FP6 “PACE” project (http://www.istpace.org/index.html) related scientific work in Vilnius University group

Quantum Mechanical Design and Construction of Photosynthetic Centers of NanoBioRobots
Arvydas Tamulis

Vilnius University Institute of Theoretical Physics and Astronomy, A. Gostauto 12, Vilnius, Lithuania, e-mail: tamulis@itpa.lt

Modeling:

1. Quantum mechanical self-assembly of artificial minimal living cells

We used quantum mechanical (QM) nonlocal gradient electron correlation interactions density functional theory (DFT) methods (i.e. high precision quantum mechanical simulations) to investigate various self-assembled photoactive bioorganic systems of artificial minimal living cells [1-13]. The cell systems studied are based on peptide nucleic acid (PNA) and consisted of up to 360 atoms (not including the associated water or methanol solvent shells) and are up to 3.0-4.2 nm in diameter. The electron correlations interactions originating the hydrogen bonds and Van der Waals weak chemical bonds that increase due to the addition of a polar solvent (water or methanol) molecules, and fatty acid (FA) and precursor fatty acid (pFA) molecules play a critical role in the QM interaction based self-assembly of the photosynthetic center and functioning of the photosynthetic processes of the artificial minimal living cells. The distances between the separated sensitizer, precursor fatty acid, and water or methanol molecules are comparable to Van der Waals and hydrogen bonding radii. As a result these nonlinear quantum interactions compress the overall system resulting in a smaller gap between the HOMO and LUMO electron energy levels and photoexcited electron tunneling occurs from the sensitizer (either a 1,4-bis(N,N-dimethylamino) naphthalene or a [Ru(bpy)₂(4,4'-Me-2-2'-bpy)]²⁺) to pFA molecules (notation used: Me = methyl; bpy = bipyridine).

2. Quantum processes in photosynthesis of artificial minimal living cells

The electron tunneling and associated light absorption of most intense transitions as calculated by the time dependent density functional theory (TD DFT) method differs from spectroscopic experiments by only 0.3 or 0.2 nm, which is within the value of experiment errors [9, 13]. This agreement implies that the quantum mechanically self-assembled structures of minimal living cells very closely approximate the realistic ones.
One successful example: we have performed calculations using TD DFT PBEPBE model with the 6-31G basis set together with COSMO water solvent model installed on our research group dual processor Opteron servers Linux cluster of the difference of electron charge density (excited-state - ground-state) for the conjugated cytosine-1,4-bis(N,N-dimethylamino)naphthalene supermolecule and six fatty acid, and two pFA molecules, and visualized the electron charge tunneling associated with certain excited state transitions (see Figure 1).

Figure 1. Visualization of quantum mechanical process of “eating” of artificial minimal living cell synthesized in Los Alamos National Laboratory. During the most intense excited state the single electron is hopping (tunneling) from cytosine-1,4-bis(N,N-dimethylamino)naphthalene supermolecule (dark blue cloud of electron hole) to one of pFA molecules (grey cloud of electron). Carbon atoms and their associated covalent bonds are shown as green sticks, hydrogens are in light grey, oxygens – red, nitrogens – blue.

Quantum mechanical electron correlation experiments of self-assembly of above described artificial minimal living cells show that these cells are complex systems because only entire ensemble of PNA, and sensitizer, and pFA, and FA and water molecules is stable and perform quantum photosynthetic processes. Removing the small part of nucleobase, FA and water molecules leads to the structural changes in comparison with realistic structures and difference in comparison with the spectroscopic values of photoexcited electron tunneling from sensitizer (1,4-bis(N,N-dimethylamino)naphthalene to pFA molecules. QM electron correlation experiments of self-assembly of artificial minimal living cells removing the main part of nucleobase, and FA and water molecules leads to the degradation of these cells [9]. We can state what the inclusion of ever more water, and fatty acid, and pFA molecules, and waste pieces of the pFA molecules and nucleobase molecules in the different artificial minimal living cells results in a shift of the absorption spectrum to the red for the artificial protocell photosynthetic centre, leading to an ever closer approach to the real experimental value and indicates the measure of the complexity of this quantum complex system, i.e. a minimal protocell. It is important to say that only QM electron correlation TD-DFT experiments with minimal living cells gives results exactly comparable with spectroscopic results and all other more simplified QM methods such as local gradient DFT or ab initio Hartree-Fock gives structures and spectra far from the experimentally measured.
The corresponding of experimental absorption spectra peaks and our QM calculated confirm that our chosen method of designing single electron nano photocells might be useful not only for artificial living organisms but also for wide implementation in the nano photodevices, and molecular computers.

