Molecular dynamics simulation: a tool for exploration and discovery using simple models

Abstract

Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by MD simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids, the Taylor-Couette and Rayleigh-Bénard instabilities, can not only be observed within the limited length and time scales accessible to MD, but even quantitative agreement can be achieved. Simulation of highly counterintuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder, and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly, and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored, and what might be discovered when sufficient resources are brought to bear on a problem.

21 pages, 20 figures (v2 - minor text addition)

References in corpus (22)

• Patterns and Collective Behavior in Granular Media: Theoretical Concepts
• Virus shapes and buckling transitions in spherical shells
• Dynamic Pathways for Viral Capsid Assembly
• Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
• Self-assembly of polyhedral shells: A molecular dynamics study
• Role of reversibility in viral capsid growth: A paradigm for self-assembly
• A Precise Packing Sequence for Self-Assembled Convex Structures
• Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus Size
• Modelling the Self-Assembly of Virus Capsids
• Transitions in the Horizontal Transport of Vertically Vibrated Granular Layers
• An irreversible growth model for virus capsid assembly
• Radial and axial segregation of granular matter in a rotating cylinder: A simulation study
• The Dynamics of Granular Segregation Patterns in a Long Drum Mixer
• Stochastic kinetics of viral capsid assembly based on detailed protein structures
• Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles
• Modeling capsid self-assembly: Design and analysis
• Enhanced molecular dynamics performance with a programmable graphics processor
• Hexagonal convection patterns in atomistically simulated fluids
• A new mechanism for granular segregation
• Stratified horizontal flow in vertically vibrated granular layers
• Simulated three-component granular segregation in a rotating drum
• Competition between Spiral-Defect Chaos and Rolls in Rayleigh-Benard Convection

Cited by in corpus (4)

• A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit
• Packaging stiff polymers in small containers: A molecular dynamics study
• Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
• Molecular Hydrodynamics: Vortex Formation and Sound Wave Propagation