Relevant bibliographies by topics / Molecular forces

Contents

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

Academic literature on the topic 'Molecular forces'

Author: Grafiati
Published: 1 February 2023

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Journal articles on the topic "Molecular forces"

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Murad, Yousif, and Isaac T. S. Li. "Quantifying Molecular Forces with Serially Connected Force Sensors." Biophysical Journal 116, no. 7 (April 2019): 1282–91. http://dx.doi.org/10.1016/j.bpj.2019.02.027.

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Murad, Yousif, Adam Yasunaga, and Isaac T. Li. "Quantifying Molecular Forces with Serially Connected Force Sensors." Biophysical Journal 118, no. 3 (February 2020): 188a. http://dx.doi.org/10.1016/j.bpj.2019.11.1145.

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Schliwa, Manfred. "Molecular motors join forces." Nature 397, no. 6716 (January 1999): 204–5. http://dx.doi.org/10.1038/16577.

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Murphy, K. P., Y. Zhao, and M. Kawai. "Molecular forces involved in force generation during skeletal muscle contraction." Journal of Experimental Biology 199, no. 12 (December 1, 1996): 2565–71. http://dx.doi.org/10.1242/jeb.199.12.2565.

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Recent advances in protein chemistry and the kinetic analysis of tension transients in skeletal muscle fibres have enabled us to elucidate the molecular forces involved in force generation by cross-bridges. On the basis of the temperature effect, we conclude that the elementary step that generates force is an endothermic reaction (the enthalpy change delta H degree = 124 kJ mol-1 at 15 degrees C), which accompanies a large entropy increase (delta S degree = 430JK-1 mol-1) and a reduction in the heat capacity (delta C p = -6.4kJ K-1 mol-1). Thus, it can be concluded that the force-generating step is an entropy-driven reaction. The above results suggest that hydrophobic interactions are the primary cause of force generation, and that polar interactions (hydrogen bonding and charge interactions) are involved to a lesser degree. On the basis of the thermodynamic data, we estimate that during force generation approximately 50 nm2 of surface area is involved for hydrophobic interactions and another 30 nm2 for polar interactions. These data suggest that both the actomyosin interaction and the cleft closure of the myosin head are essential for force generation.
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Vlcek, Lukas, Weiwei Sun, and Paul R. C. Kent. "Combining configurational energies and forces for molecular force field optimization." Journal of Chemical Physics 147, no. 16 (October 28, 2017): 161713. http://dx.doi.org/10.1063/1.4986079.

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Gaboriaud, Fabien, and Yves F. Dufrêne. "Atomic force microscopy of microbial cells: Application to nanomechanical properties, surface forces and molecular recognition forces." Colloids and Surfaces B: Biointerfaces 54, no. 1 (January 2007): 10–19. http://dx.doi.org/10.1016/j.colsurfb.2006.09.014.

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Davis, Brian K. "The forces driving molecular evolution." Progress in Biophysics and Molecular Biology 69, no. 1 (January 1998): 83–150. http://dx.doi.org/10.1016/s0079-6107(97)00034-5.

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Pirani, Fernando, Stefano Falcinelli, Franco Vecchiocattivi, Michele Alagia, Robert Richter, and Stefano Stranges. "Anisotropic forces and molecular dynamics." Rendiconti Lincei. Scienze Fisiche e Naturali 29, no. 1 (January 31, 2018): 179–89. http://dx.doi.org/10.1007/s12210-018-0668-9.

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Freikamp, Andrea, Alexander Mehlich, Christoph Klingner, and Carsten Grashoff. "Investigating piconewton forces in cells by FRET-based molecular force microscopy." Journal of Structural Biology 197, no. 1 (January 2017): 37–42. http://dx.doi.org/10.1016/j.jsb.2016.03.011.

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O'Shea, Sean J., Nitya N. Gosvami, Leonard T. W. Lim, and Wulf Hofbauer. "Liquid Atomic Force Microscopy: Solvation Forces, Molecular Order, and Squeeze-Out." Japanese Journal of Applied Physics 49, no. 8 (August 20, 2010): 08LA01. http://dx.doi.org/10.1143/jjap.49.08la01.

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Dissertations / Theses on the topic "Molecular forces"

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Dean, Delphine Marguerite Denise 1978. "Molecular electromechanics : modeling electrostatic forces between GAG molecules." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/86649.

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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.
Includes bibliographical references (p. 81-83).
by Delphine Marguerite Denise Dean.
M.Eng.and S.B.
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Eckel, Rainer. "Single molecules and nanocrystals: molecular recognition forces and optomechanical switching." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=978888227.

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Bermingham, Charlotte R. "Measurement of pico/femto-Newton scale forces using the lateral molecular force microscope." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715803.

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Wells, B. H. "Studies in intramolecular forces." Thesis, University of Oxford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355824.

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Gellert, P. R. "Spectroscopic and theoretical studies of intermolecular forces." Thesis, University of Oxford, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234945.

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Jones, Andrew. "Quantum drude oscillators for accurate many-body intermolecular forces." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4878.

