Andrzej Dobek
Adam Mickiewicz University in Poznań, Faculty of Physics, Faculty Member
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Light-gradient experiments on spherical systems (small EDTA-vesicles and large osmotically swollen thylakoids) have shown the occurrence of inversion of the photovoltage polarity depending on the wavelength of picosecond light pulses [1].... more
Light-gradient experiments on spherical systems (small EDTA-vesicles and large osmotically swollen thylakoids) have shown the occurrence of inversion of the photovoltage polarity depending on the wavelength of picosecond light pulses [1]. This observation cannot easily be explained within the earlier theory of light intensity distribution in systems of stacked planar layers, modeling the thylakoid membranes in chloroplasts, which assumed antiparallel pairs of planar photosynthetic membranes and predicted an inversion only for certain well defined values of the distance between the membranes [2,3]. Therefore, it was desirable to develop a new theory which would describe: i) the propagation of light within systems of spherical symmetry (taking into account refraction and absorption), ii) the dipole moments induced by charge separation in the reaction center (RC), knowing the light distribution in such systems, and iii) the photovoltage generated in the light-gradient experiment measured by two electrodes at different positions along the light path within the suspension [1,4].
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The study of exciton transfer and primary charge separation in photosynthesis requires excitation by picosecond flashes. If a significant fraction of the reaction centers (RCs) shall be closed by a flash, the excitation density must be... more
The study of exciton transfer and primary charge separation in photosynthesis requires excitation by picosecond flashes. If a significant fraction of the reaction centers (RCs) shall be closed by a flash, the excitation density must be chosen such high that more than one exciton resides at the same time in the pool of antenna pigments. Then excitons can be lost by singlet-singlet annihilation before they are trapped by the photochemistry in the RC. Annihilation leads to an apparent acceleration of all other reactions connected with the exciton dynamics. The quantitative treatment of this competitive deactivation path allows the bimolecular rate constant of exciton-exciton annihilation to be determined that characterizes a given antenna bed.
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The study of exciton transfer and primary charge separation in photosynthesis requires excitation by picosecond flashes. If a significant fraction of the reaction centers (RCs) shall be closed by a flash, the excitation density must be... more
The study of exciton transfer and primary charge separation in photosynthesis requires excitation by picosecond flashes. If a significant fraction of the reaction centers (RCs) shall be closed by a flash, the excitation density must be chosen such high that more than one exciton resides at the same time in the pool of antenna pigments. Then excitons can be lost by singlet-singlet annihilation before they are trapped by the photochemistry in the RC. Annihilation leads to an apparent acceleration of all other reactions connected with the exciton dynamics. The quantitative treatment of this competitive deactivation path allows the bimolecular rate constant of exciton-exciton annihilation to be determined that characterizes a given antenna bed.
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Transient absorption spectroscopy (with 120 fs time resolution) was applied to measure at room temperature the electron transfer in the reaction center of the purple photosynthetic bacterium Rb. sphaeroides R-26. Absorption changes were... more
Transient absorption spectroscopy (with 120 fs time resolution) was applied to measure at room temperature the electron transfer in the reaction center of the purple photosynthetic bacterium Rb. sphaeroides R-26. Absorption changes were measured in the range from 400 nm up to 680 nm, after excitation with a laser pulse of 80 fs duration at 800 nm. The absorbance changes characteristic of the excited state of the primary donor and extending over the whole spectral range investigated, appeared within 120 fs. They gave rise to the bleaching of the Qx absorption band of bacteriochlorophyll at 600 nm, increased further by electron transfer to bacteriopheophytin in ~ 3 ps. Photoreduction of the bacteriopheophytin acceptor detected at 546 nm and 670 nm proceeded with the same time constant. Relatively the largest were multiphase absorbance changes in the blue spectral range between 415 nm and 450 nm. Apart from the immediate absorbance increase due to excitation of the primary donor, anoth...
