In-Silico Approaches to Macromolecular Chemistry

1st Edition - February 24, 2023
Editors: Minu Elizabeth Thomas, Jince Thomas, Sabu Thomas, Haya Kornweitz
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 0 9 9 5 - 2
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 0 9 9 6 - 9

Computational approaches offer researchers unique insights into the structure, characteristics, and properties of macromolecules. However, with applications across a broad range of… Read more

In-Silico Approaches to Macromolecular Chemistry

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Computational approaches offer researchers unique insights into the structure, characteristics, and properties of macromolecules. However, with applications across a broad range of areas, various methods have been developed for exploring macromolecules in in silico; therefore, it can be difficult for researchers to select the most appropriate method for their specific needs. Covering both biopolymers and synthetic polymers, In-Silico Approaches to Macromolecular Chemistry familiarizes readers with the theoretical tools and software appropriate for such studies. In addition to providing essential background knowledge on both computational tools and macromolecules, the book presents in-depth studies of in silico macromolecule chemistry, discusses and compares these with experimental studies, and highlights the future potential for such approaches.

Written by specialists in their respective fields, this book helps students, researchers, and industry professionals gain a clear overview of the field, and furnishes them with the knowledge needed to understand and select the most appropriate tools for conducting and analyzing computational studies.

Cover image
Title page
Table of Contents
Copyright
Contributors
Chapter 1: Why are in silico approaches necessary for macromolecular chemistry?
Abstract
1: Introduction
2: Importance of computational chemistry for macromolecular studies
3: Conclusion
References
Further reading
Chapter 2: Multiscale theoretical tools for in silico macromolecular chemistry and engineering
Abstract
1: Introduction
2: Molecular scale modeling
3: Microscale modeling
4: Mesoscale modeling
5: Macro-scale modeling
6: Impact of previous scales on material level
7: Conclusions and summary of in silico tools
References
Chapter 3: Macromolecular chemistry: An introduction
Abstract
1: Introduction
2: Macromolecules chemistry
3: Proteins
4: Nucleic acids
5: Polymers
6: Lipids and fatty acids
7: Carbohydrates
8: Summary
References
Chapter 4: In silico approaches for carbohydrates
Abstract
1: Introduction
2: Selected in silico methods for carbohydrates
3: Conclusions
References
Chapter 5: In silico approaches for lipids: Interactions of membrane-active agents with lipids
Abstract
1: Introduction
2: Lipid structures and classifications
3: Lipids interact with membrane-bound agents
4: In silico numerical computation addressing the energetics of drugs in membranes
5: In silico MD simulations detecting energies of the drug-lipid interactions
6: Universal probability functions on drug-target interactions revealed by the in silico experimental results
7: Conclusions
References
Chapter 6: In silico approaches and challenges for quantum chemical calculations on macromolecules
Abstract
1: The computational scaling bottleneck of quantum calculations on large molecules
2: An introduction to the kernel energy method as a solution to the computational scaling bottleneck
3: The lead-up to the kernel energy method formalism
4: The Kernel Energy Method (KEM)
5: The scaling of the Kernel Energy Method
6: Closing remarks
References
Chapter 7: Applications of in silico quantum chemical calculations to large systems: The Kernel Energy Method
Abstract
Acknowledgments
1: The challenges of in silico quantum calculations on large systems and a solution: The Kernel Energy Method (KEM)
2: Early successes of the Kernel Energy Method: Large biomolecules
3: The Kernel Energy Method and the calculation of response properties
4: The Kernel Energy Method and the calculation of properties of atoms in molecules
5: Closing remarks
References
Chapter 8: Computational genomics for understanding of DNA-DNA and protein-protein similarity
Abstract
Authors' contributions
Funding
Availability of data and materials
Competing interests
1: Background
2: Indexing, query of reference sequence information and storage compression in sequence homology computation for local mapping and alignment
3: Algorithms for re-sequencing to indexed DNA as footprint reference
4: Amino acid substitution in modeling of evolutionary distance
5: Position-weighted matrix-based iterative methods for application to gapped sequence mapping in global alignment
6: Sequence binding affinity and position weight matrix for determination of transcription factor-sequence binding probability
7: Gapless position weight matrix application for determination of short sequence alignments
8: Genome walk clusters for modeling of restriction site or response element distribution
9: Expectation maximization for modeling of mRNA splice isoform variability, protein-protein alignment, or DNA-binding site enrichment
10: Model-based analysis of transcription factor binding response elements
11: Intergene base tropy normalization in determination of gene horizontal alignment
12: Genome assembly maps in arrangement of DNA segments
13: Advances in re-sequencing of proteome, DNA or RNA polymorphism mapping to phylogeny convergence
14: Conclusions
References
Chapter 9: In silico approaches to biomacromolecules through conformational dynamics and catalysis
Abstract
1: Introduction
2: Methods
3: Case studies in biomacromolecules
4: Conclusion
References
Further reading
Chapter 10: In silico approaches for olefin polymerization using transition metal catalyst systems
Abstract
1: Introduction
2: Procatalyst
3: Activators and catalyst activation
4: Nature of active sites
5: Olefin polymerization mechanism
6: Conclusion
References
Chapter 11: In silico approaches for elastomers
Abstract
1: Introduction
2: In silico approaches
3: Case studies
4: Concluding remarks
References
Chapter 12: In silico approaches for aerogel
Abstract
Acknowledgments
1: Introduction
2: Atomic scale
3: Nanoscale
4: Mesoscale and beyond
5: Conclusions and future perspectives
References
Chapter 13: In silico approaches for xenobiotic polymers and their degradation mechanism
Abstract
1: Introduction
2: In silico application of organic and inorganic-based compounds as a source of xenobiotic pollution in the environment
3: Application of molecular dynamics simulation of enzymes for bioremediation of xenobiotic polymers
4: Application of molecular docking and catalysis simulation of enzymes for bioremediation of xenobiotic polymers
5: Application of numerous in silico techniques and modes of action involved in the bioremediation and degradation pathways prediction using current resources for these xenobiotic polymers
6: Conclusion and future recommendation
References
Chapter 14: In silico approaches for polymeric nanocomposites
Abstract
Acknowledgments
1: Introduction
2: Establishing the structure-property-processing relationship by molecular simulations
3: Concluding remarks
References
Chapter 15: In silico studies of macromolecules as sensors
Abstract
1: Introduction
2: Materials and methods
3: Results
4: Conclusions
References
Chapter 16: Are computational approaches critically important for solving real-world problems?
Abstract
1: Introduction
2: Methods often used in in silica research of macromolecules
3: Real-world problems studied using in silico research in the last 30 years
4: Conclusion
References
Further reading
Appendix: Mathematical descriptions and methods used in the in silico macromolecular analysis
A: Vectors
B: Complex numbers
C: Matrices and determinants
D: Probability
E: Calculus
F: Differential equation
G: Power series
Index

