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Spring 2015 Seminars

In this Section

Friday, April 3, 2015

3:30 p.m.
Bertrand H. Snell Hall Room 212

Gonca Bülbül

Ph.D. Student

Clarkson University

will speak on

Development of a Universal Aptasensor for Ultrasensitive Quantification of Molecular Recognition

Abstract:

Aptamers are a class of small, single-stranded DNA or RNA nucleic acids with unique 3D structures which can recognize and bind to their targets with high specificity and affinity. They are chemically stable, cost effective, easy to modify and reusable. Additionally, they often undergo conformational changes upon target binding, which provide great flexibility in the design of biosensors with high sensitivity and selectivity. This allows for their application for detection of a broad range of targets such as proteins, peptides, amino acids, drugs, metal ions and even whole cells. These unique features make aptamers interesting molecular recognition probes as replacements for traditional antibodies.  In this seminar, I will present a newly discovered phenomenon for quantifying molecular recognition based on the reversible assembly of single-stranded DNA aptamers on redox active nanoceria particles. The method involves target tunable electrostatic and steric repulsion phenomena of the ssDNA to the surface of nanoceria which changes its spectral and functional catalytic properties upon binding of the target analyte. This approach is generally applicable for sensitive and specific detection of a wide spectrum of analytes, since any aptamer–target binding event can in principle be translated to conformational transition and be detected based on this strategy. An example for the detection of Ochratoxin A, a low molecular weight mycotoxin produced by filamentous fungi of Aspergillus and Penicillium, will be discussed. 

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Friday, March 27, 2015

3:30 p.m.
Bertrand H. Snell Hall Room 212

Linhai Jiang

Ph.D. Student

Clarkson University

will speak on

Injectable Hydrogels with Intrinsic Broad-spectrum Antimicrobial Activity

Abstract:

Hydrogels are an important class of biomaterials that have been widely utilized for a variety of biomedical/medical applications. The biological performance of hydrogels, particularly those used as wound dressing could be severely compromised when they come in contact with a variety of causative microbes during the treatment. Hydrogels with inherent antimicrobial activity are highly desirable to alleviate the safe concerns associated with microbial infections and greatly boost their therapeutic potential in various environments. In this seminar, I will discuss a new approach by using de novo designed multi-domain peptides as the molecular building blocks to generate soft hydrogels with inherent antimicrobial activity. These peptides were designed to have the ability to undergo supramolecular polymerization into highly hydrated 3-D hydrogels composed of physically crosslinked nanofibers with tailored structural morphology. Fundamentally, we will demonstrate that the supramolecular surface chemistry of the hydrogel nanofibers and the rheological property of the bulk materials dictate the antimicrobial activity, rather than the ability of individual peptides/peptide assembly to penetrate bacterial cell membrane as commonly observed in solution. Present work will be of great interests to general audiences in both science and engineering communities in terms of understanding how molecular structure can be modulated to tailor the supramolecular nanostructure and bulk mechanical properties of the self-assembled hydrogels and engineering biocompatible and highly effective antimicrobial hydrogels to treat a variety of microbial infections in various biological environments. 

Professor He Dong (right) with Ph.D. Student Linhai Jiang

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Friday, March 13, 2015

3:30 p.m.
Bertrand H. Snell Hall Room 212

Professor David Mitlin

Chemical & Biomolecular Engineering and Mechanical Engineering

Clarkson University

will speak on

Design of Electrode Microstructures that Bridge Supercapacitors and Batteries”

Abstract:

The theme of this presentation is the use of microstructural control to extend the favorable attributes of “Nano”, and minimize the undesirable ones, in relation to lithium ion batteries (LIBs), sodium ion batteries (NIBs or NABs) and electrochemical supercapacitors. In this talk I will cover several examples where proper microstructural design provides substantial improvements: A) The use of nanoscale coatings to more than double the cycling capacity retention and achieve near 100% coulombic efficiency of Si nanowire and nanotube LIB anodes; B) Fabricating improved materials for Na ion battery anodes through tailored metal alloys and pseudographitic carbons; C) Converting a common livestock biowaste, in the form of chicken eggshell membranes and inedible egg whites, to electrodes with some of the highest specific capacitances and Li storage capacities reported in literature for any carbon; D) Creating carbons with electrochemical performance on par or even better than graphene for a range of energy storage devices, from hemp fibers, banana peels and peat moss. In all cases I will detail the key synthesis – microstructure features that transform the performance of these materials from mundane to remarkable.

