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Journal articles on the topic 'MOLECULAR PRINCIPLE'

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Author: Grafiati

Published: 11 September 2023

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1

Bernasconi, M., G. L. Chiarotti, P. Focher, S. Scandolo, E. Tosatti, and M. Parrinello. "First-principle-constant pressure molecular dynamics." Journal of Physics and Chemistry of Solids 56, no. 3-4 (March 1995): 501–5. http://dx.doi.org/10.1016/0022-3697(94)00228-2.

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2

Naeim, Ihab H., J. Batle, S. Kadry, and O. Tarawneh. "Molecular Dynamics Simulations and the Landauer’s Principle." Open Systems & Information Dynamics 25, no. 02 (June 2018): 1850006. http://dx.doi.org/10.1142/s1230161218500063.

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Landauer’s principle is a fundamental link between thermodynamics and information theory, which implies that the erasure of information comes at an energetic price. In the present contribution we analyze to what extend the usual molecular dynamics (MD) simulation formalism can handle the Landauer’s bound kBT ln 2 in the simplest case of one particle treated classically. The erasure of one bit of information is performed by adiabatically varying the shape of a bistable potential in a full cycle. We will highlight the inadequacy of either the microcanonical or canonical ensemble treatments currently employed in MD simulations and propose potential solutions.

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3

Son, Joo-Hiuk. "Principle and applications of terahertz molecular imaging." Nanotechnology 24, no. 21 (April 25, 2013): 214001. http://dx.doi.org/10.1088/0957-4484/24/21/214001.

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4

Prasanna de Silva, A., and Nathan D. McClenaghan. "Proof-of-Principle of Molecular-Scale Arithmetic." Journal of the American Chemical Society 122, no. 16 (April 2000): 3965–66. http://dx.doi.org/10.1021/ja994080m.

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5

Jain, Abhinandan, In-Hee Park, and Nagarajan Vaidehi. "Equipartition Principle for Internal Coordinate Molecular Dynamics." Journal of Chemical Theory and Computation 8, no. 8 (July 26, 2012): 2581–87. http://dx.doi.org/10.1021/ct3002046.

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6

MCCONNELL, D. "C026 The principle ideas of molecular biology." Journal of the European Academy of Dermatology and Venereology 9 (September 1997): S64. http://dx.doi.org/10.1016/s0926-9959(97)89105-2.

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7

OGATA, SHIGENOBU. "First-Principle Molecular Dynamics Methods and Its Applications." NIPPON GOMU KYOKAISHI 72, no. 11 (1999): 647–52. http://dx.doi.org/10.2324/gomu.72.647.

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8

Yunusov, M. B., and R. M. Khusnutdinov. "First-Principle Molecular Dynamics Study of Methane Hydrate." Journal of Physics: Conference Series 2270, no. 1 (May 1, 2022): 012052. http://dx.doi.org/10.1088/1742-6596/2270/1/012052.

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Abstract Currently, much attention of the scientific community and the gas industry is focused on the structural, physical and thermodynamic properties of gas hydrates. This interest is explained by the fact that there is a prospect of using natural gas hydrates as a new fuel source. This article presents the results obtained during the first-principle molecular dynamic study of the thermal and electronic properties of hydrates. For hydrates of methane with cubic sI and hexagonal sH configurations, the average heat capacity Cv was computed. The densities of electronic states are studied for filled and unfilled configurations of sI and sH hydrates. The spectra of electron energy were calculated for sI hydrate, which has unfilled molecular cages. Also, for methane and ethane hydrates, the binding energies between the framework and the gas molecule are calculated.

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9

R. Kokil, Ganesh, and Prarthana V. Rewatkar. "Bioprecursor Prodrugs: Molecular Modification of the Active Principle." Mini-Reviews in Medicinal Chemistry 10, no. 14 (December 1, 2010): 1316–30. http://dx.doi.org/10.2174/138955710793564179.

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10

Duval, P., A. Raynaud, and C. Saulgeot. "The molecular drag pump: Principle, characteristics, and applications." Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films 6, no. 3 (May 1988): 1187–91. http://dx.doi.org/10.1116/1.575674.

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11

Fuentealba, P., Y. Simón-Manso, and Pratim K. Chattaraj. "Molecular Electronic Excitations and the Minimum Polarizability Principle." Journal of Physical Chemistry A 104, no. 14 (April 2000): 3185–87. http://dx.doi.org/10.1021/jp992973v.

