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Journal of Computational Chemistry, Volume 18
Volume 18, Number 1, 15 January 1997
- Christian Kölle, Karl Jug:
Solvation effects in SINDO1: Application to organic molecules. 1-8 - Elso M. Cruz, Xabier Lopez, Martín Sarobe, Fernando P. Cossío, Jesus M. Ugalde:
G2 study of triplet [H4, Si, P]+ potential energy surface: Mechanism for reaction of P+ (3P) with silane. 9-19 - Wim Klopper
:
Simple recipe for implementing computation of first-order relativistic corrections to electron correlation energies in framework of direct perturbation theory. 20-27 - Bernd Reindl, Timothy Clark, Paul von Ragué Schleyer:
Empirical force-field and ab initio calculations on delocalized open chain cations. 28-44 - Attila Bérces:
Geometry optimization of metal complexes using natural internal coordinates: Representation of skeletal degrees of freedom. 45-55 - Doyoung Lee, Chang Kon Kim, Bon-Su Lee, Ikchoon Lee, Byung Choon Lee:
A theoretical study on keto-enol tautomerization involving simple carbonyl derivatives. 56-69 - Thomas G. Metzger, David M. Ferguson, William A. Glauser:
A computational analysis of interaction energies in methane and neopentane dimer systems. 70-79 - Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick:
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. 80-85 - Richard G. A. Bone, Hugo O. Villar:
Exhaustive enumeration of molecular substructures. 86-107 - Kenneth B. Wiberg, Joseph W. Ochterski:
Comparison of different ab initio theoretical models for calculating isodesmic reaction energies for small ring and related compounds. 108-114 - Robert B. Hermann:
Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area. 115-125 - Horst M. Sulzbach, George Vacek, Peter R. Schreiner, John Morrison Galbraith, Paul von Ragué Schleyer, Henry F. Schaefer III:
NMR chemical shielding surface of N-Acetyl-N-Methylalaninamide: A density functional study. 126-138 - Christian Bartels, Peter Güntert, Martin Billeter, Kurt Wüthrich:
GARANT-a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. 139-149
Volume 18, Number 2, 30 January 1997
- Alan J. McMahon, Paul M. King:
Optimization of Carbó molecular similarity index using gradient methods. 151-158 - Antonio M. Márquez, Jaime Oviedo
Parallel computation of second derivatives of RHF energy on distributed memory computers. 159-168 - Daan M. F. van Aalten, Bert L. de Groot, John B. C. Findlay, Herman J. C. Berendsen, Andrea Amadei:
A comparison of techniques for calculating protein essential dynamics. 169-181 - Curt M. Breneman, Marlon Rhem:
QSPR analysis of HPLC column capacity factors for a set of high-energy materials using electronic van der waals surface property descriptors computed by transferable atom equivalent method. 182-197 - Ulrike Salzner
Ab initio investigation of the diels-alder reaction between 2H-phosphole and phosphaethene: A model for phosphole dimerization. 198-210 - Jörg-Rüdiger Hill:
Use of test particle calculations for the derivation of van der Waals parameters used in force fields. 211-220 - Joseph J. Pavelites, Jiali Gao, Paul A. Bash, Alexander D. MacKerell Jr.:
A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides. 221-239 - Hagai Meirovitch, Eva Meirovitch:
Efficiency of monte carlo minimization procedures and their use in analysis of NMR data obtained from flexible peptides. 240-253 - Willian R. Rocha, Wagner B. De Almeida:
Quantum-mechanical and molecular mechanics conformational analysis of 1, 5-cyclooctadiene. 254-259 - Isaac B. Bersuker:
Limitations of density functional theory in application to degenerate states. 260-267 - Robert E. Bruccoleri, Jiri Novotny, Malcolm E. Davis
Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing. 268-276 - Cheuk-San Wang:
Efficient algorithm for conformational search of macrocyclic molecules. 277-289 - Ka Fai Cedric Yiu, Kin Y. Tam, S. C. Tsang:
Crystal indexing method using a simulated annealing algorithm with particular applications in nanocrystal research. 290-299
Volume 18, Number 3, February 1997
- Matthias Krack, Andreas M. Köster, Karl Jug:
