Algorithmic Aspects of Tree Amalgamation

The amalgamation of leaf-labeled trees into a single (super)tree that “displays” each of the input trees is an important problem in classification. We discuss various approaches to this problem and show that a simple and well-known polynomial-time algorithm can be used to solve this problem whenever the input set of trees contains a minimum size subset that uniquely determines the supertree. Our results exploit a recently established combinatorial property concerning the structure of such collections of trees.     

A framework for the automated real-time detection of short tonal sounds from ocean observatories

Acquisition of acoustic data from ocean observatories is expected to play a key role for the long-term monitoring of marine mammals and anthropogenic noise. It typically requires processing of a large volume of acoustic data and it must rely on automated identification of signals. We present an algorithmic framework for the detection of short tonal sounds (e.g. cetacean calls, anthropogenic pings) intended to act as a first stage in a system for the automated real-time detection, classification, and localisation of acoustic sources. The algorithm was validated under a diversity of scenarios expected at ocean observatories. Using simulated signals that emulate a variety of cetacean call-types, perfect identification of signal position was obtained for signal to noise ratios of ?15 to ?5 dB, depending on the signal-type. Separation of real-world data segments with short tonal sounds (mainly cetacean calls) from segments with other sounds or noise resulted in Area Under the ROC Curve values between 0.96 and 0.98. The algorithm can be used to automatically identify cetacean calls and anthropogenic short tonal sounds much faster than in real-time, thereby reducing the burden put on data transmission, storage, or processing by classification and localisation algorithms.     

Thermodynamic Formalism for Contracting Lorenz Flows

We study the expansion properties of the contracting Lorenz flow introduced by Rovella via thermodynamic formalism. Specifically, we prove the existence of an equilibrium state for the natural potential [^( j)]_t(x,y,z):=-tlogJ_(x,y,z)^cu\hat{ \varphi }_{t}(x,y,z):=-t\log J_{(x,y,z)}^{cu} for the contracting Lorenz flow and for t in an interval containing [0,1]. We also analyse the Lyapunov spectrum of the flow in terms of the pressure.     

Generalizing the Cooper-pair instability to doped Mott insulators

Copper oxides become superconductors rapidly upon doping with electron holes, suggesting a fundamental pairing instability. The Cooper mechanism explains normal superconductivity as an instability of a fermi-liquid state, but high-temperature superconductors derive from a Mott-insulator normal state, not a fermi liquid. We show that precocity to pair condensation with doping is a natural property of competing antiferromagnetism and d-wave superconductivity on a singly-occupied lattice, thus generalizing the Cooper instability to doped Mott insulators, with significant implications for the high-temperature superconducting mechanism.     

Universal quenching of common fluorescent probes by water and alcohols

Although biological imaging is mostly performed in aqueous media, it is hardly ever considered that water acts as a classic fluorescence quencher for organic fluorophores. By investigating the fluorescence properties of 42 common organic fluorophores recommended for biological labelling, we demonstrate that H₂O reduces their fluorescence quantum yield and lifetime by up to threefold and uncover the underlying fluorescence quenching mechanism. We show that the quenching efficiency is significantly larger for red-emitting probes and follows an energy gap law. The fluorescence quenching finds its origin in high-energy vibrations of the solvent (OH groups), as methanol and other linear alcohols are also found to quench the emission, whereas it is restored in deuterated solvents. Our observations are consistent with a mechanism by which the electronic excitation of the fluorophore is resonantly transferred to overtones and combination transitions of high-frequency vibrational stretching modes of the solvent through space and not through hydrogen bonds. Insight into this solvent-assisted quenching mechanism opens the door to the rational design of brighter fluorescent probes by offering a justification for protecting organic fluorophores from the solvent via encapsulation.

Overtones and combinations of O–H vibrations in the solvent efficiently quench red-emitting fluorophores by resonant energy transfer.     

Characterization of VX on concrete using ion trap secondary ionization mass spectrometry

The nerve agent VX (O-ethyl S-2-diisopropylaminoethyl methyl phosphonothiolate) was analyzed on the surface of concrete samples using an ion trap secondary ion mass spectrometer (IT-SIMS). It was found that VX could be detected down to an absolute quantity of 5 ng on a concrete chip, or to a surface coverage of 0.0004 monolayers on crushed concrete. To achieve these levels of detection, the m/z 268-->128 ion fragmentation was measured using MS2, where m/z 268 corresponds to [VX + H]+, and 128 corresponds to a diisopropylvinylammonium isomer, that is formed by the elimination of the phosphonothiolate moiety. Detection at these levels was accomplished by analyzing samples that had been recently exposed to VX, i.e., within an hour. When the VX-exposed concrete samples were aged, the SIMS signature for intact VX had disappeared, which signaled the degradation of the compound on the concrete surface. The VX signature was replaced by ions which are interpreted in terms of VX degradation products, which appear to be somewhat long lived on the concrete surface. These compounds include ethylmethylphosphonic acid (EMPA), diisopropyl taurine (DIPT), diisopropylaminoethanethiol (DESH), bis(diisopropylaminoethane) disulfide [(DES)2], and a particularly tenacious compound that may correspond to diisopropylvinylamine (DIVA), or an isomer thereof. It was found that the thiolamine-derived degradation products DIPT, DESH, and (DES)2 were removed with isopropyl alcohol extraction. However, the DIVA-related degradation product was observed to strongly adhere to the concrete surface for longer than one week. Although quantitation was not possible in this set of experiments, the results clearly show the rapid degradation of VX on concrete, as well as the surface sensitivity of the IT-SIMS for intact VX and its adsorptive degradation products.     

