Project B4: Equilibrium and non-equilibrium processes in open systems via adaptive resolution simulations
Computational soft matter constitutes a major application area for simulations, with extraordinary conceptual and practical relevance. Due to the systems’ intrinsic complexity, a considerable effort in this area has focused on investigating somewhat idealised models, e.g., consisting of a few essential molecular species in explicit or implicit solvent. In reality, even the simplest experimentally relevant systems, such as (bio)macromolecules in aqueous mixtures and nanochannels, are far more complex, involving many interacting species, evolving under open-boundary and non-equilibrium conditions. Increasing the complexity and detail of the computational model for these systems poses a significant challenge. Indeed, the interplay of interactions and processes spanning a wide range of length and time scales requires a multiscale approach, including methods resolving quantum, classical, coarse-grained and continuum degrees of resolution.
However, it is often the case that a high-resolution method is only necessary to describe a relatively small portion of the system, embedded into a less detailed environment or even only a particle reservoir. In this context, the adaptive resolution simulation (AdResS) method has been developed to provide a seamless interpolation between high- and low-resolution descriptions: both concurrently present within the simulation box in a thermodynamically consistent framework. More recently, AdResS has been expanded to investigate openboundary systems and different non-equilibrium conditions. Based on this development, we plan to extend non-equilibrium simulations of driven systems and make a significant step towards quantum-classical (QM/MM) AdResS simulations, where electronic degrees of freedom are considered in a small subregion of the simulation box. From a simulation technique point of view, highly inhomogeneous systems also pose unique challenges to software development for advanced HPC architectures, especially for scaling for large systems, requiring significant parallel computing resources.
For the next funding period, we propose (i) extending the range of applicability of the AdResS method by computing free energy differences of complex molecular liquids and (ii) expanding AdResS capabilities to study non-equilibrium conditions in complex molecular systems. Furthermore, we will (iii) develop adaptive QM/MM methods where the coupling between many-electron and classical Hamiltonians constitutes a crucial step to investigate electronic quantum effects in open soft-matter systems. We intend to establish AdResS as a robust tool to simulate application relevant soft-matter systems under non-equilibrium conditions. To this aim, we will develop (iv) efficient scaling of the AdResS method in HPC environments. This goal requires an efficient implementation of novel domain decomposition strategies tailored to highly non-uniform simulation setups, also suitable for applications beyond the AdResS method.
Bottom-up synthesis of molecular nanodiamond from nanographene
I. Batatia, J. Liu, X. Yang, R.G. Brouwer, L. Kazak, R. Blinder, L. Cancellara, N.V. Tarakina, Y. Liu, T. Eklund, M. Sinha, S. Koster, S. Bhat, F. Rohmann, A. Tangemann, K.L. Gallo, R. Berger, R. Farla, A. Kubanek, K. Amann-Winkel, M. Wagner, F. Jelezko, K. Müllen, G. Csanyi, R. Cortes-Huerto, Y. Wu, T. Weil
Nature 655, 8121 (2026)
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Chemical potentials of hydrogen-bonded aqueous mixtures from adaptive resolution simulations and Kirkwood-Buff theory
Maria Duena-Herrera, Mauricio Sevilla, Diego Veloza-Diaz, Luis A. Baptista, Nancy C. Forero-Martinez, Robinson Cortes-Huerto
J. Chem. Phys. 164, 164502 (2026)
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A kinetic model to simulate charge flow through an electro-chemical half-cell
D. Veloza-Diaz, F. Schmid, R. Cortes-Huerto, P. Ballone, N.C. Forero-Martinez
J. Chem. Phys. 163, 164113 (2025)
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Density fluctuations, solvation thermodynamics, and coexistence curves in grand canonical molecular dynamics simulations
Mauricio Sevilla, Luis A. Baptista, Kurt Kremer, Robinson Cortes-Huerto
J. Chem. Phys. 162, 080901 (2025)
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Simulation Study of the Water Ordering Effect of the β-(1,3)-Glucan Callose Biopolymer
Robinson Cortes-Huerto, Nancy C. Forero-Martinez, Pietro Ballone
Biomacromolecules 26, 1748-1760 (2025)
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Code modernization strategies for short-range non-bonded molecular dynamics simulations
James Vance, Zhen-Hao Xu, Nikita Tretyakov, Torsten Stuehn, Markus Rampp, Sebastian Eible, Christoph Junghans, Andre Brinkmann
Comp. Phys. Comm. 290, 108760 (2023)
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Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol
Luis A. Baptista, Mauricio Sevilla, Manfred Wagner, Kurt Kremer, Robinson Cortes-Huerto
Eur. Phys. J. E 46, 117 (2023)
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Finite-size excess-entropy scaling for simple liquids
Mauricio Sevilla, Atreyee Banerjee, Robinson Cortes-Huerto
J. Chem. Phys. 158, 204502 (2023)
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Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?