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One of the important early applications of Quantum Mechanics was to explain the Van-der-Waal’s 1/R6 potential that is observed experimentally between two neutral species, such as noble gas atoms, in terms of correlated uncertainty between interacting dipoles, an effect that does not occur in the classical limit [London-Eisenschitz,1930]. When many-body correlations and higher-multipole interactions are taken into account they yield additional many-body and higher-multipole dispersion terms. Dispersion energies are closely related to electrostatic interactions and polarisation [Hirschfelder-Curtiss-Bird,1954]. Hydrogen bonding, the dominant force in water, is an example of an electrostatic effect, which is also strongly modified by polarisation effects. The behaviour of ions is also strongly influenced by polarisation. Where hydrogen bonding is disrupted, dispersion tends to act as a more constant cohesive force. It is the only attractive force that exists between hydrophobes, for example. Thus all three are important for understanding the detailed behaviour of water, and effects that happen in water, such as the solvation of ions, hydrophobic de-wetting, and thus biological nano-structures. Current molecular simulation methods rarely go beyond pair-wise potentials, and so lose the rich detail of many-body polarisation and dispersion that would permit a force field to be transferable between different environments. Empirical force-fields fitted in the gas phase, which is dominated by two-body interactions, generally do not perform well in the condensed (many-body) phases. The leading omitted dispersion term is the Axilrod-Teller-Muto 3-body potential, which does not feature in standard biophysical force-fields. Polarization is also usually ommitted, but it is sometimes included in next-generation force-fields following seminal work by Cochran [1971]. In practice, many-body forces are approximated using two-body potentials fitted to reflect bulk behaviour, but these are not transferable because they do not reproduce detailed behaviour well, resulting in spurious results near inhomogeneities, such as solvated hydrophobes and ions, surfaces and interfaces. The Quantum Drude Oscillator model (QDO) unifies many-body, multipole polarisation and dispersion, intrinsically treating them on an equal footing, potentially leading to simpler, more accurate, and more transferable force fields when it is applied in molecular simulations. The Drude Oscillator is simply a model atom wherein a single pseudoelectron is bound harmonically to a single pseudonucleus, that interacts via damped coulomb interactions [Drude,1900]. Path Integral [Feynman-Hibbs,1965] Molecular Dynamics (PIMD) can, in principle, provide an exact treatment for moving molecules at finite temperature on the Born- Oppenheimer surface due to their pseudo-electrons. PIMD can be applied to large systems, as it scales like N log(N), with multiplicative prefactor P that can be effectively parallelized away on modern supercomputers. There are other ways to treat dispersion, but all are computationally intensive and cannot be applied to large systems. These include, for example, Density Functional Theory provides an existence proof that a functional exists to include dispersion, but we dont know the functional. We outline the existing methods, and then present new density matrices to improve the discretisation of the path integral. Diffusion Monte Carlo (DMC), first proposed by Fermi, allows the fast computation of high-accuracy energies for static nuclear configurations, making it a useful method for model development, such as fitting repulsion potentials, but there is no straightforward way to generate forces. We derived new methods and trial wavefunctions for DMC, allowing the computation of energies for much larger systems to high accuracy. A Quantum Drude model of Xenon, fit in the gas-phase, was simulated in the condensed-phase using both DMC and PIMD. The new DMC methods allowed for calculation of the bulk modulus and lattice constant of FCC-solid Xenon. Both were in excellent agreement with experiment even though this model was fitted in the gasphase, demonstrating the power of Quantum Drudes to build transferable models by capturing many-body effects. We also used the Xenon model to test the new PIMD methods. Finally, we present the outline of a new QDO model of water, including QDO parameters fitted to the polarisabilities and dispersion coefficients of water.
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Jayachandran, Christina [Verfasser]. "Molecular DNA Sensors to Measure Distribution of Cytoskeletal Forces / Christina Jayachandran." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1217062807/34.

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Ganti, Raman S. "Microscopic forces and flows due to temperature gradients." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274324.

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Nano-scale fluid flow is unlike transport on the macro-scale. Pressure gradients typically dominate effects on a large scale while thermal gradients contribute negligibly to the motion of fluid. The situation entirely reverses on the nano-scale. At a microscopic level, flows induced by thermal gradients are caused by forces that act on atoms or molecules near an interface. These thermo-osmotic forces cannot, at present, be derived analytically or measured experimentally. Clearly, it would be useful to calculate these forces via molecular simulations, but direct approaches fail because in the steady-state, the average force per particle vanishes, as the thermo-osmotic force is balanced by a gradient in shear stress. In our journey to indirectly calculate the osmotic force, we met another unknown in the field of molecular theory at interfaces: the microscopic pressure tensor. The latter is an open problem since the microscopic pressure near an interface is not uniquely defined. Using local thermodynamics theories, we relate the thermo-osmotic force to the gradient of the microscopic pressure tensor. Yet, because the pressure is not uniquely defined, we arrive at multiple answers for the thermo-osmotic force, where at most one can be correct. To resolve the latter puzzle, we develop a direct, non-equilibrium simulation protocol to measure the thermo-osmotic force, whereby a thermal gradient is imposed and the osmotic force is measured by eliminating the shear force. Surprisingly, we find that the osmotic force cannot be derived from the gradient of well-known microscopic pressure expressions. We, therefore, derive a thermodynamic expression that gets close. In this work, we report the first, direct calculation of the thermo-osmotic force while simultaneously showing that standard microscopic pressure expressions fail to predict pressure gradients.
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Zhang, Ying. "Dynamic spatio-temporal interaction of morphogens, forces and growth in embryonic morphogenesis." [Bloomington, Ind.] : Indiana University, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3297105.