Ultrafast excited state dynamics controlling photochemical isomerization of N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium coordinated to a {Re I(CO)3(2,2'-bipyridine)} chromophore

Two multifunctional photoactive complexes [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) and [Re(MeDpe(+))(CO)(3)(bpy)](2+) (MeDpe(+)=N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium, bpy=2,2'-bipyridine) were synthesized, characterized, and their redox and photonic properties were investigated by cyclic voltammetry; ultraviolet-visible-infrared (UV/Vis/IR) spectroelectrochemistry, stationary UV/Vis and resonance Raman spectroscopy; photolysis; picosecond time-resolved absorption spectroscopy in the visible and infrared regions; and time-resolved resonance Raman spectroscopy. The first reduction step of either complex occurs at about -1.1 V versus Fc/Fc(+) and is localized at MeDpe(+). Reduction alone does not induce a trans-->cis isomerization of MeDpe(+). [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) is photostable, while [Re(MeDpe(+))(CO)(3)(bpy)](2+) and free MeDpe(+) isomerize under near-UV irradiation. The lowest excited state of [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) has been identified as the Re(Cl)(CO)(3)-->MeDpe(+ 3)MLCT (MLCT=metal-to-ligand charge transfer), decaying directly to the ground state with lifetimes of approximately 42 (73 %) and approximately 430 ps (27 %). Optical excitation of [Re(MeDpe(+))(CO)(3)(bpy)](2+) leads to population of Re(CO)(3)-->MeDpe(+) and Re(CO)(3)-->bpy (3)MLCT states, from which a MeDpe(+) localized intraligand (3)pipi* excited state ((3)IL) is populated with lifetimes of approximately 0.6 and approximately 10 ps, respectively. The (3)IL state undergoes a approximately 21 ps internal rotation, which eventually produces the cis isomer on a much longer timescale. The different excited-state behavior of the two complexes and the absence of thermodynamically favorable interligand electron transfer in excited [Re(MeDpe(+))(CO)(3)(bpy)](2+) reflect the fine energetic balance between excited states of different orbital origin, which can be tuned by subtle structural variations. The complex [Re(MeDpe(+))(CO)(3)(bpy)](2+) emerges as a prototypical, multifunctional species with complementary redox and photonic behavior.     

A systematic study of carboxylic acids in negative ion mode electrospray ionisation mass spectrometry providing a structural model for ion suppression

We report a systematic investigation of the effects and structural requirements for ion suppression in negative ion mode electrospray ionisation mass spectrometry of a series of carboxylic acids and present a structural model rationalising ion suppression effects.     

Investigating the molecular mechanisms of in-plane mechanochemistry on cantilever arrays

Free-standing cantilevers, which directly translate specific biochemical reactions into micromechanical motion, have recently attracted much attention as label-free biosensors and micro/nano robotic devices. To exploit this mechanochemical sensing technology, it is essential to develop a fundamental understanding of the origins of surface stress. Here we report a detailed study into the molecular basis of stress generation in aqueous environments focusing on the pH titration of model mercaptohexadecanoic acid self-assembled monolayers (SAMs), using in situ reference cantilevers coated with nonionizable hexadecanethiol SAMs. Semiautomated data analysis and a statistical model were developed to quantify cyclic deprotonation/protonation reactions on multiple arrays. In-plane force titrations were found to have the sensitivity to detect ionic hydrogen bond formation between protonated and nonprotonated carboxylic acid groups in the proximity of the surface pK1/2, which generated a mean tensile differential surface stress of +1.2 +/- 0.3 mN/m at pH 6.0, corresponding to 1 pN attractive force between two adjacent MHA molecules. Conversely, the magnitude of compressive differential surface stress was found to increase progressively with pH >/= 7.0, reaching a maximum of -14.5 +/- 0.5 mN/m at pH 9.0, attributed to enhanced electrostatic repulsion between deprotonated carboxylic acid groups. However, striking differences were observed in the micromechanical responses to different ionic strength and ion species present in the aqueous environment, highlighting the critical role of counter- and co-ions on surface stress. Our findings provide fundamental insights into the molecular mechanisms of in-plane mechanochemistry, which may be exploited for biosensing and nanoactuation applications.