2020

  • [DOI] S. N. Fejer, “Chapter eight – minimalistic coarse-grained modeling of viral capsid assembly,” in Computational approaches for understanding dynamical systems: protein folding and assembly, B. Strodel and B. Barz, Eds., Academic Press, 2020, vol. 170, pp. 405-434.
    [Bibtex]
    @incollection{FEJER2020405,
    title = "Chapter Eight - Minimalistic coarse-grained modeling of viral capsid assembly",
    editor = "Birgit Strodel and Bogdan Barz",
    series = "Progress in Molecular Biology and Translational Science",
    publisher = "Academic Press",
    volume = "170",
    pages = "405 - 434",
    year = "2020",
    booktitle = "Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly",
    issn = "1877-1173",
    doi = "https://doi.org/10.1016/bs.pmbts.2019.12.003",
    url = "http://www.sciencedirect.com/science/article/pii/S1877117319302091",
    author = "Szilard N. Fejer",
    keywords = "Virus capsids, Self-assembly, Energy landscapes, Minimalistic modeling",
    abstract = "The spontaneous formation of virus capsids from multiple copies of capsid proteins is a fascinating example of supramolecular self-assembling processes. Most known viruses protect their genome with icosahedral capsids, but other morphologies exist as well, including elongated, conical, tubular, head-tail structures. The mechanisms of assembly can be diverse and are still not perfectly understood. In this chapter we present theoretical models developed over the years that reproduce the basic physics of self-assembly of empty viral capsids. All these models are highly coarse-grained, as it is still not possible to access the long timescales of such processes with atomistic modeling. Very different particle-based models can result in the same overall behavior, showing that such processes are governed by the effective anisotropic interactions between protein building blocks."
    }

2019

  • M. Baibarac, M. Daescu, and S. Fejer, “Adsorption of 1, 4-phenylene diisothiocyanate onto the graphene oxide sheets functionalized with polydiphenylamine in doped state,” Scientific reports, vol. 9, iss. 1, p. 1–10, 2019.
    [Bibtex]
    @article{baibarac2019adsorption,
    title={Adsorption of 1, 4-phenylene diisothiocyanate onto the graphene oxide sheets functionalized with polydiphenylamine in doped state},
    author={Baibarac, M and Daescu, M and Fejer, SN},
    journal={Scientific reports},
    volume={9},
    number={1},
    pages={1--10},
    year={2019},
    publisher={Nature Publishing Group}
    doi={10.1038/s41598-019-48314-x},
    url={http://doi.org/10.1038/s41598-019-48314-x},
    issn={2045-2322},
    }
  • [DOI] M. Baibarac M. Daescu and S. N. Fejer, “Vibrational and photoluminescence properties of polydiphenylamine doped with silicotungstic acid heteropolyanions and their composites with reduced graphene oxide,” Journal of molecular structure, vol. 1184, p. 25–35, 2019.
    [Bibtex]
    @article{Szilard_Fejer63057301,
    title={Vibrational and photoluminescence properties of polydiphenylamine doped with silicotungstic acid heteropolyanions and their composites with reduced graphene oxide},
    journal={Journal of Molecular Structure},
    author={M. Baibarac, M. Daescu, and S. N. Fejer},
    volume={1184},
    pages={25--35},
    doi={10.1016/j.molstruc.2019.02.014},
    url={http://doi.org/10.1016/j.molstruc.2019.02.014},
    issn={0022-2860},
    year={2019}
    }

2018

  • [DOI] S. N. Fejer, R. G. Mantell, and D. J. Wales, “Designing hierarchical molecular complexity: icosahedra of addressable icosahedra,” Molecular physics, vol. 116, iss. 21-22, p. 2954–2964, 2018.
    [Bibtex]
    @article{Fejer_2018,
    doi = {10.1080/00268976.2018.1439190},
    url = {https://doi.org/10.1080%2F00268976.2018.1439190},
    year = 2018,
    month = {mar},
    publisher = {Informa {UK} Limited},
    volume = {116},
    number = {21-22},
    pages = {2954--2964},
    author = {Szilard N. Fejer and Rosemary G. Mantell and David J. Wales},
    title = {Designing hierarchical molecular complexity: icosahedra of addressable icosahedra},
    journal = {Molecular Physics}
    }

