bibliography.bib

@Article{	  bergonzo2015highly,
  title		= {Highly sampled tetranucleotide and tetraloop motifs enable
		  evaluation of common {RNA} force fields},
  author	= {Bergonzo, Christina and Henriksen, Niel M and Roe, Daniel
		  R and Cheatham III, Thomas E},
  journal	= {RNA},
  volume	= {21},
  number	= {9},
  pages		= {1578--1590},
  year		= {2015},
  publisher	= {Cold Spring Harbor Lab}
}

@Article{	  bergonzo2015improved,
  author	= {Bergonzo, Christina and Cheatham III, Thomas E},
  journal	= {J. Chem. Theory Comput.},
  number	= {9},
  pages		= {3969--3972},
  publisher	= {ACS Publications},
  title		= {Improved Force Field Parameters Lead to a Better
		  Description of {RNA} Structure},
  volume	= {11},
  year		= {2015}
}

@Article{	  sakuraba2015predicting,
  title		= {Predicting {RNA} Duplex Dimerization Free-Energy Changes
		  upon Mutations Using Molecular Dynamics Simulations},
  author	= {Sakuraba, Shun and Asai, Kiyoshi and Kameda, Tomoshi},
  journal	= {J. Phys. Chem. Lett.},
  volume	= {6},
  number	= {21},
  pages		= {4348--4351},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  bottaro2016rna,
  title		= {{{RNA}} folding pathways in stop motion},
  author	= {Bottaro, Sandro and Gil-Ley, Alejandro and Bussi,
		  Giovanni},
  journal	= {Nucleic Acids Res.},
  volume	= {44},
  number	= {12},
  pages		= {5883-5891},
  year		= {2016},
  publisher	= {Oxford University Press}
}

@Article{	  gil2016empirical,
  title		= {Empirical corrections to the {AMBER} {RNA} force field
		  with Target Metadynamics},
  author	= {Gil-Ley, Alejandro and Bottaro, Sandro and Bussi,
		  Giovanni},
  journal	= {J. Chem. Theory Comput.},
  volume	= 12,
  number	= 6,
  pages		= {2790--2798},
  year		= 2016
}

@Article{	  kuhrova2016,
  title		= {Computer folding of {RNA} tetraloops: {I}dentification of
		  key force field deficiencies},
  author	= {K{\"u}hrov{\'a}, Petra and Best, Robert B and Bottaro,
		  Sandro and Bussi, Giovanni and {\v{S}}poner,
		  Ji{\v{r}}{\'\i} and Otyepka, Michal and Ban{\'a}{\v{s}}, Pavel},
  journal	= {J. Chem. Theory Comput.},
  volume	= {12},
  number	= {9},
  pages		= {4534--4548},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  bottaro2016free,
  title		= {Free Energy Landscape of {{GAGA}} and {{UUCG}} {{RNA}}
		  Tetraloops},
  author	= {Bottaro, Sandro and Ban{\'a}{\v s}, Pavel and Ji{{\v
		  r\'\i}} {{\v S}}poner and Giovanni Bussi},
  journal	= {J. Phys. Chem. Lett.},
  volume	= {7},
  number	= 20,
  pages		= {4032--4038},
  year		= 2016
}

@Article{	  cesari2016maxent,
  title		= {Combining simulations and solution experiments as a
		  paradigm for {RNA} force field refinement},
  author	= {Cesari, A and Gil-Ley, A and Bussi, G},
  journal	= {J. Chem. Theory Comput.},
  volume	= {12},
  number	= {12},
  pages		= {6192--6200},
  year		= {2016}
}

@Article{	  yang2016predicting,
  title		= {Predicting {RNA} structures via a simple van der {W}aals
		  correction to an all-atom force field},
  author	= {Yang, Changwon and Lim, Manho and Kim, Eunae and Pak,
		  Youngshang},
  journal	= {J. Chem. Theory Comput.},
  volume	= {13},
  number	= {2},
  pages		= {395--399},
  year		= {2017},
  publisher	= {ACS Publications}
}

@Article{	  aytenfisu2017revised,
  title		= {Revised {RNA} dihedral parameters for the {AMBER} force
		  field improve {RNA} molecular dynamics},
  author	= {Aytenfisu, Asaminew H and Spasic, Aleksandar and
		  Grossfield, Alan and Stern, Harry A and Mathews, David H},
  journal	= {J. Chem. Theory Comput.},
  volume	= {13},
  number	= {2},
  pages		= {900--915},
  year		= {2017},
  publisher	= {ACS Publications}
}

