shifts towards a less differentiated maturational profile and decreases PD-1 and CTLA-4 expression. These could serve as markers of reduced mycobacterial burden. Further study is warranted. PMID:27367521

  4. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  5. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin-orbit, angular momenta, spin-rotational and spin-spin. Introducing the relevant couplings using so-called Born-Oppenheimer breakdown curves can correct non-adiabatic effects.

  6. XUV ionization of aligned molecules

    NASA Astrophysics Data System (ADS)

    Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.

    2011-11-01

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  7. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  8. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin–orbit, angular momenta, spin-rotational and spin–spin. Introducing the relevant couplings using so-called Born–Oppenheimer breakdown curves can correct non-adiabatic effects.

  9. Nanoelectronics of a DNA molecule

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Fulco, U. L.; Caetano, E. W. S.; Freire, V. N.; Lyra, M. L.; Moura, F. A. B. F.

    2014-03-01

    We investigate the nanoelectronic properties of a double-strand quasiperiodic DNA molecule, modeled by a tight-binding effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, to investigate the electronic density of states, the electronic transmissivity, and the current-voltage characteristic curves of sequences of a DNA finite segment.We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.

  10. Metal/molecule interfaces: Dispersion forces unveiled

    NASA Astrophysics Data System (ADS)

    van Ruitenbeek, Jan

    2012-10-01

    The role of dispersion forces in molecule-metal bonding has often been underestimated or ignored. Two groups now report independent single-molecule experiments that illustrate and quantify the effect of such interactions on bonding strength.

  11. Spin squeezing a cold molecule

    NASA Astrophysics Data System (ADS)

    Bhattacharya, M.

    2015-12-01

    In this article we present a concrete proposal for spin squeezing the cold ground-state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. In contrast to existing work, we consider a single, noninteracting molecule with angular momentum greater than 1 /2 . Starting from an experimentally relevant effective Hamiltonian, we identify an adiabatic regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993), 10.1103/PhysRevA.47.5138], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T. Ng, and P. T. Leung, Phys. Rev. A 63, 055601 (2001), 10.1103/PhysRevA.63.055601], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989), 10.1103/PhysRevA.39.2969]. We then consider the situation in which nonadiabatic effects are quite large and show that the effective Hamiltonian supports spin squeezing even in this case. We provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounting for the effects of field misalignment. Our results have consequences for applications such as precision spectroscopy, techniques such as magnetometry, and stereochemical effects such as the orientation-to-alignment transition.

  12. Characterization of Interstellar Organic Molecules

    SciTech Connect

    Gencaga, Deniz; Knuth, Kevin H.; Carbon, Duane F.

    2008-11-06

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  13. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K.; Hickey, Gregory S.

    1994-01-01

    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  14. Time scales for molecule formation by ion-molecule reactions

    NASA Technical Reports Server (NTRS)

    Langer, W. D.; Glassgold, A. E.

    1976-01-01

    Analytical solutions are obtained for nonlinear differential equations governing the time-dependence of molecular abundances in interstellar clouds. Three gas-phase reaction schemes are considered separately for the regions where each dominates. The particular case of CO, and closely related members of the Oh and CH families of molecules, is studied for given values of temperature, density, and the radiation field. Nonlinear effects and couplings with particular ions are found to be important. The time scales for CO formation range from 100,000 to a few million years, depending on the chemistry and regime. The time required for essentially complete conversion of C(+) to CO in the region where the H3(+) chemistry dominates is several million years. Because this time is longer than or comparable to dynamical time scales for dense interstellar clouds, steady-state abundances may not be observed in such clouds.

  15. Visualization of large elongated DNA molecules.

    PubMed

    Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong

    2015-09-01

    Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

  16. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  17. Analytical design of soliton molecules in fibers

    NASA Astrophysics Data System (ADS)

    Moubissi, A.-B.; Nse Biyoghe, S.; Mback, C. B. L.; Ekogo, T. B.; Ben-Bolie, G. H.; Kofane, T. C.; Tchofo Dinda, P.

    2016-09-01

    We present an analytical method for designing fiber systems for a highly stable propagation of soliton molecules. This analytical design uses the variational equations of the soliton molecule to determine the parameters of the most suitable fiber system for any desired soliton, thus reducing dramatically the cost of the whole procedure of design, for both the appropriate fiber system and the desired soliton molecule.

  18. Laboratory studies of astrophysical molecules

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan

    There is growing evidence that the molecules necessary for the evolution of life on earth arrived from the interstellar medium. The study of these molecules is therefore of great current interest. Two major types of signals from interstellar space, so-called unidentified interstellar infrared emission bands and the diffuse interstellar absorption bands, have intrigued and puzzled astrochemists for decades. This work has been concentrated on how to contribute to an understanding of the origins of these perplexing signals from space and help identify other molecules that may exist in outer space. Matrix isolation spectroscopy (infrared and ultraviolet-visible) combined with theoretical calculations has been employed throughout this research. Fourier transform infrared absorption spectroscopic measurements, aided by theoretical calculations and 13 C-isotope shifts, have led to the identification of eight heretofore unknown C n S m clusters: C 2 S, C 6 S, C 7 S, C 7 S 2 , C 9 S 2 , C 11 S 2 , C 13 S 2 , and C 15 S 2 . Infrared absorption studies of xenon polycarbon clusters aid in understanding the special electronic structure and reactivity of carbon clusters, which might be associated with the formation mechanism of Buckyball (C 60 ). Reaction of C3 with benzene and ammonia might be involved in the formation of more complex molecular structures, including polycyclic aromatic hydrocarbons (PAHs) and biomolecules such as the amino acids. High resolution vibrational and electronic spectra of neutral dibenzo [b,def]chrysene and its ions in 12 K argon matrices have been recorded. Spectral assignments were supported by high level theoretical calculations. A mixture of the neutral and ionic infrared spectra of dibenzo[b,def]chrysene resembles the unidentified IR bands in the reflection nebula NGC 7023. Anharmonic frequency calculations for neutral and cationic naphthalene, phenanthrene and anthracene using density functional theory have been carried out for the first time

  19. Nonadiabatic calculations on hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Komasa, Jacek; Pachucki, Krzysztof

    Since its infancy quantum mechanics has treated hydrogen molecule as a test bed. Contemporary spectroscopy is able to supply the dissociation energy (D0) of H2 with the accuracy of 3 . 7 .10-4cm-1 , while current theoretical predictions are 10-3cm-1 in error. Both the uncertainties are already smaller than the quantum electrodynamic (QED) effects contributing to D0, which poses a particular challenge to theoreticians. Undoubtedly, in order to increase the predictive power of theory one has to not only account for the multitude of the tiny relativistic and QED effects but, especially, significantly increase precision of the largest component of D0--the nonrelativistic contribution. We approach the problem of solving the Schroedinger equation, equipped with new methodology, with the target precision of D0 set at the level of 10-7cm-1 .

  20. Photoluminescence of a Plasmonic Molecule.

    PubMed

    Huang, Da; Byers, Chad P; Wang, Lin-Yung; Hoggard, Anneli; Hoener, Ben; Dominguez-Medina, Sergio; Chen, Sishan; Chang, Wei-Shun; Landes, Christy F; Link, Stephan

    2015-07-28

    Photoluminescent Au nanoparticles are appealing for biosensing and bioimaging applications because of their non-photobleaching and non-photoblinking emission. The mechanism of one-photon photoluminescence from plasmonic nanostructures is still heavily debated though. Here, we report on the one-photon photoluminescence of strongly coupled 50 nm Au nanosphere dimers, the simplest plasmonic molecule. We observe emission from coupled plasmonic modes as revealed by single-particle photoluminescence spectra in comparison to correlated dark-field scattering spectroscopy. The photoluminescence quantum yield of the dimers is found to be surprisingly similar to the constituent monomers, suggesting that the increased local electric field of the dimer plays a minor role, in contradiction to several proposed mechanisms. Aided by electromagnetic simulations of scattering and absorption spectra, we conclude that our data are instead consistent with a multistep mechanism that involves the emission due to radiative decay of surface plasmons generated from excited electron-hole pairs following interband absorption. PMID:26165983

  1. Electrokinetic concentration of charged molecules

    DOEpatents

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  2. New molecules for hippocampal development.

    PubMed

    Skutella, T; Nitsch, R

    2001-02-01

    Pathfinding by developing axons towards their proper targets is an essential step in establishing appropriate neuronal connections. Recent work involving cell culture assays and molecular biology strategies, including knockout animals, strongly indicates that a complex network of guidance signals regulates the formation of hippocampal connections during development. Outgrowing axons are routed towards the hippocampal formation by specific expression of long-range cues, which include secreted class 3 semaphorins, netrin 1 and Slit proteins. Local membrane- or substrate-anchored molecules, such as ligands of the ephrin A subclass, provide layer-specific positional information. Understanding the molecular mechanisms that underlie axonal guidance during hippocampal development might be of importance in making therapeutic use of sprouting fibers, which are produced following the loss of afferents in CNS lesion. PMID:11164941

  3. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  4. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  5. Single-molecule imaging by optical absorption

    NASA Astrophysics Data System (ADS)

    Celebrano, Michele; Kukura, Philipp; Renn, Alois; Sandoghdar, Vahid

    2011-02-01

    To date, optical studies of single molecules at room temperature have relied on the use of materials with high fluorescence quantum yield combined with efficient spectral rejection of background light. To extend single-molecule studies to a much larger pallet of substances that absorb but do not fluoresce, scientists have explored the photothermal effect, interferometry, direct attenuation and stimulated emission. Indeed, very recently, three groups have succeeded in achieving single-molecule sensitivity in absorption. Here, we apply modulation-free transmission measurements known from absorption spectrometers to image single molecules under ambient conditions both in the emissive and strongly quenched states. We arrive at quantitative values for the absorption cross-section of single molecules at different wavelengths and thereby set the ground for single-molecule absorption spectroscopy. Our work has important implications for research ranging from absorption and infrared spectroscopy to sensing of unlabelled proteins at the single-molecule level.

  6. Deformation of DNA molecules by hydrodynamic focusing

    NASA Astrophysics Data System (ADS)

    Wong, Pak Kin; Lee, Yi-Kuen; Ho, Chih-Ming

    2003-12-01

    The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil stretch transition was observed when the Deborah number (De) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.

  7. Observation of pendular butterfly Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-10-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  8. Observation of pendular butterfly Rydberg molecules

    PubMed Central

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-01-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

  9. Programmed Organic Synthesis

    ERIC Educational Resources Information Center

    Heusler, Karl

    1975-01-01

    Describes recent attempts to program computers to map synthetic routes to organic compounds. The computer is provided with structural information for many molecules and reaction descriptions; when a target compound is specified, the computer lists possible precursors, thus indicating possible synthetic routes. (MLH)

  10. Intercultural Programs Program Evaluation.

    ERIC Educational Resources Information Center

    Jones, Mary Lynne

    The report evaluates the programs of the Des Moines (Iowa) Public Schools' Office of Intercultural Programs' services. The programs are designed to provide educational equity and serve as a resource for students, parents, community, and staff in a variety of areas, including: a voluntary transfer program; paired and magnet schools; extended day…

  11. PREFACE: Processes in Isotopes and Molecules

    NASA Astrophysics Data System (ADS)

    Bogdan, Diana; Tosa, Valer

    2009-07-01

    These Proceedings present some of the Invited Lectures and Contributed Papers of the International Conference 'Processes in Isotopes and Molecules' (PIM), held in Cluj-Napoca, Romania, 24-26 September 2009. The PIM conference, started in 1999 as a local event, is now an international conference organized every two years by the National Institute for R&D of Isotopic and Molecular Technologies in Cluj-Napoca, the capital city of Transylvania, Romania. The meetings are attended by researchers in the field of atomic and molecular physics as well as those developing new materials and technologies. The scientific subjects are at the cross-roads of three fundamental research areas: physics, chemistry, and biology. The papers here are grouped according to the five conference topics: T1 - Molecular and biomolecular systems T2 - Modern techniques and technologies T3 - Environmental molecular processes T4 - Hydrogen and renewable sources of energy T5 - Nanostructured materials and nanocomposites We gratefully acknowledge the contribution of our colleagues from the Scientific Committee and Program Committee who contributed their time, energy and expertise to the refereeing process. Finally, we would like to thank people from IOP Publishing for their friendly advice and prompt help during the editing process, as well as for their efforts making the Journal of Physics: Conference Series available to the scientific community. Diana Bogdan and Valer Tosa National Institute for R&D Isotopic and Molecular Technologies, Cluj-Napoca

  12. Vibrationally Averaged Long-Range Molecule-Molecule Dispersion Coefficients from Coupled-Cluster Calculations

    NASA Astrophysics Data System (ADS)

    Schmidt, Matthew; Nooijen, Marcel

    2011-06-01

    Recent years have seen increasing interest in the structure and dynamics of molecular clusters formed when a chromophore molecule such as CO_2, OCS or N_2O is solvated by number of He atoms and/or para-H_2 molecules. A key experimental probe of their behaviour is the shift of a chromophore's vibrational transition frequency which occurs when the solvent species are attached to it. Such shifts are driven by the changes in the solvent-chromophore interaction potential upon vibrational excitation of the probe molecule. While `conventional' supermolecule calculations can often provide realistic predictions of such changes in the potential well and repulsive wall region, they become increasingly unreliable for describing the weak interactions at long range where most of the solvent species in a large cluster are located. It is therefore important to have accurate relative-orientation and monomer-stretching dependent long-range C_6, C_8 and C10 dispersion coefficients to incorporate into the models for the interaction potential and for its dependence on the chromophore's vibrational state. This paper describes how those coefficients can be obtained from calculated monomer dipole, quadrupole, and octupole polarizabilities for imaginary frequencies, and by making use of the Casimir-Polder relation and angular momentum coupling to extract orientation-dependent quantities. The calculations are performed using a modified version of the ACES2 program system which allows the calculation of dipole, quadrupole and octupole polarizabilities at the EOM-CCSD level, and of static multipole moments using CCSD(T) calculations and adequate basis sets. For each relevant level of the chromophore, vibrational averaging is performed by calculating the imaginary frequency polarizabilities at judiciously chosen geometries and performing a numerical integration using the free-molecule vibrational wavefunction. Subsequent work will involve merging this long-range part of the potential with a

  13. Small-molecule caspase inhibitors

    NASA Astrophysics Data System (ADS)

    Zhenodarova, S. M.

    2010-02-01

    The review considers low-molecular weight inhibitors of caspases, cysteine proteases being key contributors to apoptosis (programmed cell death). The inhibitors with aspartic acid residues or various heterocyclic systems (both synthetic and natural) are covered. Their possible mechanisms of action are discussed. Data on inhibitor structure-activity relationship studies are systematically surveyed. The interactions of the non-peptide fragments of an inhibitor with the enzymes are examined. Examples of the use of some inhibitors for apoptosis suppression are provided.

  14. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  15. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  16. Geochemical Origin of Biological Molecules

    NASA Astrophysics Data System (ADS)

    Bassez, Marie-Paule

    2013-04-01

    A model for the geochemical origin of biological molecules is presented. Rocks such as peridotites and basalts, which contain ferromagnesian minerals, evolve in the presence of water. Their hydrolysis is an exothermic reaction which generates heat and a release of H2 and of minerals with modified structures. The hydrogen reacts with the CO2 embedded inside the rock or with the CO2 of the environment to form CO in an hydrothermal process. With the N2 of the environment, and with an activation source arising from cosmic radiation, ferromagnesian rocks might evolve towards the abiotic formation of biological molecules, such as peptide like macromolecules which produce amino acids after acid hydrolysis. The reactions concerned are described. The production of hydrothermal CO is discussed in geological sites containing ferromagnesian silicate minerals and the low intensity of the Earth's magnetic field during Paleoarchaean Era is also discussed. It is concluded that excitation sources arising from cosmic radiation were much more abundant during Paleoarchaean Era and that macromolecular structures of biological relevance might consequently form during Archaean Eon, as a product of the chemical evolution of the rocks and of their mineral contents. This synthesis of abiotically formed biological molecules is consecutively discussed for meteorites and other planets such as Mars. This model for the geochemical origin of biological molecules has first been proposed in 2008 in the context of reactions involving catalysers such as kaolinite [Bassez 2008a] and then presented in conferences and articles [Bassez 2008b, 2009, 2012; Bassez et al. 2009a to 2012b]. BASSEZ M.P. 2008a Synthèse prébiotique dans les conditions hydrothermales, CNRIUT'08, Lyon 29-30/05/2008, Conf. and open access article:http://liris.cnrs.fr/~cnriut08/actes/ 29 mai 11h-12h40. BASSEZ M.P. 2008b Prebiotic synthesis under hydrothermal conditions, ISSOL'08, P2-6, Firenze-Italy, 24-29/08/2008. Poster at the

  17. Broadband single-molecule excitation spectroscopy

    PubMed Central

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  18. Broadband single-molecule excitation spectroscopy

    NASA Astrophysics Data System (ADS)

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy.

  19. Rotational Cooling of Trapped Polyatomic Molecules.

    PubMed

    Glöckner, Rosa; Prehn, Alexander; Englert, Barbara G U; Rempe, Gerhard; Zeppenfeld, Martin

    2015-12-01

    Controlling the internal degrees of freedom is a key challenge for applications of cold and ultracold molecules. Here, we demonstrate rotational-state cooling of trapped methyl fluoride molecules (CH_{3}F) by optically pumping the population of 16 M sublevels in the rotational states J=3, 4, 5 and 6 into a single level. By combining rotational-state cooling with motional cooling, we increase the relative number of molecules in the state J=4, K=3, M=4 from a few percent to over 70%, thereby generating a translationally cold (≈30  mK) and nearly pure state ensemble of about 10^{6} molecules. Our scheme is extendable to larger sets of initial states, other final states, and a variety of molecule species, thus paving the way for internal-state control of ever-larger molecules.

  20. Single molecule nanometry for biological physics

    PubMed Central

    Kim, Hajin; Ha, Taekjip

    2013-01-01

    Precision measurement is a hallmark of physics but the small length scale (~ nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ~ 0.3 nm precision at ~ 1 millisecond time resolution, and how these new tools are providing fundamental insights on how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate movements of multiple components. Finally, we will discuss recent progress in combining angstrom precision optical tweezers with single molecule fluorescent detection, opening new windows for multi-dimensional single molecule nanometry for biological physics. PMID:23249673

  1. Structure of small clusters of parahydrogen molecules

    SciTech Connect

    Guardiola, Rafael; Navarro, Jesus

    2006-08-15

    The ground state energies and the one-body densities of parahydrogen clusters have been systematically calculated by the diffusion Monte Carlo technique in steps of one molecule from 3 to 50 molecules. These calculations show that parahydrogen clusters exhibit a clear geometrical order which excludes any liquidlike structure. A definite confirmation of the magic size for the cluster with 13 molecules is also obtained.

  2. A new interstellar molecule - Tricarbon monoxide

    NASA Technical Reports Server (NTRS)

    Matthews, H. E.; Irvine, W. M.; Friberg, P.; Brown, R. D.; Godfrey, P. D.

    1984-01-01

    The C3O molecule, whose pure rotational spectrum has only recently been studied in the laboratory, has been detected in the cold, dark interstellar Taurus Molecular Cloud 1. Since C3O is the first interstelar carbon chain molecule to contain oxygen, its existence places an important new constraint on chemical schemes for cold interstellar clouds. The abundance of C3O can be understood in terms of purely gas-phase ion-molecule chemistry.

  3. Circular DNA Molecules in the Genus Drosophila

    PubMed Central

    Travaglini, E. C.; Schultz, J.

    1972-01-01

    The satellite DNA's from the embryos of five species of Drosophila (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) have been analyzed for the presence of closed circular duplex DNA molecules, as determined by CsCl-EBr gradients. Circular DNA molecules were found in every species but D. melanogaster. Analyses of cell fractions from adult Drosophila and organ fractions from Drosophila larvae show that fractions containing mitochondria are highly enriched in these molecules. PMID:4643820

  4. Microwave Stark decelerator for polar molecules

    SciTech Connect

    Enomoto, Katsunari; Momose, Takamasa

    2005-12-15

    We propose a method to decelerate polar molecules from a beam using a microwave field. A moving standing wave of a microwave electric field causes an ac Stark shift to polar molecules and decelerates them. The method is applicable to polar molecules in rotational ground states and can be used to directly load a microwave trap. Numerical simulations are presented indicating large phase-space acceptance volume.

  5. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented.

  6. Production and Trapping of Ultracold Polar Molecules

    SciTech Connect

    David, DeMille

    2015-04-21

    We report a set of experiments aimed at the production and trapping of ultracold polar molecules. We begin with samples of laser-cooled and trapped Rb and Cs atoms, and bind them together to form polar RbCs molecules. The binding is accomplished via photoassociation, which uses a laser to catalyze the sticking process. We report results from investigation of a new pathway for photoassociation that can produce molecules in their absolute ground state of vibrational and rotational motion. We also report preliminary observations of collisions between these ground-state molecules and co-trapped atoms.

  7. Probing individual molecules with confocal fluorescence microscopy.

    PubMed

    Nie, S; Chiu, D T; Zare, R N

    1994-11-11

    Confocal fluorescence microscopy coupled with a diffraction-limited laser beam and a high-efficiency detection system has been used to study the diffusive movement and emission process of individual fluorescent molecules in the liquid phase at room temperature. The high detection sensitivity achieved at fast data acquisition speeds (greater than 1 kilohertz) allows real-time observation of single-molecule fluorescence without statistical analysis. The results show fluorescence-cycle saturation at the single-molecule level and multiple recrossings of a single molecule into and out of the probe volume as well as the triplet state.

  8. Theoretical spectra of floppy molecules

    NASA Astrophysics Data System (ADS)

    Chen, Hua

    2000-09-01

    Detailed studies of the vibrational dynamics of floppy molecules are presented. Six-D bound-state calculations of the vibrations of rigid water dimer based on several anisotropic site potentials (ASP) are presented. A new sequential diagonalization truncation approach was used to diagonalize the angular part of the Hamiltonian. Symmetrized angular basis and a potential optimized discrete variable representation for intermonomer distance coordinate were used in the calculations. The converged results differ significantly from the results presented by Leforestier et al. [J. Chem. Phys. 106 , 8527 (1997)]. It was demonstrated that ASP-S potential yields more accurate tunneling splittings than other ASP potentials used. Fully coupled 4D quantum mechanical calculations were performed for carbon dioxide dimer using the potential energy surface given by Bukowski et al [J. Chem. Phys., 110, 3785 (1999)]. The intermolecular vibrational frequencies and symmetry adapted force constants were estimated and compared with experiments. The inter-conversion tunneling dynamics was studied using the calculated virtual tunneling splittings. Symmetrized Radau coordinates and the sequential diagonalization truncation approach were formulated for acetylene. A 6D calculation was performed with 5 DVR points for each stretch coordinate, and an angular basis that is capable of converging the angular part of the Hamiltonian to 30 cm-1 for internal energies up to 14000 cm-1. The probability at vinylidene configuration were evaluated. It was found that the eigenstates begin to extend to vinylidene configuration from about 10000 cm-1, and the ra, coordinate is closely related to the vibrational dynamics at high energy. Finally, a direct product DVR was defined for coupled angular momentum operators, and the SDT approach were formulated. They were applied in solving the angular part of the Hamiltonian for carbon dioxide dimer problem. The results show the method is capable of giving very accurate

  9. Completed Optimised Structure of Threonine Molecule by Fuzzy Logic Modelling

    NASA Astrophysics Data System (ADS)

    Sahiner, Ahmet; Ucun, Fatih; Kapusuz, Gulden; Yilmaz, Nurullah

    2016-04-01

    In this study we applied the fuzzy logic approach in order to model the energy depending on the two torsion angles for the threonine (C4H9NO3) molecule. The model is set up according to theoretical results obtained by the density functional theory (B3LYP) with a 6-31 G(d) basic set on a Gausian program. We aimed to determine the best torsion angle values providing the energy of the molecule minimum by a fuzzy logic approach and to compare them with the density functional theory results. It was concluded that the fuzzy logic approach gives information about the untested data and its best value which are expensive and time-consuming to obtain by other methods and experimentation.

  10. Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

    NASA Technical Reports Server (NTRS)

    Han, Jie

    2001-01-01

    Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

  11. Energy Transfer Involving Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Gibbons, John Paul

    three colliding pairs, the experimental results lie between the results calculated for the same two sets of potential parameters. These parameters were those calculated to match the short range Lennard-Jones potential and a set obtained by a theoretical Thomas-Fermi treatment of the molecules.

  12. Tumor suppressor molecules and methods of use

    DOEpatents

    Welch, Peter J.; Barber, Jack R.

    2004-09-07

    The invention provides substantially pure tumor suppressor nucleic acid molecules and tumor suppressor polypeptides. The invention also provides hairpin ribozymes and antibodies selective for these tumor suppressor molecules. Also provided are methods of detecting a neoplastic cell in a sample using detectable agents specific for the tumor suppressor nucleic acids and polypeptides.

  13. Optical interfacing single molecules with atomic vapor

    NASA Astrophysics Data System (ADS)

    Siyushev, Petr; Stein, Guilherme; Wrachtrup, Jörg; Gerhardt, Ilja

    2013-05-01

    Organic molecules at liquid Helium temperatures can constitute high-brightness and narrow-band single photon sources. Thus, they might form an important building block for quantum information processing. A number of quantum optical experiments were conducted with single photon sources based on single molecules. It was shown that it is possible to spectrally detune the molecules, and optical interaction between several molecules could be shown. Another important ingredient for quantum information processing is the implementation of quantum memory. Atomic vapors do not only allow for slowing down light, but also for its storage and can be used as an efficient quantum memory. In the past it was impossible to utilize the high brightness of single molecules in combination with an efficient quantum memory, since the lack of spectral overlap. Here, we present spectral tuning of a single molecule to match the resonance of the sodium D-line. We reach up to 6 ×105 detected 30 MHz narrow-band single photons per second. We are able to slow down near-resonant photons from a single molecule, and simultaneous show its single photon properties. We are further able to explore the properties of atomic vapor for its use as a narrow-band filter for single molecule studies.

  14. The Distribution of Solubilized Molecules among Micelles.

    ERIC Educational Resources Information Center

    Miller, Dennis J.

