MBN Explorer and MBN Studio related journal publications

2024

V.V. Haurylavets, V.K. Ivanov, A.V. Korol, and A.V. Solov'yov, Atomistic modelling of electron propagation and radiation emission in oriented bent ultra-thin Si and Ge crystals, Nucl. Instrum. Meth. A, vol. 1058, 168917 (2024)

2023

A.V. Verkhovtsev, Y. Erofeev, and A.V. Solov'yov, Mechanisms of radiation-induced structural transformations in deposited gold clusters, Phys. Rev. B, vol. 108, 115423 (2023)
M.D. Dickers, A.V. Verkhovtsev, N.J. Mason, and A.V. Solov’yov, Atomistic modelling and structural characterisation of coated gold nanoparticles for biomedical applications, Eur. Phys. J. D, vol. 77, 141 (2023)
W. Wu, A.V. Verkhovtsev, T. Pavloudis, A.V. Solov'yov, and R.E. Palmer, Neuromorphic nanocluster networks: Critical role of the substrate in nano-link formation, Nano Research, vol. 16, pp. 10500-10506 (2023)
B. Andreides, A.V. Verkhovtsev, J. Fedor, and A.V. Solov’yov, Role of the molecular environment in quenching the irradiation-driven fragmentation of Fe(CO)5: A reactive molecular dynamics study, J. Phys. Chem. A, vol. 127, pp. 3757-3767 (2023)
V.V. Haurylavets, A.V. Korol, G.B. Sushko, V.K. Ivanov, A.V. Solov’yov, Radiation of high-energy electrons when channeling in the bent silicon and germanium monocrystals, St. Petersburg Polytechnical State University Journal. Physics and Mathematics, vol. 16(1), pp. 33-50 (2023) (in Russian)
A.V. Korol and A.V. Solov'yov, Atomistic modeling and characterizaion of light sources based on small-amplitude short-period periodically bent crystals, Nucl. Instrum. Meth. B, vol. 537, pp. 1-13 (2023)
A. Prosvetov, A.V. Verkhovtsev, G. Sushko, and A.V. Solov'yov, Atomistic modeling of thermal effects in focused electron beam-induced deposition of Me2Au(tfac), Eur. Phys. J. D, vol. 77, 15 (2023)
G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Atomistic modeling of the channeling process with radiation reaction force included, Nucl. Instrum. Meth. B, vol. 535, pp. 117-125 (2023)

2022

G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Ultra-relativistic electron beams deflection by quasi-mosaic crystals, Eur. Phys. J. D, vol. 76, 236 (2022)
G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Extremely brilliant crystal-based light sources, Eur. Phys. J. D, vol. 76, 166 (2022)
I.A. Solov'yov, G. Sushko, I. Friis, A.V. Solov'yov, Multiscale modeling of stochastic dynamics processes with MBN Explorer, J. Comput. Chem., vol. 43, pp. 1442-1458 (2022) (selected as a journal cover image)
A. Prosvetov, A.V. Verkhovtsev, G. Sushko, and A.V. Solov'yov, Atomistic simulation of the FEBID-driven growth of iron-based nanostructures, Phys. Chem. Chem. Phys., vol. 24, pp. 10807-10819 (2022) (highlighted as 2022 PCCP HOT Article)
W. Wu, T. Pavloudis, A.V. Verkhovtsev, A.V. Solov'yov, and R.E. Palmer, Molecular dynamics simulation of nanofilament breakage in neuromorphic nanoparticle networks, Nanotechnology, vol. 33, 275602 (2022)
A.V. Verkhovtsev, A. Nichols, N.J. Mason, and A.V. Solov'yov, Molecular dynamics characterization of radiosensitizing coated gold nanoparticles in aqueous environment, J. Phys. Chem. A, vol. 126, pp. 2170-2184 (2022)
V.V. Haurylavets, A. Leukovich, A. Sytov, L. Bandiera, A. Mazzolari, M. Romagnoni, V. Guidi, G.B. Sushko, A.V. Korol, and A.V. Solov’yov, MBN Explorer atomistic simulations of 855 MeV electron propagation and radiation emission in oriented silicon bent crystal: theory versus experiment, Eur. Phys. J. Plus, vol. 137, 34 (2022)

