Predicting a Kind of Unusual Multiple-States Dimerization-Modes Transformation in Protein PD-L1 System by Computational Investigation and a Generalized Rate Theory

The new cancer immunotherapy has been carried out with an almost messianic zeal, but its molecular basis remains unclear due to the complexity of programmed death ligand 1 (PD-L1) dimerization. In this study, a new and integral multiple dimerization-modes transformation process of PD-L1s (with a new PD-L1 dimerization mode and a new transformation path discovered) and the corresponding mechanism are predicted using theoretical and computational methods. The results of the state analysis show that 5 stable binding states exist in system. A generalized inter-state transformation rate (GITR) theory is also proposed in such multiple-states self-assembly system to explore the kinetic characteristics of inter-state transformation. A “drug insertion” path was identified as the dominant path of the PD-L1 dimerization-modes transformation. Above results can provide supports for both the relative drug design and other multiple-states self-assembly system from the theoretical chemistry perspective.

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Guiding Self-Organization in Systems of Cooperative Mobile Agents

Advancing Artificial Intelligence through Biological Process Applications ◽

10.4018/978-1-59904-996-0.ch015 ◽

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.

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Study of self-assembly system of norfloxacin molecularly imprinted polymers based on simulated design

Theoretical Chemistry Accounts ◽

10.1007/s00214-020-02712-x ◽

2021 ◽

Vol 140 (1) ◽

Author(s):

Xiaoshuang Wang ◽

Wensi Zhao ◽

Junbo Liu ◽

Shanshan Tang ◽

Ruifa Jin

Keyword(s):

Molecularly Imprinted Polymers ◽

Self Assembly ◽

Assembly System ◽

Molecularly Imprinted ◽

Imprinted Polymers

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Cell Layout of Aircraft Assembly System Based on Sequence Pair

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.271-272.801 ◽

2012 ◽

Vol 271-272 ◽

pp. 801-805

Author(s):

Jia Jia Xu ◽

Yuan Li ◽

Jian Feng Yu ◽

Jie Zhang

Keyword(s):

Solution Structure ◽

Simulated Annealing Algorithm ◽

Assembly System ◽

Sequence Pair ◽

Logistics Network ◽

Aircraft Assembly ◽

System A ◽

Assembly Cell ◽

Annealing Algorithm ◽

Transportation Route

This paper aims to investigate the cell layout problem of aircraft assembly system. A mathematical model for this problem is proposed, taking into account the integration design of cell layout and logistics network. The means of logistics transportation are divided into horizontal transportation and space transportation, meanwhile, the logistics transportation route is calculated. Based on sequence pair, the presentation of solution structure for cell layout is put forward, and the solution structure is solved using simulated annealing algorithm. This method is applied successfully to the assembly cell layout of the fuselage-wing assembly system for a giant aircraft, and the result shows its feasibility and effectiveness.

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Theoretical and experimental research on self‐assembly system of molecularly imprinted polymers formed via chloramphenicol and methacrylic acid

Journal of Separation Science ◽

10.1002/jssc.201800997 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jun‐Bo Liu ◽

Guang‐Yu Wang ◽

Shan‐Shan Tang ◽

Qian Gao ◽

Da‐Dong Liang ◽

...

Keyword(s):

Experimental Research ◽

Methacrylic Acid ◽

Molecularly Imprinted Polymers ◽

Self Assembly ◽

Assembly System ◽

Molecularly Imprinted ◽

Imprinted Polymers

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The Activation of Carboxylic Acids via Self-Assembly Asymmetric Organocatalysis: A Combined Experimental and Computational Investigation

Journal of the American Chemical Society ◽

10.1021/jacs.6b09179 ◽

2016 ◽

Vol 138 (44) ◽

pp. 14740-14749 ◽

Cited By ~ 27

Author(s):

Mattia Riccardo Monaco ◽

Daniele Fazzi ◽

Nobuya Tsuji ◽

Markus Leutzsch ◽

Saihu Liao ◽

...

Keyword(s):

Carboxylic Acids ◽

Self Assembly ◽

Computational Investigation ◽

Asymmetric Organocatalysis

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True Nature of an Archetypal Self-Assembly System: Mobile Au-Thiolate Species on Au(111)

Physical Review Letters ◽

10.1103/physrevlett.97.166102 ◽

2006 ◽

Vol 97 (16) ◽

Cited By ~ 195

Author(s):

Miao Yu ◽

N. Bovet ◽

Christopher J. Satterley ◽

S. Bengió ◽

Kevin R. J. Lovelock ◽

...

Keyword(s):

Self Assembly ◽

Assembly System ◽

True Nature

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Effect of Two-Step Austempering Process on Transformation Kinetics of Nanostructured Bainitic Steel

Materials ◽

10.3390/ma12010166 ◽

2019 ◽

Vol 12 (1) ◽

pp. 166 ◽

Cited By ~ 6

Author(s):

Chunhe Chu ◽

Yuman Qin ◽

Xuemei Li ◽

Zhinan Yang ◽

Fucheng Zhang ◽

...

Keyword(s):

Activation Energy ◽

Energy Barrier ◽

Bainitic Ferrite ◽

Transformation Process ◽

Transformation Rate ◽

Bainitic Steel ◽

Transformation Kinetics ◽

Activation Energy Barrier ◽

Quenching Process ◽

Kinetics Of

The two-step austempering process has been reported to be an effective method to accelerate the bainitic transformation process by introducing martensite (Q-M-B). However, in this study, it was found that the Q-M-B process reduced the incubation time, but the transformation duration remained nearly unchanged. The notably reduced activation energy barrier for nucleation of bainitic ferrite on the preformed martensite should be responsible for the reduced duration time of the Q-M-B process. A process that both of the two steps were above, Ms (Q-B-B), has been demonstrated to increase transformation rate and improve the amount of bainitic ferrite, which probably results from the additional hysteresis free energy provided by the first quenching process.

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Anisotropic polymer nanoparticles with controlled dimensions from the morphological transformation of isotropic seeds

Nature Communications ◽

10.1038/s41467-019-13263-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Zan Hua ◽

Joseph R. Jones ◽

Marjolaine Thomas ◽

Maria C. Arno ◽

Anton Souslov ◽

...

Keyword(s):

Physical Model ◽

Self Assembly ◽

Transformation Process ◽

Polymer Nanoparticles ◽

Advanced Materials ◽

General Mechanism ◽

Morphological Transformation ◽

Functional Nanostructures ◽

Anisotropic Nanoparticles ◽

Multiple Length Scales

AbstractUnderstanding and controlling self-assembly processes at multiple length scales is vital if we are to design and create advanced materials. In particular, our ability to organise matter on the nanoscale has advanced considerably, but still lags far behind our skill in manipulating individual molecules. New tools allowing controlled nanoscale assembly are sorely needed, as well as the physical understanding of how they work. Here, we report such a method for the production of highly anisotropic nanoparticles with controlled dimensions based on a morphological transformation process (MORPH, for short) driven by the formation of supramolecular bonds. We present a minimal physical model for MORPH that suggests a general mechanism which is potentially applicable to a large number of polymer/nanoparticle systems. We envision MORPH becoming a valuable tool for controlling nanoscale self-assembly, and for the production of functional nanostructures for diverse applications.

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