    1978-01-01

    Conflicting views have been put forward on the derivation of the distribution of solubilized molecules among micelles. This stems from failure to consider the arrangement of the solubilized molecules in the micelles. In the treatment presented enthalpy effects are ignored as they are not amenable to a simple general theory. (Author/BB)

  15. Polymer physics experiments with single DNA molecules

    NASA Astrophysics Data System (ADS)

    Smith, Douglas E.

    1999-11-01

    Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

  16. Relating single-molecule measurements to thermodynamics.

    PubMed

    Keller, David; Swigon, David; Bustamante, Carlos

    2003-02-01

    Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and which are allowed to fluctuate. Thus an experiment in which the end-to-end distance of the polymer molecule is fixed and the tension fluctuates yields a different result than an experiment where the force is fixed and the end-to-end distance fluctuates. It is further shown that this difference is due to asymmetry in the distribution of end-to-end distances for a single molecule, and that the difference vanishes in the appropriate thermodynamic limit; that is, as the polymer molecule becomes long compared to its persistence length. Despite these differences, much of the thermodynamic formalism still applies on the single-molecule level if the thermodynamic free energies are replaced with appropriate potentials of mean force. The primary remaining differences are consequences of the fact that unlike the free energies, the potentials of mean force are not in general homogeneous functions of their variables. The basic thermodynamic concepts of an intensive or extensive quantity, and the thermodynamic relationships that follow from them, are therefore less useful for interpreting single-molecule experiments.

  17. Computation of generating functions for biological molecules

    SciTech Connect

    Howell, J.A.; Smith, T.F.; Waterman, M.S.

    1980-08-01

    The object of this paper is to give algorithms and techniques for computing generating functions of certain RNA configurations. Combinatorics and symbolic computation are utilized to calculate the generating functions for small RNA molecules. From these generating functions, it is possible to obtain information about the bonding and structure of the molecules. Specific examples of interest to biology are given and discussed.

  18. Quantum transport of the single metallocene molecule

    NASA Astrophysics Data System (ADS)

    Yu, Jing-Xin; Chang, Jing; Wei, Rong-Kai; Liu, Xiu-Ying; Li, Xiao-Dong

    2016-10-01

    The Quantum transport of three single metallocene molecule is investigated by performing theoretical calculations using the non-equilibrium Green's function method combined with density functional theory. We find that the three metallocen molecules structure become stretched along the transport direction, the distance between two Cp rings longer than the other theory and experiment results. The lager conductance is found in nickelocene molecule, the main transmission channel is the electron coupling between molecule and the electrodes is through the Ni dxz and dyz orbitals and the s, dxz, dyz of gold. This is also confirmed by the highest occupied molecular orbital resonance at Fermi level. In addition, negative differential resistance effect is found in the ferrocene, cobaltocene molecules, this is also closely related with the evolution of the transmission spectrum under applied bias.

  19. The symmetry of single-molecule conduction.

    PubMed

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-14

    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

  20. Single molecule sensing with carbon nanotube devices

    NASA Astrophysics Data System (ADS)

    Choi, Yongki; Sims, Patrick C.; Olsen, Tivoli J.; Iftikhar, Mariam; Corso, Brad L.; Gul, O. Tolga; Weiss, Gregory A.; Collins, Philip G.

    2013-09-01

    Nanoscale electronic devices like field-effect transistors have long promised to provide sensitive, label-free detection of biomolecules. In particular, single-walled carbon nanotubes have the requisite sensitivity to detect single molecule events and sufficient bandwidth to directly monitor single molecule dynamics in real time. Recent measurements have demonstrated this premise by monitoring the dynamic, single-molecule processivity of three different enzymes: lysozyme, protein Kinase A, and the Klenow fragment of DNA polymerase I. In each case, recordings resolved detailed trajectories of tens of thousands of individual chemical events and provided excellent statistics for single-molecule events. This electronic technique has a temporal resolution approaching 1 microsecond, which provides a new window for observing brief, intermediate transition states. In addition, the devices are indefinitely stable, so that the same molecule can be observed for minutes and hours. The extended recordings provide new insights into rare events like transitions to chemically-inactive conformations.

  1. Circumstellar and interstellar synthesis of organic molecules.

    PubMed

    Tielens, A G; Charnley, S B

    1997-06-01

    We review the formation and evolution of complex circumstellar and interstellar molecules. A number of promising chemical routes are discussed which may lead to the formation of polycyclic aromatic hydrocarbon molecules, fullerenes, and unsaturated hydrocarbon chains in the outflows from stars. Some of the problems with these chemical schemes are pointed out as well. We also review the role of grains in the formation of complex molecules in interstellar molecular clouds. This starts with the formation of simple molecules in an ice grain mantle. UV photolysis and/or thermal polymerization can convert some of these simple molecules into more complex polymeric structures. Some of these species may be released to the gas phase, particularly in the warm regions around newly formed stars. Methanol and formaldehyde seem to play an important role in this drive towards molecular complexity and their chemistry is traced in some detail.

  2. Macronuclear DNA molecules of Tetrahymena thermophila.

    PubMed Central

    Conover, R K; Brunk, C F

    1986-01-01

    The physical organization of the DNA in the macronuclei of Tetrahymena thermophila was investigated by using alternating-orthogonal-field gel electrophoresis. The genome consisted of a spectrum of molecules with lengths ranging from less than 100 to in excess of 1,500 kilobase pairs. There were about 270 different macronuclear DNA molecules, with an average size of about 800 kilobase pairs. Specific genes were mapped and were generally found on macronuclear DNA molecules of the same size in different strains of T. thermophila. This indicates that the molecular mechanisms giving rise to the macronuclear DNA molecules were precise. The fragmentation process that gave rise to macronuclear DNA molecules occurred between 11 and 19 h after the initiation of conjugation. Images PMID:3773895

  3. Chemical principles of single-molecule electronics

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Neupane, Madhav; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2016-03-01

    The field of single-molecule electronics harnesses expertise from engineering, physics and chemistry to realize circuit elements at the limit of miniaturization; it is a subfield of nanoelectronics in which the electronic components are single molecules. In this Review, we survey the field from a chemical perspective and discuss the structure-property relationships of the three components that form a single-molecule junction: the anchor, the electrode and the molecular bridge. The spatial orientation and electronic coupling between each component profoundly affect the conductance properties and functions of the single-molecule device. We describe the design principles of the anchor group, the influence of the electronic configuration of the electrode and the effect of manipulating the structure of the molecular backbone and of its substituent groups. We discuss single-molecule conductance switches as well as the phenomenon of quantum interference and then trace their fundamental roots back to chemical principles.

  4. Relationships between dipole moments of diatomic molecules.

    PubMed

    Hou, Shilin; Bernath, Peter F

    2015-02-14

    The dipole moment is one of the most important physical properties of a molecule. We present a combination rule for the dipole moments of related diatomic molecules. For molecules AB, AX, BY, and XY from two different element groups in the periodic table, if their elements make a small parallelogram, reliable predictions can be obtained. Our approach is particularly useful for systems with heavy atoms. For a large set of molecules tested, the average difference of the prediction from experimental data is less than 0.2 debye (D). The dipole moments for heavy molecules such as GaCl, InBr, SrCl, and SrS, for which no experimental data are available at present, are predicted to be 3.17, 3.76, 3.85 and 11.54 D, respectively. PMID:25588998

  5. Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

    DOEpatents

    Salafsky, Joshua S.; Eisenthal, Kenneth B.

    2005-10-11

    This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

  6. Molecules-in-molecules fragment-based method for the evaluation of Raman spectra of large molecules

    NASA Astrophysics Data System (ADS)

    Jovan Jose, K. V.; Raghavachari, Krishnan

    2015-10-01

    We present the first implementation of the evaluation Raman spectra of large molecules using the molecules-in-molecules (MIM) fragment-based method (MIM-Raman). Molecular fragments and associated overlapping subsystems are constructed by cutting the C-C bonds in the large molecule based on the connectivity information and a number-based fragmentation scheme. After saturating the dangling bonds with hydrogen link-atoms, independent energy and Raman frequency calculations are performed on each subsystem. Subsequently, link-atom-related forces, Hessian and polarisability derivative matrix elements are projected back onto the corresponding host and supporting atoms through the Jacobian projection method. In the two-layer model (MIM2), the long-range interactions, absent in the single layer model (MIM1), are taken into account through a second layer at a lower level of theory. The MIM-Raman method is benchmarked on a set of large linear and cage molecules. The MIM extrapolated energy and Raman spectra are compared with the full calculations at B3LYP/6-311G(d,p) or B3LYP/6-311+G(d,p) levels of theory. The benchmark analysis of 21 molecules at MIM2 show an accuracy improvement of 85% in energies, 74% in Raman frequencies and 66% in intensities over MIM1. The implementation and benchmark analysis validates the MIM-Raman model for exploring Raman spectra of large molecules in the future.

  7. The Origins and Evolution of Molecules in Icy Solids

    NASA Technical Reports Server (NTRS)

    Hudson, Reggie L.; Moore, Marla H.

    2010-01-01

    Astronomical observations of the past few decades have revealed the existence of a variety of molecules in extraterrestrial ices. These molecules include H2O, CO, and CO2, and organics such as CH4, CH30H, and C2H6. Some ices are dominated by polar molecules, while non-polar species appear to dominate others. Observations, mainly in the radio and IR regions, have allowed the inference of other solid-phase molecules whose formation remains difficult to explain by gas-phase chemistry alone. Several laboratory research groups have reported on extensive experiments on the solid-phase reaction chemistry of icy materials, generally as initiated by either ionizing radiation or vacuum-UV photons. These experiments not only permit molecular identifications to be made from astronomical observations, but also allow predictions of yet unidentified molecules. This laboratory approach has evolved over more than 30 years with much of the earliest work focusing on complex mixtures thought to represent either cometary or interstellar ices. Although those early experiments documented a rich solid-state photo- and radiation chemistry, they revealed few details of reactions for particular molecules, partly due to the multi-component nature of the samples. Since then, model systems have been examined that allow the chemistry of individual species and specific reactions to be probed. Reactions involving most of the smaller astronomical molecules have now been studied and specific processes identified. Current laboratory work suggests that a variety of reactions occur in extraterrestrial ices, including acid-base processes, radical dimerizations, proton transfers, oxidations, reductions, and isomerizations. This workshop presentation will focus on chemical reactions relevant to solar system and interstellar ices. While most of the work will be drawn from that to which the speaker has contributed, results from other laboratories also will be included. Suggestions for future studies will be

  8. Search for complex organic molecules in space

    NASA Astrophysics Data System (ADS)

    Ohishi, Masatoshi

    2016-07-01

    It was 1969 when the first organic molecule in space, H2CO, was discovered. Since then many organic molecules were discovered by using the NRAO 11 m (upgraded later to 12 m), Nobeyama 45 m, IRAM 30 m, and other highly sensitive radio telescopes as a result of close collaboration between radio astronomers and microwave spectroscopists. It is noteworthy that many famous organic molecules such as CH3OH, C2H5OH, (CH3)2O and CH3NH2 were detected by 1975. Organic molecules were found in so-called hot cores where molecules were thought to form on cold dust surfaces and then to evaporate by the UV photons emitted from the central star. These days organic molecules are known to exist not only in hot cores but in hot corinos (a warm, compact molecular clump found in the inner envelope of a class 0 protostar) and even protoplanetary disks. As was described above, major organic molecules were known since 1970s. It was very natural that astronomers considered a relationship between organic molecules in space and the origin of life. Several astronomers challenged to detect glycine and other prebiotic molecules without success. ALMA is expected to detect such important materials to further consider the gexogenous deliveryh hypothesis. In this paper I summarize the history in searching for complex organic molecules together with difficulties in observing very weak signals from larger species. The awfully long list of references at the end of this article may be the most useful part for readers who want to feel the exciting discovery stories.

  9. Spectroscopic and dynamical studies of highly energized small polyatomic molecules

    SciTech Connect

    Field, R.W.; Silbey, R.J.

    1993-12-01

    The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.

  10. Electron-driven excitations and dissociation of molecules

    SciTech Connect

    Miller, Greg; Orel, Ann E.

    2015-02-13

    This program studied how energy is interchanged in electron and photon collisions with molecules leading to ex-citation and dissociation. Modern ab initio techniques, both for the photoionization and electron scattering, and the subsequent nuclear dynamics studies, are used to accurately treat these problems. This work addresses vibrational ex-citation and dissociative attachment following electron impact, and the dynamics following inner shell photoionzation. These problems are ones for which a full multi-dimensional treatment of the nuclear dynamics is essential and where non-adiabatic effects are expected to be important.

  11. CHEMICAL ACTIVATION OF MOLECULES BY METALS: EXPERIMENTAL STUDIES OF ELECTRON DISTRIBUTIONS AND BONDING

    SciTech Connect

    LICHTENBERGER, DENNIS L.

    2002-03-26

    This research program is directed at obtaining detailed experimental information on the electronic interactions between metals and organic molecules. These interactions provide low energy pathways for many important chemical and catalytic processes. A major feature of the program is the continued development and application of our special high-resolution valence photoelectron spectroscopy (UPS), and high-precision X-ray core photoelectron spectroscopy (XPS) instrumentation for study of organometallic molecules in the gas phase. The study involves a systematic approach towards understanding the interactions and activation of bound carbonyls, C-H bonds, methylenes, vinylidenes, acetylides, alkenes, alkynes, carbenes, carbynes, alkylidenes, alkylidynes, and others with various monometal, dimetal, and cluster metal species. Supporting ligands include -aryls, alkoxides, oxides, and phosphines. We are expanding our studies of both early and late transition metal species and electron-rich and electron-poor environments in order to more completely understand the electronic factors that serve to stabilize particular organic fragments and intermediates on metals. Additional new directions for this program are being taken in ultra-high vacuum surface UPS, XPS, scanning tunneling microscopy (STM) and atomic force microscopy (AFM) experiments on both physisorbed and chemisorbed organometallic thin films. The combination of these methods provides additional electronic structure information on surface-molecule and molecule-molecule interactions. A very important general result emerging from this program is the identification of a close relationship between the ionization energies of the species and the thermodynamics of the chemical and catalytic reactions of these systems.

  12. Trapping and manipulating single molecules of DNA

    NASA Astrophysics Data System (ADS)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  13. Single-molecule junctions beyond electronic transport.

    PubMed

    Aradhya, Sriharsha V; Venkataraman, Latha

    2013-06-01

    The idea of using individual molecules as active electronic components provided the impetus to develop a variety of experimental platforms to probe their electronic transport properties. Among these, single-molecule junctions in a metal-molecule-metal motif have contributed significantly to our fundamental understanding of the principles required to realize molecular-scale electronic components from resistive wires to reversible switches. The success of these techniques and the growing interest of other disciplines in single-molecule-level characterization are prompting new approaches to investigate metal-molecule-metal junctions with multiple probes. Going beyond electronic transport characterization, these new studies are highlighting both the fundamental and applied aspects of mechanical, optical and thermoelectric properties at the atomic and molecular scales. Furthermore, experimental demonstrations of quantum interference and manipulation of electronic and nuclear spins in single-molecule circuits are heralding new device concepts with no classical analogues. In this Review, we present the emerging methods being used to interrogate multiple properties in single molecule-based devices, detail how these measurements have advanced our understanding of the structure-function relationships in molecular junctions, and discuss the potential for future research and applications.

  14. Stretched polyethylene films probed by single molecules.

    PubMed

    Wirtz, Alexander C; Hofmann, Clemens; Groenen, Edgar J J

    2011-06-01

    Stretched films of low-density polyethylene (LDPE) doped with 2.3,8.9-dibenzanthanthrene (DBATT) were studied using polarization-selective single-molecule spectroscopy at 1.8 K. By measuring the in-plane component of the electronic transition-dipole moments of individual chromophores, the alignment of dopant molecules is determined without averaging. The distributions of chromophore orientations reveal the presence of two fractions of dopant molecules: those oriented along the stretching direction and randomly oriented molecules. With increasing drawing ratio of the polyethylene films, the ratio of oriented to randomly oriented guest molecules increases, whereas the extent of chromophore orientation, that is, the width of the orientation distribution, remains the same. The results are consistent with the interpretation that oriented chromophores reside on the surfaces of polyethylene crystals, instead of in the amorphous polyethylene regions. Guest molecules in stretched polyethylene are oriented due to the alignment of the crystallites on which they are adsorbed. As such, the shape and width of the distributions of chromophore orientations are determined by the interaction of guest molecules with the crystal surfaces.

  15. Ultralong-range polyatomic Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Gonzalez-Ferez, Rosario

    2016-05-01

    Ultralong-range polyatomic Rydberg molecules are formed when a ground-state atom is bound to a Rydberg atom. The binding mechanism of these Rydberg molecules is based on the low-energy collisions between a Rydberg electron and a ground-state atom and leads to the unusual oscillatory behavior of the adiabatic potential energy curves. If the ground-state atom immersed into the Rydberg wave function is replaced by a heteronuclear diatomic molecule another type of polyatomic Rydberg molecules can form. In this case, the Rydberg electron is coupled to the internal states of the polar ground-state molecule. In this talk, we will explore the electronic structure and rovibrational properties of these ultralong-range polyatomic Rydberg molecule. For the second type of Rydberg molecules, the polar dimer is allowed to rotate in the electric fields generated by the Rydberg electron and Rydberg core as well as an additional external field. We will investigate the metamorphosis of the Born-Oppenheimer potential curves, essential for the binding mechanism, with varying electric field and analyze the resulting properties such as the vibrational structure and the alignment and orientation of the polar dimer.

  16. Symmetry calculation for molecules and transition states.

    PubMed

    Vandewiele, Nick M; Van de Vijver, Ruben; Van Geem, Kevin M; Reyniers, Marie-Françoise; Marin, Guy B

    2015-01-30

    The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three-dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label-stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules.

  17. Single Molecule Spectroscopy of Electron Transfer

    SciTech Connect

    Michael Holman; Ling Zang; Ruchuan Liu; David M. Adams

    2009-10-20

    The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

  18. Giant molecules composed of polar molecules and atoms in mixed dimensions

    NASA Astrophysics Data System (ADS)

    Qi, Ran; Tan, Shina

    2014-05-01

    Two or three polar molecules, confined to one or two dimensions, can form stable bound states with a single atom living in three dimensions, if the molecule and the atom can interact resonantly such that their mixed dimensional scattering length is large. We call these bound states ``giant molecules'' since it's a molecule composed of smaller molecules and atoms. We study their properties using techniques including exact numerical solution, exact qunatum diffusion Monte Carlo (QMC), Born-Oppenheimer approximation (BOA), and semiclassical approximation. These bound states have a hierarchical structure reminiscent of the celestial systems.

  19. Line broadening of confined CO gas: from molecule-wall to molecule-molecule collisions with pressure.

    PubMed

    Hartmann, J-M; Boulet, C; Auwera, J Vander; El Hamzaoui, H; Capoen, B; Bouazaoui, M

    2014-02-14

    The infrared absorption in the fundamental band of CO gas confined in porous silica xerogel has been recorded at room temperature for pressures between about 5 and 920 hPa using a high resolution Fourier transform spectrometer. The widths of individual lines are determined from fits of measured spectra and compared with ab initio predictions obtained from requantized classical molecular dynamics simulations. Good agreement is obtained from the low pressure regime where the line shapes are governed by molecule-wall collisions to high pressures where the influence of molecule-molecule interactions dominates. These results, together with those obtained with a simple analytical model, indicate that both mechanisms contribute in a practically additive way to the observed linewidths. They also confirm that a single collision of a molecule with a wall changes its rotational state. These results are of interest for the determination of some characteristics of the opened porosity of porous materials through optical soundings.

  20. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives. PMID:26606461

  1. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives.

  2. Detecting high-density ultracold molecules using atom-molecule collision

    NASA Astrophysics Data System (ADS)

    Chen, Jun-Ren; Kao, Cheng-Yang; Chen, Hung-Bin; Liu, Yi-Wei

    2013-04-01

    Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecules utilizing inelastic atom-molecule collision is demonstrated. The resonant coupling effect on the formation of the X1Σ+g ground state 85Rb2 allows for a sufficient number of more deeply bound ultracold molecules, which induced an additional trap loss and heating of the co-existing atoms owing to the inelastic atom-molecule collision. Therefore, after the photoassociation process, the ultracold molecules can be investigated using the absorption image of the ultracold rubidium atoms mixed with the molecules in a crossed optical dipole trap. The existence of the ultracold molecules was then verified, and the amount of accumulated molecules was measured. This method detects the final produced ultracold molecules, and hence is distinct from the conventional trap loss experiment, which is used to study the association resonance. It is composed of measurements of the time evolution of an atomic cloud and a decay model, by which the number density of the ultracold 85Rb2 molecules in the optical trap was estimated to be >5.2 × 1011 cm-3.

  3. Phononic Molecules Studied by Raman Scattering

    SciTech Connect

    Lanzillotti-Kimura, N. D.; Fainstein, A.; Jusserand, B.; Lemaitre, A.

    2010-01-04

    An acoustic nanocavity can confine phonons in such a way that they act like electrons in an atom. By combining two of these phononic-atoms, it is possible to form a phononic 'molecule', with acoustic modes that are similar to the electronic states in a hydrogen molecule. We report Raman scattering experiments performed in a monolithic structure formed by a phononic molecule embedded in an optical cavity. The acoustic mode splitting becomes evident through both the amplification and change of selection rules induced by the optical cavity confinement. The results are in perfect agreement with photoelastic model simulations.

  4. Life at the Single Molecule Level

    SciTech Connect

    Xie, Xiaoliang Sunny

    2011-03-04

    In a living cell, gene expression—the transcription of DNA to messenger RNA followed by translation to protein—occurs stochastically, as a consequence of the low copy number of DNA and mRNA molecules involved. Can one monitor these processes in a living cell in real time? How do cells with identical genes exhibit different phenotypes? Recent advances in single-molecule imaging in living bacterial cells allow these questions to be answered at the molecular level in a quantitative manner. It was found that rare events of single molecules can have important biological consequences.

  5. Chiral Isotropic Liquids from Achiral Molecules

    SciTech Connect

    L Hough; M Spannuth; M Nakata; D Coleman; C Jones; G Dantlgraber; C Tschierske; J Watanabe; N Clark; et al.

    2011-12-31

    A variety of simple bent-core molecules exhibit smectic liquid crystal phases of planar fluid layers that are spontaneously both polar and chiral in the absence of crystalline order. We found that because of intralayer structural mismatch, such layers are also only marginally stable against spontaneous saddle splay deformation, which is incompatible with long-range order. This results in macroscopically isotropic fluids that possess only short-range orientational and positional order, in which the only macroscopically broken symmetry is chirality - even though the phases are formed from achiral molecules. Their conglomerate domains exhibit optical rotatory powers comparable to the highest ever found for isotropic fluids of chiral molecules.

  6. Electron-impact-induced tryptophan molecule fragmentation

    NASA Astrophysics Data System (ADS)

    Tamuliene, Jelena; Romanova, Liudmila G.; Vukstich, Vasyl S.; Papp, Alexander V.; Snegursky, Alexander V.

    2015-01-01

    The fragmentation of a gas-phase tryptophan molecule by a low-energy (<70 eV) electron impact was studied both experimentally and theoretically. Various positively charged fragments were observed and analyzed. A special attention was paid to the energy characteristics of the ionic fragment yield. The geometrical parameters of the initial molecule rearrangement were also analyzed. The fragmentation observed was due to either a simple bond cleavage or more complex reactions involving molecular rearrangements. Contribution to the Topical Issue "Elementary Processes with Atoms and Molecules in Isolated and Aggregated States", edited by Friedrich Aumayr, Bratislav Marinkovic, Stefan Matejcik, John Tanis and Kurt H. Becker.

  7. Circularly Polarized Luminescence from Simple Organic Molecules

    PubMed Central

    Sánchez-Carnerero, Esther M.; Agarrabeitia, Antonia R.; Moreno, Florencio; Maroto, Beatriz L.; Muller, Gilles; Ortiz, María J.

    2015-01-01

    This article aims to show the identity of “CPL-active simple organic molecules” as a new concept in Organic Chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and nonaggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

  8. Cytochrome c Is Released in a Reactive Oxygen Species-Dependent Manner and Is Degraded via Caspase-Like Proteases in Tobacco Bright-Yellow 2 Cells en Route to Heat Shock-Induced Cell Death1

    PubMed Central

    Vacca, Rosa Anna; Valenti, Daniela; Bobba, Antonella; Merafina, Riccardo Sandro; Passarella, Salvatore; Marra, Ersilia

    2006-01-01

    To gain some insight into the mechanism of plant programmed cell death, certain features of cytochrome c (cyt c) release were investigated in heat-shocked tobacco (Nicotiana tabacum) Bright-Yellow 2 cells in the 2- to 6-h time range. We found that 2 h after heat shock, cyt c is released from intact mitochondria into the cytoplasm as a functionally active protein. Such a release did not occur in the presence of superoxide anion dismutase and catalase, thus showing that it depends on reactive oxygen species (ROS). Interestingly, ROS production due to xanthine plus xanthine oxidase results in cyt c release in sister control cultures. Maximal cyt c release was found 2 h after heat shock; later, activation of caspase-3-like protease was found to increase with time. Activation of this protease did not occur in the presence of ROS scavenger enzymes. The released cyt c was found to be progressively degraded in a manner prevented by either the broad-range caspase inhibitor (zVAD-fmk) or the specific inhibitor of caspase-3 (AC-DEVD-CHO), which have no effect on cyt c release. In the presence of these inhibitors, a significant increase in survival of the cells undergoing programmed cell death was found. We conclude that ROS can trigger release of cyt c, but do not cause cell death, which requires caspase-like activation. PMID:16531480

  9. Intercultural Programs: Program Evaluation.

    ERIC Educational Resources Information Center

    Des Moines Public Schools, IA.

    The Office of Intercultural Programs of the Des Moines public schools addresses the equity needs of the district through a wide range of equity services. The Office serves as a resource for students, parents, community, and staff, and provides service in the areas of: (1) the Voluntary Transfer Program; (2) paired and magnet schools; (3) extended…

  10. Small Molecules from the Human Microbiota

    PubMed Central

    Donia, Mohamed S.; Fischbach, Michael A.