2017

  • [DOI] Z. Antal, J. Szoverfi, and S. N. Fejer, “Predicting the initial steps of salt-stable cowpea chlorotic mottle virus capsid assembly with atomistic force fields,” Journal of chemical information and modeling, vol. 57, iss. 4, p. 910–917, 2017.
    [Bibtex]
    @article{Antal_2017,
    doi = {10.1021/acs.jcim.7b00078},
    url = {https://doi.org/10.1021%2Facs.jcim.7b00078},
    year = 2017,
    month = {apr},
    publisher = {American Chemical Society ({ACS})},
    volume = {57},
    number = {4},
    pages = {910--917},
    author = {Zoltan Antal and Janos Szoverfi and Szilard N. Fejer},
    title = {Predicting the Initial Steps of Salt-Stable Cowpea Chlorotic Mottle Virus Capsid Assembly with Atomistic Force Fields},
    journal = {Journal of Chemical Information and Modeling}
    }

2015

  • S. N. Fejer and D. J. Wales, “Design of a kagome lattice from soft anisotropic particles,” Soft matter, vol. 11, iss. 33, pp. 6663-6668, 2015.
    [Bibtex]
    @article{RID:1103150641510-22,
    title = {Design of a Kagome lattice from soft anisotropic particles},
    journal = {Soft Matter},
    year = {2015},
    author = {Fejer, Szilard N. and Wales, David J.},
    volume = {11},
    number = {33},
    pages = {6663-6668}
    }

2014

  • S. N. Fejer, D. Chakrabarti, H. Kusumaatmaja, and D. J. Wales, “Design principles for bernal spirals and helices with tunable pitch,” Nanoscale, vol. 6, iss. 16, pp. 9448-9456, 2014.
    [Bibtex]
    @article{RID:1103150641510-20,
    title = {Design principles for Bernal spirals and helices with tunable pitch},
    journal = {Nanoscale},
    year = {2014},
    author = {Fejer, S. N. and Chakrabarti, D. and Kusumaatmaja, H. and Wales, D. J.},
    volume = {6},
    number = {16},
    pages = {9448-9456}
    }
  • J. Balazs, B. Viskolcz, M. Posa, and S. N. Fejer, “Global optimization of cholic acid aggregates,” Journal of chemical physics, vol. 140, iss. 14, p. 7, 2014.
    [Bibtex]
    @article{RID:1103150641510-21,
    title = {Global optimization of cholic acid aggregates},
    journal = {Journal of Chemical Physics},
    year = {2014},
    author = {Balazs, J. and Viskolcz, B. and Posa, M. and Fejer, S. N.},
    volume = {140},
    number = {14},
    pages = {7}
    }

2013

  • S. W. Olesen, S. N. Fejer, D. Chakrabarti, and D. J. Wales, “A left-handed building block self-assembles into right-and left-handed helices,” Rsc advances, vol. 3, iss. 31, pp. 12905-12908, 2013.
    [Bibtex]
    @article{RID:1103150641510-19,
    title = {A left-handed building block self-assembles into right-and left-handed helices},
    journal = {Rsc Advances},
    year = {2013},
    author = {Olesen, Scott W. and Fejer, Szilard N. and Chakrabarti, Dwaipayan and Wales, David J.},
    volume = {3},
    number = {31},
    pages = {12905-12908}
    }
  • I. Jakli, I. G. Csizmadia, S. N. Fejer, O. Farkas, B. Viskolcz, S. K. J. Jensen, and A. Perczel, “Helix compactness and stability: electron structure calculations of conformer dependent thermodynamic functions,” Chemical physics letters, vol. 563, pp. 80-87, 2013.
    [Bibtex]
    @article{RID:1103150641510-18,
    title = {Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions},
    journal = {Chemical Physics Letters},
    year = {2013},
    author = {Jakli, Imre and Csizmadia, Imre G. and Fejer, Szilard N. and Farkas, Oedoen and Viskolcz, Bela and Jensen, Svend J. Knak and Perczel, Andras},
    volume = {563},
    pages = {80-87}
    }
  • C. J. Forman, S. N. Fejer, D. Chakrabarti, P. D. Barker, and D. J. Wales, “Local frustration determines molecular and macroscopic helix structures,” Journal of physical chemistry b, vol. 117, iss. 26, pp. 7918-7928, 2013.
    [Bibtex]
    @article{RID:1103150641510-17,
    title = {Local Frustration Determines Molecular and Macroscopic Helix Structures},
    journal = {Journal of Physical Chemistry B},
    year = {2013},
    author = {Forman, Christopher J. and Fejer, Szilard N. and Chakrabarti, Dwaipayan and Barker, Paul D. and Wales, David J.},
    volume = {117},
    number = {26},
    pages = {7918-7928}
    }

