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Journal articles on the topic 'Energy of binding'

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Published: 6 September 2023
Last updated: 7 September 2023

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1

Kızılcık, Hasan Şahin. "Does binding energy bind?" Physics Education 56, no. 3 (February 24, 2021): 033005. http://dx.doi.org/10.1088/1361-6552/abe5b7.

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2

Englert, Berthold-Georg, and Julian Schwinger. "Atomic-binding-energy oscillations." Physical Review A 32, no. 1 (July 1, 1985): 47–63. http://dx.doi.org/10.1103/physreva.32.47.

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3

Lecker, Douglas N., Sangeeta Kumari, and Arshad Khan. "Iodine binding capacity and iodine binding energy of glycogen." Journal of Polymer Science Part A: Polymer Chemistry 35, no. 8 (June 1997): 1409–12. http://dx.doi.org/10.1002/(sici)1099-0518(199706)35:8<1409::aid-pola9>3.0.co;2-u.

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4

Nadeau, M.-J., X.-L. Zhao, M. A. Garwan, and A. E. Litherland. "Ca negative-ion binding energy." Physical Review A 46, no. 7 (October 1, 1992): R3588—R3590. http://dx.doi.org/10.1103/physreva.46.r3588.

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5

Filikhin, Igor, Vladimir Suslov, and Branislav Vlahovic. "Hyperon binding energy inΛ6He andΛ7He." EPJ Web of Conferences 113 (2016): 07008. http://dx.doi.org/10.1051/epjconf/201611307008.

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6

Bizon, P., E. Malec, and N. O. Murchadha. "Binding energy for spherical stars." Classical and Quantum Gravity 7, no. 11 (November 1, 1990): 1953–59. http://dx.doi.org/10.1088/0264-9381/7/11/008.

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7

Ho, Y. K. "Binding energy of positronium molecules." Physical Review A 33, no. 5 (May 1, 1986): 3584–87. http://dx.doi.org/10.1103/physreva.33.3584.

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8

Hansen, David E., and Ronald T. Raines. "Binding energy and enzymatic catalysis." Journal of Chemical Education 67, no. 6 (June 1990): 483. http://dx.doi.org/10.1021/ed067p483.

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9

Bellert, D., T. Buthelezi, K. Dezfulian, T. Hayes, and P. J. Brucat. "The binding energy of VXe+." Chemical Physics Letters 260, no. 3-4 (September 1996): 458–64. http://dx.doi.org/10.1016/0009-2614(96)00848-2.

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10

Abdel-Raouf, Mohamed Assad. "Binding energy of protonium ions." Journal of Physics: Conference Series 194, no. 7 (November 1, 2009): 072003. http://dx.doi.org/10.1088/1742-6596/194/7/072003.

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11

Lifshitz, C. "C2 binding energy in C60." International Journal of Mass Spectrometry 198, no. 1-2 (April 2000): 1–14. http://dx.doi.org/10.1016/s1387-3806(00)00192-5.

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12

Kröger, H., and R. Perne. "Few-body binding-energy correlations." Canadian Journal of Physics 63, no. 3 (March 1, 1985): 366–70. http://dx.doi.org/10.1139/p85-057.

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Few-nucleon binding-energy correlations are discussed. The first-order correction in the propagator potential range ratio is estimated. The class of potentials is generalized from the previously considered rank-one separable potential. Similar results are predicted for few-atomic molecule clusters.
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13

Miki, Hisami. "Binding energy and mass defect." Physics Education 25, no. 6 (November 1, 1990): 322–24. http://dx.doi.org/10.1088/0031-9120/25/6/307.

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14

Suffczyński, M., and L. Wolniewicz. "Binding Energy of Muonium Hydride." Acta Physica Polonica A 83, no. 2 (February 1993): 157–59. http://dx.doi.org/10.12693/aphyspola.83.157.

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15

Kubinec, P., and J. Krištiak. "Precise deuteron binding energy calculations." Czechoslovak Journal of Physics 35, no. 2 (February 1985): 103–9. http://dx.doi.org/10.1007/bf01595622.

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16

Bitencourt-Ferreira, Gabriela, and Walter Filgueira de Azevedo Junior. "Electrostatic Potential Energy in Protein-Drug Complexes." Current Medicinal Chemistry 28, no. 24 (August 13, 2021): 4954–71. http://dx.doi.org/10.2174/0929867328666210201150842.

