scholarly journals Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology

2006 ◽  
Vol 17 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Kurt W. Kohn ◽  
Mirit I. Aladjem ◽  
John N. Weinstein ◽  
Yves Pommier
Keyword(s):  
Computer Simulation ◽  
Systems Biology ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Structure And Function ◽  
Graphical Notations ◽  
Interaction Map ◽  
And Function ◽  
Network Diagrams

A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. “Heuristic” MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. “Explicit” MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.

scholarly journals Lipidomics at the Interface of Structure and Function in Systems Biology

2011 ◽  
Vol 18 (3) ◽  
pp. 284-291 ◽  
Author(s):  
Richard W. Gross ◽  
Xianlin Han
Keyword(s):  
Systems Biology ◽  
Structure And Function ◽  
And Function

scholarly journals Computer Simulations in Service of Biology

2021 ◽  
Vol 8 ◽  
Author(s):  
Michael Levitt
Keyword(s):  
Computer Simulation ◽  
Structural Biology ◽  
Computer Simulations ◽  
Virtual World ◽  
Computer Game ◽  
Structure And Function ◽  
Important Research ◽  
Scientific World ◽  
The World ◽  
And Function

Computer simulation is an important research tool in today’s scientific world. Computers allow us to perform computations that mimic the behavior of complex (biological) systems in ways that we could not otherwise achieve. You could think of these simulations as a computer game, in which a virtual world is created that works according to certain (e.g., physical) rules. While we play the game, we learn the rules governing this virtual world and its environment, and also the way that we affect this world as players. In this article, I will explain how we use computer simulations in the world of structural biology to study the structure and function of molecules. I will also describe how I think that we could use insights from the world of biology and computer simulations to advance the society that we live in.

Aquamoleculomics: A Thermodynamic Cornerstone of Systems Biology

2021 ◽  
Author(s):  
Zilin Nie ◽  
Yanming Nie
Keyword(s):  
Systems Biology ◽  
Thermodynamic Characteristics ◽  
Living System ◽  
Structure And Function ◽  
Biological Processes ◽  
Modern Biology ◽  
Cell Tissue ◽  
Novel Concept ◽  
And Function ◽  
Current Systems

Systems biology has been established for more than a decade in the post-genomic era. With the help of the computational and mathematical tools, systems biology reconstitutes the entire scenario of the cell, tissue and even organism from the pieces data generated in the past decades. However, the modern biology is mainly focusing on the structure and function of the biomolecule, cell, tissue or organ, which are far from the essence of the life because of missing thermodynamic information. It is doubtable that the current systems biology-based omics is no-how to fully understand the dynamic courses of the structure, function and information in life. For this reason, we promote a novel concept of aquamoleculomics, in which the biological structure and function as well as thermodynamic characteristics and bioinformation of the aquamolecule complexes are included in this theoretical model of systems biology. Water is mother of life, matter and matrix of organism. Indeed, the fundamental roles of H2O molecules in biological processes might be dramatically underestimated. Extremely speaking, H2O networks in the living system might be engaged in all the biological processes including building all the biological structures, the residential places of the motherhood molecules as the honeycombs of honeybees.

A Model for the Control of the Rat Estrous Cycle

1969 ◽  
Vol 91 (2) ◽  
pp. 321-324 ◽  
Author(s):  
Neena B. Schwartz
Keyword(s):  
Computer Simulation ◽  
Theoretical Model ◽  
Estrous Cycle ◽  
Reproductive Cycle ◽  
Adaptive Significance ◽  
Structure And Function ◽  
Reproduction System ◽  
System A ◽  
Cyclic Function ◽  
And Function

This paper first reviews the basic elements of the reproduction system in female mammals and indicates the adaptive significance of the cyclicity of structure and function always observed in this system. A detailed description of the reproductive cycle in the laboratory rat is then presented, and a theoretical model of the control of the rat estrous cycle is described. The purpose of the model is to “explain” the mechanism of cyclic function of reproduction in the rat. Some examples of the heuristic value of the model are then outlined, including the beginning of computer simulation.

