Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics

In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for “biological water”, a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.     

Mixing of perfluorooctanesulfonic acid (PFOS) potassium salt with dipalmitoyl phosphatidylcholine (DPPC)

Perfluorooctane-1-sulfonic acid (PFOS) is emerging as an important persistent environmental pollutant. To gain insight into the interaction of PFOS with biological systems, the mixing behavior of dipalmitoylphosphatidylcholine (DPPC) with PFOS was studied using differential scanning calorimetry (DSC) and fluorescence anisotropy measurements. In the DSC experiments the onset temperature of the DPPC pretransition (Tp) decreased with increasing PFOS concentration, disappearing at XDPPC < or = 0.97. The main DPPC phase transition temperature showed a depression and peak broadening with increasing mole fraction of PFOS in both the DSC and the fluorescence anisotropy studies. From the melting point depression in the fluorescence anisotropy studies, which was observed at a concentration as low as 10 mg/L, an apparent partition coefficient of K = 5.7 x 10(4) (mole fraction basis) was calculated. These results suggest that PFOS has a high tendency to partition into lipid bilayers. These direct PFOS-DPPC interactions are one possible mechanism by which PFOS may contribute to adverse effects, for example neonatal mortality, in laboratory studies and possibly in humans.     

Tuning the band gap in hybrid tin iodide perovskite semiconductors using structural templating

Structural distortions within the extensive family of organic/inorganic hybrid tin iodide perovskite semiconductors are correlated with their experimental exciton energies and calculated band gaps. The extent of the in- and out-of-plane angular distortion of the SnI4(2-) perovskite sheets is largely determined by the relative charge density and steric requirements of the organic cations. Variation of the in-plane Sn-I-Sn bond angle was demonstrated to have the greatest impact on the tuning of the band gap, and the equatorial Sn-I bond distances have a significant secondary influence. Extended Hückel tight-binding band calculations are employed to decipher the crystal orbital origins of the structural effects that fine-tune the band structure. The calculations suggest that it may be possible to tune the band gap by as much as 1 eV using the templating influence of the organic cation.     

Elongated silica nanoparticles with a mesh phase mesopore structure by fluorosurfactant templating

Mesoporous silica materials with pore structures such as 2D hexagonal close packed, bicontinuous cubic, lamellar, sponge, wormhole-like, and rectangular have been made by using surfactant templating sol-gel processes. However, there are still some "intermediate" phases, in particular mesh phases, that are formed by surfactants but which have not been made into analogous silica pore structures. Here, we describe the one-step synthesis of mesoporous silica with a mesh phase pore structure. The cationic fluorinated surfactant 1,1,2,2-tetrahydroperfluorodecylpyridinium chloride (HFDePC) is used as the template. Like many fluorinated surfactants, HFDePC forms intermediate phases in water (including a mesh phase) over a wider range of compositions than do hydrocarbon surfactants. The materials produced by this technique are novel elongated particles in which the layers of the mesh phase are oriented orthogonal to the main axis of the particles.     

Subword complexes in Coxeter groups

Let (Π,Σ) be a Coxeter system. An ordered list of elements in Σ and an element in Π determine a subword complex, as introduced in Knutson and Miller (Ann. of Math. (2) (2003), to appear). Subword complexes are demonstrated here to be homeomorphic to balls or spheres, and their Hilbert series are shown to reflect combinatorial properties of reduced expressions in Coxeter groups. Two formulae for double Grothendieck polynomials, one of which appeared in Fomin and Kirillov (Proceedings of the Sixth Conference in Formal Power Series and Algebraic Combinatorics, DIMACS, 1994, pp. 183-190), are recovered in the context of simplicial topology for subword complexes. Some open questions related to subword complexes are presented.     

A scheme related to the Brauer loop model

We introduce the Brauer loop scheme, where • is a certain degeneration of the ordinary matrix product. Its components of top dimension, ⌊N²/2⌋, correspond to involutions π∈SN having one or no fixed points. In the case N even, this scheme contains the upper-upper scheme from [A. Knutson, Some schemes related to the commuting variety, J. Algebraic Geom., in press, math.AG/0306275] as a union of (N/2)! of its components. One of those is a degeneration of the commuting variety of pairs of commuting matrices.The Brauer loop model is an integrable stochastic process studied in [J. de Gier, B. Nienhuis, Brauer loops and the commuting variety, J. Stat. Mech. (2005) P01006, math.AG/0410392], based on earlier related work in [M.J. Martins, B. Nienhuis, R. Rietman, An intersecting loop model as a solvable super spin chain, Phys. Rev. Lett. 81 (1998) 504-507, cond-mat/9709051], and some of the entries of its Perron-Frobenius eigenvector were observed (conjecturally) to equal the degrees of the components of the upper-upper scheme.Our proof of this equality follows the program outlined in [P. Di Francesco, P. Zinn-Justin, Inhomogeneous model of crossing loops and multidegrees of some algebraic varieties, math-ph/0412031]. In that paper, the entries of the Perron-Frobenius eigenvector were generalized from numbers to polynomials, which allowed them to be calculated inductively using divided difference operators. We relate these polynomials to the multidegrees of the components of the Brauer loop scheme, defined using an evident torus action on E. As a consequence, we obtain a formula for the degree of the commuting variety, previously calculated up to 4×4 matrices.     

Unusual dependence of particle architecture on surfactant concentration in partially fluorinated decylpyridinium templated silica

A series of porous silica particles is prepared with different concentrations of the fluorinated cationic surfactant 1-(3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10)-heptadecafluorodecyl)pyridinium chloride (HFDePC) to trace the changes in pore structure and particle morphology as the surfactant concentration increases. At the lowest concentration studied (1.5 mmol/L), the product consists of small round particles with close-packed cylindrical mesopores. As the HFDePC concentration increases, macroporous voids are introduced to create multi-chambered hollow particles with mesoporous walls. With a still higher concentration of HFDePC the macropore volume decreases, and elongated, tactoid-like nanoparticles are formed with random mesh-phase pores oriented with silica layers perpendicular to the main axis of the particles. Further increasing the concentration of HFDePC eventually leads to the formation of round particles with disordered pores. These changes are consistent with increasing HFDePC concentration favoring increasingly oblate or disklike micelles. The process of forming the elongated particles with random mesh-phase structure is investigated by TEM of chilled and dried samples. The results indicate that the oriented tactoid-like structure forms spontaneously within 2 min by co-assembly of silica and HFDePC rather than by preferred growth perpendicular to the layers. The particle shape and layer orientation are consistent with what would be expected for a liquid-crystal particle with orientation-dependent surface tension. Finally, we compare samples prepared with a high HFDePC and with good or poor mixing. With inadequate mixing, a gel layer forms at the top of the sample which is composed of elongated mesoporous particles with a thick coating of microporous silica. The lower particulate phase contains small disordered particles similar to those obtained in a well-mixed sample. Presumably, the structure of the upper layer results from initial immiscibility of the precursor and slow diffusion of silicates out of the gel.     

Nonlinear domain-wall velocity enhancement by spin-polarized electric current

The interaction between a dc spin-polarized electric current and a magnetic domain wall in a Permalloy nanowire was studied by high-bandwidth scanning Kerr polarimetry. The full functional dependence of wall velocity on electric current and magnetic field is presented. With the pinning potential nulled by a field, current-induced velocity enhancements exceeded 35 m/s at a current density of approximately 6 x 10(11) A/m(2). This large enhancement, more than 10 times that found in pinning-dominated experiments, results in part from an interaction that is nonlinear in current and independent of current direction.