Movie by Nobel Laureate Irving Langmuir, 1927

I read about this documentary in the nice book by Patrick Coffey „Cathedrals of Science“. The movie was shot by famous physical chemist Irving Langmuir (the 1932 Nobel Prize winner) during the 5^th Solvay Conference in Brussels, October 1927. It is difficult to imagine that almost all founders of the quantum mechanics gathered at one conference: A. Einstein, M. Curie, E. Schrödinger, M. Planck, N. Bohr, W. Pauli, W. Heisenberg, P.A.M. Dirac, L. de Broglie, P. Ehrenfest, L. Brillouin, P. Debye, W.L. Bragg, H.A. Kramers, A.H. Compton, M. Born, I. Langmuir, H.A. Lorentz, P. Langevin and other great scientists.


The voiceover is by Nancy Thorndike Greenspan.

West Lafayette, Indiana, Jan-2-2010

University of Southern California (USC)

After the workshop we visited Anna Krylov's group at USC where we meet many interesting people who work on the exciting projects. Vadim Mozhayskiy investigates topology of the Jahn–Teller intersections and is the author of the ezSpectrum program which computes photoelectron/photodetachment spectra taking into account Franck-Condon factors. He also creates beautiful artworks for the journal covers. Evgeny Epifanovsky created a new library for the tensor operations which will be used for all currently available and new coupled-cluster methods and other methods which use tensor formalism within Q-Chem program package. Dr. Debashree Ghosh works on implementation of the gradients for the EFP method. We would like also thank Dr. Kadir Diri for useful advice about our computational cluster and Dr. Arik Landau for his help with basis sets employed in RI-MP2 calculations. (Photos from USC Campus)



More photos from Pasadena and San Francisco

Los Angeles, California, Dec-14-2009

Q-Chem Workshop at Berkeley

In the begging of December we attended Q-Chem Workshop at University of California Berkeley. Q-Chem developers presented and discussed recent features which will be included in the forecoming major release of Q-Chem. Peter Gill's group presented developments grounded on the dual basis method for DFT (dual grids and functionals). The group of Martin Head-Gordon presented developments in ab-initio methods for the systems with strong correlation. Anna Krylov's group reported advances in the spin-flip and EOM coupled-cluster methods. Lyudmila Slipchenko and me presented implementation of QM/MM based on effective fragment potential (EFP) force field and its applications. (Photos from Berkeley)

Berkeley, California, Dec-10-2009

Wind Turbines Farm

Wind power along with solar energy and biofuels is a source of renewable energy. This weekend I visited one of the wind farms near Brookston, Indiana. Indeed, the wind turbines are pretty large with the tower height 230–260 ft (70–80 m) and rotor diameter approximately 260 ft (80 m). The turbines operate at wind speed range 8–56 mph (3.5–25 m/s) producing 1,500 kW of electrical energy each. (Photos)

Brookston, Indiana, Nov-8-2009

Purdue Campus Tour

Finally, I have settled down in West Lafayette. There are some photos with my first impressions from the university campus. (Photos)


West Lafayette, Oct-1-2009

Prof. Slipchenko's Group Home Page

Welcome to http://www.chem.purdue.edu/slipchenko/ our group's home page! We just created a new site where you can find information about us, our research activities, useful computational chemistry resources and many other things related to our group.
West Lafayette, Oct-1-2009

Moving to Indiana

Photo by Unknown Truck Driver
On the 700 miles long way I have crossed five states: Mississippi, Tennessee, Arkansas, Illinois, and Indiana.
Mississippi–Indiana, Aug-2-2009

Graduation, 2009

Photo by Bakhtiyor Rasulev
It tooks four years to get my Ph.D and now I am very glad to go further!
Jackson, Aug-1-2009

Gordon Research Conference on Biological Molecules in the Gas Phase and in Solution

Few days ago I participated in the Gordon Research Conference on Biological Molecules in the Gas Phase and in Solution. It was held in Tilton School in New Hampshire (see photos from this trip). The conference gathered many renowned as well as young scientists. Not surprisingly that the most wanted molecules for many researches are proteins from the small peptide chains to the large enzyme complexes. I would like to mention several groups which work on experimental study of biological molecule in the gas phase. At the end of the note I decided to put a glossary of some experimental techniques widely used in these studies.

Prof. David Clemmer's group at University of Indiana use Ion Mobility Mass Spectrometry (IMMS) of proteins. They investigate conformational changes of the proteins in the gas phase.