scholarly journals Concepts to Reveal Parvovirus–Nucleus Interactions

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1306
Author(s):  
Salla Mattola ◽  
Satu Hakanen ◽  
Sami Salminen ◽  
Vesa Aho ◽  
Elina Mäntylä ◽  
...  
Keyword(s):  
Life Cycle ◽  
Molecular Interactions ◽  
Structure And Function ◽  
Dna Modification ◽  
Nuclear Entry ◽  
Dna Viruses ◽  
Chromatin Interactions ◽  
Nuclear Stage ◽  
And Function ◽  
Induced Changes

Parvoviruses are small single-stranded (ss) DNA viruses, which replicate in the nucleoplasm and affect both the structure and function of the nucleus. The nuclear stage of the parvovirus life cycle starts at the nuclear entry of incoming capsids and culminates in the successful passage of progeny capsids out of the nucleus. In this review, we will present past, current, and future microscopy and biochemical techniques and demonstrate their potential in revealing the dynamics and molecular interactions in the intranuclear processes of parvovirus infection. In particular, a number of advanced techniques will be presented for the detection of infection-induced changes, such as DNA modification and damage, as well as protein–chromatin interactions.

From protoplasmic theory to cellular systems biology: a 150-year reflection

2010 ◽  
Vol 298 (6) ◽  
pp. C1280-C1290 ◽  
Author(s):  
G. Rickey Welch ◽  
James S. Clegg
Keyword(s):  
Systems Biology ◽  
Cell Biology ◽  
Cell Structure ◽  
Structure And Function ◽  
Cellular Systems ◽  
Controversial Issues ◽  
Cell Theory ◽  
History Of ◽  
And Function

Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, “system” character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The origin of the “system” view of the cell dates to the birth of the protoplasm concept. The 150-year history of the role of “protoplasm” in cell biology is traced. It is found that the “protoplasmic theory,” not the “cell theory,” was the key 19th-century construct that drove the study of the structure-and-function of living cells and set the course for the development of modern cell biology. The evolution of the “protoplasm” picture into the 20th century is examined by looking at controversial issues along the way and culminating in the current views on the role of cytological organization in cellular activities. The relevance of the “protoplasmic theory” to 21st-century cellular systems biology is considered.

scholarly journals Integration of multiscale dendritic spine structure and function data into systems biology models

2014 ◽  
Vol 8 ◽  
Author(s):  
James J. Mancuso ◽  
Jie Cheng ◽  
Zheng Yin ◽  
Jared C. Gilliam ◽  
Xiaofeng Xia ◽  
...  
Keyword(s):  
Systems Biology ◽  
Dendritic Spine ◽  
Structure And Function ◽  
Function Data ◽  
Spine Structure ◽  
And Function

scholarly journals Study of Molecular interaction in Binary Mixtures containing N, N-Dimethylformamide and n-Butanol

2021 ◽  
Vol 17 (01) ◽  
pp. 1-8
Author(s):  
BISWAJIT SAMANTARAY ◽  
◽  
MANOJ KUMAR PRAHARAJ ◽  
SMRUTI PRAVA DAS ◽  
◽  
...  
Keyword(s):  
Experimental Data ◽  
Free Energy ◽  
Acoustic Impedance ◽  
Molecular Interaction ◽  
Polar Solvent ◽  
Adiabatic Compressibility ◽  
Structure And Function ◽  
Water Soluble ◽  
Thermodynamical Parameters ◽  
And Function

The acoustic studies of the interactions between alcohol molecules and water soluble polar solvent DMF are significant for understanding the relationships between structure and function of polar molecule like DMF, and for explaining the mechanisms of interaction of alcoholic OH group with an electronegative moiety. In this piece of work Ultrasonic velocity, density and viscosity have been measured at 298 K, 308 K, 318 K and 328 K for mixture of N,N-dimethylformamide (DMF) and n-butanol, the frequency being maintained at a constant value. The experimental data have been used to calculate the acoustical and thermodynamical parameters like adiabatic compressibility, free length, free volume, internal pressure, acoustic impedance, Gibbs free energy

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