@Article{	  gil2015,
  title		= {Enhanced conformational sampling using replica exchange
		  with collective-variable tempering},
  author	= {Gil-Ley, Alejandro and Bussi, Giovanni},
  journal	= {J. Chem. Theory Comput.},
  volume	= {11},
  number	= {3},
  pages		= {1077--1085},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  haldar2015insights,
  title		= {Insights into Stability and Folding of {GNRA} and {UNCG}
		  Tetraloops Revealed by Microsecond Molecular Dynamics and
		  Well-Tempered Metadynamics.},
  author	= {Haldar, S and K{\"u}hrov{\'a}, P and Ban{\'a}{\v{s}}, P
		  and Spiwok, V and {\v{S}}poner, J and Hobza, P and Otyepka, M},
  journal	= {J. Chem. Theory Comput.},
  volume	= {11},
  number	= {8},
  pages		= {3866},
  year		= {2015}
}

@Article{	  xue2015folding,
  title		= {Folding of {SAM-II} riboswitch explored by
		  replica-exchange molecular dynamics simulation},
  author	= {Xue, Xu and Yongjun, Wang and Zhihong, Li},
  journal	= {J. Theor. Biol.},
  volume	= {365},
  pages		= {265--269},
  year		= {2015},
  publisher	= {Elsevier}
}

@Article{	  park2015crystallographic,
  title		= {Crystallographic and Computational Analyses of {AUUCU}
		  Repeating {RNA} That Causes {S}pinocerebellar {A}taxia Type
		  10 ({SCA10})},
  author	= {Park, HaJeung and Gonz{\'a}lez, {\`A}lex L and Yildirim,
		  Ilyas and Tran, Tuan and Lohman, Jeremy R and Fang, Pengfei
		  and Guo, Min and Disney, Matthew D},
  journal	= {Biochemistry},
  volume	= {54},
  number	= {24},
  pages		= {3851},
  year		= {2015},
  publisher	= {NIH Public Access}
}

@Article{	  bergonzo2015stem,
  title		= {Stem-{L}oop {V} of {V}arkud {S}atellite {RNA} Exhibits
		  Characteristics of the {Mg}$^{2+}$ Bound Structure in the
		  Presence of Monovalent Ions},
  author	= {Bergonzo, Christina and Hall, Kathleen B and Cheatham III,
		  Thomas E},
  journal	= {J. Phys. Chem. B},
  volume	= {119},
  number	= {38},
  pages		= {12355--12364},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  radak2015characterization,
  title		= {Characterization of the three-dimensional free energy
		  manifold for the uracil ribonucleoside from asynchronous
		  replica exchange simulations},
  author	= {Radak, Brian K and Romanus, Melissa and Lee, Tai-Sung and
		  Chen, Haoyuan and Huang, Ming and Treikalis, Antons and
		  Balasubramanian, Vivekanandan and Jha, Shantenu and York,
		  Darrin M},
  journal	= {J. Chem. Theory Comput.},
  volume	= {11},
  number	= {2},
  pages		= {373--377},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  bian2015free,
  title		= {Free energy landscape and multiple folding pathways of an
		  {H}-type {RNA} pseudoknot},
  author	= {Bian, Yunqiang and Zhang, Jian and Wang, Jun and Wang,
		  Jihua and Wang, Wei},
  journal	= {PloS One},
  volume	= {10},
  number	= {6},
  pages		= {e0129089},
  year		= {2015},
  publisher	= {Public Library of Science}
}

@Article{	  di2015kissing,
  title		= {Kissing loop interaction in adenine riboswitch: {I}nsights
		  from umbrella sampling simulations},
  author	= {Di Palma, Francesco and Bottaro, Sandro and Bussi,
		  Giovanni},
  journal	= {BMC Bioinformatics},
  volume	= {16},
  number	= {Suppl 9},
  pages		= {S6},
  year		= {2015},
  publisher	= {BioMed Central Ltd}
}