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Thesis (Ph.D.)--Indiana University, Dept. of Physics, 2007.
Title from dissertation home page (viewed Sept. 29, 2008). Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0881. Adviser: James A. Glazier.
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Marla, Krishna Tej. "Molecular thermodynamics of nanoscale colloid-polymer mixures: chemical potentials and interaction forces." Available online, Georgia Institute of Technology, 2004, 2004. http://etd.gatech.edu/theses/available/etd-08102004-105655/.

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Thesis (Ph. D.)--Chemical Engineering, Georgia Institute of Technology, 2006.
Dr. J. Carson Meredith, Committee Chair ; Dr. Charles A. Eckert, Committee Member ; Dr. Clifford L. Henderson, Committee Member ; Dr. Rigoberto Hernandez, Committee Member ; Dr. Peter J. Ludovice, Committee Member. Vita. Includes bibliographical references.
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Books on the topic "Molecular forces"

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J, Wales David, ed. Intermolecular forces and clusters. Berlin: Springer, 2005.

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Interatomic forces in condensed matter. Oxford: Oxford University Press, 2010.

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Vital forces: The discovery of the molecular basis of life. San Diego: Academic Press, 2000.

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Salam, Akbar. Molecular quantum electrodynamics: Long-range intermolecular interactions. Hoboken, N.J: Wiley, 2010.

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Sarina, Bromberg, ed. Molecular driving forces: Statistical thermodynamics in chemistry and biology. New York: Garland Science, 2003.

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Kholmurodov, Kholmirzo. Molecular simulation in material and biological research. Hauppauge, NY: Nova Science Publishers, 2009.

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Salam, A. Molecular quantum electrodynamics: Theory of long-range intermolecular interactions. Hoboken, N.J: Wiley, 2010.

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Interatomic forces in condensed matter. Oxford: Oxford University Press, 2003.

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Pierandrea, Lo Nostro, ed. Molecular forces and self assembly: In colloid, nano sciences and biology. Cambridge: Cambridge University Press, 2010.

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Kaplan, I. G. Intermolecular interactions: Physical picture, computational methods and model potentials. Chichester, UK: John Wiley & Sons, 2006.

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Book chapters on the topic "Molecular forces"

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Salam, Akbar. "Intermolecular Forces." In Molecular Quantum Electrodynamics, 121–38. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9780470535462.ch3.

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Buckingham, A. D. "Intermolecular forces." In Principles of Molecular Recognition, 1–16. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-2168-2_1.

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Salam, Akbar. "Retarded Dispersion Forces." In Molecular Quantum Electrodynamics, 175–256. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9780470535462.ch5.

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Salam, Akbar. "Many-Body Forces." In Molecular Quantum Electrodynamics, 257–310. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9780470535462.ch6.

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Rademann, K. "Cluster Research with Spectroscopic Molecular Beam Techniques." In Intermolecular Forces, 297–315. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76260-4_12.

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Yamada, Shinji. "Molecular Interactions (Molecular and Surface Forces)." In Encyclopedia of Polymeric Nanomaterials, 1–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-36199-9_151-1.

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Yamada, Shinji. "Molecular Interactions (Molecular and Surface Forces)." In Encyclopedia of Polymeric Nanomaterials, 1280–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-642-29648-2_151.

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Buck, U. "Molecular Beam Scattering: Method and Results on Intermolecular Potentials." In Intermolecular Forces, 317–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76260-4_13.

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Bopp, P. "Molecular Dynamics (MD) Computer Simulations of Hydrogen-Bonded Liquids." In Intermolecular Forces, 337–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76260-4_14.

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Misevic, Gradimir N., Yannis Karamanos, and Nikola J. Misevic. "Atomic Force Microscopy Measurements of Intermolecular Binding Forces." In Methods in Molecular Biology, 143–50. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-413-1_8.

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Conference papers on the topic "Molecular forces"

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Forbes, Kayn A., and David L. Andrews. "Optical spin-orbit interactions in molecular scattering of twisted light." In Complex Light and Optical Forces XIII, edited by David L. Andrews, Enrique J. Galvez, and Jesper Glückstad. SPIE, 2019. http://dx.doi.org/10.1117/12.2509390.

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Chong, William W. F., and Hedong Zhang. "Simulating Surface Forces Between Iron Oxide Surfaces Immersed in Methyl Oleate Using Molecular Dynamics." In ASME-JSME 2018 Joint International Conference on Information Storage and Processing Systems and Micromechatronics for Information and Precision Equipment. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/isps-mipe2018-8524.

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Using Molecular Dynamics (MD) simulation, the current study determined the surface forces between iron oxide surfaces when immersed in methyl oleate. Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to model the methyl oleate molecules. For the nano-confinement simulation, the iron oxide wall was modelled from its crystal structure. The nano-confinement simulation model was setup in a manner where the confined methyl oleate molecules were in contact with the bulk molecules surrounding each side of the iron oxide walls. Through the simulation, the load-separation gap profile was obtained by reducing the separation gap between the ferric oxide walls. When the separation gap was reduced from 2.75 nm to 1.88 nm, the load is shown to increase monotonically. Such increase in load bearing ability of the contact is observed to correspond to a more densely packed methyl oleate molecules, reflected by four well-formed layers across the separation gap. As the gap is dropped from 1.88 nm to 1.63 nm, the load instead reduces, indicating deteriorating load bearing ability of the contact. However, the load bearing ability of the contact is then shown to recover when the gap was further reduced till 1.38 nm. This oscillatory load trend is shown to be as a result of a layer of methyl oleate molecules being squeezed out of contact, corroborated by the density profile change where four well-formed layers were reduced to only three layers from 1.88 nm to 1.38 nm gap. This also indicates that the simulated contact exhibits structural forces, known as solvation forces. Thus, the MD simulation discussed in this study is demonstrated to be capable of providing a foundation to allow for a multi-scale simulation, integrating various force laws at different length scales, to study larger scale tribological contacts.
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Wemhoff, Aaron P. "Molecular-Based Theory for Drag on a Circular Cylinder by a Liquid." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-87895.

