Dilip Gersappe - US grants

0079410
Gersappe
This is an award for theoretical and computational research on polymer nanocomposites. Polymer nanocomposites are a new class of materials that are formed when nanometer sized inorganic particles (fillers) are mixed into a polymer matrix. The large surface area presented by these fillers, coupled with the ability to control the interactions between the fillers and the matrix offers the possibility of the development of a new material that can find potential applications in a wide variety of areas give their extraordinary properties: their light-weight but extremely high mechanical strength, their selective filtering capacity and their high thermal stability. Indeed, polymer nanocomposites are being touted as the next generation of materials in applications as diverse as automobile parts and bone fixation materials. Yet, a fundamental knowledge of the processes by which these small nanoscale particles enhance the strength of the material is still unknown. While advances in synthetic methods have led to a precise control of structures at the nanometer scale, the development of a theoretical framework that can predict macroscopic properties of polymers in such nanostructured environments from their microstructural details has not kept pace with the synthetic advances. This is because macroscopic assumptions break down when the critical length scale of the environment is on the order of a few molecular sizes. It is this gap that will be addressed in this research. Thus, the aim is to understand the molecular mechanisms that are responsible for the extraordinary mechanical properties of the nanocomposite.

The approach to be taken here uses a combination of mean field methods and molecular dynamics simulations to extract the critical parameters necessary to bridge the gap between the nanoscale (where the critical assemblies exist) and the mesoscales (where the prediction of physical properties takes place). Numerical self-consistent field calculations combined with a netwrok formation theory will be used to focus parallel molecular dynamics simulations into those regions of phase space where one can determine the critical factors that control the response of the nanocomposite to external load.
%%%
This is an award for theoretical and computational research on polymer nanocomposites. Polymer nanocomposites are a new class of materials that are formed when nanometer sized inorganic particles (fillers) are mixed into a polymer matrix. The large surface area presented by these fillers, coupled with the ability to control the interactions between the fillers and the matrix offers the possibility of the development of a new material that can find potential applications in a wide variety of areas give their extraordinary properties: their light-weight but extremely high mechanical strength, their selective filtering capacity and their high thermal stability. Indeed, polymer nanocomposites are being touted as the next generation of materials in applications as diverse as automobile parts and bone fixation materials. Yet, a fundamental knowledge of the processes by which these small nanoscale particles enhance the strength of the material is still unknown. While advances in synthetic methods have led to a precise control of structures at the nanometer scale, the development of a theoretical framework that can predict macroscopic properties of polymers in such nanostructured environments from their microstructural details has not kept pace with the synthetic advances. This is because macroscopic assumptions break down when the critical length scale of the environment is on the order of a few molecular sizes. It is this gap that will be addressed in this research. Thus, the aim is to understand the molecular mechanisms that are responsible for the extraordinary mechanical properties of the nanocomposite.
***

Abstract
CTS-0103470

NER: A Novel Concept for Electrophoretic Separation of Long DNA Molecules with High Resolution at Nanoscale Dimensions.

Vladimir A. Samuilov and Dilip Gersappe
State University of New York Stony Brook


The recent advances in molecular biology rely on improved techniques for the separation of long (multi-kilobasepairs and megabasepairs) DNA molecules. Current methods employ electrophoresis of DNA molecules in different sieving matrixes, such as junction points in a gel and the entanglements in polymer solutions. Separation of DNA by size, in particular, is at the heart of genome mapping and sequencing and is likely to play an increasing role in diagnosis. There have been important advances in fast-developing and innovative technology like elechophoresis on microchips. In the implementation of micro-fabricated systems for electrophoresis based on silicon technology, the interaction of DNA molecules with the surfaces of the devices should be taken into account in analyzing the mechanisms of the separation. This research introduces a novel approach to the liquid-solid interface as the separation medium and to the mechanism of electrophoresis itself at nanoscale dimensions. Also, a new concept of loading of the DNA sample onto a microchip is considered.

