molecular recognition at interfaces

In order to investigate molecular recognition on surfaces, an azide- functionalized monolayer was deposited on gold. The monolayer was characterized by X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) experiments and the decomposition of the azide upon irradiation with X-ray beams was investigated. Subsequently, various alkyne-functionalized host and guest molecules were attached to the azide by 1,3-dipolar cycloaddition. These modified surfaces and their host–guest chemistry were analysed by XPS and angle-resolved NEXAFS. The reversibility of guest binding was shown for one example as a proof of principle

Coevolutionary Dynamics: From Finite to Infinite Populations

Traditionally, frequency dependent evolutionary dynamics is described by deterministic replicator dynamics assuming implicitly infinite population sizes. Only recently have stochastic processes been introduced to study evolutionary dynamics in finite populations. However, the relationship between deterministic and stochastic approaches remained unclear. Here we solve this problem by explicitly considering large populations. In particular, we identify different microscopic stochastic processes that lead to the standard or the adjusted replicator dynamics. Moreover, differences on the individual level can lead to qualitatively different dynamics in asymmetric conflicts and, depending on the population size, can even invert the direction of the evolutionary process.Comment: 4 pages (2 figs included). Published in Phys. Rev. Lett., December 200

Stochastic differential equations for evolutionary dynamics with demographic noise and mutations

We present a general framework to describe the evolutionary dynamics of an arbitrary number of types in finite populations based on stochastic differential equations (SDE). For large, but finite populations this allows to include demographic noise without requiring explicit simulations. Instead, the population size only rescales the amplitude of the noise. Moreover, this framework admits the inclusion of mutations between different types, provided that mutation rates, $\mu$, are not too small compared to the inverse population size 1/N. This ensures that all types are almost always represented in the population and that the occasional extinction of one type does not result in an extended absence of that type. For $\mu N\ll1$ this limits the use of SDE's, but in this case there are well established alternative approximations based on time scale separation. We illustrate our approach by a Rock-Scissors-Paper game with mutations, where we demonstrate excellent agreement with simulation based results for sufficiently large populations. In the absence of mutations the excellent agreement extends to small population sizes.Comment: 8 pages, 2 figures, accepted for publication in Physical Review

Critical dynamics in the evolution of stochastic strategies for the iterated Prisoner's Dilemma

The observed cooperation on the level of genes, cells, tissues, and individuals has been the object of intense study by evolutionary biologists, mainly because cooperation often flourishes in biological systems in apparent contradiction to the selfish goal of survival inherent in Darwinian evolution. In order to resolve this paradox, evolutionary game theory has focused on the Prisoner's Dilemma (PD), which incorporates the essence of this conflict. Here, we encode strategies for the iterated Prisoner's Dilemma (IPD) in terms of conditional probabilities that represent the response of decision pathways given previous plays. We find that if these stochastic strategies are encoded as genes that undergo Darwinian evolution, the environmental conditions that the strategies are adapting to determine the fixed point of the evolutionary trajectory, which could be either cooperation or defection. A transition between cooperative and defective attractors occurs as a function of different parameters such a mutation rate, replacement rate, and memory, all of which affect a player's ability to predict an opponent's behavior.Comment: 27 pages, including supplementary information. 5 figures, 4 suppl. figures. Version accepted for publication in PLoS Comp. Bio

Nitroarene Reduction by a Virus Protein Cage Based Nanoreactor

Gold nanoparticles have recently gained attention as heterogeneous catalysts in a variety of industrially relevant processes. The catalytic activity of the particles is directly related to the available surface area, which increases with decreasing particle size. However, their stability in solution decreases along with the size, and surface modifications have to be carried out to enable efficient catalysis also for elongated reaction times. To prolong catalyst lifetime and to study the substrate selectivity, we encapsulated colloidal gold nanoparticles in cowpea chlorotic mottle virus cages and catalyzed the reduction of nitroarenes with different substituents. The reduction mechanism has been investigated carefully, revealing the reduction sequence nitro → hydroxylamine → amine to take place. The reduction rate is slowed by the introduction of the diffusion barrier imposed by the virus cage, and a nonconventional relation between electronic effects and reduction rate constants is reported that originates from the limited pore sizes and charged exterior/interior of the virus cage. Finally, a significantly increased stability of the hybrid nanoreactors and their recyclability are demonstrated

Intermixed Terpyridine-Functionalized Monolayers on Gold: Nonlinear Relationship between Terpyridyl Density and Metal Ion Coordination Properties

