Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir.

In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this Letter, we show a novel approach where the latest version of the adaptive resolution scheme (AdResS), with noninteracting tracers as particles' reservoir, is combined with a fluctuating hydrodynamics (FHD) solver. The resulting algorithm, supported by a solid mathematical model, allows for a physically consistent exchange of matter and energy between the particle domain and its fluctuating continuum reservoir. Numerical tests are performed to show the validity of the algorithm. Differently from previous algorithms of the same kind, the current approach allows for simulations where, in addition to density fluctuations, also thermal fluctuations can be accounted for, thus large complex molecular systems, as, for example, hydrated biological membranes in a thermal field, can now be efficiently treated.

The physics of open systems for the simulation of complex molecular environments in soft matter.

Molecular dynamics (MD) has become one of the most powerful tools of investigation in soft matter. Despite such success, simulations of large molecular environments are mostly run using the approximation of closed systems without the possibility of exchange of matter. Due to the molecular complexity of soft matter systems, an optimal simulation strategy would require the application of concurrent multiscale resolution approaches such that each part of a large system can be considered as an open subsystem at a high resolution embedded in a large coarser reservoir of energy and particles. This paper discusses the current capability and the future perspectives of multiscale adaptive resolution MD methods to satisfy the conceptual principles of open systems and to perform simulations of complex molecular environments in soft matter.

On the formalization of asynchronous first passage algorithms.

Formalization of first passage schemes is revisited, and the emerging conceptual contradiction is underlined. We then show why, despite such a contradiction, the numerical results are not explicitly affected. Through a different formalization of the problem, we recast the current principles of the algorithm in a more solid conceptual framework and numerical evidence gives further justification to our claims.

Adaptive resolution molecular dynamics technique: Down to the essential.

We investigate the role of the thermodynamic (TD) force as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution molecular dynamics setup assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution setups, which employ switching functions in the coupling region.

Path integral-GC-AdResS simulation of a large hydrophobic solute in water: a tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space.

We perform large scale quantum (path integral) molecular dynamics simulations of a C60-like molecule in water. The path integral (PI) technique allows for the description of the delocalization of atoms in space and of its consequences on the structure and dynamics of the hydrogen bonding network around the solute. We then employ the adaptive resolution method GC-AdResS, which unambiguously defines the essential (necessary) degrees of freedom required for a certain property, to analyze the locality of the water structure around the solute. We show that the feature of locality is independent of the use of a quantum or classical model of water. However the water structure around the solute obtained from classical simulations is more ordered and rigid than the structure found in quantum simulations. With this study we mainly intend to show that GC-AdResS, besides its computational efficiency, can be used as a powerful tool of multiscale analysis; this capability, in turn, can be used to speculate about processes at larger scales. We make an example, whose current validity is restricted to the molecular models specifically used, regarding the possible role of quantum effects in the aggregation of fullerene-like molecules in water.

Towards open boundary molecular dynamics simulation of ionic liquids.

We extend the use of the adaptive resolution (AdResS) method in its grand canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a subsystem of interest with atomistic details and a reservoir of coarse-grained particles leads to satisfactory results. The challenging aspect of this study, compared to previous AdResS simulations, is the presence of charged particles and the necessity of addressing the question about the minimal physical input needed to model the coarse-grained particles in the reservoir. We propose two different approaches and show that in both cases they are sufficient to capture the decisive physical characteristics that allow a valid system-reservoir coupling. The technically satisfactory results pave the way for the multiscale analysis of ionic liquids and truly open boundary molecular simulations.

Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water.

Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

Influence of pH and sequence in peptide aggregation via molecular simulation.

We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.

Chemical potential of liquids and mixtures via adaptive resolution simulation.

We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonical-like version (GC-AdResS) [H. Wang, C. Hartmann, C. Schütte, and L. Delle Site, Phys. Rev. X 3, 011018 (2013)], to calculate the excess chemical potential, µ(ex), of various liquids and mixtures. We compare our results with those obtained from full atomistic simulations using the technique of thermodynamic integration and show a satisfactory agreement. In GC-AdResS, the procedure to calculate µ(ex) corresponds to the process of standard initial equilibration of the system; this implies that, independently of the specific aim of the study, µ(ex), for each molecular species, is automatically calculated every time a GC-AdResS simulation is performed.

Autocatalytic and cooperatively stabilized dissociation of water on a stepped platinum surface.

Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires.

Force fields for studying the structure and dynamics of ionic liquids: a critical review of recent developments.

Classical molecular dynamics simulations are a valuable tool to study the mechanisms that dominate the properties of ionic liquids (ILs) on the atomistic and molecular level. However, the basis for any molecular dynamics simulation is an accurate force field describing the effective interactions between all atoms in the IL. Normally this is done by empirical potentials which can be partially derived from quantum mechanical calculations on simple subunits or have been fitted to experimental data. Unfortunately, the number of accurate classical non-polarizable models for ILs that allow a reasonable description of both dynamical and statical properties is still low. However, the strongly increasing computational power allows one to apply computationally more expensive methods, and even polarizable-force-field-based models on time and length scales long enough to ensure a proper sampling of the phase space. This review attempts to summarize recent achievements and methods in the development of classical force fields for ionic liquids. As this class of salts covers a large number of compounds, we focus our review on imidazolium-based ionic liquids, but show that the main conclusions are valid for non-imidazolium salts, too. Insight obtained from recent electronic density functional results into the parametrization of partial charges and on the influence of polarization effects in bulk ILs is highlighted. An overview is given of different available force fields, ranging from the atomistic to the coarse-grained level, covering implicit as well as explicit modeling of polarization. We show that the recently popular usage of the ion charge as fit parameter can looked upon as treating polarization effects in a mean-field matter.

Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir.

We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point-particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space-dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms' delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.

Nuclear quantum effects in fullerene-fullerene aggregation in water.

We studied the effects of the quantum delocalization in space of the hydrogen atoms of water in the aggregation process of two fullerene molecules. We considered a case using a purely repulsive water-fullerene interaction, as such a situation has shown that water-mediated effects play a key role in the aggregation process. This study becomes feasible, at a reduced computational price, by combining the path integral (PI) molecular dynamics (MD) method with a recently developed open-system MD technique. Specifically, only the mandatory solvation shell of the two fullerene molecules was considered at full quantum resolution, while the rest of the system was represented as a mean-field macroscopic reservoir of particles and energy. Our results showed that the quantum nature of the hydrogen atoms leads to a sizable difference in the curve of the free energy of aggregation; that is, that nuclear quantum effects play a relevant role.

Momentum distribution of the homogeneous electron gas.

We calculate the off-diagonal density matrix of the homogeneous electron gas at zero temperature using unbiased reptation Monte Carlo calculations for various densities and extrapolate the momentum distribution and the kinetic and potential energies to the thermodynamic limit. Our results on the renormalization factor allow us to validate approximate G0W0 calculations concerning quasiparticle properties over a broad density region (1≤r(s)≲10) and show that, near the Fermi surface, vertex corrections and self-consistency aspects almost cancel each other out.

Depolarization of water in protic ionic liquids.

A mixture of the protic ionic liquid mono-methylammonium nitrate with 1.6 wt% water was investigated from Car-Parrinello molecular dynamics simulations. In contrast to imidazolium-based ionic liquids, the cation possesses strong directional hydrogen bonds to water and all hydrogen bonds in the mixture have a comparable strength. This results in a good incorporation of water into the hydrogen bond network of mono-methylammonium nitrate and a tetrahedral hydrogen bond coordination of water. Hence, one might expect a larger dipole moment of water in the investigated mixture compared to neat water due to the good hydrogen bond network incorporation and the charged vicinity of water in the protic ionic liquid. However, the opposite is observed pointing to strong electrostatic screening in protic ionic liquids. Additionally, the influence of water on the properties of the protic ionic liquid is discussed.

Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique.

We use the adaptive resolution simulation (AdResS) technique to estimate the region in space where water-mediated effects in molecule-molecule interactions are relevant. AdResS is employed to identify the region around the solute (solvation shell) where the atomistic details of the hydrogen bonding network are relevant while outside water plays the role of a thermodynamic bath that can be described at simplified macroscopic level. The consequence is that for the interaction of two solutes the intermolecular distance at which water mediated effects start to be relevant is represented by the sum of the radii of the two respective solvation shells identified via AdResS. The hypothesis formulated above will be proven by calculating the solute-solute potential of mean force for different solutes. As test molecules we use amino acids derived from fragments of the FCHo2-F-BAR domain protein; this choice stems from the fact that the current results, beside proving the technical capability of AdResS in this context, may provide data for future actual coarse-grained models.

From adaptive resolution to molecular dynamics of open systems.

ABSTRACT: We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

Coupling different levels of resolution in molecular simulations.

Simulation schemes for liquids or strongly fluctuating systems that allow to change the molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surroundings introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures a thermodynamic equilibrium among molecules of different representations. The robustness of the algorithm is tested for two examples, namely, an adaptive resolution simulation, atomistic/coarse grained, for a liquid of tetrahedral molecules, and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

Communication: On the locality of hydrogen bond networks at hydrophobic interfaces.

The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting the solvation structure around a hydrophobic molecule. In this context we present a molecular dynamics study of the solvation of various hydrophobic molecules where the effect of different regions around the solvent can be analyzed by employing an adaptive resolution method, which can systematically separate local and nonlocal factors in the structure of water around a hydrophobic molecule. A number of hydrophobic solutes of different sizes and two different model potential interactions between the water and the solute are investigated.

Phenylalanine near inorganic surfaces: conformational statistics vs specific chemistry.

We present a first principle density functional study of phenylalanine interacting with three different classes of surfaces, namely a purely repulsive hard wall, mildly interacting close packed surfaces of group 11 metals (Cu(111), Ag(111), and Au(111)), and strongly interacting close packed surfaces of group 10 metals (Ni(111), Pd(111), and Pt(111)). In particular, we characterize, by changing the substrate, the passage from the statistical behavior of a flexible molecule in the presence of the topological confinement of a hard wall to a purely chemical behavior where the molecule, highly deformed compared to the free state, strongly binds to the surface and statistical conformations play no longer a role. Such a comparative study allows for characterization of some of the key aspects of the adsorption process for a prototype of flexible amino acids on experimentally and technologically relevant metal surfaces.