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Colloquium

In this Section

Summer 2014

Department of Physics
Clarkson University
Colloquium

Tuesday, July 15, 2014 
11:00 AM 
Science Center (Lecture Wing) 166

Dr. Dmitry Mozyrsky
Los Alamos National Laboratory

will speak on

A new approach for modelling non-adiabatic dynamics in molecular systems

Modeling of non-adiabatic dynamics in extended molecular systems and solids is a next frontier of atomistic electronic structure theory. The underlying numerical algorithms should operate only with a few quantities that can be efficiently obtained from quantum chemistry, provide a controlled approximation which can be systematically improved and capture important phenomena such as branching (multiple products), detailed balance and evolution of electronic coherences. Here we propose a new algorithm based on Monte-Carlo sampling of classical trajectories, which satisfies the above requirements and provides a general framework for existing surface hopping methods for non-adiabatic dynamics simulations. In particular, our algorithm can be viewed as a 'post-processing' technique for analyzing numerical results obtained from the conventional surface hopping approaches. Presented numerical tests for several model problems demonstrate efficiency and accuracy of the new method.

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Department of Physics
Clarkson University
Colloquium

Wednesday, July 2, 2014
3:30 PM
Science Center (Lecture Wing) 166

Prof. Vyacheslav Gorshkov
Kiev Polytechni University (KPI) — National Technical
University of Ukraine

will speak on

Nonequilibrium kinetics of sintering in a monolayer of noble metal nanoparticles

Sintering is an important technological process which has attracted substantial efforts both in numerous experimental investigations and in modeling by various techniques ranging from continuum theories to numerical approaches. Various aspects of sintering have been studied, including the overall structure of the sintered materials and more local properties of neck formation and particle merging. Multiscale approaches to modeling involve continuum/finite-element studies, as well as more atomistic kinetic Monte Carlo and molecular dynamics methodology. Recently, there have been interesting new developments utilizing the new capabilities of synthesizing nanoparticles of well-defined size, shape, and surface morphology. Incorporation of nanoparticles can improve the resulting connectivity, and thus, conductance, in the sintering of metal particles initially dispersed in pastes and similar materials typically containing other components and additives.

            We report the results of possible applications of our kinetic Monte Carlo approach that incorporates a competition of several kinetic processes: transport of matter, on-surface restructuring, and detachment–reattachment, which when combined, typically generate nonequilibrium dynamics and are suitable for describing the evolution of the surface and shape morphological features in sintering starting from preformed nanocrystals. We explore the effect of sizes, temperature control, and certain geometrical factors on sintering involving a smaller particle placed in a void between larger particles.

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Spring 2014

 
 
Department of Physics
Clarkson University
Seminar

Friday, April 18, 2014
3:30 PM
B.H. Snell 177
 
 
Zach Hulings
Department of Physics
Clarkson University
will speak on
 
Solution of Poisson Equation in the Debye Approximation Inside a Nanochannel

 

Nanochannels in solid-state materials are devices that are used for various applications such as electrophoresis and nanoparticle separation. Here, we solve the Poissonequation inside a nanochannel with a wedge-like geometry in the Debye approximation. We study how the channel geometry and electrolyte concentration affect the electrostatic potential inside a channel with either  constant surface potential or constant surface charge. We examine the behavior of the electrostatic potential, the electric field, and the gradient of the electric field, which are the contributing factors to the dipole and the electrophoretic force on a biomolecule trapped within a channel. We found that near the wedge's vertex there is a very large variation in the electrostatic potential, suggesting a strong influence of it on particles in that region. From our results, we can deduce how the geometry of the nanochannel affects the motion of biomolecules and nanoparticles through the channel.

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Department of Chemistry and Biomolecular Science
and
Department of Physics  
Clarkson University 
 
Joint Colloquium 
 
 
Wednesday, April 2, 2014
3:30 PM
Science Center (Lecture Wing) 166
 
 
Prof. Milan N. Stojanovic 
Division of Clinical Pharmacology and Experimental Therapeutics
Department of Medicine
Columbia University
 
 
will speak on
 
Progress in Oligonucleotide-Based Devices
 
 
This presentation will focus on two topics:  Oligonucleotide-based devices for analysis of cell surfaces, and oligonucleotide-based sensors for low-epitope targets. For the former, antibody-oligonucleotide conjugates that form reaction cascades on cell surfaces will be presented, and we describe how the outcomes of these cascades depend on types of cells. For the latter topic, an approach to isolate high-affinity aptamers for traditionally challenging targets will be surveyed, and we then describe how this progress may impact clinical chemistry.    
 
