Recoiling DNA Molecule: Simulation & Experiment

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between computer simulated recoil curves, generated from the corresponding Langevin equation, and experimental recoils is used to assure the validity of data analysis.Comment: 14 pages (single column preprint), 7 figures. Major changes: data analysis method improved; dna-ethidium bromide results removed (dna-ethidium bromide protocol affected microspheres and coverglass behavior

The Logic of the Method of Agent-Based Simulation in the Social Sciences: Empirical and Intentional Adequacy of Computer Programs

The classical theory of computation does not represent an adequate model of reality for simulation in the social sciences. The aim of this paper is to construct a methodological perspective that is able to conciliate the formal and empirical logic of program verification in computer science, with the interpretative and multiparadigmatic logic of the social sciences. We attempt to evaluate whether social simulation implies an additional perspective about the way one can understand the concepts of program and computation. We demonstrate that the logic of social simulation implies at least two distinct types of program verifications that reflect an epistemological distinction in the kind of knowledge one can have about programs. Computer programs seem to possess a causal capability (Fetzer, 1999) and an intentional capability that scientific theories seem not to possess. This distinction is associated with two types of program verification, which we call empirical and intentional verification. We demonstrate, by this means, that computational phenomena are also intentional phenomena, and that such is particularly manifest in agent-based social simulation. Ascertaining the credibility of results in social simulation requires a focus on the identification of a new category of knowledge we can have about computer programs. This knowledge should be considered an outcome of an experimental exercise, albeit not empirical, acquired within a context of limited consensus. The perspective of intentional computation seems to be the only one possible to reflect the multiparadigmatic character of social science in terms of agent-based computational social science. We contribute, additionally, to the clarification of several questions that are found in the methodological perspectives of the discipline, such as the computational nature, the logic of program scalability, and the multiparadigmatic character of agent-based simulation in the social sciences.Computer and Social Sciences, Agent-Based Simulation, Intentional Computation, Program Verification, Intentional Verification, Scientific Knowledge

An Analysis of the Insertion of Virtual Players in GMABS Methodology Using the Vip-JogoMan Prototype

The GMABS (Games and Multi-Agent-Based Simulation) methodology was created from the integration of RPG and MABS techniques. This methodology links the dynamic capacity of MABS (Multi-Agent-Based Simulation) and the discussion and learning capacity of RPG (Role-Playing Games). Using GMABS, we have developed two prototypes in the natural resources management domain. The first prototype, called JogoMan (Adamatti et. al, 2005), is a paper-based game: all players need to be physically present in the same place and time, and there is a minimum needed number of participants to play the game. In order to avoid this constraint, we have built a second prototype, called ViP-JogoMan (Adamatti et. al, 2007), which is an extension of the first one. This second game enables the insertion of virtual players that can substitute some real players in the game. These virtual players can partially mime real behaviors and capture autonomy, social abilities, reaction and adaptation of the real players. We have chosen the BDI architecture to model these virtual players, since its paradigm is based on folk psychology; hence, its core concepts easily map the language that people use to describe their reasoning and actions in everyday life. ViP-JogoMan is a computer-based game, in which people play via Web, players can be in different places and it does not have a hard constraint regarding the minimum number of real players. Our aim in this paper is to present some test results obtained with both prototypes, as well as to present a preliminary discussion on how the insertion of virtual players has affected the game results.Role-Playing Games, Multi-Agent Based Simulation, Natural Resources, Virtual Players

Anisotropic superconducting properties of aligned MgB2 crystallites

Samples of aligned MgB2 crystallites have been prepared, allowing for the first time the direct identification of an upper critical field anisotropy Hc2^{ab}/Hc2^{c}= xi_{ab}/xi_{c} ~ 1.73; with xi_{o,ab} ~ 70 A, xi_{o,c} ~ 40 A, and a mass anisotropy ratio m_{ab}/m_{c} ~ 0.3. A ferromagnetic background signal was identified, possibly related to the raw materials purity.Comment: 4 pages, 4 figures; Revised version to appear in Phys. Rev. Let