Specifically the study considers the electrical transport properties of long DNA molecules at a flat liquid-semiconductor interface. One-dimensional positioning of DNA molecules on a silicon surface is accomplished by a simple physical alignment process using capillary forces applied by the receding front of an evaporating drop containing DNA molecules. A diblock-copolymer system, self-assembled with L-B technique, is used to produce patterns at the nanometer length scale, which are used as a template for introducing metal nanopatterns on semiconductor surfaces to serve as DNA separation media. Success in this effort will make possible more rapid and more precise DNA analyses for a variety of applications and provide an important new tool for genetic analyses.

NIRT: Molecular Assembly for Hybrid Electronics
Abstract

This proposal was received in response to Nanoscale Science and Engineering initiative, NSF 02-148, category NIRT. The extension of integrated circuits into sub-10-nm range promises enormous benefits for computing, networking, and signal processing. However, fabrication of such devices using current paradigms based on CMOS and current VLSI technology are not possible. We believe that this crisis may only be resolved by a radical paradigm shift, which would simultaneously change the approach to fabrication of electron devices and to VLSI circuit architecture. Our approach is to use a biologically inspired approach called "Self-Evolving Neuromorphic Networks". This approach is based on artificial models of the neocortex and is structured to have a high degree of parallelism and intrinsic redundancy. In this approach molecular circuit elements, "self-assembled" by molecular chemistry, can be allowed to grow randomly, forming circuit elements (molecular transistors), which connect lithographically patterned metal grids. However, the random aspect of molecular self-assembly has to be carefully understood and controlled. At present, there is no detailed understanding of this process. It is this crucial gap that we address in this proposal. The devices that we are proposing need molecular wires that can switch into and out of a conductive state. The molecules bridge the metal wires with inherent randomness. Our aims are to predict and control the bridging and switching, through deterministic chemistry of the molecule-metal interaction, as well as through a statistical analysis of the assembly process. To accomplish these aims, we have a diverse team, which will interact strongly across the engineering/chemistry/physics boundaries. As part of the outreach of this project we plan to use the NIRT as a forum in which we will provide new types of educational settings for students (undergraduate and graduate) and high school teachers, and adopt a flexible program of research guided by feedback between theory and experiment, chemistry and physics and engineering.

Tremendous technological advances in miniaturization have enabled more and more transistors to be packed onto a silicon chip. However, the reduction of feature size on chips is limited not just by the resolution of the fabrication process, but also by the problem of quantum and classical fluctuations. Consequently, below a limiting dimension that we have nearly reached, a new paradigm that goes beyond conventional solid state electronics has to be developed for the next generation of electronics devices. In this project, we propose a new paradigm that is based on an artificial model of the neocortex: In which molecular circuits are assembled in a manner similar to the synaptic connections present in the brain. Our paradigm if realized offers the possibility of the design of the next generation of computational devices, with speeds that, in theory, could be 10 orders of magnitude faster than the fastest existing parallel supercomputer.

DESCRIPTION (provided by applicant): We propose to develop a novel methodology to separate DNA and related biomolecules using nanostructured surfaces. We will use a combination of theoretical and experimental methods to study electrophoresis of charged biological molecules on patterned surfaces. The goal is to understand the fundamental mechanisms which control the dynamics near surfaces and to formulate predictive models which will allow the engineering of high resolution separation devices with optimum throughput and chemical selectivity. Nanoscale patterns will be imprinted using polymer self assembly, while more complicated micron scale structures with a combination of topological and chemical patterns will be manufactured by micro-contact printing. Electrophoresis will be performed and the mobility of DNA chains on these various surfaces will be observed either by confocal, near field microscopy, or CCD coupled video imaging. Fluorescence recovery after photobleaching (FRAP) coupled with Linear Dichroism detection (FDLD) will be used to measure surface relaxation times and diffusivity. The measurements will be performed as a function of pattern morphology, buffer concentration, chemical interactions, and chain structure. From these measurements we should be able to elucidate the relative importance of surface interactions, surface charges, electroosmotioc flow, and topological confinement in the surface dynamics of charged molecules. Due to the complexity of the problem, a variety of complementary theoretical treatments will be employed in order to obtain a quantitative model. Coarse grained models will be used to focus the application of more computationally intensive molecular models into those regions of phase space which control the behavior of the system. Theoretical methods used will range from Molecular dynamics simulations, to scaling analysis, to studies of flow on patterned media. The results should have broad applicability to a variety of devices and molecules including microfluidic channels, microarrays, complexed proteins, and cellular materials.