Professor Silvana Andreescu with Professor David Mitlin

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Monday, March 9, 2015

9:00 a.m.
Science Center Room 238

Dr. Dmitry Kolpashcikov

Deaprtment of Chemistry

University of Central Florida, Orlando

will speak on

“Two-component approach for recognition of nucleic acids and proteins: applications in molecular diagnostics and drug design”

Abstract:

Selective recognition of proteins and nucleic acids (biopolymers) is a challenging task, which is important for accurate detection and analysis of biopolymers as well as for design of specific drugs with minimized side effects. We develop and apply the two-component approach that improves recognition selectivity. The approach uses two pre-designed ligands that bind a biopolymer of interest at two adjacent sites. The two ligands then interact with each other in the tripartite complex ligand 1-biopolymer-ligand 2 and produce either a detectable signal or a chemical reaction.  Based on this approach we have designed a series of two-component probes for highly selective recognition of DNA and RNA sequences. The probes were applied for accurate differentiation of pathogenic bacteria and detection of human genetic variations both in PCR-based and PCR-free formats. Furthermore, DNA logic gates and theirs initial circuits were designed from two-component probes and applied for the analysis of mutations responsible for drug resistance in mycobacterium tuberculosis.  We have also demonstrated that the two-component approach is promising for the design of new types of covalent inhibitors. Potentially, these inhibitors can be used as drugs for treatment of human diseases including HIV/AIDS.

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Friday, March 6, 2015

3:30 p.m.
Bertrand H. Snell Hall Room 212

Dr. Andrey A. Yakovenko

Argonne National Laboratory, Advanced Photon Source

will speak on

In situ Synchrotron Powder Diffraction Measurements: Modern Techniques and
Methods of Structural Analysis”

Abstract:

Understanding of how the structure of the material changes during operation under real working conditions is extremely important. One of the most common and easy technique to do that is Powder X-ray Diffraction analysis (PXRD). However, the structural characterization by PXRD can be complicated by reflection overlap, large unit cell parameters, week signal and/or contamination of the samples. Hence, recently we applied and develop several successful targeted techniques which simplify structural analysis by PXRD.

To ease the structural investigations of porous materials (MOFs and zeolites), methods which apply the analysis of Structure Envelope and Difference Envelope Densities can be used. These densities can be easily generated from the structure factors of a few (1 to 10) most intense low index reflections. This allows us to study guest related issues of MOFs such as, location of guest molecules in the pores, tracking activation of MOFs and gas loading, etc.

To increase sensitivity and to study the signal that is normally hardly detectable by X-ray diffraction, Phase Sensitive Detection (PSD) technique can be used. The principle of a PSD experiment is to apply an external stimulus to the system of reference by periodically varying a parameter (e.g. gas in-flow, concentration, pH, temperature or pressure). The active structural part involved in the process changes periodically (and reversibly) with time. Oscillations of the diffracted signal can be observed and the Fourier analysis of it provides selective access to partial diffraction contributions otherwise merged into one average diffraction signal. 

Professor Mario Wreidt with Dr. Andrey Yakovenko

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Wednesday, March 4, 2015

9:00 a.m.
Science Center Room 238

Professor Julian X.X. Zhu

Deaprtment of Chemistry

McGill University

will speak on

“New polymeric biomaterials made from natural compounds”

Abstract:

The use of natural compounds may improve the biocompatibility and bioacceptance of materials intended for biomedical and pharmaceutical applications. We have used natural amphiphilic compounds including bile acids in our body, in the preparation of new polymers including hydrogels, dental resins, thermosensitive polymers and degradable elastomers with shape-memory properties. Oligomeric molecular pockets have also been made and are shown to be invertible depending on the polarity of the media.

