Santanu Ray

Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers

Antimicrobial peptides are postulated to disrupt microbial phospholipid membranes. The prevailing molecular model is based on the formation of stable or transient pores although the direct observation of the fundamental processes is lacking. By combining rational peptide design with topographical (atomic force microscopy) and chemical (nanoscale secondary ion mass spectrometry) imaging on the same samples, we show that pores formed by antimicrobial peptides in supported lipid bilayers are not necessarily limited to a particular diameter, nor they are transient, but can expand laterally at the nano-to-micrometer scale to the point of complete membrane disintegration. The results offer a mechanistic basis for membrane poration as a generic physicochemical process of cooperative and continuous peptide recruitment in the available phospholipid matrix.

Quantitative analysis of adsorbed proteins by X-ray photoelectron spectroscopy.

Protein adsorption at solid surfaces is central to many phenomena of medical and technological interest. The determination of the amount of protein attached to the surface is a critical measurement performed by using a wide range of methods. X-ray photoelectron spectroscopy (XPS) is able to provide a straightforward quantitative analysis of the amount of protein adsorbed as an overlayer on a material surface. While XPS is commonly employed to assess qualitatively the amount of adsorbed protein, this is usually expressed in terms of the elemental fraction (or at. %) of nitrogen calculated using an assumption of depth homogeneity despite the fact that this does not linearly scale with the amount of protein. In this paper, we have shown that thicknesses derived from XPS data linearly correlated with spectroscopic ellipsometry data on the same samples with a scatter of 10%. A straightforward equation to convert the concentration of nitrogen from XPS into an equivalent thickness of a protein film is presented. We highlight some discrepancies in the absolute thicknesses determined by XPS and ellipsometry on dried films and quartz crystal microbalance on wet films, which appear likely to result from the inclusion of a contribution from water in the latter two techniques.

Sample Cooling or Rotation Improves C60 Organic Depth Profiles of Multilayered Reference Samples: Results from a VAMAS Interlaboratory Study

We demonstrate two methods to improve the quality of organic depth profiling by C(60) sputtering using multilayered reference samples as part of a VAMAS (Versailles project on Advanced Materials and Standards) interlaboratory study. Sample cooling was shown previously to be useful in extending the useful depth over which organic materials can be profiled. We reinforce these findings and demonstrate that cooling results in a lower initial sputtering yield to approximately -40 degrees C, but the improvement in useful profiling depth continues as the sample is cooled further, even though there is no further reduction in the initial sputtering yield. We report, for the first time, the use of sample rotation in organic depth profiling and demonstrate that the initial sputtering yield at room temperature is maintained throughout the depth of the samples used in this study. Useful profiling depth and good depth resolution are both associated with a constant sputtering yield. The fact that rotation results in the maintenance of depth resolution underlines the fact that depth resolution is often limited by the development of ion-beam-induced topography. Constant sputtering yield results in a constant secondary-ion yield, after transient processes have occurred, and this allows simple quantification methods to be applied to organic depth profiling data.

Influence of the work of adhesion on the dynamic wetting of chemically heterogeneous surfaces.

The velocity dependence of the dynamic contact angle for a glycerol-water mixture wetting two different chemically heterogeneous surfaces (mixed thiols on gold and partially methylated titania, 16 samples in all) was studied. The molecular kinetic theory (MKT) of wetting was used to interpret the dynamic contact angle data. The equilibrium displacement frequency ( K 0) was predominantly determined by the viscous contribution from the bulk liquid, with a minor contribution from the surface. The mean distance between surface sites (lambda) decreased with increasing work of adhesion. The contact line friction coefficient zeta 0 was found to vary exponentially with the work of adhesion, enabling the unit flow volume of the liquid to be obtained.

Differentially Instructive Extracellular Protein Micro-nets

An ability to construct biological matter from the molecule up holds promise for applications ranging from smart materials to integrated biophysical models for synthetic biology. Biomolecular self-assembly is an efficient strategy for biomaterial construction which can be programmed to support desired function. A challenge remains in replicating the strategy synthetically, that is at will, and differentially, that is for a specific function at a given length scale. Here we introduce a self-assembly topology enabling a net-like architectural mimetic of native extracellular matrices capable of differential responses to cell adhesion--enhanced mammalian cell attachment and proliferation, and enhanced resistance to bacterial colonization--at the native sub-millimeter length scales. The biological performance of such protein micro-nets directly correlates with their morphological and chemical properties, offering thus an application model for differential extracellular matrices.