Prof. Steven Boxer's group at Stanford University use modifications of Förster Resonance Energy Transfer (FRET) technique which allows them to determine distance between labels attached to the molecules and thus determines conformation of the molecule [1, 2]. They also use Stark spectroscopy to investigate local electrostatic field in the protein molecules and investigate how this field affects the chemical reactivity of the proteins [3, 4].

Prof. Timothy Zwier at Purdue University use very sensitive spectroscopic techniques including double resonance spectroscopy to sample conformational space including high energy local minima of the small molecules [5].

Prof. David Pratt at University of Pittsburgh work on fundamental physical chemistry problems using high resolution UV/Vis and Stark spectroscopy to study electronic dipole moments [6] and charge transfer in the small biological molecules and their hydrogen bonded complexes.

I would also especially emphasize theoretical work by Dr. Alexandre Tkatchenko at Fritz-Haber-Institut who developed theoretical method for accurate and efficient computation of Van der Vaals interactions. The method is based on evaluation of electronic density and it is independent on the DFT functional used [7].

I have presented on the conference my recently published work on kinetic simualtion of the gas phase experiments [8].

Glossary
IMMS (Ion Mobility Mass Spectrometry)—is a combined technique where ions under an applied electrical potential gradient are first separated by drift time through some neutral gas similarly to the gas chromatography technique before being introduced into a mass spectrometer. Ion mobility is determined by the drift time which in turn is a measure of the radius relative to the charge of the ion [9]. Then separated by the drift time the ions are analyzed by mass spectrometry measuring the mass-to-charge ratio of the ions. Currently this technique is used for infestation of the protein conformations in the gas phase.



FRET (Förster Resonance Energy Transfer) spectroscopy—is a technique based on the energy transfer from electronically excited donor chromophore molecule to an acceptor situated in proximity (ca 10 nm) through non radiative dipole–dipole coupling. Thus knowing fluorescence spectra of the chromophores and fluorescence quenching due to non radiative relaxation it is possible to estimate relative positions of the donor and acceptor in the molecule. Information about relative positions of the chromophore is used to determione conformation of the large molecule. This methods is used both for investigation of proteins and nucleic acid. Sometimes several labels with different fluorescence spectra can be attached to the one large molecule and thus provide more detailed information about the conformation [10].

Stark Spectroscopy—is a high resolution UV/Vis spectroscopic technique based on the Stark effect [11]. The Stark effect is manifested in the shifting of spectral lines of a moleucle in preence of external electric field. The amount of shifting is called the Stark shift. In the spectroscopy based on Stark effect the small label molecule which has spectral lines with a large Stark shift attached to a protein or other molecules of interest. The Stark shift of spectral lines of the label molecule due to an electric field of the protein (where the label is attached) can be used as a measure of electric field of the protein. Informartion about electric field of the protein is valuable for undestanding of the protein chemical reactivity.

References
1) X. Shi et al. Biochemistry, 46, 14403 (2007); 2) K. P. Kent et al. J. Am. Chem. Soc. 130, 9664 (2008); 3) L. N. Silverman et al. J. Phys. Chem. A, 112, 10244 (2008); 4) S. G. Boxer et al. J. Phys. Chem. B, 113, 2972 (2009); 5) N. R. Pillsbury et al. J. Phys. Chem. A, 113, 126 (2009); 6) D. M. Miller et al. J. Phys. Chem. A, 113, 6964 (2009); 7) A. Tkatchenko et al. Phys. Rev. Lett. 102, 073005 (2009); 8) D. Kosenkov et al. J. Phys. Chem.  B 113, 6140 (2009); 9) Wikipedia article on Mass Spectrometry; 10) Wikipadia article on Förster Resonance Energy Transfer; 11) Wikipadia article on Stark effect.
Tilton School, New Hampshire Jul-10-2009

New England's Trip

I just got back from Tilton, New Hampshire. There are three photo galleries with New England's impressions: Tilton Village, Tilton School, and our traditional photos of chipmunks and squirrels.

Photo by Dmytro Kosenkov

Photo by Dmytro Kosenkov

Photo by Dmytro Kosenkov

Tilton, New Hampshire, Jul-10-2009

What’s Next?