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Friday, February 27, 2015

3:30 p.m.
212 B. H. Snell Hall

Dinusha Karunaratne

Ph.D. Student

Clarkson University

will speak on

“Linear polyamines with variable chain lengths as additives in Cu CMP”

Abstract:

Chemical mechanical polishing (CMP) is the most effective wafer planarization method known today in the semiconductor industry. Cu-CMP is one broad and important area in CMP. Significant part of the research on Cu-CMP involves the improvement of slurry composition, a key factor affecting the outcome of the polishing process. The introduction of copper (Cu) as interconnect material has allowed a significant reduction in the dimensions of the conductive tracks and a much improved usage of the real estate on the surface of wafers. Cu-CMP is largely chemically driven and the chemical properties of copper have brought new challenges in optimizing slurry composition. Chelating agents play a significant role in Cu-CMP by controlling material removal rates (MRR). They can act either as complexing that improve the dissolution of the abraded copper and copper oxides (existing or formed in situ) or passivating agents that interact with the surface of copper and stabilizes the zero-valent metal. A proper balance between these two compounds/functions is essential for achieving an optimum polishing process that provides an acceptable MRR (in the presence of mechanical abrasion) but lowers the static etch rates (in the absence of mechanical abrasion). 

We present the results of the investigations of homologous linear polyamines as potential chelating/passivating agents in Cu-CMP. The study reveals a strong relationship between the size of polyamine molecule and the Cu removal rate. The experimental findings show that the ability to chelate the Cu2+ ions and the passivating efficiency increases with the polyamine chain length. The complexation and passivation mechanisms for each member of the homologous series will be discussed to explain these trends. The data presented will reveal a new view of the copper polishing in which the passivation of the copper substrate dictates the outcome of the overall polishing process. 

Professor Goia (right) with Ph.D. student Dinusha Karunaratne

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Friday, February 20, 2015

3:30 p.m.
212 B. H. Snell Hall

Roshanak Aslebagh, M.S.

Ph.D. Student

Clarkson University

will speak on

“Mass Spectrometry-Based Proteomics of Human Breast Milk to Assess Breast Cancer Risk”

Abstract:

Breast cancer (BC) as the second common cancer and the second leading cause of cancer death among American women, is one of the major research concerns in the US. Detection of BC in the early stages is challenging in young women because of several reasons: first, mammography and imaging technics are less effective due to having dense breast tissue in young women. Second, there is a possible relationship between pregnancy and BC risk. One option for detection of BC is biochemical monitoring of protein markers in different types of body fluids such as sera, nipple aspirate fluid and ductal lavage fluid, tear, urine, saliva and breast milk. Breast milk provides access to breast tissue in the form of exfoliated epithelial cells that are the origins of the most types of BCs. In addition, analysis of breast milk is a noninvasive method for cancer diagnosis. Here we discuss the potential application of mass spectrometry (MS)-based proteomics in investigation of human breast milk as a mean for building a biomarker signature for early detection of BC and for monitoring its treatment. In order to do that, we performed in gel digestion of human breast milk samples coupled with nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS). Using human breast milk samples from both healthy controls and BC suffering individuals, several alterations in protein expression were identified, which might be associated with BC risk. Additional up or down-regulated proteins in either cancerous or control samples will also be discussed. 

Roshanak Aslebagh

Professor Darie (right) with Ph.D. student Roshanak Aslebagh

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Friday, February 13, 2015

3:30 p.m.
214 B. H. Snell Hall

Christopher Netzband

Clarkson University

will speak on

Synthesis of Silver Ribbons through Galvanic Displacement

Abstract:

Silver is one of the most important elements in the world. Since ancient times, its properties have drawn applications in fields such as medicine, paints, and as a form of currency. More recently, silver has been used in fields such as electronics, solar devices and catalysis. Many of these applications are possible due to surface properties of the silver particles in the bulk. By altering these surfaces through the creation of anisotropic silver particles, new materials can be made that better suits the needs of a specific application. This presentation describes the formation of anisotropic silver ribbons through galvanic displacement. The wet chemical synthesis method eliminates the need for templates, dispersing agents or non-aqueous solvents which are typical for similar anisotropic particle synthesis. Due to the flexibility of this synthesis technique, various parameters can be altered to determine their effects on the size and shape of the ribbons. We will show that concentration, pH, ratio of silver to copper, precursor size, temperature, addition time and light can be used to tune the morphology of the ribbons. 

