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.

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.

scholarly journals 3D DNA structural barcode copying and random access

2020 ◽  
Author(s):  
Filip Bošković ◽  
Alexander Ohmann ◽  
Ulrich F. Keyser ◽  
Kaikai Chen
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Random Access ◽  
Scale Production ◽  
Digital Information ◽  
Dna Nanostructures ◽  
Large Scale Production

AbstractThree-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.

scholarly journals Extra Surfactant-Assisted Self-Assembly of Highly Ordered Monolayers of BaTiO3 Nanocubes at the Air—Water Interface

Nanomaterials ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 739 ◽  
Author(s):  
Hiroki Itasaka ◽  
Ken-Ichi Mimura ◽  
Kazumi Kato
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Water Interface ◽  
Compression Pressure ◽  
Air Water Interface ◽  
Out Of Plane ◽  
Key Factor ◽  
Evaporation Induced Self Assembly ◽  
20 Nm

Assembly of nanocrystals into ordered two- or three-dimensional arrays is an essential technology to achieve their application in novel functional devices. Among a variety of assembly techniques, evaporation-induced self-assembly (EISA) is one of the prospective approaches because of its simplicity. Although EISA has shown its potential to form highly ordered nanocrystal arrays, the formation of uniform nanocrystal arrays over large areas remains a challenging subject. Here, we introduce a new EISA method and demonstrate the formation of large-scale highly ordered monolayers of barium titanate (BaTiO3, BT) nanocubes at the air-water interface. In our method, the addition of an extra surfactant to a water surface assists the EISA of BT nanocubes with a size of 15–20 nm into a highly ordered arrangement. We reveal that the compression pressure exerted by the extra surfactant on BT nanocubes during the solvent evaporation is a key factor in the self-assembly in our method. The BT nanocube monolayers transferred to substrates have sizes up to the millimeter scale and a high out-of-plane crystal orientation, containing almost no microcracks and voids.

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.

scholarly journals Elastic Three-Dimensional Graphene Sponge Fabricated by the Liquid Crystals of Controlled Large Graphene Oxide Sheets

2018 ◽  
Author(s):  
Qiuli Wei ◽  
Anaerguli Wufuer ◽  
Meisong Wang ◽  
Yuanyuan Wang ◽  
Liyi Dai
Keyword(s):  
Graphene Oxide ◽  
Liquid Crystals ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
High Porosity ◽  
Graphene Sponge ◽  
New Strategy ◽  
Facile Fabrication ◽  
Graphene Oxide Sheets

Three-dimensional graphene (3DG) sponge has attracted increasing attention because it combines the unique properties of cellular materials and the excellent performance of graphene. The preparation of 3DG sponge depends mainly on the self-assembly of graphene oxide sheets. Here, we demonstrate facile fabrication of 3DG sponge with a large-scale and ordered porous structure, exploiting the liquid crystals of large graphene oxide (LGO) and ultralarge graphene oxide (ULGO) sheets. The resulting materials exhibit a low density, high porosity and elasticity. Our work explores a new strategy for organizing the ordered alignment of controlled large GO sheets and exploring the relationship between the microstructures and mechanical properties of 3DG sponge.

scholarly journals Superior adsorption of 3D nanoporous architectures for Ni(ii) ions adsorption using polyvinyl alcohol as cross-linking agent and adsorption conveyor

RSC Advances ◽  
2018 ◽  
Vol 8 (15) ◽  
pp. 7899-7903 ◽  
Author(s):  
Haibo Wang ◽  
Wei Wang ◽  
Yufen Zhao ◽  
Zhiwei Xu ◽  
Lei Chen ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Polyvinyl Alcohol ◽  
Self Assembly ◽  
Large Scale ◽  
Low Cost ◽  
Three Dimensional ◽  
Cross Linking ◽  
Cost Approach ◽  
Assembly Method

In this study, we report a large-scale and low cost approach for the synthesis of three-dimensional (3D) polyvinyl alcohol/carbon nanotubes nanoporous architecture using self-assembly method.

scholarly journals Large-scale dissipative particle dynamics simulations of self-assembled amphiphilic systems

2014 ◽  
Vol 50 (61) ◽  
pp. 8306-8308 ◽  
Author(s):  
Xuejin Li ◽  
Yu-Hang Tang ◽  
Haojun Liang ◽  
George Em Karniadakis
Keyword(s):  
Self Assembly ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Amphiphilic Molecules ◽  
Self Assembled ◽  
Dynamics Simulations ◽  
Confined Environment

GPU-accelerated dissipative particle dynamics has been explored to probe the self-assembly of amphiphilic molecules in a soft confined environment.

Control of Colloidal Crystal Growth by External Fields

2005 ◽  
Vol 901 ◽  
Author(s):  
Elisabeth von Rhein ◽  
Andreas Bielawny ◽  
Siegmund Greulich-Weber
Keyword(s):  
Crystal Growth ◽  
Self Assembly ◽  
Large Scale ◽  
Colloidal Crystal ◽  
Three Dimensional ◽  
Particle Diffusion ◽  
Bulk Crystals ◽  
Centrifugal Field ◽  
Sonic Wave ◽  
Synthetic Opals

AbstractSynthetic opals serve as templates for the most promising three-dimensional photonic crystals, so-called inverted opals. The time consuming growth of artificial opals by self-assembly of monodisperse sub-micron spheres made of silica or organic materials resulting in fcc and hcp colloidal crystals usually yields in limited crystal qualities. The large scale fabrication and thus their application in photonics suffer from the reproducible growth of defect-free extended bulk crystals. In this paper we propose a sonic wave supported fast colloidal crystal growth in a centrifugal field. White noise acoustic irradiation is thought to realize an artificial temperature allowing particle diffusion during crystal growth.

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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