Wire-bar coating of semiconducting polythiophene/insulating polyethylene blend thin films for organic transistors

Organic blend thin films consisting of semiconducting poly(3-hexylthiophene) (P3HT) and insulating high-density polyethylene (HDPE) have been fabricated by novel application of a large area wire-bar coating technique in air. The microstructure of P3HT:HDPE blend films reveals a strong structural dependence on initial composition. Preferential segregation of P3HT toward the film surface is observed for all blend compositions, while P3HT (or P3HT-rich) columnar structures enclosed by HDPE (or HDPE-rich) lamellar matrix is distinctive for 50:50 (by weight) blends. The transistors fabricated with P3HT:HDPE blend films show a clear field effect behavior, exhibiting charge carrier mobilities up to 5 × 10−2 cm2/Vs, comparable to the values reported in spin-coated similar blends and of neat P3HT devices. The wire-bar coated blend films and devices are highly repeatable and spatially uniform over large areas (few cm by few cm), demonstrating the suitability of this technique for manufacturing of large area organic...

Arbitrary Self‐Assembly of Peptide Extracellular Microscopic Matrices

Two faces for one matrix: A single bifaceted cyclopeptide block forms highly branched, porous, and intricate fibrillar networks, which span microscopic dimensions and mimic the extracellular matrix to support cell growth and proliferation. The peptide block has two domains connected with triglycine linkers (GGG); the domains consist of positively (blue) and negatively (red) charged heptads that provide interactions between different blocks.

A De Novo Virus-Like Topology for Synthetic Virions

A de novo topology of virus-like assembly is reported. The design is a trifaceted coiled-coil peptide helix, which self-assembles into ultrasmall, monodisperse, anionic virus-like shells that encapsulate and transfer both RNA and DNA into human cells. Unlike existing artificial systems, these shells share the same physical characteristics of viruses being anionic, nonaggregating, abundant, hollow, and uniform in size, while effectively mediating gene silencing and transgene expression. These are the smallest virus-like structures reported to date, both synthetic and native, with the ability to adapt and transfer small and large nucleic acids. The design thus offers a promising solution for engineering bespoke artificial viruses with desired functions.

Quantification of variable functional-group densities of mixed-silane monolayers on surfaces via a dual-mode fluorescence and XPS label.

The preparation of aminated monolayers with a controlled density of functional groups on silica surfaces through a simple vapor deposition process employing different ratios of two suitable monoalkoxysilanes, (3-aminopropyl)diisopropylethoxysilane (APDIPES) and (3-cyanopropyl)dimethylmethoxysilane (CPDMMS), and advances in the reliable quantification of such tailored surfaces are presented here. The one-step codeposition process was carried out with binary silane mixtures, rendering possible the control over a wide range of densities in a single step. In particular, APDIPES constitutes the functional silane and CPDMMS the inert component. The procedure requires only small amounts of silanes, several ratios can be produced in a single batch, the deposition can be carried out within a few hours and a dry atmosphere can easily be employed, limiting self-condensation of the silanes. Characterization of the ratio of silanes actually bound to the surface can then be performed in a facile manner through contact angle measurements using the Cassie equation. The reliable estimation of the number of surface functional groups was approached with a dual-mode BODIPY-type fluorescence label, which allows quantification by fluorescence and XPS on one and the same sample. We found that fluorescence and XPS signals correlate over at least 1 order of magnitude, allowing for a direct linking of quantitative fluorescence analysis to XPS quantification. Employment of synchrotron-based methods (XPS; reference-free total reflection X-ray fluorescence, TXRF) made the traceable quantification of surface functional groups possible, providing an absolute reference for quantitative fluorescence measurements through a traceable measurement chain.

Neutralized Chimeric Avidin Binding at a Reference Biosensor Surface

We describe the development of a reference biosensor surface, based upon a binary mixture of oligo-ethylene glycol thiols, one of which has biotin at the terminus, adsorbed onto gold as self-assembled monolayers (SAMs). These surfaces were analyzed in detail by X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS) to establish the relationship between the thiol solution composition and the surface composition and structure. We report the use of argon cluster primary ions for the analysis of PEG-thiols, establishing that the different thiols are intimately mixed and that SIMS may be used to measure surface composition of thiol SAMs on gold with a detection limit better than 1% fractional coverage. The adsorption of neutralized chimeric avidin to these surfaces was measured simultaneously using ellipsometry and QCM-D. Comparison of the two measurements demonstrates the expected nonlinearity of the frequency response of the QCM but also reveals a strong variation in the dissipation signal that correlates with the surface density of biotin. These variations are most likely due to the difference in mechanical response of neutralized chimeric avidin bound by just one biotin moiety at low biotin density and two biotin moieties at high density. The transition between the two modes of binding occurs when the average spacing of biotin ligands approaches the diameter of the avidin molecule.