News

Opportunity: 2 Postdoctoral Openings in Theoretical Research (associated with Columbia University's newly established Energy Frontier Research Center)

We have two postdoctoral openings in theoretical research associated with Columbia University's newly established Energy Frontier Research Center (www.cise.columbia.edu/efrc/). The center unites physicists, chemists and engineers with the goal of understanding nanoscale charge and energy transfer processes fundamental for the design of new solar-based energy technology.

Both openings require a PhD in theoretical physics, chemistry or related fields, with emphasis on electronic structure theory and/or quantum dynamics. The theoretical effort will be led by Professor David Reichman (Department of Chemistry, Columbia University), Mark Hybertsen (Brookhaven National Labs) and Professor Eran Rabani (Department of Chemistry, Tel Aviv University). While these postdoctoral researchers will be based in the Chemistry Department at Columbia, research projects in the EFRC are expected to involve significant interaction with several experimental groups.

The two projects are:

a) Theoretical understanding of generation and evolution of excitons in nanocrystals and other nanoscale objects such as nanotubes. Emphasis will be placed on understanding factors that enhance or inhibit multi-exciton generation. This project will make use of large scale electronic structure techniques.

b) Theoretical understanding of optical excitations in nanoscale inorganic-organic hybrid structures, subsequent exciton dissociation and fission processes and the role of coupling to nanostructured leads. This project will involve electronic structure techniques as well as quantum dynamics approaches.

Both positions have open start dates. Please have all interested parties send a CV and 2 letters of reference to:

Professor David R. Reichman
Department of Chemistry
Columbia University
3000 Broadway,
New York, New York, 10027
e-mail:drr2103@columbia.edu

Opportunity: 2 Postdoctoral Research Openings

We are searching for two postdoctoral research associates for the theoretical modeling of the structural and electronic properties of conjugated polymers in the condensed phase. The work will be part of a newly funded effort that combines synthetic (Colin Nuckolls, Columbia), experimental (Paul Barbara and Katherine Willets, Texas) and theoretical (Richard Friesner and David Reichman, Columbia) expertise to understand the morphological properties of films and assemblies of conjugated polymers as well as the electronic and optical properties of these entities.

Two main theoretical thrusts will be initiated:

a) Understanding the electronic structure and optical properties of individual conjugated polymers as well as small aggregates of conjugated polymers. Familiarity with state-of-the art electronic structure methods is highly advantageous.

b) Molecular modeling of the morphology of individual folded polymeric units as well as the effective interactions between units in the condensed phase. This phase of research will potential involve force field development, as well as Monte Carlo and molecular dynamics simulation of the behavior of conjugated polymers in the condensed phase. A long term goal is the understanding of self-assembly of conjugate polymer units in large length scale structures.

It is expected that research associates working on these two related areas will interact with each other as well as the experimental members of the research team. The Chemistry department at Columbia offers a rich environment for theory with four full-time theoretical chemistry faculty members (Berne, Cacciuto, Friesner, Reichman) and state-of-the-art computational facilities. The positions listed will be for one year, with additional years expected upon mutual consent. Salary is negotiable, and women and minority candidates are encouraged to apply. Please have your CV and 3 letters of recommendation sent to: Ec31@columbia.edu with PD THEORY SEARCH – Postdoc’s Name (in the subject line).

!Talk: Pharmaceutical Recruitment from the Student Perspective
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Dr. Menhaji-Klotz will be discussing the Columbia pharmaceutical recruitment process and will offer her suggestions towards maximizing your own experience. Dr. Menhaji-Klotz graduated from Barnard College in 2002, conducting undergraduate research with Professor Christian Rojas. She spent a year doing research at Trinity College Dublin with David Grayson’s lab before returning to the states to begin her graduate studies. She obtained her Ph.D. in 2008 from Yale University studying under Professor John Wood. She currently holds a post-doctoral position with Professor Tristan Lambert at Columbia University and will be joining AstraZeneca as a discovery chemist in January 2010.

Refreshments will be served.

!Seminar: CHEMISTRY COLLOQUIUM - Exploring Conductance Switching Properties of Molecular Scale Devices: A Computational Approach
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Hosted by Professor Richard Friesner

!Talk: A Tale of Two Chemistries, Heterocycloadditions and Phosphonium Couplings.
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Biography:
Bill Murray received his Ph.D. at the State University of New York at Stony Brook with Professor Francis Johnson. After a Post Doctoral Fellowship in Chemistry at MIT with Professor George Buchi he joined Johnson and Johnson in 1980 as a synthetic organic chemist. He has spent most of his career in drug discovery and process chemistry. During his career at J&J, Bill has held positions of increasing responsibility in medicinal chemistry and chemical and pharmaceutical development. He has worked in numerous therapeutic areas including inflammation, cardiovascular, hematology, oncology and urology. In the late 1990’s he established the drug discovery chemistry group at J&J’s LaJolla site and built it to over 30 chemists. He then built the Raritan chemistry group to over 120 chemists. In addition to his discovery chemistry responsibilities in 2004 he lead the global Chemical and Pharmaceutical Development group for J&J’s early development effort.
Bill played a key role in the acquisition and integration of 3DP Pharmaceuticals in 2003 and the acquisition of Transform in 2005. As COO he set the strategy for Transform as an independent J&J affiliate in the Boston area. With the regional reorganization of J&J Research and Early Development Bill has returned to his role as Vice President of Chemistry for the East Coast Research and Early Development unit of J&J Pharma. Bill is author of approximately 90 refereed publications and inventor on over 50 issued US patents. He has served on the advisory boards of a number of academic institutions focused on chemical biology. He has also given numerous invited lectures in the areas of Synthetic Organic, Pharmaceutical and Medicinal Chemistry.