Experiment, Future Capabilities:

3. Quantum mechanical control of functions of artificial minimal living cells

Our goals are by using quantum mechanical experiments to predict the possibility of biochemical experimental synthesis of molecular electronics and spintronics logical elements information based artificial living organisms or nanobiorobots for nanomedicine and cleaning of nuclear, chemical and microbial pollutions.
We are creating molecular electronics logic gates regulating the photosynthesis, growing and dividing of artificial living cells and nanobiorobots [14-21]. It was performed the quantum mechanical study of G-C self-assembling energies in various H₂O molecules clusters correlating these energies with the G-C dehybridization energies due to charge transfer in the H₂O molecules clusters surrounded the photosynthetic center of artificial minimal living cell controlled by the last chain of genome, i.e. hydrogen bonded G-C supramolecule.

Implementation of quantum information bits based on spatially localized electron spins in stable molecular radicals was investigated by unrestricted time dependent functional theory methods [15, 20]. The g-tensor shift calculations of neutral radical molecules was performed for beta-diketone and syringate. beta-diketone neutral radical moiety with an attached hydrocarbon chain. Beta-diketone is suitable for construction of quantum computing processing devices because the qubit is relatively stable due to the small magnitude of g-tensor shift component that is aligned with the external magnetic field, i.e. the direction of hydrocarbon chain which provide the self-assembled monolayer an attachment of the molecule to a substrate [18].
Analysis of time dependent density functional theory method calculated absorption spectrum and images of electron transfer trajectories in the different excited states allow to separate two different logically controlled functions of molecular device consisting of guanine-cytosine-PNA-1,4-dihydroquinoxaline-1,4-bis(N,N-dimethylamino)naphthalene supermolecule and Van der Waals bonded precursor of fatty acid molecule. These two different logically controlled functions of artificial minimal living cells are: 1) initiation of metabolic fatty acid production in five excited states or 2) initiation of gene dehybridization in one excited state. This designed supermolecule works in the artificial minimal cell as molecular electronics classic OR logic function (Boolean logics OR gate) [21].
TD DFT simulations of the artificial minimal living cells with implemented molecular electronics and spintronics gates done using self-assembled neutral radical molecules beta-diketone and syringate show that it is possible to construct more general ContrlNOT and NAND logic functions suitable for the production of the nanobiorobots [19]. Designed of variety of the molecular spintronics devices will regulate photosynthesis and growth of artificial minimal living cells in the conditions of external magnetic fields, while also providing a perspective of the requirements for success in the synthesis of new forms of artificial living organisms:

http://www.daviddarling.info/encyclopedia/M/molecular_quantum_computing_cloud.html

We are planing experimental synthesis of photosynthetic centers of minimal cells, molecular logic devices and femtosecond laser spectroscopic measurements. This fundamental research needs for our goal of experimental synthesis of logically controlled minimal cells and nanobiorobots and their femtosecond laser spectroscopic measurements.

A list of PACE project related publications

[1] J. Tamuliene, M. L. Balevicius, A. Tamulis, “Search of Suitable Sensitizers” book of abstracts International conference on “ Structure and Spectroscopy” held in Vilnius , September 23-26, P9, 2004.

[2] Jelena Tamuliene, Arvydas Tamulis, “Quantum Mechanical Investigations of Self-Assembled System Consisting of Peptide Nucleic Acid, Sensitizer, and Lipid Precursor Molecules”, Lithuanian Journal of Physics, vol 45, No 3, p.p. 167-174, 2005.

