Introduction to Molecular Computation

2016 ◽  
pp. 719-743
Author(s):  
Angshuman Bagchi
Keyword(s):  
Molecular Biology ◽  
Biological Membranes ◽  
Computational Techniques ◽  
Molecular Architecture ◽  
Molecular Computation ◽  
Computation Techniques ◽  
Comparative Analyses ◽  
Molecular Logic ◽  
Computer Scientists ◽  
Molecular Computations

The present chapter deals with the topic Molecular Computation. The chapter first defines the basic terminologies associated with the processes. The chapter discusses the basic molecular biology and DNA and membranes. Emphases are given on the structural arrangements of DNA and the molecular architecture of biological membranes. The chapter also focuses on the molecular logic behind the applications of DNA and bimolecular membranes in computations. There are discussions on the current researches that are going on in the field of DNA and membrane computations. There are comparative analyses of the existing computational techniques with molecular computations. There are very few reports that deal with the underlying basics of molecular computation techniques. Thus the chapter may be a first hand guide for researchers interested in the field. The chapter is written for the benefits of both the biologists as well as computer scientists.

Establishing a model to demonstrate physical and mathematical properties of chromatin fibres in fission yeast cells - Research in the Molecular Biophysics Lab at Hiroshima University

Impact ◽  
2018 ◽  
Vol 2018 (3) ◽  
pp. 89-91
Author(s):  
Shin-ichi Tate
Keyword(s):  
Molecular Biology ◽  
Yeast Cells ◽  
Molecular Architecture ◽  
Ministry Of Education ◽  
Cellular Functions ◽  
Sports Science ◽  
Cellular Events ◽  
And Function ◽  
Education Culture ◽  
Open The Doors

The field of molecular biology has provided great insights into the structure and function of key molecules. Thanks to this area of research, we can now grasp the biological details of DNA and have characterised an enormous number of molecules in massive data bases. These 'biological periodic tables' have allowed scientists to connect molecules to particular cellular events, furthering scientific understanding of biological processes. However, molecular biology has yet to answer questions regarding 'higher-order' molecular architecture, such as that of chromatin. Chromatin is the molecular material that serves as the building block for chromosomes, the structures that carry an organism's genetic information inside of the cell's nucleus. Understanding the physical properties of chromatin is crucial in developing a more thorough picture of how chromatin's structure relate to its key cellular functions. Moreover, by establishing a physical model of chromatin, scientists will be able to open the doors into the true inner workings of the cell nucleus. Professor Shin-ichi Tate and his team of researchers at Hiroshima University's Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), are attempting to do just that. Through a five-year grant funded by the Platform for Dynamic Approaches to Living Systems from the Ministry of Education, Culture, Sports, Science and Technology, Tate is aiming to gain a clearer understanding of the structure and dynamics of chromatin.

scholarly journals Molecular Computing and Bioinformatics

Molecules ◽  
2019 ◽  
Vol 24 (13) ◽  
pp. 2358
Author(s):  
Xin Liang ◽  
Wen Zhu ◽  
Zhibin Lv ◽  
Quan Zou
Keyword(s):  
Organic Chemistry ◽  
Molecular Biology ◽  
Smart Materials ◽  
Close Relationships ◽  
Molecular Computing ◽  
The Core ◽  
Computer Scientists ◽  
Novel Algorithms ◽  
Silicon Based ◽  
Molecular Computers

Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers. Molecular computing is a branch of computing that uses DNA, biochemistry, and molecular biology hardware, instead of traditional silicon-based computer technologies. Research and development in this area concerns theory, experiments, and applications of molecular computing. The core advantage of molecular computing is its potential to pack vastly more circuitry onto a microchip than silicon will ever be capable of—and to do it cheaply. Molecules are only a few nanometers in size, making it possible to manufacture chips that contain billions—even trillions—of switches and components. To develop molecular computers, computer scientists must draw on expertise in subjects not usually associated with their field, including organic chemistry, molecular biology, bioengineering, and smart materials. Bioinformatics works on the contrary; bioinformatics researchers develop novel algorithms or software tools for computing or predicting the molecular structure or function. Molecular computing and bioinformatics pay attention to the same object, and have close relationships, but work toward different orientations.

Molecular Biology of Protein-Protein Interactions for Computer Scientists

2009 ◽  
pp. 1-13 ◽  
Author(s):  
Christian Schönbach
Keyword(s):  
Molecular Biology ◽  
Protein Interactions ◽  
Wnt Signaling Pathway ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Detection Technology ◽  
Challenges And Opportunities ◽  
Computer Scientists ◽  
Assay Methods

Advances in protein-protein interaction (PPI) detection technology and computational analysis methods have produced numerous PPI networks, whose completeness appears to depend on the extent of data derived from different PPI assay methods and the complexity of the studied organism. Despite the partial nature of human PPI networks, computational data integration and analyses helped to elucidate new interactions and disease pathways. The success of computational analyses considerably depends on PPI data understanding. Exploration of the data and verification of their quality requires basic knowledge of the molecular biology of PPIs and familiarity with the assay methods used to detect PPIs. Both topics are reviewed in this chapter. After introducing various types of PPIs the principles of selected PPI assays are explained and their limitations discussed. Case studies of the Wnt signaling pathway and splice regulation demonstrate some of the challenges and opportunities that arise from assaying and analyzing PPIs. The chapter is concluded with an extrapolation to human systems biology that offers a glimpse into the future of PPI networks.

