Ansatz for Dynamical Hierarchies

2001 ◽  
Vol 7 (4) ◽  
pp. 329-353 ◽  
Author(s):  
Steen Rasmussen ◽  
Nils A. Baas ◽  
Bernd Mayer ◽  
Martin Nilsson
Keyword(s):  
Self Assembly ◽  
Lattice Gas ◽  
Three Dimensional ◽  
Self Organization ◽  
Emergent Properties ◽  
Simulation Framework ◽  
Natural Systems ◽  
Polymer Aggregates ◽  
Physicochemical Simulation ◽  
Different Levels

Complex, robust functionalities can be generated naturally in at least two ways: by the assembly of structures and by the evolution of structures. This work is concerned with spontaneous formation of structures. We define the notion of dynamical hierarchies in natural systems and show the importance of this particular kind of organization for living systems. We then define a framework that enables us to formulate, investigate, and manipulate such dynamical hierarchies. This framework allows us to simultaneously investigate different levels of description together with their interrelationship, which is necessary to understand the nature of dynamical hierarchies. Our framework is then applied to a concrete and very simple formal, physicochemical, dynamical hierarchy involving water and monomers at level one, polymers and water at level two, and micelles (polymer aggregates) and water at level three. Formulating this system as a simple two-dimensional molecular dynamics (MD) lattice gas allows us within one dynamical system to demonstrate the successive emergence of two higher levels (three levels all together) of robust structures with associated properties. Second, we demonstrate how the framework for dynamical hierarchies can be used for realistic (predictive) physicochemical simulation of molecular self-assembly and self-organization processes. We discuss the detailed process of micellation using the three-dimensional MD lattice gas. Finally, from these examples we can infer principles about formal dynamical hierarchies. We present an ansatz for how to generate robust, higher-order emergent properties in formal dynamical systems that is based on a conjecture of a necessary minimal complexity within the fundamental interacting structures once a particular simulation framework is chosen.

Modelling the dynamics of a minimal protocell container

2005 ◽  
Vol 4 (1) ◽  
pp. 81-91 ◽  
Author(s):  
Martin Nilsson Jacobi ◽  
Steen Rasmussen ◽  
Kolbjørn Tunstrøm
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Lattice Gas ◽  
Three Dimensional ◽  
Initial Distribution ◽  
Energy Potential ◽  
Time Dynamics ◽  
Amphiphilic Molecules ◽  
Head Groups ◽  
Simplifying Assumptions

This paper is a discussion on how reaction kinetics and three-dimensional (3D) lattice simulations can be used to elucidate the dynamical properties of micelles as a possible minimal protocell container. We start with a general discussion on the role of molecular self-assembly in prebiotic and contemporary biological systems. A simple reaction kinetic model of a micellation process of amphiphilic molecules in water is then presented and solved analytically. Amphiphilic molecules are polymers with hydrophobic (water-fearing), e.g. hydrocarbon tail groups, and hydrophilic (water-loving) head groups, e.g. fatty acids. By making a few simplifying assumptions an analytical expression for the size distribution of the resulting micelles can be derived. The main part of the paper presents and discusses a lattice gas technique for a more detailed 3D simulation of molecular self-assembly of amphiphilic polymers in aqueous environments. Water molecules, hydrocarbon tail groups and hydrophilic head groups are explicitly represented on a three-dimensional discrete lattice. Molecules move on the lattice proportional to their continuous momentum. Collision rules preserve momentum and kinetic energy. Potential energy from molecular interactions are also included explicitly. The non-trivial thermodynamics of large-scale and long-time dynamics are studied. In this paper we specifically demonstrate how, from a random initial distribution, micelles are formed and grow until they destabilize and can divide. Eventually a steady state of growing and dividing micelles is formed. Towards the end of the paper we discuss the relevance of the presented results to the design of a minimal artificial protocell.

Guiding Self-Organization in Systems of Cooperative Mobile Agents

2011 ◽  
pp. 268-290
Author(s):  
Alejandro Rodríguez ◽  
Alexander Grushin ◽  
James A. Reggia
Keyword(s):  
Swarm Intelligence ◽  
Self Assembly ◽  
The Self ◽  
Self Organization ◽  
Assembly System ◽  
Global Behavior ◽  
System A ◽  
Collective Transport ◽  
Reactive Behavior ◽  
Different Levels

Drawing inspiration from social interactions in nature, swarm intelligence has presented a promising approach to the design of complex systems consisting of numerous, simple parts, to solve a wide variety of problems. Swarm intelligence systems involve highly parallel computations across space, based heavily on the emergence of global behavior through local interactions of components. This has a disadvantage as the desired behavior of a system becomes hard to predict or design. Here we describe how to provide greater control over swarm intelligence systems, and potentially more useful goal-oriented behavior, by introducing hierarchical controllers in the components. This allows each particle-like controller to extend its reactive behavior in a more goal-oriented style, while keeping the locality of the interactions. We present three systems designed using this approach: a competitive foraging system, a system for the collective transport and distribution of goods, and a self-assembly system capable of creating complex 3D structures. Our results show that it is possible to guide the self-organization process at different levels of the designated task, suggesting that self-organizing behavior may be extensible to support problem solving in various contexts.

