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Ab initio free energy calculations for adsorption and reactions in nanoporous systems

Wednesday, April 26, 2017, 4:00 PM - 5:00 PM
Joachim Sauer, Professor of Chemistry, Humboldt University Berlin

The ab initio prediction of reaction rate or equilibrium constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide-and-conquer strategy that more  »


ECE Brice Distinguished Lecture: "Novel Materials for Next Generation Photonic Devices," Dr. Michal Lipson, Columbia University, (698/699)

Tuesday, April 18, 2017, 4:00 PM - 5:00 PM
Michal Lipson, Professor, Electrical and Computer Engineering, Columbia University

Ultrafast optoelectronics devices, critical for future telecommunication and data ultra-high speed communications and data communications, have been limited in speed due to nature of the materials forming the devices. Only very few materials can be u more  »


"Architecture of Myosin V and its Motility”

Tuesday, April 18, 2017, 12:30 PM - 1:30 PM
Dave Thirumalai, Robert A. Welch Chair in Chemistry, University of Texas, Austin

Abstract: Myosin V, two-headed motor protein and a member of the myosin super family, ferries cellular cargo by walking hand-over-hand on actin filaments. Interplay between ATD-driven conformational changes in the motor head and stress due to load p more  »


Single-Molecule Spectroscopy with Catalysts, Conductive Polymers, and Optical Microresonators

Wednesday, April 12, 2017, 4:00 PM - 5:00 PM
Randall Goldsmith, Assistant Professor of Chemistry, University of Wisconsin-Madison

Measurements on individual molecules have revolutionized how chemists can perceive molecular properties and dynamics, yet single-molecule techniques can only be applied with considerable experimental constraints. The Goldsmith group develops new too more  »


“Division of Labor Among the Subunits of a Highly Coordinated Ring ATPase”

Tuesday, April 11, 2017, 12:30 PM - 1:30 PM
Carlos Bustamante, Professor, Stanford School of Medicine

Abstract: As part of their infection cycle, many viruses must package their newly replicated genomes inside a protein capsid. Bacteriophage phi29 packages its 6.6 mm long double-stranded DNA using a pentameric ring nano motor that belongs to the ASC more  »

Thesis Defense

Advanced Quantitative Analysis of Single-Walled Carbon Nanotubes

Monday, April 10, 2017, 3:00 PM - 5:00 PM
Yara Kadria-Vili, Doctoral Candidate

Single-walled carbon nanotubes (SWCNTs) have promised wide range of novel applications for containing a mixture of many tubular structures that vary in diameter size, chiral angles, and physical properties. However, their usage has been hindered by s more  »

Lecture/Lecture Series

Ken Kennedy Award Lecture: "MPI: The Once and Future King" presented by Dr. William Gropp

Tuesday, April 4, 2017, 4:00 PM - 5:00 PM
Dr. William Gropp, Acting Director and Chief Scientist at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign and the Paul and Cynthia Saylor Professor in the Department of Computer Science, University of Illinois at Urbana-Champaign

The Message Passing Interface (MPI) has been the dominant programming system for expressing highly-parallel technical applications for over 20 years. This success was due in part to a combination of careful design of the standard by the MPI Forum an more  »


“Modeling the Emergence of Clones in Populations (By Drawing Analogies with the Physics of Glasses) and the Adaptive Immune System of Bacteria (Called CRISPR)”

Tuesday, April 4, 2017, 12:30 PM - 1:30 PM
Marija Vucelja, Assistant Professor, University of Virginia

Abstract: I will present two population genetics stories where analogies from physics have been pivotal. First, I will talk about the emergence of clones in populations. Recombination reshuffles genetic material, while selection amplifies the fittest more  »

Thesis Defense

Size and Shape Control of Colloidal Al Nanocrystals for UV Plasmonics Applications

Monday, April 3, 2017, 10:30 AM - 12:30 PM
Michael McClain, Doctoral Candidate

Al nanocrystals are a cost-effective alternative to noble metal nanomaterials with their own unique plasmonic features throughout the UV, visible, and infrared spectrum. In the past two decades, generalized rules for nanocrystal growth have been esta more  »



Mimicking Enzymatic Function in Molecular Catalysts for Energy Transformations

Wednesday, March 29, 2017, 4:00 PM - 5:00 PM
Wendy Shaw, Physical & Computational Sciences Manager, Pacific Northwest National Laboratory

Enzymes are capable of shuttling gases, protons and electrons with great speed and precision. Enzymes are also capable of very specifically controlling the local environment around the catalytic active site. Using the large range of functional grou more  »


“Orthogonal Replication for Rapid Evolution and Synthetic Biology”

Tuesday, March 28, 2017, 12:30 PM - 1:30 PM
Chang Liu, Assistant Professor, Departments of Biomedical Engineering, Chemistry, Molecular Biology and Biochemistry University of California, Irvine

Abstract: We recently developed an orthogonal DNA replication (OrthoRep) system in the yeast Saccharomyces cerevisiae. OrthoRep exploits an unusual selfish DNA element consisting of a DNA plasmid–DNA polymerase pair that stably replicates in the cyto more  »

Thesis Defense

Structure, Design and Applications of Collagen-mimetic Peptides

Friday, March 24, 2017, 11:00 AM - 12:00 PM
Amanda Acevedo-Jake, Doctoral Candidate

