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Molecular Dynamics Simulations: Concept, Methods, and Applications

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Transdisciplinarity

Part of the book series: Integrated Science ((IS,volume 5))

Summary

Molecular dynamics (MD) is a computer simulation that deals with biological molecules, such as proteins and nucleic acid, and visualizes their movement in atoms and molecules. Computer simulation is executed with these atoms and molecules that are capable of interacting with each other over time and thereby can define the dynamic evolution of the system. MD simulation mimics the changes in biological molecules’ structures over a given time, giving us atomic insights into the change in structure. This data helps us understand biological functions. These simulations give us comprehensive information about the fluctuations and flexibility of the proteins and nucleic acids under study. These approaches are applied to thoroughly study the organization and dynamics of biological molecules, their complexes, and conformational changes in proteins and nucleic acids. Many mysteries, on the femtoseconds scale, have been revealed through the study of these conformational changes. These methods are applied in chemical physics, materials science, and biophysics. MD simulations are often used in computational biology to generate a comprehensive understanding of interactions between proteins and their ligands and address how much these interactions are flexible and shape conformational changes in molecules when a particular mutation is introduced. Currently, it is being used to determine the tertiary structure of proteins from x-ray crystallography and NMR (or Nuclear Magnetic Resonance, a technique used in analytical chemistry for determining the structural properties and purity of samples) experiments.

The molecular dynamics simulation process.

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Acknowledgment

We would like to acknowledge Director (Admin), Mr. Syed Sharique Hussain, Salfia Paramedical Institute Darbhanga, (SPI) Darbhanga, (director_admin@salfiainstitute.edu.in), Dr. Naima Saman (pursuing MD), Dr. Syed Abdul Hakeem, Mrs. Siddiqua Khatoon, all members of Farid/Salfia family, Faridia Hospital, Dr. Faiyaz Ahmad, Chairman, Madhubani Medical College, Madhubani, Dr. Faraz Fatmi (JD(U)), Mr. Ashraf Ali Fatmi (JD(U)), Dr. Shakeel Ahmad (Congress), Mr. Salman Akhtar, Chief Functionary, Nalanda Minority Educational and Welfare Trust, Dr. Muhammad Nezamuddin (Jawed) and Dr. Arifa Nishat, Ruston, LA, USA, Mr. Prashant Kishore, (I-PAC), Dr. David K Mills and Dr. Thomas C Bishop (Louisiana Tech University, Ruston, LA, USA), Dr. Manzoor Alam, Chairman, AIMC, Brother Aman, Aligarh Bachchon Ka Ghar, Aligarh, Hafiz Hassan Badar, Secretary, Hazrat Umar Farooque Academy, Nazra-Ranipur, Mrs. Shahnaz Badar, and motivator for Abdur Razzaque Family, Mr. Saeeduzzafar, (IDB Jeddah) and my life partner, Mrs. Rana Kamal Sufian.

Author information

Authors and Affiliations

  1. Department of Bioengineering, University of California, Riverside, CA, USA

    Mohammad Sufian Badar

  2. Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), Riverside, CA, USA

    Mohammad Sufian Badar

  3. Salfia Paramedical Institute, Darbhanga, India

    Mohammad Sufian Badar

  4. Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India

    Shazmeen Shamsi

  5. PGD (Big Data Analytics), School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India

    Shazmeen Shamsi

  6. Department of Computer Science, Jamia Hamdard University, Delhi, India

    Jawed Ahmed

  7. Jamia Hamdard, New Delhi, India

    Md. Afshar Alam

  8. School of Engineering Science and Technology, Department of Computer Science and Engineering, Jamia Hamdard, New Delhi, India

    Md. Afshar Alam

Authors
  1. Mohammad Sufian Badar
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  2. Shazmeen Shamsi
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  3. Jawed Ahmed
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  4. Md. Afshar Alam
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Corresponding author

Correspondence to Mohammad Sufian Badar .

Editor information

Editors and Affiliations

  1. Universal Scientific Education and Research Network (USERN), Stockholm, Sweden

    Nima Rezaei

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Badar, M.S., Shamsi, S., Ahmed, J., Alam, M.A. (2022). Molecular Dynamics Simulations: Concept, Methods, and Applications. In: Rezaei, N. (eds) Transdisciplinarity. Integrated Science, vol 5. Springer, Cham. https://doi.org/10.1007/978-3-030-94651-7_7

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