After the graduation in August, 2009 I will join Prof. Slipchenko’s Theoretical Chemistry Group at Purdue University as a postdoc. I am very happy to have the opportunity to work on development of new methods of quantum chemistry for simulation of biological molecules in solvents and accounts for electronic excitations.
Jackson, Jun-8-2009

Ph.D. Defense

On Friday May 29, 2009 I defended my Ph.D. thesis!
Dmytro Kosenkov Title: „Thermodynamic and Kinetic Simulations on Biological Molecules in Gas Phase and in Solution: Evaporation, Isomerization, and Hydrogen Bonding“

I am glad to complete this important step in my education! Thank for all of you who helped me during my graduate studies and supported during the defense. Special thanks to my dissertation committee who made this event possible: Dr. Jerzy Leszczynski, Dr. Paresh C. Ray, Dr. Glake Hill, Dr. Tigran V. Shahbazyan, Dr. Ming-Ju Huang, and Dr. Lеоnid Gоrb. Members of our dissertation committee
Jackson, May-29-2009

One Day Two Prizes

On April 27, we celebrated Annual Chemistry Day at Jackson State University. I was recognized with two awards: „Best Graduate Poster“ and „Best Oral Presentation at Annual Meeting of Mississippi Academy of Sciences“. I appreciate my supervisors, colleagues and friends whose support made this possible.
Jackson, Apr-27-2009

Scenic Views of Utah

Last week we attended 237^th National Meeting of American Chemical Society in Salt Lake City, Utah. After the conference we visited several interesting places in this state. It is interesting that in Utah the weather changes significantly from North to South. While in Salt Lake City it is windy and snowing, warm weather under clear sky welcomes you on South. This is due to mountain ranges which cross the state. Photo by Dmytro Kosenkov
We have visited only three of more then dozen state and national parks of Utah: Great Salt Lake, Antelope Island, and Arches National Park.
Salt Lake City, Mar-30-2009

Interdisciplinary Center for Nanotoxicity (ICN): New Center—New Web Site

A new web site (http://icnanotox.org/) for our Interdisciplinary Center for Nanotoxicity (ICN) has been launched. The web site was created by Olexandr Isayev. The site is based on the up-to-date content management system and has many other useful features. We are glad to have a brand new web site!
Jackson, Feb-05-2009

Full Moon Craters

This Friday Moon is closer to Earth this year. NASA reported that this Friday Moon was closer to Earth and thus 14% bigger and 30% brighter than other full moons of the year. Even under a hazy sky using my 6" toy telescope purchased for $90 in toy-R-us and Olympus Camedia camera without any attachments I was able to take some pictures. Well, I have got not very clear images but we still can see some craters. On the photos below North-East part of the Moon craters Hahn (84 km), Bersosus (74 km) and Bernoulli (47 km). You can find these craters on the website of The Lunar Republic Society in The Full Moon Atlas
Photo by Dmytro Kosenkov
Jackson, Dec-13-2008

Mississippi Snow: Winter Has Come!

Congratulations, winter has come! This morning we spot snow laying on the cars and grass. This is very unusual for Jackson even in December. Be careful while driving and have a nice Holyday Season!
Photo by Dmytro Kosenkov
Jackson, Dec-11-2008

Sir Norman Foster—Architect

Norman Foster is contemporary British architect and designer. Among his works I especially like Viaduc de Millau (France) and Spaceport America (New Mexico, USA). We can see buildings designed by Foster+Partners group around the world from Australia to Russia. On the photo below courtyard of Smithsonian institution in Washington D.C. designed by Foster+Partners and Smith Group
Photo by Dmytro Kosenkov
Interesting that Norman Robert Foster, Baron Foster of Thames Bank was born in working-class family and received his title of knight for his service. You can find out more details on his unusual biography in Wikipedia.
Jackson, Nov-30-2008

AmbiScript—Enhanced Ambigraphic Nucleic Acid Notation

David A. Rozak and Anthony J. Rozak proposed a new notation called AmbiScript to describe DNA sequence data. AmbiScript uses special characters instead of conventional letters (A, T, C, G) to denote nucleic acid bases. These characters have very interesting property if you rotate string describing DNA by 180° you obtain complimentary sequence. Moreover, the authors tried embed in the characters some properties of the nucleic acid bases to facilitate easier learning of nucleic acid bases properties. For example more strongly h-bonded in pairs cytosine and guanine have the solid baselines of the corresponding characters. Heavier purines (adenine and guanine) hanging below the baseline while lighter pirimidines (cytosine and thymine) rise above the line. If you interested you can download AmbiScript fonts from authors' site.
Jackson, Nov-11-2008

