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Y. N. Chirgadze, I. V. Likhachev, N. K. Balabaev & E. V. Brazhnikov. (2023) Molecular dynamics of α-helical structure: poly-l-glutamic acid. Journal of Biomolecular Structure and Dynamics 0:0, pages 1-6.
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Yuri N. Chirgadze, Kevin P. Battaile, Ilya V. Likhachev, Nikolay K. Balabaev, Roni D. Gordon, Vladimir Romanov, Andres Lin, Robert Karisch, Robert Lam, Max Ruzanov, Evgeniy V. Brazhnikov, Emil F. Pai, Benjamin G. Neel & Nickolay Y. Chirgadze. (2022) Signal transfer in human protein tyrosine phosphatase PTP1B from allosteric inhibitor P00058. Journal of Biomolecular Structure and Dynamics 40:24, pages 13823-13832.
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Yuri Konstantinovich Tovbin. (2023) Molecular Modeling of Supercritical Processes and the Lattice—Gas Model. Processes 11:9, pages 2541.
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I.V. Likhachev, V.S. Bystrov & S.V. Filippov. (2023) Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods. Mathematical Biology and Bioinformatics 18:1, pages 251-266.
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Vladimir Bystrov, Ilya Likhachev, Sergey Filippov & Ekaterina Paramonova. (2023) Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality. Nanomaterials 13:13, pages 1905.
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K. V. Shaitan. (2023) Why Do Proteins Fold into Unique 3D Structures? And Other Questions.... Russian Journal of Physical Chemistry B 17:3, pages 550-570.
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S. A. Dubrovskii & N. K. Balabaev. (2023) Molecular Dynamics Simulation of High-Field Effects in the Mobility of Protonated Poly(ethylene oxide)s in a Gas. Polymer Science, Series A 65:2, pages 213-223.
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Ilya Likhachev, Nikolay Balabaev, Vladimir Bystrov, Ekaterina Paramonova, Leon Avakyan & Natalia Bulina. (2022) Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite. Nanomaterials 12:23, pages 4244.
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Anna Y. Aksenova, Ilya V. Likhachev, Sergei Y. Grishin & Oxana V. Galzitskaya. (2022) The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study. International Journal of Molecular Sciences 23:21, pages 13502.
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S. A. Dubrovskii & N. K. Balabaev. (2022) Molecular Dynamics Simulation of the Behavior of Protonated Poly(ethylene oxide)s in Drift Tube Experiments. Polymer Science, Series A 64:5, pages 549-558.
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Mikhail Mazo, Roman Khudobin, Nikolay Balabaev, Nikolay Belov, Victoria Ryzhikh, Roman Nikiforov, Rimpa Chatterjee & Susanta Banerjee. (2022) Structure and free volume of fluorine-containing polyetherimides with Pendant di-tert-butyl groups investigated by molecular dynamics simulation. Polymer, pages 125318.
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K. V. Shaitan. (2022) Hidden Symmetry Effects in the Dynamics of Linear Polymers and Biopolymers. Biophysics 67:3, pages 386-405.
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Ilya V. Likhachev, Nikolay K. Balabaev & Oxana V. Galzitskaya. (2022) Is It Possible to Find an Antimicrobial Peptide That Passes the Membrane Bilayer with Minimal Force Resistance? An Attempt at a Predictive Approach by Molecular Dynamics Simulation. International Journal of Molecular Sciences 23:11, pages 5997.
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Vladimir Bystrov, Ilya Likhachev, Alla Sidorova, Sergey Filippov, Aleksey Lutsenko, Denis Shpigun & Ekaterina Belova. (2022) Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes. Nanomaterials 12:5, pages 861.
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Anna V. Glyakina, Ilya V. Likhachev, Nikolay K. Balabaev & Oxana V. Galzitskaya. 2022. Advances in Artificial Systems for Medicine and Education V. Advances in Artificial Systems for Medicine and Education V
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Anna V. Glyakina, Nikolai K. Balabaev & Oxana V. Galzitskaya. 2022. Computer Simulations of Aggregation of Proteins and Peptides. Computer Simulations of Aggregation of Proteins and Peptides
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Alla Sidorova, Vladimir Bystrov, Aleksey Lutsenko, Denis Shpigun, Ekaterina Belova & Ilya Likhachev. (2021) Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes. Nanomaterials 11:12, pages 3299.
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S. A. Dubrovskii & N. K. Balabaev. (2021) Simulation of the Drift of a Macromolecular Ion in a Gas under the Action of an Electric Field. Polymer Science, Series A 63:6, pages 891-901.