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12

Duval, P., A. Raynaud, and C. Saulgeot. "The molecular drag pump: principle, characteristics and applications." Vacuum 39, no. 7-8 (January 1989): 864. http://dx.doi.org/10.1016/0042-207x(89)90077-8.

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13

Uehara, K., M. Ishitobi, T. Oda, and Y. Hiwatari. "First-principle molecular dynamics calculation of selenium clusters." Zeitschrift f�r Physik D Atoms, Molecules and Clusters 40, no. 1-4 (May 1, 1997): 472–75. http://dx.doi.org/10.1007/s004600050255.

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14

Xiong, Ren-Gen, Da-Wei Fu, and Yi Zhang. "Applications of Curie symmetry principle in molecular ferroelectrics." Acta Crystallographica Section A Foundations and Advances 73, a2 (December 1, 2017): C33. http://dx.doi.org/10.1107/s2053273317095377.

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15

Luo, Xiao, Luyan Gu, Xuhong Qian, and Youjun Yang. "Molecular probe design via the “covalent-assembly” principle." Chemical Communications 56, no. 64 (2020): 9067–78. http://dx.doi.org/10.1039/d0cc00542h.

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Fluorescent probes are useful molecular tools. We summarize the recent progress with the “covalent-assembly” design principle, which warrants high-performance fluorescence probes exhibiting a highly sensitive turn-on signal from the dark background.

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16

K�nig, B. "Molecular Recognition. The principle and recent chemical examples." Journal f�r Praktische Chemie/Chemiker-Zeitung 337, no. 1 (1995): 339–46. http://dx.doi.org/10.1002/prac.19953370174.

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17

Bader, R., and P. Kramer. "The U(3) principle causes nuclear molecular resonances." Nuclear Physics A 441, no. 1 (July 1985): 174–88. http://dx.doi.org/10.1016/0375-9474(85)90174-5.

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18

Li, Jiu. "Multiscale Modeling Techniques Based on Molecular Structure and Elastic Properties." Applied Mechanics and Materials 312 (February 2013): 438–41. http://dx.doi.org/10.4028/www.scientific.net/amm.312.438.

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Based on the principle of using atomistic force field, and the use of ultra-flexible multi-scale modeling techniques to predict the polycarbonate and polyimide polymer molecular structure and the elastic properties of the system. The model combines molecular modeling and nonlinear continuum mechanics basic principles, to simulate and predict the behavior of the material properties of the polymer molecular structure. For the polymer structure and properties, using a plurality of force field simulation to predict the contrast, and binding experiments measured polymer performance value, using static and dynamic molecular simulation technology for molecular mechanics energy minimization to solve.

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19

Wang, Shao Qing. "Atomic Modeling and Simulation of AlCoCrCuFeNi Multi-Principal-Element Alloy." Materials Science Forum 749 (March 2013): 479–83. http://dx.doi.org/10.4028/www.scientific.net/msf.749.479.

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Atomic structure model of bulk AlCoCrCuFeNi multi-principal-element alloy was build by following the principle of maximum entropy. Morse pair-potentials to describe the inter-atomic interaction among neighboring atoms in the alloy were generated directly from first-principles calculations within density-functional theory. Molecular statics simulation was carried out to achieve the optimized atomic configuration of AlCoCrCuFeNi alloy. The results show that the crystallographic behavior in lattice structure observed experimentally is just caused by the average of the disordered atomic position and composition in wide range since there is neither short-range nor long-range order in the local atomic arrangement of this kind of materials.

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20

Malyshko, Ekaterina V., Ekaterina V. Semenova, Olga E. Bagrova, Alina R. Murtazina, and Vsevolod A. Tverdislov. "Chiral Dualism as a Unifying Principle in Molecular Biophysics." Biophysica 1, no. 1 (February 8, 2021): 22–37. http://dx.doi.org/10.3390/biophysica1010003.

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The origin and potential role of chiral asymmetry remain one of the most exciting issues in biology. In this paper we review the chirality of biological macromolecules, starting at the level of single molecules and continuing to the level of supramolecular assemblies. We discuss the physical and chemical consequences of the presence of chirality and their role in the self-organization and formation of structural hierarchies in cells. Homochirality may serve as an essential factor that invokes mechanisms required to control the formation of discrete structural hierarchies in macromolecules and macromolecular assemblies. Symmetry is of fundamental importance not only for all molecular biology as a systemic factor of its organization but also for pharmacology, as well as a systemic factor of drug stereospecificity.