17^th Conference on Current Trends in Computational Chemistry

Last week we have our annual conference on Current Trends in Computational Chemistry. This year Nobel Laureate Prof. Walter Kohn attended the conference. Prof. Kohn presented his documentary „The Power of The Sun“. This movie presents and discuss perspectives of solar energy use. In his work Prof. Kohn tries to attracts attention to problems of energy consumption.
Photo by Igor Pavlenko
On the photo from left to right: Dr. Bakhtiyor Rasulev, Tetyana Petrova, Yаnа Khоlоd, Prof. Walter Kohn, Dmytro Kosenkov, and Yuliya Paukku

Photo by Yаnа Khоlоd
Jackson, Oct-31-2008

Kiev The City

This fall I spent some time in Kiev. I lived in this city for twenty years. Kiev was established in V^th century A.C. Some building of X^th A.C. century can be seen in Kiev today. There are also many interesting buildings of later epochs. Photo by Dmytro Kosenkov
However, the city was heavily damaged during the Second World War and during the last decade. I tried to take pictures of some historical places of the city. Photo gallery „Kiev The City 2008“ is available through Picasa.
Kiev, Jackson, Oct-20-2008

Express Your Opinion about Quantum Chemistry

This week I have decided to establish small voting about quantum chemistry perspectives. You could express your opinion and see what other visitors think. If this voting will be interesting for you I have some more questions for the next week. You could also contact me and suggest your own question for the next voting.

Update: Voting has been finished. It appeared that only half of the people think that there are real perspectives in quntum chemistry…
Jackson, Jul-21-2008

Chipmunks at Iowa State University Campus

Yаnа Khоlоd is currently at Iowa State University in Ames, IA. She sent me couple of pictures with funny university habitants. Small chipmunks are running fast around the campus looking for nuts or other tasty food. Photo by Yаnа Khоlоd
Photo by Yаnа Khоlоd

On the last picture you can see their relative—fluffy tailed squirrel from University of Washington in Seattle, WA. Photo by Dmytro Kosenkov
Jun-22-2008

Lecture Notes on Quantum Chemistry

I see some of the site visitors looking for lecture notes on Quantum Chemistry. There are some useful links:
Introduction to Quantum Chemistry and GAMESS by Mark S. Gordon
Coupled Cluster Theory by T. Daniel Crawford and Henry F. Schaefer III
An Introduction to Theoretical Chemistry by Jack Simons
Jackson, Jun-20-2008

Congratulations to Olexandr Isayev on his Ph.D. Thesis Defense!

Photo by Yаnа Khоlоd
Alex's advisors Prof. Jerzy Leszczynski and Dr. Lеоnid Gоrb discuss some important points…
Jackson, May-2-2008

Advanced Quantum Chemistry Class

Photo by Olexandr Isayev
Prof. Andrzej Sadlej taught the course in Advanced Quantum Chemistry this spring. On the photo our class of doctorate students and Prof Sadlej (from left to right): Jason Ford-Green, Al'ona Furmanchuk, Tetyana Petrova, Prof. Andrzej Sadlej, Yаnа Khоlоd, Dmytro Kosenkov, and Mike Cato.
Jackson, May-2-2008

8^th Southern School on Computational Chemistry

The conference was held as usual in Jackson, MS. There were many interesting talks and posters on quantum chemical investigation of the nanostructures and other systems.

The presentation delivered by Prof. Andrzej Sadlej, Nicolaus Copernicus University, Poland deeply impressed me. His talk was entitled: „Explaining the Derivation and Functioning of the Two–Component Methods. A Simple Algebraic Model“. In the talk Prof. Sadlej outlined perspectives of the multireference configuration interaction and perturbation theories.

I also liked very much the presentation given by Prof. Jason Petta, Princeton University on „Quantum Circuits: Controlling the Quantum Dynamics of Electron Spins“ and Olexandr Isayev work on „Structure of Liquid Water from ab initio Molecular Dynamics at the Complete Plane Wave Basis Set Limit“. I liked very much the work presented by Yаnа Khоlоd on „Origin of Life: Viability of Pyrite Pulled Metabolism in the Iron-Sulfur World Theory. Quantum Chemical Assessment.“

My work presented on the conference was devoted to the kinetic simulation of nitroaromatic compounds decomposition. It was distinguished by The Second Place in The Student Poster Contest. The First Place was presented to Ayorinde Hassan for his poster on the study of the ineraction between metal ions with bicyclohexene and benzene. The Third Place was taken by Tetyana Petrova for her DFT study of acidities of epoxyendic amidoacid esters in ethanol.

