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Pellegrino, M. & Hess, B. (2024). Near-wall depletion and layering affect contact line friction of multicomponent liquids. Physical Review Fluids, 9(3), Article ID 034002.
Open this publication in new window or tab >>Near-wall depletion and layering affect contact line friction of multicomponent liquids
2024 (English)In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 9, no 3, article id 034002Article in journal (Refereed) Published
Abstract [en]

The main causes of energy dissipation in micro- and nanoscale wetting are viscosity and liquid-solid friction localized in the three-phase contact line region. Theoretical models predict the contact line friction coefficient to correlate with the shear viscosity of the wetting fluid. Experiments conducted to investigate such correlation have not singled out a unique scaling law between the two coefficients. We perform molecular dynamics simulations of liquid water-glycerol droplets wetting silicalike surfaces, aimed to demystify the effect of viscosity on contact line friction. The viscosity of the fluid is tuned by changing the relative mass fraction of glycerol in the mixture and it is estimated both via equilibrium and nonequilibrium molecular dynamics simulations. Contact line friction is measured directly by inspecting the velocity of the moving contact line and the microscopic contact angle. It is found that the scaling between contact line friction and viscosity is sublinear, contrary to the prediction of molecular kinetic theory. The disagreement is explained by accounting for the depletion of glycerol in the near-wall region. A correction is proposed, based on multicomponent molecular kinetic theory and the definition of a rescaled interfacial friction coefficient.

Place, publisher, year, edition, pages
American Physical Society (APS), 2024
National Category
Tribology (Interacting Surfaces including Friction, Lubrication and Wear) Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-346072 (URN)10.1103/PhysRevFluids.9.034002 (DOI)001195765500002 ()2-s2.0-85188268773 (Scopus ID)
Note

QC 20240502

Available from: 2024-05-02 Created: 2024-05-02 Last updated: 2024-05-21Bibliographically approved
Jansen, A., Aho, N., Groenhof, G., Buslaev, P. & Hess, B. (2024). phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. Journal of Chemical Information and Modeling, 64(3), 567-574
Open this publication in new window or tab >>phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS
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2024 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 64, no 3, p. 567-574Article in journal (Refereed) Published
Abstract [en]

Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Other Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:kth:diva-343938 (URN)10.1021/acs.jcim.3c01313 (DOI)001161607500001 ()38215282 (PubMedID)2-s2.0-85182581195 (Scopus ID)
Note

QC 20240305

Available from: 2024-03-05 Created: 2024-03-05 Last updated: 2024-05-14Bibliographically approved
Lundborg, M., Lidmar, J. & Hess, B. (2023). On the Path to Optimal Alchemistry. The Protein Journal, 42(5), 477-489
Open this publication in new window or tab >>On the Path to Optimal Alchemistry
2023 (English)In: The Protein Journal, ISSN 1572-3887, E-ISSN 1875-8355, Vol. 42, no 5, p. 477-489Article in journal (Refereed) Published
Abstract [en]

Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path. To address this, the notion of the length of a path or a metric is required. A metric recently introduced in the context of the accelerated weight histogram method also proves to be very useful here. We demonstrate that this metric can not only improve the efficiency of sampling along a given path, but that it can also be used to improve the actual choice of path. For a set of relevant use cases, the combination of these improvements can increase the efficiency of alchemical free energy calculations by up to a factor 16.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
Accelerated weight histogram method, Alchemical free energy calculations, Lambda path optimization
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-336556 (URN)10.1007/s10930-023-10137-1 (DOI)001185025700001 ()37651042 (PubMedID)2-s2.0-85169161633 (Scopus ID)
Note

QC 20230918

Available from: 2023-09-18 Created: 2023-09-18 Last updated: 2024-04-05Bibliographically approved
Pellegrino, M. & Hess, B. (2022). Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics. Physics of fluids, 34(10), 102010, Article ID 102010.
Open this publication in new window or tab >>Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics
2022 (English)In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 34, no 10, p. 102010-, article id 102010Article in journal (Refereed) Published
Abstract [en]