The collagen triple helix is a unique protein fold found in all domains of life where it has diverse roles from imparting structure and strength to tissue, to initiating an immune response. While many factors affecting the structure and stability of more  »

Thesis Defense

Functionalization of Carbon Materials with Metals

Wednesday, March 22, 2017, 1:00 PM - 3:00 PM
Kourtney Wright, Doctoral Candidate

The functionalization of carbon nanotubes (CNTs) with metals has been shown to produce materials with interesting and useful properties which are different from the isolated constituents. Although metal atoms and particles have been attached to CNTs more  »

Thesis Defense

Understanding Functional Roles of Transcription Factor Decoys in Gene Regulation via Mathematical Modeling

Wednesday, March 22, 2017, 2:00 PM - 4:00 PM
Zhipeng Wang, Doctoral Candidate

Gene expressions are essentially regulated by transcription factor-DNA interactions. Many transcription factors bind to DNA with remarkably low specificity, so that the functional binding sites have to compete with an enormous number of non-functiona more  »


Nanoscale gymnastics: Dynamics of protein-DNA complexes with high speed AFM

Wednesday, March 22, 2017, 4:00 PM - 5:00 PM
Yuri L Lyubchenko, Professor of Pharmaceutical Sciences, University of Nebraska Medical Center

A low data acquisition rate of AFM is a serious deficiency if AFM is applied to imaging of the majority of biological processes. For example, the translocation of RNA polymerase along DNA occurs on the second time scale, therefore the observation on more  »


In the pursuit of higher resolution in live cell imaging … and little perks of microscopy

Tuesday, March 21, 2017, 4:00 PM - 5:00 PM
Robert Pal, Research Fellow in the Department of Chemistry, Durham University

The optical probes and cellular stains commonly used in microscopy are usually fluorescent organic molecules or recombinant proteins which have been used in many areas of cellular biology leading to an enhanced understanding of cellular processes and more  »


“Understanding the Effects of Confinement on the Statistics of Biomolecules”

Tuesday, March 21, 2017, 12:30 PM - 1:30 PM
Greg Morrison, Assistant Professor, University of Houston

Abstract: The confinement of biomolecules is ubiquitous in nature, such as the spatial constraints of viral encapsulation and the binding of DNA to the surface of the histone octamer. Advances in microfluidics and nanopore fabrication have permitted more  »

Thesis Defense

Decoding biological gene regulatory networks by quantitative modeling

Monday, March 20, 2017, 9:00 AM - 11:00 AM
Bin Huang, Doctoral Candidate

Gene regulatory network is essential to regulate the biological functions of cells. With the rapid development of “omics” technologies, the network can be inferred for a certain biological function. However, it still remains a challenge to understa more  »


Using Computer Simulations to Advance our Understanding of Biological Systems at the Atomic Level

Monday, March 20, 2017, 4:00 PM - 5:00 PM
Benoit Roux, Professor, Department of Biochemistry and Molecular Biophysics, Department of Pediatrics, Institute of Molecular Pediatric Sciences, University of Chicago

Classical molecular dynamics simulations based on atomic models play an increasingly important role in a wide range of applications in physics, biology and chemistry. The approach consists of constructing detailed atomic models of the macromolecular more  »


Building Structural Complexity via Tandem Catalytic Transformations: Total Syntheses of Bioactive Macrolides and Terpenes

Wednesday, March 8, 2017, 4:00 PM - 5:00 PM
Mingji Dai, Assistant Professor of Chemistry, Purdue University

This talk will highlight elements of our recent efforts in developing novel strategies and methodologies for divergent and efficient synthesis of medicinally important natural products. Particular emphasis will be placed on two research projects. One more  »

Thesis Defense

Charge Pairs and Mutations in Collagen Mimetic Peptides

Wednesday, March 8, 2017, 3:00 PM - 5:00 PM
Katherine Clements, Doctoral Candidate

This thesis will present insights into natural type I collagen based upon studies with collagen mimetic peptides. Natural collagen is a fibrous protein with challenging properties, such as solubility, which makes it difficult to study through analyti more  »


“Studying Directed Cell Migration with Microfluidic Tools”

Tuesday, March 7, 2017, 12:30 PM - 1:30 PM
Alex Groisman, Associate Professor of Physics, University of California, San Diego

Abstract: Directed migration in response to spatial non-uniformity of various external cues takes a variety of forms, such as chemo-, photo-, thermo-, aero-, and mechano-taxis. It is vital in the bacterial search for nutrients and energy and in the s more  »


Structural Examined Through the Combined Lenses of Ultrafast and Magnetooptical Spectroscopy

Wednesday, March 1, 2017, 4:00 PM - 5:00 PM
Ken Knappenberger, Associate Professor of Chemistry and Biochemistry, Florida State University

Plasmonic nanoparticle assemblies offer unique opportunities for controlling energy at the nanoscale. Here, we describe experimental outcomes in three key areas critical to understanding nanoscale-structure-specific light-matter interactions: 1) sel more  »



“Touring the Protein Energy Landscape: The View Depends on How and When You Look”

Tuesday, February 28, 2017, 12:30 PM - 1:30 PM
Susan Marqusee, Professor of Molecular and Cell Biology, Division of Biophysics, Biochemistry and Structural Biology, University of California, Berkeley

Abstract: Understanding the structural and dynamic information encoded in the primary sequence of a protein is one of the most fundamental challenges in modern biology. The amino acid sequence of a protein encodes more than the native three-dimension more  »