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Journal articles on the topic 'Molecular computer'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Suyama, A. "Autonomous molecular computer." Seibutsu Butsuri 43, supplement (2003): S13. http://dx.doi.org/10.2142/biophys.43.s13_2.

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2

Haarer, D. "Molecular computer memory." Nature 355, no. 6358 (1992): 297–98. http://dx.doi.org/10.1038/355297a0.

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3

Stewart, Sharon D. "Computer generated molecular modeling." SIMULATION 47, no. 1 (1986): 18–23. http://dx.doi.org/10.1177/003754978604700104.

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4

McCammon, J. "Computer-aided molecular design." Science 238, no. 4826 (1987): 486–91. http://dx.doi.org/10.1126/science.3310236.

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5

Peplow, Mark. "Rebooting the Molecular Computer." ACS Central Science 2, no. 12 (2016): 874–77. http://dx.doi.org/10.1021/acscentsci.6b00376.

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6

N J White, D. "Computer-aided molecular design." Journal of Molecular Graphics 5, no. 2 (1987): 114. http://dx.doi.org/10.1016/0263-7855(87)80022-x.

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7

Graham Richards, W. "Computer-aided molecular design." Computer-Aided Design 17, no. 5 (1985): 215–18. http://dx.doi.org/10.1016/0010-4485(85)90072-7.

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8

North, Anthony C. T. "Computer-aided molecular design." Trends in Biochemical Sciences 11, no. 4 (1986): 191. http://dx.doi.org/10.1016/0968-0004(86)90143-x.

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9

Liang, Xin, Wen Zhu, Zhibin Lv, and Quan Zou. "Molecular Computing and Bioinformatics." Molecules 24, no. 13 (2019): 2358. http://dx.doi.org/10.3390/molecules24132358.

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Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies. Research and development in this area concerns theory, experiments, and applications of molecular computing. The core advantage of molecular computing is its potential to pack vastly more circuitry onto a microchip than silicon will ever be capable of—and to do it cheaply. Molecules are only a few nanometers in s

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10

Gruskin, Karen D., and Temple F. Smith. "Molecular genetics and computer analyses." Bioinformatics 3, no. 3 (1987): 167–70. http://dx.doi.org/10.1093/bioinformatics/3.3.167.

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11

Delarue, M. "Computer modelling in molecular biology." Biochimie 78, no. 1 (1996): 67. http://dx.doi.org/10.1016/s0300-9084(96)90003-6.

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12

Raugei, Simone, Daniel L. DuBois, Roger Rousseau, et al. "Toward Molecular Catalysts by Computer." Accounts of Chemical Research 48, no. 2 (2015): 248–55. http://dx.doi.org/10.1021/ar500342g.

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13

Klein, Michael L., and Roger W. Impey. "Computer simulation of molecular crystals." Journal de Chimie Physique 82 (1985): 111–15. http://dx.doi.org/10.1051/jcp/1985820111.

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14

Balasubramanian, K. "Computer Perception of Molecular Symmetry." Journal of Chemical Information and Modeling 35, no. 4 (1995): 761–70. http://dx.doi.org/10.1021/ci00026a015.

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15

Booth, AG. "Computer graphics and molecular modeling." Biochemical Education 15, no. 1 (1987): 51. http://dx.doi.org/10.1016/0307-4412(87)90169-5.

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16

Liberman, E. A., and S. V. Minina. "Molecular quantum computer of neuron." Biosystems 35, no. 2-3 (1995): 203–7. http://dx.doi.org/10.1016/0303-2647(94)01515-9.

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17

Murray-Rust, P., and J. Raftery. "Computer analysis of molecular geometry." Journal of Molecular Graphics 3, no. 2 (1985): 50–59. http://dx.doi.org/10.1016/0263-7855(85)80003-5.

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18

Gale, Julian D. "Computer session on molecular dynamics." EPJ Web of Conferences 14 (2011): 03005. http://dx.doi.org/10.1051/epjconf/20111403005.

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19

Nyborg, Jens. "Computer modelling in molecular biology." FEBS Letters 398, no. 2-3 (1996): 337. http://dx.doi.org/10.1016/0014-5793(97)81271-9.

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20

Alameri, A., I. Gutman, V. R. Kulli, A. Ayache, and M. Alsharafi. "Chemical Applications on General Zagreb Indices of Composite Graphs." international journal of mathematics and computer research 12, no. 03 (2024): 4114–18. http://dx.doi.org/10.47191/ijmcr/v12i3.06.

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A topological index is a quantity computed from the molecular graph, that finds application in chemistry, material science, computer science, and biological application-driven fields. Recently, the general Zagreb indices were studied, and methods for their calculation for composite graphs were established. In the present paper, we provide examples for chemical applications of these methods, computing the first and second general Zagreb indices of several composite molecular species, in particular of biphenyl, naphthalene, biphenylene, and bicoronylene. In this paper, we compute the Nirmala ind

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21

Lynden-Bell, R. M., D. J. C. Hutchinson, and M. J. Doyle. "Translational molecular motion and cages in computer molecular liquids." Molecular Physics 58, no. 2 (1986): 307–15. http://dx.doi.org/10.1080/00268978600101171.