Christopher Netzband

From left to right: Dr. Ajeet Kumar, graduate student Christopher Netzband, Dr. John Njagi, and graduate student Dinusha Karunaratne

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Friday, February 6, 2015

3:30 p.m.
214 B. H. Snell Hall

Ramiz S. J. Alkasir

Clarkson University

will speak on

Design of a Low Cost Portable Device for Personal Exposure Assessment to Bisphenol A

Abstract:

Bisphenol A (BPA) is found in the plastic industry and is used in a variety of commercial products.  Conventional methods for air quality monitoring use expensive platforms with high capital and operational expenditures which limit the number of samples that can be analyzed. This presentation will describe development of a compact sampling/analysis instrument for field-based measurements of BPA. The instrument incorporates interchangeable low cost portable sensors based on signal responsive materials and integrated biomolecular recognition functions to determine BPA. The system includes a paper-based sensor disk with a diameter of 0.6 cm as a test zone for BPA connected to an air-sampling cassette for sample collection. The sensing mechanism is based on the use of a BPA responsive enzyme, polyphenol oxidase immobilized on the sensing surface in conjunction with a biocompatible polymer that changes color in contact with BPA. Signal quantification was performed using a specifically designed color database based on sRGB color space and evaluated using a statistical histogram provided by Photoshop. Colorimetric response was concentration dependent with a detection limit of 0.28 µg/g.  The sensor responses were validated with the conventional Gas Chromatography – Mass Spectrometry (GC-MS) method. Results showed a linear regression (R2 = 0.9743) for real samples measured by both of the colorimetric and GC-MS methods. The instrument was used to detect BPA exposure in household dust. BPA concentrations in household dusts ranged in concentrations from 0.05 to 3.87 µg/g in 57 samples when both methods were used.  The potential of this method for field measurements of aerosol samples and further integration of this technology with the growing cyberinfrastructure to enable effective communication, data integration and interpretation will be discussed. 

Ramiz Alkasir

From left to right: graduate student Ramiz Alkasir, Distinguished Emeritus Professor Petr Zuman, and Professor Silvana Andreescu

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Friday, January 30, 2015

3:30 p.m.
214 B. H. Snell Hall

Armand G. Ngounou Wetie

PhD Candidate

Clarkson University

will speak on

 “The quest for a biomarker of autism spectrum disorder (ASD)”

Abstract:

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interaction, impaired verbal and nonverbal communication as well as stereotyped and rigid patterns of behavior and interest. In the last decades, prevalence of ASD has been on the rise. Despite increased research in this field, clear etiology is still elusive and improvements in consistent, early diagnosis are needed. To uncover possible biomarkers present in ASD, we explored nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS) - based approaches: 1) In-gel digestion coupled with nanoLC-MS/MS; 2) In-solution digestion coupled with nanoLC-MS/MS; 3) two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) coupled with nanoLC-MS/MS. Here, we present the results of three different pilot studies utilizing sera and saliva from children with ASD compared to typically-developing control participants with the aim to develop and optimize methods for biomarker discovery of ASD and ultimately diagnosis. Many of the identified putative protein markers have previously been linked to ASD or were proposed as risk factors of ASD at the genetic level. Some others are involved in pathological pathways implicated in ASD causality such as oxidative stress, lipid and cholesterol metabolism, immune system disturbances and inflammation. These data could contribute to protein signatures for ASD presence, risk and subtypes, and advance understanding of ASD cause as well as provide novel treatment targets for ASD. 