@Article{	  larsen2015thermodynamic,
  title		= {Thermodynamic insights into 2-thiouridine-enhanced {RNA}
		  hybridization},
  author	= {Larsen, Aaron T and Fahrenbach, Albert C and Sheng, Jia
		  and Pian, Julia and Szostak, Jack W},
  journal	= {Nucleic Acids Res.},
  volume	= {43},
  number	= {16},
  pages		= {7675--7687},
  year		= {2015},
  publisher	= {Oxford University Press}
}

@Article{	  yildirim2015computational,
  title		= {Computational investigation of {RNA} {CUG} repeats
		  responsible for myotonic dystrophy 1},
  author	= {Yildirim, Ilyas and Chakraborty, Debayan and Disney,
		  Matthew D and Wales, David J and Schatz, George C},
  journal	= {J. Chem. Theory Comput.},
  volume	= {11},
  number	= {10},
  pages		= {4943--4958},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  wu2015multivalent,
  title		= {Multivalent ion-mediated nucleic acid helix-helix
		  interactions: {RNA} versus {DNA}},
  author	= {Wu, Yuan-Yan and Zhang, Zhong-Liang and Zhang, Jin-Si and
		  Zhu, Xiao-Long and Tan, Zhi-Jie},
  journal	= {Nucleic Acids Res.},
  volume	= {43},
  number	= {12},
  pages		= {6156--6165},
  year		= {2015},
  publisher	= {Oxford University Press}
}

@Article{	  miner2016free,
  title		= {Free-energy landscape of a hyperstable {RNA} tetraloop},
  author	= {Miner, Jacob C and Chen, Alan A and Garc{\'\i}a, Angel E},
  journal	= {Proc. Natl. Acad. Sci. U.S.A.},
  volume	= {113},
  number	= {24},
  pages		= {6665--6670},
  year		= {2016},
  publisher	= {National Acad Sciences}
}

@Article{	  takahashi2016using,
  title		= {Using in-cell {SHAPE}-Seq and simulations to probe
		  structure--function design principles of {RNA}
		  transcriptional regulators},
  author	= {Takahashi, Melissa K and Watters, Kyle E and Gasper, Paul
		  M and Abbott, Timothy R and Carlson, Paul D and Chen, Alan
		  A and Lucks, Julius B},
  journal	= {RNA},
  volume	= {22},
  number	= {6},
  pages		= {920--933},
  year		= {2016},
  publisher	= {Cold Spring Harbor Lab}
}

@Article{	  borkar2016structure,
  title		= {Structure of a low-population binding intermediate in
		  protein--{RNA} recognition},
  author	= {Borkar, Aditi N and Bardaro, Michael F and Camilloni,
		  Carlo and Aprile, Francesco A and Varani, Gabriele and
		  Vendruscolo, Michele},
  journal	= {Proc. Natl. Acad. Sci. U.S.A.},
  volume	= {113},
  number	= {26},
  pages		= {7171--7176},
  year		= {2016},
  publisher	= {National Acad Sciences}
}

@Article{	  vukovic2016molecular,
  title		= {Molecular mechanism of processive 3' to 5' {RNA}
		  translocation in the active subunit of the {RNA} exosome
		  complex},
  author	= {Vukovic, Lela and Chipot, Christophe and Makino, Debora L
		  and Conti, Elena and Schulten, Klaus},
  journal	= {J. Am. Chem. Soc.},
  volume	= {138},
  number	= {12},
  pages		= {4069--4078},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  hayatshahi2017investigating,
  title		= {Investigating the ion dependence of the first unfolding
		  step of {GTP}ase-Associating Center ribosomal {RNA}},
  author	= {Hayatshahi, Hamed S and Bergonzo, Christina and Cheatham
		  III, Thomas E},
  journal	= {J. Biomol. Struct. Dyn.},
  pages		= {1--11},
  year		= {2017},
  publisher	= {Taylor \& Francis}
}

@Article{	  borkar2017simultaneous,
  title		= {Simultaneous {NMR} characterisation of multiple minima in
		  the free energy landscape of an {RNA} {UUCG} tetraloop},
  author	= {Borkar, Aditi N and Vallurupalli, Pramodh and Camilloni,
		  Carlo and Kay, Lewis E and Vendruscolo, Michele},
  journal	= {Phys. Chem. Chem. Phys.},
  volume	= {19},
  number	= {4},
  pages		= {2797--2804},
  year		= {2017},
  publisher	= {Royal Society of Chemistry}
}