 
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Department of Physics 
Clarkson University 
Seminar
 
 
Friday, March 14, 2014
3:30 PM
Snell 177
 
 
Sergii Domanskyi 
Department of Physics
Clarkson University
 
will speak on
 
 
Reaction-Diffusion Degradation Model for Crosslinked Polymer Materials
 
 
We develop a reaction-diffusion model for explaining features of degradation of four-fold-crosslinked polyanhydrides in aqueous environment. We investigate the nature of the reaction and diffusion processes and attempt to explain the observed separate time scale of water uptake before the onset of the degradation, experimentally measured by the group of Prof. D. A. Shipp. Explanation of the observed properties is challenging because several diffusion and reaction processes act as rate-limiting with respect to each other. Numerical studies suggest that process rates depend on the local degradation product concentrations, which may cause the steady state profile of pH emerge with delay, explaining the separate time sale of the water uptake vs. degradation.
 
 
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Department of Physics
Clarkson University
Colloquium
 
 
Wednesday, March 5, 2014
3:30 PM
Science Center (Lecture Wing) 166
 
 
Prof. He Dong 
Department of Chemistry and Biomolecular Science,
Clarkson University
 
 
will speak on
 
 
Supramolecular Polymers Enabling New Opportunities for Anticancer and Antimicrobial Therapies
 
 
Rational design and engineering of synthetic macromolecules with natural peptide/protein-like activities have great implications on modern cancer therapy and infectious disease treatments. This work aims to develop a novel class of supramolecular polymers to mimic (1) protein transduction domain with potent cell penetrating activity and (2) host defense peptide with broad spectrum antimicrobial activity. Our preliminary work demonstrates our ability to build these mimics through molecular self-assembly of de novo designed peptides to form supramolecular nanofilaments. We will show that fibrous morphology dramatically improves the transduction activity and leads to exceptional anticancer drug efficacy in mammalian cell lines. In contrast, for bacteria cells, these nanofibers appear to be less interfacially active when interacting with bacteria cell walls. A delicate balance between materials assembly and disassembly is required to achieve optimal broad spectrum antimicrobial activity. While current study demonstrated fundamental concepts, further work will be focused to gain a comprehensive understanding of the structure-activity connections between molecular composition, supramolecular chemistry and biological activity, e. g. anticancer and antimicrobial activity. The acquired knowledge will help build up a solid foundation for the rational design of supramolecular nanostructured materials, in particular nanofiber-based materials to probe various biological processes.    
 
 
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Department of Physics
Clarkson University 
Colloquium
 
 
Wednesday, February 26, 2014
3:30 PM
Science Center (Lecture Wing) 166
 
 
Prof. Ajit Achuthan 
Department of the Mechanical and Aeronautical Engineering
Clarkson University
 
 
will speak on
 
 
The order in the nucleation of discrete deformation events and its effect on the irreversible response of material systems
 
 
Irreversible response of materials under external excitation can always be linked to certain nanoscale deformation phenomena at micro-/nano-scale. As a consequence of mass conservation these deformation phenomena are continuous events in time. However, when the time scale of the measurement is much larger than the time scale of the phenomena, the continuous deformations will be observed as discrete (spontaneous) events in the material response. Often, the discrete events are characterized by an excessive deformation, disproportionate to the excitation, leading to lattice instability. In general, the spatial and temporal randomness of the nucleation of these events results in their homogenization, yielding a smooth material behavior at the macro-scale. In some systems, however, a certain order in the occurrence of nucleation events leads to several interesting characteristics in material behavior at macro-scale.

In this talk, the incipient plasticity in metals and domain switching behavior in ferroelectric materials will be discussed from an instability framework to demonstrate these differences in deformation characteristics. The discussion is based on experimental observations and molecular dynamics (MD) simulations. The complexity in the mathematical modeling of such systems will be highlighted. Possibility of changing the occurrence of the deformation events from ordered to random by introducing appropriate external conditions will also be discussed.

Bio: Dr. Ajit Achuthan is an Assistant Professor at Clarkson University in the Department of Mechanical and Aeronautical Engineering. Dr. Achuthan received his PhD from Purdue University. Prior to joining Clarkson University he worked at GE Research Center.

 
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Department of Physics,
Clarkson University 
Colloquium
 
Wednesday, January 29, 2014
3:30 PM
Science Center (Lecture Wing) 166

 

Prof. Paul J. G. Goulet
Department of Chemistry and Biomolecular Science,
Clarkson University

will speak on

Synthesis, Characterization, and Application of Noble Metal Nanoparticles

               Nanoparticles of gold, silver, platinum, and palladium are central materials in nanoscience and nanotechnology, with applications in a large number of areas including sensing, electronics, labeling, catalysis, medical therapy, diagnostics, and drug delivery. Along with relatively high nobility, they display remarkable physical, chemical, optical, and electronic properties that arise specifically from their nano dimensions. These properties can be readily tailored through changes in the size, shape, composition, aggregation, and chemical functionalization of the particles.