DESCRIPTION (provided by applicant): We propose to develop a novel methodology to separate DNA and related biomolecules using nanostructured surfaces. We will use a combination of theoretical and experimental methods to study electrophoresis of charged biological molecules on patterned surfaces. The goal is to understand the fundamental mechanisms which control the dynamics near surfaces and to formulate predictive models which will allow the engineering of high resolution separation devices with optimum throughput and chemical selectivity. Nanoscale patterns will be imprinted using polymer self assembly, while more complicated micron scale structures with a combination of topological and chemical patterns will be manufactured by micro-contact printing. Electrophoresis will be performed and the mobility of DNA chains on these various surfaces will be observed either by confocal, near field microscopy, or CCD coupled video imaging. Fluorescence recovery after photobleaching (FRAP) coupled with Linear Dichroism detection (FDLD) will be used to measure surface relaxation times and diffusivity. The measurements will be performed as a function of pattern morphology, buffer concentration, chemical interactions, and chain structure. From these measurements we should be able to elucidate the relative importance of surface interactions, surface charges, electroosmotioc flow, and topological confinement in the surface dynamics of charged molecules. Due to the complexity of the problem, a variety of complementary theoretical treatments will be employed in order to obtain a quantitative model. Coarse grained models will be used to focus the application of more computationally intensive molecular models into those regions of phase space which control the behavior of the system. Theoretical methods used will range from Molecular dynamics simulations, to scaling analysis, to studies of flow on patterned media. The results should have broad applicability to a variety of devices and molecules including microfluidic channels, microarrays, complexed proteins, and cellular materials.

The involvement of students of any age in different phases of research can be a stimulating experience for both the scientist and the student. We propose to continue a program where cutting edge research is done in partnership of faculty with students starting from high school through the post doctorate. We believe that this arrangement can be beneficial for all participants. The faculty brings the excitement of original research into the classroom, providing role models and motivation for the students. Post doctoral and graduate students, who are heavily involved in the day to day research activities also learn teaching and mentoring skills through working with the undergraduate and high school students. Becoming involved in all phases of the research, undergraduate and high school students, learn first hand what is expected if they are to chose careers in science and engineering.
A central goal of the National Nanotechnology Initiative has recently been identified by an NSF report to be the ability to create "smart" and adaptable materials with atomic level precision and control in economically viable quantities that would "be of broad benefit to industry, economy, health, environment, and society". The report pointed to "our ability to achieve a better understanding of materials at dissimilar interfaces" as a key vehicle to attaining this goal. Polymers, which can be molecularly engineered on a macroscopic scale, while retaining nanometer scale precision, play a central role in attaining this goal. This proposal therefore has two research directions: Engineering biomimetic polymer scaffolds for tissue engineering and fundamental studies of cell mechanical transduction and the desing of self extinguishing polymer nanocomposites that can withstand extreme conditions. This proposal therefore has two interrelated goals; (a) Produce original and relevant research in biomaterials and nanocomposite polymer engineering ; (b) Allow for versatile training of students from high school, undergraduate, graduate through the post-doctorate to develop necessary skills for achieving professional careers in science and engineering.

This NSF award by the Chemical and Biological Separations program supports work by Professors Dilip Gersappe and Miriam Rafailovich to develop a technology that uses patterned surfaces to separate large DNA molecules. Patterned surfaces offer significant advantages over conventional gels used to separate DNA. They are reusable, portable and most importantly do not cause breakage of large DNA fragments. Further, with the advances in patterning techniques we can engineer surfaces with the particular pattern that will optimize the separation of DNA molecules.

