First-principles molecular structure search with a genetic algorithm

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum, but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is: (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds and 1 cis/trans bond

CO Oxidation Catalysed by Pd-based Bimetallic Nanoalloys

Density functional theory based global geometry optimization has been used to demonstrate the crucial influence of the geometry of the catalytic cluster on the energy barriers for the CO oxidation reaction over Pd-based bimetallic nanoalloys. We show that dramatic geometry change between the reaction intermediates can lead to very high energy barriers and thus be prohibitive for the whole process. This introduces challenges for both the design of new catalysts, and theoretical methods employed. On the theory side, a careful choice of geometric configurations of all reaction intermediates is crucial for an adequate description of a possible reaction path. From the point of view of the catalyst design, the cluster geometry can be controlled by adjusting the level of interaction between the cluster and the dopant metal, as well as between the adsorbate molecules and the catalyst cluster by mixing different metals in a single nanoalloy particle. We show that substitution of a Pd atom in the Pd$_{5}$ cluster with a single Ag atom to form Pd$_{4}$Ag$_{1}$ leads to a potential improvement of the catalytic properties of the cluster for the CO oxidation reaction. On the other hand, a single Au atom does not enhance the properties of the catalyst, which is attributed to a weaker hybridization between the cluster's constituent metals and the adsorbate molecules. Such flexibility of properties of bimetallic nanoalloy clusters illustrates the possibility of fine-tuning, which might be used for design of novel efficient catalytic materials.Comment: 12 pages, 8 figure

Cooperative Caching and Transmission Design in Cluster-Centric Small Cell Networks

Wireless content caching in small cell networks (SCNs) has recently been considered as an efficient way to reduce the traffic and the energy consumption of the backhaul in emerging heterogeneous cellular networks (HetNets). In this paper, we consider a cluster-centric SCN with combined design of cooperative caching and transmission policy. Small base stations (SBSs) are grouped into disjoint clusters, in which in-cluster cache space is utilized as an entity. We propose a combined caching scheme where part of the available cache space is reserved for caching the most popular content in every SBS, while the remaining is used for cooperatively caching different partitions of the less popular content in different SBSs, as a means to increase local content diversity. Depending on the availability and placement of the requested content, coordinated multipoint (CoMP) technique with either joint transmission (JT) or parallel transmission (PT) is used to deliver content to the served user. Using Poisson point process (PPP) for the SBS location distribution and a hexagonal grid model for the clusters, we provide analytical results on the successful content delivery probability of both transmission schemes for a user located at the cluster center. Our analysis shows an inherent tradeoff between transmission diversity and content diversity in our combined caching-transmission design. We also study optimal cache space assignment for two objective functions: maximization of the cache service performance and the energy efficiency. Simulation results show that the proposed scheme achieves performance gain by leveraging cache-level and signal-level cooperation and adapting to the network environment and user QoS requirements.Comment: 13 pages, 10 figures, submitted for possible journal publicatio