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21

Astumian, R. Dean. "Microscopic reversibility as the organizing principle of molecular machines." Nature Nanotechnology 7, no. 11 (November 2012): 684–88. http://dx.doi.org/10.1038/nnano.2012.188.

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22

Wang, Jiaxing, Bonan Yin, and Mugen Peng. "Diffusion based molecular communication: principle, key technologies, and challenges." China Communications 14, no. 2 (February 2017): 1–18. http://dx.doi.org/10.1109/cc.2017.7868158.

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23

Van Wijk, R., and FAC Wiegant. "Postconditioning hormesis and the homeopathic Similia principle: Molecular aspects." Human & Experimental Toxicology 29, no. 7 (June 17, 2010): 561–65. http://dx.doi.org/10.1177/0960327110369860.

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Postexposure conditioning, as a part of hormesis, involves the application of a low dose of stress following exposure to a severe stress condition. Depending on whether the low-dose stress is of the same type of stress or is different from the initial high-dose stress causing the diseased state, postconditioning can be classified as homologous or heterologous, respectively. In clinical homeopathy, the same distinction is found between isopathic and homeopathic application of low-dose substances. Homeopathy is unique for its Similia principle, which implies that substances causing symptoms in healthy biological systems can be used to treat similar symptoms in diseased biological systems. The evaluation of the Similia principle in an experimental set-up requires the analysis of a complex sequence of ‘damage-disease-treatment-effect’ events. The process of recovery from an insult is then monitored and a possible beneficial effect on this recovery process, upon application of a range of substances in low dose, can subsequently be analyzed using molecular and functional parameters. It is then possible to compare the effect of treatment with the degree of similarity between the diseased state and the effects caused by homologous and/or different heterologous substances. Beneficial effects of postconditioning mild stress conditions have been described in terms of an increase of the synthesis of stress proteins. In this commentary paper, we present additional information on this aspect. The experimental data suggest that the beneficial effect of the low-dose stress condition used as heterologous postconditioning is related to similarity in molecular stress response.

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24

Kang, Hong Seok, and J. Bernholc. "First-Principle Study of Molecular Springs under Shear Deformation." Journal of Physical Chemistry A 107, no. 9 (March 2003): 1377–83. http://dx.doi.org/10.1021/jp0267353.

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25

Harde, Hermann, and Daniel Grischkowsky. "Molecular Response Theory in Terms of the Uncertainty Principle." Journal of Physical Chemistry A 119, no. 34 (August 17, 2015): 9085–90. http://dx.doi.org/10.1021/acs.jpca.5b05909.

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26

Lisowski, Bartosz, Łukasz Kuśmierz, Michał Żabicki, and Martin Bier. "“Cargo-mooring” as an operating principle for molecular motors." Journal of Theoretical Biology 374 (June 2015): 26–34. http://dx.doi.org/10.1016/j.jtbi.2015.03.007.

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27

Bertoni, C. M., R. Di Felice, and C. A. Pignedoli. "First-principle simulations of molecular processes at semiconductor surfaces." Il Nuovo Cimento D 20, no. 7-8 (July 1998): 967–74. http://dx.doi.org/10.1007/bf03185500.

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28

Rajapaksa, I., K. Uenal, and H. Kumar Wickramasinghe. "Image force microscopy of molecular resonance: A microscope principle." Applied Physics Letters 97, no. 7 (August 16, 2010): 073121. http://dx.doi.org/10.1063/1.3480608.

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29

Gros, François. "The mobility principle: How I became a molecular biologist." Journal of Biosciences 31, no. 3 (September 2006): 303–8. http://dx.doi.org/10.1007/bf02704102.

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30

Pan, Peichen, Youyong Li, Huidong Yu, Huiyong Sun, and Tingjun Hou. "Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches." Journal of Chemical Information and Modeling 53, no. 4 (April 3, 2013): 997–1006. http://dx.doi.org/10.1021/ci400066x.

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31

Seaquist, Elizabeth R., Andrew J. M. Boulton, R. Mack Harrell, George Grunberger, and Richard J. Santen. "Statement of Principle." Molecular Endocrinology 28, no. 12 (December 1, 2014): 1918. http://dx.doi.org/10.1210/me.2014-1338.

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32

Toro, M. A. "Future trends in Animal Breeding due to new genetic technologies." Advances in Animal Biosciences 1, no. 3 (January 6, 2011): 546–57. http://dx.doi.org/10.1017/s2040470010005431.

