Book contents
- Frontmatter
- Contents
- Preface
- 1 Introduction and Overview
- 2 Preparatory Concepts
- 3 The Governing Equations for an Electrically Conducting Fluid
- 4 The Essentials of Viscous Flow
- 5 Heat and Mass Transfer Phenomena in Channels and Tubes
- 6 Introduction to Electrostatics
- 7 Elements of Electrochemistry and the Electrical Double Layer
- 8 Elements of Molecular and Cell Biology
- 9 Electrokinetic Phenomena
- 10 Essential Numerical Methods
- 11 Molecular Simulations
- 12 Applications
- Appendix A Matched Asymptotic Expansions
- Appendix B Vector Operations in Curvilinear Coordinates
- Appendix C Web Sites
- Appendix D A Semester Course Syllabus
- Bibliography
- Index
11 - Molecular Simulations
Published online by Cambridge University Press: 05 February 2013
- Frontmatter
- Contents
- Preface
- 1 Introduction and Overview
- 2 Preparatory Concepts
- 3 The Governing Equations for an Electrically Conducting Fluid
- 4 The Essentials of Viscous Flow
- 5 Heat and Mass Transfer Phenomena in Channels and Tubes
- 6 Introduction to Electrostatics
- 7 Elements of Electrochemistry and the Electrical Double Layer
- 8 Elements of Molecular and Cell Biology
- 9 Electrokinetic Phenomena
- 10 Essential Numerical Methods
- 11 Molecular Simulations
- 12 Applications
- Appendix A Matched Asymptotic Expansions
- Appendix B Vector Operations in Curvilinear Coordinates
- Appendix C Web Sites
- Appendix D A Semester Course Syllabus
- Bibliography
- Index
Summary
Introduction
In this chapter, the focus is on presenting the fundamentals of molecular simulations, particularly molecular dynamics (MD) and its derivatives, particularly nonequilibrium molecular dynamics (NEMD), or MD in a system that is exposed to an external field. The number of molecular simulation tools has grown substantially over the last few years, and it would be impossible to mention all the applications that have appeared in the literature. MD simulations have been used in a variety of ways; four of the most important ways in the context of this text that such calculations have been used are as follows:
Calculating transport properties of new fluids and mixtures for which such properties have not been measured or as a test of the accuracy of such experimental measurements
Predicting the equilibrium conformation of complex biomolecules and polymers
Verifying fluid dynamics boundary conditions (Koplik et al., 1989)
Predicting the flow of pure fluids and complex mixtures in very small channels and circular pores, where the continuum approximation may break down and where direct experimental measurements are not available
Indeed, it is the last class of problems that is of particular interest in this chapter. It is certainly to be noted that while restricted to very short length and time scales, molecular simulations provide information that cannot be found any other way.
As has been seen throughout this book, ionic and biomolecular transport devices are now being used for drug development and delivery, single molecule manipulation, detection and transport, and rapid molecular analysis.
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- Chapter
- Information
- Essentials of Micro- and NanofluidicsWith Applications to the Biological and Chemical Sciences, pp. 447 - 474Publisher: Cambridge University PressPrint publication year: 2012