Relevant bibliographies by topics / Molecular integrals

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Molecular integrals'

Author: Grafiati
Published: 4 June 2021
Last updated: 14 September 2024

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Molecular integrals.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Journal articles on the topic "Molecular integrals"

1

Matsuoka, Osamu. "Molecular integrals over Laguerre Gaussian-type functions of real spherical harmonics." Canadian Journal of Chemistry 70, no. 2 (February 1, 1992): 388–92. http://dx.doi.org/10.1139/v92-055.

Full text
Abstract:
Molecular integrals are formulated over the Laguerre Gaussian-type functions (LGTF) of real spherical harmonics. They include the overlap integrals and the energy integrals of kinetic, nuclear attraction, and electron repulsion. For the nuclear-attraction integrals the formulations based on the point as well as the Gaussian nuclear charge distribution models are presented. Integral formulas over the LGTFs of real spherical harmonics are found a little more complicated than those of the LGTFs of complex spherical harmonics due to the summations over magnetic quantum numbers. Keywords: molecular integral, Gaussian-type function, spherical harmonic, solid harmonic, Sonine polynomial.
APA, Harvard, Vancouver, ISO, and other styles
2

Barnett, Michael P. "Mathscape and molecular integrals." Journal of Symbolic Computation 42, no. 3 (March 2007): 265–89. http://dx.doi.org/10.1016/j.jsc.2006.07.002.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Dawass, Noura, Peter Krüger, Sondre K. Schnell, Othonas A. Moultos, Ioannis G. Economou, Thijs J. H. Vlugt, and Jean-Marc Simon. "Kirkwood-Buff Integrals Using Molecular Simulation: Estimation of Surface Effects." Nanomaterials 10, no. 4 (April 16, 2020): 771. http://dx.doi.org/10.3390/nano10040771.

Full text
Abstract:
Kirkwood-Buff (KB) integrals provide a connection between microscopic properties and thermodynamic properties of multicomponent fluids. The estimation of KB integrals using molecular simulations of finite systems requires accounting for finite size effects. In the small system method, properties of finite subvolumes with different sizes embedded in a larger volume can be used to extrapolate to macroscopic thermodynamic properties. KB integrals computed from small subvolumes scale with the inverse size of the system. This scaling was used to find KB integrals in the thermodynamic limit. To reduce numerical inaccuracies that arise from this extrapolation, alternative approaches were considered in this work. Three methods for computing KB integrals in the thermodynamic limit from information of radial distribution functions (RDFs) of finite systems were compared. These methods allowed for the computation of surface effects. KB integrals and surface terms in the thermodynamic limit were computed for Lennard–Jones (LJ) and Weeks–Chandler–Andersen (WCA) fluids. It was found that all three methods converge to the same value. The main differentiating factor was the speed of convergence with system size L. The method that required the smallest size was the one which exploited the scaling of the finite volume KB integral multiplied by L. The relationship between KB integrals and surface effects was studied for a range of densities.
APA, Harvard, Vancouver, ISO, and other styles
4

Chang, Chia-En, Michael J. Potter, and Michael K. Gilson. "Calculation of Molecular Configuration Integrals." Journal of Physical Chemistry B 110, no. 13 (April 2006): 7083. http://dx.doi.org/10.1021/jp061244u.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Chang, Chia-En, Michael J. Potter, and Michael K. Gilson. "Calculation of Molecular Configuration Integrals." Journal of Physical Chemistry B 107, no. 4 (January 2003): 1048–55. http://dx.doi.org/10.1021/jp027149c.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Barnett, Michael P. "Molecular integrals over slater orbitals." Chemical Physics Letters 166, no. 1 (February 1990): 65–70. http://dx.doi.org/10.1016/0009-2614(90)87051-r.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Barnett, Michael P. "Molecular integrals and information processing." International Journal of Quantum Chemistry 95, no. 6 (2003): 791–805. http://dx.doi.org/10.1002/qua.10614.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Rico, J. Fernández, R. López, and G. Ramírez. "Molecular integrals with Slater basis. III. Three‐center nuclear attraction integrals." Journal of Chemical Physics 94, no. 7 (April 1991): 5032–39. http://dx.doi.org/10.1063/1.460538.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Murphy, Kevin V., Justin M. Turney, and Henry F. Schaefer. "Student-Friendly Guide to Molecular Integrals." Journal of Chemical Education 95, no. 9 (July 19, 2018): 1572–78. http://dx.doi.org/10.1021/acs.jchemed.8b00255.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Fern�ndez Rico, J., R. L�pez, G. Ram�rez, and J. I. Fern�ndez-Alonso. "Auxiliary functions for Slater molecular integrals." Theoretica Chimica Acta 85, no. 1-3 (March 1993): 101–7. http://dx.doi.org/10.1007/bf01374580.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Molecular integrals"

1

Womack, James Christopher. "Evaluating many-electron molecular integrals for quantum chemistry." Thesis, University of Bristol, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.687429.