               The unique optical properties of Au and Ag nanomaterials are of particular interest. Au and Ag nanoparticles sustain strong localized surface plasmon resonances (LSPR) when excited with visible and near infrared light. These resonances are the result of the collective oscillation of conduction electrons in the particles, and are highly sensitive to changes in adsorption and particle aggregation, which, respectively, provide the bases for LSPR and colorimetric sensing. LSPR resonances also lead to intense, highly-localized heating of the particles (the basis for plasmonic phototherapy), and huge enhancements of electromagnetic fields near the surface of particles (the basis for surface-enhanced photoprocesses including surface-enhanced Raman scattering).

              In this talk, the results of several projects on the synthesis, characterization, and application of noble metal nanoparticles will be presented. Specific topics that will be discussed include: mechanistic studies of the synthesis of thiolate-protected noble metal nanoparticles; oxidation of Au and Pt nanoparticles; thermal decomposition of tetraalkylammonium metal complexes; nanoparticle phase-transfer; surface-enhanced spectroscopy, and the synthesis of hybrid plasmonic nanoparticles 

 

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FALL 2013

 
Department of Physics
Clarkson University
Seminar
 
Friday, December 6, 2013
3:30 PM
Snell 177
 
Sergii Domanskyi
Department of Physics
Clarkson University
 
Will Speak on
 

Percolation Modeling of Self-Damaging of Composite Materials

 

            We propose the concept of autonomous self-damaging in "smart" composite materials, controlled by activation of added nanosize "damaging" capsules. Percolation-type modeling approach earlier applied to the related concept of self-healing materials, is used to investigate the behavior of the initial material's fatigue. We aim at achieving a relatively sharp drop in the material's integrity after some initial limited fatigue develops in the course of the sample's usage.

            Our theoretical study considers a two-dimensional lattice model and involves Monte Carlo simulations of the connectivity and conductance in the high-connectivity regime of percolation. We give several examples of local capsule-lattice and capsule-capsule activation rules and show that the desired self-damaging property can only be obtained with rather sophisticated "smart" material's response involving not just damaging but also healing capsules.

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Department of Physics
Clarkson University
Colloquium
 
Friday, November 22, 2013
3:30 PM
Snell 177
 
Prof. Thomas Lufkin
Bayard and Virginia Clarkson Endowed Chair in Biology
Department of Biology, Clarkson University
 
 
Will Speak on
 

A Systems Biology Approach to Building a Skeletogenic Gene Regulatory Network (GRN)

 

Our research is in the novel area of Regenerative Medicine and Stem Cell Biology with a focus on the molecular mechanisms controlling vertebral column development and an emphasis on early embryogenesis and embryonic stem cell commitment to specific differentiation pathways, but from a novel Systems Biology point of view. We are commited to understanding how the vertebral column degenerates with aging, and how this process can be reversed using stem cell based approaches. In particular we are working on understanding the gene regulatory networks (GRNs) that govern normal embryonic development of the vertebral column and intervertebral disc (IVD). We are investigating the role of transcriptional regulators in the restriction of pluripotent embryonic stem cells into specific lineages that in turn comprise functional pre and postnatal vertebral elements with the goal of applying this knowledge in regenerative medicine using patient‐specific induced pluripotent stem (iPS) cells and adult mesenchymal stem cells.

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Department of Physics and Computer Science
Joint Colloquium
 
Friday, November 15, 2013
3:30 PM
Snell 177
 
Prof. Christino Tamon
 
 
Will Speak on
Pretty Good State Transfer on Graphs
 

Given a finite graph G with adjacency matrix A, a continuous-time quantum walk on G is given by the unitary matrix U(t) = exp(-itA), where t is a time parameter. We say that G has "pretty good state transfer" from vertex u to vertex v if the magnitude of the (u,v)-entry of U(t) can be made arbitrarily close to one. This notion is motivated by problems in quantum information. In this talk, we survey basic questions and recent results related to state transfer on graphs.

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Department of Physics, and Department of Electrical and Computer Engineering
Clarkson University
 

JOINT COLLOQUIUM

Friday, November 1, 2013
Time: 3:40 PM
Location: B.H. Snell 177
 
Prof. Ming-Cheng Cheng
Department of Electrical and Computer Engineering
Clarkson University
 

will speak on     

Electro-Thermal Simulations of Semiconductor Integrated Circuit Structure

            As the integrated circuit (IC) density in semiconductor chips increases aggressively in recent years, the power density in the chips is substantially enhanced. This results in temperature escalation and formation of hot spots in the chips and leads to severe performance and reliability degradation. Heating has therefore been recognized as one of the major obstacles in developing emerging semiconductor technologies, including 3D stacked IC’s. To understand and minimize the heating effects and to take into account these effects in IC design, capability of predicting thermal profiles and hot spots in semiconductor chips is essential. Capture of the hot spots in these structures however requires detailed numerical solution that is in general prohibitive for large IC structures.