    2015-01-01

    Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of natural products from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future, and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and their biological relevance. PMID:26206939

  11. Single-Molecule Studies in Live Cells

    NASA Astrophysics Data System (ADS)

    Yu, Ji

    2016-05-01

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

  12. Synaptic Cell Adhesion Molecules in Alzheimer's Disease

    PubMed Central

    Leshchyns'ka, Iryna

    2016-01-01

    Alzheimer's disease (AD) is a neurodegenerative brain disorder associated with the loss of synapses between neurons in the brain. Synaptic cell adhesion molecules are cell surface glycoproteins which are expressed at the synaptic plasma membranes of neurons. These proteins play key roles in formation and maintenance of synapses and regulation of synaptic plasticity. Genetic studies and biochemical analysis of the human brain tissue, cerebrospinal fluid, and sera from AD patients indicate that levels and function of synaptic cell adhesion molecules are affected in AD. Synaptic cell adhesion molecules interact with Aβ, a peptide accumulating in AD brains, which affects their expression and synaptic localization. Synaptic cell adhesion molecules also regulate the production of Aβ via interaction with the key enzymes involved in Aβ formation. Aβ-dependent changes in synaptic adhesion affect the function and integrity of synapses suggesting that alterations in synaptic adhesion play key roles in the disruption of neuronal networks in AD. PMID:27242933

  13. Electronic Structure of Small Lanthanide Containing Molecules

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Ray, Manisha; Topolski, Josey E.; Chick Jarrold, Caroline

    2016-06-01

    Lanthanide-based materials have unusual electronic properties because of the high number of electronic degrees of freedom arising from partial occupation of 4f orbitals, which make these materials optimal for their utilization in many applications including electronics and catalysis. Electronic spectroscopy of small lanthanide molecules helps us understand the role of these 4f electrons, which are generally considered core-like because of orbital contraction, but are energetically similar to valence electrons. The spectroscopy of small lanthanide-containing molecules is relatively unexplored and to broaden this understanding we have completed the characterization of small cerium, praseodymium, and europium molecules using photoelectron spectroscopy coupled with DFT calculations. The characterization of PrO, EuH, EuO/EuOH, and CexOy molecules have allowed for the determination of their electron affinity, the assignment of numerous anion to neutral state transitions, modeling of anion/neutral structures and electron orbital occupation.

  14. Stochastic Models of Molecule Formation on Dust

    NASA Technical Reports Server (NTRS)

    Charnley, Steven; Wirstroem, Eva

    2011-01-01

    We will present new theoretical models for the formation of molecules on dust. The growth of ice mantles and their layered structure is accounted for and compared directly to observations through simulation of the expected ice absorption spectra

  15. Laser Spectroscopy of Atoms and Molecules.

    ERIC Educational Resources Information Center

    Schawlow, Arthur L.

    1978-01-01

    Surveys new laser techniques and a variety of spectroscopic experiments that can be used to detect, measure and study very small numbers of atoms on molecules. The range of applicability of these techniques is also included. (HM)

  16. Polyatomic molecules under intense femtosecond laser irradiation.

    PubMed

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim V; Jackson, James E; Levine, Benjamin G; Dantus, Marcos

    2014-12-11

    Interaction of intense laser pulses with atoms and molecules is at the forefront of atomic, molecular, and optical physics. It is the gateway to powerful new tools that include above threshold ionization, high harmonic generation, electron diffraction, molecular tomography, and attosecond pulse generation. Intense laser pulses are ideal for probing and manipulating chemical bonding. Though the behavior of atoms in strong fields has been well studied, molecules under intense fields are not as well understood and current models have failed in certain important aspects. Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon excitation. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a "bag of atoms" during field induced ionization. In this article we present a set of experiments and theoretical calculations exploring the behavior of a large collection of aryl alkyl ketones when irradiated with intense femtosecond pulses. Specifically, we consider to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The set of molecules studied is further divided into smaller sets, sorted by type and position of functional groups. The pump-probe time-delay scans show that among positional isomers the variations in relative energies, which amount to only a few hundred millielectronvolts, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). High level ab initio quantum chemical calculations were performed to predict molecular dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose the

  17. Protein mechanics: from single molecules to functional biomaterials.

    PubMed

    Li, Hongbin; Cao, Yi

    2010-10-19

    multidomain elastomeric proteins, and the design of novel elastomeric proteins that exhibit stimuli-responsive mechanical properties. Moving forward, we are now exploring the use of these artificial elastomeric proteins as building blocks of protein-based biomaterials. Ultimately, we would like to rationally tailor mechanical properties of elastomeric protein-based materials by programming the molecular sequence, and thus nanomechanical properties, of elastomeric proteins at the single-molecule level. This step would help bridge the gap between single protein mechanics and material biomechanics, revealing how the mechanical properties of individual elastomeric proteins are translated into the properties of macroscopic materials. PMID:20669937

  18. Intercellular adhesion molecule-1 in the heart.

    PubMed

    Niessen, Hans W M; Krijnen, Paul A J; Visser, Cees A; Meijer, Chris J L M; Hack, C Erik

    2002-11-01

    Intercellular adhesion molecule-1 (ICAM-1) belongs to the superfamily of immunoglobulin-like adhesion molecules. Up-regulation of ICAM-1 occurs in many different pathophysiological processes. Also, cardiomyocytes can express ICAM-1-for example, in acute myocardial infarction. Moreover, inhibition of ICAM-1 expression in the heart dramatically reduces infarct size. Hence, inhibitors of ICAM-1 may provide a novel therapeutic option for acute myocardial infarction.

  19. Recovery of tritium from tritiated molecules

    DOEpatents

    Swansiger, W.A.

    1984-10-17

    This invention relates to the recovery of tritium from various tritiated molecules by reaction with uranium. More particularly, the invention relates to the recovery of tritium from tritiated molecules by reaction with uranium wherein the reaction is conducted in a reactor which permits the reaction to occur as a moving front reaction from the point where the tritium enters the reactor charged with uranium down the reactor until the uranium is exhausted.

  20. Hadronic molecules in the heavy baryon spectrum

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    We study possible baryon molecules in the non-strange heavy baryon spectrum. We include configurations with a heavy-meson and a light baryon. We find several structures, in particular we can understand the Λc(2940) as a D*N molecule with JP = 3/2- quantum numbers. We also find D(*)Δ candidates for the recently discovered Xc(3250) resonance.

  1. Do triatomic molecules echo atomic periodicity?

    SciTech Connect

    Hefferlin, R. Barrow, J.

    2015-03-30

    Demonstrations of periodicity among triatomic-molecular spectroscopic constants underscore the role of the periodic law as a foundation of chemistry. The objective of this work is to prepare for another test using vibration frequencies ν{sub 1} of free, ground-state, main-group triatomic molecules. Using data from four data bases and from computation, we have collected ν{sub 1} data for molecules formed from second period atoms.

  2. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  3. Tests of Lorentz invariance using hydrogen molecules

    SciTech Connect

    Mueller, Holger; Herrmann, Sven; Saenz, Alejandro; Peters, Achim; Laemmerzahl, Claus

    2004-10-01

    We discuss the consequences of Lorentz violation (as expressed within the Lorentz-violating extension of the standard model) for the hydrogen molecule, which represents a generic model of a molecular binding. Lorentz-violating shifts of electronic, vibrational and rotational energy levels, and of the internuclear distance are calculated. This offers the possibility of obtaining improved bounds on Lorentz invariance by experiments using molecules.

  4. Auxin biology revealed by small molecules.

    PubMed

    Ma, Qian; Robert, Stéphanie

    2014-05-01

    The plant hormone auxin regulates virtually every aspect of plant growth and development and unraveling its molecular and cellular modes of action is fundamental for plant biology research. Chemical genomics is the use of small molecules to modify protein functions. This approach currently rises as a powerful technology for basic research. Small compounds with auxin-like activities or affecting auxin-mediated biological processes have been widely used in auxin research. They can serve as a tool complementary to genetic and genomic methods, facilitating the identification of an array of components modulating auxin metabolism, transport and signaling. The employment of high-throughput screening technologies combined with informatics-based chemical design and organic chemical synthesis has since yielded many novel small molecules with more instantaneous, precise and specific functionalities. By applying those small molecules, novel molecular targets can be isolated to further understand and dissect auxin-related pathways and networks that otherwise are too complex to be elucidated only by gene-based methods. Here, we will review examples of recently characterized molecules used in auxin research, highlight the strategies of unraveling the mechanisms of these small molecules and discuss future perspectives of small molecule applications in auxin biology. PMID:24252105

  5. A prototype storage ring for neutral molecules.

    PubMed

    Crompvoets, F M; Bethlem, H L; Jongma, R T; Meijer, G

    2001-05-10

    The ability to cool and manipulate atoms with light has yielded atom interferometry, precision spectroscopy, Bose-Einstein condensates and atom lasers. The extension of controlled manipulation to molecules is expected to be similarly rewarding, but molecules are not as amenable to manipulation by light owing to a far more complex energy-level spectrum. However, time-varying electric and magnetic fields have been successfully used to control the position and velocity of ions, suggesting that these schemes can also be used to manipulate neutral particles having an electric or magnetic dipole moment. Although the forces exerted on neutral species are many orders of magnitude smaller than those exerted on ions, beams of neutral dipolar molecules have been successfully slowed down in a series of pulsed electric fields and subsequently loaded into an electrostatic trap. Here we extend the scheme to include a prototype electrostatic storage ring made of a hexapole torus with a circumference of 80 cm. After injection, decelerated bunches of deuterated ammonia molecules, each containing about 106 molecules in a single quantum state and with a translational temperature of 10 mK, travel up to six times around the ring. Stochastic cooling might provide a means to increase the phase-space density of the stored molecules in the storage ring, and we expect this to open up new opportunities for molecular spectroscopy and studies of cold molecular collisions.

  6. Single Molecule Raman Spectroscopy Under High Pressure

    NASA Astrophysics Data System (ADS)

    Fu, Yuanxi; Dlott, Dana

    2014-06-01

    Pressure effects on surface-enhanced Raman scattering spectra of Rhdoamine 6G adsorbed on silver nanoparticle surfaces was studied using a confocal Raman microscope. Colloidal silver nanoparticles were treated with Rhodamine 6G (R6G) and its isotopically substituted partner, R6G-d4. Mixed isotopomers let us identify single-molecule spectra, since multiple-molecule spectra would show vibrational transitions from both species. The nanoparticles were embedded into a poly vinyl alcohol film, and loaded into a diamond anvil cell for the high-pressure Raman scattering measurement. Argon was the pressure medium. Ambient pressure Raman scattering spectra showed few single-molecule spectra. At moderately high pressure ( 1GPa), a surprising effect was observed. The number of sites with observable spectra decreased dramatically, and most of the spectra that could be observed were due to single molecules. The effects of high pressure suppressed the multiple-molecule Raman sites, leaving only the single-molecule sites to be observed.

  7. Self-Assemblies of novel molecules, VECAR

    NASA Astrophysics Data System (ADS)

    Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

    2015-03-01

    VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

  8. Nonlinear Dynamics of Atom-Molecule Conversion

    NASA Astrophysics Data System (ADS)

    Fu, Li-Bin; Liu, Jie

    2014-03-01

    The creation of ultracold molecules has opened up new possibilities for studies on molecular matter waves, strongly interacting superfluids, high-precision molecular spectroscopy and coherent molecular optics. In an atomic Bose-Einstein condensate (BEC) and a degenerate Fermi-Fermi or Fermi-Bose mixture, magnetic Feshbach resonance or optical photoassociation (PA) technique has been used to create not only diatomic molecules but also more complex molecules. In this chapter, we focus on many issues of nonlinear dynamics of atom-molecule systems. In Sec. 1, on the basis of the two-channelmean-field approach, we study the manybody effects on the Landau-Zener(LZ) picture of two-body molecular production through dramatically distorting the energy levels near the Feshbach resonance. In Sec. 2, we investigate the Feshbach resonance with modulation of an oscillating magnetic field. In Sec. 3, we include the nonlinear interparticle collisions and focus on the linear instability induced by the collisions and the adiabatic fidelity of the atom-trimer dark state in a stimulated Raman adiabatic passage (STIRAP). In Sec. 4, we theoretically investigate conversion problem from atom to N-body polyatomic molecule in an ultracold bosonic system by implementing the generalized STIRAP. In the last section, we discuss role of two-body interactions in the Feshbach conversion of fermionic atoms to bosonic molecules.

  9. Vibrational Cooling of Photoassociated Homonuclear Cold Molecules

    NASA Astrophysics Data System (ADS)

    Passagem, Henry; Ventura, Paulo; Tallant, Jonathan; Marcassa, Luis

    2015-05-01

    In this work, we produce vibrationally cold homonuclear Rb molecules using spontaneous optical pumping. The vibrationally cooled molecules are produced in three steps. In the first step, we use a photoassociation laser to produce molecules in high vibrational levels of the singlet ground state. Then in a second step, a 50 W broadband laser at 1071 nm, which bandwidth is about 2 nm, is used to transfer the molecules to lower vibrational levels via optical pumping through the excited state. This process transfers the molecules from vibrational levels around ν ~= 113 to a distribution of levels below ν = 35 . The molecules can be further cooled using a broadband light source near 685 nm. In order to obtain such broadband source, we have used a 5 mW superluminescent diode, which is amplified in a tapered amplifier using a double pass configuration. After the amplification, the spectrum is properly shaped and we end up with about 90 mW distributed in the 682-689 nm range. The final vibrational distribution is probed using resonance-enhanced multiphoton ionization with a pulsed dye laser near 670 nm operating at 4KHz. The results are presented and compared with theoretical simulations. This work was supported by Fapesp and INCT-IQ.

  10. Sol-gel method for encapsulating molecules

    DOEpatents

    Brinker, C. Jeffrey; Ashley, Carol S.; Bhatia, Rimple; Singh, Anup K.

    2002-01-01

    A method for encapsulating organic molecules, and in particular, biomolecules using sol-gel chemistry. A silica sol is prepared from an aqueous alkali metal silicate solution, such as a mixture of silicon dioxide and sodium or potassium oxide in water. The pH is adjusted to a suitably low value to stabilize the sol by minimizing the rate of siloxane condensation, thereby allowing storage stability of the sol prior to gelation. The organic molecules, generally in solution, is then added with the organic molecules being encapsulated in the sol matrix. After aging, either a thin film can be prepared or a gel can be formed with the encapsulated molecules. Depending upon the acid used, pH, and other processing conditions, the gelation time can be from one minute up to several days. In the method of the present invention, no alcohols are generated as by-products during the sol-gel and encapsulation steps. The organic molecules can be added at any desired pH value, where the pH value is generally chosen to achieve the desired reactivity of the organic molecules. The method of the present invention thereby presents a sufficiently mild encapsulation method to retain a significant portion of the activity of the biomolecules, compared with the activity of the biomolecules in free solution.

  11. Molecular Programming with DNA

    NASA Astrophysics Data System (ADS)

    Winfree, Erik

    2009-05-01

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

  12. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  13. Isomerization reactions on single adsorbed molecules.

    PubMed

    Morgenstern, Karina

    2009-02-17

    Molecular switches occur throughout nature. In one prominent example, light induces the isomerization of retinal from the compact 11-cis form to the elongated all-trans form, a conversion that triggers the transformation of light into a neural impulse in the eye. Applying these natural principles to synthetic systems offers a promising way to construct smaller and faster nanoelectronic devices. In such systems, electronic switches are essential components for storage and logical operations. The development of molecular switches on the single-molecule level would represent a major step toward incorporating molecules as building units into nanoelectronic circuits. Molecular switches must be both reversible and bistable. To meet these requirements, a molecule must have at least two different thermally stable forms and a way to repeatedly interconvert between those forms based on changes in light, heat, pressure, magnetic or electric fields, pH, mechanical forces, or electric currents. The conversion should be connected to a measurable change in electronic, optical, magnetic, or mechanical properties. Because isomers can differ significantly in physical and chemical properties, isomerization could serve as a molecular switching mechanism. Integration of molecular switches into larger circuits will probably require arranging them on surfaces, which will require a better understanding of isomerization reactions in these environments. In this Account, we describe our scanning tunneling microscopy studies of the isomerization of individual molecules adsorbed on metal surfaces. Investigating chlorobenzene and azobenzene derivatives on the fcc(111) faces of Ag, Cu, and Au, we explored the influence of substituents and the substrate on the excitation mechanism of the isomerization reaction induced by inelastically tunneling electrons. We achieved an irreversible configurational (cis-trans) isomerization of individual 4-dimethyl-amino-azobenzene-4-sulfonic acid molecules on Au

  14. Mining for Molecules in the Milky Way

    NASA Astrophysics Data System (ADS)

    2008-06-01

    Scientists are using the giant Robert C. Byrd Green Bank Telescope (GBT) to go prospecting in a rich molecular cloud in our Milky Way Galaxy. They seek to discover new, complex molecules in interstellar space that may be precursors to life. The GBT and Molecules The Robert C. Byrd Green Bank Telescope and some molecules it has discovered. CREDIT: Bill Saxton, NRAO/AUI/NSF "Clouds like this one are the raw material for new stars and planets. We know that complex chemistry builds prebiotic molecules in such clouds long before the stars and planets are formed. There is a good chance that some of these interstellar molecules may find their way to the surface of young planets such as the early Earth, and provide a head start for the chemistry of life. For the first time, we now have the capability to make a very thorough and methodical search to find all the chemicals in the clouds," said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO). In the past three years, Remijan and his colleagues have used the GBT to discover ten new interstellar molecules, a feat unequalled in such a short time by any other team or telescope. The scientists discovered those molecules by looking specifically for them. However, they now are changing their strategy and casting a wide net designed to find whatever molecules are present, without knowing in advance what they'll find. In addition, they are making their data available freely to other scientists, in hopes of speeding the discovery process. The research team presented its plan to the American Astronomical Society's meeting in St. Louis, MO. As molecules rotate and vibrate, they emit radio waves at specific frequencies. Each molecule has a unique pattern of such frequencies, called spectral lines, that constitutes a "fingerprint" identifying that molecule. Laboratory tests can determine the pattern of spectral lines that identifies a specific molecule. Most past discoveries came from identifying a molecule's pattern in

  15. What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

    PubMed

    Sen, Anik; Ganguly, Bishwajit

    2010-12-01

    This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller-Plesset second-order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K(+)/Cl(-) ion-pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion-pair [K(+)(H(2)O)(5)Cl(-)]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion-pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed.

  16. Theoretical Treatment of the Thermophysical Properties of Fluids Containing Chain-like Molecules

    SciTech Connect

    Carol K. Hall

    2008-11-14

    This research program was designed to enhance our understanding of the behavior of fluids and fluid mixtures containing chain-like molecules. The original objective was to explain and predict the experimentally observed thermophysical properties, including phase equilibria and dynamics, of systems containing long flexible molecules ranging in length from alkanes to polymers. Over the years the objectives were expanded to include the treatment of molecules that were not chain-like. Molecular dynamics and Monte Carlo computer simulations were used to investigate how variations in molecular size, shape and architecture influence the types of phase equilibria, thermodynamic properties, structure and surface interactions that are observed experimentally. The molecular insights and theories resulting from this program could eventually serve as the foundation upon which to build correlations of the properties of fluids that are both directly and indirectly related to the Nation’s energy resources including: petroleum, natural gas, and polymer solutions, melts, blends, and materials.

  17. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    SciTech Connect

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in

  18. Fluorescence Detection of Single DNA Molecules.

    PubMed

    Huang, Weidong; Wang, Yue; Wang, Zhimin

    2015-09-01

    Single-molecule detection (SMD) and single-molecule fluorescence resonance energy transfer (smFRET) were conducted using Cy3- and Cy5-labeled single-strand DNAs (ssDNAs) either immobilized on substrates or encapsulated in microdroplets. High-quality fluorescent images were obtained using a total internal reflection fluorescence microscope (TIRFM). In the substrate system, deposition of a low concentration of fluorescence molecules on substrates through electrostatic adsorption showed that most of the fluorescence spots were single molecules, and the mean value of signal to noise ratio (S/N) reached 6.9 ± 0.34. smFRET analysis was conducted through immobilization of donor- and acceptor-labeled oligonucleotides on substrates. In the droplet system, fluorophor-labeled oligonucleotides were injected into T-type microfluidics. Single and double fluorophor-labeled DNA molecules encapsulated in droplets were detected, the FRET efficiency and inter-dye distance of a single donor-acceptor pair were measured accurately. smFRET was conducted detailedly in the tortuous channel for the first time.

  19. Optimal Superpositioning of Flexible Molecule Ensembles

    PubMed Central

    Gapsys, Vytautas; de Groot, Bert L.

    2013-01-01

    Analysis of the internal dynamics of a biological molecule requires the successful removal of overall translation and rotation. Particularly for flexible or intrinsically disordered peptides, this is a challenging task due to the absence of a well-defined reference structure that could be used for superpositioning. In this work, we started the analysis with a widely known formulation of an objective for the problem of superimposing a set of multiple molecules as variance minimization over an ensemble. A negative effect of this superpositioning method is the introduction of ambiguous rotations, where different rotation matrices may be applied to structurally similar molecules. We developed two algorithms to resolve the suboptimal rotations. The first approach minimizes the variance together with the distance of a structure to a preceding molecule in the ensemble. The second algorithm seeks for minimal variance together with the distance to the nearest neighbors of each structure. The newly developed methods were applied to molecular-dynamics trajectories and normal-mode ensembles of the Aβ peptide, RS peptide, and lysozyme. These new (to our knowledge) superpositioning methods combine the benefits of variance and distance between nearest-neighbor(s) minimization, providing a solution for the analysis of intrinsic motions of flexible molecules and resolving ambiguous rotations. PMID:23332072

  20. Assembling Ultracold Polar Molecules From Single Atoms

    NASA Astrophysics Data System (ADS)

    Liu, Lee R.; Hutzler, Nicholas R.; Yu, Yichao; Zhang, Jessie T.; Ni, Kang-Kuen

    2016-05-01

    Ultracold polar molecules are promising candidates for studying quantum many-body phenomena and building quantum information systems, due to their long-range, anisotropic, and tunable interactions. This calls for a technique to create low entropy samples of ultracold polar molecules with a large dipole moment. The lowest entropy molecular gas to date was created from atomic quantum gases in bulk or in optical lattices. The entropy is limited by that of the constituent atomic gases. We propose a method that addresses this limitation by assembling sodium cesium (NaCs) molecules from individually manipulated atoms. First, we load single Na and Cs atoms in separate optical tweezers from MOTs. We will cool them to their motional ground state using Raman sideband cooling and then merge them into a single tweezer. The tweezer confinement provides enhanced wavefunction overlap between the atom pair and molecule states. Using coherent two-photon techniques, we will then transfer the atom pair into a molecule. Our method offers reduced apparatus complexity and cycle time, single-site manipulation and imaging resolution, and should be readily extended to different species.

  1. Figuration and detection of single molecules

    NASA Astrophysics Data System (ADS)

    Nevels, R.; Welch, G. R.; Cremer, P. S.; Hemmer, P.; Phillips, T.; Scully, S.; Sokolov, A. V.; Svidzinsky, A. A.; Xia, H.; Zheltikov, A.; Scully, M. O.

    2012-08-01

    Recent advances in the description of atoms and molecules based on Dimensional scaling analysis, developed by Dudley Herschbach and co-workers, provided new insights into visualization of molecular structure and chemical bonding. Prof. Herschbach is also a giant in the field of single molecule scattering. We here report on the engineering of molecular detectors. Such systems have a wide range of application from medical diagnostics to the monitoring of chemical, biological and environmental hazards. We discuss ways to identify preselected molecules, in particular, mycotoxin contaminants using coherent laser spectroscopy. Mycotoxin contaminants, e.g. aflatoxin B1 which is present in corn and peanuts, are usually analysed by time-consuming microscopic, chemical and biological assays. We present a new approach that derives from recent experiments in which molecules are prepared by one (or more) femtosecond laser(s) and probed by another set. We call this technique FAST CARS (femto second adaptive spectroscopic technique for coherent anti-Stokes Raman spectroscopy). We propose and analyse ways in which FAST CARS can be used to identify preselected molecules, e.g. aflatoxin, rapidly and economically.

  2. Small Molecule Immunosensing Using Surface Plasmon Resonance

    PubMed Central

    Mitchell, John

    2010-01-01

    Surface plasmon resonance (SPR) biosensors utilize refractive index changes to sensitively detect mass changes at noble metal sensor surface interfaces. As such, they have been extensively applied to immunoassays of large molecules, where their high mass and use of sandwich immunoassay formats can result in excellent sensitivity. Small molecule immunosensing using SPR is more challenging. It requires antibodies or high-mass or noble metal labels to provide the required signal for ultrasensitive assays. Also, it can suffer from steric hindrance between the small antigen and large antibodies. However, new studies are increasingly meeting these and other challenges to offer highly sensitive small molecule immunosensor technologies through careful consideration of sensor interface design and signal enhancement. This review examines the application of SPR transduction technologies to small molecule immunoassays directed to different classes of small molecule antigens, including the steroid hormones, toxins, drugs and explosives residues. Also considered are the matrix effects resulting from measurement in chemically complex samples, the construction of stable sensor surfaces and the development of multiplexed assays capable of detecting several compounds at once. Assay design approaches are discussed and related to the sensitivities obtained. PMID:22163605

  3. Modelling the spectroscopic behaviour of hot molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan

    2010-05-01

    At elevated temperatures the molecules absorb and emit light in a very complicated fashion which is hard to characterise on the basis of laboraroty measurement. Computed line lists of molecule transitions therefore provide a vital input for models of hot atmospheres. I will describe the calculation and use of such line lists including the BT2 water line list [1], which contains some 500 million distinct rotation-vibration transitions. This linelist proved crucial in the detection of water in extrasolar planet HD189733b and has been used extensively in atmospheric modelling. Illustrations will be given at the meeting. A new linelist for the ammonia molecule has just been completed [2] which shows that standard compilations for this molecule need to be improved. Progress on a more extensive linelist for hot ammonia and linelists for other molecules will be discussed at the meeting. [1] R.J. Barber, J. Tennyson, G.J. Harris and R.N. Tolchenov, Mon. Not. R. Astr. Soc., 368, 1087-1094 (2006) [2] S.N. Yurchenko, R.J. Barber, A. Yachmenev, W. Theil, P. Jensen and J. Tennyson, J. Phys. Chem. A, 113, 11845-11855 (2009).

