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A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartition law, and free energy changes result from entropy fluctuations only. Frequency –wave-number maps show communication between residues involved in slow and fast(More)
Experimental results on grain boundary properties and grain growth obtained using the Electron Backscattered Diffraction (EBSD) technique are compared with the Finite Element simulation results of an Al-foil with a columnar grain structure. The starting microstructure and grain boundary properties are implemented as an input for the three-dimensional grain(More)
This paper will describe modeling microstructure evolution using a combination of our gradient-weighted moving finite elements code, Grain3D and our 3-D unstructured grid generation and optimization code, LaGriT. Grain boundaries evolve by mean curvature motion, and Grain3D allows for the incorporation of grain boundary orientation dependence modeled as(More)
Axonal growth and the formation of synaptic connections are key steps in the development of the nervous system. Here, we present experimental and theoretical results on axonal growth and interconnectivity in order to elucidate some of the basic rules that neuronal cells use for functional connections with one another. We demonstrate that a unidirectional(More)
Given its biocompatibility, elasticity, and gas permeability, poly(dimethylsiloxane) (PDMS) is widely used to fabricate microgrooves and microfluidic devices for three-dimensional (3D) cell culture studies. However, conformal coating of complex PDMS devices prepared by standard microfabrication techniques with desired chemical functionality is challenging.(More)
Detailed knowledge of how the surface physical properties, such as mechanics, topography and texture influence axonal outgrowth and guidance is essential for understanding the processes that control neuron development, the formation of functional neuronal connections and nerve regeneration. Here we synthesize asymmetric surfaces with well-controlled(More)
Hierarchical assembly of self-healing adhesive proteins creates strong and robust structural and interfacial materials, but understanding of the molecular design and structure-property relationships of structural proteins remains unclear. Elucidating this relationship would allow rational design of next generation genetically engineered self-healing(More)
Analysis of x-ray crystal structures has clarified the nature of antibody-antigen interactions, and the conformational basis of specificity and affinity, but does not provide a clear picture of the dynamics of antigen recognition. In particular, we know that primary antibodies can bind a wider variety of ligands than their secondary counterparts--which are(More)
BACKGROUND Protein topology plays a key role in various types of interactions. Topological constraints of a protein are defined by a contact map. We studied the fluctuations of proteins with use of a new approach based on contact map. METHODS An annealing algorithm is used to generate a 3-dimensional protein structure from the contact map. First, we study(More)
63130 # These authors contributed equally. Abstract We report the development of a new technique to screen protein crystallinity quantitatively based on laser-probing spectroscopy with sub-picosecond resolution. First, we show theoretically that the temperature dependence of the refractive index of a polymeric protein is correlated to its crystallinity.(More)