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A simple multiscale theory is presented that predicts the inertial drag on an infinite cylindrical rod in a homogeneous liquid. The theory essentially integrates the van der Waals molecular interactions between the rod molecules and the surrounding fluid molecules, where these integrated molecular forces are influenced by the bulk motion of the surrounding fluid. The theory suggests that the drag force exhibited by the fluid onto the rod is caused by the combination of leading-edge repulsive forces and trailing-edge attractive forces, and the predicted drag coefficient increases linearly with the rod diameter. An application of the theory to the endothelial glycocalyx layer (EGL), which contains an array of 20 nm diameter protein chain fibers lining the walls of human blood vessels, predicts a substantial difference in drag coefficient when compared to a continuum theory. This result shows that theory predicts a small inertial drag force compared to viscous force on the EGL, which provides some validation of the theory.
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Li, Jiang, Haosheng Chen, and Yongjian Li. "Investigation on Surface Forces Measurement Using Force-Balanced MEMS Sensor." In 2006 1st IEEE International Conference on Nano/Micro Engineered and Molecular Systems. IEEE, 2006. http://dx.doi.org/10.1109/nems.2006.334895.

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Rivera, Monica, Whasil Lee, Piotr E. Marszalek, Daniel G. Cole, and Robert L. Clark. "Aligning Molecular Attachment Sites in Single Molecule Force Spectroscopy Measurements." In ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/detc2008-50019.

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In atomic force microscopy (AFM) -based single molecule force spectroscopy, it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Although this assumption may hold for flexible, compact molecules, studies have shown that it may not be appropriate for fairly rigid molecules, where measured forces can be a fraction of the actual values experienced by the molecule. Previously, we have proposed a method to align a molecule’s substrate and cantilever attachment sites and tested it in a simulated environment. Here we continue our work and test the alignment program in an experimental environment. In this paper we demonstrate that circling-induced force fluctuations are the result of stretching and relaxing a tethered molecule and we present the results of an alignment trial. Combined, these preliminary results demonstrate the feasibility of the alignment program and are a promising step towards correcting pulling geometry errors in single molecule force spectroscopy studies.
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Darbandi, Masoud, Hossein Reza Abbasi, Moslem Sabouri, and Rasool Khaledi-Alidusti. "Simulation of Heat Transfer in Nanoscale Flow Using Molecular Dynamics." In ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels collocated with 3rd Joint US-European Fluids Engineering Summer Meeting. ASMEDC, 2010. http://dx.doi.org/10.1115/fedsm-icnmm2010-31065.

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We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6–12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the heat transfer between wall and fluid. We implement this idea in analyzing the heat transfer in a few cases, including the shear driven and poiseuille flow with specified heat flux boundary conditions. In this method, the work done by the viscous stress (in case of shear driven flow) and the force applied to the fluid molecules (in case of poiseuille flow) produce heat in the fluid, which is dissipated from the nanochannel walls. We present the velocity profiles and temperature distributions for the both chosen test cases. As a result of interaction between the fluid molecules and their adjacent wall molecules, we can clearly observe the velocity slip in the velocity profiles and the temperature jump in the cross-sectional temperature distributions.
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Zolotoukhina, Tatiana, and Takeo Fukui. "Identification of Nucleobases of Single Stranded DNA by Nanopore Force Resolution at Different Film Thickness." In ASME/JSME 2011 8th Thermal Engineering Joint Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajtec2011-44260.

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The model of the molecular translocation of all types of DNA base molecules of cytosine, thymine, adenine and guanine through the nanoporous membrane of a solid thin film has been considered from the point of view of improving the resolution of forces by changing parameters of the membrane itself. The results of simulation of translocation process were compared for all four DNA nucleotides. The molecular dynamics (MD) method with the force field potential has been used for the atomic level modeling of the cytosine (C), thymine (T), adenine (A), and guanine (G) molecules and a configuration of the nanoporous Si membrane. With the planar structure of base molecules and cylindrical symmetry of pore, the two-dimensional projection was used in the simulation. The force field between the base molecule and atoms of nanopore has been estimated. Influence of the Si surface hydrogenization and film thickness on the force resolution for each nucleobase was evaluated vs. possible signal resolution. At 5 layer thickness of the film it was possible to cut thermal fluctuations and distinguish four nucleobase types.
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Hur, Sung Sik, Yi-Shuan Li, Joon Seok Park, Ying-Li Hu, and Shu Chien. "3-dimensional forces and molecular dynamics of live cells." In SPIE NanoScience + Engineering, edited by Hooman Mohseni and Manijeh Razeghi. SPIE, 2010. http://dx.doi.org/10.1117/12.861581.

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Lin, Yuan, Gustav Amberg, Fredrik Aldaeus, and Johan Roeraade. "Simulation of Dielectrophoretic Motion of Microparticles Using a Molecular Dynamics Approach." In ASME 4th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2006. http://dx.doi.org/10.1115/icnmm2006-96095.