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22

Bowen, J. Phillip, Paul S. Charifson, Peter C. Fox, et al. "Computer-Assisted Molecular Modeling: Indispensable Tools for Molecular Pharmacology." Journal of Clinical Pharmacology 33, no. 12 (1993): 1149–64. http://dx.doi.org/10.1002/j.1552-4604.1993.tb03915.x.

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23

Carleton, H. R. "Special-Purpose Computer for Molecular Dynamics." MRS Bulletin 11, no. 1 (1986): 38–39. http://dx.doi.org/10.1557/s088376940006975x.

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24

Padavic-Callaghan, Karmela. "Molecular computer is extremely energy efficient." New Scientist 255, no. 3394 (2022): 12. http://dx.doi.org/10.1016/s0262-4079(22)01196-4.

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25

Bărbulescu, Alina, Lucica Barbeș, and Cristian Ștefan Dumitriu. "Computer-Aided Methods for Molecular Classification." Mathematics 10, no. 9 (2022): 1543. http://dx.doi.org/10.3390/math10091543.

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The study aims to analyze the degree of similarity of some molecules belonging to two subgroups of Aminoalkylindoles. After extracting the molecules’ characteristics using Cheminformatics methods, and the computation of the Tanimoto coefficients, dendrograms and heatmaps were built to reveal the degree of similarity of the analyzed drugs. Some atom-pair similarities between the molecules in the same group were detected. The clusters determined by the k-means method divided the Benzoylindoles into two subgroups but kept all the Phenylacetylindoles together in the same set. The activity spectrum

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26

Shimoji, Mitsuo, and Toshio Itami. "3.8 "Computer Experiment" (Molecular Dynamics Technique)." Defect and Diffusion Forum 43 (January 1986): 248–57. http://dx.doi.org/10.4028/www.scientific.net/ddf.43.248.

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27

Smith, T. F., K. Gruskin, S. Tolman, and D. Faulkner. "The molecular biology computer research resource." Nucleic Acids Research 14, no. 1 (1986): 25–29. http://dx.doi.org/10.1093/nar/14.1.25.

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28

Fel’dman, T. B., Kh T. Kholmurodov, and M. A. Ostrovsky. "Molecular physiology of rhodopsin: Computer simulation." Physics of Particles and Nuclei Letters 5, no. 2 (2008): 131–44. http://dx.doi.org/10.1134/s1547477108020118.

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29

Jackson, Robert A. "Computer modelling of molecular ionic materials." Current Opinion in Solid State and Materials Science 5, no. 5 (2001): 463–67. http://dx.doi.org/10.1016/s1359-0286(01)00029-8.

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30

Stockert, JC. "Stereoscopy of computer-drawn molecular structures." Biochemical Education 22, no. 1 (1994): 23–25. http://dx.doi.org/10.1016/0307-4412(94)90160-0.

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31

Dubois, J. E., D. Laurent, and J. Weber. "Chemical ideograms and molecular computer graphics." Visual Computer 1, no. 1 (1985): 49–63. http://dx.doi.org/10.1007/bf01901269.

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32

Schutte, C. J. H. "Computer Software Review. Desktop Molecular Modeller." Journal of Chemical Information and Modeling 31, no. 1 (1991): 168. http://dx.doi.org/10.1021/ci00001a601.

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33

Dearing, A. "Trends in computer-assisted molecular design." Journal of Molecular Graphics 10, no. 1 (1992): 60. http://dx.doi.org/10.1016/0263-7855(92)80044-e.

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34

Deger, H., K. Luchner, and R. Worg. "Interactive computer simulation on molecular dynamics." European Journal of Physics 11, no. 4 (1990): 252–56. http://dx.doi.org/10.1088/0143-0807/11/4/114.

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35

Belcaid, Mahdi, and Robert J. Toonen. "Demystifying computer science for molecular ecologists." Molecular Ecology 24, no. 11 (2015): 2619–40. http://dx.doi.org/10.1111/mec.13175.

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36

Hecker, E., C. W. von der Lieth, H. Ponstingl, et al. "International symposium: Computer-assisted molecular modeling." Journal of Cancer Research and Clinical Oncology 116, no. 6 (1990): 654–61. http://dx.doi.org/10.1007/bf01637090.

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37

Della Valle, R. G., L. Halonen, and E. Venuti. "Molecular anharmonicity: A computer-aided treatment." Journal of Computational Chemistry 20, no. 16 (1999): 1716–30. http://dx.doi.org/10.1002/(sici)1096-987x(199912)20:16<1716::aid-jcc4>3.0.co;2-1.