@Article{	  warfield2017molecular,
  title		= {Molecular simulations and {M}arkov state modeling reveal
		  the structural diversity and dynamics of a
		  theophylline-binding {RNA} aptamer in its unbound state},
  author	= {Warfield, Becka M and Anderson, Peter C},
  journal	= {PloS One},
  volume	= {12},
  number	= {4},
  pages		= {e0176229},
  year		= {2017},
  publisher	= {Public Library of Science}
}

@Article{	  palermo2017crispr,
  title		= {{CRISPR}-{C}as9 conformational activation as elucidated
		  from enhanced molecular simulations},
  author	= {Palermo, Giulia and Miao, Yinglong and Walker, Ross C and
		  Jinek, Martin and McCammon, J Andrew},
  journal	= {Proc. Natl. Acad. Sci. U.S.A.},
  volume	= {114},
  number	= {28},
  pages		= {7260--7265},
  year		= {2017},
  publisher	= {National Acad Sciences}
}

@Article{	  verona2017focus,
  title		= {Focus on {PNA} Flexibility and {RNA} Binding using
		  Molecular Dynamics and Metadynamics},
  author	= {Verona, Massimiliano Donato and Verdolino, Vincenzo and
		  Palazzesi, Ferruccio and Corradini, Roberto},
  journal	= {Sci. Rep.},
  volume	= {7},
  pages		= {42799},
  year		= {2017},
  publisher	= {Nature Publishing Group}
}

@Article{	  pathak2017water,
  title		= {Water isotope effect on the thermostability of a polio
		  viral {RNA} hairpin: {A} metadynamics study},
  author	= {Pathak, Arup K and Bandyopadhyay, Tusar},
  journal	= {J. Chem. Phys.},
  volume	= {146},
  number	= {16},
  pages		= {165104},
  year		= {2017},
  publisher	= {AIP Publishing}
}

@Article{	  sun2017protonation,
  title		= {Protonation-dependent base flipping in the catalytic triad
		  of a small {RNA}},
  author	= {Sun, Zhaoxi and Wang, Xiaohui and Zhang, John ZH},
  journal	= {Chem. Phys. Lett.},
  year		= {2017},
  publisher	= {Elsevier},
  volume	= {684},
  pages		= {239--244}
}

@Article{	  pan2017structure,
  title		= {Structure and Dynamics of {DNA} and {RNA} Double Helices
		  of {CAG} and {GAC} Trinucleotide Repeats},
  author	= {Pan, Feng and Man, Viet Hoang and Roland, Christopher and
		  Sagui, Celeste},
  journal	= {Biophys. J.},
  volume	= {113},
  number	= {1},
  pages		= {19--36},
  year		= {2017},
  publisher	= {Elsevier}
}

@Article{	  miner2017equilibrium,
  title		= {Equilibrium denaturation and preferential interactions of
		  an {RNA} tetraloop with urea},
  author	= {Miner, Jacob C and Garc{\'\i}a, Angel E},
  journal	= {J. Phys. Chem. B},
  volume	= {121},
  number	= {15},
  pages		= {3734--3746},
  year		= {2017},
  publisher	= {ACS Publications}
}

@Article{	  bochicchio2015molecular,
  title		= {Molecular view of ligands specificity for {CAG} repeats in
		  anti-{H}untington therapy},
  author	= {Bochicchio, Anna and Rossetti, Giulia and Tabarrini,
		  Oriana and Krau$\beta$, Sybille and Carloni, Paolo},
  journal	= {J. Chem. Theory Comput.},
  volume	= {11},
  number	= {10},
  pages		= {4911--4922},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  panteva2015comparison,
  title		= {Comparison of structural, thermodynamic, kinetic and mass
		  transport properties of {Mg}$^{2+}$ ion models commonly
		  used in biomolecular simulations},
  author	= {Panteva, Maria T and Giamba{\c{s}}u, George M and York,
		  Darrin M},
  journal	= {J. Comput. Chem.},
  volume	= {36},
  number	= {13},
  pages		= {970--982},
  year		= {2015},
  publisher	= {Wiley Online Library}
}