Full text
Abstract:
The evaluation of molecular integrals is a vital but computationally expensive part of electronic structure calculations. This computational expense is particularly problematic for the explicitly correlated methods, in which complicated and numerous integrals over more than two-electrons must be evaluated. The successful R12/F12 methods overcome this difficulty by decomposition of these many-electron integrals by means of approximate resolutions of the identity (RIs). To obtain accurate results with this approach, however, requires large auxiliary basis sets with high angular momentum functions. To address this issue, we present a new RI-free variant of MP2-F12 theory, which uses density fitting to approximate three-electron integrals, rather than RIs. This approach demonstrates improved convergence of calculated energies with respect to the size and maximum angular momentum of the auxiliary basis set compared to the standard RI-based approach. For the systems on which the method was tested, relatively small auxiliary basis sets were sufficient to reduce errors in the correlation energy to less than a millihartree. The software implementation of the three-electron integral types needed in the new MP2-F12 variant proved to be extremely time-consuming. This difficulty inspired us to develop "Intception", a code generator which generates code for molecular integral evaluation. Intception is capable of automatically implementing code for evaluating a wide range of molecular integral types, using a general theoretical framework based on Obara-Saika-type recurrence relations [1] . To flexibly express integral definitions for use in Intception, a new domain-specific language was created. Testing revealed that the generated code evaluated integrals to a high numerical accuracy and on a reasonable timescale, though somewhat slower than existing optimized implementations. A detailed analysis of the performance of the generated code was undertaken, which suggested some possible routes to improving the efficiency of the code.
APA, Harvard, Vancouver, ISO, and other styles
2

Jensen, Daniel S. "Real-Space Approach to Time Dependent Current Density Functional Theory." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2559.

Full text
Abstract:
A real-space time-domain calculation of the frequency-dependent dielectric constant of nonmetallic crystals is outlined and the integrals required for this calculation are computed. The outline is based on time dependent current density functional theory and is partially implemented in the ab initio density functional theory FIREBALL program. The addition of a vector potential to the Hamiltonian of the system is discussed as well as the need to include the current density in addition to the particle density. The derivation of gradient integrals within a localized atomic-like orbital basis is presented for use in constructing the current density. Due to the generality of the derivation we also give the derivation of the kinetic energy, dipole, and overlap interactions.
APA, Harvard, Vancouver, ISO, and other styles
3

Sturdy, Yvette Katherine. "Molecular simulation with path integral methods." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436950.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Righi, Assis Francisco Moro. "Calculo de orbitais moleculares na molecula LiH e no ion BeH+ com tratamento algebrico das integrais." reponame:Repositório Institucional da UFSC, 1998. http://repositorio.ufsc.br/xmlui/handle/123456789/77784.

Full text
Abstract:
Tese (doutorado) - Universidade Federal de Santa Catarina, Centro de Ciencias Fisicas e Matematicas
Made available in DSpace on 2012-10-17T07:28:34Z (GMT). No. of bitstreams: 0Bitstream added on 2016-01-09T00:26:07Z : No. of bitstreams: 1 109966.pdf: 2204184 bytes, checksum: 21712f4f2c8eabccd377dde54704284a (MD5)
Técnicas de computação algébrica são utilizadas na resolução de integrais que aparecem no estudo de moléculas diatômicas. Soluções analíticas são obtidas para integrais de um e de dois centros híbridas e de Coulomb com orbitais atômicos do tipo de Slater (STO). Tratamento semelhante é usado no estudo das integrais de troca. Usando estes resultados, propriedades eletrônicas, como distância internuclear de equilíbrio e momento de dipolo, do estado fundamental da molécula LiH e do íon BeH+ são investigadas fazendo-se um cálculo variacional com uma base de orbitais moleculares. O comportamento das cargas efetivas dos orbitais atômicos é estudado em função da distância internuclear. A influência de um campo elétrico externo bastante intenso na ligação química é um fenômeno pouco discutido teoricamente. Neste trabalho, o comportamento das curvas de energia potencial da molécula LiH e do íon BeH+ em campo externo uniforme também é investigado. Os efeitos na dissociação molecular são analisados.
APA, Harvard, Vancouver, ISO, and other styles
5

Newport, Thomas. "Tools and resources for molecular simulations of integral membrane proteins." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:b6dc3047-aaf4-4236-8266-7a885fecb5d9.

Full text
Abstract:
Integral Membrane Proteins (IMPs) are an important and scientifically interesting class of protein which span the lipid bilayer surrounding cells, cell compartments and many viruses. Molecular Dynamics (MD) simulation has revealed intimate and often highly specific relationships between membrane lipids and IMPs critical to many metabolic and signalling pathways. Meanwhile, the use of Coarse-Grained (CG) MD techniques has extended capabilities of biomolecular simulation to larger proteins over longer time periods. Several tools and resources for biomolecular simulations of IMPs are presented here, as well as two MD studies of specific IMPs. The previously developed MemProtMD pipeline automates the setup of MD simulations of IMPs; major extensions to this are presented here with the MemProtMD database and web server, automating the analysis of IMP simulations. The results of this can be viewed using the MemProtMD web server, an interactive, searchable online resource containing data from simulations of over 3000 experimentally determined IMP structures in explicit lipid bilayers. Using data from analysis of the entire MemProtMD database, MemProtMetrics has been developed to automate identification and orientation of IMP structures from Protein DataBank (PDB) depositions. This is shown to effectively predict membrane protein orientations seen in MD simulations. A tool for identification and classification of membrane lipids is also described, and used to identify over 500 IMPs structures with resolved lipids. CGMD simulations have also been used to assess dependence on side-chain ionisation state of interactions between lipids and two IMPs observed in mass spectrometry experiments. The simulations reveal similar trends to those seen in experiments. Finally, using multi-scale simulations, and through the development of a novel method for altering membrane composition in MD simulations, lipid-specific scramblase activity was shown for a novel structure of the TMEM16K scramblase IMP.
APA, Harvard, Vancouver, ISO, and other styles
6

Kasahara, Kento. "Integral Equation Theories of Diffusion and Solvation for Molecular Liquids." Kyoto University, 2018. http://hdl.handle.net/2433/232056.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Silveira, Rodrigo Leandro 1986. "Aspectos moleculares da degradação de biomassa lignocelulósica : dinâmica de enzimas e nanoarquitetura de paredes celulares de plantas." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/248864.