Luis A. Baptista, Yani Zhao, Kurt Kremer, Debashish Mukherji, and Robinson Cortes-Huerto
ACS Macro Lett. 2023, 12, 841–847, (2023)
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Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions
Atreyee Banerjee, Mauricio Sevilla, Joseph F. Rudzinski, Robinson Cortes-Huerto
Soft Matter 18, 2373-2382 (2022)
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Connecting density fluctuations and Kirkwood-Buff integrals for finite-size systems
Mauricio Sevilla, Robinson Cortes-Huerto
J. Chem. Phys. 156, 044502 (2022)
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Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method
L A Baptista, R C Dutta, M Sevilla, M Heidari, R Potestio, K Kremer, R Cortes-Huerto
Journal of Physics: Condensed Matter 33 (18), 184003 (2021)
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Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators
Luca Tubiana, Hideki Kobayashi, Raffaello Potestio, Burkhard Duenweg, Kurt Kremer, Peter Virnau, Kostas Daoulas
Journal of Physics: Condensed Matter, (2021)
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Adaptive Resolution Molecular Dynamics Technique
M. Praprotnik, R. Cortes-Huerto, R. Potestio, L. Delle Site
Handbook of Materials Modeling, Pages 1443-1457, Springer International Publishing (2020)
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Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water–Ethanol and Water–Urea Mixtures?
Yani Zhao, Manjesh K. Singh, Kurt Kremer, Robinson Cortes-Huerto, Debashish Mukherji
Macromolecules 53 (6), 2101-2110 (2020)
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Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model
Yani Zhao, Robinson Cortes-Huerto, Kurt Kremer, Joseph F. Rudzinski
The Journal of Physical Chemistry B124 (20),4097-4113 (2020)
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Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations
Maziar Heidari, Kurt Kremer, Ramin Golestanian, Raffaello Potestio, Robinson Cortes-Huerto
The Journal of Chemical Physics 152 (19), 194104 (2020)
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Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach
I. Tabujew, M. Heidari, C. Freidel, M. Helm, L. Tebbe, U. Woflrum, K. Nagel-Wolfrum, K. Koynov, P. Biehl, F.H. Schacher, R. Potestio, K. Peneva
Biomacromolecules 20, 4389-4406 (2019)
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Surface of Half-Neutralized Diamine Triflate Ionic Liquids. A Molecular Dynamics Study of Structure, Thermodynamics, and Kinetics of Water Absorption and Evaporation
N. C. Forero-Martinez, R. Cortes-Huerto, J. F. Mora Cardozo, P. Ballone
The Journal of Physical Chemistry B123 (40), 8457-8471 (2019)
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Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences
Maziar Heidari, Robinson Cortes-Huerto, Raffaello Potestio, Kurt Kremer
The Journal of Chemical Physics 151 (14), 144105 (2019)
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Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method
Maziar Heidari, Kurt Kremer, Raffaello Potestio, Robinson Cortes-Huerto
Entropy 20 (4), 222 (2018)
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Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations
Maziar Heidari, Robinson Cortes-Huerto, Kurt Kremer, Raffaello Potestio
The European Physical Journal E41 (5), (2018)
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Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids
Maziar Heidari, Kurt Kremer, Robinson Cortes-Huerto, Raffaello Potestio
Journal of Chemical Theory and Computation 14 (7), 3409-3417 (2018)
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Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations
M. Heidari, K. Kremer, R. Potestio, R. Cortes-Huerto
Molecular Physics 116 (21-22), 3301-3310 (2018)
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Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles
Hamed Sharifi Dehsari, Maziar Heidari, Anielen Halda Ribeiro, Wolfgang Tremel, Gerhard Jakob, Davide Donadio, Raffaello Potestio, Kamal Asadi
Chemistry of Materials 29 (22), 9648-9656 (2017)
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Adsorption of polyiodobenzene molecules on the Pt(111) surface using van der Waals density functional theory
Karen Johnston, Rengin Pekoz, Davide Donadio
Surface Science 644, 113-121 (2016)
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From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations
Karsten Kreis, Mark E. Tuckerman, Davide Donadio, Kurt Kremer, Raffaello Potestio
Journal of Chemical Theory and Computationut. 12 (7), 3030-3039 (2016)
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Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations
M. Heidari, R. Cortes-Huerto, D. Donadio, R. Potestio
The European Physical Journal Special Topics 225 (8-9), 1505-1526 (2016)
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Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials
Jelle M. Boereboom, Raffaello Potestio, Davide Donadio, Rosa E. Bulo
Journal of Chemical Theory and Computationut. 12 (8), 3441-3448 (2016)
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Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2505-2506 (2015)
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Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2289-2304 (2015)
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