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Mechanisms controlling conformational changes of flexible proteins.

John Portman, Department of Physics.

The structural self-organization of protein molecules has fascinated biologists, chemists, and physicists for many years. One way to describe the structural order of the protein molecule as it folds is through changes in flexibility of monomers along the polymer chain. Though the folded state is considerably less flexible than the unfolded state, even folded proteins retain considerable flexibility since the conformation dynamics is essential to function for many proteins. In this talk, I will discuss the results of an analytical model that can describe the flexibility of partially folded proteins. This model is based on the statistical mechanics of a polymer inhomogeneously constrained to the native three-dimensional structure. I will discuss how this model can be used to gain insight into the mechanism of protein folding as well as the mechanism for conformational transitions between two distinct folded conformations.


Biophysics of lipid storage and transport.

Edgar Kooijman, Department of Biological Sciences. 

Neutral lipids, fats, form an important source of energy. However, they are water insoluble and thus have to be packaged in specialized structures in order to be utilized by cells. Two distinct types of structures have evolved to facilitate this packaging in mammals, both based on similar principles. Neutral lipids taken up through the diet need to be delivered to tissues for energy usage, and endogenously synthesized lipids need to be distributed to specialized cells (adipose tissue) or cleared from the body. These transport structures are called apolipoproteins or apolipoprotein particles and include the well known HDL and LDL particles. However, many different types of transport structures exist all with specialized roles in lipid metabolism. Additionally, nearly every cell type has evolved the ability to store neutral lipids intracellularly. These storage structures are named lipid droplets (LDs) and are found primarily in adipocyte tissue. Interestingly, recent cell biological results have shown that these LDs are not merely static storage devices, but are involved in a plethora of cellular functions and also play an important role in several important pathologies. LDs in adipocytes have been shown to fuse with one another to form larger mature LDs and also move around the cell. We are interested in the biophysical principles behind the storage of neutral lipids inside these storage and transport devices. Here I will give a first introduction into the fascinating cell biology of these different particles, talk about several of the many outstanding questions and show some first results on the lipid-protein interactions involved.


Laser tweezers, a tool for single molecular and single particle studies.

Hanbin Mao, Department of Chemistry. 

In this presentation I will introduce laser tweezers as a tool for single molecular and single particle investigations. Invented in the late nineteen eighties, the laser tweezers technique has been used widely in physics and biophysics. Recently, it has started to explore the property of single molecules and single particles. Here I will first discuss the mechanism of laser trapping. I will then provide most recent examples in our lab to demonstrate its application in single molecule and single particle studies.


Focusing light at nanometer scale.

Qihuo Wei, Liquid Crystal Institute.

This talk is to provide an overview of research projects in my research group, and will focus primarily on three subjects: (1) scaling laws in nanoscale bio/chemical sensors; (2) optical nanoantennas for single molecule surface enhanced Raman scattering; and (3) optical transmission through circular and spiral nanotrenches.


First-principles simulations of nanomaterials.

Lan Li, Center for Materials Informatics, Kent State University. 

The electronic structure of C60 and C60 assemblies can be tuned via contact with metals. The well-known example is the superconductivity of alkali-metal-doped C60 solids. With high electron affinity, C60 is often an electron receptor. Employing this characteristic, the I-V characteristics of metal-doped fullerene thin film can be altered by controlling the thickness of metal. Here, we performed first-principles calculations based on density functional theory to investigate the structure, electronic structure and magnetic properties of Fen-C60 complexes. Interfaces that consist of a C60 monolayer, a supporting h-BN/Ni (111) layers, and the transition metal Fen (n = 1−4 & 15) have been thoroughly characterized. Electron transfer has been observed from the Fe ions to the C60 molecules, which leads to the domination of ionic character on the Fe-C60 bonding. Furthermore, the Fen-doped C60 systems show strong hybridizations between s-, d- orbitals of Fe atoms and p-orbital (p-like) of C atoms. The spin of the net transferred electrons from Fen to C60­ is spin minority, which leads to a magnetic moment in C60 opposite to the total magnetic moment of the system.