  4. Feshbach molecule production in fermionic atomic gases

    NASA Astrophysics Data System (ADS)

    Gurarie, V.

    2009-08-01

    This paper examines the problem of molecule production in an atomic fermionic gas close to an s -wave Feshbach resonance by means of a magnetic field sweep through the resonance. In the solvable case of a narrow resonance, the density of molecules at the end of the process is derived for a slow sweep. It is shown that the density of the produced molecules is lower than what an application of a naive Landau-Zener formula for level crossing would imply. However, in the limit of a very slow sweep it is still possible to achieve full conversion of fermions into the molecules. It appears that the origin of the failure of the Landau-Zener picture of the molecule production is due to the fact that the sweep goes through a quantum phase transition in the limit of an infinitely narrow resonance, in agreement with general results recently discussed in the literature. However, the precise connection of this problem to other problems with this feature is not established.

  5. Medium Effects in Single Molecule Electronics

    NASA Astrophysics Data System (ADS)

    Higgins, Simon

    2010-03-01

    We use STM-based techniques for measuring the electrical properties of metal|molecule|metal junctions. For a family of molecules HS(CH2)6-Ar-(CH2)6SH (Ar = substituted benzene), we found that the single molecule conductances varied significantly with substituent, being higher for electron-donating substituents [1]. Later, we studied the effect of increasing conjugation on this system by examining oligothiophenes HS(CH2)6-[C4H4S]x-(CH2)6SH (x = 1, 2, 3, 5). We found that the conductances of junctions involving these molecules depended upon the medium in which the measurements were made. In fact, for x = 3, the conductance was two orders of magnitude higher in the presence of water than in anhydrous conditions [2]. This presentation will outline these studies, together with the results of transport calculations that rationalise these unusual findings, and will set the results in the context of existing literature on medium effects in single molecule conductance determinations. In collaboration with Edmund Leary and Richard Nichols, University of Liverpool; Colin Lambert, Iain Grace, and Chris Finch, University of Lancaster; and Wolfgang Haiss, University of Liverpool.

  6. Mining for Molecules in the Milky Way

    NASA Astrophysics Data System (ADS)

    2008-06-01

    Scientists are using the giant Robert C. Byrd Green Bank Telescope (GBT) to go prospecting in a rich molecular cloud in our Milky Way Galaxy. They seek to discover new, complex molecules in interstellar space that may be precursors to life. The GBT and Molecules The Robert C. Byrd Green Bank Telescope and some molecules it has discovered. CREDIT: Bill Saxton, NRAO/AUI/NSF "Clouds like this one are the raw material for new stars and planets. We know that complex chemistry builds prebiotic molecules in such clouds long before the stars and planets are formed. There is a good chance that some of these interstellar molecules may find their way to the surface of young planets such as the early Earth, and provide a head start for the chemistry of life. For the first time, we now have the capability to make a very thorough and methodical search to find all the chemicals in the clouds," said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO). In the past three years, Remijan and his colleagues have used the GBT to discover ten new interstellar molecules, a feat unequalled in such a short time by any other team or telescope. The scientists discovered those molecules by looking specifically for them. However, they now are changing their strategy and casting a wide net designed to find whatever molecules are present, without knowing in advance what they'll find. In addition, they are making their data available freely to other scientists, in hopes of speeding the discovery process. The research team presented its plan to the American Astronomical Society's meeting in St. Louis, MO. As molecules rotate and vibrate, they emit radio waves at specific frequencies. Each molecule has a unique pattern of such frequencies, called spectral lines, that constitutes a "fingerprint" identifying that molecule. Laboratory tests can determine the pattern of spectral lines that identifies a specific molecule. Most past discoveries came from identifying a molecule's pattern in

  7. Ultracold molecules from the bottom-up

    NASA Astrophysics Data System (ADS)

    Zhang, Jessie T.; Hutzler, Nicholas R.; Liu, Lee R.; Yu, Yichao; Ni, Kang-Kuen

    2016-05-01

    Ultracold polar molecules exhibit strong, long-range, and tunable dipole-dipole interactions that may be utilized for a wide range of studies in quantum simulation and quantum information processing. To realize the full potential of these studies, it is desirable to have a low entropy sample of ultracold polar molecules with full control over both internal and external states, as well as inter-particle interactions. We work toward this goal with a new, bottom-up approach using the highly polar NaCs molecule. The key steps of our scheme are trapping single Na and Cs atoms in optical dipole traps, cooling the atoms to their motional ground state using Raman sideband cooling, and finally coherently transferring them to ground state NaCs molecules via a two-photon process. This approach should enable creation of low entropy samples with full control over all degrees of freedom, as well as realizing the possibility of single-site read-out and manipulation of molecules.

  8. Metastable States of small-molecule solutions.

    PubMed

    He, Guangwen; Tan, Reginald B H; Kenis, Paul J A; Zukoski, Charles F

    2007-12-27

    Metastable states such as gels and glasses that are commonly seen in nanoparticle suspensions have found application in a wide range of products including toothpaste, hand cream, paints, and car tires. The equilibrium and metastable state behavior of nanoparticle suspensions are often described by simple fluid models where particles are treated as having hard cores and interacting with short-range attractions. Here we explore similar models to describe the presence of metastable states of small-molecule solutions. We have recently shown that the equilibrium solubilities of small hydrogen-bonding molecules and nanoparticles fall onto a corresponding-states solubility curve suggesting that with similar average strengths of attraction these molecules have similar solubilities. This observation implies that metastable states in small-molecule solutions may be found under conditions similar to those where metastable states are observed in nanoparticle and colloidal suspensions. Here we seek confirmation of this concept by exploring the existence of metastable states in solutions of small molecules.

  9. Simple treatment of ultracold polar molecule collisions

    NASA Astrophysics Data System (ADS)

    Bohn, John; Quèmèner, Goulven; Idziaszek, Zbigniew; Julienne, Paul

    2010-03-01

    Collisions of polar molecules at ultracold (< μK) temperatures open the way for prospects of manipulating collision dynamics, including chemical reactions, by by varying an electric field. To understand such processes, one needs a scattering theory that accounts sufficiently accurately for the long-range van der Waals and dipolar forces acting between the molecules, but that also has a reasonable parametrization of the short-range physics when the molecules actually encounter one another. In this presentation we discuss a theory that marries a quantum-defect-theory parametrization of short-range physics, to a modified Langevin-like model that has successfully estimated the effect of electric fields. We discuss the character of the resulting scattering, including field-dependent chemical reaction rates and resonances.

  10. Electron Transport Through Single Fullerene Molecules (abstract)

    NASA Astrophysics Data System (ADS)

    Stróżecka, Anna; Muthukumar, Kaliappan; Larsson, J. Andreas; Voigtländer, Bert

    2009-04-01

    Fullerenes show potential for applications in nanotechnology due to the possibility of tuning their properties by doping or functionalization. In particular, the endohedral doping of the hollow carbon cage with metal atoms allows changing the electronic and magnetic properties of the molecule without distorting the geometry of the outer shell. Here we present a low temperature scanning tunneling microscopy (STM) and spectroscopy study of the vibrational and transport properties of Ce2atC80 metallofullerenes. We observe that electron transport through the endohedral fullerene is strongly mediated by excitation of molecular vibrations, especially the dynamics of encapsulated atoms. We measure the conductance of the single-molecule junction upon contact between the molecule and the STM tip. To determine the role of doping atoms we compare the results obtained for the endohedrally doped species with those for a hollow fullerene. Analysis shows that localization of electron density on encapsulated atoms hinders the conduction process through the fullerene.

  11. Conformational dynamics of peptide T molecule

    NASA Astrophysics Data System (ADS)

    Akverdieva, Gulnare; Godjayev, Niftali; Akyuz, Sevim

    2002-05-01

    Using a method of the theoretical conformational analysis, a conformational dynamics of the side chains of the amino acid residues of peptide T, a competitor of the human immuno-deficiency virus in the binding to human T cells, was investigated. For this purpose, the conformational maps of the potential surfaces were constructed over the angles of the side chains for the preferable conformations of peptide T molecule. Permissible deviations of these angles from the optimal values were determined. It has been found that the angles of the side chains of the amino acid residues involved in physiologically active fragment Thr4-Thr8 are more rigid than in the other segment of the molecule. This fact confirms the existence of such a regular structure as β-turn revealed previously in studies of the spatial structure of the peptide T molecule.

  12. Featured Molecules: Ascorbic Acid and Methylene Blue

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-05-01

    The WebWare molecules of the month for May are featured in several articles in this issue. "Arsenic: Not So Evil After All?" discusses the pharmaceutical uses of methylene blue and its development as the first synthetic drug used against a specific disease. The JCE Classroom Activity "Out of the Blue" and the article "Greening the Blue Bottle" feature methylene blue and ascorbic acid as two key ingredients in the formulation of the blue bottle. You can also see a colorful example of these two molecules in action on the cover. "Sailing on the 'C': A Vitamin Titration with a Twist" describes an experiment to determine the vitamin C (ascorbic acid) content of citrus fruits and challenges students, as eighteenth-century sea captains, to decide the best fruit to take on a long voyage. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  13. Complex molecules in the galactic center

    NASA Astrophysics Data System (ADS)

    Requena-Torres, Miguel Angel; Martin-Pintado, Jesus; Martin, Sergio; Amo-Baladron, Arancha

    2007-04-01

    Recently the number of complex organic molecules observed in hot cores has been increased by observing the Sgr B2N hot core, located in the GC molecular clouds. But in the inner 200pc of the center of our Galaxy complex organic molecules seems to widespread distributed along the Galactic plane. Last year large aldehydes where observed in the cm range with the Green Bank Telescope. These molecules where detected not in the hot core, but in the envelope of the SgrB2 molecular clouds and in two different positions in SgrA molecular cloud. We have not reach the maximum in the chemical complexity that these molecular clouds can show up. The next step would be to detect the more complex esters and ethers observed in hot cores and to obtain a better estimation of the physical conditions of the aldehydes observing more transitions in the mm range.

  14. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect

    Baker, David

    2014-09-14

    We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

  15. Ionization of glycerin molecule by electron impact

    NASA Astrophysics Data System (ADS)

    Zavilopulo, A. N.; Shpenik, O. B.; Markush, P. P.; Kontrosh, E. E.

    2015-07-01

    The methods and results of studying the yield of positive ions produced due to direct and dissociative electron impact ionization of the glycerin molecule are described. The experiment is carried out using two independent setups, namely, a setup with a monopole mass spectrometer employing the method of crossing electron and molecular beams and a setup with a hypocycloidal electron spectrometer with the gas-filled cell. The mass spectra of the glycerin molecule are studied in the range of mass numbers of 10-95 amu at various temperatures. The energy dependences of the effective cross sections of the glycerin molecular ions produced by a monoenergetic electron beam are obtained and analyzed; using these dependences, the appearance energies of fragment ions are determined. The dynamics of the glycerin molecule fragment ions formation is investigated in the temperature range of 300-340 K.

  16. Berry connection in atom-molecule systems

    SciTech Connect

    Cui Fucheng; Wu Biao

    2011-08-15

    In the mean-field theory of atom-molecule systems, where bosonic atoms combine to form molecules, there is no usual U(1) symmetry, presenting an apparent hurdle for defining the Berry phase and Berry curvature for these systems. We define a Berry connection for this system, with which the Berry phase and Berry curvature can be naturally computed. We use a three-level atom-molecule system to illustrate our results. In particular, we have computed the mean-field Berry curvature of this system analytically, and compared it to the Berry curvature computed with the second-quantized model of the same system. An excellent agreement is found, indicating the validity of our definition.

  17. Electrostatic trapping of metastable NH molecules

    SciTech Connect

    Hoekstra, Steven; Metsaelae, Markus; Zieger, Peter C.; Scharfenberg, Ludwig; Gilijamse, Joop J.; Meijer, Gerard; Meerakker, Sebastiaan Y. T. van de

    2007-12-15

    We report on the Stark deceleration and electrostatic trapping of {sup 14}NH (a{sup 1}{delta}) radicals. In the trap, the molecules are excited on the spin-forbidden A{sup 3}{pi}<-a{sup 1}{delta} transition and detected via their subsequent fluorescence to the X{sup 3}{sigma}{sup -} ground state. The 1/e trapping time is 1.4{+-}0.1 s, from which a lower limit of 2.7 s for the radiative lifetime of the a{sup 1}{delta}, v=0, J=2 state is deduced. The spectral profile of the molecules in the trapping field is measured to probe their spatial distribution. Electrostatic trapping of metastable NH followed by optical pumping of the trapped molecules to the electronic ground state is an important step toward accumulation of these radicals in a magnetic trap.

  18. Genetically engineered antibody molecules and their application.

    PubMed

    Morrison, S L; Wims, L; Wallick, S; Tan, L; Oi, V T

    1987-01-01

    Immunoglobulin genes can be efficiently expressed following transfection into myeloma cells. Using protoplast fusion, transfection frequencies greater than 10(-3) can be achieved. Compatible plasmids containing two different selectible markers are used to simultaneously deliver heavy and light chain genes to the same cell. To produce molecules with differing specificities the rearranged and expressed variable regions can be cloned from the appropriate hybridoma. In some cases, variable regions from cDNAs can be inserted into the expression vectors. It is possible to manipulate the immunoglobulin genes and produce novel antibody molecules. Antibodies have been produced in which the variable regions from mouse antibodies have been joined to human constant regions. In addition, antibodies with altered constant regions have been produced. These genetically engineered antibodies provide a unique set of reagents to study structure-function relationships within the molecule. They also can potentially be used in the diagnosis and therapy of human disease.

  19. Profiling protein function with small molecule microarrays

    PubMed Central

    Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

    2002-01-01

    The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

  20. Stochastic models for surface diffusion of molecules

    SciTech Connect

    Shea, Patrick Kreuzer, Hans Jürgen

    2014-07-28

    We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

  1. Hydrodynamic trapping of molecules in lipid bilayers

    PubMed Central

    Jönsson, Peter; McColl, James; Clarke, Richard W.; Ostanin, Victor P.; Jönsson, Bengt; Klenerman, David

    2012-01-01

    In this work we show how hydrodynamic forces can be used to locally trap molecules in a supported lipid bilayer (SLB). The method uses the hydrodynamic drag forces arising from a flow through a conical pipette with a tip radius of 1–1.5 μm, placed approximately 1 μm above the investigated SLB. This results in a localized forcefield that acts on molecules protruding from the SLB, yielding a hydrodynamic trap with a size approximately given by the size of the pipette tip. We demonstrate this concept by trapping the protein streptavidin, bound to biotin receptors in the SLB. It is also shown how static and kinetic information about the intermolecular interactions in the lipid bilayer can be obtained by relating how the magnitude of the hydrodynamic forces affects the accumulation of protein molecules in the trap. PMID:22699491

  2. Photostability of Organic Molecules in Circumstellar Environment

    NASA Astrophysics Data System (ADS)

    Monfredini, T.; Wolf, W.; Mendoza, E.; Rocco, M. L.; Lago, A.; Boechat-Roberty, H. M.

    2014-10-01

    Aromatic Infrared Bands, the footprint of molecules like neutral and ionic Polycyclic Aromatic Hydrocarbons (PAHs), have been observed in several astrophysical environments.We present the experimental results of the photoionization and photodissociation of the methyl-benzene (or toluene) molecule, a basic unit for the methylated PAHs, using synchrotron radiation at C1s resonance, ˜ 285 eV (soft X-ray) and time-of-flight mass-spectrometry. Absolute photoionization and photodissociation cross sections have been determined. Then the ionization and destruction rates and half-life of the toluene molecule were also obtained for the X-ray photon flux of the pre-planetary nebula CRL 618.

  3. Hydrogen sulfide and polysulfides as signaling molecules

    PubMed Central

    KIMURA, Hideo

    2015-01-01

    Hydrogen sulfide (H2S) is a familiar toxic gas that smells of rotten eggs. After the identification of endogenous H2S in the mammalian brain two decades ago, studies of this molecule uncovered physiological roles in processes such as neuromodulation, vascular tone regulation, cytoprotection against oxidative stress, angiogenesis, anti-inflammation, and oxygen sensing. Enzymes that produce H2S, such as cystathionine β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase have been studied intensively and well characterized. Polysulfides, which have a higher number of inner sulfur atoms than that in H2S, were recently identified as potential signaling molecules that can activate ion channels, transcription factors, and tumor suppressors with greater potency than that of H2S. This article focuses on our contribution to the discovery of these molecules and their metabolic pathways and mechanisms of action. PMID:25864468

  4. T Cell Cosignaling Molecules in Transplantation.

    PubMed

    Ford, Mandy L

    2016-05-17

    The ultimate outcome of alloreactivity versus tolerance following transplantation is potently influenced by the constellation of cosignaling molecules expressed by immune cells during priming with alloantigen, and the net sum of costimulatory and coinhibitory signals transmitted via ligation of these molecules. Intense investigation over the last two decades has yielded a detailed understanding of the kinetics, cellular distribution, and intracellular signaling networks of cosignaling molecules such as the CD28, TNF, and TIM families of receptors in alloimmunity. More recent work has better defined the cellular and molecular mechanisms by which engagement of cosignaling networks serve to either dampen or augment alloimmunity. These findings will likely aid in the rational development of novel immunomodulatory strategies to prolong graft survival and improve outcomes following transplantation.

  5. Chiral Molecules Revisited by Broadband Microwave Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schnell, Melanie

    2014-06-01

    Chiral molecules have fascinated chemists for more than 150 years. While their physical properties are to a very good approximation identical, the two enantiomers of a chiral molecule can have completely different (bio)chemical activities. For example, the right-handed enantiomer of carvone smells of spearmint while the left-handed one smells of caraway. In addition, the active components of many drugs are of one specific handedness, such as in the case of ibuprofen. However, in nature as well as in pharmaceutical applications, chiral molecules often exist in mixtures with other chiral molecules. The analysis of these complex mixtures to identify the molecular components, to determine which enantiomers are present, and to measure the enantiomeric excesses (ee) remains a challenging task for analytical chemistry, despite its importance for modern drug development. We present here a new method of differentiating enantiomers of chiral molecules in the gas phase based on broadband rotational spectroscopy. The phase of the acquired signal bares the signature of the enantiomer, as it depends upon the combined quantity, μ_a μ_b μ_c, which is of opposite sign between enantiomers. It thus also provides information on the absolute configuration of the particular enantiomer. Furthermore, the signal amplitude is proportional to the ee. A significant advantage of our technique is its inherent mixture compatibility due to the fingerprint-like character of rotational spectra. In this contribution, we will introduce the technique and present our latest results on chiral molecule spectroscopy and enantiomer differentiation. D. Patterson, M. Schnell, J.M. Doyle, Nature 497 (2013) 475-477 V.A. Shubert, D. Schmitz, D. Patterson, J.M. Doyle, M. Schnell, Angewandte Chemie International Edition 53 (2014) 1152-1155

  6. Molecule capture by olfactory antennules: mantis shrimp.

    PubMed

    Stacey, Mark T; Mead, Kristina S; Koehl, Mimi A R

    2002-01-01

    A critical step in the process of olfaction is the movement of odorant molecules from the environment to the surface of a chemosensory structure. Many marine crustaceans capture odorant molecules with arrays of chemosensory sensilla (aesthetascs) on antennules that they flick through the water. We developed a model to calculate molecule flux to the surfaces of aesthetascs in order to study how the size, aesthetasc spacing, and flick kinematics of olfactory antennules affect their performance in capturing molecules from the surrounding water. Since the three-dimensional geometry of an aesthetasc-bearing antennule is complex, dynamically-scaled physical models can often provide an efficient method of determining the fluid velocity field through the array. Here we present a method to optimize the incorporation of such measured velocity vector fields into a numerical simulation of the advection and diffusion of odorants to aesthetasc surfaces. Furthermore, unlike earlier models of odorant interception by antennae, our model incorporates odorant concentration distributions that have been measured in turbulent ambient flows. By applying our model to the example of the olfactory antennules of mantis shrimp, we learned that flicking velocity can have profound effects on odorant flux to the aesthetascs if they operate in the speed range in which the leakiness of the gaps between the aesthetascs to fluid movement is sensitive to velocity. This sensitivity creates an asymmetry in molecule fluxes between outstroke and return stroke, which results in an antennule taking discrete samples in space and time, i.e. "sniffing". As stomatopods grow and their aesthetasc Reynolds number increases, the aesthetasc arrangement on the antennule changes in a way that maintains these asymmetries in leakiness and molecule flux between the outstroke and return stroke, allowing the individual to continue to take discrete samples as it develops. PMID:11942523

  7. Molecules and Clusters in Intense Laser Fields

    NASA Astrophysics Data System (ADS)

    Posthumus, Jan

    2001-06-01

    Preface; 1. Ultra-high intensity based on Ti:Sapphire Philip F. Taday and Andrew J. Langley; 2. Diatomic molecules in intense laser fields Jan H. Posthumus and James F. McCann; 3. Small polyatomic molecules in intense laser fields C. Cornaggia; 4. Coherent control in intense laser fields Eric Charron and Brian Sheehy; 5. Experimental studies of laser-heated rare gas clusters M. Lezius and M. Schmidt; 6. Single cluster explosions and high harmonic generation John W. G. Tisch and Emma Springate; 7. Intense laser interaction with extended cluster media Roland A. Smith and Todd Ditmire.

  8. Molecules and Clusters in Intense Laser Fields

    NASA Astrophysics Data System (ADS)

    Posthumus, Jan

    2009-09-01

    Preface; 1. Ultra-high intensity based on Ti:Sapphire Philip F. Taday and Andrew J. Langley; 2. Diatomic molecules in intense laser fields Jan H. Posthumus and James F. McCann; 3. Small polyatomic molecules in intense laser fields C. Cornaggia; 4. Coherent control in intense laser fields Eric Charron and Brian Sheehy; 5. Experimental studies of laser-heated rare gas clusters M. Lezius and M. Schmidt; 6. Single cluster explosions and high harmonic generation John W. G. Tisch and Emma Springate; 7. Intense laser interaction with extended cluster media Roland A. Smith and Todd Ditmire.

  9. Adsorption of polar molecules on krypton clusters.

    PubMed

    Rosso, A; Pokapanich, W; Ohrwall, G; Svensson, S; Björneholm, O; Tchaplyguine, M

    2007-08-28

    The formation process of binary clusters has been studied using synchrotron based core level photoelectron spectroscopy. Free neutral krypton clusters have been produced by adiabatic expansion and doped with chloromethane molecules using the pickup technique. The comparison between the integrated intensities, linewidths, and level shifts of the cluster features of pure krypton and of chloromethane-krypton clusters has been used to obtain information about the cluster geometry. We have shown that most of the chloromethane molecules remain on the surface of the clusters.

  10. Metastable feshbach molecules in high rotational states.

    PubMed

    Knoop, S; Mark, M; Ferlaino, F; Danzl, J G; Kraemer, T; Nägerl, H-C; Grimm, R

    2008-02-29

    We experimentally demonstrate Cs2 Feshbach molecules well above the dissociation threshold, which are stable against spontaneous decay on the time scale of 1 s. An optically trapped sample of ultracold dimers is prepared in a high rotational state and magnetically tuned into a region with a negative binding energy. The metastable character of these molecules arises from the large centrifugal barrier in combination with negligible coupling to states with low rotational angular momentum. A sharp onset of dissociation with increasing magnetic field is mediated by a crossing with a lower rotational dimer state and facilitates dissociation on demand with a well-defined energy. PMID:18352621

  11. Newly detected molecules in dense interstellar clouds.

    PubMed

    Irvine, W M; Avery, L W; Friberg, P; Matthews, H E; Ziurys, L M

    1988-01-01

    The last year or so has seen the identification of several new interstellar molecules, including C2S, C3S, C5H, C6H, and (probably) HC2CHO in the cold, dark cloud TMC-1; and the discovery of the first interstellar phosphorous-containing molecule, PN, in the Orion "plateau" source. Further interesting results include the observations of 13C3H2 and C3HD, and the first detection of HCOOH (formic acid) in a cold cloud.

  12. Nonadiabatic transitions in electrostatically trapped ammonia molecules

    SciTech Connect

    Kirste, Moritz; Schnell, Melanie; Meijer, Gerard; Sartakov, Boris G.

    2009-05-15

    Nonadiabatic transitions are known to be major loss channels for atoms in magnetic traps but have thus far not been experimentally reported upon for trapped molecules. We have observed and quantified losses due to nonadiabatic transitions for three isotopologues of ammonia in electrostatic traps by comparing the trapping times in traps with a zero and a nonzero electric field at the center. Nonadiabatic transitions are seen to dominate the overall loss rate even for the present samples that are at relatively high temperatures of 30 mK. It is anticipated that losses due to nonadiabatic transitions in electric fields are omnipresent in ongoing experiments on cold molecules.

  13. Electrostatic propulsion using C60 molecules

    NASA Technical Reports Server (NTRS)

    Leifer, Stephanie D.; Rapp, Donald; Saunders, Winston A.

    1992-01-01

    An evaluation is made of the potential benefits of C60 molecules as a basis for ion propulsion. Because C60 is storable, its use may result in a larger usable propellant fraction than previous methods of cluster ion propulsion. C60 may also relax such engineering constraints as grid spacing, which restrict the performance of noble gas ion propulsion. The behavior of C60 in a plasma discharge environment, as well as various electron impact cross sections of the molecule, will greatly afftect the feasibility of the concept.

  14. Accurate density functional thermochemistry for larger molecules.

    SciTech Connect

    Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.

    1997-06-20

    Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).

  15. Cold Light from Hot Atoms and Molecules

    SciTech Connect

    Lister, Graeme; Curry, John J.

    2011-05-11

    The introduction of rare earth atoms and molecules into lighting discharges led to great advances in efficacy of these lamps. Atoms such as Dy, Ho and Ce provide excellent radiation sources for lighting applications, with rich visible spectra, such that a suitable combination of these elements can provide high quality white light. Rare earth molecules have also proved important in enhancing the radiation spectrum from phosphors in fluorescent lamps. This paper reviews some of the current aspects of lighting research, particularly rare earth chemistry and radiation, and the associated fundamental atomic and molecular data.