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effect of mono- and divalent cations on Tetrahymena thermophila telomeric repeat fragment. A photon correlation spectroscopy study
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Predictions of hyperfine structure in hydrogen-like 229Th89+ ions are presented for both the 5/2+ ground state of the nucleus and the 3.5 eV 3/2+ isomeric state. The effect of nuclear spin mixing and mixing oscillations is analyzed.... more
Predictions of hyperfine structure in hydrogen-like 229Th89+ ions are presented for both the 5/2+ ground state of the nucleus and the 3.5 eV 3/2+ isomeric state. The effect of nuclear spin mixing and mixing oscillations is analyzed. Perspectives of experimental verification of these predictions are briefly discussed.
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The supersonic free-jet expansion technique has been used in different fields of physics, chemical physics and chemistry to study vibrational and rotational molecular structures in both ground and excited electronic energy states as well... more
The supersonic free-jet expansion technique has been used in different fields of physics, chemical physics and chemistry to study vibrational and rotational molecular structures in both ground and excited electronic energy states as well as in studies of neutral–neutral interactions. The technique exploits a source of monokinetic, rotationally and vibrationally cold molecules that are very weakly bound in their ground electronic states. Recently, the method is applied as a source of pairs of entangled atoms to test Bell’s inequalities.
The three papers on the statistical description of thermal equilibrium published by Albert Einstein in the years 1902–1904 in Annalen der Physik are reviewed. W kolejnych latach 1902, 1903 i 1904 ukazały się w czasopiśmie Annalen der... more
The three papers on the statistical description of thermal equilibrium published by Albert Einstein in the years 1902–1904 in Annalen der Physik are reviewed. W kolejnych latach 1902, 1903 i 1904 ukazały się w czasopiśmie Annalen der Physik trzy prace Alberta Einsteina poświęcone podstawom fizyki statystycznej. Postawione w nich zostało zasadnicze zagadnienie wyprowadzenia praw termodynamiki z mechanicznego modelu układów fizycznych w ścisłym powiązaniu z rachunkiem prawdopodobieństwa. W refleksji Einsteina nad tym problemem istotną rolę odegrały oryginalne koncepcje teorii kinetycznej rozwinięte przez Maxwella i Boltzmanna. Jest to szczególnie widoczne w pracy [1] z 1902 r. W kolejnym artykule [2], opublikowanym w roku 1903, Einstein postawił już sobie za cel sformułowanie podstaw termodynamiki opartych na ogólniejszych założeniach; szczególną ilustracją tych podstaw miała być teoria kinetyczna gazów. Wreszcie, w 1904 roku ukazało się ważne uzupełnienie [3], zawierające m.in. anali...
The structure of the Tetrahymena thermophila telomeric sequence d(TGGGGT)(4) was studied by photon correlation spectroscopy (PCS) in aqueous solution in the presence of NaCl, KCl and SrCl(2). The sample studied was polydisperse in all... more
The structure of the Tetrahymena thermophila telomeric sequence d(TGGGGT)(4) was studied by photon correlation spectroscopy (PCS) in aqueous solution in the presence of NaCl, KCl and SrCl(2). The sample studied was polydisperse in all conditions studied. Translational diffusion coefficients D(T) describing the diffusion modes observed were determined. On the basis of a comparison between the experimental D(T) values with those calculated assuming the bead model, two forms were identified as telomeric quadruplex structures: monomer and tetramer. In the presence of SrCl(2) formation of aggregates was observed, with a size that reached several micrometres. The relative weighted concentrations of the structures observed for different concentrations of a salt and DNA were determined. The results obtained in the presence of monovalent ions were qualitatively similar and could be presented in a coherent plot in which the concentration of salt was expressed by the number of ions per DNA mol...
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Nonlinear THz pump – optical probe (THz – OKE) measurements in deionized, distilled and buffered (PBS) water are reported. A laser system that produces pulses at 800 nm, 30 fs...