!Talk: From one amino acid to another:
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Refreshments will be served.
Dr. Sheppard will meet with students in Altschul 514 after the seminar.

Seminar: Physical Chemistry Seminar - Time-Resolved Study of CN Radical Reactions in Solution: The Role of CN-Solvent Complexes
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Abstract: Time-resolved studies using 100-fs laser pulses generate CN radicals photolytically in solution and probe their subsequent reaction with solvent molecules by monitoring both radical loss and product formation. The experiments use both single wavelength and broadband detection to follow the CN reactants by transient electronic spectroscopy at 400 nm and to monitor the HCN products by transient vibrational spectroscopy near 3.07 microns. The observation that CN disappears more slowly than HCN appears shows that the two processes are decoupled kinetically and suggests that the CN radicals rapidly form two different types of complexes that have different reactivities. Electronic structure calculations find two bound complexes between CN and a typical solvent molecule (CH2Cl2) that are consistent with this picture. The more weakly bound complex is linear with CN bound to an H atom through the N atom and is primarily responsible for the rapid HCN signal rise. The more strongly bound complex has a structure in which the CN bridges Cl and H atoms of the solvent and is primarily responsible for the more slowly decaying CN signal. These complexes form the basis for examining CN radical reactivity with seven different chlorinated solvents, where both linear and bridging CN-solvent complexes tend to react more slowly with solvents with more Cl substituents.

Seminar: D. E. Shaw Research Seminar Series - "Refinement and validation of models of the Kv1.2 channel and calculation of the gating charge using molecular dynamics simulations."
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Molecular dynamics (MD) simulations are carried out to refine atomic models of the active and resting state of the Kv1.2 channel in an explicit lipid membrane environment. The full tetrameric channel and the isolated voltage-sensor domain (VSD) are simulated for an aggregate time of more than 350 ns in the presence of transmembrane voltages bias. The total gating charge of the channel, determined from 500 ns of MD simulation of the full tetrameric channel, is 10.3 elementary charge, in good accord with experimental estimates, indicating that the refined models offer a realistic depiction of voltage-gating. During the simulation of the closed state model, the extracellular end of the S4 segment spontaneously converted into a 3-10 helix over a stretch of ten residues (294-304). This conformation is energetically favored because it orients the positively charged side chains of S4 toward the water-filled crevice at the center of the voltage-sensing domain where they can also form favorable salt bridges interactions with the negatively charged residues along the S2 and S3 segments. The change in the salt bridges pattern in the closed and active conformations reflects a whole-body movement of the S4 segment, where the positively charged residue of S4 associates sequentially with lipid headgroups as well as with highly conserved acidic residues in S2 and S3. The fraction of the membrane potential acting upon key charged residues in the voltage sensor, calculated using free energy all-atom MD simulations, reveals that the applied field varies rapidly over a narrow region of about 10-15 Angstroms, corresponding roughly to the outer leaflet of the bilayer. The focused transmembrane field enables the transfer of a large effective gating charge without a full translocation of the S4 segment across the membrane.

Attendance is limited, so please RSVP by November 3 to Cheryl.Erskine@DEShawResearch.com.

!Talk: “Understanding Science for Public Choices”
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Martin Chalfie, Professor of Biological Sciences, Columbia University, 2008 Nobel Prize in Chemistry

Jean Salençon, Professor Emeritus at the Ecole Polytechnique, President of the French Academie des Sciences

Claude Henry, Professor of Sustainable Development, Sciences Po & Columbia University

This event is open to the public. Please RSVP to the Alliance Program if you are planning to attend: mj2412@columbia.edu

Communicating the meaning of science to public policy-makers is a delicate and necessary challenge. In this panel discussion, Martin Chalfie, Jean Salençon and Claude Henry present the risks and rewards of helping policy-makers understand scientific relationships so that public policy decision-making reflects scientific integrity.

Martin Chalfie is a Professor of Biological Sciences at Columbia University, where he is also the Department Chair. In 2008, he won the Nobel Prize in Chemistry with Osamu Shimomura and Roger Y. Tsien for their discovery and development of the green fluorescent protein (GFP). Dr. Chalfie’s work investigates aspects of nerve cell development and function.

Jean Salençon is a Professor Emeritus at Ecole Polytechnique. In 2008, he was elected President of the French Academy of Sciences, and he is currently the chairman of the Institut de France. Dr. Salençon’s research focuses on structure analysis, soil mechanics, and continuum mechanics.

