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Richard Clark

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Richard Clark
Assistant Professor

International Center for Science and Engineering Program (ICSEP)
Faculty of Science & Engineering
Electrical Engineering & Bioscience
Waseda University

Email:  clark (at) aoni.waseda.jp



Research Interests

Research Specialty: Computational Physics Tools for Quantum Biology
My research focuses on the development of computational methods that allow scientists to explore biomolecule interactions inside cells.  The two primary methods are:
“molecular dynamics” (MD) - a computational tool which simulates atom dynamics based on classical physics, thermodynamics, and “fit” energy equations.
“density functional theory” (DFT) - a method which calculates the energy of a small number of atoms by using quantum mechanics, electrostatics (first-principles).
Using these tools, we have gained new insight into both natural cellular processes (such as clarifying the role of enzymes in DNA deamination – a process linked to cancer) as well as novel synthetic biomolecules (such as discovering an externally-driven structural transition in tailor-made peptide nanotubes, PNTs; a molecule that may provide direct control over ion transport into cells and act as a structural backbone for molecular-scale structures).  My current work focuses on the development of efficient methods for exploring “excited state chemistry” reactions in biomolecules.

Keywords: computational physics, molecular dynamics, density functional theory, multi-scale simulation, quantum biology, excited-state chemistry, peptide nanotube, DNA deamination

Classes Taught at Waseda University

Vector Analysis (Math) (Fall)
Calculus in 3 dimensions focusing on science and engineering application.  
Main topics: Vector Math, Vector Calculus, Divergence Theorems, Curvilinear Coordinates.

Intermediate Electricity & Magnetism (Physics) (Fall)
Extension of the basic E&M principles based on full vector calculus.  
Main topics: Static electrostatics/magnetostatics in vacuum.

Advanced Electricity & Magnetism (Physics) (Spring)
Extends the Intermediate class to include materials and an introduction to electrodynamics.  
Main topics: Material effects on E&M (Conductors, Dielectrics, Dia/Para/Ferromagnetism), Faraday’s Law, Light.

Introduction to Computational Physics (Computer Science/Physics) (Spring)
Introduction to the Computer Simulation/Modeling Techniques used to model a wide-range of problems.  Includes an optional C/Fortran project-based weekly tutorial.  
Main topics: Computational Math, Molecular Dynamics, Monte Carlo, Grid-based Methods, Potential Energy Surface (PES) Methods, and Multi-scale “Bridging” techniques.