Full text
Abstract:
Orientador: Munir Salomão Skaf
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química
Made available in DSpace on 2018-08-25T19:29:24Z (GMT). No. of bitstreams: 1 Silveira_RodrigoLeandro_D.pdf: 21325666 bytes, checksum: e2332474509730ff297050a513a97a70 (MD5) Previous issue date: 2014
Resumo: A produção de bioetanol a partir da biomassa lignocelulósica integra processos físico-químicos e enzimáticos que comprometem sua viabilidade econômica. A biomassa possui uma estrutura recalcitrante composta de celulose, hemicelulose e lignina. Tal estrutura, bem como os mecanismos das enzimas, não são bem compreendidos. Nesta tese, simulações de dinâmica molecular e a teoria mecânico-estatística 3D-RISM foram utilizada para investigar aspectos moleculares da degradação de biomassa, incluindo: (1) dinâmica estrutural de celulases; (2) base molecular da termofilicidade de laminarinaes; (3) disrupção não-hidrolítica de biomassa por expansinas; (4) nanoarquitetura da parede ceular primária; e (5) forças termodinâmicas da parede celular secundária. No tópico (1), observou-se que a acessibilidade ao substrato em celulases pode ser modulada por alterações na estrutura primária, com consequências para a atividade enzimática. Observou-se também que a inibição por produto está relacionada a alterações conformacionais de resíduos próximos ao sítio de ligação. Adicionalmente, alterações na dinâmica intrínseca das enzimas ocorrem conforme a etapa do processo de hidrólise. No tópico (2), os resultados mostraram que a conformação do sítio de ligação ao substrato de laminarinases é sensível a variações de temperatura. No tópico (3), observou-se que a expansina pode transladar sobre a superfície da celulose e induzir torções em cadeias de glucano, sugerindo a possibilidade de romper ligações de hidrogênio celulose-celulose e/ou celulose/xiloglucano como um zíper. No tópico (4), observou-se que a agregação de nanofibrilas de celulose se dá através de suas faces hidrofílicas e que a presença de hemicelulose estabiliza tal agregação. No tópico (5), os resultados mostraram que as forças de coesão da parede celular secundária são de natureza entrópica e que a composição química da lignina modula as interações lignina-lignina e lignina-hemicelulose
Abstract: Biofuel production from lignocellulosic biomass involves physico-chemical and enzymatic processes that challenge its economic viability. The lignocellulosic biomass is recalcitrant against degradation and is made up of cellulose, hemicellulose and lignin. This structure and the enzyme mechanisms are not fully understood. In this thesis, molecular dynamics simulations and the statistical mechanical theory 3D-RISM were employed to assess molecular aspects of the biomass degradation, including: (1) structural dynamics of cellulases; (2) molecular basis of the thermophilicity of laminarinases; (3) non-hydrolytic disruption of biomass by expansins; (4) primary cell wall nanoarchitecture; and (5) thermodynamic forces of the secondary cell wall. In the topic (1), we observed that cellulase substrate accessibility can be modulated through changes in its primary structure, with consequences to the enzymatic activity. Moreover, the product inhibition is related to conformational changes of residues located close to the substrate binding site. In addition, changes of the intrinsic dynamics allow cellulases change their function according to the hydrolysis step. In the topic (2), we show that the substrate binding site conformation of laminarinases is sensitive to temperature variations. In the topic (3), we observed that the expansin can translade over the cellulose surface and induce torsions in free glucan chains, suggesting the possibility of disruption of cellulose-cellulose and cellulose-xyloglucan hydrogen bonds as a ziper. In the topic (4), the results showed that the aggregation of cellulose nanofibrils takes place through their hydrophilic face and that hemicellulose plays roles in stabilizing such aggregation. In the topic (5), we observed that the cohesion forces within the secondary cell wall are of entropic origin and that the lignin chemical composition modulates the lignin-lignin and lignin-hemicellulose interactions
Doutorado
Físico-Química
Doutor em Ciências
APA, Harvard, Vancouver, ISO, and other styles
8

Spura, Thomas [Verfasser]. "Ab initio path integral molecular dynamics : theory and applications / Thomas Spura." Paderborn : Universitätsbibliothek, 2015. http://d-nb.info/1078666504/34.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Niegowski, Damian. "Structural biology of integral membrane proteins from methods to molecular mechanisms /." Doctoral thesis, Stockholm : Department of Biochemistry and Biophysics, Stockholm Univeristy, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-30069.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Phan, Isabelle Q. H. "Structural studies of modular proteins by NMR and molecular modelling." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294330.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Books on the topic "Molecular integrals"

1

Center, Langley Research, ed. Solution of multi-center molecular integrals of Slater-type orbitals. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1989.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
2

