Bibliography

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

[plumID:19.082] V. Rizzi, D. Polino, E. Sicilia, N. Russo, M. Parrinello, The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study, Angewandte Chemie International Edition 58, 3976–3980 (2019)

[plumID:19.081] P. M. Piaggi, M. Parrinello, Calculation of phase diagrams in the multithermal-multibaric ensemble, The Journal of Chemical Physics 150, 244119 (2019)

[plumID:19.078] F. Giberti, B. Cheng, G. A. Tribello, M. Ceriotti, Iterative Unbiasing of Quasi-Equilibrium Sampling, Journal of Chemical Theory and Computation (2019)

[plumID:19.075] T. Giorgino, PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python, Journal of Open Source Software 4, 1773 (2019)

[plumID:19.074] F. Colizzi et al., Asymmetric base-pair opening drives helicase unwinding dynamics, Proceedings of the National Academy of Sciences 116, 22471–22477 (2019)

[plumID:19.073] L. Kollias, D. Cantu, V.-A. Glezakou, R. Rousseau, M. Salvalaglio, On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units, (2019)

[plumID:19.071] V. Marinova, M. Salvalaglio, Time-independent free energies from metadynamics via mean force integration, The Journal of Chemical Physics 151, 164115 (2019)

[plumID:19.070] S. Bottaro, P. J. Nichols, B. Vögeli, M. Parrinello, K. Lindorff-Larsen, Unexpected Dynamics in the UUCG RNA Tetraloop, (2019)

[plumID:19.069] V. Marinova, G. P. F. Wood, I. Marziano, M. Salvalaglio, Solvent Dynamics and Thermodynamics at the Crystal–Solution Interface of Ibuprofen, Crystal Growth & Design 19, 6534–6541 (2019)

[plumID:19.067] J. Rydzewski, R. Jakubowski, W. Nowak, H. Grubmüller, Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways, Journal of Chemical Theory and Computation 14, 2843–2851 (2018)

[plumID:19.066] J. Rydzewski, O. Valsson, Finding multiple reaction pathways of ligand unbinding, The Journal of Chemical Physics 150, 221101 (2019)

[plumID:19.065] W. Chen, A. L. Ferguson, Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration, Journal of Computational Chemistry 39, 2079–2102 (2018)

[plumID:19.064] J. Sampath, J. Pfaendtner, Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations, Molecular Physics 117, 3642–3650 (2019)

[plumID:19.063] M. Bernetti, M. Masetti, M. Recanatini, R. E. Amaro, A. Cavalli, An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes, Journal of Chemical Theory and Computation 15, 5689–5702 (2019)

[plumID:19.062] J. Smith, P. McMullen, Z. Yuan, J. Pfaendtner, S. Jiang, Elucidating Molecular Design Principles for Charge-Alternating Peptides, Biomacromolecules (2019)

[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 123, 21011–21021 (2019)

[plumID:19.060] L. Bonati, Y.-Y. Zhang, M. Parrinello, Neural networks-based variationally enhanced sampling, Proceedings of the National Academy of Sciences 116, 17641–17647 (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:19.057] C. Paissoni, A. Jussupow, C. Camilloni, Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics., (2019)

[plumID:19.056] J. Rydzewski, maze: Heterogeneous ligand unbinding along transient protein tunnels, Computer Physics Communications 247, 106865 (2020)

[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:19.054] G. Piccini, M. Parrinello, Accurate Quantum Chemical Free Energies at Affordable Cost, The Journal of Physical Chemistry Letters 10, 3727–3731 (2019)

[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:19.038] A. Achour et al., Biochemical and biophysical comparison of human and mouse beta‐2 microglobulin reveals the molecular determinants of low amyloid propensity, The FEBS Journal (2019)

[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. L. Ribeiro, P. Tiwary, Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics, Nature Communications 10 (2019)

[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)