Claude Henry is a Professor of Sustainable Development at Sciences Po and a regular Visiting Professor at Columbia University. He is a member of the Committee on the Measure of Economic Performance and Social Progress, led by Joseph Stiglitz and Jean-Paul Fitoussi. In 1970, Claude Henry was the first scholar to articulate the ‘precautionary principle.’ He has taught at the Ecole Polytechnique for more than 30 years.

The Alliance Program is a partnership between Columbia University and three French universities, the Ecole Polytechnique, Sciences Po and the Universite Paris I Pantheon Sorbonne. For further information please visit: http://www.columbia.edu/cu/alliance

Seminar: Physical Chemistry Seminar - Quantum diffusion of hydrogen atoms in water and ice
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Abstract: We have recently used the ring polymer molecular dynamics method to study the diffusion of muonium, hydrogen and deuterium atoms in liquid water and hexagonal ice over a wide temperature range (8-361 K). Quantum effects are found to dramatically reduce the diffusion of muonium in water relative to that predicted by classical simulation. This leads to a simple explanation for the lack of any significant isotope effect in the observed diffusion coefficients of these species in the room temperature liquid. Our results indicate that the mechanism of the diffusion in liquid water is similar to the intercavity hopping mechanism observed in ice, supplemented by the diffusion of the cavities in the liquid. Within the same model, we have also been able to simulate the observed crossover in the c-axis diffusion coefficients of hydrogen and deuterium in hexagonal ice. Finally, we have been able to obtain good agreement with experimental data on the diffusion of muonium in hexagonal ice at 8 K, where the diffusion is dominated by quantum mechanical tunneling. This talk will review these developments and show how experimental measurements throughout the 8-361 K temperature range can be explained in terms of the swelling of the Mu, H and D solute atoms owing to thermal quantum fluctuations.

Seminar: Elmer L. Gaden Lecture Series - "How enzymes adapt: lessons from artificial selection of cytochrome P450"
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When making his case for the key role of natural selection in evolution, Darwin pointed to the enormous phenotypic variation that could be achieved in relatively few generations of artificial selection. Today, artificial selection (or 'directed evolution') applied to proteins allows us to observe how readily the functional molecules of life adapt in the face of defined selection pressures. Circumventing our profound ignorance of how sequence encodes function, directed evolution is a powerful approach to generating useful new biological molecules. Here I will describe our efforts to evolve a cytochrome P450 enzyme (CYP102A1 from Bacillus megaterium). Properties such as catalytic activity or stability can frequently be enhanced by single amino acid substitutions, and accumulating relatively few beneficial mutations (as little as 1-2% of the sequence) can make very significant changes to enzyme function. I will show how a P450 fatty acid hydroxylase has been converted into a whole family of catalysts for oxidation of small alkanes to carbohydrate synthesis and drug lead diversification. Where natural evolution has gone (e.g. impressive diversification of function in the P450 enzyme superfamily), directed evolution can follow. Even more interesting are the catalysts nature may not care about, but chemists dream of. While yielding useful biocatalysts for chemical synthesis, these studies provide new insights into the mechanisms underlying evolution of natural enzymes.

Announcement: CONGRATULATIONS To Jing Zhang. Jing Has Been Awarded The Blanche R. & David Kasindorf Fellowship
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The Blanche R. & David Kasindorf Fellowship is awarded to an outstanding graduate student in the Department of Chemistry with a preference for a student of Physical Chemistry.

!Opportunity: Call for Applicants - ACS Graduate Student Awards in Computational Chemistry
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Call for Applicants
ACS Graduate Student Awards in Computational Chemistry
This is an announcement for two Awards in Computational Chemistry that are open to current graduate students. We are grateful to the National Center for Supercomputing Applications for their support of these awards. The competition is open to any graduate student (regardless of citizenship) who began graduate study after August 1, 2005, and who is an ACS member (or whose advisor is an ACS member). These awards are designed to encourage graduate work in computational chemistry, to recognize research accomplishments, and to stimulate interest in the Subdivision of Theoretical Chemistry and the Physical Chemistry Division of the American Chemistry Society. An Awards Committee will consider all the applicants. The awards applications should be sent by e-mail to acspchem@chemistry.ohio-state.edu with the applicant's name and "student award" in the subject line of the email. The deadline for applications is August 1. 2009.

One award will be for up to 30,000 service units and the second award will be for up to 60,000 service units on NCSA's Teragrid resources. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. Applicants should prepare a written description of a computational chemistry research project that requires high-performance computing, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript, are required. The proposal, including the vita, should not exceed four double-spaced pages. In addition, a faculty person (typically the applicant's research advisor) responsible for the applicant's use of the NCSA Teragrid resources must be identified.

Opportunity: ACS Graduate Student Awards in Computational Chemistry
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This is an announcement for two Awards in Computational Chemistry that are open to current graduate students. We are grateful to the National Center for Supercomputing Applications for their support of these awards. The competition is open to any graduate student (regardless of citizenship) who began graduate study after August 1, 2005, and who is an ACS member (or whose advisor is an ACS member). These awards are designed to encourage graduate work in computational chemistry, to recognize research accomplishments, and to stimulate interest in the Subdivision of Theoretical Chemistry and the Physical Chemistry Division of the American Chemistry Society. An Awards Committee will consider all the applicants. The awards applications should be sent by e-mail to acspchem@chemistry.ohio-state.edu with the applicant's name and "student award" in the subject line of the email. The deadline for applications is August 1. 2009.

