Comment on "pumping of confined water in carbon nanotubes by rotation-translation coupling"

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

In the last quarter-century, the field of molecular dynamics (MD) has undergone a remarkable transformation, propelled by substantial enhancements in software, hardware, and underlying methodologies. In this Perspective, we contemplate the future trajectory of MD simulations and their possible look at the year 2050. We spotlight the pivotal role of artificial intelligence (AI) in shaping the future of MD and the broader field of computational physical chemistry. We outline critical strategies and initiatives that are essential for the seamless integration of such technologies. Our discussion delves into topics like multiscale modeling, adept management of ever-increasing data deluge, the establishment of centralized simulation databases, and the autonomous refinement, cross-validation, and self-expansion of these repositories. The successful implementation of these advancements requires scientific transparency, a cautiously optimistic approach to interpreting AI-driven simulations and their analysis, and a mindset that prioritizes knowledge-motivated research alongside AI-enhanced big data exploration. While history reminds us that the trajectory of technological progress can be unpredictable, this Perspective offers guidance on preparedness and proactive measures, aiming to steer future advancements in the most beneficial and successful direction.

Electrokinetic, electrochemical, and electrostatic surface potentials of the pristine water liquid-vapor interface

Although conceptually simple, the air-water interface displays rich behavior and is subject to intense experimental and theoretical investigations. Different definitions of the electrostatic surface potential as well as different calculation methods, each relevant for distinct experimental scenarios, lead to widely varying potential magnitudes and sometimes even different signs. Based on quantum-chemical density-functional-theory molecular dynamics (DFT-MD) simulations, different surface potentials are evaluated and compared to force-field (FF) MD simulations. As well explained in the literature, the laterally averaged electrostatic surface potential, accessible to electron holography, is dominated by the trace of the water molecular quadrupole moment, and using DFT-MD amounts to +4.35 V inside the water phase, very different from results obtained with FF water models which yield negative values of the order of -0.4 to -0.6 V. Thus, when predicting potentials within water molecules, as relevant for photoelectron spectroscopy and non-linear interface-specific spectroscopy, DFT simulations should be used. The electrochemical surface potential, relevant for ion transfer reactions and ion surface adsorption, is much smaller, less than 200 mV in magnitude, and depends specifically on the ion radius. Charge transfer between interfacial water molecules leads to a sizable surface potential as well. However, when probing electrokinetics by explicitly applying a lateral electric field in DFT-MD simulations, the electrokinetic ζ-potential turns out to be negligible, in agreement with predictions using continuous hydrodynamic models. Thus, interfacial polarization charges from intermolecular charge transfer do not lead to significant electrokinetic mobility at the pristine vapor-liquid water interface, even assuming these transfer charges are mobile in an external electric field.

The good, the bad and the user in soft matter simulations

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Molecular dynamics study of nanoconfined water flow driven by rotating electric fields under realistic experimental conditions

In our recent work, J. Chem. Phys. 2013, 138, 154712, we demonstrated the feasibility of unidirectional pumping of water, exploiting translational-rotational momentum coupling using nonequilibrium molecular dynamics simulations. Flow can be sustained when the fluid is driven out of equilibrium by an external spatially uniform rotating electric field and confined between two planar surfaces exposing different degrees of hydrophobicity. The permanent dipole moment of water follows the rotating field, thus inducing the molecules to spin, and the torque exerted by the field is continuously injected into the fluid, enabling a steady conversion of spin angular momentum into linear momentum. The translational-rotational coupling is a sensitive function of the rotating electric field parameters. In this work, we have found that there exists a small energy dissipation region attainable when the frequency of the rotating electric field matches the inverse of the dielectric relaxation time of water and when its amplitude lies in a range just before dielectric saturation effects take place. In this region, that is, when the frequency lies in a small window of the microwave region around ∼20 GHz and amplitude ∼0.03 V Å(-1), the translational-rotational coupling is most effective, yielding fluid velocities of magnitudes of ∼2 ms(-1) with only moderate fluid heating. In this work, we also confine water to a realistic nanochannel made of graphene giving a hydrophobic surface on one side and β-cristobalite giving a hydrophilic surface on the other, reproducing slip-and-stick velocity boundary conditions, respectively. This enables us to demonstrate that in a realistic environment, the coupling can be effectively exploited to achieve noncontact pumping of water at the nanoscale. A quantitative comparison between nonequilibrium molecular dynamics and analytical solutions of the extended Navier-Stokes equations, including an external rotating electric field has been performed, showing excellent agreement when the electric field parameters match the aforementioned small energy dissipation region.

Asymmetric transport of water molecules through a hydrophobic conical channel

Unlike macroscale systems, symmetry breaking could lead to surprising results for nanoscale systems.

How fast does water flow in carbon nanotubes?