Motion of three-phase contact lines is one of the most relevant research topics of micro- and nano-fluidics. According to many hydrodynamic and molecular models, the dynamics of contact lines is assumed overdamped and dominated by localized liquid-solid friction, entailing the existence of a mobility relation between contact line speed and microscopic contact angle. We present and discuss a set of non-equilibrium atomistic molecular dynamics simulations of water nanodroplets spreading on or confined between silica-like walls, showing the existence of the aforementioned relation and its invariance under wetting modes ( "spontaneous " or "forced "). Upon changing the wettability of the walls, it has been noticed that more hydrophilic substrates are easier to wet rather than de-wet; we show how this asymmetry can be automatically captured by a contact line friction model that accounts for the molecular transport between liquid layers. A simple examination of the order and orientation of near-contact-line water molecules corroborates the physical foundation of the model. Furthermore, we present a way to utilize the framework of multicomponent molecular kinetic theory to analyze molecular contributions to the motion of contact lines. Finally, we propose an approach to discriminate between contact line friction models which overcomes the limitations of experimental resolution. This work constitutes a stepping stone toward demystifying wetting dynamics on high-friction hydrophilic substrates and underlines the relevance of contact line friction in modeling the motion of three-phase contact lines.

Place, publisher, year, edition, pages
AIP Publishing, 2022
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-321632 (URN)10.1063/5.0121144 (DOI)000877985900006 ()2-s2.0-85141198405 (Scopus ID)
Note

QC 20221118

Available from: 2022-11-18 Created: 2022-11-18 Last updated: 2024-05-21Bibliographically approved
Buslaev, P., Aho, N., Jansen, A., Bauer, P., Hess, B. & Groenhof, G. (2022). Best Practices in Constant pH MD Simulations: Accuracy and Sampling. Journal of Chemical Theory and Computation, 18(10), 6148-6160
Open this publication in new window or tab >>Best Practices in Constant pH MD Simulations: Accuracy and Sampling
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2022 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 10, p. 6148-6160Article in journal (Refereed) Published
Abstract [en]

Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the A-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys. 1996, 105, 2414-2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput. 2022, DOI: 10.1021 /acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on how to set up and perform long time scale constant pH MD simulations. We found that barriers associated with the torsions of side chains in the CHARMM36m force field are too high for reaching convergence in constant pH MD simulations on microsecond time scales. To avoid the high computational cost of extending the sampling, we propose small modifications to the force field to selectively reduce the torsional barriers. We demonstrate that with such modifications we obtain converged distributions of both protonation and torsional degrees of freedom and hence consistent pK(a) estimates, while the sampling of the overall configurational space accessible to proteins is unaffected as compared to normal MD simulations. We also show that the results of constant pH MD depend on the accuracy of the correction potentials. While these potentials are typically obtained by fitting a low-order polynomial to calculated free energy profiles, we find that higher order fits are essential to provide accurate and consistent results. By resolving problems in accuracy and sampling, the work described in this and the accompanying paper paves the way to the widespread application of constant pH MD beyond pK(a) prediction.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2022
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-322879 (URN)10.1021/acs.jctc.2c00517 (DOI)000897361300001 ()36107791 (PubMedID)2-s2.0-85138973066 (Scopus ID)
Note

QC 20230126

Available from: 2023-01-26 Created: 2023-01-26 Last updated: 2024-06-20Bibliographically approved
Lācis, U., Pellegrino, M., Sundin, J., Amberg, G., Zaleski, S., Hess, B. & Bagheri, S. (2022). Nanoscale sheared droplet: volume-of-fluid, phase-field and no-slip molecular dynamics. Journal of Fluid Mechanics, 940, Article ID A10.
Open this publication in new window or tab >>Nanoscale sheared droplet: volume-of-fluid, phase-field and no-slip molecular dynamics
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2022 (English)In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 940, article id A10Article in journal (Refereed) Published
Abstract [en]

The motion of the three-phase contact line between two immiscible fluids and a solid surface arises in a variety of wetting phenomena and technological applications. One challenge in continuum theory is the effective representation of molecular motion close to the contact line. Here, we characterize the molecular processes of the moving contact line to assess the accuracy of two different continuum two-phase models. Specifically, molecular dynamics simulations of a two-dimensional droplet between two moving plates are used to create reference data for different capillary numbers and contact angles. We use a simple-point-charge/extended water model. This model provides a very small slip and a more realistic representation of the molecular physics than Lennard-Jones models. The Cahn–Hilliard phase-field model and the volume-of-fluid model are calibrated against the drop displacement from molecular dynamics reference data. It is shown that the calibrated continuum models can accurately capture droplet displacement and droplet break-up for different capillary numbers and contact angles. However, we also observe differences between continuum and atomistic simulations in describing the transient and unsteady droplet behaviour, in particular, close to dynamical wetting transitions. The molecular dynamics of the sheared droplet provide insight into the line friction experienced by the advancing and receding contact lines. The presented results will serve as a stepping stone towards developing accurate continuum models for nanoscale hydrodynamics.