Molecular computation: Molecular logic gets loaded

2005 ◽  
Vol 4 (1) ◽  
pp. 15-16 ◽  
Author(s):  
A. P. De Silva
Keyword(s):  
Molecular Computation ◽  
Molecular Logic

scholarly journals Parasites and their (endo)symbiotic microbes

Parasitology ◽  
2018 ◽  
Vol 145 (10) ◽  
pp. 1261-1264 ◽  
Author(s):  
Vyacheslav Yurchenko ◽  
Julius Lukeš
Keyword(s):  
Molecular Biology ◽  
Microbial Ecology ◽  
Host Cell ◽  
High Frequency ◽  
Symbiotic Bacteria ◽  
Biological Complexity ◽  
Comparative Analyses ◽  
Modern Molecular Biology ◽  
The Impact

AbstractThanks to modern molecular biology methods, our understanding of the impact of (endo)symbiotic bacteria on parasitic protists and helminths is growing fast. In this issue, 9 papers have been brought together that describe various facets of the relationships between these microorganisms, reveal their range and high frequency, as well as their capacity to create novel biological complexity. Comparative analyses of these host–endosymbiont interactions indicate that there may be no discrete types of relationships but rather a continuum ranging from a dispensable endosymbiont minimally integrated within the host cell to organelles, such as mitochondria and plastids that evolved into an indispensable, deeply integrated components of the cell. We hope that this series of studies on parasites and (endo)symbiotic bacteria will increase awareness about these relationships and their representation in microbial ecology models.

scholarly journals The 1st international workshop on computational social choice

2008 ◽  
Vol 23 (2) ◽  
pp. 213-215 ◽  
Author(s):  
ULLE ENDRISS
Keyword(s):  
Artificial Intelligence ◽  
Social Choice ◽  
Computer Science ◽  
Multiagent Systems ◽  
Choice Theory ◽  
International Workshop ◽  
Social Choice Theory ◽  
Computational Techniques ◽  
Computational Social Choice ◽  
Computer Scientists

AbsractComputational social choice is a new discipline currently emerging at the interface of social choice theory and computer science. It is concerned with the application of computational techniques to the study of social choice mechanisms, and with the integration of social choice paradigms into computing. The first international workshop specifically dedicated to this topic took place in December 2006 in Amsterdam, attracting a mix of computer scientists, people working in artificial intelligence and multiagent systems, economists, game and social choice theorists, logicians, mathematicians, philosophers, and psychologists as participants.

scholarly journals Fluorescent logic systems for sensing and molecular computation: structure–activity relationships in edge-detection

2015 ◽  
Vol 185 ◽  
pp. 337-346 ◽  
Author(s):  
Jue Ling ◽  
Gaowa Naren ◽  
Jessica Kelly ◽  
Adam Qureshi ◽  
A. Prasanna de Silva
Keyword(s):  
Edge Detection ◽  
Molecular Computation ◽  
Structure Activity Relationships ◽  
Molecular Logic ◽  
Structure Activity ◽  
Detection Of Objects ◽  
Logic Systems ◽  
New Applications

Molecular logic-based computation continues to throw up new applications in sensing and switching, the newest of which is the edge detection of objects. The scope of this phenomenon is mapped out by the use of structure–activity relationships, where several structures of the molecules and of the objects are examined. The different angles and curvatures of the objects are followed with good fidelity in the visualized edges, even when the objects are in reverse video.

Electron Diffraction of Wet Biological Membranes

1974 ◽  
Vol 32 ◽  
pp. 158-159
Author(s):  
S.W. Hui ◽  
D.F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Biological Membranes ◽  
Small Areas ◽  
Electron Diffraction Technique ◽  
Electron Microscopes ◽  
Collection Time ◽  
Camera Length

The development of the hydration stages for electron microscopes has opened up the application of electron diffraction in the study of biological membranes. Membrane specimen can now be observed without the artifacts introduced during drying, fixation and staining. The advantages of the electron diffraction technique, such as the abilities to observe small areas and thin specimens, to image and to screen impurities, to vary the camera length, and to reduce data collection time are fully utilized. Here we report our pioneering work in this area.

Electron Microscopy in Molecular Biology

1967 ◽  
Vol 25 ◽  
pp. 2-3
Author(s):  
Cecil E. Hall
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Noise Level ◽  
Molecular Structures ◽  
Material Structure ◽  
The Arts ◽  
Shadow Casting ◽  
Electron Image ◽  
High Degree ◽  
Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

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