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Authors |
Title |
Journal |
Comments |
| 1. |
Dieter Cremer, Peder Svensson, Elfi Kraka,
Zoran Konkoli, and Per Ahlberg:
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Exploration of the Potential Energy Surface of C9H9+ by ab initio Methods II. Is
the 1,4-Bishomotropilium Cation a Bishomoaromatic Prototype,
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J. Am. Chem. Soc. 115, 7457-7464 (1993) |
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2. |
Elfi Kraka, Zoran Konkoli, and Dieter Cremer, Joseph Fowler and Henry F. Schaefer
III |
Diflourodioxirane - An Unusual Cyclic Peroxide |
J. Am. Chem. Soc. 118, 10595-10608 (1996) |
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3.
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Zoran Konkoli, Elfi Kraka, and Dieter Cremer |
The Unified Reaction
Valley Approach. Mechanism of the reaction CH3+H2 CH4+H,
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J. Phys. Chem. A 101, 1742-1757
(1997). |
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4. |
Zoran Konkoli, Zhi He and Dieter Cremer
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On the role of single excitations
in Quasi-degenerate Perturbation Theory,
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Theoret. Chem. Accounts 96, 71-74 (1997). |
One of the problems that are still close to my heart, though I do not see any solution
to it: given that your wave function is of the multiconfiguration type (not single
determinant) how to do perturbation theory? This paper showed that one has to be
extremely careful. |
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5. |
Zoran Konkoli, Dieter Cremer, and Elfi Kraka
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Diabatic ordering of vibrational
normal modes in reaction valley studies,
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J. Comput. Chem. 18, 1282-1294 (1997). |
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6.
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Zoran Konkoli and Dieter Cremer
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A new way of analysis vibrational spectra I.
Derivation of Adiabatic internal modes,
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Int. J. Quant. Chem. 67, 1-9 (1998). |
First of the series of papers that tried to solve nuclear coordinate problem. What
is really a C-H vibration mode? How to characterize it? How our intuition of nuclear
motion relates to reality? |
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7.
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Zoran Konkoli, Andreas J. Larsson, and Dieter Cremer |
A new way of analysis vibrational
spectra II. Comparison of internal mode frequencies,
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Int. J. Quant. Chem. 67, 11-27
(1998).
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ibid, second paper |
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8.
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Zoran Konkoli and Dieter Cremer |
A new way of analysis vibrational spectra
III. Characterization of normal vibrational modes in terms of internal vibrational
modes,
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Int. J. Quant. Chem. 67, 29-40 (1998). |
ibid, third paper |
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9.
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Zoran Konkoli, Andreas J. Larsson, and Dieter Cremer |
A new way of analysis vibrational spectra IV. Application and
testing of adiabatic modes within the concept of the characterization of normal
modes,
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Int. J. Quant. Chem. 67, 41-55 (1998).
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ibid, fourht paper |
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10. |
Zoran Konkoli, Henrik Johannesson
and Benjamin P. Lee
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Fluctuation Effects in Steric Reaction-Diffusion Systems,
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Phys.
Rev. E 59, R3787 (1999).
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We studied diffusion controlled model A+A, A+B, B+B. Inspiration came from up to
date work on steric effects (molecules need to have particular orientation in order
to react). Field theory is used together with Monte Carlo simulation. We showed
that system exhibits both d/2 and d/4 decays characteristic of A+A and A+B systems. |
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11. |
Zoran Konkoli and Henrik Johannesson |
Two-species
reaction-diffusion system with equal diffusion constants: Anomalous density decay
at large times,
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Phys. Rev E 62, 3276 (2000)
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Same as 10. but with non-equal initial concentrations. This worked showed how fluctuation
dominated kinetics leads to complete break-down of classical (mean field) kinetics.
According to classical kinetics ration nA/nB should saturate either to infinity
or zero, while correct results is that this ratio should saturate to constant value. |
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12. |
Zoran Konkoli, John Hertz and Silvio Franz
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Random heteropolymer dynamics,
. |
Phys. Rev. E 64, 051910 (2001) |
Is it possible to do a pencil-and-paper study of protein dynamics? We (like many
before us) showed that it is. This was one of the first dynamic calculations (no
replicas as in static calculation, just Langevin equation). |
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13. |
Tobias
Ambjörnsson, Peter S. Apell, Zoran Konkoli, Edmund A. Di Marzio, John J. Kasianowicz
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Charged polymer membrane translocation,
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J. Chem. Phys. 117, 4063-4073 (2002).