2021

A.V. Pavlov, A.V. Korol, V.K. Ivanov, and A.V. Solov'yov, Channeling and radiation of electrons and positrons in the diamond heterocrystals, St. Petersburg Polytechnical State University Journal. Physics and Mathematics, vol. 14(4), pp. 190–201 (2021)
I. Friis, A.V. Verkhovtsev, I.A. Solov'yov, and A.V. Solov'yov, Lethal DNA damage caused by ion-induced shock waves in cells, Phys. Rev. E, vol. 104, 054408 (2021); see also Synopsis in Physics, vol. 14, s153 (2021)
A. Prosvetov, A.V. Verkhovtsev, G. Sushko, and A.V. Solov'yov, Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4, Beilstein J. Nanotechnol., vol. 12, pp. 1151–1172 (2021)
Y. Fortouna, P. de Vera, A.V. Verkhovtsev, and A.V. Solov'yov, Molecular dynamics simulations of sodium nanoparticle deposition on magnesium oxide, Theor. Chem. Acc., vol. 140, 84 (2021)
A.V. Korol, G.B. Sushko, and A.V. Solov'yov, All-atom relativistic molecular dynamics simulations of channeling and radiation processes in oriented crystals, Eur. Phys. J. D, vol. 75, 107 (2021)
C. Kexel and A.V. Solov'yov, Predicting dipole orientations in spontelectric methyl formate, Eur. Phys. J. D, vol. 75, 89 (2021)

2020

P. de Vera, M. Azzolini, G. Sushko, I. Abril, R. Garcia-Molina, M. Dapor, I.A. Solov'yov, and A.V. Solov'yov , Multiscale simulation of the focused electron beam induced deposition process, Scientific Reports, vol. 10, 20827 (2020)
A.V. Verkhovtsev, Y. Erofeev, and A.V. Solov'yov, Soft landing of metal clusters on graphite: a molecular dynamics study, Eur. Phys. J. D, vol. 74, 205 (2020)
A.V. Korol and A.V. Solov'yov, Crystal-based intensive gamma-ray light sources (Topical Review), Eur. Phys. J. D, vol. 74, 201 (2020)
I. Friis, A. Verkhovtsev, I.A. Solov’yov, and A.V. Solov'yov, Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field, J. Comput. Chem., vol. 41, pp. 2429-2439 (2020)
A.V. Verkhovtsev, A.V. Korol, G.B. Sushko, S. Schramm, and A.V. Solov'yov, Generalized correction to embedded-atom potentials for simulation of equilibrium and nonequilbrium properties of metals, St. Petersburg Polytechnical State University Journal. Physics and Mathematics, vol. 13(3), pp. 23-41 (2020)
A.V. Pavlov, A.V. Korol, V.K. Ivanov, and A.V. Solov'yov, Channeling of electrons and positrons in straight and periodically bent diamond(110) crystals, Eur. Phys. J. D, vol. 74, 21 (2020)

2019

E. Surdutovich and A.V. Solov'yov, Exploration of multifragmentation of Ar clusters with incident protons, Eur. Phys. J. D, vol. 73, 241 (2019)
A.V. Pavlov, V.K. Ivanov, A.V. Korol, and A.V. Solov'yov, Radiation of 375 MeV electrons and positrons curing channeling in straight and periodically bent diamond crystals, St. Petersburg State Polytechnical University Journal. Physics and Mathematics, vol. 12(4), pp. 108-118 (2019) (in Russian)
P. de Vera, A. Verkhovtsev, G. Sushko, and A.V. Solov'yov, Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation, Eur. Phys. J. D, vol. 73, 215 (2019)
A.V Korol and A.V Solov'yov, Multiscale modelling of complex dynamical processes in solids with MBN Explorer and MBN Studio, Proceedings, vol. 26, 23 (2019)
P. de Vera, E. Surdutovich, and A.V. Solov'yov, The role of shock waves on the biodamage induced by ion beam radiation, Cancer Nanotechnology, vol. 10, 5 (2019)
A.V. Pavlov, A.V Korol, V.K. Ivanov, and A.V Solov'yov, Interplay and specific features of radiation mechanisms of electrons and positrons in crystalline undulators, J. Phys. B: At. Mol. Opt. Phys., vol. 52, 11LT01 (2019)
G.B.Sushko, I.A. Solov'yov, and A.V. Solov'yov, Modeling MesoBioNano systems with MBN Studio made easy, J. Mol. Graph. Model., vol. 88, pp. 247-260 (2019)