One award will be for up to 30,000 service units and the second award will be for up to 60,000 service units on NCSA's Teragrid resources. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. Applicants should prepare a written description of a computational chemistry research project that requires high-performance computing, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript, are required. The proposal, including the vita, should not exceed four double-spaced pages. In addition, a faculty person (typically the applicant's research advisor) responsible for the applicant's use of the NCSA Teragrid resources must be identified.

Celebration: CONGRATULATIONS LINGLE! Lingle Wang Wins the Jack Miller, Chemistry Teaching Award!
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You’re cordially invited to attend the reception to honor the winners of the 2009 Jack Miller, Pegram and Hammett awards.
Thursday, June 11, 2009
At 5:00pm
Havemeyer 7th Floor Lounge

**Refreshments will be served!!**

Event: Chemistry Happy Hour
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!Group meeting: Mandatory Theory Group Meeting
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Talk: Atwal Career Symposium
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Atwal Career Symposium
Transforming the Culture of Organic Chemistry Learning
To Teach or not to Teach: Careers in Education Panel

This event will feature a presentation by Assistant Professor Karen Phillips of Hunter College on new educational methods for teaching undergraduate organic chemistry courses.
Following the presentation will be a panel discussion of professors on careers in education. The panel will feature:

Luis Avila, Ph.D, Lecturer, Columbia University
Brenton DeBoef, Ph.D, Assistant Professor of Chemistry, University of Rhode Island
Ruben L. Gonzalez, Jr., Ph.D, Assistant Professor of Chemistry, Columbia University
Emily McLaughlin, Ph.D, Assistant Professor of Chemistry, Bard College

Announcement: Final Examinations
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Friday, May 8th through Friday, May 15
Final Examinations

Talk: The Science Behind Angels and Demons: Hollywood Meets High Energy Physics
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Opportunity: KnowItAll U training
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KnowItAll U training is Wed., May 6th from 11:00am to 12noon at 209 Hav.
Come and you will have a chance to win an Apple iPod Nano!

Announcement: Study Days
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Study Days:
Tuesday, May 5 through Thursday, May 7

Talk: The Gilbert Stork Lecture - Evolution of a Fully Synthetic Route to the Tetracyclines and its Implementation in the Discovery of New Antibiotics
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Tea & cookies will be served prior to the lecture.

Announcement: Organic Problem Session
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Talk: Chemistry Colloquium - Hosted by Graduate Students
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Announcement: Organic Problem Session
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For further information regarding this event, please contact Dani Farrell by sending email to mdf2105@columbia.edu or by calling 212-854-2202.

Talk: The Ramabrahman and Balamani Guthikonda Memorial Lecture - Carbon nanotubes and graphene nanoribbons
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Tea & cookies will be served prior to the lecture.

!Event: Take a Girl to College Day!
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It's time for Take a Girl to College Day! We'll take girls around to classes, have lunch with them, run hands-on experiments, and just have good old fashioned fun. We need:

Undergraduate volunteers to take girls to classes and/or help escort them around campus
Graduate student / post-doc volunteers to run experiments with girls (a Girls' Science Day experiment, for example)
ANY volunteers for a variety of other activities
Please respond to this email ASAP if you can help with any of the above. It should be a lot of fun!

Thanks,
Teresa and Michelle

Event: Happy Hour This Friday!
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Talk: Entropy-Driven Phase Transition in DNA-linked Colloids
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The bi-weekly Physical Chemistry Seminar will be held today, Tuesday, April 7th, 2009. The Physical Chemistry Student Seminar Series encourages pedagogy and speaker-audience interaction, with education as a key goal.

Abstract: We report grand-canonical Monte Carlo simulations of an equimolar mixture of hard colloids coated with long polymers that have a complementary functionalization. Such systems have the potential to function as self-healing materials. Under conditions where the complementary polymer ends are strongly associated, we observe a first-order vapor-liquid transition from a dilute gas of colloidal dimers to a dense, liquid-like phase. This transition is driven exclusively by the increase in entropy associated with bond disorder

Talk: Chemistry Colloquium - Complex Alkaloid Total Synthesis
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Hosted by Prof. James Leighton

