Evolution with recombination as Gibbs sampling.

This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions without resorting to diffusion approximations. Tractability is achieved by generating new offspring using n-parent rather than 2-parent recombination.

Nonequilibrium correlations in minimal dynamical models of polymer copying.

Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these nonequilibrium states are created and analyze the accuracy and efficiency of a family of dynamical models that produce persistent copies. For the weakest chemical driving, when polymer growth occurs in equilibrium, both the copy accuracy and, more surprisingly, the efficiency vanish.

Small heat shock proteins sequester misfolding proteins in near-native conformation for cellular protection and efficient refolding.

Small heat shock proteins (sHsp) constitute an evolutionary conserved yet diverse family of chaperones acting as first line of defence against proteotoxic stress. sHsps coaggregate with misfolded proteins but the molecular basis and functional implications of these interactions, as well as potential sHsp specific differences, are poorly explored. In a comparative analysis of the two yeast sHsps, Hsp26 and Hsp42, we show in vitro that model substrates retain near-native state and are kept physically separated when complexed with either sHsp, while being completely unfolded when aggregated without sHsps.

Self-Assembly and Conformational Changes of Hydrophobin Classes at the Air-Water Interface.

We use surface-specific vibrational sum-frequency generation spectroscopy (VSFG) to study the structure and self-assembling mechanism of the class I hydrophobin SC3 from Schizophyllum commune and the class II hydrophobin HFBI from Trichoderma reesei. We find that both hydrophobins readily accumulate at the water-air interface and form rigid, highly ordered protein films that give rise to prominent VSFG signals. We identify several resonances that are associated with β-sheet structures and assign them to the central β-barrel core present in both proteins.

Dose-Response Analysis of Chemotactic Signaling Response in Salmonella typhimurium LT2 upon Exposure to Cysteine/Cystine Redox Pair.

The chemotaxis system enables motile bacteria to search for an optimum level of environmental factors. Salmonella typhimurium senses the amino acid cysteine as an attractant and its oxidized dimeric form, cystine, as a repellent. We investigated the dose-response dependence of changes in chemotactic signaling activity upon exposure to cysteine and cystine of S.

Orientation of polar molecules near charged protein interfaces.

We study the orientation of water and urea molecules and protein amide vibrations at aqueous α-lactalbumin and α-lactalbumin/urea interfaces using heterodyne-detected vibrational sum frequency generation. We vary the net charge of the protein by changing the pH. We find that the orientation of the water and urea molecules closely follows the net charge of the protein at the surface of the solution.

Heterodyne-detected sum frequency generation spectroscopy of polyacrylic acid at the air/water-interface.

The conformational and hydration behavior of polyacrylic acid (PAA) at the air/water interface is studied using heterodyne-detected vibrational sum frequency generation spectroscopy (HD-VSFG). The amount of adsorption at the water-air interface and the influence of PAA on the water structure at the interface are found to be highly dependent on the degree of ionization (acid dissociation) of the carboxylic acid groups. At a low degree of ionization PAA is surface active and remains in a dense packing arrangement with intrachain hydrogen bonds.

Investigation of the Ice-Binding Site of an Insect Antifreeze Protein Using Sum-Frequency Generation Spectroscopy.

We study the ice-binding site (IBS) of a hyperactive antifreeze protein from the beetle Dendroides canadensis (DAFP-1) using vibrational sum-frequency generation spectroscopy. We find that DAFP-1 accumulates at the air-water interface due to the hydrophobic character of its threonine-rich IBS while retaining its highly regular β-helical fold. We observe a narrow band at 3485 cm(-1) that we assign to the O-H stretch vibration of threonine hydroxyl groups of the IBS.

Structure and dynamics of a salt-bridge model system in water and DMSO.

We study the interaction between the ions methylguanidinium and trifluoroacetate dissolved in D2O and dimethylsulfoxide with linear infrared spectroscopy and femtosecond two-dimensional infrared spectroscopy. These ions constitute model systems for the side chains of arginine and glutamic and aspartic acid that are known to form salt bridges in proteins. We find that the salt-bridge formation of methylguanidinium and trifluoroacetate leads to a significant acceleration of the vibrational relaxation dynamics of the antisymmetric COO stretching vibration of the carboxyl moiety of trifluoroacetate.

Femtosecond mid-infrared study of the dynamics of water molecules in water-acetone and water-dimethyl sulfoxide mixtures.

We study the vibrational relaxation dynamics and the reorientation dynamics of HDO molecules in binary water-dimethyl sulfoxide (DMSO) and water-acetone mixtures with polarization-resolved femtosecond mid-infrared spectroscopy. For low solute concentrations we observe a slowing down of the reorientation of part of the water molecules that hydrate the hydrophobic methyl groups of DMSO and acetone. For water-DMSO mixtures the fraction of slowed-down water molecules rises much steeper with solute concentration than for water-acetone mixtures, showing that acetone molecules show significant aggregation already at low concentrations.

Observation of vibrational energy exchange in a type-III antifreeze protein.

We performed time- and polarization-resolved pump-probe and two-dimensional infrared (2D-IR) experiments to study the dynamics of the amide I vibration of a 7 kDa type-III antifreeze protein. In the pump-probe experiments, we used femtosecond mid-infrared pulses to investigate the vibrational relaxation dynamics of the amide mode. The transient spectra show the presence of two spectral components that decay with different lifetimes, indicative of the presence of two distinct amide subbands.

