Matej Praprotnik

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecules atomic and coarse-grained levels of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, and the other containing only one-particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The hybrid and the atomistically resolved systems have the same statistical properties at the same physical conditions.

Adaptive resolution simulation of liquid water

Water plays a central role in biological systems and processes, and is equally relevant in a large range of industrial and technological applications. Being the most important natural solvent, its presence uniquely influences biological function as well as technical processes. Because of their importance, aqueous solutions are among the most experimentally and theoretically studied systems. However, many questions still remain open. Both experiments and theoretical models are usually restricted to specific cases. In particular all-atom simulations of biomolecules and materials in water are computationally very expensive and often not possible, mainly due to the computational effort to obtain water–water interactions in regions not relevant for the problem under consideration. In this paper we present a coarse-grained model that can reproduce the behaviour of liquid water at a standard temperature and pressure remarkably well. The model is then used in a multiscale simulation of liquid water, where a spatially adaptive molecular resolution procedure allows one to change from a coarse-grained to an all-atom representation on-the-fly. We show that this approach leads to the correct description of essential thermodynamic and structural properties of liquid water. Our adaptive multiscale scheme allows for significantly greater extensive simulations than existing approaches by taking explicit water into account only in the regions where the atomistic details are physically relevant.

Concurrent triple-scale simulation of molecular liquids

We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolution scheme (AdResS), which couples the atomic and mesoscopic scales, and a hybrid continuum-molecular dynamics scheme (HybridMD). The combined AdResS-HybridMD scheme successfully sorts out the problem of large molecule insertion in the hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of truly open molecular liquid systems.

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.

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.

A macromolecule in a solvent: Adaptive resolution molecular dynamics simulation

The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymers center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on the fly. The authors show that their approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water

We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic model owing to the conservation of linear momentum by the adaptive resolution forces. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under nonequilibrium conditions.

Adaptive molecular resolution via a continuous change of the phase space dimensionality

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or by far too small time scales. To overcome this problem multiscale techniques are being developed. However, in almost all cases, the regions and molecules of different resolution are kept fixed and are not in equilibrium with each other. We here give a basic theoretical framework for an efficient and flexible coupling of the different regimes. The approach leads to a concept, which can be seen as a geometry-induced phase transition, and to a counterpart of the equipartition theorem for fractional degrees of freedom. This represents the initial step in developing a general theoretical framework for computer simulation methods applying simultaneously different levels of resolution.

Fractional dimensions of phase space variables: a tool for varying the degrees of freedom of a system in a multiscale treatment

A pre-assembled self-erecting display of corrugated paper or the like includes a rear display panel, a front display panel and an easel member which is fastened in part to the back side of the rear display panel. Resilient members such as rubber bands are connected across a vertical fold of the easel member. This causes a wing panel of the easel member to fold rearward for support means and an edge of the rear display panel to fold forward to create a concave configuration. Hinged panels folding out of the easel member urge an inner portion of the rear display panel away from the easel member, thus causing the rear display panel to obtain a convex configuration. The other edge of the rear display panel is attached to a part of a second wing panel of the easel member, inversely causing it to unfold rearward, also for support means. A part of the easel member passes through a slot in the rear display panel and is fastened to the back side of the front display panel, thus causing a multiple level configuration. Included are one or more horizontal folds permitting the entire display to be folded over to reduce its size for shipping.

Simulation approaches to soft matter: Generic statistical properties vs. chemical details

Abstract The relation between atomistic structure, architecture, molecular weight and material properties is a basic concern of modern soft material science. This by now goes far beyond standard properties of bulk materials. A typical additional focus is on surface or interface aspects or on the relation between structure and function in nanoscopic molecular assemblies. This all implies a thorough understanding on many length and correspondingly time scales ranging from (sub-)atomic to macroscopic. At this point computer simulations are playing an increasingly important, if not the central role. Traditionally simulations have been separated in two main groups, namely simplified models to deal with generic or universal aspects of polymers, i.e. critical exponents, and those employing classical force field simulations with (almost) all atomistic detail, i.e. for the diffusion of small additives in a small “sample”. Still characteristic problems, which require huge systems and/or long times in combination with a chemistry specific model, cannot be tackled by these methods alone. More recently with the development of scale bridging or multiscale simulation techniques, these different approaches have been combined into an emerging rather powerful tool. It is the purpose of this contribution to give a few examples of how such an approach can be used to understand specific material properties.