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I.V. Likhachev & V.S. Bystrov. (2021) Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator. Mathematical Biology and Bioinformatics 16:2, pages 244-255.
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Arlette R. C. Baljon, Gerardo Mendoza, N. K. Balabaev & A. V. Lyulin. (2021) Glass-Transition Temperature of Cyclic Polystyrene: A Computational Study. Polymer Science, Series A 63:3, pages 356-362.
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Sergey A. Milenin, Elizaveta V. Selezneva, Pavel A. Tikhonov, Viktor G. Vasil’ev, Alexander I. Buzin, Nikolay K. Balabaev, Andrey O. Kurbatov, Maxim V. Petoukhov, Eleonora V. Shtykova, Lev A. Feigin, Elena A. Tatarinova, Elena Yu. Kramarenko, Sergey N. Chvalun & Aziz M. Muzafarov. (2021) Hybrid Polycarbosilane-Siloxane Dendrimers: Synthesis and Properties. Polymers 13:4, pages 606.
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Andrey O. Kurbatov, Nikolay K. Balabaev, Mikhail A. Mazo & Elena Yu. Kramarenko. (2021) Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number. Polymers 13:4, pages 552.
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A.S. Shigaev, I.V. Lihachev & V.D. Lakhno. (2020) DNA Model with Non-Local Inter-Site Interaction in Collisional Thermostat. Mathematical Biology and Bioinformatics 15:2, pages 129-137.
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G. M. Agayan, N. K. Balabaev & M. N. Rodnikova. (2020) Structure Description of Liquid 1,3-Propanediol and Ethylene Glycol by Graph Theory and Percolation Methods. Russian Journal of Physical Chemistry A 94:6, pages 1143-1148.
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Andrey O. Kurbatov, Nikolay K. Balabaev, Mikhail A. Mazo & Elena Yu. Kramarenko. (2020) Effects of generation number, spacer length and temperature on the structure and intramolecular dynamics of siloxane dendrimer melts: molecular dynamics simulations. Soft Matter 16:15, pages 3792-3805.
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I. V. Likhachev, N. K. Balabaev & O. V. Galzitskaya. 2020. Advances in Computer Science for Engineering and Education II. Advances in Computer Science for Engineering and Education II
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Ilya Viatcheslavovitch Likhachev & Victor Dmitrievitch Lakhno. (2019) Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. The European Physical Journal B 92:11.
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I.V. Likhachev & V.D. Lakhno. (2019) The direct investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. Chemical Physics Letters 727, pages 55-58.
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M.N. Rodikova, G.M. Agayan & N.K. Balabaev. (2019) Description of the spatial networks of hydrogen bonds in liquids by topological methods. Journal of Molecular Liquids 283, pages 374-379.
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Mikhail Mazo, Nikolay Balabaev, Alexandre Alentiev, Ivan Strelnikov & Yury Yampolskii. (2019) Structure and Properties of High and Low Free Volume Polymers Studied by Molecular Dynamics Simulation. Computation 7:2, pages 27.
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Anna V. Glyakina, Nicolai I. Strizhov, Mikhail V. Karpov, Nikita V. Dovidchenko, Bakhyt T. Matkarimov, Ludmila V. Isaeva, Vera S. Efimova, Mikhail A. Rubtsov, Ludmila A. Novikova, Marina V. Donova & Oxana V. Galzitskaya. (2019) Ile351, Leu355 and Ile461 residues are essential for catalytic activity of bovine cytochrome P450scc (CYP11A1). Steroids 143, pages 80-90.
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Andrey Kurbatov, Nikolay Balabaev, Mikhail Mazo & Elena Kramarenko. (2018) A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations. Polymers 10:8, pages 838.
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S. A. Dubrovskii & N. K. Balabaev. (2018) Computer Simulation of High-Frequency Heating of a Protonated Poly(ethylene oxide) Chain in a Vacuum. Polymer Science, Series A 60:3, pages 404-416.
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N. K. Balabaev, Yu. V. Novakovskaya & M. N. Rodnikova. (2018) Repeated Elements of the Structure of Liquid Monoethanolamine. Doklady Physical Chemistry 479:1-2, pages 47-51.
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Anna V. Glyakina, Ilya V. Likhachev, Nikolay K. Balabaev & Oxana V. Galzitskaya. (2018) Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. Journal of Structural Biology 201:2, pages 162-170.
