The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes.

Behavior is critical for animal survival and reproduction, and possibly for diversification and evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental and widespread behavioral trait, exploratory behavior, in one of the largest adaptive radiations on Earth, the cichlid fishes of Lake Tanganyika.

Local Environments Created by the Ligand Coating of Nanoparticles and Their Implications for Sensing and Surface Reactions.

ConspectusThe ligand shells of colloidal nanoparticles (NPs) can serve different purposes. In general, they provide colloidal stability by introducing steric repulsion between NPs. In the context of biological applications, the ligand shell plays a critical role in targeting, enabling NPs to achieve specific biodistributions.

Machine learning of an implicit solvent for dynamic Monte Carlo simulations.

The Bond Fluctuation Model (BFM) is a highly efficient and versatile method for simulating polymers, membranes, and soft matter. Due to its coarse-grained nature, the BFM is employed to understand the universal properties of polymers. Solvent effects are often mediated by explicit solvent particles, while implicit solvent models have had limited use as they may lead to frozen states and, thus, ergodicity-related problems.

Efficient enumeration-selection computational strategy for adaptive chemistry.

Design problems of finding efficient patterns, adaptation of complex molecules to external environments, affinity of molecules to specific targets, dynamic adaptive behavior of chemical systems, reconstruction of 3D structures from diffraction data are examples of difficult to solve optimal design or inverse search problems. Nature inspires evolution strategies to solve design problems that are based on selection of successful adaptations and heritable traits over generations. To exploit this strategy in the creation of new materials, a concept of adaptive chemistry was proposed to provide a route for synthesis of self-adapting molecules that can fit to their environment.

Decoding Interaction Patterns from the Chemical Sequence of Polymers Using Neural Networks.

The relation between chemical sequences and the properties of polymers is considered using artificial neural networks with a low-dimensional bottleneck layer of neurons. These encoder-decoder architectures may compress the input information into a meaningful set of physical variables that describe the correlation between distinct types of data. In this work, neural networks were trained to translate a sequence of hydrophilic and hydrophobic segments into the effective free energy landscape of a copolymer interacting with a lipid membrane.

Protein corona modulates interaction of spiky nanoparticles with lipid bilayers.

The impact of protein corona on the interactions of nanoparticles (NPs) with cells remains an open question. This question is particularly relevant to NPs which sizes, ranging from tens to hundreds nanometers, are comparable to the sizes of most abundant proteins in plasma. Protein sizes match with typical thickness of various coatings and ligands layers, usually present at the surfaces of larger NPs.

The multi-faceted mechano-bactericidal mechanism of nanostructured surfaces.

The mechano-bactericidal activity of nanostructured surfaces has become the focus of intensive research toward the development of a new generation of antibacterial surfaces, particularly in the current era of emerging antibiotic resistance. This work demonstrates the effects of an incremental increase of nanopillar height on nanostructure-induced bacterial cell death. We propose that the mechanical lysis of bacterial cells can be influenced by the degree of elasticity and clustering of highly ordered silicon nanopillar arrays.

Unexpected Cholesterol-Induced Destabilization of Lipid Membranes near Transmembrane Carbon Nanotubes.

Cholesterol is a crucial component of mammalian cell membranes that takes part in many vital processes. It is generally accepted that cholesterol stabilizes the membrane and induces transitions into ordered states. In contrast to expectations, we demonstrate that cholesterol can destabilize the membrane by creating a nanodomain around a perpendicularly embedded ultrashort carbon nanotube (CNT), and we show that cholesterol triggers the translocation of an ultrashort CNT through the cell membrane.

Simulations of Protein Adsorption on Nanostructured Surfaces.

Recent technological advances have allowed the development of a new generation of nanostructured materials, such as those displaying both mechano-bactericidal activity and substrata that favor the growth of mammalian cells. Nanomaterials that come into contact with biological media such as blood first interact with proteins, hence understanding the process of adsorption of proteins onto these surfaces is highly important. The Random Sequential Adsorption (RSA) model for protein adsorption on flat surfaces was modified to account for nanostructured surfaces.

