Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Socio-Economic Mechanisms to Coordinate the Internet of Services: The Simulation Environment SimIS

Visions of 21st century information systems show highly specialized digital services and resources, which interact continuously and with a global reach. Especially with the emergence of technologies, such as the semantic web or software agents, intelligent services within these settings can be implemented, automatically communicating and negotiating over the Internet about digital resources without human intervention. Such environments will eventually realize the vision of an open and global Internet of Services (IoS). In this paper we present an agent-based simulation model and toolkit for the IoS: 'SimIS - Simulating an Internet of Services'. Employing SimIS, distributed management mechanisms and protocols can be investigated in a simulated IoS environment before their actual deployment.Multi-Agent Simulation, Internet, Simulation Tools

Simulation of complex environments:the Fuzzy Cognitive Agent

The world is becoming increasingly competitive by the action of liberalised national and global markets. In parallel these markets have become increasingly complex making it difficult for participants to optimise their trading actions. In response, many differing computer simulation techniques have been investigated to develop either a deeper understanding of these evolving markets or to create effective system support tools. In this paper we report our efforts to develop a novel simulation platform using fuzzy cognitive agents (FCA). Our approach encapsulates fuzzy cognitive maps (FCM) generated on the Matlab Simulink platform within commercially available agent software. We firstly present our implementation of Matlab Simulink FCMs and then show how such FCMs can be integrated within a conceptual FCA architecture. Finally we report on our efforts to realise an FCA by the integration of a Matlab Simulink based FCM with the Jack Intelligent Agent Toolkit

Object oriented design of a thermo-mechanical FEM code

An object oriented design is presented for a computer program that can perform\ud thermo-mechanically coupled analyzes. The target of the design is a \ud exible and robust\ud computer program. It should be easy to adapt and extend, re-using existing code, without\ud interfering with already established algorithms.\ud The program uses publicly available toolkits that are currently emerging as C++ pack-\ud ages. First of all the Standard C++ Library (formerly Standard Template Library) is\ud used for packing items in container classes. Secondly the matrix and vector operations\ud are derived from the Template Numerical Toolkit (TNT) and �nally (not essentially for\ud the numerical part) a graphical user interface is made, based on the wxWindows package,\ud that can generate a GUI for Motif and MS-Windows with the same code.\ud Attention is given to the design of classes such as speci�c elements and material classes\ud based on more general classes. A hierarchy of classes is constructed where general behavior\ud is put high in the hierarchy and speci�c behavior low. The choice between inheritance and\ud aggregation is made at several levels

GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet

Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl. ac.uk or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press