Tea & cookies will be served prior to the lecture

!Talk: Novel Approaches to Drug Discovery and Cancer Metabolomics
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Abstract:
The growing number of predicted protein structures requires robust methods that can utilize low-quality receptor structures for protein function identification and ligand screening. Here, FINDSITE, a new method for ligand-binding site prediction and functional annotation based on binding site similarity across groups of weakly homologous template structures identified from threading is described. For crystal structures, considering a cutoff distance of 4 Å as the hit criterion, the success rate is 70.9% for identifying the best of top five predicted ligand-binding sites. The ability to accurately assign a molecular function to the protein model and to predict the binding site is sustained when approximate protein models (<35% sequence identity to the closest template structure) are used, showing a 67.3% success rate. FINDSITE tolerates inaccuracies in protein models up to a root-mean-square-deviation, RMSD, from the crystal structure of 8-10 Å, because many of these models have a local RMSD from the native binding site < 2 Å. Furthermore, the chemical properties of template-bound ligands can be used to select ligands from large compound libraries. This approach is completed by Q-DOCK, a low-resolution structure-based flexible ligand docking/ranking approach. In docking against distorted receptor models with a RMSD from native of ~3 Å, Q-Dock recovers on average 15-20% more specific contacts and 25-35% more binding residues than all-atom methods. Finally, we describe a recent approach to cancer metabolomics, COMET, that shows considerable ability to predict metabolites with significant antiproliferative activities in cancer cell lines.

!Announcement: Michelle Lynn Hall Wins the ACS Physical Chemistry Division Outstanding Student Poster Award at the Spring 2009 National ACS Meeting in Salt Lake City, Utah. Congratulations Michelle!
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Localized orbital corrections for the calculation of barrier heights in density functional theory Michelle Lynn Hall, mlh2130@columbia.edu, Artem Bochevarov, and Richard A. Friesner.

An empirical localized orbital correction model (B3LYP-LOC) is developed which improves the accuracy of density functional theory (DFT) methods for the prediction of barrier heights for molecules of first and second row elements. This method has already been successfully applied to atomization energies, ionization potentials, electron affinities, and reaction enthalpies; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. The method significantly reduces the number of outliers and overall MAD to error levels below that achieved with canonical B3LYP for a data set of over 100 barrier heights. Although the model is heuristic and is based on a multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation.

Announcement: Organic Problem Session
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For further information regarding this event, please contact Dani Farrell by sending email to mdf2105@columbia.edu or by calling 212-854-2202.

Seminar: Grandpierre Memorial Lecture: Towards Synthetic Biology: Functional De Novo Proteins from a Designed Artificial Proteome
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Hosted by The Chandler Society

Tea & cookies will be served prior to the lecture.

Seminar: Coupling of Ribosomal L1 Stalk and tRNA Dynamics During Translation Elongation
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The bi-weekly Physical Chemistry Seminar will be held today, March 24th, 2009. Today's seminar on single-molecule studies of ribosome dynamics will touch on both physical chemistry and biochemistry, and thus encourage an interdisciplinary audience. As a reminder, the Physical Chemistry Student Seminar Series encourages pedagogy and speaker-audience interaction, with education as a key goal.

Abstract: Translation elongation necessarily requires large-scale movements of transfer RNAs (tRNAs) through the ribosome in order to synthesize polypeptides from individual amino acids based on the genetic codes on the message RNA (mRNA). While it is likely that these highly-coordinated tRNA movements are directed by conformational changes of the translating ribosome, data directly correlating ribosome and tRNA conformational dynamics are lacking. Using single-molecule ribosome- ribosome and ribosome-tRNA Forster resonance energy transfer (sm-FRET) signals, we have characterized the intrinsic conformational dynamics of the ribosomal L1 stalk as well as the coupling of L1 stalk and tRNA dynamics during translation elongation.

!Event: Happy Hour
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Please welcome our prospective graduate students visiting the department today.

Announcement: Spring Recess
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Spring Recess
Monday, March 16th through Friday, March 20th

Announcement: Organic Problem Session - CANCELLED
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For further information regarding this event, please contact Dani Farrell by sending email to mdf2105@columbia.edu or by calling 212-854-2202.

Talk: The Brian Bent Memorial Lecture: Semiconductor nanowires for energy conversion
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Tea & cookies will be served prior to the lecture.

Seminar: Excitation Wavelength Dependent Solvation Dynamics in Organized Assemblies
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Abstract

Solvation plays an important role in controlling the structure and properties of various organized assemblies like micelles, reverse micelles, lipid vesicles, proteins, etc. I will discuss how one can spatially resolve dynamics in different regions of such assemblies. In an organized assembly, the polarity and hence, the absorption and emission maxima of a solvatochromic probe are different in different regions. Consequently, the probe molecules in different locations of an organized assembly may be selectively excited by varying the excitation wavelength. At short wavelength (“blue edge”) the probe molecules in a relatively nonpolar environment are excited and give rise to a blue shifted emission spectrum. Excitation at longer wavelength (“red edge”) selects the probe in a relatively polar environment and gives rise to red-shifted emission spectrum. Such an excitation wavelength dependence of emission maximum is known as red edge excitation shift (REES). We apply excitation wavelength dependence to explore solvation dynamics at different regions of a triblock copolymer micelle and lipid vesicle.

Refreshments will be served.

Talk: Feedback and Redundancy in Oncoprotein-Activated Signaling Networks: Basic and Therapeutic Implications
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Biological Sciences Departmental Seminar

Host: Prof. Dana Pe’er

Refreshments will be served in the 7th floor gallery at 11:50 am

Celebration: Happy Hour
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Happy Hour
Mingle and meet with the Visiting Students and Unwind.

