55,498 research outputs found
A framework and simulation engine for studying artificial life
The area of computer-generated artificial life-forms is a relatively recent
field of inter-disciplinary study that involves mathematical modelling, physical
intuition and ideas from chemistry and biology and computational science.
Although the attribution of “life” to non biological systems is still controversial,
several groups agree that certain emergent properties can be ascribed to
computer simulated systems that can be constructed to “live” in a simulated
environment. In this paper we discuss some of the issues and infrastructure
necessary to construct a simulation laboratory for the study of computer generated
artificial life-forms. We review possible technologies and present some
preliminary studies based around simple models
Multi-level agent-based modeling - A literature survey
During last decade, multi-level agent-based modeling has received significant
and dramatically increasing interest. In this article we present a
comprehensive and structured review of literature on the subject. We present
the main theoretical contributions and application domains of this concept,
with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic
statistics updated. v7 Change of the name of the paper to reflect what it
became, many refs and text added, bibliographic statistics update
Investigating biocomplexity through the agent-based paradigm.
Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex
Molecular dynamics simulation: a tool for exploration and discovery using simple models
Emergent phenomena share the fascinating property of not being obvious
consequences of the design of the system in which they appear. This
characteristic is no less relevant when attempting to simulate such phenomena,
given that the outcome is not always a foregone conclusion. The present survey
focuses on several simple model systems that exhibit surprisingly rich emergent
behavior, all studied by MD simulation. The examples are taken from the
disparate fields of fluid dynamics, granular matter and supramolecular
self-assembly. In studies of fluids modeled at the detailed microscopic level
using discrete particles, the simulations demonstrate that complex hydrodynamic
phenomena in rotating and convecting fluids, the Taylor-Couette and
Rayleigh-B\'enard instabilities, can not only be observed within the limited
length and time scales accessible to MD, but even quantitative agreement can be
achieved. Simulation of highly counterintuitive segregation phenomena in
granular mixtures, again using MD methods, but now augmented by forces
producing damping and friction, leads to results that resemble experimentally
observed axial and radial segregation in the case of a rotating cylinder, and
to a novel form of horizontal segregation in a vertically vibrated layer.
Finally, when modeling self-assembly processes analogous to the formation of
the polyhedral shells that package spherical viruses, simulation of suitably
shaped particles reveals the ability to produce complete, error-free assembly,
and leads to the important general observation that reversible growth steps
contribute to the high yield. While there are limitations to the MD approach,
both computational and conceptual, the results offer a tantalizing hint of the
kinds of phenomena that can be explored, and what might be discovered when
sufficient resources are brought to bear on a problem.Comment: 21 pages, 20 figures (v2 - minor text addition
Simulation modelling and visualisation: toolkits for building artificial worlds
Simulations users at all levels make heavy use of compute resources to drive computational
simulations for greatly varying applications areas of research using different simulation
paradigms. Simulations are implemented in many software forms, ranging from highly standardised
and general models that run in proprietary software packages to ad hoc hand-crafted
simulations codes for very specific applications. Visualisation of the workings or results of a
simulation is another highly valuable capability for simulation developers and practitioners.
There are many different software libraries and methods available for creating a visualisation
layer for simulations, and it is often a difficult and time-consuming process to assemble a
toolkit of these libraries and other resources that best suits a particular simulation model. We
present here a break-down of the main simulation paradigms, and discuss differing toolkits and
approaches that different researchers have taken to tackle coupled simulation and visualisation
in each paradigm
To boldly go:an occam-π mission to engineer emergence
Future systems will be too complex to design and implement explicitly. Instead, we will have to learn to engineer complex behaviours indirectly: through the discovery and application of local rules of behaviour, applied to simple process components, from which desired behaviours predictably emerge through dynamic interactions between massive numbers of instances. This paper describes a process-oriented architecture for fine-grained concurrent systems that enables experiments with such indirect engineering. Examples are presented showing the differing complex behaviours that can arise from minor (non-linear) adjustments to low-level parameters, the difficulties in suppressing the emergence of unwanted (bad) behaviour, the unexpected relationships between apparently unrelated physical phenomena (shown up by their separate emergence from the same primordial process swamp) and the ability to explore and engineer completely new physics (such as force fields) by their emergence from low-level process interactions whose mechanisms can only be imagined, but not built, at the current time
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