Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as - ΔH (kJ mole^-1) decreases as: m⁹Gua (- 59.5) > m ¹Cyt (- 57.0) > m ⁹Ade (- 52.0) ≫m ¹Ura (- 40.6). We have determined that in the double stranded DNA only purine bases can be recognized. Received 5 February 2002 and Received in final form 14 March 2002 Published online 13 September 2002     

The interplay between surface micro-topography and -mechanics of type I collagen fibrils in air and aqueous media: An atomic force microscopy study

Calf skin type I collagen fibrils were regenerated from acidic solution and imaged with contact mode atomic force microscopy in air, water, and buffer solution. When imaged in air at a contact force of 20-150 nN, collagen fibrils exhibited a distinct transverse banding pattern with a period of 65 nm, consisting of high ridges and shallow grooves. The force dependence of the images suggests that such banding pattern is attributed to the transverse contraction of the fibril upon dehydration during sample preparation, which reflects the tangential mass density across the fibril. Imaging in water and phosphate buffer solution at a contact force of 15-80 nN revealed hydrated collagen fibrils with smooth surfaces. The rigidity of the collagen fibrils decreased considerably upon hydration. Scanning the cantilever tip in an aqueous medium at a contact force of 90-280 nN enabled us to probe subunit arrangement in the bulk region of the collagen fibril. The results indicate that the molecular assembly in the hydrated fibril is akin to that in the intact form. The image resolution was improved by stabilizing the collagen molecules through crosslinking with glutaraldehyde, which served to resolve microfibril-like structure on the fibril surface. Received 28 March 2000 and Received in final form 15 June 2001     

Photoexcitation of rare-gas neon and argon clusters doped with <Emphasis Type="Bold">H</Emphasis><Subscript><Emphasis Type="Bold">2</Emphasis></Subscript><Emphasis Type="Bold">O</Emphasis>

We have studied the fluorescence of electronically excited OH^*, H^* and H₂O^+* dissociation fragments after VUV excitation ( h ν≥11.6 eV) of rare-gas clusters (Rg = Ne, Ar) doped with H₂O molecules. In contrast to a free molecule, where Balmer H-series dominate the UV-visible spectra, only the OH ^* ( A ² Σ ⁺ ↦ X ² Π) emission band is observed in neon clusters. No emission of excited water ions has been observed. We find that while higher excitation energies (Ne vs. Ar) induce higher vibrational excitation of the OH^* ( A ) fragment, the rotational temperature is lower. This effect is attributed to the difference in the geometric position of the H₂O molecule on the surface or inside the Rg-cluster. The rotational relaxation in neon clusters is rapid while the vibrational relaxation is slow because of the coupling with the low energy matrix phonons. Received 7 March 2002 / Received in final form 27 May 2002 Published online 19 July 2002     

Photoreflectance investigation of hydrogenated (InGa)(AsN)/GaAs heterostructures

The optical response of as grown and hydrogenated In_0.32Ga_0.68As_1-yN_y/GaAs single quantum wells (y = 0, 0.027) has been investigated from T = 80 K to room temperature by photoreflectance. Three excitonic spectral features detected in the N free sample shift to lower energy in the N containing sample and back to higher energy upon H irradiation of the N containing sample. In the hydrogenated sample, a progressive change with increasing temperature of the nature of the lowest energy transition from an excitonic to a band-to-band character has been explained in terms of an increasing release of carriers from traps formed by H and N clusters. A reduction in the oscillator strength of the lowest energy transition and an increase in the binding energy of the heavy-hole exciton have been explained in terms of an increase in the electron effective mass upon N introduction into the In_xGa_1-xAs lattice. Received 23 June 2002 Published online 19 November 2002     

Vertical water distribution during the drying of polymer films cast from aqueous emulsions

We present a systematic study of the vertical uniformity of water distribution during the drying of waterborne colloidal films, testing the predictions of a Peclet number Pe defined for this system. Pe indicates the relative contributions of water evaporation and Brownian diffusion in determining the concentration profile in the vertical direction (i.e. normal to the substrate). When Pe < 1, the water concentration in films cast from an alkyd emulsion is found via magnetic-resonance profiling to be uniform with depth, which is consistent with expectations. When Pe > 1, a gradient in the water concentration develops, with less water near the interface with air. The water profiles reveal that the alkyd particles do not coalesce immediately upon contact in close-packing. At later times, a concentrated surface layer develops, but particles are not coalesced in this layer to form a continuous “skin”, but rather the structure is likely to be that of a biliquid foam. Received 20 March 2002 and Received in final form 12 June 2002     

Tautomer contributions to the near UV spectrum of guanine: towards a refined picture for the spectroscopy of purine molecules

By using depopulation laser techniques, like IR-UV population labeling coupled to mass-selected R2PI detection, we confirm that four tautomers are responsible for the near UV spectroscopy (310-280 nm) of guanine: two enol and two keto forms, each pair having a 7NH and a 9NH form. Besides the UV spectroscopy of each tautomer, additional information on the excited state nature and dynamics is obtained from fluorescence studies. In particular, the quenching of fluorescence beyond 285 nm, the existence of a background absorption, as well as the existence of a strongly red-shifted component in the fluorescence emission provides evidence for a strong electronic mixing in the excited state together with an efficient non-radiative process. The details of these features are found to be tautomer-dependent. Comparison of the present results with literature data on other purine molecules, like adenine or 9-substituted guanines, enables us to propose a new insight on the spectroscopy and dynamics of the purine molecules. First, a large variability of the tautomer distribution in the gas phase is found within the purine family, in particular a molecular change, as simple as a 9-methylation on guanine, can reduce the tautomer distribution to a single species (enol form). Since the absorption spectrum is tautomer-dependent as well as substituent-dependent, it turns out that the tautomer population is one of the major parameters that control the overall shape of the UV spectrum. Second, the excited state model, often evoked in the literature, which involves electronic coupling between excited states of different natures, namely ππ^* and nπ^* states, might account for the present fluorescence measurements on guanine, providing an extensive excited state electronic mixing is assumed for these systems. Received 24 June 2002 Published online 13 September 2002     

Spectroscopy of the regenerative soot

The mechanisms and processes of the formation of the regenerative soot in a graphite hollow cathode discharge that produces and emits carbon clusters are presented. Mass spectrometry with a specially designed E×B velocity filter analyzes the entire range of the charged clusters from C ₁ to ∼C ₄₃₀₀. The state of the carbon vapour within the source is evaluated by using the characteristic line emissions from the carbonaceous discharge whose formative mechanisms depend upon the kinetic and potential sputtering of the sooted cathode. The carbonaceous discharge generates atomic and ionic C and its clusters C _m (m≥ 2), noble gas metastable atoms and ions, energetic electrons and photons in the cavity of the graphite hollow cathode. The parameters of soot formation and its recycling depend critically on the discharge parameters, the geometry of the hollow cathode and 3D profile of the cusp magnetic field contours. Received 2nd July 2001 and Received in final form 10 September 2001     

Prompt dipole γ-ray emission in fusionlike heavy-ion reactions

The ³²S + ¹⁰⁰Mo and ³⁶S + ⁹⁶Mo fusionlike reactions were studied at incident energy of E _lab = 298 MeV and 320 MeV, respectively, with the aim of probing the influence of the entrance channel charge asymmetry on the dipole γ-ray emission. The excitation energy and spin distribution of the compound nucleus created in these reactions were identical, the only difference being associated with the unequal charge asymmetry of the two entrance channels. High-energy γ-rays were detected in an array of 9 seven-pack BaF₂ clusters. Coincidence with fusionlike residues detected in four PPAC ensured the selection of central reaction events. By studying the differential γ-ray multiplicity associated with the two reactions it was shown that the dipole strength excited in the compound nucleus increases with the entrance channel charge asymmetry. From the linearized spectra, the increase of the GDR γ-ray intensity was found to be ∼ 25% for the more charge asymmetric system. The results are discussed and compared with those of previous data obtained at different incident energies. Received: 21 October 2002 / Accepted: 23 December 2002 / Published online: 1 April 2003     

Fragmentation of water clusters: Molecular-dynamics simulation study

The fragmentation of water clusters, [(H ₂ O)_n;n = 2-8], have been investigated by using molecular-dynamics simulation method. In the simulations a polarizable-dissociable potential energy function for water has been used. Particular attention has bee paid to investigate the effect of structural properties and cluster size on the fragmentation. Received 27 April 2000 and Received in final form 6 October 2000     

Spectra of baryons containing two heavy quarks

Doubly heavy baryons, i.e., the baryons containing two heavy quarks are treated in the adiabatic approximation, considering the motion of the light quark as a relativistic motion. The binding energy and mass spectra of doubly heavy baryons are calculated solving the two-center Dirac equation the one-centre Schr?dinger equation for Coulomb plus linear potential. The binding energy of the light quark as a function of the distance between heavy quarks is found. Received: 16 January 2002 / Accepted: 7 February 2002     