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A. O. Kurbatov, N. K. Balabaev, M. A. Mazo & E. Yu. Kramarenko. (2018) Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups. The Journal of Chemical Physics 148:1.
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Alexey V. Lyulin, Nikolay K. Balabaev, Arlette R. C. Baljon, Gerardo Mendoza, Curtis W. Frank & Do Y. Yoon. (2017) Interfacial and topological effects on the glass transition in free-standing polystyrene films. The Journal of Chemical Physics 146:20.
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N. K. Balabaev, M. A. Mazo & E. Yu. Kramarenko. (2016) Insight into the Structure of Polybutylcarbosilane Dendrimer Melts via Extensive Molecular Dynamics Simulations. Macromolecules 50:1, pages 432-445.
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Anna V. Glyakina, Nikolai K. Balabaev & Oxana V. Galzitskaya. (2016) Dataset of the molecular dynamics simulations of bilayers consisting of short amyloidogenic peptide VDSWNVLVAG from Bgl2p–glucantransferase of S. cerevisiae cell wall. Data in Brief 9, pages 597-601.
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A V Lankin. (2016) Ion recombination in dense gases. Journal of Physics: Conference Series 774, pages 012143.
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N. K. Balabaev, S. V. Kraevskii, M. N. Rodnikova & I. A. Solonina. (2016) On the structures of ethylene glycol, monoethanolamine, and ethylenediamine in the liquid phase. Russian Journal of Physical Chemistry A 90:5, pages 1000-1005.
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D. K. Belashchenko, M. N. Rodnikova, N. K. Balabaev & I. A. Solonina. (2015) Molecular dynamics models of pores in the liquid monoethanolamine structure. Russian Journal of Physical Chemistry A 90:1, pages 100-104.
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Anna V. Glyakina, Ilya V. Likhachev, Nikolay K. Balabaev & Oxana V. Galzitskaya. (2015) Mechanical stability analysis of the protein L immunoglobulin‐binding domain by full alanine screening using molecular dynamics simulations. Biotechnology Journal 10:3, pages 386-394.
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I. A. Strelnikov, M. A. Mazo, N. K. Balabaev & E. F. Oleinik. (2014) Computer simulation of rearrangements in chains of glassy polymethylene subjected at low temperature inelastic deformation. Polymer Science Series A 56:4, pages 511-521.
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I. A. Strelnikov, M. A. Mazo, N. K. Balabaev, E. F. Oleinik & A. A. Berlin. (2014) Energy storage in plastic deformation of glassy polymethylene. Doklady Physical Chemistry 457:1, pages 108-111.
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Anna V. Glyakina, Ilya V. Likhachev, Nikolay K. Balabaev & Oxana V. Galzitskaya. (2014) Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins. Proteins: Structure, Function, and Bioinformatics 82:1, pages 90-102.
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A. Lankin & G. Norman. (2013) Recombination in Dense Ion Plasmas. Contributions to Plasma Physics 53:10, pages 711-720.
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Ilya Viatcheslavovich Lihachev, Oksana V. Galzitskaya & Nikolai K. Balabaev. (2013) Investigation of C-Cadherin mechanical properties by Molecular Dynamics. Computer Research and Modeling 5:4, pages 727-735.
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D. K. Belashchenko, M. N. Rodnikova, N. K. Balabaev & I. A. Solonina. (2013) Studying the cavities in liquid ethyleneglycol. Russian Journal of Physical Chemistry A 87:7, pages 1145-1150.
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E. A. Zubova, N. K. Balabaev, A. I. Musienko, E. B. Gusarova, M. A. Mazo, L. I. Manevitch & A. A. Berlin. (2012) Simulation of melting in crystalline polyethylene. The Journal of Chemical Physics 136:22.
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Igor L. Kanev, Nikolay K. Balabaev, Anna V. Glyakina & Victor N. Morozov. (2012) Computer Simulation of Gas-Phase Neutralization of Electrospray-Generated Protein Macroions. The Journal of Physical Chemistry B 116:20, pages 5872-5881.
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N. T. Moldogazieva, A. A. Terentiev, M. Yu. Antonov, A. N. Kazimirsky & K. V. Shaitan. (2012) Correlation between biological activity and conformational dynamics properties of tetra- and pentapeptides derived from fetoplacental proteins. Biochemistry (Moscow) 77:5, pages 469-484.