  16. Molecular spintronics using single-molecule magnets.

    PubMed

    Bogani, Lapo; Wernsdorfer, Wolfgang

    2008-03-01

    A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

  17. Single-molecule electrophoresis. Final report

    SciTech Connect

    Castro, A.; Shera, E.B.

    1996-05-22

    A novel method for the detection and identification of single molecules in solution has been devised, computer-simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required by individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed beforehand in order to estimate the experimental feasibility of the method, and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented.

  18. The origin of life. [genetically important molecules

    NASA Technical Reports Server (NTRS)

    Horowitz, N. H.; Hubbard, J. S.

    1974-01-01

    Research in the areas of precambrian paleontology, chemical evolution of genetically important monomers, prebiotic dehydration-condensation reactions, organic compounds in meteorites and interstellar space, and biological exploration of the planets is summarized. Fossils in precambrian cherts and findings of eukaryotic cells are described, and recent investigations of prebiotic conditions, energy sources, and starting materials for genetic molecules are outlined. Studies of homogeneous and heterogeneous dehydrations and of nonaqueous thermal dehydrations are described. The detection of amino acids, purines, and pyrimidines in meteorites and of biologically significant molecules in interstellar clouds is discussed, as well as the possibilities of life on Jupiter, Mars, and Titan.

  19. Photoassociative production of ultracold heteronuclear ytterbium molecules

    SciTech Connect

    Borkowski, Mateusz; Ciurylo, Roman; Yamazaki, Rekishu; Takahashi, Yoshiro; Hara, Hideaki; Taie, Shintaro; Sugawa, Seiji; Takasu, Yosuke; Enomoto, Katsunari

    2011-09-15

    We report observations of photoassociation (PA) spectra near the intercombination line in isotopic mixtures of ultracold ytterbium gases. Several heteronuclear bound states have been found for the excited {sup 170}Yb{sup 174}Yb and {sup 174}Yb{sup 176}Yb molecules. We develop a single-channel mass-scaled interaction model for the excited state molecule which well reproduces the measured bound state energies. This is an important step toward optical control of interactions in mixtures of ultracold ytterbium gases using heteronuclear optical Feshbach resonances. The model developed is applicable in collisions of other similar systems, such as cadmium and mercury.

  20. Evidence of water molecules--a statistical evaluation of water molecules based on electron density.

    PubMed

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias

    2015-04-27

    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

  1. Strategy to discover diverse optimal molecules in the small molecule universe.

    PubMed

    Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

    2015-03-23

    The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

  2. Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

    PubMed Central

    2015-01-01

    The small molecule universe (SMU) is defined as a set of over 1060 synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc.2013, 135, 7296–730323548177) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 105 molecules. PMID:25594586

  3. Polarization of excitation light influences molecule counting in single-molecule localization microscopy.

    PubMed

    Chen, Ye; Lin, Han; Ludford-Menting, Mandy J; Clayton, Andrew H; Gu, Min; Russell, Sarah M

    2015-01-01

    Single-molecule localization microscopy has been widely applied to count the number of biological molecules within a certain structure. The percentage of molecules that are detected significantly affects the interpretation of data. Among many factors that affect this percentage, the polarization state of the excitation light is often neglected or at least unstated in publications. We demonstrate by simulation and experiment that the number of molecules detected can be different from -40 up to 100% when using circularly or linearly polarized excitation light. This is determined mainly by the number of photons emitted by single fluorescent molecule, namely the choice of fluorescence proteins, and the background noise in the system, namely the illumination scheme. This difference can be further exaggerated or mitigated by various fixation methods, magnification, and camera settings We conclude that the final choice between circularly or linearly polarized excitation light should be made experimentally, based on the signal to noise ratio of the system.

  4. Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions

    NASA Technical Reports Server (NTRS)

    Shortt, Brian; Chutjian, Ara; Orient, Otto

    2008-01-01

    A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

  5. Complex organic molecules and star formation

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2014-12-01

    Star forming regions are characterised by the presence of a wealth of chemical species. For the past two to three decades, ever more complex organic species have been detected in the hot cores of protostars. The evolution of these molecules in the course of the star forming process is still uncertain, but it is likely that they are partially incorporated into protoplanetary disks and then into planetesimals and the small bodies of planetary systems. The complex organic molecules seen in star forming regions are particularly interesting since they probably make up building blocks for prebiotic chemistry. Recently we showed that these species were also present in the cold gas in prestellar cores, which represent the very first stages of star formation. These detections question the models which were until now accepted to account for the presence of complex organic molecules in star forming regions. In this article, we shortly review our current understanding of complex organic molecule formation in the early stages of star formation, in hot and cold cores alike and present new results on the formation of their likely precursor radicals.

  6. Molecules of significance in planetary aeronomy

    NASA Technical Reports Server (NTRS)

    Mohan, H.

    1979-01-01

    This monograph is basically devoted to spectroscopic information of the molecules of planetary interest. Only those molecules have been dealt with which have been confirmed spectroscopically to be present in the atmosphere of major planets of our solar system and play an important role in the aeronomy of the respective planets. An introduction giving the general conditions of planets and their atmospheres including the gaseous molecules is given. Some typical planetary spectra is presented and supported with a discussion on some basic concepts of optical absorption and molecular parameters that are important to the study of planetary atmospheres. Quantities like dipole moments, transition probabilities, Einstein coefficients and line strengths, radiative life times, absorption cross sections, oscillator strengths, line widths and profiles, equivalent widths, growth curves, bond strengths, electronic transition moments, Franck-Condon factors and r-centroids, etc., are discussed. Spectroscopic information and relevant data of 6 diatomic (HF, HCL, CO, H2, O2, N2) and 6 polyatomic (CO2, N2), O3, HeO, NH3, CH4) molecules are presented.

  7. Langmuir Films of Chiral Molecules on Mercury

    SciTech Connect

    Tamam, L.; Menahem, T; Mastai, Y; Sloutskin, E; Yefet, S; Deustch, M

    2009-01-01

    Homo- and heterochiral Langmuir films of a chiral derivative of stearic acid are studied in situ on the surface of liquid mercury as a function of surface coverage by surface tensiometry and surface-specific synchrotron X-ray diffraction and reflectivity. A transition from a phase of surface-parallel molecules to a phase of standing-up molecules is found. The former shows no surface-parallel long-range order. The standing-up phase of both homochiral and heterochiral compositions exhibit long-range order. However, the former has an oblique unit cell with parallel molecular planes, and the later has a centered rectangular unit cell with a herringbone molecular packing. For both cases, the standing-up molecules are tilted by 44 from the surface normal and pack at a density of 19.5 Angstroms2/molecule in the plane normal to the molecular long axis. Important differences are found, and discussed, between this behavior and that of a Langmuir film of the nonchiral stearic acid on mercury.

  8. Manipulation of fullerene molecules on graphene

    NASA Astrophysics Data System (ADS)

    Glukhova, O. E.; Mitrofanov, V. V.; Slepchenkov, M. M.; Shunaev, V. V.

    2015-03-01

    Due to the increasing demand for functionalization of graphene and its application as a functional element of real electronic and / or mechanical devices, as well as due to its unique adhesive and sensory abilities the actual problem is the use of graphene as a substrate on which the assembly of supramolecular structures. Elements of such structures can be different molecules driven by external factors, and can be easily transported on graphene. These molecules primarily include miniature spheroidal fullerenes easy to navigate on the surface of graphene, in particular icosahedral C60. The aim of this work was to find an effective method of manipulation of fullerene C60 on graphene. As such method we proposed to introduce in graphene sheet structural defect of the atomic framework namely defect Stone-Wales (pentagon-heptagon pairs). Another structural defect studied in this paper is adsorbed on the Stone-Wales defect hydrogen atom. Molecular dynamics and tight binding method were applied to calculate the location of the molecule C60 on graphene sheet and its movement. To identify the regulatities of behavior of fullerene on graphene sheet we carried out a series of numerical experiments at different temperatures. In this paper we calculated the energy profile of interaction between fullerene and graphene sheet. Obtained results showed that forming on the surface of the graphene sheet defects in a certain way, one can control the trajectory of molecules on graphene.

  9. Proteins Are the Body's Worker Molecules

    MedlinePlus

    ... Each "bead" is a small molecule called an amino acid. There are 20 standard amino acids, each with its own shape, size, and properties. Proteins typically contain from 50 to 2,000 amino acids hooked end-to-end in many combinations. Each ...

  10. Collisions of trapped molecules with slow beams

    SciTech Connect

    Tscherbul, T. V.; Dalgarno, A.; Pavlovic, Z.; Sadeghpour, H. R.; Cote, R.

    2010-08-15

    We present a theoretical study of molecular-trap loss induced by collisions with slow atomic beams based on an explicit analysis of collision kinematics in the laboratory frame and a rigorous quantum description of atom-molecule scattering in external fields. The theory is applied to elucidate the effects of nonuniform magnetic and optical trapping fields on low-temperature collisions of OH (J=3/2,M{sub J}=3/2,f) molecules with {sup 4}He atoms. Our calculations quantify the extent to which both elastic and inelastic cross sections are suppressed by external trapping fields, clarify the role of small-angle scattering in trap loss, and may benefit future experiments on collisional cooling of molecules in electromagnetic traps. The calculated cross sections for trap loss in {sup 4}He + OH collisions are consistent with recent experimental observations at low beam energies [B. C. Sawyer et al., Phys. Rev. Lett. 101, 203203 (2008)], demonstrating the importance of including the effects of nonuniform trapping fields in theoretical simulations of cold collision experiments with trapped molecules and slow atomic beams.

  11. Photochromism of diarylethene molecules and crystals

    PubMed Central

    IRIE, Masahiro

    2010-01-01

    Photochromism is defined as a reversible transformation of a chemical species between two isomers upon photoirradiation. Although vast numbers of photochromic molecules have been so far reported, photochromic molecules which exhibit thermally irreversible photochromic reactivity are limited to a few examples. The thermal irreversibility is an indispensable property for the application of photochromic molecules to optical memories and switches. We have developed a new class of photochromic molecules named “diarylethenes”, which show the thermally irreversible photochromic reactivity. The well designed diarylethene derivatives provide outstanding photochromic performance: both isomers are thermally stable for more than 470,000 years, photoinduced coloration/decoloration can be repeated more than 105 cycles, the quantum yield of cyclization reaction is close to 1 (100%), and the response times of both coloration and decoloration are less than 10 ps. This review describes theoretical background of the photochromic reactions, color changes of the derivatives in solution as well as in the single crystalline phase, and application of the crystals to light-driven actuators. PMID:20467213

  12. Polypetide signaling molecules in plant development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intercellular communication mediated by small signaling molecules is a key mechanism for coordinating plant growth and development. In the past few years, polypeptide signals have been shown to play prominent roles in processes as diverse as shoot and root meristem maintenance, vascular differentiat...

  13. A new interstellar molecule: tricarbon monoxide.

    PubMed

    Matthews, H E; Irvine, W M; Friberg, P; Brown, R D; Godfrey, P D

    1984-07-12

    The cold dark interstellar Taurus Molecular Cloud One (TMC-1) is a rich source of acetylenic and polyacetylenic molecular species. As well as linear closed-shell molecules (H(C triple bond C)nCN) and symmetric rotors (CH3C triple bond CH, CH3C triple bond CCN), several radicals (C triple bond CH, C triple bond CCN, (C triple bond C2H) have also been identified, many of which had not been studied previously in the laboratory. Whether the observed abundances can be understood in terms of purely gas-phase ion-molecule chemical schemes, which produce reasonable agreement for the simplest polyatomic species, is unclear; alternative models involving the particulate interstellar grains as catalysts or sources have also been suggested. We now report the detection in TMC-1 of a new molecule, tricarbon monoxide (C3O), whose pure rotational spectrum has only very recently been studied in the laboratory. As C3O is the first known interstellar carbon chain molecule to contain oxygen, its existence places an important new constraint on chemical schemes for cold interstellar clouds. In fact, the observed abundance of tricarbon monoxide fits quite well into our model of galactochemistry.

  14. Leishmania molecules that mediate intracellular pathogenesis.

    PubMed

    Kima, Peter E

    2014-09-01

    Parasites of the Leishmania genus are the causative agents of a complex disease called leishmaniasis. Many activities of infected cells including their responses to a range of stimuli are modulated by Leishmania parasites. This review will profile some of the parasite molecules that target host cell processes for which there has been recent progress.

  15. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  16. Adsorption of small organic molecules on graphene.

    PubMed

    Lazar, Petr; Karlický, František; Jurečka, Petr; Kocman, Mikuláš; Otyepková, Eva; Šafářová, Klára; Otyepka, Michal

    2013-04-24

    We present a combined experimental and theoretical quantification of the adsorption enthalpies of seven organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate, hexane, and toluene) on graphene. Adsorption enthalpies were measured by inverse gas chromatography and ranged from -5.9 kcal/mol for dichloromethane to -13.5 kcal/mol for toluene. The strength of interaction between graphene and the organic molecules was estimated by density functional theory (PBE, B97D, M06-2X, and optB88-vdW), wave function theory (MP2, SCS(MI)-MP2, MP2.5, MP2.X, and CCSD(T)), and empirical calculations (OPLS-AA) using two graphene models: coronene and infinite graphene. Symmetry-adapted perturbation theory calculations indicated that the interactions were governed by London dispersive forces (amounting to ∼60% of attractive interactions), even for the polar molecules. The results also showed that the adsorption enthalpies were largely controlled by the interaction energy. Adsorption enthalpies obtained from ab initio molecular dynamics employing non-local optB88-vdW functional were in excellent agreement with the experimental data, indicating that the functional can cover physical phenomena behind adsorption of organic molecules on graphene sufficiently well.

  17. Molecules into Cells: Specifying Spatial Architecture

    PubMed Central

    Harold, Franklin M.

    2005-01-01

    A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth. PMID:16339735

  18. Uranium-mediated activation of small molecules.

    PubMed

    Arnold, Polly L

    2011-08-28

    Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power.

  19. Trapping polar molecules in an ac trap

    SciTech Connect

    Bethlem, Hendrick L.; Veldhoven, Jacqueline van; Schnell, Melanie; Meijer, Gerard

    2006-12-15

    Polar molecules in high-field seeking states cannot be trapped in static traps as Maxwell's equations do not allow a maximum of the electric field in free space. It is possible to generate an electric field that has a saddle point by superposing an inhomogeneous electric field to an homogeneous electric field. In such a field, molecules are focused along one direction, while being defocused along the other. By reversing the direction of the inhomogeneous electric field the focusing and defocusing directions are reversed. When the fields are being switched back and forth at the appropriate rate, this leads to a net focusing force in all directions. We describe possible electrode geometries for creating the desired fields and discuss their merits. Trapping of {sup 15}ND{sub 3} ammonia molecules in a cylindrically symmetric ac trap is demonstrated. We present measurements of the spatial distribution of the trapped cloud as a function of the settings of the trap and compare these to both a simple model assuming a linear force and to full three-dimensional simulations of the experiment. With the optimal settings, molecules within a phase-space volume of 270 mm{sup 3} (m/s){sup 3} remain trapped. This corresponds to a trap depth of about 5 mK and a trap volume of about 20 mm{sup 3}.

  20. SMPDB: The Small Molecule Pathway Database.

    PubMed

    Frolkis, Alex; Knox, Craig; Lim, Emilia; Jewison, Timothy; Law, Vivian; Hau, David D; Liu, Phillip; Gautam, Bijaya; Ly, Son; Guo, An Chi; Xia, Jianguo; Liang, Yongjie; Shrivastava, Savita; Wishart, David S

    2010-01-01

    The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in clinical metabolomics, transcriptomics, proteomics and systems biology. SMPDB provides exquisitely detailed, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the Human Metabolome Database (HMDB) or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca. PMID:19948758

  1. Electrostatic Propulsion Using C60 Molecules

    NASA Technical Reports Server (NTRS)

    Leifer, Stephanie D.; Saunders, Winston A.

    1993-01-01

    Report proposes use of C60 as propellant material in electrostatic propulsion system of spacecraft. C60, C70, and similar molecules, have recently been found to have characteristics proving advantageous in electrostatic propulsion. Report discusses these characteristics and proposes experiments to determine feasibility of concept.

  2. Molecule diagram from earth-grown crystals

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Like many chemicals in the body, the three-dimensional structure of insulin is extremely complex. When grown on the ground, insulin crystals do not grow as large or as ordered as researchers desire--obscuring the blueprint of the insulin molecules.

  3. The Molecules of the Cell Membrane.

    ERIC Educational Resources Information Center

    Bretscher, Mark S.

    1985-01-01

    Cell membrane molecules form a simple, two-dimensional liquid controlling what enters and leaves the cell. Discusses cell membrane molecular architecture, plasma membranes, epithelial cells, cycles of endocytosis and exocytosis, and other topics. Indicates that some cells internalize, then recycle, membrane area equivalent to their entire surface…

  4. Small molecule control of bacterial biofilms

    PubMed Central

    Worthington, Roberta J.; Richards, Justin J.

    2012-01-01

    Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: 1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, 2) chemical library screening for compounds with anti-biofilm activity, and 3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity. PMID:22733439

  5. Small molecule control of bacterial biofilms.

    PubMed

    Worthington, Roberta J; Richards, Justin J; Melander, Christian

    2012-10-01

    Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis patients, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: (1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, (2) chemical library screening for compounds with anti-biofilm activity, and (3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity. PMID:22733439

  6. Progress in searches for prebiotic interstellar molecules

    NASA Astrophysics Data System (ADS)

    Hjalmarson, Å.; Bergman, P.; Nummelin, A.

    2001-08-01

    Recent progress in our searches for complex interstellar molecules, which may be important for the origin of life on habitable planets, is reviewed. The molecular abundance ranges and current search limits observed in a number of "hot core" sources are tabulated and discussed. The abundance limits reached in searches for most complex interstellar molecules are not much lower than the detection levels of other large molecules. While our detection of c-C2H4O (ethylene oxide, oxirane) may suggest the interstellar presence of the next larger similar ring c-C4H4O (furan - the core of the simple sugars ribose and deoxyribose, which form the backbones of RNA and DNA), our current search limits are just barely lower than the abundance level of ethylene oxide. Really deep searches for prebiotic molecules in compact cloud cores will have to await the erection of the very sensitive aperture synthesis instrument ALMA, the Atacama Large Millimetre Array, to be located in the Chilean Andes.

  7. Organic chemistry: Precision pruning of molecules

    NASA Astrophysics Data System (ADS)

    Yang, Kin S.; Engle, Keary M.

    2016-05-01

    If organic molecules were trees, then the numerous carbon-hydrogen bonds within them would be leaves. A catalyst that targets one 'leaf' out of many similar other ones looks set to be a huge leap for synthetic chemistry. See Letter p.230

  8. Organic molecules in translucent interstellar clouds.

    PubMed

    Krełowski, Jacek

    2014-09-01

    Absorption spectra of translucent interstellar clouds contain many known molecular bands of CN, CH+, CH, OH, OH(+), NH, C2 and C3. Moreover, one can observe more than 400 unidentified absorption features, known as diffuse interstellar bands (DIBs), commonly believed to be carried by complex, carbon-bearing molecules. DIBs have been observed in extragalactic sources as well. High S/N spectra allow to determine precisely the corresponding column densities of the identified molecules, rotational temperatures which differ significantly from object to object in cases of centrosymmetric molecular species, and even the (12)C/(13)C abundance ratio. Despite many laboratory based studies of possible DIB carriers, it has not been possible to unambiguously link these bands to specific species. An identification of DIBs would substantially contribute to our understanding of chemical processes in the diffuse interstellar medium. The presence of substructures inside DIB profiles supports the idea that DIBs are very likely features of gas phase molecules. So far only three out of more than 400 DIBs have been linked to specific molecules but none of these links was confirmed beyond doubt. A DIB identification clearly requires a close cooperation between observers and experimentalists. The review presents the state-of-the-art of the investigations of the chemistry of interstellar translucent clouds i.e. how far our observations are sufficient to allow some hints concerning the chemistry of, the most common in the Galaxy, translucent interstellar clouds, likely situated quite far from the sources of radiation (stars). PMID:25467771

  9. Comprehensive Map of Molecules Implicated in Obesity.

    PubMed

    Jagannadham, Jaisri; Jaiswal, Hitesh Kumar; Agrawal, Stuti; Rawal, Kamal

    2016-01-01

    Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in "bow-tie" architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome.

  10. Electron-atom /molecule/ collision processes

    NASA Technical Reports Server (NTRS)

    Trajmar, S.

    1980-01-01

    Electron-atom (molecule) collision processes at low and intermediate energies, from near threshold to a few hundred electron volts, are discussed. Attention is given to experimental techniques and procedures, electron impact cross sections, impact excitation and electron-atom scattering in laser fields. Specific examples are presented that illustrate various experimental techniques and interpretations of observations.

  11. Stability of Matter-Antimatter Molecules

    SciTech Connect

    Wong, Cheuk-Yin; Lee, Teck-Ghee

    2011-01-01

    We examine the stability of matter-antimatter molecules by reducing the four-body problem into a simpler two-body problem with residual interactions. We find that matter-antimatter molecules with constituents (m{sub 1}{sup +}, m{sub 2}{sup -}, {bar m}{sub 2}{sup +}, {bar m}{sub 1}{sup -}) possess bound states if their constituent mass ratio m{sub 1}/m{sub 2} is greater than about 4. This stability condition suggests that the binding of matter-antimatter molecules is a rather common phenomenon. We evaluate the binding energies and eigenstates of matter-antimatter molecules ({mu}{sup +}e{sup 0})-(e{sup +}{mu}{sup -}), ({pi}{sup +}e{sup -})-(e{sup +}{pi}{sup -}), (K{sup +}e{sup -})-(e{sup +}K{sup -}), (pe{sup -})-(e{sup +}{bar p}), (p{mu}{sup -})-({mu}{sup +}{bar p}), and (K{sup +}{mu}{sup -})-({mu}{sup +}K{sup -}), which satisfy the stability condition. We estimate the molecular annihilation lifetimes in their s states.

  12. Predicting the Stability of Hypervalent Molecules

    ERIC Educational Resources Information Center

    Mitchell, Tracy A.; Finnocchio, Debbie; Kua, Jeremy

    2007-01-01

    An exercise is described which introduces students to using concepts in thermochemistry to predict relative stability of a hypervalent molecule. Students will compare the energies of formation for both fluoride and the hydride by calculations and they will also explore the issue of partial ionic character in polar covalent bonds.

  13. Self and directed assembly: people and molecules.

    PubMed

    James, Tony D

    2016-01-01

    Self-assembly and directed-assembly are two very important aspects of supramolecular chemistry. As a young postgraduate student working in Canada with Tom Fyles my introduction to Supramolecular Chemistry was through the self-assembly of phospholipid membranes to form vesicles for which we were developing unimolecular and self-assembling transporter molecules. The next stage of my development as a scientist was in Japan with Seiji Shinkai where in a "Eureka" moment, the boronic acid templating unit (directed-assembly) of Wulff was combined with photoinduced electron transfer systems pioneered by De Silva. The result was a turn-on fluorescence sensor for saccharides; this simple result has continued to fuel my research to the present day. Throughout my career as well as assembling molecules, I have enjoyed bringing together researchers in order to develop collaborative networks. This is where molecules meet people resulting in assemblies worth more than the individual "molecule" or "researcher". My role in developing networks with Japan was rewarded by the award of a Daiwa-Adrian Prize in 2013 and I was recently rewarded for developing networks with China with an Inaugural CASE Prize in 2015.

  14. Organic molecules in translucent interstellar clouds.

    PubMed

    Krełowski, Jacek

    2014-09-01

    Absorption spectra of translucent interstellar clouds contain many known molecular bands of CN, CH+, CH, OH, OH(+), NH, C2 and C3. Moreover, one can observe more than 400 unidentified absorption features, known as diffuse interstellar bands (DIBs), commonly believed to be carried by complex, carbon-bearing molecules. DIBs have been observed in extragalactic sources as well. High S/N spectra allow to determine precisely the corresponding column densities of the identified molecules, rotational temperatures which differ significantly from object to object in cases of centrosymmetric molecular species, and even the (12)C/(13)C abundance ratio. Despite many laboratory based studies of possible DIB carriers, it has not been possible to unambiguously link these bands to specific species. An identification of DIBs would substantially contribute to our understanding of chemical processes in the diffuse interstellar medium. The presence of substructures inside DIB profiles supports the idea that DIBs are very likely features of gas phase molecules. So far only three out of more than 400 DIBs have been linked to specific molecules but none of these links was confirmed beyond doubt. A DIB identification clearly requires a close cooperation between observers and experimentalists. The review presents the state-of-the-art of the investigations of the chemistry of interstellar translucent clouds i.e. how far our observations are sufficient to allow some hints concerning the chemistry of, the most common in the Galaxy, translucent interstellar clouds, likely situated quite far from the sources of radiation (stars).

  15. Lesser-Known Molecules in Ovarian Carcinogenesis

    PubMed Central

    Lozneanu, Ludmila; Cojocaru, Elena; Giuşcă, Simona Eliza; Cărăuleanu, Alexandru; Căruntu, Irina-Draga

    2015-01-01

    Currently, the deciphering of the signaling pathways brings about new advances in the understanding of the pathogenic mechanism of ovarian carcinogenesis, which is based on the interaction of several molecules with different biochemical structure that, consequently, intervene in cell metabolism, through their role as regulators in proliferation, differentiation, and cell death. Given that the ensemble of biomarkers in OC includes more than 50 molecules the interest of the researchers focuses on the possible validation of each one's potential as prognosis markers and/or therapeutic targets. Within this framework, this review presents three protein molecules: ALCAM, c-FLIP, and caveolin, motivated by the perspectives provided through the current limited knowledge on their role in ovarian carcinogenesis and on their potential as prognosis factors. Their structural stability, once altered, triggers the initiation of the sequences characteristic for ovarian carcinogenesis, through their role as modulators for several signaling pathways, contributing to the disruption of cellular junctions, disturbance of pro-/antiapoptotic equilibrium, and alteration of transmission of the signals specific for the molecular pathways. For each molecule, the text is built as follows: (i) general remarks, (ii) structural details, and (iii) particularities in expression, from different tumors to landmarks in ovarian carcinoma. PMID:26339605

  16. Comprehensive Map of Molecules Implicated in Obesity

    PubMed Central

    Agrawal, Stuti

    2016-01-01

    Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in “bow-tie” architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome. PMID:26886906

  17. NASA's Exobiology Program.

    PubMed

    DeVincenzi, D L

    1984-01-01

    The goal of NASA's Exobiology Program is to understand the origin, evolution, and distribution of life, and life-related molecules, on Earth and throughout the universe. Emphasis is focused on determining how the rate and direction of these processes were affected by the chemical and physical environment of the evolving planet, as well as by planetary, solar, and astrophysical phenomena. This is accomplished by a multi-disciplinary program of research conducted by over 60 principal investigators in both NASA and university laboratories. Major program thrusts are in the following research areas: biogenic elements; chemical evolution; origin of life; organic geochemistry; evolution of higher life forms; solar system exploration; and the search for extraterrestrial intelligence (SETI).