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Molecular mass of the iron-dextran complex (M(w)=1133 kDa), diameter of its particles (∼8.3 nm) and the content of iron ions in the complex core (N(Fe)=6360) were determined by static light scattering, measurements of refractive index... more
Molecular mass of the iron-dextran complex (M(w)=1133 kDa), diameter of its particles (∼8.3 nm) and the content of iron ions in the complex core (N(Fe)=6360) were determined by static light scattering, measurements of refractive index increment and the Cotton-Mouton effect in solution. The known number of iron ions permitted the calculation of the permanent magnetic dipole moment value to be μ(Fe)=3.17×10(-18) erg Oe(-1) and the determination of anisotropy of linear magneto-optical polarizabilities components as Δχ=9.2×10(-21) cm(3). Knowing both values and the value of the mean linear optical polarizability α=7.3×10(-20) cm(3), it was possible to show that the total measured CM effect was due to the reorientation of the permanent and the induced magnetic dipole moments of the complex. Analysis of the measured magneto-optical birefringence indicated very small optical anisotropy of linear optical polarizability components, κ(α), which suggested a homogeneous structure of particles of spherical symmetry.
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The effect of 0.01-1 M sodium ions on the conformation of the folded brewer’s yeast tRNA
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ABSTRACT The optical Kerr effect (OKE) of tRNA solutions induced by picosecond light pulses of a YAG-Nd3+ laser, λ = 1060 nm, was investigated. A weak He-Ne laser light beam, λ = 632.8 nm, served as the measuring beam. The experimentally... more
ABSTRACT The optical Kerr effect (OKE) of tRNA solutions induced by picosecond light pulses of a YAG-Nd3+ laser, λ = 1060 nm, was investigated. A weak He-Ne laser light beam, λ = 632.8 nm, served as the measuring beam. The experimentally determined molecular Kerr constants BmolNL, and previously obtained values of the molecular total Kerr constants BmolTOT, allowed for the calculation of the molecular orientational-redistributional components BmolOR+RE of the OKE constants. The mean third-order optical polarizabilities cai were also determined. The BmolNL, BmolOR + RE and cai parameters estimated for tRNA macromolecules in water and in two different buffer solutions with and without magnesium ions are discussed in the light of data obtained by other methods. For different tRNA structures, different values of the optical Kerr constants and third-order optical polarizabilities were observed. It was found that the linear optical parameters, i.e., optical polarizability a and anisotropy δa, obtained in the present studies, are much smaller in comparison with corresponding values obtained from the static light-scattering measurements. The relative nonlinear optical Kerr constants in pure water and salt buffers were measured, and are found to be opposite in sign. The relative values of the optical Kerr constants of both buffer solvents obtained in our picosecond measurements are smaller by a factor of two than those obtained in nanosecond studies.
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ABSTRACT The optical Kerr effect (OKE) of tRNA solutions induced by picosecond light pulses of a YAG-Nd3+ laser, λ = 1060 nm, was investigated. A weak He-Ne laser light beam, λ = 632.8 nm, served as the measuring beam. The experimentally... more
ABSTRACT The optical Kerr effect (OKE) of tRNA solutions induced by picosecond light pulses of a YAG-Nd3+ laser, λ = 1060 nm, was investigated. A weak He-Ne laser light beam, λ = 632.8 nm, served as the measuring beam. The experimentally determined molecular Kerr constants BmolNL, and previously obtained values of the molecular total Kerr constants BmolTOT, allowed for the calculation of the molecular orientational-redistributional components BmolOR+RE of the OKE constants. The mean third-order optical polarizabilities cai were also determined. The BmolNL, BmolOR + RE and cai parameters estimated for tRNA macromolecules in water and in two different buffer solutions with and without magnesium ions are discussed in the light of data obtained by other methods. For different tRNA structures, different values of the optical Kerr constants and third-order optical polarizabilities were observed. It was found that the linear optical parameters, i.e., optical polarizability a and anisotropy δa, obtained in the present studies, are much smaller in comparison with corresponding values obtained from the static light-scattering measurements. The relative nonlinear optical Kerr constants in pure water and salt buffers were measured, and are found to be opposite in sign. The relative values of the optical Kerr constants of both buffer solvents obtained in our picosecond measurements are smaller by a factor of two than those obtained in nanosecond studies.
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ABSTRACT
Raman spectra of baker's yeast tRNA in NaCl aqueous solutions were measured as a function of sodium ion concentration throughout the 0–1.0 M range. Strong variations in intensity of the various bands allowed observation of the ionic... more
Raman spectra of baker's yeast tRNA in NaCl aqueous solutions were measured as a function of sodium ion concentration throughout the 0–1.0 M range. Strong variations in intensity of the various bands allowed observation of the ionic strength‐dependent conformational transitions of the tRNA. The experimental data obtained point to the existence of five distinct conformations of the tRNA molecules in the range of Na+ concentration investigated.