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N. T. Moldogazieva, K. V. Shaitan, M. Yu. Antonov, I. K. Vinogradova & A. A. Terentiev. (2011) Influence of intramolecular interactions on conformational and dynamic properties of analogs of heptapeptide AFP14–20. Biochemistry (Moscow) 76:12, pages 1321-1336.
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N. K. Balabaev, I. P. Borodin, T. I. Borodina & T. N. Khazanovich. (2011) Viscoelasticity of a stretched polymer chain with ends exposed to a constant force. Polymer Science Series A 53:11, pages 1086-1096.
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Alexey V. Lyulin, Dmitri Hudzinskyy, Eric Janiaud & Antoine Chateauminois. (2011) Competition of time and spatial scales in polymer glassy dynamics: Rejuvenation and confinement effects. Journal of Non-Crystalline Solids 357:2, pages 567-574.
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Yu. K. Tovbin. (2010) Molecular statistical theory and multiscale modeling of physicochemical processes in nanotechnologies. Nanotechnologies in Russia 5:11-12, pages 715-747.
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Yu. K. Tovbin & R. Ya. Tugazakov. (2010) Molecular flows in narrow pores at small initial perturbations. Theoretical Foundations of Chemical Engineering 44:6, pages 902-912.
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N. K. Balabaev, I. P. Borodin & T. N. Khazanovich. (2010) Stretching of a semiflexible chain composed of elastic bonds. Polymer Science Series A 52:6, pages 655-661.
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N. K. Balabaev, M. A. Mazo, A. V. Lyulin & E. F. Oleinik. (2010) Plastic deformation of glassy polymethylene: Computer-aided molecular-dynamic simulation. Polymer Science Series A 52:6, pages 633-644.
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Anna Vladimirovna Glyakina, Oksana V. Galzitskaya & Nikolai K. Balabaev. (2010) Investigation of the mechanical properties of immunoglobulinbinding domains of proteins L and G using the molecular dynamics simulations. Computer Research and Modeling 2:1, pages 73-81.
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A. V. Glyakina, N. K. Balabaev & O. V. Galzitskaya. (2009) Mechanical unfolding of proteins L and G with constant force: Similarities and differences. The Journal of Chemical Physics 131:4.
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N. K. Balabaev & T. N. Khazanovich. (2009) Extension of chains composed of freely joined elastic segments. Russian Journal of Physical Chemistry B 3:2, pages 242-246.
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Stanislav Falkovich, Anatolii Darinskii, Nikolai Balabaev & Igor Neelov. (2009) Simulation of the Mechanical Unfolding of the Ubiquitin by Pulling in Different Directions with Constant Speed. Macromolecular Symposia 278:1, pages 105-113.
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A. V. Glyakina, N. K. Balabaev & O. V. Galzitskaya. (2009) Comparison of transition states obtained upon modeling of unfolding of immunoglobulin-binding domains of proteins L and G caused by external action with transition states obtained in the absence of force probed by experiments. Biochemistry (Moscow) 74:3, pages 316-328.
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N. K. Balabaev, I. P. Borodin & T. N. Khazanovich. (2008) Viscoelasticity of stretched polymer chains: Analytical theory and computer-aided simulation. Polymer Science Series A 50:12, pages 1238-1247.
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K. V. Shaitan, M. Yu. Antonov, Ye. V. Tourleigh, O. V. Levtsova, K. B. Tereshkina, I. N. Nikolaev & M. P. Kirpichnikov. (2008) Comparative study of molecular dynamics, diffusion, and permeability for ligands in biomembranes of different lipid composition. Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology 2:1, pages 73-81.
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Mikhail A. Mazo, Leonid I. Manevitch, Elena B. Gusarova, Mikhail Yu. Shamaev, Alexander A. Berlin, Nikolay K. Balabaev & Gregory C. Rutledge. (2008) Molecular Dynamics Simulation of Thermomechanical Properties of Montmorillonite Crystal. 1. Isolated Clay Nanoplate. The Journal of Physical Chemistry B 112:10, pages 2964-2969.
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E. A. Zubova, A. I. Musienko, N. K. Balabaev, E. B. Gusarova, M. A. Mazo, L. I. Manevich & Al. Al. Berlin. (2011) High-temperature quasi-hexagonal phase in the simplest model of a polymer crystal. Doklady Physical Chemistry 418:2, pages 15-18.
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N. T. Moldogazieva, K. V. Shaitan, K. B. Tereshkina, Yu. M. Antonov & A. A. Terentiev. (2007) Molecular dynamics of human alpha-fetoprotein fragment LDSYQCT and its analogs at different dielectric constants. Biophysics 52:4, pages 365-374.