  18. NASA's Exobiology Program

    NASA Technical Reports Server (NTRS)

    Devincenzi, D. L.

    1984-01-01

    The goal of NASA's Exobiology Program is to understand the origin, evolution, and distribution of life, and life-related molecules, on earth and throughout the universe. Emphasis is focused on determining how the rate and direction of these processes were affected by the chemical and physical environment of the evolving planet, as well as by planetary, solar, and astrophysical phenomena. This is accomplished by a multi-disciplinary program of research conducted by over 60 principal investigators in both NASA and university laboratories. Major program thrusts are in the following research areas: biogenic elements; chemical evolution; origin of life; organic geochemistry; evolution of higher life forms; solar system exploration; and the search for extraterrestrial intelligence (SETI).

  19. Molecules as magnetic probes of starspots

    NASA Astrophysics Data System (ADS)

    Afram, N.; Berdyugina, S. V.

    2015-04-01

    Context. Stellar dynamo processes can be explored by measuring the magnetic field. This is usually obtained using the atomic and molecular Zeeman effect in spectral lines. While the atomic Zeeman effect can only access warmer regions, the use of molecular lines is of advantage for studying cool objects. The molecules MgH, TiO, CaH, and FeH are suited to probe stellar magnetic fields, each one for a different range of spectral types, by considering the signal that is obtained from modeling various spectral types. Aims: We have analyzed the usefulness of different molecules (MgH, TiO, CaH, and FeH) as diagnostic tools for studying stellar magnetism on active G-K-M dwarfs. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and present synthetic Stokes profiles for the modeled spectral type. Methods: We modeled a star with a spot size of 10% of the stellar disk and a spot comprising either only longitudinal or only transverse magnetic fields and estimated the strengths of the polarization Stokes V and Q signals for the molecules MgH, TiO, CaH, and FeH. We combined various photosphere and spot models according to realistic scenarios. Results: In G dwarfs, the molecules MgH and FeH show overall the strongest Stokes V and Q signals from the starspot, whereas FeH has a stronger Stokes V signal in all G dwarfs with a spot temperature of 3800 K. In K dwarfs, CaH signals are generally stronger, and the TiO signature is most prominent in M dwarfs. Conclusions: Modeling synthetic polarization signals from starspots for a range of G-K-M dwarfs leads to differences in the prominence of various molecular signatures in different wavelength regions, which helps to efficiently select targets and exposure times for observations.

  20. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  1. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-06-06

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  2. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-05-30

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  3. Chiral Sensitivity in Electron-Molecule Interactions

    NASA Astrophysics Data System (ADS)

    Dreiling, Joan

    2015-09-01

    All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found respectively in L- and D-enantiomers only. The primordial origin of this enantiomeric excess is unknown. One possible explanation is given by the Vester- Ulbricht hypothesis, which suggests that left-handed electrons present in beta-radiation, produced by parity-violating weak decays, interacted with biological precursors and preferentially destroyed one of the two enantiomers. Experimental tests of this idea have thus far yielded inconclusive results. We show direct evidence for chirally-dependent bond breaking through a dissociative electron attachment (DEA) reaction when spin-polarized electrons are incident on gas-phase chiral molecules. This provides unambiguous evidence for a well-defined, chirally-sensitive destructive molecular process and, as such, circumstantial evidence for the Vester-Ulbricht hypothesis. I will also present the results of our systematic study of the DEA asymmetry for different chiral halocamphor molecules. Three halocamphor molecules were investigated: 3-bromocamphor (C10H15BrO), 3-iodocamphor(C10H15IO), and 10-iodocamphor. The DEA asymmetries collected for bromocamphor and iodocamphor are qualitatively different, suggesting that the atomic number of the heaviest atom in the molecule plays a crucial role in the asymmetric interactions. The DEA asymmetry data for 3- and 10-iodocamphor have the same qualitative behavior, but the 10-iodocamphor asymmetry is about twice as large at the lowest energies investigated, so the location of the heavy atom in the camphor molecule also affects the asymmetries. This work was performed at the University of Nebraska-Lincoln. This project is funded by NSF Grant PHY-1206067.

  4. Microarray analysis at single molecule resolution

    PubMed Central

    Mureşan, Leila; Jacak, Jarosław; Klement, Erich Peter; Hesse, Jan; Schütz, Gerhard J.

    2010-01-01

    Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state of the art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack in appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of two to 20 micrometers and quantifies the abundance of target molecules by determining average pixel intensities, a novel high resolution approach [1] directly visualizes individual bound molecules as diffraction limited peaks. The now possible quantification via counting is less susceptible to labeling artifacts and background noise. We have developed an approach for the analysis of high-resolution microarray images. It consists first of a single molecule detection step, based on undecimated wavelet transforms, and second, of a spot identification step via spatial statistics approach (corresponding to the segmentation step in the classical microarray analysis). The detection method was tested on simulated images with a concentration range of 0.001 to 0.5 molecules per square micron and signal-to-noise ratio (SNR) between 0.9 and 31.6. For SNR above 15 the false negatives relative error was below 15%. Separation of foreground/background proved reliable, in case foreground density exceeds background by a factor of 2. The method has also been applied to real data from high-resolution microarray measurements. PMID:20123580

  5. Postsecondary Programs.

    ERIC Educational Resources Information Center

    American Annals of the Deaf, 2002

    2002-01-01

    This article lists postsecondary programs specifically for people with deafness and other postsecondary programs with supportive services for students with deafness. Alphabetized by state, contact information is provided for each of the programs, along with date the program was founded, programs, degrees, and number of students and staff with…

  6. Anharmonicity and infrared bands of Polycyclic Aromatic Hydrocarbon (PAH) molecules

    NASA Astrophysics Data System (ADS)

    Petrignani, Annemieke; Maltseva, Elena; Candian, Alessandra; Mackie, Cameron; Huang, Xinchuan; Lee, Timothy J.; Tielens, Alexander; Oomens, Jos; Buma, Wybren Jan

    2015-08-01

    We present a systematic laboratory study of the CH stretching region in Polycyclic Aromatic Hydrocarbon (PAH) molecules of different shapes and sizes to investigate anharmonic behaviour and address the reliability of the never-validated but universally accepted scaling factors employed in astronomical PAH models. At the same time, new anharmonic theoretical quantum chemistry studies have been performed with the software program Spectro using our experimental data as benchmark. We performed mass and conformational-resolved, high-resolution spectroscopy of cold (~10K) linear and compact PAH molecules starting with naphthalene (C10H8) in the 3-µm CH stretching region. Surprisingly, the measured infrared spectra show many more strong modes than expected. Measurements of the deuterated counterparts demonstrate that these bands are the result of Fermi Resonances. First comparisons with harmonic and anharmonic DFT calculations using Gaussian 09 show that both approximations are not able to reproduce in detail the observed molecular reality. The improved anharmonic calculations performed with Spectro now include the effects of Fermi resonances and have been applied to PAHs for the first time. The analysis of the experimental data is greatly aided by these new theoretical quantum chemistry studies. Preliminary assignments are presented, aided by comparison between the observed rotational contour and the symmetry of candidate bands.

  7. Variation in the Single-Molecule Conductance of Oligothiophenes

    NASA Astrophysics Data System (ADS)

    Capozzi, Brian; Dell, Emma; Dubay, Kateri; Moreno, Jose; Berkelbach, Timothy; Reichman, David; Campos, Luis; Venkataraman, Latha

    2013-03-01

    Thiophenes are ubiquitous in organic electronic and photovoltaic applications; yet, they have received minimal attention in single molecule transport studies. Here, we carry out single molecule conductance measurements on a family of methyl sulfide-terminated oligothiophenes using the scanning tunneling microscope based break-junction technique. We find a non-exponential decay in conductance with the number of thiophene units (2 through 6) in the chain, which cannot be explained by a simple tunneling or hopping mechanism. We also find that the oligothiophenes exhibit a rather broad conductance distribution when compared to oligophenyls. Using a combination of experiment and molecular dynamics simulations, we show that this increased breadth is most likely due to different thiophene confomers sampled in the experiments, which do not necessarily maintain conjugation along the backbone. These measurements therefore reinforce the importance of conformation and conjugation effects in thiophene-based organic electronic devices where highly conducting molecular components are required. The experimental work was funded by NSF-DMR-1206202 and the theory was funded by the EFRC program of the U.S. Department of Energy under Award No. DESC0001085.

  8. Living is information processing: from molecules to global systems.

    PubMed

    Farnsworth, Keith D; Nelson, John; Gershenson, Carlos

    2013-06-01

    We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function-to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, information at lower levels to appear at higher levels in complex systems (emergence). We show how information patterns, are united by the creation of mutual context, generating persistent consequences, to result in 'functional information'. This constructive process forms arbitrarily large complexes of information, the combined effects of which include the functions of life. Molecules and simple organisms have already been measured in terms of functional information content; we show how quantification may be extended to each level of organisation up to the ecological. In terms of a computer analogy, life is both the data and the program and its biochemical structure is the way the information is embodied. This idea supports the seamless integration of life at all scales with the physical universe. The innovation reported here is essentially to integrate these ideas, basing information on the 'general definition' of information, rather than simply the statistics of information, thereby explaining how functional information operates throughout life. PMID:23456459

  9. A Supramolecular Approach to Medicinal Chemistry: Medicine Beyond the Molecule

    NASA Astrophysics Data System (ADS)

    Smith, David K.

    2005-03-01

    This article focuses on the essential roles played by intermolecular forces in mediating the interactions between chemical molecules and biological systems. Intermolecular forces constitute a key topic in chemistry programs, yet can sometimes seem disconnected from real-life applications. However, by taking a "supramolecular" view of medicinal chemistry and focusing on interactions between molecules, it is possible to come to a deeper understanding of recent developments in medicine. This allows us to gain a real insight into the interface between biology and chemistry—an interdisciplinary area that is crucial for the development of modern medicinal products. This article emphasizes a conceptual view of medicinal chemistry, which has important implications for the future, as the supramolecular approach to medicinal-chemistry products outlined here is rapidly allowing nanotechnology to converge with medicine. In particular, this article discusses recent developments including the rational design of drugs such as Relenza and Tamiflu, the mode of action of vancomycin, and the mechanism by which bacteria develop resistance, drug delivery using cyclodextrins, and the importance of supramolecular chemistry in understanding protein aggregation diseases such as Alzheimer's and Creutzfield Jacob. The article also indicates how taking a supramolecular approach will enable the development of new nanoscale medicines.

  10. Modeling the Infrared Emission Spectra of Specific PAH Molecules in Interstellar Space

    NASA Astrophysics Data System (ADS)

    Li, Aigen

    2007-05-01

    The 3.3, 6.2, 7.7, 8.6 and 11.3 micron emission features ubiquitously seen in a wide variety of Galactic and extragalactic objects, are generally attributed to polycyclic aromatic hydrocarbon (PAH) molecules. Although the PAH hypothesis is quite successful in explaining the general pattern of the observed emission spectra, so far there is no actual precise identification of a single specific PAH molecule in interstellar space. Therefore, when modeling the observed PAH emission spectra, astronomers usually take an empirical approach by constructing 'astro-PAHs' which do not represent any specific material, but approximate the actual absorption properties of the PAH mixture in astrophysical regions. We propose a Spitzer Theory Program to study the photoexcitation of specific PAH molecules and their ions in interstellar space, taking a statistical-mechanical (instead of thermal) approach. For most of the specific PAH molecules selected for this research (with a small number of vibrational degrees of freedom), thermal approximation is not valid. Using available laboratory and quantum-chemical data (e.g. vibrational frequencies, UV/visible/IR absorption cross sections), we will calculate the emission spectra of 21 representative specific PAH molecules and their ions, ranging from naphthalene to circumcoronene, illuminated by interstellar radiation fields of a wide range of intensities. This program will create a web-based 'library' of the emission spectra of 21 specific PAH molecules and their ions as a function of starlight intensities. This 'library' will be made publicly available by October 2008 on the internet at http://www.missouri.edu/~lia/. By comparing observed PAH spectra with model spectra produced by co-adding the emission spectra of different PAH molecules available in this 'library' (with different weights for different species), one will be able to estimate the total PAH mass and relative abundances of each PAH species, using real PAH properties.

  11. Spin transport in molecules studied by Fe3O4/molecule nanoparticles

    NASA Astrophysics Data System (ADS)

    Yue, F. J.; Wang, S.; Wu, D.

    2013-05-01

    In this work, we synthesize single molecular layer coated Fe3O4 nanoparticles to form the network of the molecular junction spin valves. The Fe3O4 nanoparticles chemically bond with molecules without any physically absorbed molecules, leading to one monolayer molecule coated on nanoparticles. The magnetoresistance (MR) of cold-pressed Fe3O4/oleic acid nanoparticles is more than two times larger than bare Fe3O4 nanoparticles, indicating weaker spin scattering in molecules. Furthermore, the MR ratio is as high as ˜21 % at room temperature for Fe3O4/alkane molecule nanoparticles. Interestingly, even though the resistance spans about two decades as the alkane molecular length varies from 0.7 to 2.5 nm, the MR ratio stays approximately constant. This molecular length independent spin valve MR, originated from the weaker hyperfine interaction strength of the σ-electrons in alkane molecules, entails room-temperature spin-conserving transport in molecular materials. Using the size of ˜500 nm Fe3O4 nanoparticles, a large MR is achieved in a relatively low magnetic field. This feature opens a door for the development of future spin-based molecular electronics. Moreover, spin injection at the interface of Fe3O4/stearic acid molecule is investigated in a comparative study between Fe3O4 nanoparticles chemically bonded (ChemNPs) and physically absorbed (PhyNPs) molecules. A MR of 12 % at room temperature is observed in ChemNPs, in sharp contrast to the zero MR ratio in PhyNPs, reflecting that the chemical bonding is crucial for spin injection. These results show that the hybrid nanoparticles provide a simple approach to study the spin transport in molecules.

  12. SLIMP: Strong laser interaction model package for atoms and molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Zhao, Zengxiu

    2015-07-01

    We present the SLIMP package, which provides an efficient way for the calculation of strong-field ionization rate and high-order harmonic spectra based on the single active electron approximation. The initial states are taken as single-particle orbitals directly from output files of the general purpose quantum chemistry programs GAMESS, Firefly and Gaussian. For ionization, the molecular Ammosov-Delone-Krainov theory, and both the length gauge and velocity gauge Keldysh-Faisal-Reiss theories are implemented, while the Lewenstein model is used for harmonic spectra. Furthermore, it is also efficient for the evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment and calculation of orbital integrations. This package can be applied to quite large basis sets and complex molecules with many atoms, and is implemented to allow easy extensions for additional capabilities.

  13. Advances in targeting cell surface signalling molecules for immune modulation

    PubMed Central

    Yao, Sheng; Zhu, Yuwen; Chen, Lieping

    2013-01-01

    The past decade has witnessed a surge in the development of immunomodulatory approaches to combat a broad range of human diseases, including cancer, viral infections, autoimmunity and inflammation as well as in the prevention of transplant rejection. Immunomodulatory approaches mostly involve the use of monoclonal antibodies or recombinant fusion proteins that target cell surface signalling molecules on immune cells to drive immune responses towards the desired direction. Advances in our understanding of the human immune system, along with valuable lessons learned from the first generation of therapeutic biologics, are aiding the design of the next generation of immunomodulatory biologics with better therapeutic efficacy, minimized adverse effects and long-lasting clinical benefit. The recent encouraging results from antibodies targeting programmed cell death protein 1 (PD1) and B7 homolog 1 (B7H1; also known as PDL1) for the treatment of various advanced human cancers show that immunomodulatory therapy has come of age. PMID:23370250

  14. The function of a novel immunophenotype candidate molecule PD-1 in chronic lymphocytic leukemia.

    PubMed

    Grzywnowicz, Maciej; Karabon, Lidia; Karczmarczyk, Agnieszka; Zajac, Malgorzata; Skorka, Katarzyna; Zaleska, Joanna; Wlasiuk, Paulina; Chocholska, Sylwia; Tomczak, Waldemar; Bojarska-Junak, Agnieszka; Dmoszynska, Anna; Frydecka, Irena; Giannopoulos, Krzysztof

    2015-01-01

    Programmed death-1 (PD-1) is a negative receptor expressed on lymphocytes including malignant B cells in chronic lymphocytic leukemia (CLL). In this work, we found that patients with CLL had a higher expression of PD-1 transcript (PDCD1) than healthy volunteers (p < 0.0001). PDCD1 expression was comparable between CLL cells from accumulation (peripheral blood) and proliferation (bone marrow) disease compartments. In blood samples of patients with mutated IGHV genes PDCD1 expression was higher than with unmutated IGHV (p = 0.0299). We demonstrated that phosphorylation of SYK and LYN, key B-cell receptor signaling kinases, was independent of PD-1 expression in patients with CLL, while ZAP-70 phosphorylation in negative tyrosine residue 292 showed strong inverse correlation (r = - 0.8, p = 0.0019). No associations between five single nucleotide polymorphisms of PDCD1, their expressions and susceptibility to CLL were found. In conclusion, PD-1 might be an independent, universal marker of CLL cells and a part of their activated phenotype, and subsequently might modulate the function of ZAP-70.

  15. Synthesis of single-molecule nanocars.

    PubMed

    Vives, Guillaume; Tour, James M

    2009-03-17

    The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new

  16. Computation of Atomic Solvent Accessible Surface Areas and Gradients for the Calculation of Solvation Energy and Forces on Molecules

    NASA Astrophysics Data System (ADS)

    Hummel, Michelle; Fennel, Christopher; Coutsias, Evangelos; Dill, Kenneth; Brini, Emiliano

    2014-03-01

    Many models for the calculation of solvation energy and forces on a molecule involve atomic solvent accessible surface areas and their gradients. We present analytical formulas for such areas and gradients which utilize the Delaunay tetrahedrization of a molecule and its subset called the α-complex. These formulas have been implemented in a fast computer program in conjunction with a solvation approach called Semi Explicit Assembly (SEA), and has shown to produce quick and physically accurate results.

  17. Exploring X(5568) as a meson molecule

    NASA Astrophysics Data System (ADS)

    Agaev, S. S.; Azizi, K.; Sundu, H.

    2016-10-01

    The parameters, i.e. the mass and current coupling of the exotic X(5568) state observed by the D0 Collaboration as well as the decay width of the process X → B_s0π+, are explored using the Boverline{K} molecule assumption on its structure. Employed computational methods include QCD two-point and light-cone sum rules, the latter being considered in the soft-meson approximation. The obtained results are compared with the data of the D0 Collaboration as well as with the predictions of the diquark-antidiquark model. This comparison strengthens a diquark-antidiquark picture for the X(5568) state rather than a meson molecule structure.

  18. Interaction between hydrogen molecules and metallofullerenes.

    SciTech Connect

    Yoon, Mina; Yang, Shenyuan; Zhang, Zhenyu

    2009-01-01

    Within first-principles density functional theory, we explore the feasibility of using metallofullerenes as efficient hydrogen storage media. In particular, we systematically investigate the interaction between hydrogen molecules and La encapsulated all-carbon fullerenes, Cn (20≤n≤82), focusing on the role of transferred charges between the metal atoms and fullerenes on the affinity of hydrogen molecules to the metallofullerenes. Our calculations show that three electrons are transferred from La atom to fullerene cages, while the induced charges are mostly screened by the fullerene cages. We find the local enhancement of molecular hydrogen affinity to the fullerenes to be sensitively dependent on the local bonding properties, rather than on the global charging effects.

  19. Interaction between hydrogen molecules and metallofullerenes

    NASA Astrophysics Data System (ADS)

    Yoon, Mina; Yang, Shenyuan; Zhang, Zhenyu

    2009-08-01

    Within first-principles density functional theory, we explore the feasibility of using metallofullerenes as efficient hydrogen storage media. In particular, we systematically investigate the interaction between hydrogen molecules and La encapsulated all-carbon fullerenes, Cn (20≤n≤82), focusing on the role of transferred charges between the metal atoms and fullerenes on the affinity of hydrogen molecules to the metallofullerenes. Our calculations show that three electrons are transferred from La atom to fullerene cages, while the induced charges are mostly screened by the fullerene cages. We find the local enhancement of molecular hydrogen affinity to the fullerenes to be sensitively dependent on the local bonding properties, rather than on the global charging effects.

  20. Interaction between hydrogen molecules and metallofullerenes.

    PubMed

    Yoon, Mina; Yang, Shenyuan; Zhang, Zhenyu

    2009-08-14

    Within first-principles density functional theory, we explore the feasibility of using metallofullerenes as efficient hydrogen storage media. In particular, we systematically investigate the interaction between hydrogen molecules and La encapsulated all-carbon fullerenes, C(n) (20 < or = n < or = 82), focusing on the role of transferred charges between the metal atoms and fullerenes on the affinity of hydrogen molecules to the metallofullerenes. Our calculations show that three electrons are transferred from La atom to fullerene cages, while the induced charges are mostly screened by the fullerene cages. We find the local enhancement of molecular hydrogen affinity to the fullerenes to be sensitively dependent on the local bonding properties, rather than on the global charging effects.

  1. Atomic Rydberg Reservoirs for Polar Molecules

    NASA Astrophysics Data System (ADS)

    Zhao, B.; Glaetzle, A. W.; Pupillo, G.; Zoller, P.

    2012-05-01

    We discuss laser-dressed dipolar and van der Waals interactions between atoms and polar molecules, so that a cold atomic gas with laser admixed Rydberg levels acts as a designed reservoir for both elastic and inelastic collisional processes. The elastic scattering channel is characterized by large elastic scattering cross sections and repulsive shields to protect from close encounter collisions. In addition, we discuss a dissipative (inelastic) collision where a spontaneously emitted photon carries away (kinetic) energy of the collision partners, thus providing a significant energy loss in a single collision. This leads to the scenario of rapid thermalization and cooling of a molecule in the mK down to the μK regime by cold atoms.

  2. The X(3872) boson: Molecule or charmonium

    SciTech Connect

    Suzuki, Mahiko

    2005-08-01

    It has been argued that the mystery boson X(3872) is a molecular state consisting of primarily D{sup 0}{bar D}*{sup 0} + {bar D}{sup 0}D*{sup 0}. In contrast, apparent puzzles and potential difficulties have been pointed out for the charmonium assignment of X(3872). They examine several aspects of these alternatives by semi-quantitative methods since quantitatively accurate results are often hard to reach on them. they point out that some of the observed properties of X(3872), in particular, the binding and the production rates are incompatible with the molecule interpretation. Despite puzzles and obstacles, X(3872) may fit more likely to the excited {sup 3}P{sub 1} charmonium than to the molecule after the mixing of c{bar c} with D{bar D}* + {bar D}D* is taken into account.

  3. Transport of fullerene molecules along graphene nanoribbons

    PubMed Central

    Savin, Alexander V.; Kivshar, Yuri S.

    2012-01-01

    We study the motion of C60 fullerene molecules and short-length carbon nanotubes on graphene nanoribbons. We reveal that the character of the motion of C60 depends on temperature: for T < 150 K the main type of motion is sliding along the surface, but for higher temperatures the sliding is replaced by rocking and rolling. Modeling of the buckyball with an included metal ion demonstrates that this molecular complex undergoes a rolling motion along the nanoribbon with the constant velocity under the action of a constant electric field. The similar effect is observed in the presence of the heat gradient applied to the nanoribbon, but mobility of carbon structures in this case depends largely on their size and symmetry, such that larger and more asymmetric structures demonstrate much lower mobility. Our results suggest that both electorphoresis and thermophoresis can be employed to control the motion of carbon molecules and fullerenes. PMID:23259049

  4. Theory of single molecule emission spectroscopy

    SciTech Connect

    Bel, Golan; Brown, Frank L. H.

    2015-05-07

    A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive “detection” based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach. Applications to two different models for molecular dynamics are considered: a simple two-level system and a two-level absorber subject to spectral diffusion.

  5. Automated imaging system for single molecules

    DOEpatents

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  6. Small-molecule inhibitors of myosin proteins

    PubMed Central

    Bond, Lisa M; Tumbarello, David A; Kendrick-Jones, John; Buss, Folma

    2014-01-01

    Advances in screening and computational methods have enhanced recent efforts to discover/design small-molecule protein inhibitors. One attractive target for inhibition is the myosin family of motor proteins. Myosins function in a wide variety of cellular processes, from intracellular trafficking to cell motility, and are implicated in several human diseases (e.g., cancer, hypertrophic cardiomyopathy, deafness and many neurological disorders). Potent and selective myosin inhibitors are, therefore, not only a tool for understanding myosin function, but are also a resource for developing treatments for diseases involving myosin dysfunction or overactivity. This review will provide a brief overview of the characteristics and scientific/therapeutic applications of the presently identified small-molecule myosin inhibitors before discussing the future of myosin inhibitor and activator design. PMID:23256812

  7. Late Stage Azidation of Complex Molecules

    PubMed Central

    2016-01-01

    Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

  8. Imaging Genetic Molecules At Atomic Resolution

    NASA Technical Reports Server (NTRS)

    Coles, L. Stephen

    1993-01-01

    Proposed method of imaging informational polymeric biological molecules at atomic resolution enables determination of sequences of component monomers about 10 to the 3rd power to 10 to the 4th power times as fast as conventional methods do. Accelerates research on genetic structures of animals and plants. Also contributes significantly to imaging processes like scanning electron microscopy (SEM), atomic-force microscopy (AFM), and scanning tunneling microscopy (STM) in cases in which necessary to locate or identify small specimens on relatively large backgrounds and subtract background images to obtain images of specimens in isolation. V-grooves on silicon wafer laid out in square pattern, intersections of which marked to identify coordinates. Specimen molecules held in grooves for reproducible positioning and scanning by AFM or STM.