2018

K.B. Agap'ev, V.K. Ivanov, A.V. Korol, and A.V. Solov'yov, Channeling of ultrarelativistic particles in a diamond crystal, St. Petersburg State Polytechnical University Journal. Physics and Mathematics, vol. 11, pp. 139-150 (2018) (in Russian)
P. de Vera, E. Surdutovich, N.J. Mason, F.J. Currell, and A.V. Solov'yov, Simulation of the ion-induced shock waves effects on the transport of chemically reactive species in ion tracks, Eur. Phys. J. D, vol. 72, 147 (2018)
V.G. Bezchastnov, A.V. Korol, and A.V. Solov'yov, Reply to Comment on "Radiation from multi-GeV electrons and positrons in periodically bent silicon crystal", J. Phys. B: At. Mol. Opt. Phys., vol. 51, 168002 (2018)
K. Haume, P. de Vera, A. Verkhovtsev, E. Surdutovich, N.J. Mason and A.V. Solov'yov, Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles, Eur. Phys. J. D, vol. 72, 116 (2018)
H. Shen, Q. Zhao, F.S. Zhang, G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Channeling and radiation of 855 MeV electrons and positrons in straight and bent tungsten (110) crystals, Nucl. Instrum. Meth. D, vol. 424, pp. 26-36 (2018)

2017

E. Surdutovich, A. Verkhovtsev, and A.V. Solov’yov, Ion-impact-induced multifragmentation of liquid droplets, Eur. Phys. J. D, vol. 71, 285 (2017)
P. de Vera, E. Surdutovich, N.J. Mason, and A.V. Solov’yov, Radial doses around energetic ion tracks and the onset of shock waves on the nanoscale, Eur. Phys. J. D, vol. 71, 281 (2017)
A.V. Verkhovtsev, A.V. Korol, and A.V. Solov'yov, Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions, Eur. Phys. J. D, vol. 71, 212 (2017)
A.V. Korol, V.G. Bezchastnov, and A.V. Solov'yov, Channeling and radiation of the 855 MeV electrons enhanced by the re-channeling in a periodically bent diamond crystal, Eur. Phys. J. D, vol. 71, 174 (2017)

2016

C. Kexel, A.V. Verkhovtsev, G.B. Sushko, A.V. Korol, S. Schramm, and A.V. Solov’yov, Toward the exploration of the NiTi phase diagram with a classical force field, J. Phys. Chem. C, vol. 120, pp. 25043-25052 (2016)
G.B. Sushko, I.A. Solov'yov, A.V. Solov'yov, Molecular dynamics for irradiation driven chemistry: application to the FEBID process, Eur. Phys. J. D, vol. 70, 217 (2016)
A.V. Korol, V.G. Bezchastnov, G.B. Sushko, A.V. Solov'yov, Simulation of channeling and radiation of 855 MeV electrons and positrons in a small-amplitude short-period bent crystal, Nucl. Instrum. Meth. B, vol. 387, pp. 41-53 (2016)
P. de Vera, N.J. Mason, F.J. Currell, and A.V. Solov’yov, Molecular dynamics study of accelerated ion-induced shock waves in biological media, Eur. Phys. J. D, vol. 70, 183 (2016)
K. Haume, N.J. Mason, and A.V. Solov’yov, Modeling of nanoparticle coatings for medical applications, Eur. Phys. J. D, vol. 70, 181 (2016)
G.B. Sushko, A.V. Verkhovtsev, C. Kexel, A.V. Korol, S. Schramm, and A.V. Solov’yov, Reconciling simulated melting and ground-state properties of metals with a modified embedded-atom method potential, J. Phys.: Condens. Matter, vol. 28, 145201 (2016)
G.B. Sushko, I.A. Solov'yov, A.V. Verkhovtsev, S.N. Volkov, and A.V. Solov’yov, Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology, Eur. Phys. J. D, vol. 70, 12 (2016)