While this proposal addresses the development of a methodology to separate large DNA fragments, the broader impact of this work is that we ultimately aim to use this methodology to sort whole chromosomes. Chromosome sorting is a tool of great value but one that is available in only a very few institutions worldwide. Furthermore, it requires great skill and training and relies on the use of expensive equipment. Many workers experience is that it is extremely difficult to obtain custom sorted chromosomes from the relevant institutions. If chromosome sorting were available on a wider scale, and at low cost, it would be used much more routinely to answer fundamental questions in genetics, questions for which alternative (and often much less suitable) methods have had to be developed over the years.

As part of this project, we will host high school students in our lab over the summer and (when possible) over the school year. We propose to add a module on surface dielectrophoresis within the framework of the Research Scholar Program run in our Department. Undergraduate students will also act as mentors for the high school students in this module. The students will gain hands-on experience in patterning of surfaces and will perform dielectrophoresis experiments. The graduate students (following the methodology adopted by the Center) will mentor the undergraduate students. In this manner, graduate students will get valuable experience learning how to manage a small team, undergraduate students will gain mentorship experience and high school students will get involved in cutting edge research.

This INSPIRE award by the Biomaterials program in the Division of Materials Research to the State University of New York Stony Brook is in developing novel materials transport systems, and a general method for creating (and tuning the properties of) aqueous nanocluster dispersions of interest for technologies that range from drug delivery to biofuel production, as well as a theoretical understanding of the mechanism for cluster formation and stability. This award is cofunded by the Biomaterials and the Polymer programs in the Division of Materials Research and International Science and Engineering program in the Office of International and Integrative Activities. In addition, the following programs in the Engineering Directorate - Biomedical Engineering, Particulate and Multiphase Processes and Interfacial Processes and Thermodynamics - all in the Division of Chemical, Bioengineering, Environmental, and Transport Systems are also cofunding this award. The primary focus of this project is fundamental science approaches in developing a synthetic structure that has all the properties of its biological counterpart that can respond in a controlled manner to an external stimulus, by using synthetic polymer-peptide constructs on a patterned surface, manipulated by electric fields to achieve spatial control of cell migration and differentiation. These responsive surfaces would have a clear impact for the development of surfaces that can template biomineralization and scaffolds that direct the outcome of embryogenesis. This project would lead to a new interdisciplinary and potentially transformative research at the interface of colloid and interface science, multiscale modeling and statistical mechanics, biophysical characterization, materials sciences, drug delivery, interfacial processes, molecular engineering, multiphase processing and nanotechnology. Using an iterative process, theoretical models will be continuously probed and refined, and this would enable obtaining the optimal structures in designing the cell experiments using stem cells, human epithelial and endothelial cells. Significant advances could be expected as the result of this investment in inter- and multi-disciplinary research at the intersection of the engineering and material sciences, and synthetic biology that focus on advancing the fundamental experimental and theoretical answers to important fundamental questions about the possibility of forming aqueous dispersions of equilibrium nanoclusters with tunable size, shape and dissociation properties.

The broader technological impact of this project is in developing a model fundamental process of organ development, tissue organization, stem cell differentiation, and designing and synthesizing novel polymeric and dynamic surfaces with tailored properties that could have many industrial applications, if the project is successful. With respect to educational and outreach activities, the project is for the seamless integration of research and education, with a robust mentoring program, where contact with the students is often maintained throughout their educational and professional development. With the proposed model system, students learn by doing, observing, and participating fully in the research efforts from concepts through publications, and are evaluated by metrics for standard research proposals, i.e. innovation, impact, and publication. The planned high school program includes structured activities, which provide the students with the basic skill required for independent research, including statistics modules, data mining, proper reference notation, skills in keeping laboratory notebooks, awareness of intellectual property issues, filing for patents, ethics in education and sciences, and working within a group on environmental questions and awareness, and providing safety training courses in handling and disposal of hazardous chemicals and biological wastes. As part of the International activity, the project plans to initiate collaborations with University of Dortmund, Germany, where the education and outreach models practiced at the SUNY campus will be replicated. In addition, the project plans to expand these outreach activities in Europe and Asia by collaborating with Universities and High Schools in these areas.