Some photos form the conference taken by our colleagues will be posted soon.
Jackson, May-2-2008

Journey to Seattle

Recent photos from my visit to Seattle available through Picasa. There are photos from University of Washington Campus, Downtown Seattle views, Olympic National Park and Pacific Ocean s hore. It was really impressive trip.
Seattle, Apr-21-2008

Typography Week

Recently I read several brilliant books on typography. The first „Thinking with Type: A Critical Guide for Designers, Editors, and Students“ by Ellen Lupton. The book gave sound introduction to typography. It consists of three sections:
Letter
The section contains history of type and classification of typefaces.
Text
Basic concepts of text formatting and relates typography and Jack Derrida′s philosophy of deconstruction were considered.
Grid
The most interesting for me part of the book. This section deals with principles underlying the organization of any printed book: how text is organized in the book. The idea of the typographic grid was from the beginning of printing, however contemporary modular grid owe Dutch De Stiji group, Jan Tschichold (Germany), Josef Müller-Brockmann, Bayer and Renner (Switzerland). This design now called „Swiss“. Some concept of nowadays web design also is considered. In the appendix useful recommendations about text formatting are given.

Symbol	Description	Example
m-dash	A break in the flow of a sentence, no spaces used around m-dashes	Adobe InDesign—enable typographic refinements such as ligatures and oldstyle figures
n-dash	Connects two numbers, no spaces are used around n-dashes	John Baskerville (1706–1775) was a printer in Birmingham, England.
Hyphen	Naturally in the hyphenated words.	I was a do-it-yourself curator, hanging my own shows.

The second book is „Stop Stealing Sheep & Find Out How Type Works“ by Erik Spiekermann and E. M. Ginger. Since contribution from German typographers and printers difficult overestimate it was very interesting to read the book German designer. Spiekermann well known for his world-recognized fonts: FF Meta and ITC Officina. It was also interesting, one of the popular fonts and discussed in each book is type of road signs. Funny story was told in the book and widely cited on the internet. In 1936, Frederic Goudy was in New York City to receive an award for excellence in type design. Upon accepting a certificate, he took one look at it and declared that: „Anyone who would letterspace blackletter would steal sheep“. (More commonly misquoted as: „Anyone who would letterspace lowercase would steal sheep“).
Jackson, Jan-10-2008

Common Typographic Diseases

A funny list of  „Common Typographic Diseases“ instead of standard Lorem ipsum can be found in the examples of „Thinking with Type“ book by Ellen Lupton.

Common Typographic Diseases
Various forms of dysfunction appear among populations exposed to typography for long periods of time. Listed here are a number of frequently observed afflictions.
Typophilia
An excessive attachment to and fascination with the shape of letters, often to the exclusion of other interests and object choices. Typophiliacs usually die penniless and alone.
Typophobia
The irrational dislike of letterforms, often marked by a preference for icons, dingbats, and-in fatal cases-bullets and daggers. The fears of the typophobe can often be quieted (but not cured) by steady doses of Helvetica and Times Roman.
Typochondria
A persistent anxiety that one has selected the wrong typeface. This condition is often paired with OKD (optical kerning disorder), the need to constantly adjust and readjust the spaces between letters.
Typothermia
The promiscuous refusal to make a lifelong commitment to a single typeface-or even to five or six, as some doctors recommend. The typothermiac is constantly tempted to test drive „hot“ new fonts, often without a proper license.
Jackson, Jan-10-2008

Treat of Empirical Approach to Science

Empirical models are very popular now. As these models and assumptions become more convoluted to fit the data, they provide less and less insight. However this insight in turn is the core of the science itself. We should always understand limitations of the empirical approach and develop basic science as well.
Jackson, July-6-2007

Feynman's Thesis

A very good edited by Laurie M. Brown book. The first published Feynman's PhD thesis. The book gives sound introduction to path integrals formulation of quantum mechanics. The book help us understand how Richard Feynman developed his formulation of quantum mechanics. Richard P. Feynman partly published his thesis in Rev. Mod. Phys. 20, 367-387 (1948)
Jackson, May-4-2007

Dali Museum in Saint Petersburg, Florida

I was really impressed by a really great collection of the paintings in Salvador Dali museum. Especially late works from Salvador Dali's classical period. These paintings are very different form Dali's „Melted Watch“ or lips and pyramids of the „Salvador Dali“ perfume. This museum has much more impressive paintings of the artist. „The Discovery of America by Christopher Columbus“, „The Hallucinogenic Toreador“ are large geometrically perfect. Salvador Dali was known for his precise brush. These paintings are larger and more complex than his earlier works. I could advise everyone who likes art visit this museum.
Saint-Petersburg, FL, April-4-2007