Spectral diffusion at the water/lipid interface revealed by two-dimensional fourth-order optical spectroscopy: a classical simulation study

Using a classical simulation protocol for nonlinear optical signals, we predict the two-dimensional (2D) spectra of water near a monolayer of [1,2-dimytristoyl-sn-glycero-3-phosphatidylcholine] (DMPC) generated by three IR probe pulses followed by one visible probe pulse. Sum-frequency-generation 1D spectra show two peaks of the OH stretch representing two environments: near-bulk water nonadjacent to DMPC and top-layer water adjacent to DMPC. These peaks create a 2D pattern in the fourth-order signal. The asymmetric cross-peak pattern with respect to the diagonal line is a signature of coherence transfer from the higher- to the lower-frequency modes. The nodal lines in the imaginary part of the 2D spectrum show that the near-bulk water has fast spectral diffusion resembling that of bulk water despite the orientation by the strong electrostatic field of DMPC. The top-layer water has slower spectral diffusion.     

Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges

The stimulated Raman component of the pump-probe spectrum of trans-N-methylacetamide obtained in response to two soft x-ray pulses is calculated by treating the core excitations at the Hartree-Fock static-exchange level. The signal reveals the dynamics of valence-electron wave packets prepared and detected in the vicinity of a selected atom (either nitrogen or oxygen). The evolving electronic charge density as well as electronic coherence of the doorway and the window created by the two pulses are visualized using a time-dependent basis set of natural orbitals, which reveals that the wave packets consist of several entangled valence particle-hole pairs.     

Coherent control protocol for separating energy-transfer pathways in photosynthetic complexes by chiral multidimensional signals

Adaptive optimizations performed using a genetic algorithm are employed to construct optimal laser pulse configurations that separate spectroscopic features associated with the two main energy-transfer pathways in the third-order nonlinear optical response simulated for the Fenna-Matthews-Olson (FMO) photosynthetic complex from the green sulfur bacterium Chlorobium tepidum. Superpositions of chirality-induced tensor components in both collinear and noncollinear pulse configurations are analyzed. The optimal signals obtained by manipulating the ratios of various 2D spectral peaks reveal detailed information about the excitation dynamics.     

Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study

We report a first principles study of two dimensional electronic spectroscopy of aromatic side chain transitions in the 32-residue β-amyloid (Aβ(9-40)) fibrils in the near ultraviolet (250-300 nm). An efficient exciton Hamiltonian with electrostatic fluctuations (EHEF) algorithm is used to compute the electronic excitations in the presence of environmental fluctuations. The through-space inter- and intra-molecular interactions are calculated with high level quantum mechanics (QM) approaches, and interfaced with molecular mechanics (MM) simulations. Distinct two dimensional near ultraviolet (2DNUV) spectroscopic signatures are identified for different aromatic transitions, and the couplings between them. 2DNUV signals associated with the transition couplings are shown to be very sensitive to the change of residue-residue interactions induced by residue mutations. Our simulations suggest that 2DNUV spectra could provide a useful local probe for the structure and kinetics of fibrils.     

Q-switching an all-fiber laser using acousto-optic null coupler

A new method for Q-switching an all-fiber laser is presented. It is based on induced acoustic long period grating operating on a null coupler, which acts as acoustically controlled tunable output coupler. Q-switching is achieved by switching on and off the acoustic wave in a burst mode, thereby generating laser pulses that are ~400 times shorter than the acoustically controlled coupler’s rise time. Output pulse energy of 22 μJ and temporal width of ~100 ns were measured at a wavelength of 1.54 μm.     

The Formation of Pd Nanocrystals from Pd2(dba)3 Microcrystals

As‐grown platelets formed from tris‐(dibenzylideneacetone) dipalladium(0) [Pd₂(dba)₃] precursor in the presence of Pd17 RNA are investigated before and after thermal annealing. Results show that as‐grown platelets are disordered crystals of Pd₂(dba)₃ containing 1?2 nm Pd clusters and platelets grown in the absence of RNA are morphologically and structurally similar to those formed with RNA. The initially formed crystals are so sensitive to environmental variables that the degree of crystallinity can not be determined accurately by electron diffraction. X‐ray crystallography on as‐grown platelets gives a crystal structure consistent with Pd₂(dba)₃, but reveals a composition of ≈Pd_1.07(dba)₃, indicating one Pd atom in Pd₂(dba)₃ is lost from the structure. Both electron beam and thermally induced decomposition of as‐grown Pd₂(dba)₃ platelets having a hexagonal habit on the micrometer scale produces elemental Pd platelets having a hexagonal habit on the nanometer scale. These hexagonal platelets are composed of a partially sparse form of Pd₂(dba)₃ that is initially crystalline but rapidly degrades due to the loss of Pd atoms from organic ligand cages. Once released, Pd atoms aggregate to form Pd clusters, which grow and transform into well‐formed Pd nanocrystals under electron‐beam irradiation or through thermal annealing.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

A model for phase transitions in Tetrathiafulvalene-Tetracyanoquinodimethane (TTF-TCNQ)

The observed phase transitions in Tetrathiafulvalene-Tetracyanoquinodimethane (TTF-TCNQ) are discussed using a simple model for the interchain coupling of charge density waves. Estimates based on Coulomb energies show that for 38 K < T < 49 K the components $\text{q}{}_{\mathrm{x}}\text{=}\text{π}\text{a}\text{+ q′}{}_{\mathrm{x}}$ and q_z of the wave vector associated with the charge density wave satisfy $\text{q}{}_{\mathrm{z}}\text{c}\text{q′}{}_{\mathrm{x}}\text{a?0.1}$, with $\text{q′}{}_{\mathrm{x}}\text{a～(T}{}_2\text{? T)}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ and T₂ = 49 K. A possible mechanism for the first order transition at 38 K is proposed. The results are compared with neutron and X-ray scattering and with isotope shifts of the transition temperatures.