Plasmonic band structure controls single-molecule fluorescence.

Plasmonics and photonic crystals are two complementary approaches to tailor single-emitter fluorescence, using strong local field enhancements near metals on one hand and spatially extended photonic band structure effects on the other hand. Here, we explore the emergence of spontaneous emission control by finite-sized hexagonal arrays of nanoapertures milled in gold film. We demonstrate that already small lattices enable highly directional and enhanced emission from single fluorescent molecules in the central aperture.

Focusing and scanning microscopy with propagating surface plasmons.

Here we demonstrate a novel surface plasmon polariton (SPP) microscope which is capable of imaging below the optical diffraction limit. A plasmonic lens, generated through phase-structured illumination, focuses SPPs down to their diffraction limit and scans the focus with steps as small as 10 nm. This plasmonic lens is implemented on a metallic nanostructure consisting of alternating hole array gratings and bare metal arenas.

Coherent and broadband enhanced optical absorption in graphene.

We experimentally demonstrate a broadband enhancement of the light absorption in graphene over the whole visible spectrum. This enhanced absorption is obtained in a multilayer structure by using an Attenuated Total Reflectance (ATR) configuration and it is explained in terms of coherent absorption arising from interference and dissipation. The interference mechanism leading to the phenomenon of coherent absorption allows for its precise control by varying the refractive index and/or thickness of the medium surrounding the graphene.

Hybrid plasmonic-photonic modes in diffractive arrays of nanoparticles coupled to light-emitting optical waveguides.

We study the hybridized plasmonic-photonic modes supported by two-dimensional arrays of metallic nanoparticles coupled to light-emitting optical waveguides. Localized surface plasmon polaritons in the metallic nanoparticles can couple to guided modes in the underlying waveguide, forming quasi-guided hybrid modes, or to diffracted orders in the plane of the array, forming surface lattice resonances. We consider three kinds of samples: one sustains quasi-guided modes only, another sustains surface lattice resonances only, and a third sample sustains both modes.

Spatiotemporal focusing in opaque scattering media by wave front shaping with nonlinear feedback.

We experimentally demonstrate spatiotemporal focusing of light on single nanocrystals embedded inside a strongly scattering medium. Our approach is based on spatial wave front shaping of short pulses, using second harmonic generation inside the target nanocrystals as the feedback signal. We successfully develop a model both for the achieved pulse duration as well as the observed enhancement of the feedback signal.

Nanowire antenna emission.

We experimentally demonstrate the directional emission of polarized light from single semiconductor nanowires. The directionality of this emission has been directly determined with Fourier microphotoluminescence measurements of vertically oriented InP nanowires. Nanowires behave as efficient optical nanoantennas, with emission characteristics that are not only given by the material but also by their geometry and dimensions.

Rare switching events in non-stationary systems.

Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a set of rate constants. We consider the question how to extend such a coarse-grained description to non-stationary systems and to systems with finite memory.

Non-stationary forward flux sampling.

We present a method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform sampling of trajectories in phase space and time, leading to accurate estimates for time-dependent switching propensities and time-dependent phase space probability densities. It is suitable for equilibrium or non-equilibrium systems, in or out of stationary state, including non-Markovian or externally driven systems.

Optical control of plasmonic Bloch modes on periodic nanostructures.

We study and actively control the coherent properties of surface plasmon polaritons (SPPs) optically excited on a nanohole array. Amplitude and phase of the optical excitation are externally controlled via a digital spatial light modulator (SLM) and SPP interference fringe patterns are designed and observed with high contrast. Our interferometric observations reveal SPPs dressed with the Bloch modes of the periodic nanostructure.

High-reactivity matrices increase the sensitivity of matrix enhanced secondary ion mass spectrometry.

Secondary ion mass spectrometry (SIMS) is a desorption/ionization method in which ions are generated by the impact of a primary ion beam on a sample. Classic matrix assisted laser desorption and ionization (MALDI) matrices can be used to increase secondary ion yields and decrease fragmentation in a SIMS experiment, which is referred to as matrix enhanced SIMS (ME-SIMS). Contrary to MALDI, the choice of matrices for ME-SIMS is not constrained by their photon absorption characteristics.

Anisotropic water reorientation around ions.

We study the reorientation dynamics of water molecules around ions using terahertz dielectric relaxation spectroscopy and polarization-resolved femtosecond infrared pump-probe spectroscopy. The results are discussed in relation to the ion-specific Hofmeister series and the concomitant "structure-making" and "structure-breaking" effects of ions on water. We show that when a dissolved salt consists of a strongly hydrated ion with a weakly hydrated counterion the reorientation of water molecules around the strongly hydrated ion is anisotropic, in the sense that differently charged ions affect reorientation along different molecular axes: cations mainly slow the reorientation dynamics of the water dipole vectors, and anions mainly slow down the reorientation dynamics of the hydroxyl group that points toward the anion.

High dynamic range bio-molecular ion microscopy with the Timepix detector.

Highly parallel, active pixel detectors enable novel detection capabilities for large biomolecules in time-of-flight (TOF) based mass spectrometry imaging (MSI). In this work, a 512 × 512 pixel, bare Timepix assembly combined with chevron microchannel plates (MCP) captures time-resolved images of several m/z species in a single measurement. Mass-resolved ion images from Timepix measurements of peptide and protein standards demonstrate the capability to return both mass-spectral and localization information of biologically relevant analytes from matrix-assisted laser desorption ionization (MALDI) on a commercial ion microscope.