Center, Langley Research, ed. Solution of multi-center molecular integrals of Slater-type orbitals. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1989.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
3

Center, Langley Research, ed. Solution of multi-center molecular integrals of Slater-type orbitals. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1989.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
4

Center, Langley Research, ed. Solution of multi-center molecular integrals of Slater-type orbitals. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1989.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
5

Becchetti, Andrea. Integrins and ion channels: Molecular complexes and signaling. New York: Springer Science+Business Media, 2010.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
6

Larsson, Kilian. Stark effect for a linear rigid polar rotator treated by means of a general phase-integral method. Uppsala: Uppsala University, 1987.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
7

L, Leach P. G., and Steeb W. -H, eds. Proceedings of the Workshop on Finite Dimensional Integrable Nonlinear Dynamical Systems: Johannesburg, South Africa, 11-15 January 1988. Singapore: World Scientific, 1988.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
8

A, Horton Michael, ed. Adhesion receptors as therapeutic targets. Boca Raton, Fla: CRC Press, 1996.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
9

International Conference on "Structure and Function of Molecules Involved in Leukocyte Adhesion II" (1991 Titisee, Germany). Structure, function, and regulation of molecules involved in leukocyte adhesion: Proceedings of the Second International Conference on "Structure and Function of Molecules Involved in Leukocyte Adhesion II," held in Titisee, Germany, October 2-6, 1991. Edited by Lipsky Peter E. New York: Springer-Verlag, 1993.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
10

Jun-Lin, Guan, ed. Signaling through cell adhesion molecules. Boca Raton, Fla: CRC Press, 1999.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Book chapters on the topic "Molecular integrals"

1

Harris, Frank E., and H. H. Michels. "The Evaluation of Molecular Integrals for Slater-Type Orbitals." In Advances in Chemical Physics, 205–66. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007. http://dx.doi.org/10.1002/9780470140154.ch8.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Partridge, Harry, James R. Stallcop, and Eugene Levin. "Potential Energies and Collision Integrals for the Interactions of Air Components." In Molecular Physics and Hypersonic Flows, 323–38. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0267-1_19.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Stallcop, James R., Harry Partridge, and Eugene Levin. "Potential Energies and Collision Integrals for the Interactions of Air Components." In Molecular Physics and Hypersonic Flows, 339–49. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-0267-1_20.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Wilson, S. "Practical AB Initio Methods for Molecular Electronic Structure Studies. III. Molecular Integrals Over Gaussian-Type Functions." In Problem Solving in Computational Molecular Science, 159–84. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-009-0039-4_5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Lehmann-Szweykowska, A., R. J. Wojciechowski, J. Barnaś, and P. E. Wigen. "Anisotropy of the Hopping Integrals of Calcium Doped Yttrium Iron Garnet." In Molecular Low Dimensional and Nanostructured Materials for Advanced Applications, 297–300. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-010-0349-0_35.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Yasui, Jun. "Analytical Expression of Molecular Integrals over Slater-Type Functions for Generating Their Polynomial Expressions." In The DV-Xα Molecular-Orbital Calculation Method, 49–106. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11185-8_3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Weniger, E. Joachim, and E. Otto Steinborn. "Nonlinear Sequence Transformations for the Efficient Evaluation of Auxiliary Functions for GTO Molecular Integrals." In Numerical Determination of the Electronic Structure of Atoms, Diatomic and Polyatomic Molecules, 341–46. Dordrecht: Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-2329-4_27.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Helgaker, Trygve, Poul Jørgensen, and Jeppe Olsen. "Molecular Integral Evaluation." In Molecular Electronic-Structure Theory, 336–432. Chichester, UK: John Wiley & Sons, Ltd, 2014. http://dx.doi.org/10.1002/9781119019572.ch9.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Deymier, Pierre A., Keith Runge, Ki-Dong Oh, and G. E. Jabbour. "Path Integral Molecular Dynamics Methods." In Multiscale Paradigms in Integrated Computational Materials Science and Engineering, 13–106. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-24529-4_2.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Matsuno, Koichiro. "Time in Biology as a Marker of the Class Identity of Molecules." In Integral Biomathics, 269–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-28111-2_26.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Molecular integrals"

1

Stolyarov, A. V., E. A. Pazyuk, I. V. Ushakov, and R. S. Ferber. "Molecular constant error propagations into Franck-Condon integrals." In High Resolution Molecular Spectroscopy: 11th Symposium and School, edited by Alexander I. Nadezhdinskii, Yu V. Ponomarev, and Leonid N. Sinitsa. SPIE, 1994. http://dx.doi.org/10.1117/12.166198.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Groll, Rodion. "Computational Modeling of Molecular Gas Convection With a c2-z2 Model." In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2008. http://dx.doi.org/10.1115/icnmm2008-62008.