Spin configuration transformation in laterally coupled few-electron artificial molecules

Artificial molecules, namely laterally coupled quantum dots with a three-dimensional spherical confinement potential well of radius R and depth V ₀, were studied by the unrestricted Hartree-Fock-Roothaan (UHFR) method. By varying the distance d between the centers of the two coupled quantum dots, the transition from the strong coupling situation to the weak one is realized. Hund's rule, suitable for a single quantum dot is destroyed in certain conditions in the artificial molecule. For example, in the few-electron system of the strongly coupled quantum-dot molecule, a transformation of spin configuration has been found. Received 8 March 2002 / Received in final form 29 May 2002 Published online 17 September 2002     

Fragmentation and reliable size distributions of large ammonia and water clusters

The interaction of large ammonia and water clusters in the size range from <n> = 10 to 3 400 with electrons is investigated in a reflectron time-of-flight mass spectrometer. The clusters are generated in adiabatic expansions through conical nozzles and are nearly fragmentation free detected by single photon ionization after they have been doped by one sodium atom. For ammonia also the (1+1) resonance enhanced two photon ionization through the state with v = 6 operates similarly. In this way reliable size distributions of the neutral clusters are obtained which are analyzed in terms of a modified scaling law of the Hagena type [Surf. Sci. 106, 101 (1981)]. In contrast, using electron impact ionization, the clusters are strongly fragmented when varying the electron energy between 150 and 1 500 eV. The number of evaporated molecules depends on the cluster size and the energy dependence follows that of the stopping power of the solid material. Therefore we attribute the operating mechanism to that which is also responsible for the electronic sputtering of solid matter. The yields, however, are orders of magnitude larger for clusters than for the solid. This result is a consequence of the finite dimensions of the clusters which cannot accommodate the released energy. Received 21 November 2001     

Self-averaging in complex brain neuron signals

Nonlinear statistical properties of Ventral Tegmental Area (VTA) of limbic brain are studied in vivo. VTA plays key role in generation of pleasure and in development of psychological drug addiction. It is shown that spiking time-series of the VTA dopaminergic neurons exhibit long-range correlations with self-averaging behavior. This specific VTA phenomenon has no relation to VTA rewarding function. Last result reveals complex role of VTA in limbic brain. Received 17 April 2002 / Received in final form 30 September 2002 Published online 31 December 2002     

Transverse fluctuation analysis of single extended DNA molecules

We observed fluctuations of elongated DNA molecules by fluorescence microscopy. The molecules are fixed at both ends and undulate. Mode analysis of the thermally excited undulations of the labeled DNA molecules gives access to the spectral density of the amplitude fluctuations. From these measurements we estimate the tension acting on the DNA molecules. We found the forces to be within the entropic elasticity range of a typical DNA molecule (measured on the single-molecule level). Received: 11 November 2002 / Accepted: 12 May 2002 / Published online: 4 June 2003 RID="a" ID="a"Present address: Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. e-mail: zoherg@rockefeller.edu     

Ultrafast dynamics in the excited hydrogen atom transfer states of ammonia clusters

Neutral ammonia clusters (NH₃)_m are photo-excited to the electronic state by a deep UV femtosecond laser pump pulse. Within a few hundred femtoseconds a significant fraction of the clusters rearrange to form an H-transfer state (NH₃)_m-2NH₄(3s)NH₂ with the subunit NH₄ in its 3s electronic ground state. This state is then electronically excited by a time-delayed infrared control pulse of variable wavelength. Finally, a third (probe) pulse in the UV ionizes the clusters for detection. The lifetime of the excited (NH₃)_m-2NH₄(3p)NH₂ states is found to vary between 2.7 and 0.13 ps depending on cluster size and excitation energy. It increases drastically upon deuteration. The corresponding cluster size-dependent photoelectron spectra allow us to disentangle the underlying energetics of the excitation and ionization process and reveal additional processes, such as nonresonant ionization or dissociative ionization. The experimental findings suggest that the excited H-transfer ammonia complexes with m > 2 are deactivated by an internal conversion process back to the electronically lowest H-transfer state followed by fast dissociation. Received 22 September 2001 and Received in final form 31 January 2002     

