**Meet the editor**

Lichang Wang, Ph.D., is Professor of Chemistry and Biochemistry at Southern Illinois University Carbondale and the founder and president of MASIS, Inc. Her research activities encompass the area of molecular modeling, such as developing molecular dynamics simulation tools for complex systems and performing dynamics simulations and electronic structure calculations

to study various systems of chemical and energy interests: (a) Transition metal nanoparticles, their toxicity to humans, and their catalytic activities for dehydrogenation of CH4, reduction of O2, direct conversion of coal to liquid fuel, and reactions of ethanol; and (b) Organic dyes for solar cell applications. Details of her research can be found on the website: http:// www.chem.siu.edu/wang. The ultimate goal of her research activities is to replace as many bench top R & D experiments as possible by molecular modeling in order to achieve a greener, as well as economically better, R & D in Chemical and Energy Industries.

Contents

**Preface IX** 

**Part 1 Molecular Dynamics Theory and Development 1** 

**Orbital-Based Molecular Dynamics (FMO-MD) Simulations 3**  Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano and Hirotoshi Mori

**the Formation of Transition Metal Nanoparticles 25** 

Chapter 1 **Recent Advances in Fragment Molecular** 

Chapter 2 **Advanced Molecular Dynamics Simulations on** 

Lichang Wang and George A. Hudson

Ikuo Fukuda and Séverine Queyroy

**Based on a Geometric View and Application to Molecular Dynamics Simulations 43** 

**Dynamics Simulation to Small Systems 57**  Víctor M. Rosas-García and Isabel Sáenz-Tavera

**Thermal Transport at the Nano-Scale 73**  Konstantinos Termentzidis and Samy Merabia

**for** *Ab Initio* **Path-Integral Simulations 107** 

**Dynamics and Nuclear Structure 133**  Gaotsiwe J. Rampho and Sofianos A. Sofianos

**Beyond Classical Treatment 105** 

Chapter 3 **Numerical Integration Techniques** 

Chapter 5 **Molecular Dynamics Simulations and** 

**Part 2 Molecular Dynamics Theory** 

Kin-Yiu Wong

Chapter 7 **Antisymmetrized Molecular** 

Chapter 6 **Developing a Systematic Approach** 

Chapter 4 **Application of Molecular** 