Full text
Abstract:
Modelling micro channel flows momentum and heat diffusion / convection are recent parameters modelling the molecule velocity distribution. Macroscopic models describe velocity and energy / enthalpie with integrals of mass increments. Using microscopic models motion and forces of a molecular flow have to be computed by models of physical properties, whose are described by statistical power moments of the molecule velocity. Therefore dilute flows have to be investigated in small channels with a mean free path length of molecules higher than the channel width of the the micro channel itself (λ0 ≥ H0). Modelling this process by a continuous flow the boundary conditions have to be modified (e.g. [9]). Instead of a simple Dirichlet boundary condition with a neglecting velocity directly at the channel wall, given slip models define a slip velocity of the ducted fluid depending on the shear stress at the wall. The present model uses the statistical approximation of the molecule velocity distribution to simulate the behaviour of this discrete flow with a weighted averaged molecule velocity ξ˜i, its standard deviation σ and the characterisic molecule collision rate z. The number density n of molecules N per volume V near one position is used for the weighting factor averaging method describing the mean molecule velocity. The present model is validated computing Poiseuille and Couette flows with different Knudsen numbers. Showing the advantages of the present model the simulation results are compared with simulation results of the wall-distance depending diffusivity model of Lockerby and Reese [5] and BGK results of a Lattice-Boltzmann simulation.
APA, Harvard, Vancouver, ISO, and other styles
3

Chen, Tingwei, Jianpeng Chen, and Dawei Zhou. "3D-FuM: Benchmarking 3D Molecule Learning with Functional Groups." In Thirty-Third International Joint Conference on Artificial Intelligence {IJCAI-24}. California: International Joint Conferences on Artificial Intelligence Organization, 2024. http://dx.doi.org/10.24963/ijcai.2024/997.

Full text
Abstract:
Molecular graph representation learning plays a crucial role in various domains, such as drug discovery and chemical reaction prediction, where molecular graphs are typically depicted as 2D topological structures. However, recent insights highlight the critical role of 3D geometric information and functional groups in accurately predicting molecular properties, aspects often neglected in existing molecular graph benchmark datasets. To bridge the research gap, we introduce a comprehensive molecular learning benchmark named 3D-FUM, which incorporates both 3D geometric information and functional groups of a large number of molecules. 3D-FUM integrates 18 state-of-the-art algorithms and 19 evaluation metrics on three molecular learning tasks, including general molecule generation, conditional molecule generation, and property predictions. 3D-FUM, for the first time, take into consideration both 3D geometric information and molecular functional groups, which enables researchers and practitioners to effectively and impartially evaluate newly proposed methods in comparison to existing baselines across diverse datasets. Furthermore, we design a user interface for user-friendly interaction and development with the benchmark for evaluation metrics selection, parameter adjustment, and leaderboard comparison. To ensure accessibility and reproducibility, we opensource our benchmark 3D-FUM and experimental results at https://3dfunctiongroupmoleculedataset.github.io/3D-FuM/#/Home.
APA, Harvard, Vancouver, ISO, and other styles
4

Xue, S., P. Proulx, M. I. Boulos, and T. Murphy. "A Thermal and Chemical Non-Equilibrium Model for Multi-Component Ar-H2 Plasma." In ITSC2005, edited by E. Lugscheider. Verlag für Schweißen und verwandte Verfahren DVS-Verlag GmbH, 2005. http://dx.doi.org/10.31399/asm.cp.itsc2005p0305.

Full text
Abstract:
Abstract A thermal and chemical non-equilibrium model is developed for the modelling of multi-component supersonic induction Ar-H2 plasma flows. The species included in the modelling are electrons(e), hydrogen ion(H+), hydrogen atoms(H), hydrogen molecules(H2), Argon ions(Ar+) and Argon atoms(Ar). The negative hydrogen ions(H-), molecular hydrogen ions(H2+) and second order ionisation are neglected. The chemical reactions considered in the modelling are the H2 dissociations and the corresponding recombination, induced by Ar atom and H2, and the ionisations of the hydrogen and Argon and the corresponding recombination. All the heavy species are assumed to have the same temperature (Ti). The electron temperature (Te) is allowed to deviate from that of heavy species. The energies for these chemical reactions have been treated as the source terms for energy conservation equations. As a result, the contributions of these chemical reactions to the total enthalpy are removed. Therefore, the heavy species temperature can be obtained by solving the thermal kinetic energy equation, rather than the total enthalpy equation. Yos’s mixing law is used to calculate the contribution of vibrational and rotational energies of hydrogen molecules to the thermal conductivity of heavy species. The transport properties are calculated using the formulas derived by Hirschfelder, Curtiss and Bird. The data of collision integrals or collision cross-sections between species in the mixture are taken from Murphy, Devoto and Mason’s publications. The binary mass diffusion coefficients between the species in the mixture are also calculated from these collision integral data. The mass diffusion of species in the mixture are modelled under the dilute approximation at present since the mole fraction of the principal species, Argon, in the whole computational region is more than 90%. For charged species, Ambipolar diffusion coefficients are used. Mass balance equations are solved to obtain the mass fractions or mole fractions or the number densities of all the species except for electrons. The electron number density is determined by the condition of electrical neutrality. The developed model is applied to the modelling of inductive plasma flow, generated by the Tekna PL-35 torch model, under different pressures and then to the supersonic plasma flow. The model has been validated by comparing the transport properties under the LTE conditions from this model with the corresponding published values.
APA, Harvard, Vancouver, ISO, and other styles
5

Curely, J., and A. Mokrani. "Theory of superexchange for 3dn-Ions (1≤n≤9) involved in natural and artificial magnets II- derivation of the various exchange energies Ji vs key molecular integrals." In 2008 11th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM). IEEE, 2008. http://dx.doi.org/10.1109/optim.2008.4602336.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Kai, Li, Zhang Wei, and Gao Ming. "Molecular Design Method based on New Molecular Representation and Variational Auto-encoder." In 4th International Conference on Natural Language Processing, Information Retrieval and AI. Academy and Industry Research Collaboration Center (AIRCC), 2023. http://dx.doi.org/10.5121/csit.2023.130303.