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We model and simulate dielectrophoresis of micro-scale particles using the finite element method. A soft sphere system molecular dynamics model is presented, which solves a set of equations for the motion of every particle. The model couples most of the significant forces, i.e. the dielectrophoresis (DEP) forces, the particle-particle electrostatic forces, particle-particle interfacial repulsive forces, particle-wall repulsive forces and the hydrodynamic forces in Stokes flow. Since the system of equations is stiff, an implicit scheme is used. To obtain the particle trajectories, a constant time-step is applied. We present some numerical tests computing hydrodynamic force, electrostatic force and DEP force using our model, including simulated trapping of particles in a micro channel by dielectrophoresis. The results are in agreement with the theories and the experimental observations.
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Leong, Yee-Kwong. "Relationship between Inter- and Intra-molecular Forces of Adsorbed Additives and Surface Forces in Dispersions." In 14th Asia Pacific Confederation of Chemical Engineering Congress. Singapore: Research Publishing Services, 2012. http://dx.doi.org/10.3850/978-981-07-1445-1_065.

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Reports on the topic "Molecular forces"

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Davidson, Irit, Hsing-Jien Kung, and Richard L. Witter. Molecular Interactions between Herpes and Retroviruses in Dually Infected Chickens and Turkeys. United States Department of Agriculture, January 2002. http://dx.doi.org/10.32747/2002.7575275.bard.

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Tumors in commercial poultry are caused mainly by infection with avian herpes and retroviruses, the herpesvirus Marek's disease virus (MDV) and the retroviruses, reticuloendotheliosis (REV), lymphoid leukosis, subgroups A-I and J (ALV and ALV-J) in chickens, or Iymphoprolipherative disease (LPDV) in turkeys. Infection with one virus aggravates the clinical outcome of birds that are already infected by another oncogenic virus. As these viruses do not interfere for infection, MDV and one or more retroviruses can infect the same flock, the same bird and the same cell. While infecting the same cell, herpes and retroviruses might interact in at least three ways: a) Integration of retrovirus genomes, or genomic fragments (mainly the LTR) into MDV;b) alteration of LTR-driven expression of retroviral genes by MDV immediate- early genes, and c) by herpesvirus induced cellular transcriptional factors. The first type of molecular interaction have been demonstrated to happen efficiently in vitro by Dr. Kung, in cases multiple infection of cell cultures with MDV and REV or MDV and ALV. Moreover, Dr. Witter showed that an in vitro-created recombinant, RM1, had altered in vitro replication and in vivo biological properties. A more comprehensive characterization of RM1 was carried out in the present project. We sought to highlight whether events of such integrations occur also in the bird, in vivo. For that, we had first to determine the prevalence of dually-infected individual birds in commercial flocks, as no systematic survey has been yet reported. Surprisingly, about 25% of the commercial flocks infected with avian oncogenic viruses had a multiple virus infection and 5% of the total samples ana lysed had multiple virus sequences. Then, we aimed to evaluate and characterize biologically and molecularly the resulting recombinants, if formed, and to analyse the factors that affect these events (virus strains, type and age of birds and time interval between the infection with both viruses). The perception of retrovirus insertions into herpesviruses in vivo is not banal, as the in vivo and in vitro systems differ in the viral-target cells, lymphocytes or fibroblasts, in the MDV-replicative type, transforming or productive, and the immune system presence. We realized that previous methods employed to study in vitro created recombinant viruses were not adequate for the study of samples taken directly from the bird. Therefore, the Hot Spot-combined PCR was developed based on the molecularly known RM1 virus. Also, the PFGE that was used for tissue cultured-MDV separation was inefficient for separating MDV from organs, but useful with feather tips as a source of bird original MDV. Much attention was dedicated now to feathers, because if a recombinant virus would be formed in vivo, its biological significance would be evident by horizontal dissemination through the feathers. Major findings were: a) not only in vitro, but also in vivo MDV and retrovirus co-infections lead to LTR integrations into MDV. That was shown by the detection of chimeric molecules. These appeared in low quantities and as quasispecies, thus interfering with sequence analysis of cloned gel-purified chimeric molecules. Mainly inserts were located in the repeat long MDV fragments. In field birds chimeric molecules were detected at a lower frequency (2.5%) than in experimentally infected birds (30-50%). These could be transmitted experimentally to another birds by inoculation with chimeric molecules containing blood. Several types of chimeric molecules were formed, and same types were detected in birds infected by a second round. To reproduce viral integrations, in vivo infection trials were done with field inoculate that contained both viruses, but the chimeric molecule yield was undetectable.
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Gafni, Yedidya, and Vitaly Citovsky. Inactivation of SGS3 as Molecular Basis for RNA Silencing Suppression by TYLCV V2. United States Department of Agriculture, November 2013. http://dx.doi.org/10.32747/2013.7593402.bard.