!Talk: Discovery and Application of Nickel-Catalyzed C-C Bond-Forming Processes
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Tea & cookies will be served prior to the lecture.

Talk: Reactions of non-porous cyrstals with gases: changes in covalent bonding of coordination compounds
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Event: ACS Workshop: Preparing for Life After Graduate School
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Sign up to participate in this workshop by emailing Lisa at la2245@columbia.edu by Friday, February 27. Space is limited to 30 people and, if needed, priority will be given to upper level graduate students

ACS Workshop:
Preparing for Life After
Graduate School

Tuesday March 10 and Wednesday March 11

This ACS sponsored workshop will be presented by Dr. James Burke. This two-day workshop is designed to inform graduate students on chemistry career opportunities and how to prepare for the job search.

Day 1: defining career options, outlining non-technical skills, finding employment opportunities
Day 2: mock interviews, resume reviews

Dr. Burke received his Ph.D. degree in Organic Chemistry in 1965 at the University of California at Berkeley and then did his post-doc here at Columbia University. At Rohm and Haas Company, Dr. Burke was Manager of Technical Recruiting and University Relations, with responsibility for scientific and engineering recruiting for the company's U.S. locations. He also managed the company's university relations program. Besides working in synthesis and product development research laboratories, he has accumulated over 25 years of experience in recruiting and career development programs. He retired from Rohm and Haas Company in 2001. He has given about 300 lectures on these and related topics at various colleges and universities, college placement conferences, and ACS meetings.

Talk: Nanostructural Design of Photocatalysts and Photoelectrochemical Cells
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Presented by Thomas Mallouk, Penn State University

Hosted by Prof. Jack Norton

Tea & cookies will be served prior to the lecture.

Talk: Mass Transport Through Individual Carbon Nanotubes
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The bi-weekly Physical Chemistry Seminar will be held today, Tuesday, February 24th, 2009 at 5:30pm. Today, we have the second part of our exchange with City College. Haitao Liu, a postdoc in the Nuckolls and Brus groups, will give a talk on the City College campus. We encourage our students and postdocs to come out to support our own. We will meet at 5pm in the Havemeyer lobby to travel as a group.

Meet: Havemeyer Lobby at 5pm to travel there as a group, or meet us there.

Abstract: We study mass transport through individual carbon nanotubes (CNT). We fabricate nano-fluidic devices that consist of two liquid reservoirs bridged by a single CNT. We demonstrate electrical driven mass transport of aqueous KCl solution through the CNT. The rate of mass transport is significantly higher than what classical theory predicts. Finally, we discuss the translocation of DNA molecules through individual CNT.

Talk: Complex Natural Products as a Driving Force for Discovery in Organic Chemistry
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Chemistry Colloquium - Brian Stoltz

Presented by Brian Stoltz, California Institute of Technology

Hosted by Prof. Tristan Lambert

Tea & cookies will be served prior to the lecture.

Talk: Chemistry / Biological Sciences Student Seminars at the Chemistry/Biology Interface
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Student Seminars at the Chemistry/Biology Interface
Co-sponsored by the Departments of Chemistry and Biological Sciences

for more information, or to get on our mailing list please contact
Ruben Gonzalez (rlg2118@columbia.edu)

Tuesday, February 24th
12 pm
700 Fairchild
Pizza will be served at 11:45 am in 700 Fairchild

JiaGuo
Four-color DNA sequencing with 3’-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides&

JianWu
Molecular engineering of novel nucleotide analogues for DNA sequencing by synthesis

Seminar: Colloquium
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Colloquium
Klaus S. Lackner, Ph.D.
Ewing-Worzel Professor of Geophysics
Dept. of Earth & Environmental Engineering
Director, Lenfest Center for Sustainable Energy of
The Earth Institute at Columbia University

"Sustainable Energy: Options for the Future.
Stabilizing the Carbon Dioxide Content of the Atmosphere”

4:30 P.M. Room 209 Havemeyer
Host: Professor Bruce Berne

Talk: Pyridine single molecule switching: interplay of mechanics and chemistry
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We measure the conductance of single molecules by mechanically forming and breaking Au point contacts with a modified STM in a solution of molecules ...

Seminar: “How proteins find their target sites in vivo: Implications for epigenetic inheritance”
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Host: Prof. James Manley

Refreshments will be served in the 7th floor gallery at 11:50 am

Talk: The Changing Farmaceutical Industry
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STVhelp@columbia.edu
Please RSVP if you plan to attend.
Contact phone number: 212-854-8444

As head of research and later chairman and CEO of Merck, Roy Vagelos, a physician and biochemist, led the company through an unprecedented period of drug discovery and financial success. In Fortune magazine’s annual surveys, Merck was voted “America’s most admired corporation” for seven consecutive Vagelos-led years. During his tenure, Merck developed such successful drugs as Mevacor (first statin approved in the world) and Zocor, cholesterol-lowering agents; Vasotec, an angiotensin-converting enzyme inhibitor for high blood pressure and heart failure; and Recombivax HB, a recombivant vaccine to protect against hepatitis B. While at Merck, Dr. Vagelos was also responsible for making the historic decision to donate the drug, Mectizan, to prevent river blindness; to-date, more than 530 million people worldwide have received the drug.