@Article{	  liberman2015structural,
  title		= {Structural analysis of a class {III} pre{Q}1 riboswitch
		  reveals an aptamer distant from a ribosome-binding site
		  regulated by fast dynamics},
  author	= {Liberman, Joseph A and Suddala, Krishna C and Aytenfisu,
		  Asaminew and Chan, Dalen and Belashov, Ivan A and Salim,
		  Mohammad and Mathews, David H and Spitale, Robert C and
		  Walter, Nils G and Wedekind, Joseph E},
  journal	= {Proc. Natl. Acad. Sci. U.S.A.},
  volume	= {112},
  number	= {27},
  pages		= {E3485--E3494},
  year		= {2015},
  publisher	= {National Acad Sciences}
}

@Article{	  cunha2016ions,
  title		= {Unraveling {Mg}$^{2+}$--{RNA} binding with atomistic
		  molecular dynamics},
  author	= {Cunha, Richard A and Bussi, Giovanni},
  journal	= {RNA},
  volume	= {23},
  number	= {5},
  pages		= {628--638},
  year		= {2017},
  publisher	= {Cold Spring Harbor Lab}
}

@Article{	  lemkul2016characterization,
  title		= {Characterization of {Mg}$^{2+}$ Distributions around {RNA}
		  in Solution},
  author	= {Lemkul, Justin A and Lakkaraju, Sirish Kaushik and
		  MacKerell Jr, Alexander D},
  journal	= {ACS omega},
  volume	= {1},
  number	= {4},
  pages		= {680--688},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  hayatshahi2017computational,
  title		= {Computational assessment of potassium and magnesium ion
		  binding to a buried pocket in {GTP}ase-associating center},
  author	= {Hayatshahi, Hamed S and Roe, Daniel R and Galindo-Murillo,
		  Rodrigo and Hall, Kathleen B and Cheatham III, Thomas E},
  journal	= {RNA},
  volume	= {121},
  number	= {3},
  pages		= {451--462},
  year		= {2017},
  publisher	= {ACS Publications}
}

@Article{	  hu2017ligand,
  title		= {Ligand Selectivity Mechanism and Conformational Changes in
		  Guanine Riboswitch by Molecular Dynamics Simulations and
		  Free Energy Calculations},
  author	= {Hu, Guodong and Ma, Aijing and Wang, Jihua},
  journal	= {J. Chem. Inf. Model.},
  volume	= {57},
  number	= {4},
  pages		= {918--928},
  year		= {2017},
  publisher	= {ACS Publications}
}

@Article{	  radak2015assessment,
  title		= {Assessment of metal-assisted nucleophile activation in the
		  hepatitis delta virus ribozyme from molecular simulation
		  and {3D}-{RISM}},
  author	= {Radak, Brian K and Lee, Tai-Sung and Harris, Michael E and
		  York, Darrin M},
  journal	= {RNA},
  volume	= {21},
  number	= {9},
  pages		= {1566--1577},
  year		= {2015},
  publisher	= {Cold Spring Harbor Lab}
}

@Article{	  zhang2015role,
  title		= {Role of the active site guanine in the {\it {glmS}}
		  ribozyme self-cleavage mechanism: {Q}uantum
		  mechanical/molecular mechanical free energy simulations},
  author	= {Zhang, Sixue and Ganguly, Abir and Goyal, Puja and
		  Bingaman, Jamie L and Bevilacqua, Philip C and
		  Hammes-Schiffer, Sharon},
  journal	= {J. Am. Chem. Soc.},
  volume	= {137},
  number	= {2},
  pages		= {784--798},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  swadling2015structure,
  title		= {Structure, dynamics, and function of the hammerhead
		  ribozyme in bulk water and at a clay mineral surface from
		  replica exchange molecular dynamics},
  author	= {Swadling, Jacob B and Wright, David W and Suter, James L
		  and Coveney, Peter V},
  journal	= {Langmuir},
  volume	= {31},
  number	= {8},
  pages		= {2493--2501},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  thaplyal2015inverse,
  title		= {Inverse thio effects in the hepatitis delta virus ribozyme
		  reveal that the reaction pathway is controlled by metal ion
		  charge density},
  author	= {Thaplyal, Pallavi and Ganguly, Abir and Hammes-Schiffer,
		  Sharon and Bevilacqua, Philip C},
  journal	= {Biochemistry},
  volume	= {54},
  number	= {12},
  pages		= {2160--2175},
  year		= {2015},
  publisher	= {ACS Publications}
}