Constructive Molecular Dynamics Lattice Gases: Three-Dimensional Molecular Self-Assembly

2003 ◽  
Author(s):  
Martin Nilsson ◽  
Steen Rasmussen
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Lattice Gas ◽  
Chemical Properties ◽  
Special Kind ◽  
Lattice Gases ◽  
Living Systems ◽  
Self Organization ◽  
Assembly Systems ◽  
Formal Systems

Realistic molecular dynamics and self-assembly is represented in a lattice simulation where water, water-hydrocarbons, and water-amphiphilic systems are investigated. The details of the phase separation dynamics and the constructive self-assembly dynamics are discussed and compared to the corresponding experimental systems. The method used to represent the different molecular types can easily be expended to include additional molecules and thus allow the assembly of more complex structures. This molecular dynamics (MD) lattice gas fills a modeling gap between traditional MD and lattice gas methods. Both molecular objects and force fields are represented by propagating information particles and all microscopic interactions are reversible. Living systems, perhaps the ultimate constructive dynamical systems, is the motivation for this work and our focus is a study of the dynamics of molecular self-assembly and self-organization. In living systems, matter is organized such that it spontaneously constructs intricate functionalities at all levels from the molecules up to the organism and beyond. At the lower levels of description, chemical reactions, molecular selfassembly and self-organization are the drivers of this complexity. We shall, in this chapter, demonstrate how molecular self-assembly and selforganization processes can be represented in formal systems. The formal systems are to be denned as a special kind of lattice gas and they are in a form where an obvious correspondence exists between the observables in the lattice gases and the experimentally observed properties in the molecular self-assembly systems. This has the clear advantage that by using these formal systems, theory, simulation, and experiment can be conducted in concert and can mutually support each other. However, a disadvantage also exists because analytical results are difficult to obtain for these formal systems due to their inherent complexity dictated by their necessary realism. The key to novelt simpler molecules (from lower levels), dynamical hierarchies are formed [2, 3]. Dynamical hierarchies are characterized by distinct observable functionalities at multiple levels of description. Since these higher-order structures are generated spontaneously due to the physico-chemical properties of their building blocks, complexity can come for free in molecular self-assembly systems. Through such processes, matter apparently can program itself into structures that constitute living systems [11, 27, 30].

scholarly journals Mimosa Origami: A nanostructure-enabled directional self-organization regime of materials

2016 ◽  
Vol 2 (6) ◽  
pp. e1600417 ◽  
Author(s):  
William S. Y. Wong ◽  
Minfei Li ◽  
David R. Nisbet ◽  
Vincent S. J. Craig ◽  
Zuankai Wang ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Soft Materials ◽  
Inorganic Materials ◽  
Living Systems ◽  
Self Organization ◽  
Mimosa Pudica ◽  
Flow Rates ◽  
Immense Potential ◽  
Spontaneous Motion

One of the innate fundamentals of living systems is their ability to respond toward distinct stimuli by various self-organization behaviors. Despite extensive progress, the engineering of spontaneous motion in man-made inorganic materials still lacks the directionality and scale observed in nature. We report the directional self-organization of soft materials into three-dimensional geometries by the rapid propagation of a folding stimulus along a predetermined path. We engineer a unique Janus bilayer architecture with superior chemical and mechanical properties that enables the efficient transformation of surface energy into directional kinetic and elastic energies. This Janus bilayer can respond to pinpoint water stimuli by a rapid, several-centimeters-long self-assembly that is reminiscent of the Mimosa pudica’s leaflet folding. The Janus bilayers also shuttle water at flow rates up to two orders of magnitude higher than traditional wicking-based devices, reaching velocities of 8 cm/s and flow rates of 4.7 μl/s. This self-organization regime enables the ease of fabricating curved, bent, and split flexible channels with lengths greater than 10 cm, demonstrating immense potential for microfluidics, biosensors, and water purification applications.

scholarly journals Self-assembly, buckling and density-invariant growth of three-dimensional vascular networks

2019 ◽  
Vol 16 (159) ◽  
pp. 20190517 ◽  
Author(s):  
Julius B. Kirkegaard ◽  
Bjarke F. Nielsen ◽  
Ala Trusina ◽  
Kim Sneppen
Keyword(s):  
Cell Polarity ◽  
Self Assembly ◽  
Planar Cell Polarity ◽  
Vascular System ◽  
Initial Density ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Emergent Properties ◽  
Vascular Density ◽  
Convergent Extension

The experimental actualization of organoids modelling organs from brains to pancreases has revealed that much of the diverse morphologies of organs are emergent properties of simple intercellular ‘rules’ and not the result of top-down orchestration. In contrast to other organs, the initial plexus of the vascular system is formed by aggregation of cells in the process known as vasculogenesis. Here we study this self-assembling process of blood vessels in three dimensions through a set of simple rules that align intercellular apical–basal and planar cell polarity. We demonstrate that a fully connected network of tubes emerges above a critical initial density of cells. Through planar cell polarity, our model demonstrates convergent extension, and this polarity furthermore allows for both morphology-maintaining growth and growth-induced buckling. We compare this buckling with the special vasculature of the islets of Langerhans in the pancreas and suggest that the mechanism behind the vascular density-maintaining growth of these islets could be the result of growth-induced buckling.