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Photon Correlation Spectroscopy (PCS) was used to study the dynamics and structure of Tetrahymena telomeric sequence d(5'-TGGGGT-3')4. Two different modes were observed, corresponding to the following structures: intermolecular... more
Photon Correlation Spectroscopy (PCS) was used to study the dynamics and structure of Tetrahymena telomeric sequence d(5'-TGGGGT-3')4. Two different modes were observed, corresponding to the following structures: intermolecular (tetramolecular) G-quadruplex and intramolecular (monomeric) G-quartet. Experimental values of translational diffusion coefficients DT were obtained for each structural form. The value of DT for the monomer equals to 1.4 x 10(6) (cm2/s), while for the tetramolecular structure, to 0.8 x 10(6) (cm2/s). The relative weight concentrations of these two forms were analyzed versus the concentration of NaCl varied from 10 mM to 500 mM. The values of experimentally determined diffusion coefficients were compared with those calculated assuming the "bead model" and with the atomic coordinates from the NMR and X-ray crystallographic data. For both structures the experimental and calculated values of DT were in reasonable agreement. In the entire NaCl co...
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The sodium ion concentration dependent conformational changes of transfer RNA (unfractionated tRNA from baker's yeast) have been studied in unbuffered aqueous solutions by Rayleigh light scattering. Changes of the optical parameters... more
The sodium ion concentration dependent conformational changes of transfer RNA (unfractionated tRNA from baker's yeast) have been studied in unbuffered aqueous solutions by Rayleigh light scattering. Changes of the optical parameters of the molecule indicated the following conformational changes of tRNA with increasing NaCl concentration: in salt-free solution tRNA molecules have an irregular hairpin loop-like structure in which the orientation of base rings is not correlated. Upon addition of a small amount of NaCl (0.005 M) an increasing ordering of this structure is observed. In 0.1 M-NaCl the molecule has an extended structure with ordered regions (arms). Further increase of sodium ion concentration up to 2 M results in folding of the extended structure and formation of a compact and rigid conformation in which most of the bases are nearly perpendicular to the symmetry axis of the molecule.
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The structure of the Tetrahymena thermophila telomeric sequence d(TGGGGT)(4) was studied by photon correlation spectroscopy (PCS) in aqueous solution in the presence of NaCl, KCl and SrCl(2). The sample studied was polydisperse in all... more
The structure of the Tetrahymena thermophila telomeric sequence d(TGGGGT)(4) was studied by photon correlation spectroscopy (PCS) in aqueous solution in the presence of NaCl, KCl and SrCl(2). The sample studied was polydisperse in all conditions studied. Translational diffusion coefficients D(T) describing the diffusion modes observed were determined. On the basis of a comparison between the experimental D(T) values with those calculated assuming the bead model, two forms were identified as telomeric quadruplex structures: monomer and tetramer. In the presence of SrCl(2) formation of aggregates was observed, with a size that reached several micrometres. The relative weighted concentrations of the structures observed for different concentrations of a salt and DNA were determined. The results obtained in the presence of monovalent ions were qualitatively similar and could be presented in a coherent plot in which the concentration of salt was expressed by the number of ions per DNA mol...
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The temperature dependence of charge recombination of the pair P(+)HA(-) in isolated reaction centers from the purple bacterium Rhodobacter sphaeroides with prereduced quinone QA was studied by sub-nanosecond to microsecond time-scale... more
The temperature dependence of charge recombination of the pair P(+)HA(-) in isolated reaction centers from the purple bacterium Rhodobacter sphaeroides with prereduced quinone QA was studied by sub-nanosecond to microsecond time-scale transient absorption. Overall, the kinetics slowed down substantially upon cooling from room temperature to ∼200 K, and then remained virtually unchanged down to 77 K, indicating the coexistence of two competitive pathways of charge recombination, a thermally-activated pathway appearing only above ~200 K and a temperature-independent pathway. In our modelling, the thermally activated pathway includes an uphill electron transfer from HA(-) to BA(-) leading to transient formation of the state P(+)BA(-), whereas the temperature-independent pathway is due to direct downhill electron transfer from HA(-) to P(+). At all temperatures studied, the kinetics could be approximated by a four-component decay. Detailed analysis of the lifetimes and amplitudes of par...