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The Israeli isolate of Tomato yellow leaf curl geminivirus(TYLCV-Is) is a major tomato pathogen, causing extensive crop losses in Israel and in the south-eastern U.S. Yet, little is known about the molecular mechanisms of its interaction with tomato cells. One of the most interesting aspects of such interaction is how the invading virus counteracts the RNA silencing response of the plant. In the former BARD project, we have shown that TYLCV-Is V2 protein is an RNA silencing suppressor, and that this suppression is carried out via the interaction of V2 with the SGS3 component of the plant RNA silencing machinery. This reported project was meant to use our data as a foundation to elucidate the molecular mechanism by which V2 affects the SGS3 activity. While this research is likely to have an important impact on our understanding of basic biology of virus-plant interactions and suppression of plant immunity, it also will have practical implications, helping to conceive novel strategies for crop resistance to TYLCV-Is. Our preliminary data in regard to V2 activities and our present knowledge of the SGS3 function suggest likely mechanisms for the inhibitory effect of V2 on SGS3. We have shown that V2 possess structural and functional hallmarks of an F-box protein, suggesting that it may target SGS3 for proteasomal degradation. SGS3 contains an RNA-binding domain and likely functions to protect the cleavage produces of the primary transcript for subsequent conversion to double-stranded forms; thus, V2 may simply block the RNA binding activity of SGS3. V2 may also employ a combination of these mechanisms. These and other possibilities were tested in this reported project.
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LAST, JULIE A., TINA HUBER, DARRYL Y. SASAKI, BRIAN SALVATORE, and SALVATORE J. TURCO. Atomic Force Microscopy Studies of Lipophosphoglycan (LPG) Molecules in Lipid Bilayers. Office of Scientific and Technical Information (OSTI), March 2003. http://dx.doi.org/10.2172/809989.

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4

Bunte, Steven W., and Huai Sun. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field. Fort Belvoir, VA: Defense Technical Information Center, November 2000. http://dx.doi.org/10.21236/ada393318.

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5

LaBonte, Don, Etan Pressman, Nurit Firon, and Arthur Villordon. Molecular and Anatomical Characterization of Sweetpotato Storage Root Formation. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7592648.bard.

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Original objectives: Anatomical study of storage root initiation and formation. Induction of storage root formation. Isolation and characterization of genes involved in storage root formation. During the normal course of storage root development. Following stress-induced storage root formation. Background:Sweetpotato is a high value vegetable crop in Israel and the U.S. and acreage is expanding in both countries and the research herein represents an important backstop to improving quality, consistency, and yield. This research has two broad objectives, both relating to sweetpotato storage root formation. The first objective is to understand storage root inductive conditions and describe the anatomical and physiological stages of storage root development. Sweetpotato is propagated through vine cuttings. These vine cuttings form adventitious roots, from pre-formed primordiae, at each node underground and it is these small adventitious roots which serve as initials for storage and fibrous (non-storage) “feeder” roots. What perplexes producers is the tremendous variability in storage roots produced from plant to plant. The marketable root number may vary from none to five per plant. What has intrigued us is the dearth of research on sweetpotato during the early growth period which we hypothesize has a tremendous impact on ultimate consistency and yield. The second objective is to identify genes that change the root physiology towards either a fleshy storage root or a fibrous “feeder” root. Understanding which genes affect the ultimate outcome is central to our research. Major conclusions: For objective one, we have determined that the majority of adventitious roots that are initiated within 5-7 days after transplanting possess the anatomical features associated with storage root initiation and account for 86 % of storage root count at 65 days after transplanting. These data underscore the importance of optimizing the growing environment during the critical storage root initiation period. Water deprivation during this phenological stage led to substantial reduction in storage root number and yield as determined through growth chamber, greenhouse, and field experiments. Morphological characterization of adventitious roots showed adjustments in root system architecture, expressed as lateral root count and density, in response to water deprivation. For objective two, we generated a transcriptome of storage and lignified (non-storage) adventitious roots. This transcriptome database consists of 55,296 contigs and contains data as regards to differential expression between initiating and lignified adventitious roots. The molecular data provide evidence that a key regulatory mechanism in storage root initiation involves the switch between lignin biosynthesis and cell division and starch accumulation. We extended this research to identify genes upregulated in adventitious roots under drought stress. A subset of these genes was expressed in salt stressed plants.
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O'Neill, Sharman, Abraham Halevy, and Amihud Borochov. Molecular Genetic Analysis of Pollination-Induced Senescence in Phalaenopsis Orchids. United States Department of Agriculture, 1991. http://dx.doi.org/10.32747/1991.7612837.bard.

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The project investigated the molecular genetic and biochemical basis of pollination-induced senescence of Phalaenopsis flowers. This experimental system offered unique advantages in that senescence is strictly regulated by pollination, providing the basis to experimentally initiate and synchronize senescence in populations of flowers. The postpollination syndrome in the Phalaenopsis orchid system was dissected by investigating the temporal and spatial regulation of ACC synthase gene expression. In the stigma, pollen-borne auxin induces the expression of the auxin-regulated ACC synthase (PS-ACS2) gene, resulting in ACC synthesis within 1 h following pollination. Newly formed ACC is oxidized by basal constitutive ACC oxidase to ethylene, which then induces the expression of the ethylene-regulated ACC synthase(PS-ACS1) and oxidase (ACO1) genes for further autocatalytic production of ethylene. It is speculated that during the 6-h period following pollination, emasculation leads to the production or release of a sensitivity factor that sensitizes the cells of the stigma to ethylene. ACC and ethylene molecules are translocated from the stigma to the labellum and perianth where ethylene induces the expression of PS-ACS1 and ACO1 resulting in an increased production of ACC and ethylene. Organ-localized ethylene is responsible for inrolling and senescence of the labellum and perianth. The regulation of ethylene sensitivity and signal transduction events in pollinated flowers was also investigated. The increase in ethylene sensitivity appeared in both the flower column and the perianth, and was detected as early as 4 h after pollination. The increase in ethylene sensitivity following pollination was not dependent on endogenous ethylene production. Application of linoleic and linoleic acids to Phalaenopsis and Dendrobium flowers enhanced their senescence and promoted ethylene production. Several major lipoxygenase pathway products including JA-ME, traumatic acid, trans-2-hexenal and cis-3-hexenol, also enhanced flower senescence. However, lipoxygenase appears to not be directly involved in the endogenous regulation of pollination-induced Phalaenopsis and Dendrobium flower senescence. The data suggest that short-chain saturated fatty acids may be the ethylene "sensitivity factors" produced following pollination, and that their mode of action involves a decrease in the order of specific regions i the membrane lipid bilayer, consequently altering ethylene action. Examination of potential signal transduction intermediates indicate a direct involvement of GTP-binding proteins, calcium ions and protein phosphorylation in the cellular signal transduction response to ethylene following pollination. Modulations of cytosolic calcium levels allowed us to modify the flowers responsiveness to ethylene.
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Rocheford, Torbert, Yaakov Tadmor, Robert Lambert, and Nurit Katzir. Molecular Marker Mapping of Genes Enhancing Tocol and Carotenoid Composition of Maize Grain. United States Department of Agriculture, December 1995. http://dx.doi.org/10.32747/1995.7571352.bard.