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Background: Electrostatic interactions are one of the forces guiding the binding of molecules to proteins. The assessment of this interaction through computational approaches makes it possible to evaluate the energy of protein-drug complexes. Objective: Our purpose here is to review some the of methods used to calculate the electrostatic energy of protein-drug complexes and explore the capacity of these approaches for the generation of new computational tools for drug discovery using the abstraction of scoring function space. Method: Here we present an overview of AutoDock4 semi-empirical scoring function used to calculate binding affinity for protein-drug complexes. We focus our attention on electrostatic interactions and how to explore recently published results to increase the predictive performance of the computational models to estimate the energetics of protein-drug interactions. Public data available at Binding MOAD, BindingDB, and PDBbind were used to review the predictive performance of different approaches to predict binding affinity. Results: A comprehensive outline of the scoring function used to evaluate potential energy available in docking programs is presented. Recent developments of computational models to predict protein-drug energetics were able to create targeted-scoring functions to predict binding to these proteins. These targeted models outperform classical scoring functions and highlight the importance of electrostatic interactions in the definition of the binding. Conclusion: Here, we reviewed the development of scoring functions to predict binding affinity through the application of a semi-empirical free energy scoring function. Our studies show the superior predictive performance of machine learning models when compared with classical scoring functions and the importance of electrostatic interactions for binding affinity.
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17

Ortiz, Angel R., M. Teresa Pisabarro, Federico Gago, and Rebecca C. Wade. "Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis." Journal of Medicinal Chemistry 38, no. 14 (July 1995): 2681–91. http://dx.doi.org/10.1021/jm00014a020.

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18

Mentes, Ahmet, Nan-Jie Deng, R. S. K. Vijayan, Junchao Xia, Emilio Gallicchio, and Ronald M. Levy. "Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation." Journal of Chemical Theory and Computation 12, no. 5 (April 26, 2016): 2459–70. http://dx.doi.org/10.1021/acs.jctc.6b00134.

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19

Taqi, A. "Binding energy of excitons in parabolic quantum wells in uniform electric and magnetic fields." Semiconductor Physics Quantum Electronics and Optoelectronics 15, no. 1 (March 29, 2012): 21–25. http://dx.doi.org/10.15407/spqeo15.01.021.

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20

Neoustroev, S. A. "Binding Energy of Cubic Carbon Atoms." Proceedings of Universities. Electronics 26, no. 6 (December 2021): 580–83. http://dx.doi.org/10.24151/1561-5405-2021-26-6-580-583.

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Energy spectrum of gas particles in plasma is broad, ranging from fractions to 10s of electron volts. Proportion of particles with required energetic parameters, participating in cubic carbon c-C synthesis, is small. External energy deposition can transfer an inert carbon atom to active state and change its electronic configuration. Binding energy of c-C atom depends on energy sources interaction. In this work, the calculations found the binding energy value that was compared with value of energy of the bond between the carbon atoms in ethane. The advisability of external source, activated carbon atoms generator, is marked. It has been established that by adding accelerated carbon atoms with energy of 9,687 eV into reactor it is possible to increase productivity of films, coatings and bulk crystals growth.
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21

ACKLEH, E. S., G. D. MAHAN, and JI-WEI WU. "DONOR BINDING ENERGY IN TWO DIMENSIONS." Modern Physics Letters B 08, no. 17 (July 20, 1994): 1041–43. http://dx.doi.org/10.1142/s0217984994001035.

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We calculate numerically the binding energy of an electron bound to a proton in two-dimensional electron gas. Unlike the case in three dimensions, in 2D the binding energy is nonzero for all values of electron density.
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22

Lee, Lee-Peng, and Bruce Tidor. "Optimization of electrostatic binding free energy." Journal of Chemical Physics 106, no. 21 (June 1997): 8681–90. http://dx.doi.org/10.1063/1.473929.

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23

Hall, Richard L., and Wolfgang Lucha. "Binding energy of semirelativisticN-boson systems." Journal of Physics A: Mathematical and Theoretical 40, no. 23 (May 22, 2007): 6183–92. http://dx.doi.org/10.1088/1751-8113/40/23/012.

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24

Takemiya, T. "Binding Energy for Three-Nucleon System." Progress of Theoretical Physics 94, no. 1 (July 1, 1995): 143–46. http://dx.doi.org/10.1143/ptp/94.1.143.

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25

Kristensen, P., U. V. Pedersen, V. V. Petrunin, T. Andersen, and K. T. Chung. "Binding energy of the metastableHe−ion." Physical Review A 55, no. 2 (February 1, 1997): 978–83. http://dx.doi.org/10.1103/physreva.55.978.

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26

Pedersen, U. V., H. H. Andersen, T. Andersen, and L. Veseth. "Binding energy of the metastableAr−ion." Physical Review A 58, no. 1 (July 1, 1998): 258–63. http://dx.doi.org/10.1103/physreva.58.258.