2011

  • D. Chakrabarti, S. N. Fejer, D. J. Wales, and E. Bichoutskaia, “Self-assembly of nanoclusters: an energy landscape perspective,” Computational nanoscience, iss. 4, pp. 58-81, 2011.
    [Bibtex]
    @article{RID:1103150641511-23,
    title = {Self-Assembly of Nanoclusters: An Energy Landscape Perspective},
    journal = {Computational Nanoscience},
    year = {2011},
    author = {Chakrabarti, Dwaipayan and Fejer, Szilard N. and Wales, David J. and Bichoutskaia, E},
    number = {4},
    pages = {58-81}
    }
  • S. N. Fejer, D. Chakrabarti, and D. J. Wales, “Self-assembly of anisotropic particles,” Soft matter, vol. 7, iss. 7, pp. 3553-3564, 2011.
    [Bibtex]
    @article{RID:1103150641510-16,
    title = {Self-assembly of anisotropic particles},
    journal = {Soft Matter},
    year = {2011},
    author = {Fejer, Szilard N. and Chakrabarti, Dwaipayan and Wales, David J.},
    volume = {7},
    number = {7},
    pages = {3553-3564}
    }

2010

  • S. N. Fejer, D. Chakrabarti, and D. J. Wales, “Emergent complexity from simple anisotropic building blocks: shells, tubes, and spirals,” Acs nano, vol. 4, iss. 1, pp. 219-228, 2010.
    [Bibtex]
    @article{RID:1103150641511-1,
    title = {Emergent Complexity from Simple Anisotropic Building Blocks: Shells, Tubes, and Spirals},
    journal = {Acs Nano},
    year = {2010},
    author = {Fejer, Szilard N. and Chakrabarti, Dwaipayan and Wales, David J.},
    volume = {4},
    number = {1},
    pages = {219-228}
    }
  • M. S. Bauer, B. Strodel, S. N. Fejer, E. F. Koslover, and D. J. Wales, “Interpolation schemes for peptide rearrangements,” Journal of chemical physics, vol. 132, iss. 5, 2010.
    [Bibtex]
    @article{RID:1103150641511-4,
    title = {Interpolation schemes for peptide rearrangements},
    journal = {Journal of Chemical Physics},
    year = {2010},
    author = {Bauer, Marianne S. and Strodel, Birgit and Fejer, Szilard N. and Koslover, Elena F. and Wales, David J.},
    volume = {132},
    number = {5}
    }
  • E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. N. Fejer, and D. J. Wales, “Symmetrization of the amber and charmm force fields,” Journal of computational chemistry, vol. 31, iss. 7, pp. 1402-1409, 2010.
    [Bibtex]
    @article{RID:1103150641511-5,
    title = {Symmetrization of the AMBER and CHARMM Force Fields},
    journal = {Journal of Computational Chemistry},
    year = {2010},
    author = {Malolepsza, Edyta and Strodel, Birgit and Khalili, Mey and Trygubenko, Semen and Fejer, Szilard N. and Wales, David J.},
    volume = {31},
    number = {7},
    pages = {1402-1409}
    }