Aiming at the functionalization of surfaces with terpyridine anchors for the coordinative deposition of additional layers, mixed self-assembled monolayers (SAMs) were prepared from binary solutions of 12-(2,2′:6′,2″-terpyridine-4′-yl)­dodecane-1-thiol (TDT) and 1-decanethiol (DT). The SAMs and the order of the constituting molecules were analyzed by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and time-of-flight-secondary ion mass spectrometry (ToF-SIMS). The composition of the (TDT/DT)-SAMs and with it the surface density of terpyridyl groups correlates linearly with the relative concentrations of the two compounds in the solution used for depositing them. In marked contrast, the amount of terpyridine-coordinated Pd^II ions significantly deviates from this trend with an optimum at a 1:3 ratio of TDT/DT. This indicates a major fraction of the terpyridines in TDT-rich SAMs not to be accessible for Pd^II ion coordination. In agreement, NEXAFS spectroscopy reveals the alkyl backbones in TDT-rich SAMs not to be ordered, while they are preferentially upright oriented in the optimal 1:3-(TDT/DT)-SAMs. We interpret this in terms of terpyridine backfolding in TDT-rich SAMs, while they are located in accessible positions on top of the SAM in the 1:3-(TDT/DT)-SAM. While the alkyl backbones in the 1:3-(TDT/DT)-SAM are ordered, NEXAFS spectroscopy shows the terpyridyl groups not to have a preferential orientation in this SAM and thus retain enough flexibility to adjust to molecules that are deposited on top of the mixed SAM. In conclusion, the novel SAM does not undergo phase separation and consists predominantly of intermixed phases with adjustable surface density of quite flexible terpyridine anchor groups. The terpyridine–Pd^II anchors are not only available for a future deposition of the next layer, but the metal ions also represent a sensitive probe for the accessibility of the terpyridyl groups

Sequence-Programmable Multicomponent Multilayers of Nanometer-Sized Tetralactam Macrocycles on Gold Surfaces

Multicomponent multilayers have been deposited on gold surfaces by metal-ion-mediated layer-by-layer self-assembly of differently functionalized tetralactam macrocycles. The layer stack can be programmed with respect to the sequences of metal ions and macrocycles by the deposition sequence

Deposition of Ordered Layers of Tetralactam Macrocycles and Ether Rotaxanes on Pyridine-Terminated Self-Assembled Monolayers on Gold

The deposition of tetralactam macrocycles and the corresponding benzyl ether rotaxanes on gold substrates is investigated for the first time exploiting metallo-supramolecular chemistry. Two pyridine-terminated self-assembled monolayers (SAMs) are developed that are used as well-ordered template layers. The two SAMs differ with respect to the rigidity of the terminal pyridines as shown by angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The template layers are then used for the metal-mediated self-assembly of macrocylces and rotaxanes on solid supports. The SAM with the more rigid terminal pyridine shows a higher coverage with the macrocycles and is therefore preferable. Angle-resolved NEXAFS spectroscopy also shows the deposited supramolecules to be oriented preferentially upright. This order is only achieved for the macrocycles through the deposition on the more rigid SAM template, whereas rotaxanes form oriented layers on both SAMs. Time-of-flight secondary-ion mass spectrometry analysis was used to determine the deposition time required for the self-assembly process

Protein Cages as Containers for Gold Nanoparticles

Abundant and highly diverse, viruses offer new scaffolds in nanotechnology for the encapsulation, organization, or even synthesis of novel materials. In this work the coat protein of the cowpea chlorotic mottle virus (CCMV) is used to encapsulate gold nanoparticles with different sizes and stabilizing ligands yielding stable particles in buffered solutions at neutral pH. The sizes of the virus-like particles correspond to <i>T</i> = 1, 2, and 3 Caspar–Klug icosahedral triangulation numbers. We developed a simple one-step process enabling the encapsulation of commercially available gold nanoparticles without prior modification with up to 97% efficiency. The encapsulation efficiency is further increased using bis-p-(sufonatophenyl)­phenyl phosphine surfactants up to 99%. Our work provides a simplified procedure for the preparation of metallic particles stabilized in CCMV protein cages. The presented results are expected to enable the preparation of a variety of similar virus-based colloids for current focus areas

Structural Characterization of Native and Modified Encapsulins as Nanoplatforms for in Vitro Catalysis and Cellular Uptake

Recent years have witnessed the emergence of bacterial semiorganelle encapsulins as promising platforms for bio-nanotechnology. To advance the development of encapsulins as nanoplatforms, a functional and structural basis of these assemblies is required. Encapsulin from Brevibacterium linens is known to be a protein-based vessel for an enzyme cargo in its cavity, which could be replaced with a foreign cargo, resulting in a modified encapsulin. Here, we characterize the native structure of B. linens encapsulins with both native and foreign cargo using cryo-electron microscopy (cryo-EM). Furthermore, by harnessing the confined enzyme (i.e., a peroxidase), we demonstrate the functionality of the encapsulin for an in vitro surface-immobilized catalysis in a cascade pathway with an additional enzyme, glucose oxidase. We also demonstrate the in vivo functionality of the encapsulin for cellular uptake using mammalian macrophages. Unraveling both the structure and functionality of the encapsulins allows transforming biological nanocompartments into functional systems