Full text
Abstract:
Based on the traditional VAE, a novel neural network model is presented, with the latest molecular representation, SELFIES, to improve the effect of generating new molecules. In this model, multi-layer convolutional network and Fisher information are added to the original encoding layer to learn the data characteristics and guide the encoding process, which makes the features of the data hiding layer more aggregated, and integrates the Long Short Term Memory neural network (LSTM) into the decoding layer for better data generation, which effectively solves the degradation phenomenon generated by the encoding layer and decoding layer of the original VAE model. Through experiments on zinc molecular data sets, it is found that the similarity in the new VAE is 8.47% higher than that of the original ones. SELFIES are better at generating a variety of molecules than the traditional molecular representation, SELFIES. Experiments have shown that using SELFIES and the new VAE model presented in this paper can improve the effectiveness of generating new molecules.
APA, Harvard, Vancouver, ISO, and other styles
7

Cannon, James, and Ortwin Hess. "Non-Equilibrium Studies of Molecular Flow Through Carbon Nanotubes." In ASME 2008 6th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2008. http://dx.doi.org/10.1115/icnmm2008-62265.

Full text
Abstract:
Carbon nanotubes are likely to form an integral part of future nano-fluidic devices. In order to realise such devices, an understanding of the dynamics of molecular flow through nanotubes is crucial. We have conducted continuous-flow non-equilibrium molecular dynamics simulations of argon and hydrogen flow through nanotubes, in order to decipher the fundamental driving forces behind the flow dynamics, upon which the motions of more complex molecules are based. We detail the fundamental mechanisms of flow in the nano-confined space of a carbon nanotube, and demonstrate how this knowledge can be utilised to control the flow-rate and even convert from smooth to pulsed flow.
APA, Harvard, Vancouver, ISO, and other styles
8

Hendricks, Adam G., Bogdan I. Epureanu, and Edgar Meyho¨fer. "Synchronization of Motor Proteins Coupled Through a Shared Load." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-15752.

Full text
Abstract:
Kinesin-1 is a processive molecular motor that converts the energy from adenosine triphosphate (ATP) hydrolysis and thermal fluctuations into motion along microtubules. This motion can be interpreted as a result of ATP-fueled nonlinear nonsmooth oscillations of coupled motor domains which interact with a microtubule to transport a cargo. This class of nano-scale motors transport cargoes for distances of several micrometers in cells. This transport can also be achieved in vitro, opening the possibility of developing robust and extremely versatile nano-scale actuators or sensors based on the machinery used by biological systems. These devices could be used in a range of nano-scale applications such as drug delivery and lab-on-a-chip. However, to design such systems, a quantitative, in-depth understanding of molecular motors is essential. Single-molecule techniques have allowed the experimental characterization of kinesin-1 in vitro at a range of loads and ATP concentrations. Existing models of kinesin movement are stochastic in nature and are not well suited to describing transient dynamics. However, kinesin-1 is expected to undergo transient dynamics when external perturbations (e.g. interaction with other kinesin molecules) cause the load to vary in time. It is thought that in the cell, several kinesin motors work cooperatively to transport a common load. Thus, a transient description is integral to capturing kinesin behavior. This paper presents a mechanistic model that describes, deterministically, the average motion of kinesin-1. The structure of the kinesin-1 molecule is approximated with a simplified geometry, explicitly describing the coupling between its two heads. The diffusion is modeled using a novel approach based on the mean first-passage time, where the potential in which the free head diffuses is time varying and updated at each instant during the motion. The mechanistic model is able to predict existing force-velocity data over a wide range of ATP concentrations (including the interval 1μM to 10 mM). More importantly, the model provides a transient description, allowing predictions of kinesin-1 pulling time-varying loads and coordinated transport involving several kinesin-1 molecules. The deterministic approach is validated by comparing results to experiments and Monte Carlo simulations of the stochastic dynamics. Furthermore, using this model, the synchronization of several kinesin-1 molecules transporting a common load is investigated. Novel methods to characterize synchronization, tailored to the particularities of these nonsmooth systems, are presented.
APA, Harvard, Vancouver, ISO, and other styles
9

Georganopoulos, Markos. "Eddington-class blazar flares: beyond the molecular torus." In 10th INTEGRAL Workshop: A Synergistic View of the High-Energy Sky. Trieste, Italy: Sissa Medialab, 2015. http://dx.doi.org/10.22323/1.228.0011.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Nagashima, Hiroki, Shin-ichi Tsuda, Nobuyuki Tsuboi, Mitsuo Koshi, A. Koichi Hayashi, and Takashi Tokumasu. "A Molecular Dynamics Analysis of Quantum Effect on the Thermodynamic Properties of Liquid Hydrogen." In ASME 2013 11th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/icnmm2013-73161.