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How does the long polymer move through a narrow hole? This question is extremely
relevant for understanding intake of long molecules by the living cell. |
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14. |
Zoran Konkoli and John Hertz |
Embedding The Native State into the Random Heteropolymer
Model: The Dynamic Approach,
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Phys. Rev. E 67, 051915 (2003).
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Second attmept to look at protein folding. This time with native state present.
How to build a native state information into a protein model? We showed that glassy
phase is hard to get rid off (even with largest possible value of free parameters).
In light of this the fact that real proteins are not glassy becomes more puzzling... |
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15. |
Zoran Konkoli, A. Karlsson, O. Orwar |
The pair approach applied to kinetics in restricted geometries:
strengths and weaknesses of the method,
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J. Phys. Chem B 107, 14077 (2003). |
Here we used many-body density funtion formalism developed by Kotomin-Kuzovkov to
describe diffusion controlled reactions in small volumes. This is a pure method
development paper. |
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16. |
Zoran Konkoli |
Application of the Bogolyubov's theory of weakly non-ideal Bose gas
on the A+A, A+B, B+B reaction-diffusion system,
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Phys. Rev. E 69, 11106 (2004). |
Another pure method development paper. Using long forgotten tehcnique (weakly non-ideal
Bose gass theory, originally suggested by Ovchinikov among others) to solve
a field theory for typical diffusion-controlled reactions. I would call it "Russian
school". |
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17.
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Mattias Karlsson, Max Davidson, Roger Karlsson, Anders Karlsson, Johan Bergenholtz,
Zoran Konkoli, Aldo Jesorka, Tatsiana Lobovkina, Johan Hurtig, Marina Voinova, and
Owe Orwar |
Biomimetic nanoscale reactors and networks,
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Ann. Rev. Phys. Chem. 55,
613 (2004). |
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18. |
Anders Karlsson, Kristin Sott, Martin Markström, Max Davidson,
Zoran Konkoli, and Owe Orwar
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Controlled Initiation of Enzymatic Reactions in Micrometer-Sized
Biomimetic Compartments,
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J. Phys. Chem. B 109, 1609 (2005).
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19. |
Zoran Konkoli
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The interplay between chemical reactions and transport in structured spaces,
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Phys.
Rev. E 72, 011917 (2005). |
This work is inspired by an attempt to understnad how structure of the underlying
reaction container influences reaction dynamics (kinetics). Such study is relevant
for understanding living cell biochemistry in general. |
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20. |
Ludvig Lizana and Zoran Konkoli |
Diffusive transport
in networks built of containers and tubes,
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Phys. Rev. E 72, 026305 (2005). |
How to desribe diffusive transport in structured space? Do we need to solve diffusion
equation all the time? Such approach would be unwise for large and complicated structures.
Are there better alternatives? We showed that indeed there are... |
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21. |
Kristin Sott, Tatsiana Lobovkina, Ludvig Lizana, Michal Tokarz, Brigitte Bauer,
Zoran Konkoli, and Owe Orwar
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Controlling enzymatic reactions by geometry in a biomimetic
nanoscale network.
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Nano Lett. 6(2), 209 (2006).
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This is experimental follow up of theoretical paper no. 15. There we showed that
theory of diffuson-controlled reactions can be used to describe real biochemical
problem. (To my great surprise there are still people around who doubt this...) |
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22. |
L. Lizana, Z. Konkoli, and O. Orwar
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Tunable Filtering of Chemical Signals in a Simple Nanoscale Reaction-Diffusion Network
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Accepted for publication in J. Phys. Chem. B; to appear in late April or early May
2007 issues.
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Study of biocomputing by diffusion controlled reactions. A first step in this direction
where structured geometry is used together with transport. One can make things more
complicated by adding reactions. |
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23. |
Zoran Konkoli: |
Diffusion-controlled reactions
in small and structured spaces as a tool for describing living cell biochemistry,
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Journal of Physics: Condensed Matter 19(6): 065149 (2007). |
By invitation; special issue on Chemical
Kinetics Beyond the Textbook: Fluctuations, Many-Particle Effects and Anomalous Dynamics |