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The overall objective of this research was to identify chromosomal regions and candidate genes associated with control of concentration and forms of carotenoids (includes pro-Vitamin A) and tocopherols (Vitamin E), which are both antioxidants and are associated with health advantages. Vitamin A and E are included in animal feeding supplements and the eventual goal is to increase levels of these compounds in maize grain so that the cost of these supplements can be reduced or eliminated. Moreover, both compounds are antioxidants that protect unsaturated fatty acids from oxidation and thus maintaining maize oil quality for longer periods. We identified three SSR markers that are associated with 38% of the variation for total carotenoids and three SSR markers associated with 44% of the variation for total tocopherols in the cross W64a x A632. We identified two candidate genes associated with levels of carotenoids: phytoene synthase and zeta carotene desaturase. Evaluation of (Illinois High Oil x B73) B73 BC 1S1 population for tocopherols detected additional chromosomal regions influencing the level of total tocopherols, and detected a common region on chromosome 5 associated with ratio of the more desirable alpha from to the gamma form of tocopherol. The results suggest molecular marker assisted selection for higher levels of these antioxidants in corn grain should be feasible.
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Sadka, Avi, Mikeal L. Roose, and Yair Erner. Molecular Genetic Analysis of Citric Acid Accumulation in Citrus Fruit. United States Department of Agriculture, March 2001. http://dx.doi.org/10.32747/2001.7573071.bard.

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The acid content of the juice sac cells is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Pulp acidity is thought to be dependent on two mechanisms: the accumulation of citric acid in the vacuoles of the juice sac cells, and acidification of the vacuole. The major aim of the project was to direct effort toward understanding the mechanism of citric acid accumulation in the fruit. The following objectives were suggested: Measure the activity of enzymes likely to be involved in acid accumulation and follow their pattern of expression in developing fruit (Sadka, Erner). Identify and clone genes which are associated with high and low acid phenotypes and with elevated acid level (Roose, Sadka, Erner). Convert RAPD markers that map near a gene that causes low acid phenotype to specific co dominant markers (Roose). Use genetic co segregation to test whether specific gene products are responsible for low acid phenotype (Roose and Sadka). Objective 1 was fully achieved. Most of the enzymes of organic acid metabolism were cloned from lemon pulp. Their expression was studied during fruit development in low and high acid varieties. The activity and expression of citrate synthase, aconitase and NADP-isocitrate dehydrogenase (IDH) were studied in detail. The role that each enzyme plays in acid accumulation and decline was evaluated. As a result, a better understanding of the metabolic changes that contribute to acid accumulation was achieved. It was found that the activity of the mitochondrial aconitase is greatly reduced early in high-acid fruits, but not in acidless ones, suggesting that this enzyme plays an important role in acid accumulation. In addition, it was demonstrated that increases in the cytosolic forms of aconitase and NADP-IDH towards fruit maturation play probably a major role in acid decline. Our studies also demonstrated that the two mechanisms that contribute to fruit acidity, vacuolar acidification and citric acid accumulation, are independent, although they are tightly co-regulated. Additional, we demonstrated that sodium arsenite, which reduce fruit acidity, causes a transient inhibition in the activity of citrate synthase, but an induction in the gene expression. This part of the work has resulted in 4 papers. Objective 3 was also fully achieved. Using bulked segregant analysis, three random amplified polymorphic DNA (RAPD) markers were identified as linked to acitric, a gene controlling the acidless phenotype of pummelo 2240. One of them, which mapped 1.2 cM from acitric was converted into sequence characterized amplified region (SCAR marker, and into co dominant restriction length polymorphism (RFLP) marker. These markers were highly polymorphic among 59 citrus accessions, and therefore, they should be useful for selecting seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 and other citrus genotypes. This part of the project resulted in one paper. Objective 4 was also fully achieved. Clones isolated by the Israeli group were sent to the American laboratory for co segregation analysis. However, none of them seemed to co segregate with the low acid phenotype. Both laboratories invested much effort in achieving the goals of Objective 2, namely the isolation of genes that are elevated in expression in low and high acid phenotypes, and in tissue cultures treated with arsenite (a treatment which reduces fruit acidity). However, conventional differential display and restriction fragment differential display analyses could not identify any differentially expressed genes. The isolation of such genes was the major aim of a continuation project, which was recently submitted.
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Murray, Chris, Keith Williams, Norrie Millar, Monty Nero, Amy O'Brien, and Damon Herd. A New Palingenesis. University of Dundee, November 2022. http://dx.doi.org/10.20933/100001273.