[3] Jelena Tamuliene, Arvydas Tamulis, Peter Nielsen, “Quantum mechanical investigations of flexibility of E and E^(ag) nucleobases”, book of abstracts of 36th Lithuanian National Physics Conference, Vilnius, June 16-18, 2005, p. 140-141.

[4] A. Tamulis, V. Tamulis A. Graja. “Quantum mechanical modeling of self-assembly and photoinduced electron transfer in PNA based artificial living organism”, Journal of Nanoscience and Nanotechnology, 6, 965-973 (2006).

[5] Arvydas Tamulis, Vykintas Tamulis, "Measure of Complexity and Photoinduced Electron Tunneling in Photosynthetic Systems of PNA Based Self-Assembled Protocells", book of abstracts of Third Annual Meeting COST Action P10 "Physics of Risk" & Workshop on "Complex System Science", Vilnius Lithuania, 13-16 May 2006, pages 59-60.

[6] Arvydas Tamulis, abstract of presentation „Basic Questions about the Origin of Life“, Question 9: Artificial life“, book of abstracts of International School on Complexity – 4th Course, Italy, Erice, 2-5 October, 2006, page 92.
[7] J. Tamuliene, M.L. Balevicius. „Search for sensitizer to peptide nucleic acid sequence with adenine and guanine bases“, Viva Origino, vol. 34. p.p. 112-115, 2006.

[8] Arvydas Tamulis, Vykintas Tamulis, „Quantum processes in photosynthetic systems of artificial minimal cells“, book of abstracts of conference “Chembiogenesis 2006”, Barcelona, Spain, December 14 – 17, 2006, p. 24.

[9] A. Tamulis, V. Tamulis, H. Ziock, S. Rasmussen, “Influence of Water and Fatty Acid Molecules on Quantum Photoinduced Electron Tunnelling in Photosynthetic Systems of PNA Based Self-Assembled Protocells”, Chapter #2 in “Multi-scale Simulation Methods for Nanomaterials”, eds. R. Ross and S. Mohanty, John Wiley & Sons, Inc., New Jersey, pages 9-28, January 2008.
[10] Arvydas Tamulis and Vykintas Tamulis, "Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic System of Minimal Living Cell", Viva Origino, vol. 35, p.p. 66-72, 2007.
[11] Arvydas Tamulis, Vykintas Tamulis, „Quantum mechanical modeling of artificial minimal living cells“ , book of abstracts of 37^th Lithuanian national physics conference, June 11-13, 2007, page 128.
[12] Arvydas Tamulis and Vykintas Tamulis, "Question 9: Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic Systems of Artificial Minimal Living Cells", Origins of Life and Evolution of Biospheres, vol. 37, No 4-5, p.p. 473-476, 2007.
[13] S. Rasmussen, J. Bailey, J. Boncella, L. Chen, G. Collins, S. Colgate, M. DeClue, H. Fellermann, G. Goranovic, Y. Jiang, C. Knutson, P.-A. Monnard, F. Moufouk, P. Nielsen, A. Sen, A. Shreve, A. Tamulis, B. Travis, P. Weronski, W. Woodruff, J. Zhang, X. Zhou, and H. Ziock, “Assembly of a minimal protocell”, in MIT Press book, “Protocells: Bridging nonliving and living matter”, eds S. Rasmussen, M. Bedau, L. Chen, D. Krakauer, D. Deamer, N. Packard, and P. Stadler, 2007 in press.
[14] Arvydas Tamulis, Jelena Tamuliene, Vykintas Tamulis, Aiste Ziriakoviene, “Quantum Mechanical Design of Molecular Computers Elements Suitable for Self-Assembling to Quantum Computing Living Systems”, Solid State Phenomena, Scitec Publications, Switzerland, Vols. 97-98, p.p. 175-180, 2004.
[15] J. Tamuliene, A. Tamulis, J. Kulys “Electronic Structure of Dodecyl Syringate Radical Suitable for ESR Molecular Quantum Computers”, Nonlinear Analysis: Modeling and Control, Vol. 9, No 2, p.p. 185-196 (2004).
[16] A. Tamulis, V. Tamulis, “Variety of Self-Replicating Complex Living System Based on Quantum Information”, book of abstracts of conference “Chembiogenesis 2005”, Venice, Italy, Sept. 28 – Oct. 01, 2005, page 18.
[17] Jelena Tamuliene, Arvydas Tamulis, Aiste Ziriakoviene, Andrzej Graja. „Quantum Chemical Design of Two Logical Functions Molecular Device“, Lithuanian Journal of Physics, vol. 46, p.p. 163-167 (2006).
[18] Z. Rinkevicius, Arvydas Tamulis, Jelena Tamuliene. “Beta-Diketo Structure for Quantum Information Processing”, Lithuanian Journal of Physics, vol. 46, p.p. 413-416 (2006).
[19] Arvydas Tamulis, Vykintas Tamulis, „Quantum Mechanical Self-Assembling of Artificial Minimal Cells and Control by Molecular Electronics and Spintronics Logical Devices”, book of abstracts of COST D27 Final Evaluation conference “Prebiotic Chemistry and Early Evolution”, Inter – University Center, Dubrovnik, Croatia, May 11 - 13, 2007, pages 30-31.
[20] A. Tamulis, V. I. Tsifrinovich, S. Tretiak, G. P. Berman, D. L. Allara, ”Neutral Radical Molecules Ordered in Self-Assembled Monolayer Systems for Quantum Information Processing”, Chemical Physics Letters, vol. 436, p.p. 144 - 149 (2007).
[21] Arvydas Tamulis and Vykintas Tamulis, “Quantum Mechanical Design of Molecular Electronics OR Gate for Regulation of Minimal Cell Functions”, Journal of Computational and Theoretical Nanoscience, vol. 5 No4, p.p. 545-553, 2008.