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The Darwin theory of evolution by natural selection is based on three principles: (a) variation; (b) inheritance; and (c) natural selection. Here, I take these principles as an excuse to review some topics related to the future research prospects in Animal Breeding. With respect to the first principle I describe two forms of variation different from mutation that are becoming increasingly important: variation in copy number and microRNAs. With respect to the second principle I comment on the possible relevance of non-mendelian inheritance, the so-called epigenetic effects, of which the genomic imprinting is the best characterized in domestic species. Regarding selection principle I emphasize the importance of selection for social traits and how this could contribute to both productivity and animal welfare. Finally, I analyse the impact of molecular biology in Animal Breeding, the achievements and limitations of quantitative trait locus and classical marker-assisted selection and the future of genomic selection.

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33

Stark, Alan E. "The Hardy-Weinberg principle." Genetics and Molecular Biology 28, no. 3 (September 2005): 485. http://dx.doi.org/10.1590/s1415-47572005000300027.

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34

Fink, Gerald R. "A Transforming Principle." Cell 120, no. 2 (January 2005): 153–54. http://dx.doi.org/10.1016/j.cell.2005.01.004.

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35

Janoušek, B., and J. Žlůvová. "Mapping of non-recombining regions via molecular markers." Plant, Soil and Environment 53, No. 7 (January 7, 2008): 321–24. http://dx.doi.org/10.17221/2207-pse.

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The lack of recombination in some genomic regions represents a serious obstacle in mapping studies. In this review, we describe methods that are currently used to overcome this problem. Main attention is given to the comparison of methods that are based on the principle of radiation hybrid mapping. We also discuss a strategy called HAPPY mapping (mapping based on the analysis of approximately HAPloid DNA samples using the PolYmerase chain reaction). In addition to reviewing the methods used by other authors, we also summarize our experience with deletion mapping of Y-chromosome in dioecious model plant species (<i>Silene latifolia</i>).

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36

Wang, Yue, Jianhua Xuan, Rujirutana Srikanchana, and Peter L. Choyke. "Modeling and Reconstruction of Mixed Functional and Molecular Patterns." International Journal of Biomedical Imaging 2006 (2006): 1–9. http://dx.doi.org/10.1155/ijbi/2006/29707.

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Functional medical imaging promises powerful tools for the visualization and elucidation of important disease-causing biological processes in living tissue. Recent research aims to dissect the distribution or expression of multiple biomarkers associated with disease progression or response, where the signals often represent a composite of more than one distinct source independent of spatial resolution. Formulating the task as a blind source separation or composite signal factorization problem, we report here a statistically principled method for modeling and reconstruction of mixed functional or molecular patterns. The computational algorithm is based on a latent variable model whose parameters are estimated using clustered component analysis. We demonstrate the principle and performance of the approaches on the breast cancer data sets acquired by dynamic contrast-enhanced magnetic resonance imaging.

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37

Shi, Ping-Ping, Yuan-Yuan Tang, Peng-Fei Li, Wei-Qiang Liao, Zhong-Xia Wang, Qiong Ye, and Ren-Gen Xiong. "Symmetry breaking in molecular ferroelectrics." Chemical Society Reviews 45, no. 14 (2016): 3811–27. http://dx.doi.org/10.1039/c5cs00308c.

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Symmetry breaking occurs between the high-temperature, high-symmetry paraelectric phase and the low-temperature, low-symmetry ferroelectric phase along with a reduction in the number of symmetry elements, obeying the Curie symmetry principle and relating to the ferroelectricity.

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38

Van Wijk, R., and F. A. C. Wiegant. "Stimulation of self-recovery by similia principle?" British Homeopathic Journal 84, no. 03 (July 1995): 131–39. http://dx.doi.org/10.1016/s0007-0785(05)80063-8.

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AbstractThis paper describes how the similia principle can be studied best in fundamental research. 2 questions are raised: ‘What is known about the regulatory principles at which homoeopathic treatment is directed?’ and ‘In what kind of conditions can these regulatory principles be studied best?’ The vision of Hahnemann and ideas related to the ‘field concept’ developed in this century are discussed.With respect to the first question, the phenomenon of ‘self-recovery’ takes a central position. The essence of homoeopathy is stimulation of self-recovery by application of the similia principle. By analysing self-recovery on different levels, we conclude that research on the molecular and cell biological level can use low potencies only (containing molecules of the original substance). We consider whether stimulation of disturbed self-repair occurs by application of low doses of the disturbing agent.At the cellular level ‘self-repair’ can be defined as a supplementation of protector proteins, an enhancement of resistance to the disturbing agent and a temporary stimulation of proliferation in order to compensate for cell death. These parameters are clearly defined and can be measured using highly standardised and validated cell biological techniques.