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Robert Duncan Milne (1844-99), from Cupar, Fife, was a pioneering author of science fiction stories, most of which appeared in San Francisco’s Argonaut magazine in the 1880s and ’90s. SF historian Sam Moskowitz credits Milne with being the first full-time SF writer, and his contribution to the genre is arguably greater than anyone else including Stevenson and Conan Doyle, yet it has all but disappeared into oblivion. Milne was fascinated by science. He drew on the work of Scottish physicists and inventors such as James Clark Maxwell and Alexander Graham Bell into the possibilities of electromagnetic forces and new communications media to overcome distances in space and time. Milne wrote about visual time-travelling long before H.G. Wells. He foresaw virtual ‘tele-presencing’, remote surveillance, mobile phones and worldwide satellite communications – not to mention climate change, scientific terrorism and drone warfare, cryogenics and molecular reengineering. Milne also wrote on alien life forms, artificial immortality, identity theft and personality exchange, lost worlds and the rediscovery of extinct species. ‘A New Palingenesis’, originally published in The Argonaut on July 7th 1883, and adapted in this comic, is a secular version of the resurrection myth. Mary Shelley was the first scientiser of the occult to rework the supernatural idea of reanimating the dead through the mysterious powers of electricity in Frankenstein (1818). In Milne’s story, in which Doctor S- dissolves his terminally ill wife’s body in order to bring her back to life in restored health, is a striking, further modernisation of Frankenstein, to reflect late-nineteenth century interest in electromagnetic science and spiritualism. In particular, it is a retelling of Shelley’s narrative strand about Frankenstein’s aborted attempt to shape a female mate for his creature, but also his misogynistic ambition to bypass the sexual principle in reproducing life altogether. By doing so, Milne interfused Shelley’s updating of the Promethean myth with others. ‘A New Palingenesis’ is also a version of Pygmalion and his male-ordered, wish-fulfilling desire to animate his idealised female sculpture, Galatea from Ovid’s Metamorphoses, perhaps giving a positive twist to Orpheus’s attempt to bring his corpse-bride Eurydice back from the underworld as well? With its basis in spiritualist ideas about the soul as a kind of electrical intelligence, detachable from the body but a material entity nonetheless, Doctor S- treats his wife as an ‘intelligent battery’. He is thus able to preserve her personality after death and renew her body simultaneously because that captured electrical intelligence also carries a DNA-like code for rebuilding the individual organism itself from its chemical constituents. The descriptions of the experiment and the body’s gradual re-materialisation are among Milne’s most visually impressive, anticipating the X-raylike anatomisation and reversal of Griffin’s disappearance process in Wells’s The Invisible Man (1897). In the context of the 1880s, it must have been a compelling scientisation of the paranormal, combining highly technical descriptions of the Doctor’s system of electrically linked glass coffins with ghostly imagery. It is both dramatic and highly visual, even cinematic in its descriptions, and is here brought to life in the form of a comic.
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Kapulnik, Yoram, and Donald A. Phillips. Isoflavonoid Regulation of Root Bacteria. United States Department of Agriculture, January 1996. http://dx.doi.org/10.32747/1996.7570561.bard.

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The overall objective of this project was to develop a conceptual framework for enhancing root colonization by beneficial bacteria. To accomplish this aim we tested the hypothesis that production and excretion of the plant phytoalexin medicarpin can be used for creation of a special niche along the legume roots, where beneficial microorganism, such as rhizobium, will have a selective advantage. On the Israeli side it was shown that higher medicarpin levels are exuded following the application of Rhizobium meliloti to the rhizosphere but the specific biochemical pathway governing medicarpin production was not induced significantly enough to support a constant production and excretion of this molecule to the rhizosphere. Furthermore, pathogenic bacteria and chemical elicitors were found to induce higher levels of this phytoalexin and it became important to test its natural abundance in field grown plants. On the US side, the occurrence of flavonoids and nucleosides in agricultural soils has been evaluated and biologically significant quantities of these molecules were identified. A more virulent Agrobacterium tumefaciens strain was isolated from alfalfa (Medicago sativa L.) which forms tumors on a wide range of plant species. This isolate contains genes that increase competitive colonization abilities on roots by reducing the accumulation of alfalfa isoflavonoids in the bacterial cells. Following gene tagging efforts the US lab found that mutation in the bacterial efflux pump operons of this isolate reduced its competitive abilities. This results support our original hypothesis that detoxification activity of isoflavenoids molecules, based on bacterial gene(s), is an important selection mechanism in the rhizosphere. In addition, we focused on biotin as a regulatory element in the rhizosphere to support growth of some rhizosphere microorganisms and designed a bacterial gene construct carrying the biotin-binding protein, streptavidin. Expressing this gene in tobacco roots did not affect the biotin level but its expression in alfalfa was lethal. In conclusion, the collaborative combination of basic and applied approaches toward the understanding of rhizosphere activity yielded new knowledge related to the colonization of roots by beneficial microorganisms in the presence of biological active molecules exuded from the plant roots.
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