            In this talk, two different thermal modeling methods for different levels of IC design will be presented. These methods provide efficient approaches to capture hot spots accurately. The first model is based on the concept of characteristic thermal length to account for heat losses and thermal couplings for heat flow along wires and fins. This physics-based thermal model has been applied to different semiconductor device and circuit structures, including SOI MOSFETs and FinFETs. Electro-thermal simulations for some analog CMOS ICs will also be presented. The second model is based on a reduced order modeling technique using proper orthogonal decomposition (POD). The approach projects the problem onto a functional space in order to reduce the numerical degrees of freedom. The POD model has been applied to 3D metal-wire and FinFET structures subjected to power pulses initiated by digital signals. It has been demonstrated that the POD model offers accurate thermal solution as detailed as numerical simulation and is able to reduce numerical degrees of freedom by 5 to 6 orders of magnitude in 3D structure. Application of a block-based approach using the POD model for large IC structure will also be discussed.

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Department of Physics

Department of Chemistry & Biomolecular Science

JOINT COLLOQUIUM

Friday, October 25, 2013
Time: 3:30 PM
Location: B.H. Snell 214
 
Dr. Victor Zhirnov
Semiconductor Research Corporation, Director
Durham, North Carolina
 

will speak on     

Future Microsystems for Information Processing: Limits and Lessons from the Living Systems

The presentation will address the impact of the physics of extremely scaled information processing devices and systems, with a focus on energy minimization. The fundamental limiting factors for electronic information processors are: 1) the tunneling limit on the minimal size due to small mass of electrons, 2) excessive energy consumption in metal wires used for rigid interconnect systems, and 3) heat generation in a small volume. There are also proposals for alternative future information processing technologies based on information carriers other than electrons, however the potential for using them in future ICT systems remains unclear.

In the second part of the presentation, entirely new information processing concepts are discussed based on learning from examples in nature, specifically, the individual living cell will be considered in the context of information processing. In the paper, a bacterial cell, such as E.coli of about one cubic micrometer volume is shown to be a very efficient and powerful information processor, far surpassing conceivable performance in the same volume by an ultimately scaled semiconductor system. Advances in the science of synthetic biology are beginning to suggest possible pathways for future information processing technologies. It might be possible that some of the physical limits faced by semiconductor technology may in fact be overcome by borrowing from synthetic biology principles.

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Friday, October 4th, 2013
Time: 3:30 PM
Location: B.H. Snell 177
Speaker: Prof. Jan Scrimgeour

will speak on     

Probing Macromolecule Dynamics in Complex Biological Systems

Single molecule fluorescence microscopy, with the ability to track molecules and particles in space with 1 nm precision and millisecond time resolution, has significantly enhanced our understanding of the mechanics of biomolecule function. This has been particularly true in in vitro experiments where molecular complexes are well isolated and their environment is very well controlled. The goal of my research is to probe biomolecule interactions in their native, crowded and complex surroundings using "light-sheet" excitation techniques that allow high contrast fluorescence imaging in samples like tissue and small organisms. My talk will discuss the application of advanced optical microscopy for the visualization and characterization of nanostructured biological interfaces. Specifically the pericelluar coat, a nanostructured polymer brush performs many important functions at scales ranging from the single cell to whole tissues, by controlling access to the cell surface, acting as a filter and store for proteins, and plays an active role in controlling tissue-immune system interactions.

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Friday, September 27, 2013
Time: 3:30 PM
Location: B.H. Snell 177
Speaker:  Prof. Michael Ramsdell


will speak on

Using Pre-College Readiness Surveys as an Evidence-Base for Curriculum Modifications to Support Retention

To provide high level focus on curricular issues related to retention and academic success the First Year Council has used the Mathematics Readiness Survey (MRS), in conjunction with the Force Concepts Inventory (FCI), to develop a more precise predictor of STEM-readiness and likely persistence. An independent retention study done for Clarkson by consultants Noel-Levitz in 2011 determined that the strongest single predictor of persistence is the MRS while the best five parameter model included both the MRS and Math SAT scores, and our own studies demonstrate that the combined MRS-FCI data provides an excellent two-parameter predictor for success. Based on that analyses which highlighted the importance of foundational math and science skills, we made curriculum modifications to support our students in building that foundation.  Preliminary analyses of the first two years results will be discussed in terms of students’ retention, persistence and academic performance.

 

 

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