2009

  • S. N. Fejer, T. R. James, J. Hernandez-Rojas, and D. J. Wales, “Energy landscapes for shells assembled from pentagonal and hexagonal pyramids,” Physical chemistry chemical physics, vol. 11, iss. 12, pp. 2098-2104, 2009.
    [Bibtex]
    @article{RID:1103150641511-13,
    title = {Energy landscapes for shells assembled from pentagonal and hexagonal pyramids},
    journal = {Physical Chemistry Chemical Physics},
    year = {2009},
    author = {Fejer, Szilard N. and James, Tim R. and Hernandez-Rojas, Javier and Wales, David J.},
    volume = {11},
    number = {12},
    pages = {2098-2104}
    }
  • D. Chakrabarti, S. N. Fejer, and D. J. Wales, “Rational design of helical architectures,” Proceedings of the national academy of sciences of the united states of america, vol. 106, iss. 48, pp. 20164-20167, 2009.
    [Bibtex]
    @article{RID:1103150641511-15,
    title = {Rational design of helical architectures},
    journal = {Proceedings of the National Academy of Sciences of the United States of America},
    year = {2009},
    author = {Chakrabarti, Dwaipayan and Fejer, Szilard N. and Wales, David J.},
    volume = {106},
    number = {48},
    pages = {20164-20167}
    }

2007

  • S. N. Fejer and D. J. Wales, “Helix self-assembly from anisotropic molecules,” Physical review letters, vol. 99, iss. 8, 2007.
    [Bibtex]
    @article{RID:1103150641511-14,
    title = {Helix self-assembly from anisotropic molecules},
    journal = {Physical Review Letters},
    year = {2007},
    author = {Fejer, Szilard N. and Wales, David J.},
    volume = {99},
    number = {8}
    }
  • B. Viskoicz, S. N. Fejer, S. K. J. Jensen, A. Perczel, and I. G. Csizmadia, “Information accumulation in helical oligopeptide structures,” Chemical physics letters, vol. 450, iss. 1-3, pp. 123-126, 2007.
    [Bibtex]
    @article{RID:1103150641512-2,
    title = {Information accumulation in helical oligopeptide structures},
    journal = {Chemical Physics Letters},
    year = {2007},
    author = {Viskoicz, Bela and Fejer, Szilard N. and Jensen, Svend J. Knak and Perczel, Andras and Csizmadia, Imre G.},
    volume = {450},
    number = {1-3},
    pages = {123-126}
    }
  • B. Viskolcz, M. Szori, R. Izsak, S. N. Fejer, and I. G. Csizmadia, “Thermodynamic functions of conformational changes, part iv: functional analysis of conformational entropy of substituted ethane and methanol,” International journal of quantum chemistry, vol. 107, iss. 8, pp. 1826-1834, 2007.
    [Bibtex]
    @article{RID:1103150641512-24,
    title = {Thermodynamic functions of conformational changes, Part IV: Functional analysis of conformational entropy of substituted ethane and methanol},
    journal = {International Journal of Quantum Chemistry},
    year = {2007},
    author = {Viskolcz, Bela and Szori, Milan and Izsak, Robert and Fejer, Szilard N. and Csizmadia, Imize G.},
    volume = {107},
    number = {8},
    pages = {1826-1834}
    }