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39

Yuan Zhe, He Chun-Long, Wang Xiao-Lu, Liu Hai-Tao, and Li Jia-Ming. "First-principle molecular dynamics study of clusters:optimum valence bond scheme." Acta Physica Sinica 54, no. 2 (2005): 628. http://dx.doi.org/10.7498/aps.54.628.

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40

Michalak, Artur, and Tom Ziegler. "First-Principle Molecular Dynamic Simulations along the Intrinsic Reaction Paths." Journal of Physical Chemistry A 105, no. 17 (May 2001): 4333–43. http://dx.doi.org/10.1021/jp0041297.

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41

Magnasco, Valerio. "On the principle of maximum overlap in molecular orbital theory." Chemical Physics Letters 407, no. 1-3 (May 2005): 213–16. http://dx.doi.org/10.1016/j.cplett.2005.03.101.

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42

Peters, Jürgen, Anne-Marie Schönegge, Beate Rockel, and Wolfgang Baumeister. "Molecular ruler of tripeptidylpeptidase II: Mechanistic principle of exopeptidase selectivity." Biochemical and Biophysical Research Communications 414, no. 1 (October 2011): 209–14. http://dx.doi.org/10.1016/j.bbrc.2011.09.058.

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43

Borah, Sangkha, and P. Padma Kumar. "First-Principle Molecular Dynamics Investigation of Waterborne As-V Species." Journal of Physical Chemistry B 122, no. 12 (March 2018): 3153–62. http://dx.doi.org/10.1021/acs.jpcb.7b12482.

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44

Turco, A., D. Passerone, and F. Cardin. "Tonelli Principle: Finite Reduction and Fixed Energy Molecular Dynamics Trajectories." Multiscale Modeling & Simulation 7, no. 3 (January 2009): 1171–91. http://dx.doi.org/10.1137/080724319.

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45

Hulliger, Jürg, Thomas Wüst, Khadidja Brahimi, Matthias Burgener, and Hanane Aboulfadl. "A stochastic principle behind polar properties of condensed molecular matter." New Journal of Chemistry 37, no. 8 (2013): 2229. http://dx.doi.org/10.1039/c3nj40935j.

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46

Goldman, Saul, and Bijoy Kumar. "The use of the variational principle in molecular perturbation theory." Journal of Chemical Physics 82, no. 9 (May 1985): 4276–82. http://dx.doi.org/10.1063/1.448818.

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47

KOENIG, B. "ChemInform Abstract: Molecular Recognition. The Principle and Recent Chemical Examples." ChemInform 26, no. 45 (August 17, 2010): no. http://dx.doi.org/10.1002/chin.199545291.

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48

Fuxe, K., M. Canals, M. Torvinen, D. Marcellino, A. Terasmaa, S. Genedani, G. Leo, et al. "Intramembrane receptor–receptor interactions: a novel principle in molecular medicine." Journal of Neural Transmission 114, no. 1 (October 27, 2006): 49–75. http://dx.doi.org/10.1007/s00702-006-0589-0.

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49

Daivis, Peter, and Billy Todd. "Challenges in Nanofluidics—Beyond Navier–Stokes at the Molecular Scale." Processes 6, no. 9 (September 1, 2018): 144. http://dx.doi.org/10.3390/pr6090144.

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The fluid dynamics of macroscopic and microscopic systems is well developed and has been extensively validated. Its extraordinary success makes it tempting to apply Navier–Stokes fluid dynamics without modification to systems of ever decreasing dimensions as studies of nanofluidics become more prevalent. However, this can result in serious error. In this paper, we discuss several ways in which nanoconfined fluid flow differs from macroscopic flow. We give particular attention to several topics that have recently received attention in the literature: slip, spin angular momentum coupling, nonlocal stress response and density inhomogeneity. In principle, all of these effects can now be accurately modelled using validated theories. Although the basic principles are now fairly well understood, much work remains to be done in their application.

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50

Yang, Weitao, Chengteh Lee, and Swapan K. Ghosh. "Molecular softness as the average of atomic softnesses: companion principle to the geometric mean principle for electronegativity equalization." Journal of Physical Chemistry 89, no. 25 (December 1985): 5412–14. http://dx.doi.org/10.1021/j100271a019.

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