Metal-C60 complex is also a candidate for hydrogen storage and hydrogen sensor. Pd is a good catalyst for dissociation and storage of hydrogen on the Pd-C60 complex. Hydrogen is sufficiently dissociated in the presence of the Pd atoms/clusters, which assists in bonding of the individual H atoms to the complex.

Like C60, single-walled carbon nanotubes (SWNTs) have many unique properties. To use SWNTs in electronics, we must be able to control whether a nanotube is semiconducting or metallic and if it is semiconducting, to control its band gap. This requires us to control its diameter and its chirality. It is generally believed that a SWNT nucleates as a carbon cap on the catalyst surface, and the SWNT then grows by the root growth mechanism rather than adding atoms to an open tube (tip growth mechanism). We suggest that chirality control can only be achieved at the early nucleation stage, because each cap grows into a particular nanotube. If an epitaxial relationship favors particular caps on a solid catalyst, this would allow to preferentially grow one (n,m) nanotube. We study this idea by first-principles calculations of nanotube caps on the Ni (111) surface. This catalyst could select metallic nanotubes at lower growth temperatures.


Concentrated dyes: media of many uses for light microscopy.

Michael Model, Department of Biological Sciences. 

Dyes at high concentrations have properties that can be used in applications as diverse as 3D profilometry of biological cells and materials, volume measurements, quantitative fluorescence microscopy and quality control of a confocal microscope.

A typical biological cell has significant thickness in the direction of the optical axis (z) of a microscope. However, the microscope shows only the xy plane of a specimen, and information about the z dimension of a cell cannot be easily obtained. Likewise, there are no simple optical methods to measure cellular volume, even though the latter plays an important role in many processes. We address the problem by keeping cells in a shallow chamber and adding a strongly absorbing and nontoxic dye to the medium. Transmission image of such a specimen shows contrast that directly and quantitatively represents cell thickness. We currently work on applications of this technique to several biological systems. A similar approach can be used in materials studies to image the relief of transparent surfaces, in which case nanometer vertical resolution is possible.

The other direction of my research is the development of efficient methods to measure fluorescence. Fluorescence microscopy has traditionally been regarded as a semi-quantitative technique due to problems related to standardization and quantification. However, we now have the ability to compare fluorescence intensities obtained on different wide field and confocal microscopes using moderately fluorescent concentrated dyes as a standard. Furthermore, we can measure the absolute numbers of fluorescent molecules associated with each particular cell in the image. We plan to apply this method to quantification of cancer markers.


Introduction to visual simulation, analysis and acceleration.

Ye Zhao, Department of Computer Science.

Visual simulation models real-world phenomena with physically-based modeling methods. Thanks to the rapidly increasing computational power, it has achieved success in many aspects of computer graphics and visualization. On the other hand, the paradigm also emerges contributing to many scientific domains, to provide fast, interactive and visual tools for numerical solution, information recognition, analysis and decision making. In this talk, we present a concrete example about applying physical models on simulating fluids on consumer PCs with contemporary graphics hardware, an affordable parallel machine, so as to illustrate the start-of-the-art and potential of visual simulation.

The advances in applying physical models and numerical PDE (Partial Differential Equation) solvers for flow simulation, along with the rapid increase in computer power, open a new era in a variety of fields and application domains in computer graphics and visualization. As a unique explicit, simple and inherently-parallel scheme, the lattice Boltzmann method (LBM) has developed into a promising numerical method for simulating fluid flows and modeling physics in fluids. It has achieved great success in the world of computational physics both from the analytical and practical points of view. The LBM scheme excels due to its very efficient and simple computing process for modeling fluid dynamics even in the presence of very complex boundary conditions, such as arbitrarily-shaped obstacles, moving objects, free surfaces and the like. Due to its discrete nature, the LBM lends itself well to efficient interface tracking as to adaptive and multi-resolution approaches, which are both critical for flow simulations in realistic graphics applications. Moreover, its computational pattern, which is similar to cellular automata, is easily parallelizable. This makes the LBM very amenable to acceleration on parallel computers, such as single GPUs (Graphics Processing Unit) and for GPU clusters, enabling it to achieve interactive or real-time flow simulation performance in a scalable fashion.