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K. V. Shaitan, A. Li, K. B. Tereshkina & M. P. Kirpichnikov. (2007) Acetylcholine receptor pore permeability studied by molecular dynamics simulation. Biophysics 52:3, pages 301-306.
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N. T. Moldogazieva, A. A. Terentiev, A. N. Kazimirsky, M. Yu. Antonov & K. V. Shaitan. (2007) Conformational dynamics of human α-fetoprotein-derived heptapeptide LDSYQCT analogs. Biochemistry (Moscow) 72:5, pages 529-539.
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D.Yu. Mordvitsev, Ya.L. Polyak, D.A. Kuzmin, O.V. Levtsova, Ye.V. Tourleigh, Yu.N. Utkin, K.V. Shaitan & V.I. Tsetlin. (2007) Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors. Computational Biology and Chemistry 31:2, pages 72-81.
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E.A. Zubova, N.K. Balabaev & L.I. Manevitch. (2007) Molecular mechanisms of the chain diffusion between crystalline and amorphous fractions in polyethylene. Polymer 48:6, pages 1802-1813.
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Ye.V. Tourleigh, K.V. Shaitan & N.K. Balabaev. (2007) Diffusion of Molecules at the Interface of Water-Membrane Structures. Defect and Diffusion Forum 261-262, pages 109-126.
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K.V. Shaitan, Y.V. Tourleigh, D.N. Golik & M.P. Kirpichnikov. (2006) Computer-aided molecular design of nanocontainers for inclusion and targeted delivery of bioactive compounds. Journal of Drug Delivery Science and Technology 16:4, pages 253-258.
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D.Yu. Mordvintsev, Ya.L. Polyak, O.V. Levtsova, Ye.V. Tourleigh, I.E. Kasheverov, K.V. Shaitan, Yu.N. Utkin & V.I. Tsetlin. (2005) A model for short α-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: Comparison with long-chain α-neurotoxins and α-conotoxins. Computational Biology and Chemistry 29:6, pages 398-411.
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A. L. Rabinovich, N. K. Balabaev, M. G. Alinchenko, V. P. Voloshin, N. N. Medvedev & P. Jedlovszky. (2005) Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers. The Journal of Chemical Physics 122:8.
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Anatoly A. Darinskii, Anna Zarembo, Nikolai K. Balabaev, Igor M. Neelov & Franciska Sundholm. (2004) Molecular dynamics simulation of a flexible polymer network in a liquid crystalline solvent; dynamical properties. Polymer 45:26, pages 8901-8911.
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Alexandre Lemak, James Lepock & Jeff Chen. 2004. Soft Materials. Soft Materials
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Anatoly A. Darinskii, Anna Zarembo, Nikolai K. Balabaev, Igor M. Neelov & Franciska Sundholm. (2004) Molecular dynamics simulation of a flexible polymer network in a liquid crystal solvent; structure and equilibrium properties. Polymer 45:14, pages 4857-4866.
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Doros Theodorou & Michael Kotelyanskii. 2004. Simulation Methods for Polymers. Simulation Methods for Polymers.
Oleg L. Manevitch & Gregory C. Rutledge. (2003) Elastic Properties of a Single Lamella of Montmorillonite by Molecular Dynamics Simulation. The Journal of Physical Chemistry B 108:4, pages 1428-1435.
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Alexandre S. Lemak, James R. Lepock & Jeff Z. Y. Chen. (2003) Molecular dynamics simulations of a protein model in uniform and elongational flows. Proteins: Structure, Function, and Genetics 51:2, pages 224-235.
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A. L. Rabinovich, P. O. Ripatti, N. K. Balabaev & F. A. M. Leermakers. (2003) Molecular dynamics simulations of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to self-consistent field modeling. Physical Review E 67:1.
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Brendan W. Arbuckle & Paulette Clancy. (2002) Effects of the Ewald sum on the free energy of the extended simple point charge model for water. The Journal of Chemical Physics 116:12, pages 5090.
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Alexander S. Lemak, Nikolai K. Balabaev, Yuliya N. Karnet & Yurii G. Yanovsky. (1998) The effect of a solid wall on polymer chain behavior under shear flow. The Journal of Chemical Physics 108:2, pages 797-806.
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K Binder. (1997) Applications of Monte Carlo methods to statistical physics. Reports on Progress in Physics 60:5, pages 487-559.
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