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27

Koc, P., and E. Malec. "Binding energy for charged spherical bodies." Classical and Quantum Gravity 7, no. 9 (September 1, 1990): L199—L201. http://dx.doi.org/10.1088/0264-9381/7/9/003.

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28

Karkowski, Janusz, and Edward Malec. "Binding energy of static perfect fluids." Classical and Quantum Gravity 21, no. 16 (August 3, 2004): 3923–32. http://dx.doi.org/10.1088/0264-9381/21/16/007.

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29

Singh, Jai, D. Birkedal, V. G. Lyssenko, and J. M. Hvam. "Binding energy of two-dimensional biexcitons." Physical Review B 53, no. 23 (June 15, 1996): 15909–13. http://dx.doi.org/10.1103/physrevb.53.15909.

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30

Parra, R. D., and H. H. Farrell. "Binding Energy of Metal Oxide Nanoparticles." Journal of Physical Chemistry C 113, no. 12 (March 3, 2009): 4786–91. http://dx.doi.org/10.1021/jp807070a.

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31

Peeters, F. M., and J. E. Golub. "Binding energy of the barbell exciton." Physical Review B 43, no. 6 (February 15, 1991): 5159–62. http://dx.doi.org/10.1103/physrevb.43.5159.

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32

Kraner, Stefan, Giacomo Prampolini, and Gianaurelio Cuniberti. "Exciton Binding Energy in Molecular Triads." Journal of Physical Chemistry C 121, no. 32 (August 9, 2017): 17088–95. http://dx.doi.org/10.1021/acs.jpcc.7b03923.

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33

Blake, Russ. "The Architecture of Nuclear Binding Energy." Physics Procedia 22 (2011): 40–55. http://dx.doi.org/10.1016/j.phpro.2011.11.007.

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34

Sprague, D. T., N. Alikacem, P. A. Sheldon, and R. B. Hallock. "Binding energy of3He in thin4He films." Physica B: Condensed Matter 194-196 (February 1994): 629–30. http://dx.doi.org/10.1016/0921-4526(94)90644-0.

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35

Buthelezi, T., D. Bellert, T. Hayes, and P. J. Brucat. "The adiabatic binding energy of NbAr+." Chemical Physics Letters 262, no. 3-4 (November 1996): 303–7. http://dx.doi.org/10.1016/0009-2614(96)01095-0.

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36

Cenni, R., F. Conte, and G. Dillon. "Nuclear binding energy and pion dynamics." Lettere Al Nuovo Cimento Series 2 43, no. 1 (May 1985): 39–44. http://dx.doi.org/10.1007/bf02749493.

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37

Chen, B., M. Gao, J. M. Zuo, S. Qu, B. Liu, and Y. Huang. "Binding energy of parallel carbon nanotubes." Applied Physics Letters 83, no. 17 (October 27, 2003): 3570–71. http://dx.doi.org/10.1063/1.1623013.

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38

Sedhain, A., T. M. Al Tahtamouni, J. Li, J. Y. Lin, and H. X. Jiang. "Beryllium acceptor binding energy in AlN." Applied Physics Letters 93, no. 14 (October 6, 2008): 141104. http://dx.doi.org/10.1063/1.2996977.

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39

PIN-ZHEN, BI. "BINDING ENERGY AND DEEP INELASTIC SCATTERING." Modern Physics Letters A 03, no. 07 (June 1988): 653–59. http://dx.doi.org/10.1142/s0217732388000787.

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It is found that, by a simple assumption that was used to explain the EMC effect, the accuracy of the original Weizsäcker-Fermi mass formula can be greatly improved for light and intermediate nuclei, by merely adding one more parameter to the original five parameters.
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40

Nam, Phan Thành. "Binding energy of homogeneous Bose gases." Letters in Mathematical Physics 108, no. 1 (September 7, 2017): 141–59. http://dx.doi.org/10.1007/s11005-017-0992-5.

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41

Asher, R. L., D. Bellert, T. Buthelezi, G. Weerasekera, and P. J. Brucat. "The binding energy of Ni+·CO2." Chemical Physics Letters 228, no. 4-5 (October 1994): 390–92. http://dx.doi.org/10.1016/0009-2614(94)00970-8.

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42

Bellert, D., T. Buthelezi, V. Lewis, K. Dezfulian, and P. J. Brucat. "The binding energy of Ni+·N2O." Chemical Physics Letters 240, no. 5-6 (July 1995): 495–98. http://dx.doi.org/10.1016/0009-2614(95)00548-i.