Dr. Vagelos is a member of the Institute of Medicine, the National Academy of Sciences, the American Academy of Arts & Sciences, and the American Philosophical Society. He received his undergraduate degree from the University of Pennsylvania and his M.D. from Columbia (P&S '54) and has since received 14 honorary doctorates from numerous universities, including Columbia, University of Pennsylvania, Washington University, Harvard and Princeton.

Celebration: First 2009 Chemistry "Happy Hour"
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Dear Chemistry Department,

We are happy to announce the first Columbia University Chemistry
Department Happy Hour of 2009. Come celebrate yet another year of
imbibing free beers with your fellow chemists. This event will be held
on Friday, Jan. 30th on the 7th Floor lounge of Havemeyer. This event
welcomes all members of the department (21 or over, of course). So if you've been unable to attend in the past, start the semester off right with us. See y'all there.
Jeff Meisner
"Remember, don't drink and drive!"

Announcement: Thursday Night Organic Problem Session
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Don't miss tonight's Thursday Night Organic Problem Session, aka Thursday Night Entertainment

Presented by Prof. Scott Snyder

Tonight at 8:00pm in 209 Havemeyer

Seminar: Analysis and design of membrane proteins
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Tea & cookies will be served in the Miller Room 328 Havemeyer prior to the lecture.

The Wyeth Lecture Reception
7th Floor Lounge Havemeyer
Immediately following the lecture

Talk: Life in the Trenches: Glassy Dynamics in Liquids and Beyond
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Glassy dynamics have been observed in fields ranging from chemistry and physics to evolution, computer science, and biology. In contrast to a dilute solution, the interior of a living cell is crowded on many length scales. Recent experiments have measured subdiffusive motion of tracer particles in living bacterial cells, where a particle's mean-squared displacement grows sublinearly with time, as ~ t^alpha . Experimentally, alpha is close to 2/3 and is robust to severe physiological perturbations. Is this value of a the result of evolutionary optimization or a mere coincidence? I will present a theory to answer this question and discuss how a subdiffusive environment might alter familiar concepts of chemical reactions in vivo.

In the second part of the talk, I will discuss the dynamics of a structural glass former. Dynamical heterogeneity, where particles separated by only a few molecular diameters relax on timescales that differ by orders of magnitude, is a hallmark of the glass transition. Two qualitatively different models of dynamic heterogeneity have come to dominate the discussion
of supercooled liquids in the last few years. These two models borrow ideas from critical phenomena, and make different predictions for how the evolution of certain dynamical quantities depends on dimensionality. We have developed an atomistic model of a supercooled liquid in four spatial dimensions to test these predictions.

Talk: Seeing the Unseen with Super-resolution Fluorescence Microscopy
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As one of the most powerful imaging techniques for studying cellular processes, fluorescence microscopy allows noninvasive imaging of live samples with molecular specificity. However, the spatial resolution of conventional fluorescence microscopy is limited by the diffraction of light to about 200-300 nm in the lateral directions and 500-700 nm in the axial direction, leaving many biological structures too small to be observed in detail. To overcome this limit, we have developed the Stochastic Optical Reconstruction Microscopy (STROM) technique. Labeling the sample with photoswitchable fluorophores, it repetitively activates small, optically resolvable subsets of probe molecules and determines their positions with high precision. Accumulation of a sufficient number of localization points allows reconstruction of a super-resolution image with an order of magnitude improvement in spatial resolution (20-30 nm lateral) for cellular imaging. The incorporation of three-dimensional!

(3D) single molecule localization and z-scanning further enables 3D imaging of a whole cell with 50-60 nm axial resolution. We have also created photoswitchable fluorophores for multicolor imaging by combinatorial pairing of various activator dyes and reporter dyes. 3D two color imaging has revealed details in the interaction between organelles and cytoskeleton in mammalian cells. Live cell imaging has been demonstrated using photoswitchable probes staining the plasma membrane, which allows characterizing cell morphologies and lipid diffusion in the plasma membrane.

Talk: New Immunochemistry
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Hosted by Prof. Nicholas Turro

!Talk: Understanding Charge Transfer and Exciton/Polaron Interactions in Conjugated Polymer on the Nanoscale
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Hosted by Prof. Rich Friesner

Seminar: The role of developmental gene regulatory change in human evolution
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BIOLOGICAL SCIENCES DEPARTMENTAL SEMINAR

Host: Prof Dana Pe’er
Refreshments will be served in the 7th floor gallery at 11:50 am

Seminar: “Toward Understanding Biology: RNA at the Systems and Molecular Scale”
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BIOLOGICAL SCIENCES DEPARTMENTAL SEMINAR
Host: Prof Harmen Bussemaker
Refreshments will be served in the 7th floor gallery at 11:50 am

Talk: Rates and States: A Bayesian Approach Understanding FRET Data
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This pedagogical talk will discuss foundations of rigorous statistical data analysis. This is designed to be an interactive talk, designed to convey information applicable to your work.