Full text
Abstract:
Liquid Hydrogen plays an important role in hydrogen energy society. Therefore it is important to understand its thermal and transport properties accurately. However cryogenic hydrogen has unusual thermodynamic properties because of its quantum nature. The thermal de Broglie wavelength of cryogenic hydrogen molecule becomes the same order as molecular diameter. Therefore, each molecular position and its momentum cannot be defined classically. Because of this nature, hydrogen molecules show higher diffusivity than classical counterpart. Until now, the effects of quantum nature of hydrogen and its mechanism on the thermodynamic properties have not been clarified in detail. Especially, how the quantum nature would effect on the energy transfer in molecular scale has not been clarified. An accurate understanding of the effect and mechanism of quantum nature is important for hydrogen storage method and energy devices which use hydrogen as a fuel. In this study, therefore, we investigated the effect of this quantum nature and its mechanism on the thermodynamic and transport properties of cryogenic hydrogen using classical Molecular Dynamics (MD) method and quantum molecular dynamics method. We applied path integral Centroid Molecular Dynamics (CMD) method for the analysis. First, we have conducted thermodynamic estimation of cryogenic hydrogen using the MD methods. This simulation was performed across a wide density-temperature range. Using these results, equations of state (EOS) were obtained by Kataoka’s method, and these were compared with experimental data according to the principle of corresponding states. As a result, it was confirmed that both quantitative and qualitative effect of the quantum nature on the thermodynamic properties of hydrogen are large. It was also found that taking account the quantum nature makes larger virial pressure and weaker intermolecular interaction energy. Second, we have calculated the diffusion coefficient of liquid hydrogen to clarify the effect of the quantum nature on the transport properties. We used Green-Kubo form for the calculation using velocity autocorrelation function. The simulation was performed across a wide temperature range. CMD simulation results were compared with classical simulation results and experimental data. We clarified the effect of quantum nature on the transport properties of liquid hydrogen.
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "Molecular integrals"

1

Lopez, Rafael, Ignacio Ema, Guillermo Ramirez, and Jaime Fernandez Rico. Molecular Slater Integrals for Electronic Energy Calculations. Fort Belvoir, VA: Defense Technical Information Center, October 2010. http://dx.doi.org/10.21236/ada531785.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Alzeer, Jawad. Beyond Disorder: A New Perspective on Entropy in Chemistry. Science Repository, March 2024. http://dx.doi.org/10.31487/j.ajmc.2024.01.01.

Full text
Abstract:
The concept of entropy, a fundamental principle in the field of chemistry, has traditionally been oversimplified as a mere measure of disorder. However, this simplistic perspective fails to capture the intricate and multifaceted nature of entropy, along with its profound influence on various phenomena. This paper seeks to delve deeper into the understanding of entropy by moving beyond the conventional disorder-centric viewpoint and adopting a more nuanced approach that integrates both disorder and energy considerations. Through the redefinition of potential energy and microstates as integral components of entropy, the study explores the intricate interplay between disorder, energy, and molecular transformations within chemical systems. The implications of this refined conceptualization extend beyond the boundaries of chemistry, impacting fields such as physics, biology, and medicine. The potential transformative effects of this enhanced understanding hold promise for advancing scientific knowledge and applications across diverse disciplines.
APA, Harvard, Vancouver, ISO, and other styles
3

Cardo-Vila, Marina. Isolation of Signaling Molecules Involved in Angiogenic Pathways Mediated Alpha v Integrins. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada435432.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

Full text
Abstract:
Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
APA, Harvard, Vancouver, ISO, and other styles
5

Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

Full text
Abstract:
Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
APA, Harvard, Vancouver, ISO, and other styles
6

Samach, Alon, Douglas Cook, and Jaime Kigel. Molecular mechanisms of plant reproductive adaptation to aridity gradients. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7696513.bard.

Full text
Abstract:
Annual plants have developed a range of different mechanisms to avoid flowering (exposure of reproductive organs to the environment) under adverse environmental conditions. Seasonal environmental events such as gradual changes in day length and temperature affect the timing of transition to flowering in many annual and perennial plants. Research in Arabidopsis and additional species suggest that some environmental signals converge on transcriptional regulation of common floral integrators such as FLOWERING LOCUS T (FT). Here we studied environmental induction of flowering in the model legume Medicago truncatula. Similarly to Arabidopsis, the transition to flowering in M. truncatula is hastened by long photoperiods and long periods of vernalization (4°C for 2-3 weeks). Ecotypes collected in Israel retain a vernalization response even though winter temperatures are way above 4°C. Here we show that this species is also highly responsive (flowers earlier) to mild ambient temperatures up to 19°C simulating winter conditions in its natural habitat. Physiological experiments allowed us to time the transition to flowering due to low temperatures, and to compare it to vernalization. We have made use of natural variation, and induced mutants to identify key genes involved in this process, and we provide here data suggesting that an FT gene in M.truncatula is transcriptionally regulated by different environmental cues. Flowering time was found to be correlated with MtFTA and MtFTB expression levels. Mutation in the MtFTA gene showed a late flowering phenotype, while over-expressing MtFTA in Arabidopsis complemented the ft- phenotype. We found that combination of 4°C and 12°C resulted in a synergistic increase in MtFTB expression, while combining 4°C and long photoperiods caused a synergistic increase in MtFTA expression. These results suggest that the two vernalization temperatures work through distinct mechanisms. The early flowering kalil mutant expressed higher levels of MtFTA and not MtFTB suggesting that the KALIL protein represses MtFTA specifically. The desert ecotype Sde Boker flowers earlier in response to short treatments of 8-12oc vernalization and expresses higher levels of MtFTA. This suggests a possible mechanism this desert ecotype developed to flower as fast as possible and finish its growth cycle before the dry period. MtFTA and FT expression are induced by common environmental cues in each species, and expression is repressed under short days. Replacing FT with the MtFTA gene (including regulatory elements) caused high MtFTA expression and early flowering under short days suggesting that the mechanism used to repress flowering under short days has diversified between the two species.The circadian regulated gene, GIGANTEA (GI) encodes a unique protein in Arabidopsis that is involved in flowering mechanism. In this research we characterized how the expression of the M.truncatula GI ortholog is regulated by light and temperature in comparison to its regulation in Arabidopsis. In Arabidopsis GI was found to be involved in temperature compensation to the clock. In addition, GI was found to be involved in mediating the effect of temperature on flowering time. We tested the influence of cold temperature on the MtGI gene in M.truncatula and found correlation between MtGI levels and extended periods of 12°C treatment. MtGI elevation that was found mostly after plants were removed from the cold influence preceded the induction of MtFT expression. This data suggests that MtGI might be involved in 12°C cold perception with respect to flowering in M.truncatula. GI seems to integrate diverse environmental inputs and translates them to the proper physiological and developmental outputs, acting through several different pathways. These research enabled to correlate between temperature and circadian clock in M.truncatula and achieved a better understanding of the flowering mechanism of this species.
APA, Harvard, Vancouver, ISO, and other styles
7

Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

Full text
Abstract:
Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
APA, Harvard, Vancouver, ISO, and other styles
8

Osburn, Bennie, Marius Ianconescu, Geoffrey Akita, and Rozalia Kaufman. Rapid, Sensitive Bluetongue Virus Serogroup and Serotype Detection Using Polymerase Chain Reaction. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7612836.bard.

Full text
Abstract:
The objectives of this proposal were to enhance animal health by 1) development of a BTV serogroup diagnostic assay using polymerase chain reaction (PCR) and 2) development of a BTV serotype specific diagnostic PCR assay. A PCR assay for diagnosis of bluetongue virus (BTV) serogroup from clinical samples meeting the criteria of objective 1 was developed. This PCR assay is more sensitive than virus isolation and has been adopted by both the U.S. and Israeli collaborating laboratories of this project, as well as at least one other U.S. laboratory for routine diagnosis of BTV infection in ruminants. The basic BTV PCR protocol has also become an essential tool in BTV molecular research in both collaborating laboratories. During development of the BTV serotype specific PCR we had the opportunity to investigate a nationwide outbreak of abortions and fatal disease in dogs in the U.S. purportedly due to BTV infection via a BTV contaminated canine vaccine. The BTV serogroup PCR was integral in confirming BTV in tissues from affected dogs and in lots of the suspect vaccine. This led to the first published report of BTV infection in dogs. We discovered that BTV can produce silent persistent infection in canine cell culture. This indicated a need for more stringent screening of biologics for occult BTV infection. A novel mixed cell culture method was developed to identify occult BTV and other occult viral infection cell cultures. Serotype specific primers for PCR detection of all U.S. BTV serotypes and two Israel serotypes (BTV-2 and 10) have been evaluated and are available. A subsequent collaboration would logically include sequencing of the L2 genes of Israel BTV-4, 6 and 16, allowing incorporation of these Israel BTV serotypes into a multiplex PCR assay.
APA, Harvard, Vancouver, ISO, and other styles
9

Olivieira, Renato, Vitória Martins, Paulo Costa, Izabela Mendes, Silvia Barreto, José Bitencourt, Santelmo Vasconcelos Júnior, Gisele Nunes, Guilherme Oliveira, and Alexandre Aleixo. Manual para o monitoramento de Biodiversidade por meio de DNA ambiental (eDNA metabarcoding). ITV, 2023. http://dx.doi.org/10.29223/prod.tec.itv.ds.2023.24.oliveira.

Full text
Abstract:
O Brasil, reconhecido por sua rica biodiversidade, enfrenta desafios significativos para mapear e conservar sua vasta fauna e flora, devido à grandeza e diversidade de seu território. A escassez de taxonomistas agrava a situação, tornando os levantamentos de biodiversidade mais raros e custosos. Nesse contexto, o DNA metabarcoding surge como uma solução inovadora, permitindo a identificação simultânea de múltiplas espécies através da análise do DNA ambiental encontrado em amostras de solo, água, sedimentos e/ou tecidos biológicos. A eficiência da técnica se depende de bancos de dados de códigos de barra de DNA, gerados a partir do sequenciamento de marcadores moleculares específicos de espécimes previamente identificados por especialistas, garantindo assim a confiabilidade dos resultados. Esta abordagem vem revolucionando os projetos de monitoramento ambiental e conservação da biodiversidade, oferecendo resultados rápidos e precisos. Além disso, a técnica tem se mostrado essencial para estratégias de manejo eficazes e para atender a diversos propósitos regulatórios e de preservação. Este manual integra métodos de monitoramento de flora e ictiofauna, propondo-se a exemplificar a aplicação prática da técnica de DNA metabarcoding, visando sua adoção no Projeto Genômica da Biodiversidade Brasileira (GBB). A iniciativa representa um passo crucial para gerar conhecimento aprofundado da biodiversidade brasileira, essencial para minimizar impactos ambientais e orientar esforços de conservação.
APA, Harvard, Vancouver, ISO, and other styles
10

Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

Full text
Abstract:
To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Molecular integrals' for particular source types:
Journal articles Dissertations / Theses Books
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography