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M A Ratner

Publications and source records attributed to M A Ratner.

11 recordsLinked to original sources
PubMed2003

Anomalous surface diffusion in nanoscale direct deposition processes.

We report the first observation of anomalous diffusion in nanometer scale direct deposition processes utilizing dip-pen nanolithography (DPN). DPN permits quite general nanostructure patterns to be drawn on flat surfaces. Here we demonstrate experimentally, and discuss theoretically, the situation in which the molecular ink in DPN binds weakly to the surface. We observe, for the weak-binding case of 1-dodecylamine on mica, that anomalous diffusion occurs, leading to nearly fractal deposition patterns.

Journal Article↗
PubMed2002

Photoinduced electron-transfer processes along molecular wires based on phenylenevinylene oligomers: a quantum-chemical insight.

Quantum-chemical techniques are applied to model the mechanisms of photoinduced charge transfer from a pi-electron donating group (tetracene, D) to a pi-electron-acceptor moiety (pyromellitimide, A) separated by a bridge of increasing size (p-phenylenevinylene oligomers, B). Correlated Hartree-Fock semiempirical approaches are exploited to calculate the four main parameters controlling the transfer rate (k(RP)) in the framework of Marcus-Jortner-Levich's formalism: (i) the electronic coupling between the initial and final states; (ii) and (iii) the internal and external reorganization energy terms; and (iv) the variation of the free Gibbs energy. The charge transfer is shown to proceed in these compounds through two competing mechanisms, coherent (superexchange) versus incoherent (bridge-mediated) pathways. While superexchange is the dominant mechanism for short bridges, incoherent transfer through hopping along the phenylene vinylene segment takes over in longer chains (for ca. three phenylenevinylene repeat units). The influence of the chemical structure of the pi-conjugated phenylenevinylene bridge on the electronic properties and the rate of charge transfer is also investigated.

Journal Article↗
PubMed2001

Model for a random laser.

The laser action in random media is studied numerically for a planar system of resonant scatterers pumped by an external laser. The eigenmodes of the finite system (quasistates) are "lossy" in the absence of gain because of the leakage of light outside the medium and can be characterized by their decay rates. Lasing occurs when the gain compensates the decay rate of the quasistate with the longest lifetime. The dependence of the lasing threshold on the number of scatterers (size of the system) is found to be I varies with 1/square root of (N), which agrees with recent experiments. We demonstrate that this dependence is strongly related to the fluctuations of quasistate decay rates and discuss the nature of these fluctuations.

Journal Article↗
PubMed2001

Conformational gating of long distance electron transfer through wire-like bridges in donor-bridge-acceptor molecules.

A series of five donor-bridge-acceptor (DBA) molecules in which the donor is tetracene, the acceptor is pyromellitimide, and the bridge molecules are oligo-p-phenylenevinylenes (OPV) of increasing length has been shown to undergo electron transfer (ET) by means of two mechanisms. When the bridge is short, strongly distance dependent superexchange dynamics dominates, whereas when the bridge is longer, bridge-assisted hopping dynamics prevails. The latter mechanism results in relatively soft distance dependence for ET in which the OPV oligomers act effectively as molecular wires. We now report studies on the critical influence that bridge dynamics have on electron transfer through these oligomers. The temperature dependence of the charge separation (CS) rates in all five molecules does not appear to obey the predictions of standard ET theories based upon the Condon approximation. All five molecules show behavior consistent with CS being "gated" by torsional motion between the tetracene donor and the first bridge phenyl ring. This is based on the near equivalence of the CS activation energies measured for all five molecules with the frequency of a known vibrational mode in 5-phenyltetracene. In the molecule containing a trans-stilbene bridge, a competition occurs between the tetracene-phenyl torsional motion and one that occurs between the vinyl group and the phenyls linked to it. This results in complex temperature-dependent CS that exhibits both activated and negatively activated regimes. The charge recombination (CR) reactions within the molecules which have the two shortest bridges, namely phenyl and trans-stilbene, show a weaker dependence on these molecular motions. The three molecules with the longest bridges all display complex temperature dependencies in both their rates of CS and CR, most likely because of the complex torsional motions, which arise from the multiple phenyl-vinyl linkages. The data show that long-distance electron transfer and therefore wire-like behavior within conjugated bridge molecules depend critically on these low-frequency torsional motions. Molecular device designs that utilize such bridges will need to address these issues.

Journal Article↗
PubMed2001

Conformationally tuned large two-photon absorption cross sections in simple molecular chromophores.

We investigate here the relationship between molecular architecture and two-photon absorption (TPA) processes in a class of alkyl-substituted 4-quinopyran chromophores. We find that TPA cross sections diverge as the one-photon gap energy nears one-half of the two-photon gap. The molecular strategy proposed here to tune these two-excitation gaps for maximizing TPA cross sections is to twist the molecule about the bond connecting the chromophore donor and acceptor phenylene fragments. Extremely large TPA cross sections, determined by the absorption bandwidth, can then be realized (imaginary part of the third-order polarizability approximately 2.6 x 10(5) x 10(-36) esu) for fundamental photon energies near 1.0 eV, when the torsional angle approaches 104 degrees. The required torsional angle is achieved by introduction of sterically encumbered 2,2',2' ',2' " tertiary alkyl substituents.

Journal Article↗
PubMed2001

Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase.

Molecular dynamics (MD) simulations have been performed to study the rehydration of compact and unfolded cytochrome c ions in the vapor phase. Experimental studies have shown that the compact conformations adsorb many more water molecules than unfolded ones when exposed to water vapor. MD simulations performed with up to 150 water molecules reproduce the key experimental observations, including a partial refolding caused by hydration. According to the calculations it is more energetically favorable to hydrate the compact conformation in the initial stages of hydration, because it is easier for a water molecule to interact simultaneously with several polar groups (due to their proximity). The protonated side chains are not favored hydration sites in the simulations because they have "self-solvation" shells which must be disrupted for the water to penetrate. For both conformations, the adsorbed water molecules are mainly located in surface crevices.

Computer Simulation↗
PubMed2001

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.

Base Pairing↗
PubMed1999

Conformations of Gly(n)H+ and Ala(n)H+ peptides in the gas phase.

High-resolution ion mobility measurements and molecular dynamics simulations have been used to probe the conformations of protonated polyglycine and polyalanine (Gly(n)H and Ala(n)H+, n = 3-20) in the gas phase. The measured collision integrals for both the polyglycine and the polyalanine peptides are consistent with a self-solvated globule conformation, where the peptide chain wraps around and solvates the charge located on the terminal amine. The conformations of the small peptides are governed entirely by self-solvation, whereas the larger ones have additional backbone hydrogen bonds. Helical conformations, which are stable for neutral Alan peptides, were not observed in the experiments. Molecular dynamics simulations for Ala(n)H+ peptides suggest that the charge destabilizes the helix, although several of the low energy conformations found in the simulations for the larger Ala(n)H+ peptides have small helical regions.

Biophysical Phenomena↗
PubMed1997

Cadmium disrupts the signal transduction pathway of both inhibitory and stimulatory receptors regulating chloride secretion in the shark rectal gland.

The heavy metal cadmium causes nephrotoxicity and alters the transport function of epithelial cells. In the shark rectal gland, chloride secretion is regulated by secretagogues and inhibitors acting through receptors coupled to G proteins and the cyclic AMP-protein kinase A pathway. We examined the effects of cadmium on the response to the inhibitory peptide somatostatin (SRIF), and to the stimulatory secretagogues forskolin and vasoactive intestinal peptide (VIP). In control experiments, SRIF (100 nM) entirely inhibited the chloride secretory response to 10 microM forskolin (maximum chloride secretion with forskolin 1984 +/- 176 microEq/h/g; with forskolin + SRIF 466 +/- 93 microEq/h/g, P < 0.001). Cadmium (25 microM) entirely reversed the inhibitory response to SRIF (chloride secretion 2143 +/- 222 microEq/h/g) and caused an overshoot (2917 +/- 293 microEq/h/g) that exceeded the response to forskolin (P < 0.01). Cadmium also enhanced forskolin-stimulated chloride secretion (2628 +/- 418 vs. 1673 +/- 340 microEq/h/g, P < 0.02) and reversed the declining phase of the forskolin response. Cadmium had a concentration-dependent, biphasic effect on the response to VIP. Cd (10-100 microM) increased both chloride secretion and tissue cyclic AMP content, whereas higher concentrations (1 mM) inhibited chloride secretion and cyclic AMP accumulation. Our findings provide evidence that Cd disrupts the signal transduction pathways of both inhibitory receptors and secretagogues regulating cAMP mediated transport in an intact epithelia. The results are consistent with direct effects of cadmium on adenylate cyclase and/or phosphodiesterase activity in this marine epithelial model.

Adenylyl Cyclases↗
PubMed1995

Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI.

The harmonic approximation for the potential energy of proteins is known to be inadequate for the calculation of many protein properties. To study the effect of anharmonic terms on protein vibrations, the anharmonic wave functions for the ground state and low-lying excited states of the bovine pancreatic trypsin inhibitor (BPTI) were calculated. The results suggest that anharmonic treatments are essential for protein vibrational spectroscopy. The calculation uses the vibrational self-consistent field approximation, which includes anharmonicity and interaction among modes in a mean-field sense. Properties obtained include the quantum coordinate fluctuations, zero-point energies, and the vibrational absorption spectrum.

Aprotinin↗