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38

Asprion, Norbert, André Bardow, Jonas Mairhofer, and Johannes Schilling. "Computer‐Aided Molecular and Process Design." Chemie Ingenieur Technik 95, no. 3 (2023): 299. http://dx.doi.org/10.1002/cite.202370302.

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39

Grest, Gary S., Martin-D. Lacasse, and Michael Murat. "Molecular-Dynamics Simulations of Polymer Surfaces and Interfaces." MRS Bulletin 22, no. 1 (1997): 27–31. http://dx.doi.org/10.1557/s0883769400032309.

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From a single chain in a dilute solution to an entangled polymer melt, from bulk systems to more complex interfacial problems, computer simulations have played a critical role not only in testing the basic assumptions of various theoretical models but also in interpreting experimental results. Early computer simulations of polymers were mostly carried out on a lattice using Monte Carlo methods. This approach has led to significant progress in recent years and will continue to do so in many areas. In some cases however, for example in the study of shear, lattice models have serious limitations.

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40

Ourique, J. E., and A. Silva Telles. "Computer-aided molecular design with simulated annealing and molecular graphs." Computers & Chemical Engineering 22 (March 1998): S615—S618. http://dx.doi.org/10.1016/s0098-1354(98)00108-2.

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41

Mc Phie, Peter. "Current communications in molecular biology: Computer graphics and molecular modeling." Analytical Biochemistry 160, no. 1 (1987): 240. http://dx.doi.org/10.1016/0003-2697(87)90636-1.

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42

Narumi, Tetsu, Ryutaro Susukita, Toshikazu Ebisuzaki, Geoffrey McNiven, and Bruce Elmegreen. "Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations." Molecular Simulation 21, no. 5-6 (1999): 401–15. http://dx.doi.org/10.1080/08927029908022078.

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43

Soares, C. M., and O. Tapia. "Computer assisted simulations and molecular graphics methods in molecular design." Molecular Engineering 4, no. 4 (1994): 415–30. http://dx.doi.org/10.1007/bf01019471.

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44

Navío, PilarFlorido, and José Molina Molina. "Molecular interaction by computer-aided molecular modeling and molecular mechanics calculations: an introduction." Journal of Molecular Graphics 9, no. 1 (1991): 68. http://dx.doi.org/10.1016/0263-7855(91)80086-f.

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45

Wu, Jingui, and Youhong Zhang. "A Review of Computer Simulation-Assisted Molecularly Imprinted Polymers." International Journal of Biology and Life Sciences 10, no. 1 (2025): 127–39. https://doi.org/10.54097/tjn9qv33.

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Molecularly imprinted polymers(MIPs) are synthesized using molecular imprinting technology(MIT) to achieve specific recognition and selective adsorption of template molecules and their analogs. Optimizing the polymerization conditions can significantly enhance their recognition capabilities. However, relying solely on experimental methods for this optimization is resource-intensive and laborious. Computational simulation offers a more convenient, environmentally friendly, and accurate alternative. This paper reviews recent advancements in computational simulation and software used in MIP devel

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46

Bekono, Boris D., Akori E. Esmel, Brice Dali, et al. "Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models." Scientia Pharmaceutica 89, no. 4 (2021): 44. http://dx.doi.org/10.3390/scipharm89040044.

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In this work, antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) are proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities ( IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure–activity relationships (QSAR) model based on a l

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47

Chu, Dominique, Mikhail Prokopenko, and J. Christian J. Ray. "Computation by natural systems." Interface Focus 8, no. 6 (2018): 20180058. http://dx.doi.org/10.1098/rsfs.2018.0058.

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Computation is a useful concept far beyond the disciplinary boundaries of computer science. Perhaps the most important class of natural computers can be found in biological systems that perform computation on multiple levels. From molecular and cellular information processing networks to ecologies, economies and brains, life computes. Despite ubiquitous agreement on this fact going back as far as von Neumann automata and McCulloch–Pitts neural nets, we so far lack principles to understand rigorously how computation is done in living, or active, matter. What is the ultimate nature of natural co

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48

ITAI, Akiko, and Nobuo TOMIOKA. "Present stage of computer-assisted molecular design." Journal of Synthetic Organic Chemistry, Japan 45, no. 11 (1987): 1119–28. http://dx.doi.org/10.5059/yukigoseikyokaishi.45.1119.

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49

Silverman, B. "Molecular Moments for Computer-Aided Drug Discovery." Mini-Reviews in Medicinal Chemistry 1, no. 1 (2001): 1–4. http://dx.doi.org/10.2174/1389557013407386.

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50

Kataoka, Yosuke, and Mitsuhiro Matsumoto. "An Introduction to Molecular Dynamics Computer Simulation." Netsu Bussei 7, no. 3 (1993): 165–70. http://dx.doi.org/10.2963/jjtp.7.165.

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