Armand Ngounou

Professor Darie (right) with Ph.D. student Armand Ngounou

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Friday, January 23, 2015

3:30 p.m.
214 B. H. Snell Hall

Olivia Z Durham

PhD Candidate

Clarkson University

will speak on

"Water-Borne Polymer Particles Prepared by ‘Click’ Thiol-Ene and Thiol-Yne Suspension Polymerizations"

Abstract:

We have demonstrated the successful synthesis of water-borne crosslinked polymer particles using thiol-ene chemistry in a suspension photopolymerization. Thiol-ene chemistry is considered a ‘click’ reaction, which can be defined as a process both facile and simple that offers high yields, limited to no side products, easy product separation, and orthogonality with other chemistries. Thiol-ene polymerization is well understood and follows a step-growth mechanism, where polymer growth is dependent on the coupling of functional groups, offering the potential for the development of highly crosslinked functional materials with high conversions. Here we show the impact of various parameters on the development of thiol-ene polymer particles, and demonstrate here the development of thiol-yne crosslinked polymer particles, which can be considered the sister reaction of thiol-ene chemistry. The development of ‘clickable’ thiol-ene/yne polymer particles offers an expedient means to synthesize versatile materials for a variety of potential applications, including paints and coatings, cosmetics, diagnostics, and drug delivery.

Olivia Z Durham

Professor Partch with Ph.D. student Olivia Durham

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Friday, January 16, 2015

3:30 p.m.
214 B. H. Snell Hall

Dawei Xu

Clarkson University

will speak on

"Peptide-based Supramolecular Materials: From Molecular Design to Therapeutic Development"

Abstract:

Peptide-based supramolecular assemblies represent an important class of soft nanomaterials with hierarchical structural control down to the molecular level. The well-defined molecular structure plays important roles in regulating the supramolecular nanostructure, property and various biological activities. In this seminar, I will discuss a self-assembling system inspired by natural amyloid nanofibers with desirable features of controlled assembly, nanostructured dimensions, well-defined molecular secondary structure and atomically precise localization of chemical functionality and their therapeutic implications as drug and gene carriers. We believe the acquired knowledge through these studies will help build a solid foundation for the rational design of supramolecular nanostructured materials, in particular nanofiber-based materials for various other applications, not limited to drug/gene delivery in the biological arena. They can be useful for vaccine delivery and antimicrobial materials design and development, all of which require advanced control over both the molecular structure and nanostructure.

Dawei Xu Seminar

Professor He Dong (right) with Ph.D. student Dawei Xu

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Friday, January 9, 2015 

3:30 p.m.
214 B. H. Snell Hall

Jennifer Sidletsky

PhD Candidate, Clarkson University

will speak on

"Mechanistic Studies into the Brust-Schiffrin Synthesis of Thiolate-Protected Palladium and Platinum Nanoparticles"

Abstract:

The two-phase Brust-Schiffrin synthesis was developed in 1994 to produce alkanethiolate-protected gold nanoparticles that are dispersible in organic media.  It has since been widely employed as a reliable technique for generating small nanoparticles (1-10 nm) of a variety of different metals, including Ag, Cu, Ir, Pd, and Pt.  In these syntheses, metal halide anions (eg. AuCl4-, PtCl42-) are phase-transferred from water to toluene using a phase-transfer agent (typically tetraoctylammonium bromide), generating an ion-pair complex in the organic phase. This phase is then isolated and thiol ligands are added. Finally, a two-phase reduction process is initiated with the addition of an aqueous solution of sodium borohydride. The thiolate-protected metal nanoparticle products of these syntheses are typically highly stable, relatively monodisperse, and can be dried, stored indefinitely, and redispersed without significant change. Over the years, they have been studied extensively and thoroughly characterized by several groups. Far less attention, however, has been paid to developing thorough mechanistic understanding of the relatively complex, three-step syntheses, or to the important differences that exist between the various metals that are used. As a result, synthetic control is currently lacking. In this seminar, several mechanistic studies into the Brust-Schiffrin synthesis of thiolate-protected Pd and Pt nanoparticles will be presented. In these studies, common analytical techniques (UV-visible absorption, infrared absorption, Raman scattering, 1H NMR, TGA, and TEM) are being employed toward developing an inventory of the chemical species present, and the reactions/processes occurring, at each stage of these syntheses. It is expected that the insights gained from this work will significantly improve understanding of these complex syntheses, and provide greater control over their nanoparticle products.

Chemistry Seminar

Professor Goulet (right) with Ph.D. student Jennifer Sidletsky