  9. Artifacts in single-molecule localization microscopy.

    PubMed

    Burgert, Anne; Letschert, Sebastian; Doose, Sören; Sauer, Markus

    2015-08-01

    Single-molecule localization microscopy provides subdiffraction resolution images with virtually molecular resolution. Through the availability of commercial instruments and open-source reconstruction software, achieving super resolution is now public domain. However, despite its conceptual simplicity, localization microscopy remains prone to user errors. Using direct stochastic optical reconstruction microscopy, we investigate the impact of irradiation intensity, label density and photoswitching behavior on the distribution of membrane proteins in reconstructed super-resolution images. We demonstrate that high emitter densities in combination with inappropriate photoswitching rates give rise to the appearance of artificial membrane clusters. Especially, two-dimensional imaging of intrinsically three-dimensional membrane structures like microvilli, filopodia, overlapping membranes and vesicles with high local emitter densities is prone to generate artifacts. To judge the quality and reliability of super-resolution images, the single-molecule movies recorded to reconstruct the images have to be carefully investigated especially when investigating membrane organization and cluster analysis.

  10. Challenges in quantitative single molecule localization microscopy.

    PubMed

    Shivanandan, A; Deschout, H; Scarselli, M; Radenovic, A

    2014-10-01

    Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.

  11. Interstellar molecules - Formation in solar nebulae

    NASA Technical Reports Server (NTRS)

    Anders, E.

    1973-01-01

    Herbig's (1970) hypothesis that solar nebulae might be the principal source of interstellar grains and molecules is investigated. The investigation includes the determination of physical and chemical conditions in the early solar system. The production of organic compounds in the solar nebula is studied, and the compounds in meteorites are compared with those obtained in Miller-Urey and Fischer-Tropsch-type (FTT) reactions, taking into consideration aliphatic hydrocarbons, aromatic hydrocarbons, purines, pyrimidines, amino acids, porphyrins, and aspects of carbon-isotope fractionation. It is found that FTT reactions account reasonably well for all well-established features of organic matter in meteorites investigated. The distribution of compounds produced by FTT reactions is compared with the distribution of interstellar molecules. Biological implications of the results are considered.

  12. Computer display and manipulation of biological molecules

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

    1978-01-01

    This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

  13. Multichannel quantum defect theory for polar molecules

    NASA Astrophysics Data System (ADS)

    Elfimov, Sergei V.; Dorofeev, Dmitrii L.; Zon, Boris A.

    2014-02-01

    Our work is devoted to developing a general approach for nonpenetrating Rydberg states of polar molecules. We propose a method to estimate the accuracy of calculation of their wave functions and quantum defects. Basing on this method we estimate the accuracy of Born-Oppenheimer (BO) and inverse Born-Oppenheimer (IBO) approximations for these states. This estimation enables us to determine the space and energy regions where BO and IBO approximations are valid. It depends on the interplay between l coupling (due to dipole potential of the core) and l uncoupling (due to rotation the core). Next we consider the intermediate region where both BO and IBO are not valid. For this intermediate region we propose a modification of Fano's multichannel quantum defect theory to match BO and IBO wave functions and show that it gives more reliable results. They are demonstrated on the example of SO molecule.

  14. Electron correlation dynamics in atoms and molecules.

    PubMed

    Nest, M; Ludwig, M; Ulusoy, I; Klamroth, T; Saalfrank, P

    2013-04-28

    In this paper, we present quantum dynamical calculations on electron correlation dynamics in atoms and molecules using explicitly time-dependent ab initio configuration interaction theory. The goals are (i) to show that in which cases it is possible to switch off the electronic correlation by ultrashort laser pulses, and (ii) to understand the temporal evolution and the time scale on which it reappears. We characterize the appearance of correlation through electron-electron scattering when starting from an uncorrelated state, and we identify pathways for the preparation of a Hartree-Fock state from the correlated, true ground state. Exemplary results for noble gases, alkaline earth elements, and selected molecules are provided. For Mg we show that the uncorrelated state can be prepared using a shaped ultrashort laser pulse.

  15. Photoluminescence of a quantum-dot molecule

    SciTech Connect

    Kruchinin, Stanislav Yu.; Rukhlenko, Ivan D.; Baimuratov, Anvar S.; Leonov, Mikhail Yu.; Turkov, Vadim K.; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun'ko, Yurii K.

    2015-01-07

    The coherent coupling of quantum dots is a sensitive indicator of the energy and phase relaxation processes taking place in the nanostructure components. We formulate a theory of low-temperature, stationary photoluminescence from a quantum-dot molecule composed of two spherical quantum dots whose electronic subsystems are resonantly coupled via the Coulomb interaction. We show that the coupling leads to the hybridization of the first excited states of the quantum dots, manifesting itself as a pair of photoluminescence peaks with intensities and spectral positions strongly dependent on the geometric, material, and relaxation parameters of the quantum-dot molecule. These parameters are explicitly contained in the analytical expression for the photoluminescence differential cross section derived in the paper. The developed theory and expression obtained are essential in interpreting and analyzing spectroscopic data on the secondary emission of coherently coupled quantum systems.

  16. Computational mass spectrometry for small molecules

    PubMed Central

    2013-01-01

    The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

  17. Photodestruction rates for cometary parent molecules

    NASA Astrophysics Data System (ADS)

    Crovisier, J.

    1994-02-01

    New evaluations of the photodestruction rates for several molecules of cometary interest are presented along with a critical comparison with other estimations from 1976 to 1993, and a summary of the need for future laboratory measurements. Photodestruction rates for a heliocentric distance of 1 AU (assuming the quiet Sun reference spectrum of Huebner and Carpenter) are tabulated for molecules from the water group, hydrocarbons, CO group, CHO species, nitrogen compounds, and sulfur compounds. Inspection of the table shows reasonable agreement between new and previously calculated photodestruction rates. Further work is needed on unstable species, photodissociation channel and quantum yields, temperature effects, kinematics and anistropic ejection of the fragments, and the effects of solar radiation field variations.

  18. Quantum interference of large organic molecules

    PubMed Central

    Gerlich, Stefan; Eibenberger, Sandra; Tomandl, Mathias; Nimmrichter, Stefan; Hornberger, Klaus; Fagan, Paul J.; Tüxen, Jens; Mayor, Marcel; Arndt, Markus

    2011-01-01

    The wave nature of matter is a key ingredient of quantum physics and yet it defies our classical intuition. First proposed by Louis de Broglie a century ago, it has since been confirmed with a variety of particles from electrons up to molecules. Here we demonstrate new high-contrast quantum experiments with large and massive tailor-made organic molecules in a near-field interferometer. Our experiments prove the quantum wave nature and delocalization of compounds composed of up to 430 atoms, with a maximal size of up to 60 Å, masses up to m=6,910 AMU and de Broglie wavelengths down to λdB=h/mv≃1 pm. We show that even complex systems, with more than 1,000 internal degrees of freedom, can be prepared in quantum states that are sufficiently well isolated from their environment to avoid decoherence and to show almost perfect coherence. PMID:21468015

  19. 'Single molecule': theory and experiments, an introduction.

    PubMed

    Riveline, Daniel

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins--molecular motors--have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'.

  20. 'Single molecule': theory and experiments, an introduction

    PubMed Central

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

  1. DNA, the central molecule of aging.

    PubMed

    Lenart, Peter; Krejci, Lumir

    2016-04-01

    Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.

  2. Single molecules as whispering galleries for electrons

    NASA Astrophysics Data System (ADS)

    Reecht, G.; Bulou, H.; Schull, G.; Scheurer, F.

    2016-04-01

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations.

  3. Circular Intensity Differential Scattering of chiral molecules

    SciTech Connect

    Bustamante, C.J.

    1980-12-01

    In this thesis a theory of the Circular Intensity Differential Scattering (CIDS) of chiral molecules as modelled by a helix oriented with respect to the direction of incidence of light is presented. It is shown that a necessary condition for the existence of CIDS is the presence of an asymmetric polarizability in the scatterer. The polarizability of the scatterer is assumed generally complex, so that both refractive and absorptive phenomena are taken into account.

  4. Collision integrals for isotopic hydrogen molecules.

    NASA Technical Reports Server (NTRS)

    Brown, N. J.; Munn, R. J.

    1972-01-01

    The study was undertaken to determine the effects of reduced mass and differences in asymmetry on the collision integrals and thermal diffusion factors of isotopic hydrogen systems. Each system selected for study consisted of two diatoms, one in the j = 0 rotation state and the other in the j = 1 state. The molecules interacted with a Lennard-Jones type potential modified to include angular terms. A set of cross sections and collision integrals were obtained for each system.

  5. Small Talk: Children's Everyday `Molecule' Ideas

    NASA Astrophysics Data System (ADS)

    Jakab, Cheryl

    2013-08-01

    This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

  6. Single Molecule Dynamics of Branched DNA Polymers

    NASA Astrophysics Data System (ADS)

    Mai, Danielle; Sing, Charles; Schroeder, Charles

    This work focuses on extending the field of single polymer dynamics to topologically complex polymers. Here, we report the direct observation of DNA-based branched polymers. Recently, we recently demonstrated a two-step synthesis method to generate star, H-shaped, and comb polymers for single molecule visualization. Following synthesis, we use single-color or dual-color single molecule fluorescence microscopy to directly visualize branched polymer dynamics in flow, in particular tracking side branches and backbones independently. In this way, our imaging method allows for characterization of molecular properties, including quantification of polymer contour length and branch distributions. Moving beyond characterization, we use molecular rheology and single molecule techniques to study the dynamics of single branched polymers in flow. Here, we utilize precision microfluidics to directly observe branched DNA polymer conformations during transient stretching, steady-state extension, and relaxation from high stretch. We specifically measure backbone end-to-end distance as a function of time. Experiments and Brownian dynamics simulations show that branched polymer relaxation is a strong function of the number of branches and position of branch points along the main chain backbone.

  7. The missing organic molecules on Mars.

    PubMed

    Benner, S A; Devine, K G; Matveeva, L N; Powell, D H

    2000-03-14

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  8. Model systems for single molecule polymer dynamics

    PubMed Central

    Latinwo, Folarin

    2012-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

  9. Single-Molecule Imaging of Cellular Signaling

    NASA Astrophysics Data System (ADS)

    De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

    Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

  10. (Aerodynamic focusing of particles and heavy molecules)

    SciTech Connect

    de la Mora, J.F.

    1990-01-08

    By accelerating a gas containing suspended particles or large molecules through a converging nozzle, the suspended species may be focused and therefore used to write fine lines on a surface. Our objective was to study the limits on how narrow this focal region could be as a function of particle size. We find that, for monodisperse particles with masses m{sub p} some 3.6 {times} 10{sup 5} times larger than the molecular mass m of the carrier gas (diameters above some 100{angstrom}), there is no fundamental obstacle to directly write submicron features. However, this conclusion has been verified experimentally only with particles larger than 0.1 {mu}m. Experimental, theoretical and numerical studies on the defocusing role of Brownian motion for very small particles or heavy molecules have shown that high resolution (purely aerodynamic) focusing is impossible with volatile molecules whose masses are typically smaller than 1000 Dalton. For these, the minimal focal diameter after optimization appears to be 5{radical}(m/m{sub p}) times the nozzle diameter d{sub n}. But combinations of focused lasers and aerodynamic focusing appear as promising for direct writing with molecular precursors. Theoretical and numerical schemes capable of predicting the evolution of the focusing beam, including Brownian motion effects, have been developed, although further numerical work would be desirable. 11 refs.

  11. Introduction to nucleocytoplasmic transport: molecules and mechanisms.

    PubMed

    Peters, Reiner

    2006-01-01

    Nucleocytoplasmic transport, the exchange of matter between nucleus and cytoplasm, plays a fundamental role in human and other eukaryotic cells, affecting almost every aspect of health and disease. The only gate for the transport of small and large molecules as well as supramolecular complexes between nucleus and cytoplasm is the nuclear pore complex (NPC). The NPC is not a normal membrane transport protein (transporter). Composed of 500 to 1000 peptide chains, the NPC features a mysterious functional duality. For most molecules, it constitutes a molecular sieve with a blurred cutoff at approx 10 nm, but for molecules binding to phenylalanine-glycine (FG) motifs, the NPC appears to be a channel of approx 50 nm diameter, permitting bidirectional translocation at high speed. To achieve this, the NPC cooperates with soluble factors, the nuclear transport receptors, which shuttle between nuclear contents and cytoplasm. Here, we provide a short introduction to nucleocytoplasmic transport by describing first the structure and composition of the nuclear pore complex. Then, mechanisms of nucleocytoplasmic transport are discussed. Finally, the still essentially unresolved mechanisms by which nuclear transport receptors and transport complexes are translocated through the nuclear pore complex are considered, and a novel translocation model is suggested.

  12. Evaluating enzymatic synthesis of small molecule drugs.

    PubMed

    Moura, Matthew; Finkle, Justin; Stainbrook, Sarah; Greene, Jennifer; Broadbelt, Linda J; Tyo, Keith E J

    2016-01-01

    There have been many achievements in applying biochemical synthetic routes to the synthesis of commodity chemicals. However, most of these endeavors have focused on optimizing and increasing the yields of naturally existing pathways. We sought to evaluate the potential for biosynthesis beyond the limits of known biochemistry towards the production of small molecule drugs that do not exist in nature. Because of the potential for improved yields compared to total synthesis, and therefore lower manufacturing costs, we focused on drugs for diseases endemic to many resource poor regions, like tuberculosis and HIV. Using generalized biochemical reaction rules, we were able to design biochemical pathways for the production of eight small molecule drugs or drug precursors and identify potential enzyme-substrate pairs for nearly every predicted reaction. All pathways begin from native metabolites, abrogating the need for specialized precursors. The simulated pathways showed several trends with the sequential ordering of reactions as well as the types of chemistries used. For some compounds, the main obstacles to finding feasible biochemical pathways were the lack of appropriate, natural starting compounds and a low diversity of biochemical coupling reactions necessary to synthesize molecules with larger molecular size.

  13. Fixman compensating potential for general branched molecules

    PubMed Central

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-01-01

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules. PMID:24387353

  14. The missing organic molecules on Mars

    PubMed Central

    Benner, Steven A.; Devine, Kevin G.; Matveeva, Lidia N.; Powell, David H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m2 of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life. PMID:10706606

  15. Fluorescence Polarization Assays in Small Molecule Screening

    PubMed Central

    Lea, Wendy A.; Simeonov, Anton

    2011-01-01

    Importance of the field Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field has been symbolized by the facile adoption of FP in high-throughput screening (HTS) and small molecule drug discovery of an increasing range of target classes. Areas covered in this review The article provides a brief overview on the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including G-protein coupled receptors (GPCRs), enzymes and protein-protein interactions (PPIs). The strengths and weaknesses of this method, practical considerations in assay design, novel applications, and future directions are also discussed. What the reader will gain The reader will be informed of the most recent advancements and future directions of FP application to small molecule screening. Take home message In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor binding studies. PMID:22328899

  16. Self and directed assembly: people and molecules

    PubMed Central

    2016-01-01

    Summary Self-assembly and directed-assembly are two very important aspects of supramolecular chemistry. As a young postgraduate student working in Canada with Tom Fyles my introduction to Supramolecular Chemistry was through the self-assembly of phospholipid membranes to form vesicles for which we were developing unimolecular and self-assembling transporter molecules. The next stage of my development as a scientist was in Japan with Seiji Shinkai where in a “Eureka” moment, the boronic acid templating unit (directed-assembly) of Wulff was combined with photoinduced electron transfer systems pioneered by De Silva. The result was a turn-on fluorescence sensor for saccharides; this simple result has continued to fuel my research to the present day. Throughout my career as well as assembling molecules, I have enjoyed bringing together researchers in order to develop collaborative networks. This is where molecules meet people resulting in assemblies worth more than the individual “molecule” or “researcher”. My role in developing networks with Japan was rewarded by the award of a Daiwa-Adrian Prize in 2013 and I was recently rewarded for developing networks with China with an Inaugural CASE Prize in 2015. PMID:27340435

  17. Abundance of complex organic molecules in comets

    NASA Astrophysics Data System (ADS)

    Biver, N.; Bockelée-Morvan, D.; Debout, V.; Crovisier, J.; Moreno, R.; Boissier, J.; Lis, D.; Colom, P.; Paubert, G.; Dello Russo, N.; Vervack, R.; Weaver, H.

    2014-07-01

    The IRAM-30m submillimetre radio telescope has now an improved sensitivity and versality thanks to its wide-band EMIR receivers and high-resolution FFT spectrometer. Since 2012, we have undertaken ~70 GHz wide spectral surveys in the 1-mm band in several comets: C/2009 P1 (Garradd), C/2011 L4 (PanSTARRS), C/2012 F6 (Lemmon), C/2012 S1 (ISON), and C/2013 R1 (Lovejoy). Since their discovery in comet C/1995 O1 (Hale-Bopp) in 1997 (Bockelée-Morvan et al. 2000, Crovisier et al. 2004a, 2004b), we have detected complex CHO(N)-molecules such as formic acid (HCOOH), formamide (NH_2CHO), acetaldehyde (CH_3CHO), and ethylene glycol ((CH_2OH)_2) in several other comets. HCOOH has now been detected in 6 other comets since 2004, and formamide, ethylene glycol, and acetaldehyde were re-detected for the first time in comets Lemmon or Lovejoy in 2013 (Biver et al. 2014). We will present the abundances relative to water we derive for these species, and the sensitive upper limits we obtain for other complex CHO-bearing molecules. We will discuss the implication of these findings on the origin of cometary material in comparison with observations of such molecules in the interstellar medium.

  18. Transport Fluctuations in Metal-Molecule Junctions

    NASA Astrophysics Data System (ADS)

    Malen, Jonathan; Baheti, Kanhayalal; Doak, Peter; Segalman, Rachel; Majumdar, Arun

    2008-03-01

    Thermopower of metal-molecule junctions is an alternative transport characteristic to conductance that can be experimentally measured. A scanning tunneling microscope break junction was used to measure the thermopower of such molecular junctions. Temperature bias applied between gold contacts across the bridging molecules generates a thermoelectric voltage. Hitherto, the statistical analysis of the data from both thermopower and conductance measurements has focused on the histogram peaks rather than the spread of the data. We find that the full width half maximums (FWHM) of the voltage histograms are finite at zero temperature bias and increase in proportion to the temperature bias. Johnson Noise is the most likely cause of the zero bias FWHM, and its magnitude is thereby related to the junction conductance. For 1,4,Benzenedithiol (BDT) the junction conductance associated with the zero bias FWHM is 0.02G0, in close agreement with prior conductance measurements of BDT. The dependence of FWHM on temperature bias may provide further insight to the origin of stochastic fluctuations in metal molecule junctions.

  19. The missing organic molecules on Mars

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Devine, K. G.; Matveeva, L. N.; Powell, D. H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  20. Electron attachment to the phthalide molecule

    SciTech Connect

    Asfandiarov, N. L.; Pshenichnyuk, S. A.; Vorob’ev, A. S.; Nafikova, E. P.; Lachinov, A. N.; Kraikin, V. A.; Modelli, A.

    2015-05-07

    Phthalide, the simplest chain of conductive polymer thin film, was investigated by means of Electron Transmission Spectroscopy, Negative Ion Mass Spectrometry, and density functional theory quantum chemistry. It has been found that formation of gas-phase long-lived molecular anions of phthalide around 0.7 eV takes place through cleavage of a C–O bond of the pentacyclic ring of the parent molecular anion to give a vibrationally excited (electronically more stable) open-ring molecular anion. The energy of the transition state for ring opening of the parent negative ion is calculated to be 0.65 eV above the neutral ground state of the molecule. The energy (2.64 eV) evaluated for the corresponding transition state in the neutral molecule is much higher, so that the process of electron detachment from the anion must lead to a neutral molecule with its initial pentacyclic structure. The average lifetime of the molecular negative ions formed at an electron energy of 0.75 eV and 80 °C is measured to be about 100 μs. The known switching effect of thin phthalide films could stem from the presence of a similar open/closed transition state also in the polymer.

  1. Origins of the handedness of biological molecules.

    PubMed

    Mason, S F

    1991-01-01

    Pasteur (1860) showed that many organic molecules form enantiomeric pairs with non-superposable mirror-image shapes, characterized by their oppositely signed optical rotation but otherwise apparently identical. Equal numbers of left-handed and right-handed molecules resulted from laboratory synthesis, whereas biosynthetic processes afforded only one of the two enantiomers, leading Pasteur to conclude that biosynthesis involves a chiral force. Fischer demonstrated (1890-1919) that functional biomolecules are composed specifically of the D-sugars and the L-amino acids and that the laboratory synthetic reactions of such molecules propagate with chiral stereoselectivity. Given a primordial enantiomer, biomolecular homochirality follows without the intervention of a chiral natural force, except prebiotically. Chiral forces known at the time were found to be even handed on a time and space average, exemplifying parity conservation (1927). The weak nuclear force, shown to violate parity (1956), was unified with electro-magnetism in the electroweak force (1970). Ab initio estimations including the chiral electroweak force indicate that the L-amino acids and the D-sugars are more stable than the corresponding enantiomers. The small energy difference between these enantiomeric pairs, with Darwinian reaction kinetics in a flow reactor, account for the choice of biomolecular handedness made when life began.

  2. Signaling Molecules: Hydrogen Sulfide and Polysulfide

    PubMed Central

    2015-01-01

    Abstract Significance: Hydrogen sulfide (H2S) has been recognized as a signaling molecule as well as a cytoprotectant. It modulates neurotransmission, regulates vascular tone, and protects various tissues and organs, including neurons, the heart, and kidneys, from oxidative stress and ischemia-reperfusion injury. H2S is produced from l-cysteine by cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3MST) along with cysteine aminotransferase. Recent Advances: In addition to these enzymes, we recently identified a novel pathway to produce H2S from d-cysteine, which involves d-amino acid oxidase (DAO) along with 3MST. These enzymes are localized in the cytoplasm, mitochondria, and peroxisomes. However, some enzymes translocate to organelles under specific conditions. Moreover, H2S-derived potential signaling molecules such as polysulfides and HSNO have been identified. Critical Issues: The physiological stimulations, which trigger the production of H2S and its derivatives and maintain their local levels, remain unclear. Future Directions: Understanding the regulation of the H2S production and H2S-derived signaling molecules and the specific stimuli that induce their release will provide new insights into the biology of H2S and therapeutic development in diseases involving these substances. Antioxid. Redox Signal. 22, 362–376. PMID:24800864

  3. Dissociative excitation study of iron pentacarbonyl molecule

    NASA Astrophysics Data System (ADS)

    Ribar, Anita; Danko, Marián; Országh, Juraj; Ferreira da Silva, Filipe; Utke, Ivo; Matejčík, Štefan

    2015-04-01

    The processes of dissociative excitation (DE) and dissociative ionisation with excitation (DIE) of iron pentacarbonyl, Fe(CO)5, have been studied using a crossed electron-molecule beam experimental apparatus (Electron Induced Fluorescence Apparatus, EIFA). Using EIFA we were able to record the emission spectrum of the molecule in the UV-VIS range, as well as the photon efficiency curves initiated by electron impact. The emission spectrum of Fe(CO)5 initiated by impact of 50 eV electrons was recorded in the spectral range between 200 nm and 470 nm. It shows a high density of emission lines and bands (mainly iron lines and carbonyl bands). Additionally, we have measured photon efficiency curves (PECs) as a function of the electron impact energy for several lines and bands. On the basis of the PECs we have discussed the reaction mechanism and the energetics of the reactions associated with the DE and DIE processes. Contribution to the Topical Issue "Elementary Processes with Atoms and Molecules in Isolated and Aggregated States", edited by Friedrich Aumayr, Bratislav Marinkovic, Štefan Matejčík, John Tanis and Kurt H. Becker.

  4. Rydberg States of Atoms and Molecules

    NASA Astrophysics Data System (ADS)

    Stebbings, R. F.; Dunning, F. B.

    2011-03-01

    List of contributors; Preface; 1. Rydberg atoms in astrophysics A. Dalgarno; 2. Theoretical studies of hydrogen Rydberg atoms in electric fields R. J. Damburg and V. V. Kolosov; 3. Rydberg atoms in strong fields D. Kleppner, Michael G. Littman and Myron L. Zimmerman; 4. Spectroscopy of one- and two-electron Rydberg atoms C. Fabre and S. Haroche; 5. Interaction of Rydberg atoms with blackbody radiation T. F. Gallagher; 6. Theoretical approaches to low-energy collisions of Rydberg atoms with atoms and ions A. P. Hickman, R. E. Olson and J. Pascale; 7. Experimental studies of the interaction of Rydberg atoms with atomic species at thermal energies F. Gounand and J. Berlande; 8. Theoretical studies of collisions of Rydberg atoms with molecules Michio Matsuzawa; 9. Experimental studies of thermal-energy collisions of Rydberg atoms with molecules F. B. Dunning and R. F. Stebbings; 10. High-Rydberg molecules Robert S. Freund; 11. Theory of Rydberg collisions with electrons, ions and neutrals M. R. Flannery; 12. Experimental studies of the interactions of Rydberg atoms with charged particles J. -F. Delpech; 13. Rydberg studies using fast beams Peter M. Koch; Index.

  5. Electrophoresis of Large DNA Molecules in Microcontractions

    NASA Astrophysics Data System (ADS)

    Doyle, Patrick; Randall, Greg; Kim, Ju Min

    2006-03-01

    The ability to controllably position and stretch large DNA molecules in a microfluidic format is important for gene mapping technologies such as Direct Linear Analysis (DLA). Current technologies developed for DLA use controlled hydrodynamic flows created in a microfluidic device. The downside to this approach is that the imposition of the no-slip condition at the channel walls generates vorticity which can lead to DNA chain tumbling and incomplete stretching. We have recently shown that electric field gradients can be readily generated in a microfluidic device and the resulting field is purely elongational. We present here single molecule studies of DNA molecules driven by an electric field through a microfabricated contraction. Analogous to the hydrodynamic deformation of DNA, we can define an electrophoretic Deborah number (De) for our problem. We will discuss the effectiveness of the device to fully stretch DNA as a function of De and compare to stretching achieved in hydrodynamic flows. A detailed analysis of molecular stretching and the role of a non-homogeneous electric field will be discussed.

