Bibliography

Here is the complete list of the published papers connected to the projects deposited in PLUMED-NEST:

[plumID:19.061] E. Jackson, M. Miklitz, Q. Song, G. A. Tribello, K. E. Jelfs, Computational Evaluation of the Diffusion Mechanisms for C8 Aromatics in Porous Organic Cages, The Journal of Physical Chemistry C (2019)

[plumID:19.058] V. Santolini, G. A. Tribello, K. E. Jelfs, Predicting solvent effects on the structure of porous organic molecules, Chemical Communications 51, 15542–15545 (2015)

[plumID:19.055] Z. Šućur, V. Spiwok, Sampling Enhancement and Free Energy Prediction by the Flying Gaussian Method, Journal of Chemical Theory and Computation 12, 4644–4650 (2016)

[plumID:19.053] E. Baldi, M. Ceriotti, G. A. Tribello, Extracting the interfacial free energy and anisotropy from a smooth fluctuating dividing surface, Journal of Physics: Condensed Matter 29, 445001 (2017)

[plumID:19.052] B. Cheng, G. A. Tribello, M. Ceriotti, The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit, The Journal of Chemical Physics 147, 104707 (2017)

[plumID:19.051] B. Cheng, G. A. Tribello, M. Ceriotti, Solid-liquid interfacial free energy out of equilibrium, Physical Review B 92 (2015)

[plumID:19.050] J. Klug, C. Triguero, M. G. Del Pópolo, G. A. Tribello, Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes, The Journal of Physical Chemistry B 122, 6417–6422 (2018)

[plumID:19.049] G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations, Journal of Chemical Theory and Computation 13, 1317–1327 (2017)

[plumID:19.048] G. Mattedi, F. Deflorian, J. S. Mason, C. de Graaf, F. L. Gervasio, Understanding Ligand Binding Selectivity in a Prototypical GPCR Family, Journal of Chemical Information and Modeling 59, 2830–2836 (2019)

[plumID:19.047] J. Pazúriková, A. Křenek, V. Spiwok, M. Šimková, Reducing the number of mean-square deviation calculations with floating close structure in metadynamics, The Journal of Chemical Physics 146, 115101 (2017)

[plumID:19.046] Z. F. Brotzakis, V. Limongelli, M. Parrinello, Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables, Journal of Chemical Theory and Computation 15, 743–750 (2018)

[plumID:19.045] M. De La Pierre, P. Raiteri, A. G. Stack, J. D. Gale, Uncovering the Atomistic Mechanism for Calcite Step Growth, Angewandte Chemie International Edition 56, 8464–8467 (2017)

[plumID:19.044] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle, Physical Review Letters 122 (2019)

[plumID:19.043] G. Piccini, D. Mendels, M. Parrinello, Metadynamics with Discriminants: A Tool for Understanding Chemistry, Journal of Chemical Theory and Computation 14, 5040–5044 (2018)

[plumID:19.042] D. Mendels, G. Piccini, M. Parrinello, Collective Variables from Local Fluctuations, The Journal of Physical Chemistry Letters 9, 2776–2781 (2018)

[plumID:19.041] C. M. Mao, J. Sampath, K. G. Sprenger, G. Drobny, J. Pfaendtner, Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces, Langmuir 35, 5911–5920 (2019)

[plumID:19.040] L. Hovan, F. Comitani, F. L. Gervasio, Defining an Optimal Metric for the Path Collective Variables, Journal of Chemical Theory and Computation 15, 25–32 (2018)

[plumID:19.037] R. Drori et al., A Supramolecular Ice Growth Inhibitor, Journal of the American Chemical Society 138, 13396–13401 (2016)

[plumID:19.036] D. Meral, D. Provasi, M. Filizola, An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber, The Journal of Chemical Physics 149, 224101 (2018)

[plumID:19.035] D. Meral et al., Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations, Scientific Reports 8 (2018)

[plumID:19.034] A. Pérez de Alba Ortíz, A. Tiwari, R. C. Puthenkalathil, B. Ensing, Advances in enhanced sampling along adaptive paths of collective variables, The Journal of Chemical Physics 149, 072320 (2018)

[plumID:19.033] A. Pérez de Alba Ortíz, A. Tiwari, R. C. Puthenkalathil, B. Ensing, Advances in enhanced sampling along adaptive paths of collective variables, The Journal of Chemical Physics 149, 072320 (2018)

[plumID:19.032] F. Pietrucci, A. M. Saitta, Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios, Proceedings of the National Academy of Sciences 112, 15030–15035 (2015)

[plumID:19.031] S. Pipolo et al., Navigating at Will on the Water Phase Diagram, Physical Review Letters 119 (2017)

[plumID:19.030] M. Lelimousin, V. Limongelli, M. S. P. Sansom, Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations, Journal of the American Chemical Society 138, 10611–10622 (2016)

[plumID:19.029] P. Marinelli et al., A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation, Redox Biology 14, 566–575 (2018)