The purpose of this paper is threefold. First, we review the existing literature on flow rates of water in carbon nanotubes. Data for the slip length which characterizes the flow rate are scattered over 5 orders of magnitude for nanotubes of diameter 0.81-10 nm. Second, we precisely compute the slip length using equilibrium molecular dynamics (EMD) simulations, from which the interfacial friction between water and carbon nanotubes can be found, and also via external field driven non-equilibrium molecular dynamics simulations (NEMD). We discuss some of the issues in simulation studies which may be reasons for the large disagreements reported. By using the EMD method friction coefficient to determine the slip length, we overcome the limitations of NEMD simulations. In NEMD simulations, for each tube we apply a range of external fields to check the linear response of the fluid to the field and reliably extrapolate the results for the slip length to values of the field corresponding to experimentally accessible pressure gradients. Finally, we comment on several issues concerning water flow rates in carbon nanotubes which may lead to some future research directions in this area.

Effect of calcium and magnesium on phosphatidylserine membranes: experiments and all-atomic simulations

It is known that phosphatidylserine (PS(-)) lipids have a very similar affinity for Ca(2+) and Mg(2+) cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca(2+) or Mg(2+) induces very different aggregation behavior for PS(-) liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca(2+) or Mg(2+) cations. These puzzling results suggest that although these two cations have a similar affinity for PS(-) lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS(-) membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca(2+) and Mg(2+) cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca(2+) cations present a peak at a distance ~2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg(2+) cations has two different peaks, located a few angstroms before and after the Ca(2+) peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca(2+) and Mg(2+), respectively.

Ultralow liquid/solid friction in carbon nanotubes: comprehensive theory for alcohols, alkanes, OMCTS, and water

In this work, we perform a theoretical study of liquid flow in graphitic nanopores of different sizes and geometries. Molecular dynamics flow simulations of different liquids (water, decane, ethanol, and OMCTS) in carbon nanotubes (CNT) are shown to exhibit flow velocities 1-3 orders of magnitude higher than those predicted from the continuum hydrodynamics framework and the no-slip boundary condition. These results support previous experimental findings obtained by several groups that reported exceptionally high liquid flow rates in CNT membranes. The liquid/graphite friction coefficient is identified as the crucial parameter for this fast mass transport in CNT. The friction coefficient is found to be very sensitive to wall curvature: friction is independent of confinement for liquids between flat graphene walls with zero curvature, whereas it decreases with increasing positive curvature (liquid inside CNT), and it increases with increasing negative curvature (liquid outside CNT). Furthermore, we present a theoretical approximate expression for the friction coefficient, which predicts qualitatively and semiquantitatively its curvature dependent behavior. The proposed theoretical description, which works well for different kinds of liquids (alcohols, alkanes, and water), sheds light on the physical mechanisms at the origin of the ultra low liquid/solid friction in CNT. In fact, it is due to their perfectly ordered molecular structure and their atomically smooth surface that carbon nanotubes are quasiperfect liquid conductors compared to other membrane pores like nanochannels in amorphous silica.

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

Molecular dynamics (MD) simulation has become a common technique to study biological systems. Transport of small molecules through carbon nanotubes and membrane proteins has been an intensely studied topic, and MD simulations have been able to provide valuable predictions, many of which have later been experimentally proven. Simulations of such systems pose challenges, and unexpected problems in commonly used protocols and methods have been found in the past few years. The two main reasons why some were not found before are that most of these newly discovered errors do not lead to unstable simulations. Furthermore, some of them manifest themselves only after relatively long simulation times. We assessed the reliability of the most common simulations protocols by MD and stochastic dynamics (SD) or Langevin dynamics, simulations of an alpha hemolysin nanochannel embedded in a palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer. Our findings are that (a) reaction field electrostatics should not be used in simulations of such systems, (b) local thermostats should be preferred over global ones since the latter may lead to an unphysical temperature distribution,

Nanoscale pumping of water by AC electric fields

Using molecular dynamics simulations we demonstrate pumping of water through a carbon nanotube by time-dependent electric fields. The fields are generated by electrodes with oscillating charges in a broad gigahertz frequency range that are attached laterally to the tube. The key ingredient is a phase shift between the electrodes to break the spatiotemporal symmetry. A microscopic theory based on a polarization-dragging mechanism accounts quantitatively for our numerical findings.

Effect of electric field on liquid infiltration into hydrophobic nanopores

Understanding the variation of nanofluidic behavior in the presence of an external electric field is critical for controlling and designing nanofluidic devices. By studying the critical infiltration pressure of liquids into hydrophobic nanopores using molecular dynamics (MD) simulations and experiments, important insights can be gained on the variation of the effective liquid-solid interfacial tension with the magnitude and sign of electric field, as well as its coupling with the pore size and the solid and liquid species. It is found that the effective hydrophobicity reduces with the increase of electric intensity and/or pore size, and the behavior is asymmetric with respect to the direction of the electric field. The underlying molecular mechanisms are revealed via the study of the density profile, contact angle, and surface tension of confined liquid molecules.