  6. Classification models for safe drug molecules.

    PubMed

    Madan, A K; Bajaj, Sanjay; Dureja, Harish

    2013-01-01

    Frequent failure of drug candidates during development stages remains the major deterrent for an early introduction of new drug molecules. The drug toxicity is the major cause of expensive late-stage development failures. An early identification/optimization of the most favorable molecule will naturally save considerable cost, time, human efforts and minimize animal sacrifice. (Quantitative) Structure Activity Relationships [(Q)SARs] represent statistically derived predictive models correlating biological activity (including desirable therapeutic effect and undesirable side effects) of chemicals (drugs/toxicants/environmental pollutants) with molecular descriptors and/or properties. (Q)SAR models which categorize the available data into two or more groups/classes are known as classification models. Numerous techniques of diverse nature are being presently employed for development of classification models. Though there is an increasing use of classification models for prediction of either biological activity or toxicity, the future trend will naturally be towards the development of classification models capable of simultaneous prediction of biological activity, toxicity, and pharmacokinetic parameters so as to accelerate development of bioavailable safe drug molecules. PMID:23086839

  7. MONA – Interactive manipulation of molecule collections

    PubMed Central

    2013-01-01

    Working with small‐molecule datasets is a routine task for cheminformaticians and chemists. The analysis and comparison of vendor catalogues and the compilation of promising candidates as starting points for screening campaigns are but a few very common applications. The workflows applied for this purpose usually consist of multiple basic cheminformatics tasks such as checking for duplicates or filtering by physico‐chemical properties. Pipelining tools allow to create and change such workflows without much effort, but usually do not support interventions once the pipeline has been started. In many contexts, however, the best suited workflow is not known in advance, thus making it necessary to take the results of the previous steps into consideration before proceeding. To support intuition‐driven processing of compound collections, we developed MONA, an interactive tool that has been designed to prepare and visualize large small‐molecule datasets. Using an SQL database common cheminformatics tasks such as analysis and filtering can be performed interactively with various methods for visual support. Great care was taken in creating a simple, intuitive user interface which can be instantly used without any setup steps. MONA combines the interactivity of molecule database systems with the simplicity of pipelining tools, thus enabling the case‐to‐case application of chemistry expert knowledge. The current version is available free of charge for academic use and can be downloaded at http://www.zbh.uni‐hamburg.de/mona. PMID:23985157

  8. Programs To Aid FORTRAN Programming

    NASA Technical Reports Server (NTRS)

    Ragosta, Arthur E.

    1987-01-01

    Program-development time decreased while program quality increased. FORTRAN Programming Tools are series of programming tools used to support development and maintenance of FORTRAN 77 source codes. Included are debugging aid, central-processing-unit time-monitoring program, source-code maintenance aids, print utilities, and library of useful, well-documented programs. Tools assist in reducing development time and encouraging high-quality programming. Although intended primarily for FORTRAN programmers, some tools used on data files and other programming languages. Written in FORTRAN 77.

  9. Impact of Oxidative Stress in Fetal Programming

    PubMed Central

    Thompson, Loren P.; Al-Hasan, Yazan

    2012-01-01

    Intrauterine stress induces increased risk of adult disease through fetal programming mechanisms. Oxidative stress can be generated by several conditions, such as, prenatal hypoxia, maternal under- and overnutrition, and excessive glucocorticoid exposure. The role of oxidant molecules as signaling factors in fetal programming via epigenetic mechanisms is discussed. By linking oxidative stress with dysregulation of specific target genes, we may be able to develop therapeutic strategies that protect against organ dysfunction in the programmed offspring. PMID:22848830

  10. Direct patterning of rhodamine 6G molecules on mica by dip-pen nanolithography [rapid communication

    NASA Astrophysics Data System (ADS)

    Zhou, Hualan; Li, Zhuang; Wu, Aiguo; Wei, Gang; Liu, Zhiguo

    2004-09-01

    Dip-pen nanolithography (DPN) has been developed to pattern monolayer film of various molecules on suitable substrate through the controlled movement of ink-coated atomic force microscopy (AFM) tip, which makes DPN a potentially powerful tool for making the functional nanoscale devices. In this paper, the direct patterning of rhodamine 6G on mica by dip-pen nanolithography was demonstrated. R6G features patterned on the mica was successfully achieved with different tip movement which can be programmed by Nanoscript™ language. From the AFM image of R6G patterns, we know that R6G molecule is flatly binding to the mica surface through electrostatic interaction, thus stable R6G nanostructures could be formed on mica. The influence of translation speed and contact time on DPN was discussed. The method can be extended to direct patterning of many other organic molecules, and should open many opportunities for miniaturized optical device and site-specific biological staining.

  11. Switching Off Key Signaling Survival Molecules to Switch On the Resolution of Inflammation

    PubMed Central

    Perez, Denise Alves; Athayde, Rayssa Maciel; Reis, Alesandra Corte; Teixeira, Mauro Martins; Sousa, Lirlândia Pires; Pinho, Vanessa

    2014-01-01

    Inflammation is a physiological response of the immune system to injury or infection but may become chronic. In general, inflammation is self-limiting and resolves by activating a termination program named resolution of inflammation. It has been argued that unresolved inflammation may be the basis of a variety of chronic inflammatory diseases. Resolution of inflammation is an active process that is fine-tuned by the production of proresolving mediators and the shutdown of intracellular signaling molecules associated with cytokine production and leukocyte survival. Apoptosis of leukocytes (especially granulocytes) is a key element in the resolution of inflammation and several signaling molecules are thought to be involved in this process. Here, we explore key signaling molecules and some mediators that are crucial regulators of leukocyte survival in vivo and that may be targeted for therapeutic purposes in the context of chronic inflammatory diseases. PMID:25136148

  12. Complex molecules in galactic dust cores: Biologically interesting molecules and dust chemistry

    NASA Astrophysics Data System (ADS)

    Liu, Shen-Yuan

    2000-06-01

    The astronomical study of molecules has been an essential research field since the development of radio astronomy. Presently nearly 120 molecules have been identified in interstellar and circumstellar environments. The complexity of molecular species, and particularly organic molecules, that can be synthesized in the interstellar medium (ISM) leads to one interesting and important subfield in interstellar molecular studies, namely, the search and study for molecules of possible biological interest. Observationally, complex and most saturated molecules are observed exclusively toward compact hot, dense regions, often called ``hot cores'', in molecular clouds. To account for the observed amount of saturated organic molecules, interstellar dust particles play an important role. It has often been suggested that solid state reactions on grain surfaces provide an efficient way to synthesis saturated organic molecules. The objective of this study is to obtain observational data on biologically interesting molecules and to study important complex interstellar molecules. Since hot molecular cores are inherently compact, interferometric observations are therefore an ideal approach to study these sources. All our observations were all made with the Berkeley-Illinois-Maryland-Association (BIMA) Array. We conducted the first survey of formic acid (HCOOH) with an interferometric array, and identified at least three sources. HCOOH is found with column densities above 1015 cm-2 in these sources. The correlation between HCOOH and HCOOCH3 emission implies a surface chemistry origin of HCOOH. Details of the results are given in Chapter 2. Meanwhile, we continued to search for molecules of biological interest, namely urea, acetic acid, and glycine. In Chapter 3, the results of column density limits set by our observations are discussed. We have also investigated properties of individual hot molecular cores. It is very important to obtain the physical and chemical properties of these

  13. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

  14. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  15. Single Molecule Studies on Dynamics in Liquid Crystals

    PubMed Central

    Täuber, Daniela; von Borczyskowski, Christian

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

  16. Contacting organic molecules by soft methods: towards molecule-based electronic devices.

    PubMed

    Haick, Hossam; Cahen, David

    2008-03-01

    Can we put organic molecules to use as electronic components? The answer to this question is to no small degree limited by the ability to contact them electrically without damaging the molecules. In this Account, we present some of the methods for contacting molecules that do not or minimally damage them and that allow formation of electronic junctions that can become compatible with electronics from the submicrometer to the macroscale. In "Linnaean" fashion, we have grouped contacting methods according to the following main criteria: (a) is a chemical bond is required between contact and molecule, and (b) is the contact "ready-made", that is, preformed, or prepared in situ? Contacting methods that, so far, seem to require a chemical bond include spin-coating a conductive polymer and transfer printing. In the latter, a metallic pattern on an elastomeric polymer is mechanically transferred to molecules with an exposed terminal group that can react chemically with the metal. These methods allow one to define structures from several tens of nanometers size upwards and to fabricate devices on flexible substrates, which is very difficult by conventional techniques. However, the requirement for bifunctionality severely restricts the type of molecules that can be used and can complicate their self-assembly into monolayers. Methods that rely on prior formation of the contact pad are represented by two approaches: (a) use of a liquid metal as electrode (e.g., Hg, Ga, various alloys), where molecules can be adsorbed on the liquid metal and the molecularly modified drop is brought into contact with the second electrode, the molecules can be adsorbed on the second electrode and then the liquid metal brought into contact with them, or bilayers are used, with a layer on both the metal and the second electrode and (b) use of preformed metal pads from a solid substrate and subsequent pad deposition on the molecules with the help of a liquid. These methods allow formation of

  17. Oligomer Molecules for Efficient Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhan, Xiaowei

    2016-02-16

    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability

  18. Oligomer Molecules for Efficient Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhan, Xiaowei

    2016-02-16

    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability

  19. Robot programming

    SciTech Connect

    Lozano-Perez, T.

    1982-12-01

    The industrial robot's principal advantage over traditional automation is programmability. Robots can perform arbitrary sequences of pre-stored motions or of motions computed as functions of sensory input. This paper reviews requirements for and developments in robot programming systems. The key requirements for robot programming systems examined in the paper are in the areas of sensing, world modeling, motion specification, flow of control, and programming support. Existing and proposed robot programming systems fall into three broad categories: guiding systems in which the user leads a robot through the motions to be performed, robot-level programming systems in which the user writes a computer program specifying motion and sensing, and task-level programming systems in which the user writes a computer program specifying motion and sensing, and task-level programming systems in which the user specifies operations by their desired effect on objects. A representative sample of systems in each of these categories is surveyed in the paper.

  20. Intercellular adhesion molecule 1 is the major adhesion molecule expressed during schistosome granuloma formation.

    PubMed Central

    Ritter, D M; McKerrow, J H

    1996-01-01

    Endothelial cell adhesion molecules play a key role in inflammation by initiating leukocyte trafficking. One of the most complex inflammatory responses is the formation of a cellular granuloma. Expression of adhesion molecules during granuloma formation was investigated by using the murine host reaction to schistosome parasite eggs deposited in the liver as a model. By both immunohistochemistry and lymphocyte adhesion assays, the predominant interaction identified was between intercellular adhesion molecule 1 (ICAM-1) and its cognate integrin, leukocyte functional antigen 1 (LFA-1). ICAM-1 expression on sinusoidal endothelium was induced when eggs were first deposited in the liver, peaked in parallel with granuloma size, and was downregulated with modulation of the granuloma. Polyacrylamide beads coated with soluble parasite egg antigens could induce ICAM-1 expression on endothelial cells in vitro only in the presence of tumor necrosis factor alpha, a cytokine previously shown to be key to granuloma formation. A role for ICAM-1 in recruiting lymphocytes to the hepatic granuloma was also supported by the observation that lymphocytes preincubated with anti-LFA-1 antibody did not bind to granulomas in tissue sections. While ICAM-1 is the predominant adhesion molecule in schistosome egg granuloma formation in wild-type mice, when the ICAM-1 gene is knocked out, vascular cell adhesion molecule 1 is upregulated and granuloma formation is preserved. PMID:8890229

  1. Single-Molecule Enzymatic Conformational Dynamics: Spilling Out the Product Molecules

    PubMed Central

    2015-01-01

    Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses. PMID:25025461

  2. The Multiphoton Multiple Ionization of Molecules.

    NASA Astrophysics Data System (ADS)

    Hatherly, P. A.

    Available from UMI in association with The British Library. The multiphoton multiple ionization of a number of molecular systems has been studied using the picosecond laser facility at the Rutherford Appleton Laboratory. The laser produced 0.6ps pulses at 600nm, and 6ps at 248nm when used in conjunction with an excimer laser. The focused intensity in each case was >=q10 ^{15}W/cm^2 . A time of flight mass spectrometer designed and built at Reading University was capable of ion kinetic energy measurement, permitting the molecular dissociation dynamics to be investigated. One major question approached concerned the mode of multiphoton ionization of xenon. Specifically, does the ionization proceed in a sequential (single electron) or a collective (many electron) manner? To this end, experiments were performed with the isoelectronic molecule hydrogen iodide. The results, which were interpreted in terms of a Coulomb explosion mechanism, demonstrated the process to be sequential, rather than collective. Similar experiments on the isoelectronic pair, nitrogen and carbon monoxide tended to confirm this conclusion. These molecules were also studied at a number of laser wavelengths and pulse widths. Although the wavelength was found to have a minimal effect, the pulse width was of great importance. The results for hydrogen and deuterium contrasted with these results for other molecules, in that the energies could not be reconciled with a Coulomb explosion mechanism. Rather, dissociative autoionization or neutral dissociation followed by ionization of the atoms were considered to be the dominant processes. Finally, the existence of high energy protons (~eq100eV) from residual hydrocarbons in the vacuum chamber lead to a study of the alkanes from butane to dodecane. At 600nm, 0.6ps pulse width, the fragment energies were found to vary linearly with carbon chain length. At 248nm, 5ps though, only low energy protons were observed, independent of chain length.

  3. Femtosecond Isomerization Dynamics in the Ethylene Molecule

    NASA Astrophysics Data System (ADS)

    Belkacem, Ali

    2009-05-01

    The ethylene molecule plays a fundamental and prototypical role for the understanding of photo-isomerizaton processes and particularly for ultrafast energy conversion through nonadiabatic transitions and state crossing via conical intersections. We have developed a high power femtosecond laser based pump-probe system to study femtosecond isomerization dynamics in various model molecules. By focusing 25-mJ laser pulses into a 5-cm-long xenon-filled gas cell, we can deliver about 10^9 photons per harmonic per pulse onto a target gas, with the photons ranging in energy from 8 to 40 eV. In this talk I will present the results of our studies of the dynamics in the excited ethylene cation (C2H4^+) using a high intensity high harmonic source. The dynamics in the excited ethylene cation leads, among other channels, to isomerization to the ethyledene configuration (CH3CH^+), which is predicted to be a transient configuration for electronic relaxation. With an intense femtosecond EUV pulse as pump, and a NIR (near infra-red) pulse as probe, we measure a time scale of 45±10 fs for formation of the transient ethylidene configuration (lifetime of 60±15 fs ) through detection of the NIR-induced fragmentation to CH3^+ and CH^+. Also, a H2-stretch transient configuration (believed to succeed ethylidene), yielding H2^+, is found to be populated after 100±10 fs. These studies were also extended to excited state dynamics in the neutral ethylene using a recently developed split mirror technique enabling XUV pump - XUV probe capability. In order to achieve this we optimized our high harmonic system for high power in order to produce a very intense source of high harmonics that allows multiphoton (XUV) absorption by a single molecule. In particular, we were able to measure two-photon double-ionization of Ethelyne and argon and three-photon double ionization of neon.

  4. Raman scattering mediated by neighboring molecules

    NASA Astrophysics Data System (ADS)

    Williams, Mathew D.; Bradshaw, David S.; Andrews, David L.

    2016-05-01

    Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

  5. Raman scattering mediated by neighboring molecules.

    PubMed

    Williams, Mathew D; Bradshaw, David S; Andrews, David L

    2016-05-01

    Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

  6. A New Interstellar Cyclic Molecule, Ethylene Oxide

    NASA Astrophysics Data System (ADS)

    Dickens, J. E.; Irvine, W. M.; Ohishi, M.; Ikeda, M.; Ishikawa, S.; Nummelin, A.; Hjalmarson, A.

    1997-12-01

    Ethylene oxide (c-C2H4O) is only the fourth known ring molecule identified in the interstellar medium, detected in the Galactic Center cloud SgrB2(N) by Dickens et al. (1997). It is the higher energy isomer of both the more familiar interstellar species acetaldehyde (CH3CHO) and the as yet undetected molecule vinyl alcohol (CH2CHOH). Dickens et al. (1997) reported a c-C2H4O molecular column density about an order of magnitude less than that reported for CH3CHO in SgrB2(N). This is a factor of 200 larger than the predictions of the new standard gas phase chemistry model of Lee, Bettens, and Herbst (1996), suggesting that the formation of c-C2H4O may be related to molecular formation on interstellar grains. We present observations of the c-C2H4O to CH3CHO abundance ratio in 5 additional molecular clouds. The data were taken in October 1997 with the Swedish-European Submillimeter Telescope in Chile. The confirmation of ethylene oxide in molecular clouds provides an appealing scenario for the first link in the chain of reactions leading to the origin of life, since it has been suggested as a possible pathway to the formation of the related cyclic molecule oxiranecarbonitrile (c-C3H3NO; cf., Dickens et al. 1996), a precursor to the synthesis of sugar phosphates which comprise the backbone of our molecular genetic structure. References: Dickens, J.E., Irvine, W.M., Ohishi, M., Ikeda, M., Ishikawa, S., Nummelin, A., and Hjalmarson, A. 1997, Astrophys. J., 489 (in press). Dickens, J.E. et al. 1996, Orig. Life Evol. Biosphere, 26, 97. Lee, H.-H., Bettens, R.P.A., and Herbst, E. 1996, Astron. Astrophys. Supp., 119, 111.

  7. Raman scattering mediated by neighboring molecules.

    PubMed

    Williams, Mathew D; Bradshaw, David S; Andrews, David L

    2016-05-01

    Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process. PMID:27155637

  8. Studies of atmospheric molecules by multiphoton spectroscopy

    NASA Astrophysics Data System (ADS)

    Johnson, P. M.

    1990-12-01

    Resonance ionization processes can play an important role in understanding molecules important in combustion processes. They are a reflection of the dynamic as well as the static properties of atomic and molecular species. Due to the sequential or quasisequential nature of photon absorption in resonant multiphoton events, the lifetimes of the intermediate states play an essential role in the overall cross-sections if they are short enough to be competitive with subsequent photon interactions. In molecules, this is particularly important because there are many dissociative and other radiationless pathways which can contribute to a competitive channel. Under those conditions it should be possible to obtain information about the nature of the dynamics of the intermediate state from the multiphoton ionization process. This will involve looking at not only the ionization cross-section but also other observables such as the kinetic energy of the ejected electrons and possibly the distribution of fragment ions produced in the ionization event. Whether the ionization amplitude is affected or not, the time scales of the dynamic events which alter the ionization path can vary over a large range from the femtoseconds of dissociation to the microseconds of some radiationless transitions in large molecules. When the competing channel has a time scale shorter than the laser pulse length, the kinetics of the ionization are intimately tied into the precise nature of the laser pulse. For time scales longer than the laser pulse, pump-probe ionization schemes in which one laser prepares a state while another does the ionization provide a particularly simple method for investigating the dynamics of the intermediate state. Here the author discusses examples from each of these regimes. CO2 and pyrazine are examined.

  9. Observation of ultralong range Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Shaffer, James

    2009-05-01

    In 1934, Enrico Fermi described the scattering of a low energy electron from a neutral atom by using the ideas of scattering length and pseudopotential. Although the long range potential for an electron-atom interaction is always attractive, Fermi realized that the s-wave scattering length that characterizes the low energy collision can be either positive or negative. For a positive scattering length, the wavefunction of the electron is shifted away from the atom, the electron is repelled; whereas for a negative scattering length, the wavefunction of the electron is shifted to the atom, the electron is attracted. Based on Fermi's approach, Greene and co-workers predicted a novel molecular binding mechanism where a low energy Rydberg electron is scattered from a ground state atom in the case of negative scattering length. In this situation, the interaction between the electron and ground state atom is attractive and results in the formation of bound states of the ground state atom and the Rydberg atom. Molecules bound by electron scattering can have an internuclear separation of several thousand Bohr radii and are very different from molecules formed by 2 Rydberg atoms where the binding is the result of multipolar forces between the atoms alone. In this talk, we present experimental data on the observation of these exotic molecular states for Rb Rydberg atoms in S states for principal quantum numbers n between 34 and 40. The spectroscopic results for the vibrational ground and first excited state of the dimer Rb(5S)-Rb(nS) are presented and the s-wave scattering length for electron-Rb(5S) scattering in the low energy regime where the kinetic energy is less than 100 meV. Finally, we discuss and present data on the lifetimes and decay mechanisms of these molecules in a magnetic trap.

  10. Assembling molecular electronic junctions one molecule at a time.

    PubMed

    Bonifas, Andrew P; McCreery, Richard L

    2011-11-01

    Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (β) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules.

  11. Bringing Molecules Back into Molecular Evolution

    PubMed Central

    Wilke, Claus O.

    2012-01-01

    Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events. PMID:22761562

  12. Configurations of the amphiphilic molecules in micelles

    SciTech Connect

    Dill, K.A.

    1982-04-29

    Several theoretic models aim to account for the properties of micelles in terms of the configurations of the constituent amphiphilic chain molecules. Recent /sup 13/C NMR measurement of one property of the configuration distribution of the the hydrocarbon chain segments allows critical evaluation of these theories. It is concluded that the interphase and singly-bent chain theories, which fully account for chain continuity and for intermolecular constraints imposed by hydrophobic and steric forces, give a more satisfactory description of micellar molecular organization than models in which chains are ordered and radially aligned, or in which they have the complete disorder characteristic of an amorphous hydrocarbon liquid.

  13. Indirect observation of unobservable interstellar molecules

    NASA Technical Reports Server (NTRS)

    Herbst, E.; Green, S.; Thaddeus, P.; Klemperer, W.

    1977-01-01

    It is suggested that the abundances of neutral non-polar interstellar molecules unobservable by radio astronomy can be systematically determined by radio observation of the protonated ions. As an example, observed N2H(+) column densities are analyzed to infer molecular nitrogen abundances in dense interstellar clouds. The chemistries and expected densities of the protonated ions of O2, C2, CO2, C2H2 and CH4 are then discussed. Microwave transition frequencies fo HCO2(+) and C2H3(+) are estimated, and a preliminary astronomical search for HCO2(+) is described.

  14. Sugar amino acids in designing new molecules.

    PubMed

    Chakraborty, Tushar Kanti; Srinivasu, Pothukanuri; Tapadar, Subhasish; Mohan, Bajjuri Krishna

    2005-03-01

    Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create 'nature-like' and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature's molecular arsenal. This article describes some of our works on various sugar amino acids and many other related building blocks, like furan amino acids, pyrrole amino acids etc. used in wide-ranging peptidomimetic studies. PMID:16133829

  15. Kondo tunneling through real and artificial molecules.

    PubMed

    Kikoin, K; Avishai, Y

    2001-03-01

    When an asymmetric double dot is hybridized with itinerant electrons, its singlet ground state and lowly excited triplet state cross, leading to a competition between the Zhang-Rice mechanism of singlet-triplet splitting in a confined cluster and the Kondo effect (which accompanies the tunneling through quantum dot under a Coulomb blockade restriction). The rich physics of an underscreened S = 1 Kondo impurity in the presence of low-lying triplet-singlet excitations is exposed and estimates of the magnetic susceptibility and the electric conductance are presented, together with applications for molecule chemisorption on metallic substrates.

  16. Non-equilibrium processes in interstellar molecules

    NASA Technical Reports Server (NTRS)

    Strelnitskiy, V. S.

    1979-01-01

    The types of nonequilibrium emission and absorption by interstellar molecules are summarized. The observed brightness emission temperatures of compact OH and H2O sources are discussed using the concept of maser amplification. A single thermodynamic approach was used in which masers and anti-masers are considered as heat engines for the theoretical interpretation of the cosmic maser and anti-maser phenomena. The requirements for different models of pumping are formulated and a classification is suggested for the mechanisms of pumping, according to the source and discharge of energy.

  17. 1 mm ultrafast superconducting stripline molecule detector

    NASA Astrophysics Data System (ADS)

    Zen, N.; Casaburi, A.; Shiki, S.; Suzuki, K.; Ejrnaes, M.; Cristiano, R.; Ohkubo, M.

    2009-10-01

    Superconducting stripline detectors (SSLDs) are promising for detecting keV molecules at nanosecond response times and with mass-independent detection efficiency. However, a fast response time is incompatible with practical centimeter detector size. A parallel configuration of striplines provides a means to address this problem. Experimental results and simulation for promisingly large 1-mm-square parallel niobium SSLDs show that nanosecond pulses are produced by superconducting-normal transition within only one of the parallel striplines instead of cascade switching of all the parallel striplines. Successful detection of a series of multimers of immunoglobulin G up to 584 kDa supports the mass-independent efficiency for mass spectrometry.

  18. Nonrelativistic Lamb shift for muonic molecules

    NASA Astrophysics Data System (ADS)

    Bukowski, Robert; Jeziorski, Bogumil

    1993-03-01

    A recently developed formula [R. Bukowski and B. Jeziorski, Phys. Rev. A46 (1992) 5437]. has been applied to estimate the soft-photon Lamb shift contribution to the energies of the muonic molecules ppμ, ddμ, ttμ, pdμ, ptμ and dtμ. The corresponding corrections to the dissociation energies for the excited P states of ddμ and dtμ have been found to be almost identical and equal to 0.048 meV. The magnitude of this stabilizing effect is too small to affect seriously the formation rates predictions.

  19. Identification of cell density signal molecule

    DOEpatents

    Schwarz, Richard I.

    1998-01-01

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS) between 25 and 35 kD, which is secreted by fibroblastic primary avian tendon cells in culture, and causes the cells to self-regulate their proliferation and the expression of differentiated function. It effects an increase of procollagen production in avian tendon cell cultures of ten fold while proliferation rates are decreased. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use.

  20. Molecular-beam spectroscopy of interhalogen molecules

    SciTech Connect

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.