Preparation and characterization of cobalt-based nanostructured materials

Nano-sized cobalt clusters passivated by alkane-thiol molecules were obtained by the action of concentrated thiol solutions on micrometric cobalt particles. Thiol molecules caused an erosive process on the metal grains with the consequent formation of nano-sized metal debris and cobalt thiolate as by-product. The final material microstructure was composed by cobalt clusters embedded into a continuum cobalt thiolate matrix. Depending on the thiol molecule length, the material texture ranged from rubbery to waxy. These new types of nanocomposite materials were found to be crystalline, thermally stable up to ca. 300 ^°C, intensely red colored, and high hydrophobic. In addition, they generated polymeric structures when dissolved in non-polar solvents. Received 27 September 2002 Published online 6 March 2003 RID="a" ID="a"e-mail: giancaro@unina.it     

On N-wave type systems and their gauge equivalent

The class of nonlinear evolution equations (NLEE) - gauge equivalent to the N-wave equations related to the simple Lie algebra are derived and analyzed. They are written in terms of (x, t) ∈ satisfying r = rank nonlinear constraints. The corresponding Lax pairs and the time evolution of the scattering data are found. The Zakharov-Shabat dressing method is appropriately modified to construct their soliton solutions. Received 20 October 2001 / Received in final form 30 April 2002 Published online 2 October 2002 RID="a" ID="a"e-mail: gerjikov@inrne.bas.bg     

Mixing and sorting of bidisperse two-dimensional bubbles

We have examined a number of candidates for the minimum-surface-energy arrangement of two-dimensional clusters composed of N bubbles of area 1 and N bubbles of area λ ( λ≤1). These include hexagonal bubbles sorted into two monodisperse honeycomb tilings, and various mixed periodic tilings with at most four bubbles per unit cell. We identify, as a function of λ, the minimal configuration for N → ∞. For finite N, the energy of the external (i.e., cluster-gas) boundary and that of the interface between honeycombs in “phase-separated” clusters have to be taken into account. We estimate these contributions and find the lowest total energy configuration for each pair (N,λ). As λ is varied, this alternates between a circular cluster of one of the mixed tilings, and “partial wetting” of the monodisperse honeycomb of bubble area 1 by the monodisperse honeycomb of bubble area λ. Received 1 August 2002 RID="a" ID="a"e-mail: paulo@ist.utl.pt     

Intracluster electron transfer from a metal atom/cluster followed by anionic oligomerization of vinyl molecules

Intracluster electron transfer and oligomerization reaction were investigated by mass spectrometry of clusters of alkali metal atom (M) with acrylonitrile (AN; CH₂=CHCN). In the photoionization mass spectra of M(AN)_n, magic numbers were clearly observed at n = 3k (k = 1-4 for M = Na and K, k = 1 for M = Li). The results of photodissociation of neutral K(AN)_n indicate that the n = 3 cluster has an anomalous stability relative to other sizes of clusters. The C=C bond in vinyl molecules is also found to be necessary to form the magic numbers by measuring the photoionization mass spectrum of K atom with propionitrile. These results strongly support the intracluster anionic oligomerization reaction initiated by electron transfer from the alkali atom. The quantum chemical calculations have revealed that the evaporation induced by excess energy generated by intracluster oligomerization is important to form the magic numbers in the present clusters. Received 29 November 2000     

Directed spiral site percolation on the square lattice

A new site percolation model, directed spiral percolation (DSP), under both directional and rotational (spiral) constraints is studied numerically on the square lattice. The critical percolation threshold p _c ≈ 0.655 is found between the directed and spiral percolation thresholds. Infinite percolation clusters are fractals of dimension d _f ≈ 1.733. The clusters generated are anisotropic. Due to the rotational constraint, the cluster growth is deviated from that expected due to the directional constraint. Connectivity lengths, one along the elongation of the cluster and the other perpendicular to it, diverge as p → p _c with different critical exponents. The clusters are less anisotropic than the directed percolation clusters. Different moments of the cluster size distribution P _s(p) show power law behaviour with | p - p _c| in the critical regime with appropriate critical exponents. The values of the critical exponents are estimated and found to be very different from those obtained in other percolation models. The proposed DSP model thus belongs to a new universality class. A scaling theory has been developed for the cluster related quantities. The critical exponents satisfy the scaling relations including the hyperscaling which is violated in directed percolation. A reasonable data collapse is observed in favour of the assumed scaling function form of P _s(p). The results obtained are in good agreement with other model calculations. Received 10 November 2002 / Received in final form 20 February 2003 Published online 23 May 2003 RID="a" ID="a"e-mail: santra@iitg.ernet.in