@Article{	  gaines2016ribozyme,
  title		= {Ribozyme catalysis with a twist: {A}ctive state of the
		  twister ribozyme in solution predicted from molecular
		  simulation},
  author	= {Gaines, Colin S and York, Darrin M},
  journal	= {J. Am. Chem. Soc.},
  volume	= {138},
  number	= {9},
  pages		= {3058--3065},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  zhang2016assessing,
  title		= {Assessing the Potential Effects of Active Site {Mg}$^{2+}$
		  Ions in the {\it {glmS}} Ribozyme--Cofactor Complex},
  author	= {Zhang, Sixue and Stevens, David R and Goyal, Puja and
		  Bingaman, Jamie L and Bevilacqua, Philip C and
		  Hammes-Schiffer, Sharon},
  journal	= {J. Phys. Chem. Lett.},
  volume	= {7},
  number	= {19},
  pages		= {3984--3988},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  casalino2016activates,
  title		= {Who activates the nucleophile in ribozyme catalysis? {A}n
		  answer from the splicing mechanism of group {II} introns},
  author	= {Casalino, Lorenzo and Palermo, Giulia and Rothlisberger,
		  Ursula and Magistrato, Alessandra},
  journal	= {J. Am. Chem. Soc.},
  volume	= {138},
  number	= {33},
  pages		= {10374--10377},
  year		= {2016},
  publisher	= {ACS Publications}
}

@Article{	  mlynsky2016inline,
  title		= {Understanding in-line probing experiments by modeling
		  cleavage of nonreactive {RNA} nucleotides},
  author	= {Ml{\'y}nsk{\'y}, Vojt{\v{e}}ch and Bussi, Giovanni},
  journal	= {RNA},
  volume	= {23},
  number	= {5},
  pages		= {712--720},
  year		= {2017},
  publisher	= {Cold Spring Harbor Lab}
}

@Article{	  bingaman2017glcn6p,
  title		= {The {G}lc{N6P} cofactor plays multiple catalytic roles in
		  the {\it {glmS}} ribozyme},
  author	= {Bingaman, Jamie L and Zhang, Sixue and Stevens, David R
		  and Yennawar, Neela H and Hammes-Schiffer, Sharon and
		  Bevilacqua, Philip C},
  journal	= {Nat. Chem. Biol.},
  volume	= {13},
  number	= {4},
  pages		= {439--445},
  year		= {2017},
  publisher	= {Nature Research}
}

@Article{	  schuabb2017pressure,
  title		= {Pressure modulates the self-cleavage step of the hairpin
		  ribozyme.},
  author	= {Schuabb, C and Kumar, N and Pataraia, S and Marx, D and
		  Winter, R},
  journal	= {Nat. Commun.},
  volume	= {8},
  pages		= {14661},
  year		= {2017}
}

@Article{	  chen2017divalent,
  title		= {Divalent metal ion activation of a guanine general base in
		  the hammerhead ribozyme: {I}nsights from molecular
		  simulations},
  author	= {Chen, Haoyuan and Giese, Timothy J and Golden, Barbara L
		  and York, Darrin M},
  journal	= {Biochemistry},
  volume	= {56},
  number	= {24},
  pages		= {2985--2994},
  year		= {2017},
  publisher	= {ACS Publications}
}

@article{grasso2017free,
  title={Free energy landscape of si{RNA}-polycation complexation:              {E}lucidating the effect of molecular geometry, polymer flexibility, and charge neutralization},
  author={Grasso, Gianvito and Deriu, Marco Agostino and Patrulea, Viorica and  Borchard, Gerrit and M{\"o}ller, Michael and Danani, Andrea},
  journal={PloS One},
  volume={12},
  number={10},
  pages={e0186816},
  year={2017},
  publisher={Public Library of Science}
}

@article{panteva2015force,
  title={Force field for {Mg}$^{2+}$, {Mn}$^{2+}$, {Zn}$^{2+}$, and {Cd}$^{2+}$ ions that have balanced interactions with nucleic acids},
  author={Panteva, Maria T and Giambasu, George M and York, Darrin M},
  journal={J. Phys. Chem. B},
  volume={119},
  number={50},
  pages={15460--15470},
  year={2015},
  publisher={ACS Publications}
}