2006

  • M. A. Sahai, S. N. Fejer, B. Viskolcz, E. F. Pai, and I. G. Csizmadia, “First-principle computational study on the full conformational space of l-threonine diamide, the energetic stability of cis and trans isomers,” Journal of physical chemistry a, vol. 110, iss. 40, pp. 11527-11536, 2006.
    [Bibtex]
    @article{RID:1103150641512-10,
    title = {First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers},
    journal = {Journal of Physical Chemistry a},
    year = {2006},
    author = {Sahai, Michelle A. and Fejer, Szilard N. and Viskolcz, Bela and Pai, Emil F. and Csizmadia, Imre G.},
    volume = {110},
    number = {40},
    pages = {11527-11536}
    }
  • B. Viskolcz, S. Fejer, M. Szori, and I. Csizmadia, “Thermodynamic functions of conformational changes i. a comparative first principles study of 1,2-disubstituted ethanes,” Molecular physics, vol. 104, iss. 5-7, pp. 795-803, 2006.
    [Bibtex]
    @article{RID:1103150641512-12,
    title = {Thermodynamic functions of conformational changes I. A comparative first principles study of 1,2-disubstituted ethanes},
    journal = {Molecular Physics},
    year = {2006},
    author = {Viskolcz, B and Fejer, SN and Szori, M and Csizmadia, IG},
    volume = {104},
    number = {5-7},
    pages = {795-803}
    }
  • B. Viskolcz, S. Fejer, and I. Csizmadia, “Thermodynamic functions of conformational changes. 2. conformational entropy as a measure of information accumulation,” Journal of physical chemistry a, vol. 110, iss. 10, pp. 3808-3811, 2006.
    [Bibtex]
    @article{RID:1103150641512-9,
    title = {Thermodynamic functions of conformational changes. 2. Conformational entropy as a measure of information accumulation},
    journal = {Journal of Physical Chemistry a},
    year = {2006},
    author = {Viskolcz, B and Fejer, SN and Csizmadia, IG},
    volume = {110},
    number = {10},
    pages = {3808-3811}
    }
  • S. N. Fejer, I. G. Csizmadia, and B. Viskolcz, “Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation,” Journal of physical chemistry a, vol. 110, iss. 49, pp. 13325-13331, 2006.
    [Bibtex]
    @article{RID:1103150641529-11,
    title = {Thermodynamic functions of conformational changes: Conformational network of glycine diamide folding, entropy lowering, and informational accumulation},
    journal = {Journal of Physical Chemistry a},
    year = {2006},
    author = {Fejer, Szilard N. and Csizmadia, Imre G. and Viskolcz, Bela},
    volume = {110},
    number = {49},
    pages = {13325-13331}
    }

2005

  • C. Nagy, S. Fejer, L. Berek, J. Molnar, and B. Viskolcz, “Hydrogen bondings in deoxynivalenol (don) conformations – a density functional study,” Journal of molecular structure-theochem, vol. 726, iss. 1-3, pp. 55-59, 2005.
    [Bibtex]
    @article{RID:1103150641529-8,
    title = {Hydrogen bondings in deoxynivalenol (DON) conformations - A density functional study},
    journal = {Journal of Molecular Structure-Theochem},
    year = {2005},
    author = {Nagy, CM and Fejer, SN and Berek, L and Molnar, J and Viskolcz, B},
    volume = {726},
    number = {1-3},
    pages = {55-59}
    }
  • J. Law, S. Fejer, D. Setiadi, G. Chass, and B. Viskolcz, “Molecular orbital computations on lipids: an ab initio exploratory study on the conformations of glycerol and its fluorine congeners,” Journal of molecular structure-theochem, vol. 722, iss. 1-3, pp. 79-96, 2005.
    [Bibtex]
    @article{RID:1103150641529-7,
    title = {Molecular orbital computations on lipids: an ab initio exploratory study on the conformations of glycerol and its fluorine congeners},
    journal = {Journal of Molecular Structure-Theochem},
    year = {2005},
    author = {Law, JMS and Fejer, SN and Setiadi, DH and Chass, GA and Viskolcz, B},
    volume = {722},
    number = {1-3},
    pages = {79-96}
    }

2003

  • S. Fejer, Z. Jenei, and G. Paragi, “Conformational effects of the valine sidechain on the beta(l)beta(l) extended and type i beta turn backbone structures of meco-val-ala-nhme and meco-ala-val-nhme. an ab initio exploratory conformational study,” Journal of molecular structure-theochem, vol. 666, pp. 303-310, 2003.
    [Bibtex]
    @article{RID:1103150641529-6,
    title = {Conformational effects of the valine sidechain on the beta(L)beta(L) extended and Type I beta turn backbone structures of MeCO-Val-Ala-NHMe and MeCO-Ala-Val-NHMe. An ab initio exploratory conformational study},
    journal = {Journal of Molecular Structure-Theochem},
    year = {2003},
    author = {Fejer, SN and Jenei, ZA and Paragi, G},
    volume = {666},
    pages = {303-310}
    }