We present a hierarchical approach that combines atomistic and mesoscopic simulations that can generally be applied to vinyl polymers. As a test case, the approach is applied to atactic polystyrene (PS). First, a specific model for atactic PS is chosen. The bonded parameters in the coarse-grained force field, based on data obtained from atomistic simulations of isolated PS dimers, are chosen in a way which allows to differentiate between meso and racemic dyads. This approach in principle allows to study isotactic and syndiotactic melts as well. Nonbonded interactions between coarse-grained beads were chosen as purely repulsive. The proposed mesoscopic model reproduces both the local structure and the chain dimensions properly. An explicit time mapping is performed, based on the atomistic and CG mean-square displacements of short chains, demonstrating an effective speed up of about 3 orders of magnitude compared to brute force atomistic simulations. Finally the equilibrated coarse-grained chains are back mapped onto the atomistic systems. This opens new routes for obtaining well equilibrated high molecular weight polymeric systems and also providing very long dynamic trajectories at the atomistic level for these polymers.

Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.

The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)(2), and a proteinogenic beta(3)-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding-unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.

Although experimental and theoretical studies have addressed the question of the wetting properties of graphene, the actual value of the contact angle of water on an isolated graphene monolayer remains unknown. While recent experimental literature indicates that the contact angle of water on graphite is in the range 90-95°, it has been suggested that the contact angle on graphene may either be as high as 127° or moderately enhanced in comparison with graphite. With the support of classical molecular dynamics simulations using empirical force-fields, we develop an argumentation to show that the value of 127° is an unrealistic estimate and that a value of the order of 95-100° should be expected. Our study establishes a connection between the variation of the work of adhesion of water on graphene-based surfaces and the interaction potential between individual water molecules and these surfaces. We show that a variation of the contact angle from 90° on graphite to 127° on graphene would imply that both of the first two carbon layers of graphite contribute approximately the same interaction energy with water. Such a situation is incompatible with the short-range nature of the interaction between water and this substrate. We also show that the interaction potential energy between water and the graphene-based substrates is the main contribution to the work of adhesion of water with a relative magnitude that is independent of the number of graphene layers. We introduce the idea that the remaining contribution is entropic in nature and is connected to the fluctuations in the water-substrate interaction energy.

We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.

Biological organization depends on a sensitive balance of noncovalent interactions, in particular also those involving interactions between ions. Ion-pairing is qualitatively described by the law of ''matching water affinities.'' This law predicts that cations and anions (with equal valence) form stable contact ion pairs if their sizes match. We show that this simple physical model fails to describe the interaction of cations with (molecular) anions of weak carboxylic acids, which are present on the surfaces of many intraand extracellular proteins. We performed molecular simulations with quantitatively accurate models and observed that the order K ؉ < Na ؉ < Li ؉ of increasing binding affinity with carboxylate ions is caused by a stronger preference for forming weak solventshared ion pairs. The relative insignificance of contact pair interactions with protein surfaces indicates that thermodynamic stability and interactions between proteins in alkali salt solutions is governed by interactions mediated through hydration water molecules.aqueous systems ͉ Hofmeister series ͉ ion pairing ͉ ion-protein interaction ͉ molecular simulation I on-specific effects are important to a wealth of phenomena in biology, chemistry, and physics (1-5). The first observation of selective interactions between simple ions and proteins dates back to the late 19th century, when Hofmeister (6) described the selective ''salting in'' and ''salting out'' of chicken egg white protein by addition of various salts to the solution. Since then, there have been many studies that report the effects of different salts on properties, such as surface tension, enzymatic activity, protein stability, and protein-protein interactions. In many of these studies, ions have been ranked in a specific series (Hofmeister series) of increasing effect on the observed property. A key physical phenomenon used to explain many of the observed Hofmeister effects is the pairing of simple ions with charged macromolecular surfaces or, when thermodynamic properties of aqueous electrolyte solutions are considered, the pairing between small ions in water. Usually, the notion of ion-pairing remains qualitative owing to experimental limitations in characterizing the structural details and the free-energy of pairing. This also holds for ''simple'' electrolyte solutions. Evidenced by the lack of orientation polarization of water molecules more than 2 water molecules away from even di-and trivalent ions (7-11), it has been suggested that long-range electrostatic fields emanating from ions in solution must be weak compared to water-water interactions (7, 11). Hence, the dominant forces on ions in water are not of long-range electrostatic nature but of short-range chemical nature instead. To rationalize ion-specific phenomena and ion-pairing, Collins introduced the qualitative law of matching water affinities (11-13), where relative affinity of ions in solution depends on the matching of their hydration enthalpies. When the latter are assumed to be proportional to the ions' surface...

Multiscale modelling of soft matter is an emerging field that has made rapid progress in the past decade.Several methods for systematic coarse-graining of molecular liquids and soft matter systems have been proposed in recent years. Herein, we review these methods and discuss a selected number of applications as well as limitations of the models and remaining challenges in developing representative and transferable pair potentials.

We present a detailed study of a new, optimized coarse‐grained (CG) model of polystyrene (PS) and compare it with a recently published one (Harmandaris et al., Macromolecules 2006, 39, 6708). By implementing a different mapping scheme, the new model, augmented with softer nonbonded interactions, better reproduces the local chain conformations and melt packing observed in atomistic simulations of atactic PS. Both models properly predict the bonded distributions and are capable of simulating different tacticities without needing sidegroups. Both CG models fit dynamic data from long atomistic simulations after determining the scale factor for the simulation time. Together with a rigorous back‐mapping procedure from the mesoscopic to atomistic description, this opens up a very feasible way for generating very long atomistic trajectories.magnified image