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Research Interests: Obstetrics, Rheology, Pregnancy, Humans, Placenta, and 15 moreFemale, Redistribution, High risk pregnancy, Blood Flow, Circulation, Internal medicine Doppler ultrasonography, Fetus, Perinatal Outcome, Uterus, Blood Flow Velocity, power Doppler, Reference Value, Pregnancy Outcome, Pulsatile Flow, and Middle Cerebral Artery
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The effect of different ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy (PCS) and circular dichroism (CD). The saturation and... more
The effect of different ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy (PCS) and circular dichroism (CD). The saturation and melting curves obtained in the presence of K(+), Na(+), Rb(+), Li(+), Cs(+), and Sr(2+) ions were recorded by CD spectroscopy and indicated the formation of monomeric quadruplexes. Analysis of the saturation curves obtained at 2 degrees C has shown that the presence of a single Sr(2+) ion per oligomer is sufficient for the formation of a monomeric quadruplex of the DNA sequence studied. In the presence of SrCl(2) at a concentration of 50 mM, the formation of tetrameric quadruplexes has been detected. The effect of Sr(2+) ions on the formation of quadruplex structures by the human telomere sequence d(TTAGGG)(4) is stronger and different from that of the other ions tested. The paper also presents results of a study of electrostatic interactions in solution. The translation diffusion coefficients D(T) of the structures present in solution have been determined by photon correlation spectroscopy and the effective charges on the structures have been calculated by combining the experimental data with the results based on the coupled mode theory. Analysis of the melting points monitored by the CD method has permitted a determination of Deltan, the number of ions released in the process of thermal denaturation. All the results are in good agreement with the predictions based on the theory of polyelectrolytes. The effect of ions on the formation and behavior of quadruplex structures of the human telomere sequence d(TTAGGG)(4) has been studied by photon correlation spectroscopy and circular dichroism.
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Analysis of the Kinetics of P + H A – Recombination in Membrane-Embedded Wild-Type and Mutant Rhodobacter sphaeroides Reaction Centers between 298 and 77 K Indicates That the Adjacent Negatively Charged Q A Ubiquinone Modulates the Free Energy of P + H A – and May Influence the Rate of the Protei...more
Time-resolved spectroscopic studies of recombination of the P(+)HA(-) radical pair in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides give an opportunity to study protein dynamics triggered by light and occurring over... more
Time-resolved spectroscopic studies of recombination of the P(+)HA(-) radical pair in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides give an opportunity to study protein dynamics triggered by light and occurring over the lifetime of P(+)HA(-). The state P(+)HA(-) is formed after the ultrafast light-induced electron transfer from the primary donor pair of bacteriochlorophylls (P) to the acceptor bacteriopheophytin (HA). In order to increase the lifetime of this state, and thus increase the temporal window for the examination of protein dynamics, it is possible to block forward electron transfer from HA(-) to the secondary electron acceptor QA. In this contribution, the dynamics of P(+)HA(-) recombination were compared at a range of temperatures from 77 K to room temperature, electron transfer from HA(-) to QA being blocked either by prereduction of QA or by genetic removal of QA. The observed P(+)HA(-) charge recombination was significantly slower in the QA-deficient RCs, and in both types of complexes, lowering the temperature from RT to 77 K led to a slowing of charge recombination. The effects are explained in the frame of a model in which charge recombination occurs via competing pathways, one of which is thermally activated and includes transient formation of a higher-energy state, P(+)BA(-). An internal electrostatic field supplied by the negative charge on QA increases the free energy levels of the state P(+)HA(-), thus decreasing its energetic distance to the state P(+)BA(-). In addition, the dielectric response of the protein environment to the appearance of the state P(+)HA(-) is accelerated from ∼50-100 ns in the QA-deficient mutant RCs to ∼1-16 ns in WT RCs with a negatively charged QA(-). In both cases, the temperature dependence of the protein dynamics is weak.