Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

Exploring energy landscapes: from molecular to mesoscopic systems.

We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed.

Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules.

We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential.

Simulations of nematic homopolymer melts using particle-based models with interactions expressed through collective variables.

We develop a hybrid Monte Carlo approach for modelling nematic liquid crystals of homopolymer melts. The polymer architecture is described with a discrete worm-like chain model. A quadratic density functional accounts for the limited compressibility of the liquid, while an additional quadratic functional of the local orientation tensor of the segments captures the nematic ordering. The approach can efficiently address large systems parametrized according to volumetric and conformational properties, representative of real polymeric materials. The results of the simulations regarding the influence of the molecular weight on the isotropic-nematic transition are compared to predictions from a Landau-de Gennes free energy expansion. The formation of the nematic phase is addressed within Rouse-like dynamics, realized using the current model.

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors.

Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor.

A multiscale description of charge transport in conjugated oligomers.

By relating inter- and intrachain ordering to charge dynamics a correlation between the morphology and charge mobility of neutral and doped states of a conjugated polymer, in this case polypyrrole, is established. Morphologies are generated using an all-atom force field, while charge dynamics is simulated within the framework of high temperature nonadiabatic Marcus theory. For short oligomers, charge carrier mobility is insensitive to the orientational molecular ordering and is determined by the threshold transfer integral which connects percolating clusters of molecules, forming interconnected networks. The value of this transfer integral can be estimated from the radial distribution function. We therefore find that charge mobility is mainly determined by the local molecular packing and is independent of global morphology, at least in such a noncrystalline state of a polymer.

Versatile Object-Oriented Toolkit for Coarse-Graining Applications.

Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. Several coarse-graining techniques have so far been developed, such as iterative Boltzmann inversion, force-matching, and inverse Monte Carlo. However, there is no unified framework that implements these methods and that allows their direct comparison. We present a versatile object-oriented toolkit for coarse-graining applications (VOTCA) that implements these techniques and that provides a flexible modular platform for the further development of coarse-graining techniques. All methods are illustrated and compared by coarse-graining the SPC/E water model, liquid methanol, liquid propane, and a single molecule of hexane.

Calcitonin receptor-like receptor (CLR), receptor activity-modifying protein 1 (RAMP1), and calcitonin gene-related peptide (CGRP) immunoreactivity in the rat trigeminovascular system: differences between peripheral and central CGRP receptor distribution.

Calcitonin gene-related peptide (CGRP) is a key mediator in primary headaches including migraine. Animal models of meningeal nociception demonstrate both peripheral and central CGRP effects; however, the target structures remain unclear. To study the distribution of CGRP receptors in the rat trigeminovascular system we used antibodies recognizing two components of the CGRP receptor, the calcitonin receptor-like receptor (CLR) and the receptor activity-modifying protein 1 (RAMP1). In the cranial dura mater, CLR and RAMP1 immunoreactivity (-ir) was found within arterial blood vessels, mononuclear cells, and Schwann cells, but not sensory axons. In the trigeminal ganglion, besides Schwann and satellite cells, CLR- and RAMP1-ir was found in subpopulations of CGRP-ir neurons where colocalization of CGRP- and RAMP1-ir was very rare ( approximately 0.6%). CLR- and RAMP1-ir was present on central, but not peripheral, axons. In the spinal trigeminal nucleus, CLR- and RAMP1-ir was localized to "glomerular structures," partly colocalized with CGRP-ir. However, CLR- and RAMP1-ir was lacking in central glia and neuronal cell bodies. We conclude that CGRP receptors are associated with structural targets of known CGRP effects (vasodilation, mast cell degranulation) and targets of unknown function (Schwann cells). In the spinal trigeminal nucleus, CGRP receptors are probably located on neuronal processes, including primary afferent endings, suggesting involvement in presynaptic regulation of nociceptive transmission. Thus, in the trigeminovascular system CGRP receptor localization suggests multiple targets for CGRP in the pathogenesis of primary headaches.