2015

G.B. Sushko, A.V. Korol, and A.V. Solov'yov, A small-amplitude crystalline undulator based on 20 GeV electrons and positrons: Simulations, St. Petersburg Polytechnical University Journal: Physics and Mathematics, vol. 1, pp. 341-345 (2015); original text: St. Petersburg State Polytechnical University Journal. Physics and Mathematics, vol. 3(225), pp. 185-192 (2015)
G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Electron and positron propagation in straight and periodically bent axial and planar silicon channels, St. Petersburg Polytechnical University Journal: Physics and Mathematics, vol. 1, pp. 332-340 (2015); original text: St. Petersburg State Polytechnical University Journal. Physics and Mathematics, vol. 3(225), pp. 173-184 (2015)
C. Kexel, S. Schramm and A.V. Solov'yov, Atomistic simulation of martensite-austenite phase transition in nanoscale nickel-titanium crystals, Eur. Phys. J. B, vol. 88, 221 (2015)
R.G. Polozkov, V.K. Ivanov, G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Channeling of ultra-relativistic positrons in bent diamond crystals, St. Petersburg Polytechnical University Journal: Physics and Mathematics, vol. 1, pp. 212-218 (2015); original text: St. Petersburg State Polytechnical University Journal. Physics and Mathematics, vol. 2(218), pp. 167-178 (2015) (in Russian)
G.B. Sushko, A.V. Korol, and A.V Solov'yov, Multi-GeV electron and positron channeling in bent silicon crystals, Nucl. Instrum. Meth. B, vol. 355, pp. 39-43 (2015)

2014

V.G. Bezchastnov, A.V. Korol, and A.V. Solov'yov, Radiation from multi-GeV electrons and positrons in periodically bent silicon crystal, J. Phys. B: At. Mol. Opt. Phys., vol. 47, 195401 (2014)
R.G. Polozkov, V.K. Ivanov, G.B. Sushko, A.V. Korol, and A.V. Solov'yov, Radiation emission by electrons channeling in bent silicon crystals, Eur. Phys. J. D, vol. 68, 268 (2014)
A.V. Verkhovtsev, S. Schramm, and A.V. Solov'yov, Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle, Eur. Phys. J. D, vol. 68, 246 (2014)
G.B. Sushko, A.V. Verkhovtsev, and A.V. Solov'yov, Validation of classical force fields for the description of thermo-mechanical properties of transition metal materials, J. Phys. Chem. A, vol. 118, pp. 8426-8436 (2014)
G.B. Sushko, A.V. Verkhovtsev, A.V. Yakubovich, S. Schramm, and A.V. Solov'yov, Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface, J. Phys. Chem. A, vol. 118, pp. 6685-6691 (2014)
P. Moskovkin, M. Panshenskov, S. Lucas, and A.V. Solov’yov, Simulation of nanowire fragmentation by means of kinetic Monte Carlo approach: 2D case, Phys. Stat. Sol. B, vol. 251, pp. 1456-1462 (2014)
M. Panshenskov, I.A. Solov'yov, and A.V. Solov'yov, Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics, J. Comput. Chem., vol. 35, pp. 1317-1329 (2014)
I.A. Solov’yov, A.V. Solov’yov, N. Kebaili, A. Masson, and C. Brechignac, Thermally induced morphological transition of silver fractals, Phys. Stat. Sol. B, vol. 251, pp. 609-622 (2014)

2013

E. Surdutovich, A.V. Yakubovich, and A.V. Solov’yov, Biodamage via shock waves initiated by irradiation with ions, Scientific Reports, vol. 3, 1289 (2013)
A.V. Yakubovich, I.A. Solov’yov and A.V. Solov’yov, Molecular dynamics simulations of bio-nano systems with MBN Explorer, Physics Procedia, vol. 40, pp. 93-99 (2013)
A.V. Verkhovtsev, A.V. Yakubovich, G. Sushko, M. Hanauske, and A.V. Solov’yov, Molecular dynamics simulations of nanoindentation process of titanium crystal, Comput. Mater. Sci., vol. 76, pp. 20-26 (2013)
A.V. Yakubovich, A.V. Verkhovtsev, M. Hanauske, and A.V. Solov’yov, Computer simulation of diffusion process at interfaces of nickel and titanium crystals, Comput. Mater. Sci., vol. 76, pp. 60-64 (2013)
A.V. Verkhovtsev, M. Hanauske, A.V. Yakubovich, and A.V. Solov’yov, Characterization of small pure and Ni-doped titanium clusters: ab initio versus classical approaches, Comput. Mater. Sci., vol. 76, pp. 80-88 (2013)
A.V. Yakubovich, G. Sushko, S. Schramm, and A.V. Solov’yov, Kinetics of liquid-solid phase transition in large nickel clusters, Phys. Rev. B, vol. 88, 035438 (2013)
G.B. Sushko, V.G. Bezchastnov, I.A. Solov’yov, A.V. Korol, W. Greiner, and A.V. Solov’yov, Simulation of ultra-relativistic electrons and positrons channeling in crystals with MBN Explorer, J. Comput. Phys., vol. 252, pp. 404–418 (2013)
I.A. Solov'yov and A.V. Solov'yov, Simulation of nanofractal dynamics with MBN Explorer, J. Phys.: Conf. Ser., vol. 438, 012006 (2013)
G.B. Sushko, A.V. Korol, W. Greiner, and A.V Solov'yov, Sub-GeV electron and positron channeling in straight, bent and periodically bent silicon crystals, J. Phys.: Conf. Ser., vol. 438, 012018 (2013)
G.B. Sushko, V.G. Bezchastnov, A.V. Korol, W. Greiner, A.V. Solov'yov, R.G. Polozkov, and V.K. Ivanov, Simulations of electron channeling in bent silicon crystal, J. Phys.: Conf. Ser., vol. 438, 012019 (2013)
G.B. Sushko, A.V. Verkhovtsev, A.V. Yakubovich, and A.V. Solov'yov, Molecular dynamics simulation of nanoindentation of nickel-titanium crystal, J. Phys.: Conf. Ser., vol. 438, 012021 (2013)
A.V. Verkhovtsev, G.B. Sushko, A.V. Yakubovich, and A.V. Solov'yov, Benchmarking of classical force fields by ab initio calculations of atomic clusters: Ti and Ni-Ti case, Comput. Theor. Chem., vol. 1021, pp. 101-108 (2013)