Approximate molecular electrostatic potentials from semiempirical wavefunctions. 301-312 - M. Luz Sánchez, Manuel Angel Aguilar Espinosa, Francisco Javier Olivares del Valle:
Study of solvent effects by means of averaged solvent electrostatic potentials obtained from molecular dynamics data. 313-322 - Zhiqiang Wang, Ruth Pachter:
Prediction of peptide conformation: The adaptive simulated annealing approach. 323-329 - Gábor I. Csonka, Krisztina Éliás, Imre G. Csizmadia:
Ab initio and density functional study of the conformational space of 1C4 ALFA -L-fucose. 330-342 - Laurent David, Martin J. Field:
Basis set approach to solution of poisson equation for small molecules immersed in solvent. 343-350 - Dino R. Ferro, Paolo Pumilia, Massimo Ragazzi:
An improved force field for conformational analysis of sulfated polysaccharides. 351-367 - Konrad Hinsen, Benoît Roux:
A potential function for computer simulation studies of proton transfer in acetylacetone. 368-380 - Mario E. Fajardo, Jerry A. Boatz:
Monte Carlo simulations of Na atoms in dynamically disordered Ar systems: Solid, liquid, and critical-point fluid Ar. 381-392 - Sergey Vyazovkin:
Evaluation of activation energy of thermally stimulated solid-state reactions under arbitrary variation of temperature. 393-402 - Kenneth D. Gibson, Harold A. Scheraga:
Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. 403-415 - Sergei F. Vyboishchikov, Anibal Sierraalta, Gernot Frenking:
Topological analysis of electron density distribution taken from a pseudopotential calculation. 416-429 - Holger Dachsel, Hans Lischka, Ron L. Shepard, Jarek Nieplocha, Robert J. Harrison:
A massively parallel multireference configuration interaction program: The parallel COLUMBUS program. 430-448
Volume 18, Number 4, March 1997
- Volkhard Helms, Rebecca C. Wade:
Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. 449-462 - Uwe Eichler, Christoph M. Kölmel, Joachim Sauer:
Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs. 463-477 - Mark R. Wilson, Michael P. Allen, Mark A. Warren, Alain Sauron, William Smith:
Replicated data and domain decomposition molecular dynamics techniques for simulation of anisotropic potentials. 478-488 - Guntram Rauhut, Andrzej A. Jarzecki, Peter Pulay:
Density functional based vibrational study of conformational isomers: Molecular rearrangement of benzofuroxan. 489-500 - Kian-Tat Lim, Sharon Brunett, Mihail Iotov, Richard B. McClurg, Nagarajan Vaidehi, Siddharth Dasgupta, Stephen Taylor, William A. Goddard III:
Molecular dynamics for very large systems on massively parallel computers: The MPSim program. 501-521 - L. Young, Igor A. Topol, A. A. Rashin, Stanley K. Burt:
Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors. 522-532 - Bernd Reindl, Timothy Clark, Paul von Ragué Schleyer:
Empirical force field and ab initio calculations on allyl cations. 533-551 - Ajay C. Limaye:
Parallel MP2-energy evaluation: Simulated shared memory approach on distributed memory parallel machines. 552-561 - Stephen P. Greatbanks, Ian H. Hillier, Paul Sherwood:
Comparison of embedded cluster models to study zeolite catalysis: Proton transfer reactions in acidic chabazite. 562-568 - Yury N. Vorobjev, Harold A. Scheraga:
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. 569-583 - D. B. Chesnut, K. M. Davis:
Resonance revisited: A consideration of the calculation of cyclic conjugation energies. 584-593 - Aaron F. Stanton, Richard E. Bleil, Sabre Kais:
A new approach to global minimization. 594-599
Volume 18, Number 5, 15 April 1997
- Jacek Styszynki, Xiaoping Cao, Gulzari L. Malli, Lucas Visscher:
Relativistic all-electron Dirac-Fock-Breit calculations on xenon fluorides (XeFn, n = 1, 2, 4, 6). 601-608 - László Nyulaszi, Péter Várnai, Wolfgang Eisfeld
Regioselectivity in cycloaddition reaction between phosphaacetylene and diazomethane: An ab initio study. 609-616 - Gianfranco Pacchioni, Anna Maria Ferrari, Antonio M. Márquez, Francesc Illas:
Importance of Madelung potential in quantum chemical modeling of ionic surfaces. 617-628 - K. Pointet, A. Milliet, S. Hoyau, M. F. Renou-Gonnord:
Proton affinities of polybenzenoid aromatic hydrocarbons and those with five-membered rings. 629-637 - J. Willem M. Nissink, Marcel L. Verdonk, Jan Kroon, Thomas Mietzner, Gerhard Klebe:
Superposition of molecules: Electron density fitting by application of fourier transforms. 638-645 - Petr Bour, Jana Sopková, Lucie Bednárová, Petr Malon
Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra. 646-659 - H. Dufner, Stefan M. Kast, Jürgen Brickmann, Michael Schlenkrich:
Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids: A quantitative study. 660-676 - Marco Nonella:
Effect of charge distribution on electrostatic chromophore - protein interactions in Bacteriorhodopsin. 677-693 - Béla Paizs, Sándor Suhai:
Extension of SCF and DFT versions of chemical Hamiltonian approach to N interacting subsystems and an algorithm for their efficient implementation. 694-701 - Clifford E. Dykstra, Troy A. Van Voorhis:
Quantum monte carlo vibrational dynamics in a property-based interaction potential scheme for weakly bound clusters. 702-711 - Maria Cristina Andreazza Costa, Yuji Takahata:
Conformational analysis of synthetic neolignans active against leishmaniasis, using the molecular mechanics method (MM2). 712-721
Volume 18, Number 6, 30 April 1997
- Amedeo Caflisch, Stefan Fischer, Martin Karplus:
Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. 723-743 - Bernd Beck, Timothy Clark, Robert C. Glen:
VESPA: A new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods. 744-756 - Jos P. M. Lommerse, Sarah L. Price, Robin Taylor:
Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups. 757-774 - Andrew C. Scheiner, Jon Baker, Jan W. Andzelm:
Molecular energies and properties from density functional theory: Exploring basis set dependence of Kohn - Sham equation using several density functionals. 775-795 - Tap Ha Duong, Krystyna Zakrzewska:
Calculation and analysis of low frequency normal modes for DNA. 796-811 - Mihaly Mezei:
Optimal position of solute for simulations. 812-815 - Krzysztof Wolinski, Robert Haacke, James F. Hinton, Peter Pulay:
Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation, multi-Fock algorithm, and pseudodiagonalization. 816-825 - Pere Constans, Lluís Amat, Ramon Carbó-Dorca:
Toward a global maximization of the molecular similarity function: Superposition of two molecules. 826-846
Volume 18, Number 7, May 1997
- Adam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga:
A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. 849-873 - Adam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga:
A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization. 874-887 - Arnaud J. A. Soirat, Chung F. Wong, Roman Osman, Harel Weinstein:
Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix. 888-901 - Randall J. Radmer, Peter A. Kollman:
Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes. 902-919 - Ulrich H. E. Hansmann, Yuko Okamoto:
Numerical comparisons of three recently proposed algorithms in the protein folding problem. 920-933 - Jordi Mestres
MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches. 934-954 - Dennis S. Marynick:
Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges. 955-969
Volume 18, Number 8, June 1997
- Xiaoping Cao, Yan Wang:
Molecular symmetry and ab initio calculations: IV. Symmetry-matrix and symmetry-supermatrix in calculations of two-electron repulsion integrals. 971-979 - Robert Soliva, Modesto Orozco, F. Javier Luque:
Suitability of density functional methods for calculation of electrostatic properties. 980-991 - Josep Maria Anglada, Josep Maria Bofill:
A reduced-restricted-quasi-Newton-Raphson method for locating and optimizing energy crossing points between two potential energy surfaces. 992-1003 - Struan H. Robertson, Michael J. Pilling, Kevin E. Gates, Sean C. Smith:
Application of inverse iteration to 2-dimensional master equations. 1004-1010 - J. Papadakis, George S. Fanourgakis, Stavros C. Farantos, M. Founargiotakis:
Comparison of line search minimization algorithms for exploring topography of multidimensional potential energy surfaces: Mg+Arn case. 1011-1022 - Rainer Glaser, Grace Shiahuy Chen, Hansjög Grützmacher:
Effects of electron correlation and spin projection on rotational barriers of trithiocarbenium ion [C(SH)3]+ and Radical Dication [C(SH)3], 2+. 1023-1035 - Bouke P. van Eijck, Jan Kroon:
Fast clustering of equivalent structures in crystal structure prediction. 1036-1042 - Delphine Flatters, Krystyna Zakrzewska, Richard Lavery:
Internal coordinate modeling of DNA: Force field comparisons. 1043-1055 - Marc C. Nicklaus:
Conformational energies calculated by the molecular mechanics program CHARMm. 1056-1060 - Jiali Gao:
Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model. 1061-1071 - Joseph D. Augspurger, Harold A. Scheraga:
An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation. 1072-1078 - Jon Baker:
Constrained optimization in delocalized internal coordinates. 1079-1095 - Wayne J. Pullan:
Energy minimization of mixed argon-xenon microclusters using a genetic algorithm. 1096-1111
Volume 18, Number 9, 15 July 1997
- Andrean Goede
Voronoi cell: New method for allocation of space among atoms: Elimination of avoidable errors in calculation of atomic volume and density. 1113-1123 - Leticia González, Otilia Mó, Manuel Yáñez:
High-level ab initio versus DFT calculations on (H2O2)2 and H2O2-H2O complexes as prototypes of multiple hydrogen bond systems. 1124-1135 - Pavel Hobza, Martin Kabelác, Jirí Sponer
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results. 1136-1150 - Mark A. Murcko, B. Govinda Rao, Roberto Gomperts:
Conformational analysis of HIV-1 protease inhibitors: 2. Thioproline P1 Residue in the potent inhibitor KNI-272. 1151-1166 - Shijun Zheng, Lingpeng Meng, Xinhua Cai, Zhenfeng Xu, Xiaoyuan Fu:
Topological studies on IRC paths of X+H2XH+H reactions. 1167-1174 - Todd J. A. Ewing, Irwin D. Kuntz:
Critical evaluation of search algorithms for automated molecular docking and database screening. 1175-1189 - Sanja Sekusak, Aleksandar Sabljic:
Reactivity of haloethanes with hydroxyl radicals: Effects of basis set and correlation energy on reaction energetics. 1190-1199 - Alexander V. Mitin, Gerhard Hirsch, Robert J. Buenker:
Accurate atomic Gaussian basis functions for second-row atoms: Small split-valence 3-21SP and 4-22SP basis sets. 1200-1210 - Renate Griffith, John B. Bremner, Stephen J. Titmuss:
Molecular mechanics study of transannular amine-ketone (NC˭O) interaction in medium-sized heterocycles. 1211-1221 - Jooyoung Lee, Harold A. Scheraga, Shelly Rackovsky:
New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. 1222-1232 - John Arthur Niesse, Howard R. Mayne:
Global optimization of atomic and molecular clusters using the space-fixed modified genetic algorithm method. 1233-1244 - Nidhi Arora, B. Jayaram:
Strength of hydrogen bonds in helices. 1245-1252
Volume 18, Number 10, 30 July 1997
- David Ayma, Jean Pierre Campillo, Michel Rérat, Mauro Causà:
Ab initio calculation of dynamic polarizability and dielectric constant of carbon and silicon cubic crystals. 1253-1263 - Jörg Weiser, Max C. Holthausen, Lutz Fitjer:
HUNTER: A conformational search program for acyclic to polycyclic molecules with special emphasis on stereochemistry. 1264-1281 - Zoran Konkoli, Dieter Cremer, Elfi Kraka:
Diabatic ordering of vibrational normal modes in reaction valley studies. 1282-1294 - Gianpaolo Bravi, Emanuela Gancia, Andrea Zaliani, Monica Pegna:
SONHICA (Simple optimized non-HIerarchical Cluster Analysis): A new tool for analysis of molecular conformations. 1295-1311 - Robert Berger, Martin Klessinger:
Algorithms for exact counting of energy levels of spectroscopic transitions at different temperatures. 1312-1319 - Masahiro Kinoshita, Yuko Okamoto, Fumio Hirata:
Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm. 1320-1326 - Xuefeng Zhou:
Reviews in Computational Chemistry, Volume 7. 1327 - Ernest R. Davidson:
Modern Electronic Structure Theory. 1328
Volume 18, Number 11, August 1997
- Laura Gagliardi, Gian Luigi Bendazzoli, Stefano Evangelisti:
Direct-list algorithm for configuration interaction calculations. 1329-1343 - Martin F. Parretti, Romano T. Kroemer, Jeffrey H. Rothman, W. Graham Richards:
Alignment of molecules by the Monte Carlo optimization of molecular similarity indices. 1344-1353 - Alexey K. Mazur:
Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers. 1354-1364 - Zhuo-Min Chen, Tahir Çagin, William A. Goddard III:
Fast Ewald sums for general van der Waals potentials. 1365-1370 - Guyan Liang, Xiannong Chen, John A. Dustman, Anita H. Lewin, J. Phillip Bowen:
Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines. 1371-1391 - Fillmore Freeman, Choonsun Lee, Warren J. Hehre, Henry N. Po:
Ab initio molecular orbital calculations of 3, 4-dihydro-1, 2-dioxin, 3, 6-dihydro-1, 2-dioxin, 4H-1, 3-dioxin (1, 3-diox-4-ene), and 2, 3-dihydro-1, 4-dioxin (1, 4-dioxene). 1392-1406 - Geraldo Magela e Silva, Paulo Hora Acioli, Antonio Carlos Pedroza:
Estimating correlation energy of diatomic molecules and atoms with neural networks. 1407-1414 - Kerstin Möhle, Martin Gußmann, Hans-Jörg Hofmann:
Structural and energetic relations between turns. 1415-1430
Volume 18, Number 12, September 1997
- Miroslav Kohout, Andreas Savin:
Influence of core-valence separation of electron localization function. 1431-1439 - Shun Zhou Wan, Cun Xin Wang, Zhe Xin Xiang, Yun Yu Shi:
Stochastic dynamics simulation of alanine dipeptide: Including solvation interaction determined by boundary element method. 1440-1449 - Christian Bartels, Martin Karplus:
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations. 1450-1462 - Berk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije:
LINCS: A linear constraint solver for molecular simulations. 1463-1472 - Frank Eckert, Peter Pulay, Hans-Joachim Werner:
Ab initio geometry optimization for large molecules. 1473-1483 - Christian D. Berweger, Wilfred F. van Gunsteren, Florian Müller-Plathe:
Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations. 1484-1495 - Peter L. Cummins, Jill E. Gready:
Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution. 1496-1512 - Robert E. Tuzun, Donald W. Noid, Bobby G. Sumpter:
Treatment of multibody interactions in molecular simulations of systems with general bond networks. 1513-1522 - Soo Gyeong Cho
Rotational barriers of disilane, hexafluorodisilane, and hexamethyldisilane: Ab initio, density functional, and molecular mechanics (MM3) studies. 1523-1533 - Gábor I. Csonka
Simple tests for density functional methods. 1534-1545 - Yuto Komeiji, Masami Uebayasi, Ryo Takata, Akihiro Shimizu, Keiji Itsukashi, Makoto Taiji:
Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer. 1546-1563
Volume 18, Number 13, October 1997
- F. E. Jorge, E. V. R. De Castro, A. B. F. Da Silva:
A universal Gaussian basis set for atoms cerium through lawrencium generated with the generator coordinate Hartree-Fock method. 1565-1569 - Christian M. Cortis, Richard A. Friesner:
An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation. 1570-1590 - Christian M. Cortis, Richard A. Friesner:
Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes. 1591-1608 - T. Nguyen Dzung, Andrew C. Scheiner, Jan W. Andzelm, Suzanne W. Sirois, Dennis R. Salahub, Arnold T. Hagler:
A density functional study of the glycine molecule: Comparison with post-Hartree-Fock calculations and experiment. 1609-1631 - Richard W. Dixon, Peter A. Kollman:
Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. 1632-1646 - Emilio Martínez-Núñez, Saulo A. Vázquez, Ricardo A. Mosquera:
Conformational analysis of model compounds of vitamin D by theoretical calculations. 1647-1655 - Yoshifumi Fukunishi, Makoto Suzuki:
Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method. 1656-1663 - Sean A. C. McDowell:
Relation of the force constant of a bond to the electric field at a nucleus. 1664-1667 - Adam Liwo, Dariusz Dyl, Danuta Jeziorek, Magorzata Nowacka, Tadeusz Ossowski, Wiesaw Wonicki:
MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups. 1668-1681 - Dennis S. Marynick:
Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: II. Electrostatic potentials inside the molecular van der Waals envelope. 1682-1693
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