High-throughput 3D visualization of nanoparticles attached to the surface of red blood cells.

Blood circulation is the main distribution route for systemic delivery and the possibility to manipulate red blood cells (RBCs) by attaching nanoparticles to their surface provides a great opportunity for cargo delivery into tissues. Nanocarriers attached to RBCs can be delivered to specific organs orders of magnitude faster than if injected directly into the bloodstream. Another advantage is a shielding from recognition by the immune system, thereby increasing the efficiency of delivery.

The pyrrolopyrimidine colchicine-binding site agent PP-13 reduces the metastatic dissemination of invasive cancer cells in vitro and in vivo.

Standard chemotherapies that interfere with microtubule dynamics are a chemotherapeutic option used for the patients with advanced malignancies that invariably relapse after targeted therapies. However, major efforts are needed to reduce their toxicity, optimize their efficacy, and reduce cancer chemoresistance to these agents. We previously identified a pyrrolo[2,3d]pyrimidine-based microtubule-depolymerizing agent (PP-13) that binds to the colchicine site of β-tubulin and exhibits anticancer properties in solid human cancer cells, including chemoresistant subtypes.

Tension-Induced Translocation of an Ultrashort Carbon Nanotube through a Phospholipid Bilayer.

Increasing awareness of bioeffects and toxicity of nanomaterials interacting with cells puts in focus the mechanisms by which nanomaterials can cross lipid membranes. Apart from well-discussed energy-dependent endocytosis for large objects and passive diffusion through membranes by solute molecules, other translocation mechanisms based on physical principles can exist. We show the importance of membrane tension on the translocation through lipid bilayers of ultrashort carbon nanotubes (USCNTs).

Pillars of Life: Is There a Relationship between Lifestyle Factors and the Surface Characteristics of Dragonfly Wings?

Dragonfly wings are of great interest to researchers investigating biomimetic designs for antiwetting and antibacterial surfaces. The waxy epicuticular layer on the membrane of dragonfly wings possesses a unique surface nanoarchitecture that consists of irregular arrays of nanoscale pillars. This architecture confers superhydrophobic, self-cleaning, antiwetting, and antibiofouling behaviors.

Bridging molecular simulation models and elastic theories for amphiphilic membranes.

The Single Chain Mean Field theory is used to link coarse-grained models of amphiphilic molecules with analytical models for membrane elasticity, where phenomenological parameters are deduced from explicit molecular models and force fields. We estimate the elastic constants based on the free energy of the amphiphilic bilayer in planar and cylindrical geometries on the example of four amphiphilic molecules that differ in length and stiffness. We study how these variations affect the equilibrium bilayer structure, the equilibrium free energy, and the elastic constants.

High Aspect Ratio Nanostructures Kill Bacteria via Storage and Release of Mechanical Energy.

The threat of a global rise in the number of untreatable infections caused by antibiotic-resistant bacteria calls for the design and fabrication of a new generation of bactericidal materials. Here, we report a concept for the design of antibacterial surfaces, whereby cell death results from the ability of the nanofeatures to deflect when in contact with attaching cells. We show, using three-dimensional transmission electron microscopy, that the exceptionally high aspect ratio (100-3000) of vertically aligned carbon nanotubes (VACNTs) imparts extreme flexibility, which enhances the elastic energy storage in CNTs as they bend in contact with bacteria.

Structure and Chemical Organization in Damselfly Calopteryx haemorrhoidalis Wings: A Spatially Resolved FTIR and XRF Analysis with Synchrotron Radiation.

Insects represent the majority of known animal species and exploit a variety of fascinating nanotechnological concepts. We investigated the wings of the damselfly Calopteryx haemorrhoidalis, whose males have dark pigmented wings and females have slightly pigmented wings. We used scanning electron microscopy (SEM) and nanoscale synchrotron X-ray fluorescence (XRF) microscopy analysis for characterizing the nanostructure and the elemental distribution of the wings, respectively.