Minu Elizabeth Thomas

Minu Elizabeth Thomas is a researcher with the division of physical chemistry at Mahatma Gandhi University. She has particular expertise in the field of computational chemistry, using quantum chemistry methods to model and analyze the characteristics and properties of molecular structures. She has authored 3 publications.

Affiliations and expertise

Researcher, School of Chemical Sciences, Mahatma Gandhi University, Kerala, India

Jince Thomas

Dr. Jince Thomas is the Chief Minister's Nava Kerala Post-Doctoral Fellow at the International and Inter University Centre for Nanoscience and Nanotechnology at Mahatma Gandhi University in Kerala, India. Previously, he worked as an Assistant Professor on contract at the same institution. He earned his Ph.D. in Chemistry from Mahatma Gandhi University in 2022 under the guidance of Prof. Sabu Thomas. During 2016-2017, he worked as a project assistant on an Indo-Malaysian project in collaboration with University Technology Mara, Malaysia. Additionally, he was a visiting student at Ariel University in Israel and the University of Tennessee Knoxville, USA. Dr. Jince has contributed to numerous publications, book chapters, and edited books, with his research interests focused on polymeric membranes, electrolytes, polymer nanocomposites, and electrochemistry.

Affiliations and expertise

Post-Doctoral Fellow, International and Inter University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kerala, India

Sabu Thomas

Prof. Sabu Thomas is a Professor of Polymer Science and Engineering and the Director of the School of Energy Materials at Mahatma Gandhi University, India. Additionally, he is the Chairman of the Trivandrum Engineering Science & Technology Research Park (TrEST Research Park) in Thiruvananthapuram, India. He is the founder director of the International and Inter-university Centre for Nanoscience and Nanotechnology at Mahatma Gandhi University and the former Vice-Chancellor of the same institution.

Prof. Thomas is internationally recognized for his contributions to polymer science and engineering, with his research interests encompassing polymer nanocomposites, elastomers, polymer blends, interpenetrating polymer networks, polymer membranes, green composites, nanocomposites, nanomedicine, and green nanotechnology. His groundbreaking inventions in polymer nanocomposites, polymer blends, green bionanotechnology, and nano-biomedical sciences have significantly advanced the development of new materials for the automotive, space, housing, and biomedical fields. Dr. Thomas has been conferred with Honoris Causa (DSc) by the University of South Brittany, France.

Affiliations and expertise

Professor and Director, International and Interuniversity Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, India

Haya Kornweitz

Prof. Haya Kornweitz is head of the Department of Chemical Science at Airel University, Israel. She has expertise in the fields of Computational Chemistry (molecular and solid state), Theoretical chemistry and Molecular dynamics, studying the geometry and thermodynamics of molecules and exploring the mechanisms of considered reactions. Prof Kornweitz has published 42 papers in the field and was an editor of two journal special issues (J. Coord. Chem. and in Israel Journal of Chemistry).

Affiliations and expertise

Head of the Department of Chemical Sciences, Airel University, Israel

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In-Silico Approaches to Macromolecular Chemistry

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Minu Elizabeth Thomas

Jince Thomas

Sabu Thomas

Haya Kornweitz

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