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Jan Jensen
Works at University of Copenhagen
Attended Iowa State University
Lives in Copenhagen
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Jan Jensen

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Here's a great feature of how +Janus Juul Eriksen and his team have been using +OpenACC on +NVIDIA GPUs at +Oak Ridge National Laboratory.
For this interview, I reached out to Janus Juul Eriksen, a Ph.D. fellow at Aarhus University in Denmark. Janus is a chemist by trade without any formal education in computer science; but he is gett...
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Revival of an old basis set project
During the stillness in the summer months I've revived an old project regarding the construction of a new basis set optimized for calculating spin-spin coupling constants. It is the aug-cc-pVTZ-J basis set family I hope to contribute to and I am deriving ba...
During the stillness in the summer months I've revived an old project regarding the construction of a new basis set optimized for calculating spin-spin coupling constants. It is the aug-cc-pVTZ-J basis set family I hope to co...
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Last year I wrote a post on the possibility of a stable hypercoordinated carbon in the C(CH3)5+ molecule as proposed by Schleyer and Schaefer. Kozuch has re-examined this molecule with an eye towards examining the lifetime of this proposed “fleeting” molecule. The computed barriers for either ...
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Does this experiment measure ΔH° or ΔA°?
I recently came across this interesting paper from 1974 in which they measure the equilibrium constants for hydrogen bond formation between methanol and amines in the gas phase.  I find it interesting because it's a concrete example the practical considerat...
I recently came across this interesting paper from 1974 in which they measure the equilibrium constants for hydrogen bond formation between methanol and amines in the gas phase. I find it interesting because it's a concrete example the practical considerations that underlying thermodynamics - in ...
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Computational Chemistry Highlights: June issue
The June issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is ...
The June issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for ...
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Grimme, S. and Hansen, A., Angew Chem Int Edit, (2015) Contributed by Tobias Schwabe The question of how to deal with multireference (MR) cases in DFT has a longstanding history. Of course, the exact functional would also include multireference effects (or non-dynamical/non-local/static electron ...
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Jan Jensen

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Best to ask your question on the GAMESS list:  https://groups.google.com/forum/#!forum/gamess
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Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method
Hiroya Nakata, Dmitri G. Fedorov, Takeshi Nagata, Kazuo Kitaura, and Shinichiro Nakamura. Journal of Chemical Theory and Computation  2015, 11, 3053−3064 Contributed by  +Jan Jensen Reprinted (adapted) with permission from J. Chem. Theory Comput. 2015, 11, ...
I am highlighting this paper because it is the first paper I have come across that reports the optimized TS, free energy barrier, and IRC for an enzymatic reaction using an all-QM description of the entire enzyme. The underlying method is the frozen domain with dimers (FDD) formulation of the ...
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Planned papers for 2015 - six months in
In January I wrote about the papers I plan to publish and made this list: Submitted 1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the therm...
In January I wrote about the papers I plan to publish and made this list: Submitted 1. Søs Torpenholt, Leonardo De Maria, Mats H. M. Olsson, Lars H. Christensen, Michael Skjøt, Peter Westh, Jan H. Jensen and Leila Lo Leggio "Effect of mutations on the thermostability of Aspergillus aculeatus β-1 ...
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The mind-blowing power of randomness

Here's a puzzle:

I write down two different numbers that are completely unknown to you, and hold one in my left hand and one in my right. You have absolutely no idea how I generated these two numbers. Which is larger?

You can point to one of my hands, and I will show you the number in it. Then you can decide to either select the number you have seen or switch to the number you have not seen, held in the other hand.  Is there a strategy that will give you a greater than 50% chance of choosing the larger number, no matter which two numbers I write down?

At first it seems the answer is no.  Whatever number you see, the other number could be larger or smaller.  There's no way to tell.  So obviously you can't get a better than 50% chance of picking the hand with the largest number - even if you've seen one of those numbers!

But "obviously" is not a proof.  Sometimes "obvious" things are wrong!

It turns out that, amazingly, the answer to the puzzle is yes.  You can find a strategy to do better than 50%.  But the strategy uses randomness.

I'd seen this puzzle before - do you know who invented it? 

If you want to solve it yourself, stop now or read Quanta magazine for some clues - they offered a small prize for the best answer. 

Otherwise, you can read Greg Egan's answer, which seems like the best answer to me. 

I'll paraphrase it here:

Pick some function f(x) defined for all real numbers, such that:

the limit as x → -∞ of f(x) is 0,

the limit as x → +∞ of f(x) is 1,

whenever x > y, f(x) > f(y).

(There are lots of functions like this; choose any one.)

Next, pick one hand at random. If the number you are shown is x, compute f(x). Then generate a uniform random number z between 0 and 1.  If z is less than or equal to f(x) guess that x is the larger number, but if z is greater than f(x) guess that the larger number is in the other hand.

The probability of guessing correctly can be calculated as the probability of seeing the larger number initially and then, correctly, sticking with it, plus the probability of seeing the smaller number initially and then, correctly, choosing the other hand.

This is

0.5 f(x) + 0.5 (1 - f(y)) = 0.5 + 0.5(f(x) – f(y))

This is strictly greater than 0.5, since x > y so f(x) - f(y) > 0.

So, you have a more than 50% chance of winning!  But as you play the game, there's no way to tell how much more than 50%.  If the numbers on the other players hands are very large, or very small, your chance will be just slightly more than 50%.

Puzzle 1: Prove that no deterministic strategy can guarantee you have a more than 50% chance of choosing the larger number.

Puzzle 2: There are perfectly specific but 'algorithmically random' sequences of bits, which can't predicted well by any program.  If we use these to generate a uniform algorithmically random number between 0 and 1, and use the strategy Egan describes, will our chance of choosing the larger number be more than 50%, or not?
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Accurately Modeling Nanosecond Protein Dynamics Requires at least Microseconds of Simulation
Gregory R. Bowman  Journal of Computational Chemistry 2015 Contributed by  +Jan Jensen This papers compares computed and experimental order parameters for two proteins, ubiquitin and RNase H, computed using 10, 100, 1000, and 10000 ns (10 $\mu$s) explicit m...
Gregory R. Bowman Journal of Computational Chemistry 2015. Contributed by +Jan Jensen This papers compares computed and experimental order parameters for two proteins, ubiquitin and RNase H, computed using 10, 100, 1000, and 10000 ns (10 $\mu$s) explicit molecular dynamics simulations.
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In what is seen as the opening shot of a global superstar revolt against the establishment, Taylor Swift announced on her twitter feed earlier today that she was no longer content to review papers for
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Work
Employment
  • University of Copenhagen
    Professor of Bio-Computational Chemistry, present
  • University of Iowa
    1997 - 2006
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Introduction
I am a computational chemist working at the University of Copenhagen.  I work on protein design, quantum chemistry methods, and visualization
Education
  • Iowa State University
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