Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

De/construction sites: Romans and the digital playground

The Roman world as attested to archaeologically and as interacted with today has its expression in a great many computational and other media. The place of visualisation within this has been paramount. This paper argues that the process of digitally constructing the Roman world and the exploration of the resultant models are useful methods for interpretation and influential factors in the creation of a popular Roman aesthetic. Furthermore, it suggests ways in which novel computational techniques enable the systematic deconstruction of such models, in turn re-purposing the many extant representations of Roman architecture and material culture

Negotiating Reality

Our understanding of research through design is demonstrated by a close examination of the methods used in the project lifeClipper2. This design research project investigates the applicability of immersive outdoor Augmented Reality (AR). lifeClipper2 offers an audiovisual walking experience in a virtually extended public space and focuses on audiovisual perception as well as on the development of the appropriate technology. The project involves contributions of partners from different fields of research. Thus, lifeClipper2 is able to test the potential of AR for visualizing architecture and archaeological information and to challenge our understanding of perception and interaction. Using examples from our research, the paper reflects on how scenario design contributes to the production of design knowledge and explores the possibilities and variations of AR. Finally, the paper drafts our approach to design research. The three tenets of our work are: the use of scenarios as a tool of interdisciplinary research, the experimental exploration of media and the intention to make design knowledge explicit. Keywords: augmented reality; locative media; hybrid environment; immersion; perception; experience design; research through design; scenario design</p

Shape interpretation with design computing

How information is interpreted has significant impact on how it can be used. This is particularly important in design where information from a wide variety of sources is used in a wide variety of contexts and in a wide variety of ways. This paper is concerned with the information that is created, modified and analysed during design processes, specifically with the information that is represented in shapes. It investigates how design computing seeks to support these processes, and the difficulties that arise when it is necessary to consider alternative interpretations of shape. The aim is to establish the problem of shape interpretation as a general challenge for research in design computing, rather than a difficulty that is to be overcome within specific processes. Shape interpretations are common characteristics of several areas of enquiry in design computing. This paper reviews these, brings an integrated perspective and draws conclusions about how this underlying process can be supported

Exploring the Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics (MICA)

We describe the Meta-Institute for Computational Astrophysics (MICA), the first professional scientific organization based exclusively in virtual worlds (VWs). The goals of MICA are to explore the utility of the emerging VR and VWs technologies for scientific and scholarly work in general, and to facilitate and accelerate their adoption by the scientific research community. MICA itself is an experiment in academic and scientific practices enabled by the immersive VR technologies. We describe the current and planned activities and research directions of MICA, and offer some thoughts as to what the future developments in this arena may be.Comment: 15 pages, to appear in the refereed proceedings of "Facets of Virtual Environments" (FaVE 2009), eds. F. Lehmann-Grube, J. Sablating, et al., ICST Lecture Notes Ser., Berlin: Springer Verlag (2009); version with full resolution color figures is available at http://www.mica-vw.org/wiki/index.php/Publication

Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

Interactive Chemical Reactivity Exploration

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.Comment: 36 pages, 14 figure