A list of press releases

1. Arvydas Tamulis, Vykintas Tamulis, “Self-assembling of artificial programmable cells and their growing and control” (in Lithuanian language), Lithuanian journal “Mokslas ir Gyvenimas” (“Science and Life”), 2006 No 12, page 32 http://ausis.gf.vu.lt/mg/ .
2. Arvydas Tamulis, “Scientists meet new challenges in nanoecology and nanomedicine (PACE project)” (in Lithuanian language), in the book: “Participation of Lithuania in the FP6 of European Union, examples of successes”, issued by Agency for International Science and Development Programs in Lithuania, pages 32-33, 2007 http://www.tpa.lt/publikacijos.htm
3. Arvydas Tamulis, “Artificial cell was modeled in Lithuania” (in Lithuanian language), placed in Lithuanian WEBserver “Science News” on January 30, 2007 at: http://mokslasplius.lt/mokslo-
naujienos/2007/01/30/sukurta-dirbtine-lastele
4. Arvydas Tamulis proposed idea of Molecular Quantum Computing Life is publishing in the Lithuanian WEBsite: http://mokslasplius.lt/mokslo-naujienos/2007/04/04/kvantine-gyvybe and in the The Encyclopedia of Astrobiology, Astronomy and Spaceflight: http://www.daviddarling.info/encyclopedia/M/molecular_quantum_computing_cloud.html
5. Arvydas Tamulis, “Artificial living cells and nanobiorobots” (in Lithuanian language), Lithuanian journal “Mokslas ir Technika” (“Science and Technology”), 2007 No 12, pages 26-28 http://www.ktl.mii.lt/mt/
6. Arvydas Tamulis, A talk about quantum mechanical control of artificial living cells in Lithuanian TV movie on March 29 (see http://www.tv.lt/mconsole.asp?category_id=157, Negali Buti LRT 2008-03-29 and click on the Siusk (Send)). A. Tamulis contribution is in the second part of this movie after TV advertisement.