Driven lattice gases as the ASEP are useful tools for the modeling of various stochastic transport processes carried out by self-driven particles, such as molecular motors or vehicles in road traffic. Often these processes take place in onedimensional systems offering several tracks to the particles, and in many cases the particles are able to change track with a given rate. In this work we consider the case of strong coupling where the hopping rate along the tracks and the exchange rates are of the same order, and show how a phenomenological approach based on a domain wall theory can describe the dynamics of the system. In particular, the domain walls on the different tracks form pairs, whose dynamics dominate the behavior of the system.

We present a series of capping-potentials designed as link atoms to saturate dangling bonds at the quantum/classical interface within density functional theory-based hybrid QM/MM calculations. We aim at imitating the properties of different carbon-carbon bonds by means of monovalent analytic pseudopotentials. These effective potentials are optimized such that the perturbations of the quantum electronic density are minimized. This optimization is based on a stochastic scheme, which helps to avoid local minima trapping. For a series of common biomolecular groups, we find capping-potentials that outperform the more common hydrogen-capping in view of structural and spectroscopic properties. To demonstrate the transferability to complex systems, we also benchmark our potentials with a hydrogen-bonded dimer, yielding systematic improvements in structural and spectroscopic parameters.

We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules.

Different hydrogen bonding networks, same principle: hydrogen bonds are the most common fundamental structural driving forces, which determine structural and dynamical properties of numerous functional materials. First-principles calculations of spectroscopic parameters can help to understand local geometric motifs, but also more complex processes such as hydrogen bond lifetimes and ion transport processes in condensed phases. In this feature article, we review the relevance of structure-spectroscopy-relationships, we discuss recent ab initio calculations eludicating the structure of supramolecular assemblies, and highlight the importance of incorporating atomic and molecular mobility by means of molecular dynamics (MD) simulations.Complex hydrogen bonding networks: vinyl-phosphonic acid polymers (left) and aqueous hydrochloric acid (right).1 Sensitivity of spectroscopic signatures to structure Any simulation of a molecular system is based on the computed potential energy surface (PES). This surface, however, is not directly experimentally accessible. One of the first actual observables in a numerical calculation is the atomic structure, be it at equilibrium or as an ensemble average. As a consequence, approximations and errors in the calculation of the PES propagate immediately to structural parameters. Even a highly corrugated landscape is full of local energy minima, at which the atomic forces vanish; hence, the PES is locally quadratic in all coordinates at those points. This in turn results in a strong effect of small perturbative forces on computed geometries near equilibrium.It turns out that many spectroscopic observables exhibit a very different behavior close to the equilibrium geometry: small structural variations can lead to considerable changes in (experimental as well as computed) spectra. As an example from nuclear magnetic resonance spectroscopy (NMR), the 1 H NMR chemical shift calculated for the H-bonding proton in an imidazole dimer is shown in Fig. 1 (top). The slope of d H at equilibrium (indicated by the dashed line) is about 8 ppm/Å ; assuming a conservative estimate for the theoretical/experimental resolution of 0.1 ppm, this corresponds to a spectroscopic distance resolution of almost 0.01 Å [1]. In comparison to this, the energetic resolution of a standard ab initio calculation (assuming a systematic error of 1 kcal/mol and a typical H-bond strength) is roughly 0.1 Å . It is not feasible to reliably compute the energy differences due to small geometric changes more accurately than this, except by means of very resource-intensive quantumchemical reference methods. Hence, the variation of the NMR chemical shift considerably magnifies alterations of Phys. Status Solidi B 249, No. 2, 368-375 (2012)