Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems

Author: Kim, Hyungjun

Year: 2009

Degree: Dissertation (Ph.D.)

Advisor: Goddard, William A., III

Committee Members: McKoy, Basil Vincent; Heath, James R.; Beauchamp, Jesse L.; Davis, Mark E.; Goddard, William A., III

Option: Chemistry; Physics

DOI: 10.7907/0PFF-R531

Abstract

Multiscale and multiphysics simulation strategy is important to investigate complex problems in nature because it provides a systematic method to understand underpinning physics of the systems depending on the size. In this thesis, we discuss how such multiscale and multiphysics simulation framework can explain and rationalize the experimental observations in several nano- and biosystems. Furthermore, we exhibit the computational simulation methods that play major roles to rationally design novel materials with desired properties in next generation nano electronic devices, alternative energy materials, life science, and so on.

Chapter 1 reviews the significance of multiscale and multiphysics simulation strategy. In this chapter, we briefly discuss the multiscale and multiphysics natures in nano- and bio-systems, and detailed examples are contained in the next chapters. Chapter 2 introduces an electric field induced conformational change mechanism, which is responsible for the unique current-voltage (I-V) behavior of nano device, negative differential resistance (NDR). In Chapter 3, the on/off kinetics of the Stoddart-Heath rotaxane-based programmable molecular electronic switch is discussed in terms of the free energy quantities. Chapter 4 explores sodium diffusion through the aluminum-doped zeolite BEA system, and the effect of water uptake amount is thoroughly discussed. This has importance for the application of zeolite to proton exchange membranes for fuel cells (PEMFC). In Chapters 5 and 6, the ion mobilities of tertiary and quaternary ammonium cations (precursors for lipids), and phosphatidylcholine (PC) lipid cations are investigated, respectively. In order to compute the ion mobilities of the precursors and entire lipids, we develop a modified trajectory (TJ) method dealing with the complicated integrals of interaction terms. QM and MD simulations are performed to determine the structures and charge distributions. In Chapter 7, we study how the model lung system of lipid monolayer with surfactant protein B (SP-B) responds to ozone introduction. In parallel with the field induced droplet ionization (FIDI) mass spectrometry study, MD simulations identify the distinct ozone reaction mechanism at the interface, and the role of SP-B at the pulmonary surfactant (PS) system on the oxidative stresses.

From these studies, we suggest various multiscale and multiphysics modeling approaches depending on the characteristics of systems and objectives. These efforts allow us to overcome the limited time- and length-scales of the monoscale simulations. In addition, we expect that an establishment of such multiscale modeling procedures will invoke interdisciplinary studies by tightly combining the developments occurring independently across fields.

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