scholarly journals “Crawling” on the self-assembly system: A molecular simulation of peptide position adjusting over self-assembly block

2018 ◽  
Vol 189 ◽  
pp. 02002
Author(s):  
Tong Zhang ◽  
Baoying Shen ◽  
Xinghua Shi
Keyword(s):  
Self Assembly ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Reaction Coordinate ◽  
The Self ◽  
System A ◽  
Assembly Structure ◽  
Non Equilibrium Molecular Dynamics ◽  
Weighted Histogram ◽  
Weighted Histogram Analysis

By combining non-equilibrium molecular dynamics(NEMD), umbrella sampling, and weighted histogram analysis method(WHAM), we calculated the potential of mean force of histidine peptide moving over a self-assembly structure. The reaction coordinate is along the main chain direction of the histidine peptide in the self-assembly structure. It is found that the energy needed for the histidine peptide with 3 and 5 residues while moving along the reaction coordinate is around -2.2 kCal/mol and -7.4 kCal/mol, respectively. And the histidine peptide crawls along the reaction coordinate, performing a snake-like movement. This result could illustrate how histidine peptide adjusts its position during self-assembly process.

scholarly journals Hydrophobicity of small alkane molecules (propane dimer) in solvents: a classical molecular dynamics study

BIBECHANA ◽  
2020 ◽  
Vol 17 ◽  
pp. 1-12
Author(s):  
Bikash Panthi ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Histogram Analysis ◽  
Analysis Method ◽  
Classical Molecular Dynamics ◽  
Solvent Environment ◽  
Weighted Histogram ◽  
Weighted Histogram Analysis

Molecular Dynamics (MD) simulations of propane dimer in different solvents (water, acetonitrile and methanol) were performed by using CHARMM platform for modeling the solute and solvents. A series of Umbrella sampling MD simulations were carried out in each solvent separately and potential of mean force (PMFs) were calculated by using Weighted Histogram Analysis Method. Results show that two minima (contact minima and solvent separated minima) characterize the PMF of propane dimer in all three solvent environments. The contact minima are deeper and less sensitive to solvent environment for its position. However, significant effect in the position of second minima, solvent separated minima, was observed. Our study reveals that the interaction between propane dimer is softer in methanol and acetonitrile than in water. BIBECHANA 17 (2020) 1-12  

scholarly journals Crystalline modification of a rare earth nucleating agent for isotactic polypropylene based on its self-assembly

2018 ◽  
Vol 5 (5) ◽  
pp. 180247 ◽  
Author(s):  
Yuanming Zhang ◽  
Tingting Sun ◽  
Wei Jiang ◽  
Guangting Han
Keyword(s):  
Hydrogen Bond ◽  
Rare Earth ◽  
Isotactic Polypropylene ◽  
Self Assembly ◽  
Dendritic Structure ◽  
Nucleating Agent ◽  
The Self ◽  
Structure Evolution ◽  
Crystalline Modification ◽  
Assembly Structure

In this paper, the crystalline modification of a rare earth nucleating agent (WBG) for isotactic polypropylene (PP) based on its supramolecular self-assembly was investigated by differential scanning calorimetry, wide-angle X-ray diffraction and polarized optical microscopy. In addition, the relationship between the self-assembly structure of the nucleating agent and the crystalline structure, as well as the possible reason for the self-assembly behaviour, was further studied. The structure evolution of WBG showed that the self-assembly structure changed from a needle-like structure to a dendritic structure with increase in the content of WBG. When the content of WBG exceeded a critical value (0.4 wt%), it self-assembled into a strip structure. This revealed that the structure evolution of WBG contributed to the K β and the crystallization morphology of PP with different content of WBG. In addition, further studies implied that the behaviour of self-assembly was a liquid–solid transformation of WBG, followed by a liquid–liquid phase separation of molten isotactic PP and WBG. The formation of the self-assembly structure was based on the free molecules by hydrogen bond dissociation while being heated, followed by aggregation into another structure by hydrogen bond association while being cooled. Furthermore, self-assembly behaviour depends largely on the interaction between WBG themselves.

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.

Simulation study on the assembly of rod-coil diblock copolymers within coil-selective nanoslits

e-Polymers ◽  
2016 ◽  
Vol 16 (4) ◽  
pp. 343-349 ◽  
Author(s):  
Ya-Juan Su ◽  
Ze-Xin Ma ◽  
Jian-Hua Huang
Keyword(s):  
Phase Diagram ◽  
Self Assembly ◽  
Diblock Copolymers ◽  
Dissipative Particle Dynamics ◽  
Orientational Order ◽  
Particle Dynamics ◽  
The Self ◽  
Ordered Structures ◽  
Assembly Structure ◽  
Dynamics Simulations

AbstractDissipative particle dynamics simulations are performed to study the self-assembly of rod-coil (RC) diblock copolymers confined in a slit with two coil-selective surfaces. The effect of rod length and slit thickness on the assembly structure is investigated. A morphological phase diagram as a function of slit thickness and rod length is presented. We observe several ordered structures, such as perpendicular cylinders, parallel cylinders, and puck-shaped structure. In the assembly structures, long-range rod-rod orientational order is observed when the rod length exceeds a critical rod length. Our results show that the coil-selective slit influences the assembly structure as well as the rod orientation of RC diblock copolymers.

scholarly journals The Self-assembly Structure of Pyrazine Derivative on Highly Oriented Pyrolytic Graphite

2005 ◽  
Vol 21 (08) ◽  
pp. 925-928 ◽  
Author(s):  
AN Shi-yan ◽  
◽  
XU Shan-dong ◽  
ZENG Qing-dao ◽  
TAN Zhong-yin ◽  
...  
Keyword(s):  
Self Assembly ◽  
Pyrolytic Graphite ◽  
The Self ◽  
Highly Oriented Pyrolytic Graphite ◽  
Pyrazine Derivative ◽  
Assembly Structure

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.

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