2012

I.A. Solov’yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, and A.V. Solov’yov, MesoBioNano Explorer - a universal program for multiscale computer simulations of complex molecular structure and dynamics, J. Comput. Chem., vol. 33, pp. 2412-2439 (2012)

2011

V.V. Dick, I.A. Solov'yov, and A.V. Solov'yov, Fragmentation pathways of nanofractal structures on surface, Phys. Rev. B, vol. 84, 115408 (2011)

2010

J. Geng, I.A. Solov'yov, D.G. Reid, P. Skelton, A.E.H. Wheatley, A.V. Solov'yov, and B.F.G. Johnson, Fullerene-based one-dimensional crystalline nanopolymer formed through topochemical transformation of the parent nanowire, Phys. Rev. B, vol. 81, 214114 (2010)
V.V. Dick, I.A. Solov'yov, and A.V. Solov'yov, Nanoparticles dynamics on a surface: fractal pattern formation and fragmentation, J. Phys.: Conf. Ser., vol. 248, 012025 (2010)

2009

I.A. Solov'yov, J. Geng, A.V. Solov'yov, and B.F.G. Johnson, On the possibility of the electron polarization to be the driving force for the C60-TMB nanowire growth, Chem. Phys. Lett., vol. 472, pp.166-170 (2009)
V.V. Dick, I.A. Solov'yov, and A.V. Solov'yov, Theoretical study of fractal growth and stability on surface, AIP Conf. Proc., vol. 1197, pp.76-88 (2009)
I.A. Solov'yov, J. Geng, A.V. Solov'yov, and B.F.G. Johnson, Understanding the formation process of exceptionally long fullerene-based nanowires, AIP Conf. Proc., vol. 1197, pp.89-102 (2009)
J. Geng, I.A. Solov'yov, W. Zhou, A.V. Solov'yov, and B.F.G. Johnson, Uncovering a solvent-controlled preferential growth of buckminsterfullerene (C60) nanowires, J. Phys. Chem. C, vol. 113, pp. 6390-6397 (2009)

2008

I.A. Solov'yov, M. Mathew, A.V. Solov'yov, and W. Greiner, Liquid surface model for carbon nanotube energetics, Phys. Rev. E, vol. 78, 051601 (2008)

2005

O.I. Obolensky, I.A. Solov'yov, A.V. Solov'yov, and W. Greiner, Fusion and fission of atomic clusters: recent advances, Comput. Lett., vol. 1, pp.313-318 (2005)

2004

I.A. Solov'yov, A.V. Solov'yov, and W. Greiner, Fusion process of Lennard-Jones clusters: global minima and magic numbers formation, Int. J. Mod. Phys. E, vol. 13, pp. 697-736 (2004)

2003

A. Koshelev, A. Shutovich, I. A. Solov'yov, A. V. Solov'yov, and W. Greiner, Formation of global energy minimum structures in the growth process of Lennard-Jones clusters, Proceedings of International Workshop "From Atomic to Nano-scale", Old Dominion University, pp.184-194 (2003)
I.A. Solov'yov, A.V. Solov'yov, W. Greiner, A. Koshelev, and A. Shutovich, Cluster growing process and a sequence of magic numbers, Phys. Rev. Lett., vol. 90, 053401 (2003)