Model selection is an important component of biophysical data analysis that often does not receive enough attention. Most parameter estimation techniques are based on maximizing the likelihood of the data ­ a method that is naturally prone to overfitting. Empirical Bayes is an alternative technique for parameter estimation that has been gaining popularity in the machine learning community ...

Talk: Small molecule-mediated signaling between organisms
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Hosted by Prof. Brent Stockwell

Seminar: “Small GTPase regulation of receptor trafficking”
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Host: Prof Dana Pe’er.
Refreshments will be served in the 7th floor gallery at 11:50 am

Talk: “Chaperonin-Mediated Protein Folding”
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Talk: “Chaperone-mediated protein folding: Mechanisms and significance in disease”
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Talk: "A tribute to Rosalind Franklin, Ph.D. (1920-1958): her science, her life and her legacy"
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Talk: "A new strategy in synthetic biology: from enzyme inhibition, natural products synthesis to PET imaging by 6p-azaelectrocyclication"
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Seminar: “The two faces of Ras: oncogene and inhibitor of the malignant phenotype”
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BIOLOGICAL SCIENCES DEPARTMENTAL SEMINAR
Host: Dr. Lewis Brown
Refreshments will be served in the 7th floor gallery at 11:50 am

Seminar: H₃⁺ and the Interstellar Cosmic-Ray Ionization Rate
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H₃⁺ has long been recognized as playing a key role in dense interstellar clouds as the initiator of ion-molecule chemistry, which leads to the production of well over one hundred interstellar molecules. The detection of H₃⁺ in diffuse interstellar clouds came as a surprise, however, and suggested a serious problem in the simple model of diffuse cloud chemistry. In particular, this observation raised questions as to the applicability of laboratory measurements of the H₃⁺ dissociative recombination rate to interstellar conditions. We have measured the dissociative recombination rate of rotationally cold H₃⁺ ions in an ion storage ring, and observed H₃⁺ in a large sample of diffuse clouds. This combination of new laboratory measurements and astronomical observations has eliminated two of the primary uncertainties in the chemical model, and implies a previously unrecognized and significant enhancement in the cosmic-ray ionization rate in the diffuse interstellar medium. However, ...

(Cheese and Wine in Room 1402 after Colloquium)

Seminar: "Understanding Energy Transduction of Molecular Motors"
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Molecular motors play crucial roles in diverse biological processes ranging from gene replication, muscle contraction to cell division. They convert chemical energy such as energy from ATP hydrolysis cycle into mechanical work. Our goal is to understand the energy transduction mechanism of these proteins. We use statistical mechanics and molecular simulation to study the conformational equilibrium and dynamics of several different molecular motors. I will show both our previous results and our current research directions in studying molecular motors.

Seminar: “Stem Cell Self-Renewal, Aging and Cancer”
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Host: Prof Daniel Kalderon
Refreshments will be served in the 7th floor gallery at 11:50 am

Seminar: "The continuing saga of the marine polyether biotoxins"
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Tea and cookies - 4 PM in 328 Havemeyer
Reception to follow on the 7th floor

Talk: "Conformational transitions upon protein adsorption studied using Monte-Carlo simulations"
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Other: Happy Hour
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DON'T forget to wear your best costume!

Talk: "Palladium- and Ruthenium-catalyzed Redox Reactions in Selective Organic Synthesis"
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Talk: "Climate, Oceans, Infectious Disease, and Human Health: The Saga of Cholera"
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Lee C. Bollinger
President of Columbia University

Geraldine Downey
Vice Provost for Diversity Initiatives and Professor of Psychology at Columbia University

and

Robin E. Bell
Director of the ADVANCE Program at the Earth Institute and Doherty Senior Research
Scientist in the Lamont-Doherty Earth Observatory at Columbia University

cordially invite you to attend this presidential lecture.

Talk: "Designing Polymers for Chemo- and Immuno-Therapy"
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Talk: “Visualizing the Dynamics of Chromatin”
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In eukaryotic cells, genome maintenance, replication and transcription are carried out on DNA that is organized into condensed chromatin. Specialized proteins must often be employed to modify chromatin before tasks critical for cell viability can be carried out. Nucleosomes, comprised of histones H2A, H2B, H3, and H4 or their variants, represent the fundamental unit of chromatin, and as such are important regulatory targets. We use a single molecule TIRF microscopy assay to directly visualize single nucleosomes and nucleosome arrays in real time ...

Talk: "Potential of mean force calculations of ion permeation in the gramicidin A channel"
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The potential of mean force (PMF) for K+ ion permeation through the gramicidin A (gA) channel were calculated from the molecular dynamics (MD) simulations with four different force fields (FF): CHARMM27, CHARMM27 with dihedral-based cor-rection map (CHARMM27+CMAP), CHARMM27 with a improved FF parameters for tryptophan indole ring (CHARMM27+Trp), and CHARMM27 with the CMAP and the improved FF parameters for Trp (CHARMM27+CMAP+Trp) ...

Seminar: “Understanding and Modulating Cell Death"
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