scholarly journals Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

2007 ◽  
Vol 20 (4) ◽  
pp. 205-214 ◽  
Author(s):  
Alexei Kurakin
Keyword(s):  
Molecular Recognition ◽  
Self Organization ◽  
Design Charts

Self-Organization of 2,5-Di-n-Alkoxy-1,4-benzoquinones in the Solid State:  Molecular Recognition Involving Intermolecular Dipole−Dipole, Weak C−H···OC Hydrogen Bond and van der Waals Interactions

1996 ◽  
Vol 8 (5) ◽  
pp. 1092-1105 ◽  
Author(s):  
Erik M. D. Keegstra ◽  
Valentijn van der Mieden ◽  
Jan W. Zwikker ◽  
Leonardus W. Jenneskens ◽  
Arie Schouten ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Molecular Recognition ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Self Organization

scholarly journals Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 271
Author(s):  
Masatake Sugita ◽  
Itaru Onishi ◽  
Masayuki Irisa ◽  
Norio Yoshida ◽  
Fumio Hirata
Keyword(s):  
Molecular Recognition ◽  
Statistical Mechanics ◽  
Self Assembly ◽  
The Self ◽  
Self Organization ◽  
Molecular Processes ◽  
Molecular Liquids ◽  
Organization Process ◽  
Structural Fluctuation ◽  
Life Phenomena

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

Self-organization versus Watchmaker: stochastic dynamics of cellular organization

2005 ◽  
Vol 386 (3) ◽  
pp. 247-254 ◽  
Author(s):  
Alexei Kurakin
Keyword(s):  
Experimental Evidence ◽  
Stochastic Dynamics ◽  
Molecular System ◽  
Living Cells ◽  
Integrated System ◽  
Self Organization ◽  
Cellular Organization ◽  
Time Dynamics ◽  
Design Charts ◽  
Growing Body

AbstractThe cell, as a molecular system, is often interpreted in terms of complex clockworks, and the design charts of mechanical and electrical engineering are assumed to provide adequate approximations for the description of cellular organization. However, a growing body of experimental evidence obtained through the observation and analysis of real-time dynamics of fluorescently labeled molecules inside living cells is increasingly inconsistent with the classico-mechanistic perception of the cell. An overview of recent studies favors an emerging alternative image of the cell as a dynamic integrated system of interconnected and interdependent metastable molecular organizations realized through stochasticity and self-organization.

scholarly journals Self-organization, entropy and allostery

2018 ◽  
Vol 46 (3) ◽  
pp. 587-597 ◽  
Author(s):  
Alexandr P. Kornev
Keyword(s):  
Protein Folding ◽  
Molecular Recognition ◽  
Molecular Mechanism ◽  
Broad Spectrum ◽  
Regulatory Mechanism ◽  
Signal Transmission ◽  
Self Organization ◽  
Common Root ◽  
The Cross ◽  
Polypeptide Chains

Allostery is a fundamental regulatory mechanism in biology. Although generally accepted that it is a dynamics-driven process, the exact molecular mechanism of allosteric signal transmission is hotly debated. We argue that allostery is as a part of a bigger picture that also includes fractal-like properties of protein interior, hierarchical protein folding and entropy-driven molecular recognition. Although so far all these phenomena were studied separately, they stem from the same common root: self-organization of polypeptide chains and, thus, has to be studied collectively. This merge will allow the cross-referencing of a broad spectrum of multi-disciplinary data facilitating progress in all these fields.

scholarly journals Molecular recognition and self-organization of three-way DNA junctions and supramolecular helicates

2008 ◽  
Vol 64 (a1) ◽  
pp. C105-C105
Author(s):  
R. Boer ◽  
J.M.C.A. Kerckhoffs ◽  
Y. Parajo ◽  
M. Pascu ◽  
A. Oleksy ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Self Organization ◽  
Dna Junctions
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