Study of melanin localization in the mature male Calopteryx haemorrhoidalis damselfly wings.

Damselflies Calopteryx haemorrhoidalis exhibiting black wings are found in the western Mediterranean, Algeria, France, Italy, Spain and Monaco. Wing pigmentation is caused by the presence of melanin, which is involved in physiological processes including defence reactions, wound healing and sclerotization of the insect. Despite the important physiological roles of melanin, the presence and colour variation among males and females of the C.

Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context.

Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and the alteration of biological function. Nature and humans use different design strategies to create nanomaterials: biological objects have emerged from billions of years of evolution and from adaptation to their environment resulting in high levels of structural complexity; in contrast, synthetic nanomaterials result from minimalistic but controlled design options limited by the authors' current understanding of the biological world. This conceptual mismatch makes it challenging to create synthetic nanomaterials that possess desired functions in biological media.

Formation and stabilization of pores in bilayer membranes by peptide-like amphiphilic polymers.

We study pore formation in models of lipid bilayer membranes interacting with amphiphilic copolymers mimicking anti-microbial peptides using Monte Carlo simulations and we rationalize our results by a simple brush-model for the fluid membrane. In our study a weak tension on the membrane is required to observe pore-formation induced by the adsorption of flexible amphiphilic copolymers. The copolymers enhance the pore stability by decreasing the line tension due to weak adsorption along the rim of the pore.

Dynamic studies of the interaction of a pH responsive, amphiphilic polymer with a DOPC lipid membrane.

Deeper understanding of the molecular interactions between polymeric materials and the lipid membrane is important across a range of applications from permeation for drug delivery to encapsulation for immuno-evasion. Using highly fluidic microcavity supported lipid bilayers, we studied the interactions between amphiphilic polymer PP50 and a DOPC lipid bilayer. As the PP50 polymer is pH responsive the studies were carried out at pH 6.

Thermal Tunneling of Homopolymers through Amphiphilic Membranes.

We propose a theory to predict the passive translocation of flexible polymers through amphiphilic membranes. By using a generic model for the potential felt by a monomer across the membrane we calculate the free energy profile for homopolymers as a function of their hydrophobicity. Our model explains the translocation window and the translocation rates as a function of chain hydrophobicity in quantitative agreement with simulation results.

Translocation and induced permeability of random amphiphilic copolymers interacting with lipid bilayer membranes.

We investigate adsorption and passive translocation of random amphiphilic copolymers interacting with a self-assembled lipid bilayer membrane. By using the bond fluctuation model with explicit solvent, we consider random copolymers under variation of the fraction, H̅, of hydrophobic sites and chain length. Our results indicate a point of balanced hydrophobicity, where a slight excess of hydrophobic monomers compensates an additional insertion barrier due to the self-organized packing of the bilayer.

Single polymer chains in poor solvent: using the bond fluctuation method with explicit solvent.

We use the bond fluctuation model with explicit solvent to study single polymer chains under poor solvent conditions. Static and dynamic properties of the bond fluctuation model with explicit solvent are compared with the implicit solvent model, and the Θ-temperatures are determined for both solvent models. We show that even in the very poor solvent regime, dynamics is not frozen for the explicit solvent model.

Nanoparticle-induced permeability of lipid membranes.

Monte Carlo simulations using the bond fluctuation method with explicit solvent reveal the mechanism of enhanced permeability of lipid bilayers induced by the adsorption of nanoparticles with controlled hydrophobicity. Simulation results indicate an adsorption transition of nanoparticles on the bilayer in a certain range of relative degree of hydrophobicity. In this range the nanoparticles can translocate through the bilayer, reversibly destabilizing the structure of the bilayer and inducing enhanced permeability for water and small solutes.