### Refine

#### Document Type

- Article (9)
- ZIB-Report (4)

#### Keywords

- Alanine dipeptide (1)
- Coarse graining (1)
- Electric field (1)
- Floquet theory (1)
- Girsanov transformation (1)
- Markov states model (1)
- Non-equilibrium (1)
- adaptive resolution (1)
- change of measure (1)
- chemical potential (1)

#### Institute

- Linear response theory and optimal control for a molecular system under nonequilibrium conditions (2013)
- In this paper, we propose a straightforward generalization of linear response theory to systems in nonequilibrium that are subject to nonequilibrium driving. We briefly revisit the standard linear response result for equilibrium systems, where we consider Langevin dynamics as a special case, and then give an alternative derivation using a change-of-measure argument that does not rely on any stationarity or reversibility assumption. This procedure moreover easily enables us to calculate the second order correction to the linear response formula (which may or may not be useful in practice). Furthermore, we outline how the novel nonequilibirum linear response formula can be used to compute optimal controls of molecular systems for cases in which one wants to steer the system to maximize a certain target expectation value. We illustrate our approach with simple numerical examples.

- Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique (2013)

- Linear response theory and optimal control for a molecular system under nonequilibrium conditions (2013)

- Chemical potential of liquids and mixtures via Adaptive Resolution Simulation (2014)
- We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonicallike version (GC-AdResS) [Wang et al. 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.

- Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation (2014)
- In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal effects of the field. For the constant field different time-scales are identified in the conformational, dipole moment, and orientational dynamics. Moreover, we prove that the solvent structure only marginally changes when the external field is switched on. In the case of oscillatory field, the conformational changes are shown to be as strong as in the previous case, and nontrivial nonequilibrium circular paths in the conformation space are revealed by calculating the integrated net probability fluxes.

- Building Markov State Models for Periodically Driven Non-Equilibrium Systems (2014)
- Recent years have seen an increased interest in non-equilibrium molecular dynamics (NEMD) simulations, especially for molecular systems with periodic forcing by external fields, e.g., in the context of studying effects of electromagnetic radiation on the human body tissue. Lately, an NEMD methods with local thermostating has been proposed that allows for studying non-equilibrium processes in a statistically reliable and thermodynamically consistent way. In this article, we demonstrate how to construct Markov State Models (MSMs) for such NEMD simulations. MSM building has been well-established for systems in equilibrium where MSMs with just a few (macro-)states allow for accurate reproduction of the essential kinetics of the molecular system under consideration. Non-equilibrium MSMs have been lacking so far. The article presents how to construct such MSMs and illustrates their validity and usefulness for the case of conformation dynamics of alanine dipeptide in an external electric field.