Optimal prediction of folding rates and transition state placement from native state geometry

A variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well with the contact order, a measure of contact locality. Our investigation focuses on identifying additional topologic properties that correlate with experimentally measurable quantities, such as folding rates and transition state placement, for both two- and three-state folders. The validation against data from forty experiments shows that a particular topologic property which measures the interdepedence of contacts, termed cliquishness or clustering coefficient, can account with significant accuracy both for the transition state placement and especially for folding rates, the linear correlation coefficient being $r=0.71$. This result can be further improved to $r=0.74$, by optimally combining the distinct topologic information captured by cliquishness and contact order.Comment: Revtex, 15 pages, 8 figure

Injecting, Controlling, and Storing Magnetic Domain Walls in Ferromagnetic Nanowires

Domain walls in ferromagnetic nanowires are important for proposed devices in recording, logic, and sensing. The realization of such devices depends in part on the ability to quickly and accurately control the domain wall from creation until placement. Using micromagnetic computer simulation we demonstrate how a combination of externally applied magnetic fields is used to quickly inject, move, and accurately place multiple domain walls within a single wire for potential recording and logical operations. The use of a magnetic field component applied perpendicular to the principle domain wall driving field is found to be critical for increased speed and reliability. The effects of the transverse field on the injection and trapping of the domain wall will be shown to be of particular importance

Multiple centrality assessment in Parma : a network analysis of paths and open spaces

One of the largest of Europe, the recently realized university campus 'Area of the Sciences' in Parma, northern Italy, has been planned for a comprehensive programme of renovation and revitalization with a special focus on vehicular accessibility and the quality of open spaces. As part of the problem setting phase, the authors, with Rivi Engineering, applied Multiple Centrality Assessment (MCA) - a process of network analysis based on primal graphs, a set of different centrality indices and the metric computation of distances - in order to understand why the existent system of open spaces and pedestrian paths is so scarcely experienced by students as well as faculty and staff members and why it appears so poorly supportive of social life and human exchange. In the problem-solving phase MCA was also applied, turning out to offer a relevant contribution to the comparative evaluation of two alternative proposed scenarios, leading to the identification of one final solution of urban design. In the present paper, the first professional application of MCA, an innovative approach to the network analysis of geographic complex systems, is presented and its relevance in the context of a problem of urban design illustrated

Enabling Bidirectional Interoperability between BIM and BPS through Lightweight Topological Models

Building Performance Simulation (BPS) tools have become prevalent in the Architecture, Engineering, Construction, and Operation (AECO) sector to assess building performance for various purposes. However, some challenges persist in achieving full interoperability between BPS and Building Information Modeling (BIM). This paper proposes a different approach to BIM-BPS interoperability based on creating space-based Topological Models (TM) for data exchange using Visual Programming (VP) algorithms. The VP approach allows for complex geometrical operations, the automatic reflection of changes made to the BIM model in the BPS model, and easy synchronous modification of these models to encourage design exploration. The proposed workflow is tested on the heritage building of the Faculty of Engineering in Bologna, Italy, with the aim of establishing the basis for developing a Digital Twin (DT) of the building for optimising its energy management. This approach can also be used for the early-stage analysis of new constructions, providing a comprehensive view of building performance

Area topology for road extraction and topographic data validation

CISRG discussion paper ; 1

Topology generated non-fungible tokens: blockchain as infrastructure for a circular economy in architectural design.

The paper presents a new digital infrastructure layer for buildings and architectural assets. The infrastructure layer consists of a combination of topology graphs secured on a decentralised ledger. The topology graphs organise non-fungible digital tokens which each represent and correspond to building components, and in the root of the graph to the building itself. The paper presents background research in the relationship of building representation in the form of graphs with topology, of both manifold and non manifold nature. In parallel we present and analyse the relationship between digital representation and physical manifestation of a building, and back again. Within the digital representations the paper analyses the securing and saving of information on decentralised ledger technologies (such as blockchain). We then present a simple sample of generating and registering a non-manifold topology graph on the Ethereum blockchain as an EC721 token, i.e. a digital object that is unique, all through the use of dynamo and python scripting connected with a smart contract on the Ethereum blockchain. Ownership of this token can then be transferred on the blockchain smart contracts. The paper concludes with a discussion of the possibilities that this integration brings in terms of material passports and a circular economy and smart contracts as an infrastructure for whole-lifecycle BIM and digitally encapsulates of value in architectural design

Mathematical models of games of chance: Epistemological taxonomy and potential in problem-gambling research

Games of chance are developed in their physical consumer-ready form on the basis of mathematical models, which stand as the premises of their existence and represent their physical processes. There is a prevalence of statistical and probabilistic models in the interest of all parties involved in the study of gambling – researchers, game producers and operators, and players – while functional models are of interest more to math-inclined players than problem-gambling researchers. In this paper I present a structural analysis of the knowledge attached to mathematical models of games of chance and the act of modeling, arguing that such knowledge holds potential in the prevention and cognitive treatment of excessive gambling, and I propose further research in this direction

Automated generation of geometrically-precise and semantically-informed virtual geographic environnements populated with spatially-reasoning agents

La Géo-Simulation Multi-Agent (GSMA) est un paradigme de modélisation et de simulation de phénomènes dynamiques dans une variété de domaines d'applications tels que le domaine du transport, le domaine des télécommunications, le domaine environnemental, etc. La GSMA est utilisée pour étudier et analyser des phénomènes qui mettent en jeu un grand nombre d'acteurs simulés (implémentés par des agents) qui évoluent et interagissent avec une représentation explicite de l'espace qu'on appelle Environnement Géographique Virtuel (EGV). Afin de pouvoir interagir avec son environnement géographique qui peut être dynamique, complexe et étendu (à grande échelle), un agent doit d'abord disposer d'une représentation détaillée de ce dernier. Les EGV classiques se limitent généralement à une représentation géométrique du monde réel laissant de côté les informations topologiques et sémantiques qui le caractérisent. Ceci a pour conséquence d'une part de produire des simulations multi-agents non plausibles, et, d'autre part, de réduire les capacités de raisonnement spatial des agents situés. La planification de chemin est un exemple typique de raisonnement spatial dont un agent pourrait avoir besoin dans une GSMA. Les approches classiques de planification de chemin se limitent à calculer un chemin qui lie deux positions situées dans l'espace et qui soit sans obstacle. Ces approches ne prennent pas en compte les caractéristiques de l'environnement (topologiques et sémantiques), ni celles des agents (types et capacités). Les agents situés ne possèdent donc pas de moyens leur permettant d'acquérir les connaissances nécessaires sur l'environnement virtuel pour pouvoir prendre une décision spatiale informée. Pour répondre à ces limites, nous proposons une nouvelle approche pour générer automatiquement des Environnements Géographiques Virtuels Informés (EGVI) en utilisant les données fournies par les Systèmes d'Information Géographique (SIG) enrichies par des informations sémantiques pour produire des GSMA précises et plus réalistes. De plus, nous présentons un algorithme de planification hiérarchique de chemin qui tire avantage de la description enrichie et optimisée de l'EGVI pour fournir aux agents un chemin qui tient compte à la fois des caractéristiques de leur environnement virtuel et de leurs types et capacités. Finalement, nous proposons une approche pour la gestion des connaissances sur l'environnement virtuel qui vise à supporter la prise de décision informée et le raisonnement spatial des agents situés