SWARM INTELLIGENCE SYSTEMS USING GUIDED SELF-ORGANIZATION FOR COLLECTIVE PROBLEM SOLVING

2007 ◽  
Vol 10 (supp01) ◽  
pp. 5-34 ◽  
Author(s):  
ALEJANDRO RODRÍGUEZ ◽  
ALEXANDER GRUSHIN ◽  
JAMES A. REGGIA
Keyword(s):  
Problem Solving ◽  
Swarm Intelligence ◽  
Self Assembly ◽  
The Self ◽  
Self Organization ◽  
Ongoing Research ◽  
System A ◽  
Collective Transport ◽  
Reactive Behavior ◽  
Different Levels

Drawing inspiration from social interactions in nature, the field of swarm intelligence has presented a promising approach to the design of complex systems consisting of numerous, usually homogeneous, simple parts, to solve a wide variety of problems. Like cellular automata, swarm-intelligence systems involve highly parallel computations across space, based heavily on self-organization, the emergence of global behavior through local interactions of components, and the absence of centralized or global control. However, this has a disadvantage as the desired behavior of a system becomes hard to predict or design based on its local interaction rules. In our ongoing research, we propose to provide greater control over a system, and potentially more useful, goal-oriented behavior, by introducing layered, hierarchical controllers in the particles or components. The layered controllers allow each particle to extend their reactive behavior in a more goal-oriented style, while keeping the locality of the interactions and the general simplicity of the system. In this paper, we present three systems designed using this approach: a competitive foraging system, a system for the collective transport and distribution of goods, and a self-assembly system capable of creating complex structures in a 3D world. Our simulation results show that in all three cases it was possible to guide the self-organization process at different levels of the designated task, suggesting that the self-organizing behavior of swarm-intelligence systems may be extendable to support problem solving in various contexts, such as coordinated robotic teams.

scholarly journals A class of organic cages featuring twin cavities

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhenyu Yang ◽  
Chunyang Yu ◽  
Junjie Ding ◽  
Lihua Chen ◽  
Huiyu Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Porous Materials ◽  
Self Assembly ◽  
Rational Design ◽  
Three Dimensional ◽  
The Self ◽  
Emergent Properties ◽  
Dynamics Simulations ◽  
Single Cavity

AbstractA variety of organic cages with different geometries have been developed during the last decade, most of them exhibiting a single cavity. In contrast, the number of organic cages featuring a pair of cavities remains scarce. These structures may pave the way towards novel porous materials with emergent properties and functions.We herein report on rational design of a three-dimensional hexaformyl precursor 1, which exhibits two types of conformers, i.e. Conformer-1 and -2, with different cleft positions and sizes. Aided by molecular dynamics simulations, we select two triamino conformation capturers (denoted CC). Small-sized CC-1 selectively capture Conformer-1 by matching its cleft size, while the large-sized CC-2 is able to match and capture both conformers. This strategy allows the formation of three compounds with twin cavities, which we coin diphane. The self-assembly of diphane units results in superstructures with tunable proton conductivity, which reaches up to 1.37×10-5 S cm-1.

scholarly journals Cellular Automata for Simulating Molecular Self-Assembly

2003 ◽  
Vol DMTCS Proceedings vol. AB,... (Proceedings) ◽  
Author(s):  
Martin Nilsson ◽  
Steen Rasmussen
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Lattice Gas ◽  
Three Dimensional ◽  
Initial Distribution ◽  
Energy Potential ◽  
Time Dynamics ◽  
Head Groups ◽  
Long Time ◽  
International Audience

International audience We present a lattice gas technique for simulating molecular self-assembly of amphiphilic polymers in aqueous environments. Water molecules, hydrocarbons tail-groups and amphiphilic head-groups are explicitly represented on a three dimensional discrete lattice. Molecules move on the lattice proportional to their continuous momentum. Collision rules preserve momentum and kinetic energy. Potential energy from molecular interactions are also included explicitly. Non-trivial thermodynamics of large scale and long time dynamics are studied. In this paper we specifically demonstrate how, from a random initial distribution, micelles are formed, and grow until they destabilize and divide. Eventually a steady state of growing and dividing micelles is formed.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

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