1. Problem Statement and Motivation Key Achievements and Future Goals Technical Approach Investigator: Hui Lu, Ph.D., Bioengineering, Collaborators: Julio Fernandez (Columbia University), Hongbin Li (U of British Columbia) Mechanical signals play key role in physiological processes by controlling protein conformational changes Uncover design principles of mechanical protein stability Relationship between protein structure and mechanical response; Deterministic design of proteins Atomic level of understanding is needed from biological understanding and protein design principles Identified key force-bearing patch that controlled the mechanical stability of proteins. Discovered a novel pathway switch mechanism for tuning protein mechanical properties. Calculated how different solvent affect protein’s mechanical resistance. Goal: Computationally design protein molecules with specific mechanical properties for bio-signaling and bio-materials. All-atom computational simulation for protein conformational changes – Steered Molecular Dynamics Free energy reconstruction from non-equilibrium protein unfolding trajectories Force partition calculation for mechanical load analysis Modeling solvent-protein interactions for different molecules Coarse-grained model with Molecular dynamics and Monte Carlo simulations

2. Problem Statement and Motivation Key Achievements and Future Goals Technical Approach G.Ali Mansoori, Bio & Chem Eng Depts Prime Grant Support: ARO, KU, UMSL, ANL Diamondoids and Gold Nanoparticle - based nanobiotechnology - Applications for Drug Delivery. Quantum and statistical mechanics of small systems - Development of ab initio models and equations of state of nanosystems. Phase transitions, fragmentations. Molecular dynamics simulation of nano systems - Non-extensivity and internal pressure anomaly. DNA-Dendrimers nano-cluster formation. DNA-Dendrimer Nano-Cluster Electrostatics (CTNS, 2005) Nonextensivity and Nonintensivity in Nanosystems - A Molecular Dynamics Sumulation J Comput & Theort Nanoscience (CTNS,2005) Principles of Nanotechnology (Book) World Scientific Pub. Co (2005) Statistical Mechanical Modeling and its Application to Nanosystems Handbook of Theor & Comput Nanoscience and Nanotechnology (2005) Phase-Transition and Fragmentation in Nano-Confined Fluids J Comput & Theort Nanoscience (2005). Interatomic Potential Models for Nanostructures" Encycl Nanoscience & Nanotechnology (2004). Nanoparticles-Protein Attachment Nano-Imaging (AFM & STM), Microelectrophoresis Ab Initio computations (Applications of Gaussian 98) Nano-Systems Simulations (Molecular Dynamics) Nano-Thermodynamics and Statistical Mechanics

3. Problem Statement and Motivation Key Achievements and Future Goals Technical Approach Investigators: M. Stroscio, ECE and BioE; M. Dutta, ECE Prime Grant Support: ARO, NSF, AFOSR, SRC, DARPA, DHS Coupling manmade nanostructures with biological structures to monitor and control biological processes. For underlying concepts see Biological Nanostructures and Applications of Nanostructures in Biology: Electrical, Mechanical, & Optical Properties, edited by Michael A. Stroscio and Mitra Dutta (Kluwer, New York, 2004). Numerous manmade nanostructures have been functionalized with biomolecules Nanostructure-biomolecule complexes have been used to study a variety of biological structures including cells Interactions between nanostructures with biomolecules and with biological environments have been modeled for a wide variety of systems Ultimate goal is controlling biological systems at the nanoscale Synthesis of nanostructures Binding nanostructures to manmade structures Modeling electrical, optical and mechanical properties of nanostructures Experimental characterization of integrated manmade nanostructure- biological structures