[plumID:19.028] Y. Wang, J. M. Lamim Ribeiro, P. Tiwary, Past–future information bottleneck framework for simultaneously sampling biomolecular reaction coordinate, thermodynamics and kinetics, (2018)

[plumID:19.027] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle, Physical Review Letters 122 (2019)

[plumID:19.026] G. C. Sosso et al., Unravelling the origins of ice nucleation on organic crystals, Chemical Science 9, 8077–8088 (2018)

[plumID:19.025] T. Löhr, A. Jussupow, C. Camilloni, Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide, The Journal of Chemical Physics 146, 165102 (2017)

[plumID:19.024] M. Deighan, M. Bonomi, J. Pfaendtner, Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble, Journal of Chemical Theory and Computation 8, 2189–2192 (2012)

[plumID:19.023] A. Gil-Ley, G. Bussi, Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering, Journal of Chemical Theory and Computation 11, 1077–1085 (2015)

[plumID:19.022] H. Chen, H. Fu, X. Shao, C. Chipot, W. Cai, ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines, Journal of Chemical Information and Modeling 58, 1315–1318 (2018)

[plumID:19.021] G. M. Hocky, T. Dannenhoffer-Lafage, G. A. Voth, Coarse-Grained Directed Simulation, Journal of Chemical Theory and Computation 13, 4593–4603 (2017)

[plumID:19.020] M. Bernetti et al., Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations, The Journal of Physical Chemistry B 121, 9572–9582 (2017)

[plumID:19.019] Y. Wang, O. Valsson, P. Tiwary, M. Parrinello, K. Lindorff-Larsen, Frequency adaptive metadynamics for the calculation of rare-event kinetics, The Journal of Chemical Physics 149, 072309 (2018)

[plumID:19.018] C. Cozza, M. Bonomi, A. Pietropaolo, A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes, Journal of Chemical Theory and Computation 14, 5441–5445 (2018)

[plumID:19.017] R. Capelli, P. Carloni, M. Parrinello, Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics, The Journal of Physical Chemistry Letters 10, 3495–3499 (2019)

[plumID:19.016] P. Lucaioli et al., Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction, CrystEngComm 20, 3971–3977 (2018)

[plumID:19.015] V. Marinova, G. P. F. Wood, I. Marziano, M. Salvalaglio, Dynamics and Thermodynamics of Ibuprofen Conformational Isomerism at the Crystal/Solution Interface, Journal of Chemical Theory and Computation 14, 6484–6494 (2018)

[plumID:19.014] L. Kollias et al., Molecular Level Understanding of the Free Energy Landscape in Early Stages of Metal–Organic Framework Nucleation, Journal of the American Chemical Society 141, 6073–6081 (2019)

[plumID:19.013] A. Cesari et al., Fitting Corrections to an RNA Force Field Using Experimental Data, Journal of Chemical Theory and Computation 15, 3425–3431 (2019)

[plumID:19.012] C. Paissoni, A. Jussupow, C. Camilloni, Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data, Journal of Applied Crystallography 52, 394–402 (2019)

[plumID:19.011] T. Giorgino, How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation, Computer Physics Communications 228, 258–263 (2018)

[plumID:19.010] B. Weber et al., The Antibody Light-Chain Linker Regulates Domain Orientation and Amyloidogenicity, Journal of Molecular Biology 430, 4925–4940 (2018)

[plumID:19.009] S. Bottaro, P. Banáš, J. Šponer, G. Bussi, Free Energy Landscape of GAGA and UUCG RNA Tetraloops, The Journal of Physical Chemistry Letters 7, 4032–4038 (2016)

[plumID:19.008] D. Trapl et al., Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations, Frontiers in Molecular Biosciences 6 (2019)

[plumID:19.007] L. Eshun-Wilson et al., Effects of α-tubulin acetylation on microtubule structure and stability, Proceedings of the National Academy of Sciences 116, 10366–10371 (2019)

[plumID:19.006] P. Kříž, Z. Šućur, V. Spiwok, Free-Energy Surface Prediction by Flying Gaussian Method: Multisystem Representation, The Journal of Physical Chemistry B 121, 10479–10483 (2017)

[plumID:19.005] G. T. Heller et al., Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide, Journal of Molecular Biology 429, 2772–2779 (2017)

[plumID:19.004] M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo, Metainference: A Bayesian inference method for heterogeneous systems, Science Advances 2, e1501177 (2016)

[plumID:19.003] S. Vahidi et al., Reversible inhibition of the ClpP protease via an N-terminal conformational switch, Proceedings of the National Academy of Sciences 115, E6447–E6456 (2018)

[plumID:19.002] M. Bonomi, R. Pellarin, M. Vendruscolo, Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy, Biophysical Journal 114, 1604–1613 (2018)

[plumID:19.001] V. Mlýnský, G. Bussi, Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility, The Journal of Physical Chemistry Letters 9, 313–318 (2018)

[plumID:19.000] M. Invernizzi, M. Parrinello, Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation, Journal of Chemical Theory and Computation 15, 2187–2194 (2019)