Place, publisher, year, edition, pages
Cambridge University Press (CUP), 2022
National Category
Fluid Mechanics and Acoustics
Identifiers
urn:nbn:se:kth:diva-311053 (URN)10.1017/jfm.2022.219 (DOI)000778572600001 ()2-s2.0-85129201165 (Scopus ID)
Funder
Swedish Research Council, VR-2014-5680
Note

QC 20220425

Available from: 2022-04-14 Created: 2022-04-14 Last updated: 2024-05-21Bibliographically approved
Aho, N., Buslaev, P., Jansen, A., Bauer, P., Groenhof, G. & Hess, B. (2022). Scalable Constant pH Molecular Dynamics in GROMACS. Journal of Chemical Theory and Computation, 18(10), 6148-6160
Open this publication in new window or tab >>Scalable Constant pH Molecular Dynamics in GROMACS
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2022 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 10, p. 6148-6160Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2022
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-346446 (URN)10.1021/acs.jctc.2c00516 (DOI)000861595500001 ()36128977 (PubMedID)2-s2.0-85138860798 (Scopus ID)
Funder
Swedish Research Council, 2019-04477European Commission, H2020-INFRAEDI-02-2018-823830Academy of Finland, 311031Academy of Finland, 332743
Note

QC 20240515

Available from: 2024-05-14 Created: 2024-05-14 Last updated: 2024-05-15Bibliographically approved
Lundborg, M., Wennberg, C., Lidmar, J., Hess, B., Lindahl, E. & Norlen, L. (2022). Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophysical Journal, 121(20), 3837-3849
Open this publication in new window or tab >>Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates
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2022 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 121, no 20, p. 3837-3849Article in journal (Refereed) Published
Abstract [en]

A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates in the accelerated weight histogram method, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for 20 permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the obtained log KPexp-calc mean square difference was 0.9 cm(2) h(-2)

Place, publisher, year, edition, pages
Elsevier BV, 2022
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-324466 (URN)10.1016/j.bpj.2022.09.009 (DOI)000928435100009 ()36104960 (PubMedID)2-s2.0-85138811844 (Scopus ID)
Note

QC 20230405

Available from: 2023-04-05 Created: 2023-04-05 Last updated: 2023-04-05Bibliographically approved
Lundborg, M., Lidmar, J. & Hess, B. (2021). The accelerated weight histogram method for alchemical free energy calculations. Journal of Chemical Physics, 154(20), Article ID 204103.
Open this publication in new window or tab >>The accelerated weight histogram method for alchemical free energy calculations
2021 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 20, article id 204103Article in journal (Refereed) Published
Abstract [en]

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.

Place, publisher, year, edition, pages
AIP Publishing, 2021
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-302010 (URN)10.1063/5.0044352 (DOI)000692823300002 ()34241154 (PubMedID)2-s2.0-85106877320 (Scopus ID)
Note

QC 20210916

Available from: 2021-09-16 Created: 2021-09-16 Last updated: 2022-06-25Bibliographically approved
Johansson, P. & Hess, B. (2020). Electrowetting diminishes contact line friction in molecular wetting. Physical Review Fluids, 5(6), Article ID 064203.
Open this publication in new window or tab >>Electrowetting diminishes contact line friction in molecular wetting
2020 (English)In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 5, no 6, article id 064203Article in journal (Refereed) Published
Abstract [en]

We use large-scale molecular dynamics to study the dynamics at the three-phase contact line in electrowetting of water and electrolytes on no-slip substrates. Under the applied electrostatic potential the line friction at the contact line is diminished. The effect is consistent for droplets of different sizes as well as for both pure water and electrolyte solution droplets. We analyze the electric field at the contact line to show how it assists ions and dipolar molecules to advance the contact line. Without an electric field, the interaction between a substrate and a liquid has a very short range, mostly affecting the bottom, immobilized layer of liquid molecules which leads to high friction since mobile molecules are not pulled towards the surface. In electrowetting, the electric field attracts charged and polar molecules over a longer range, which diminishes the friction.

Place, publisher, year, edition, pages
American Physical Society (APS), 2020
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-278603 (URN)10.1103/PhysRevFluids.5.064203 (DOI)000543942500003 ()2-s2.0-85087963862 (Scopus ID)
Note

QC 20200729

Available from: 2020-07-29 Created: 2020-07-29 Last updated: 2022-06-26Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7498-7763

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