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43

Eremeev, S. V., A. G. Lipnitskii, A. I. Potekaev, and E. V. Chulkov. "Divacancy binding energy at metal surfaces." Russian Physics Journal 40, no. 6 (June 1997): 579–83. http://dx.doi.org/10.1007/bf02766392.

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44

Re, Suyong, Hiraku Oshima, Kento Kasahara, Motoshi Kamiya, and Yuji Sugita. "Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape." Proceedings of the National Academy of Sciences 116, no. 37 (August 26, 2019): 18404–9. http://dx.doi.org/10.1073/pnas.1904707116.

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Modern drug discovery increasingly focuses on the drug-target binding kinetics which depend on drug (un)binding pathways. The conventional molecular dynamics simulation can observe only a few binding events even using the fastest supercomputer. Here, we develop 2D gREST/REUS simulation with enhanced flexibility of the ligand and the protein binding site. Simulation (43 μs in total) applied to an inhibitor binding to c-Src kinase covers 100 binding and unbinding events. On the statistically converged free-energy landscapes, we succeed in predicting the X-ray binding structure, including water positions. Furthermore, we characterize hidden semibound poses and transient encounter complexes on the free-energy landscapes. Regulatory residues distant from the catalytic core are responsible for the initial inhibitor uptake and regulation of subsequent bindings, which was unresolved by experiments. Stabilizing/blocking of either the semibound poses or the encounter complexes can be an effective strategy to optimize drug-target residence time.
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45

Bovolenta, Giulia M., Stefan Vogt-Geisse, Stefano Bovino, and Tommaso Grassi. "Binding Energy Evaluation Platform: A Database of Quantum Chemical Binding Energy Distributions for the Astrochemical Community." Astrophysical Journal Supplement Series 262, no. 1 (August 24, 2022): 17. http://dx.doi.org/10.3847/1538-4365/ac7f31.

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Abstract The quality of astrochemical models is highly dependent on reliable binding energy (BE) values that consider the morphological and energetic variety of binding sites on the surface of ice-grain mantles. Here, we present the Binding Energy Evaluation Platform (BEEP) and database that, using quantum chemical methods, produces full BE distributions of molecules bound to an amorphous solid water (ASW) surface model. BEEP is highly automatized and allows one to sample binding sites on a set of water clusters and to compute accurate BEs. Using our protocol, we computed 21 BE distributions of interstellar molecules and radicals on an amorphized set of 15–18 water clusters of 22 molecules each. The distributions contain between 225 and 250 unique binding sites. We apply a Gaussian fit and report the mean and standard deviation for each distribution. We compare with existing experimental results and find that the low- and high-coverage experimental BEs coincide well with the high-BE tail and mean value of our distributions, respectively. Previously reported single BE theoretical values are broadly in line with ours, even though in some cases significant differences can be appreciated. We show how the use of different BE values impacts a typical problem in astrophysics, such as the computation of snow lines in protoplanetary disks. BEEP will be publicly released so that the database can be expanded to other molecules or ice models in a community effort.
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46

Ganotra, Gaurav K., and Rebecca C. Wade. "Prediction of Drug–Target Binding Kinetics by Comparative Binding Energy Analysis." ACS Medicinal Chemistry Letters 9, no. 11 (October 4, 2018): 1134–39. http://dx.doi.org/10.1021/acsmedchemlett.8b00397.

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47

Almudallal, Ahmad M., Ivan Saika-Voivod, and John M. Stewart. "Folding and binding energy of a calmodulin-binding cell antiproliferative peptide." Journal of Molecular Graphics and Modelling 61 (September 2015): 281–89. http://dx.doi.org/10.1016/j.jmgm.2015.08.002.

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48

Chen, Thomas, Vitali Vougalter, and Semjon A. Vugalter. "The increase of binding energy and enhanced binding in nonrelativistic QED." Journal of Mathematical Physics 44, no. 5 (May 2003): 1961–70. http://dx.doi.org/10.1063/1.1562007.

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49

Henrich, Stefan, Isabella Feierberg, Ting Wang, Niklas Blomberg, and Rebecca C. Wade. "Comparative binding energy analysis for binding affinity and target selectivity prediction." Proteins: Structure, Function, and Bioinformatics 78, no. 1 (August 17, 2009): 135–53. http://dx.doi.org/10.1002/prot.22579.

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50

Wei, Y. B., Y. G. Ma, W. Q. Shen, G. L. Ma, K. Wang, X. Z. Cai, C. Zhong, W. Guo, and J. G. Chen. "Exploring binding energy and separation energy dependences of HBT strength." Physics Letters B 586, no. 3-4 (April 2004): 225–31. http://dx.doi.org/10.1016/j.physletb.2004.02.021.

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