Allan Variance Analysis as Useful Tool to Determine Noise in Various Single-Molecule Setups

One limitation on the performance of optical traps is the noise inherently present in every setup. Therefore, it is the desire of most experimentalists to minimize and possibly eliminate noise from their optical trapping experiments. A step in this direction is to quantify the actual noise in the system and to evaluate how much each particular component contributes to the overall noise. For this purpose we present Allan variance analysis as a straightforward method. In particular, it allows for judging the impact of drift which gives rise to low-frequency noise, which is extremely difficult to pinpoint by other methods. We show how to determine the optimal sampling time for calibration, the optimal number of data points for a desired experiment, and we provide measurements of how much accuracy is gained by acquiring additional data points. Allan variances of both micrometer-sized spheres and asymmetric nanometer-sized rods are considered.Comment: 14 pages, 6 figures, presented at SPIE Optics+Photonics 2009 in San Diego, CA, US

A Minimalistic, Synthetic Cell‐Inspired Metamaterial for Enabling Reversible Strain‐Stiffening

Strain-stiffening, i.e. the nonlinear stiffening of a material in response to a strain, is an intrinsic feature of many biological systems, including skin, blood vessels, and single cells. To avoid a mismatch in mechanical properties, synthetic materials in contact with such biological systems should also be strain-stiffening. Conventional strain-stiffening materials are either highly dependent on the applied strain-rate, or only available for a limited stiffness regime. Both aspects limit the applicability of these materials. In contrast, living cells employ a dynamic strain-stiffening mechanism that is based on the cross-linking of cytoskeletal fibers in response to external stress. This strain-stiffening of the cytoskeleton is mimicked in a mechanical metamaterial by a minimalistic structure consisting of parallel slats connected to backbones. Herein, it is demonstrated experimentally that the structures can be adapted such that the strain required for stiffening, the final stiffness, as well as the degree of stiffening can be tuned, particularly by combining several strain-stiffening elements. These properties make the structure promising for the development of devices that should resemble the mechanical properties of human soft tissues, e.g., skin-integrated flexible electronics and blood vessel grafts

Controlled Self-Assembly of Hexagonal Nanoparticle Patterns on Nanotopographies

Diblock copolymer micelle nanolithography (BCML) is a versatile and efficient method to cover large surface areas with hexagonally ordered arrays of metal nanoparticles, in which the nanoparticles are equally spaced. However, this method falls short of providing a controlled allocation of such regular nanoparticle arrays with specific spacing into micropatterns. We present here a quick and high-throughput method to generate quasi-hexagonal nanoparticle structures with well-defined interparticle spacing on segments of nanotopographic Si substrates. The topographic height of these segments plays a dominant role in dictating the spacing between the gold nanoparticles, as the nanoparticle arrangement is controlled by immersion forces and by their self-assembly within the segments. Our novel strategy of employing a single-step BCML routine is a highly promising method for the fabrication of regular gold nanopatterns in micropatterns for a wide range of applications

Adhesion forces and mechanics in mannose-mediated acanthamoeba interactions

The human pathogenic amoeba Acanthamoeba castellanii (A. castellanii) causes severe diseases, including acanthamoeba keratitis and encephalitis. Pathogenicity arises from the killing of target-cells by an extracellular killing mechanism, where the crucial first step is the formation of a close contact between A. castellanii and the target-cell. This process is medi- ated by the glycocalix of the target-cell and mannose has been identified as key mediator. The aim of the present study was to carry out a detailed biophysical investigation of man- nose-mediated adhesion of A. castellanii using force spectroscopy on single trophozoites. In detail, we studied the interaction of a mannose-coated cantilever with an A. castellanii tro- phozoite, as mannose is the decisive part of the cellular glycocalix in mediating pathogenic- ity. We observed a clear increase of the force to initiate cantilever detachment from the trophozoite with increasing contact time. This increase is also associated with an increase in the work of detachment. Furthermore, we also analyzed single rupture events during the detachment process and found that single rupture processes are associated with mem- brane tether formation, suggesting that the cytoskeleton is not involved in mannose binding events during the first few seconds of contact. Our study provides an experimental and conceptual basis for measuring interactions between pathogens and target-cells at different levels of complexity and as a function of interaction time, thus leading to new insights into the biophysical mechanisms of parasite pathogenicity

Cardiomyocyte behavior on biodegradable polyurethane/gold nanocomposite scaffolds under electrical stimulation

Following a myocardial infarction (MI), cardiomyocytes are replaced by scar tissue, which decreases ventricular contractile function. Tissue engineering is a promising approach to regenerate such damaged cardiomyocyte tissue. Engineered cardiac patches can be fabricated by seeding a high density of cardiac cells onto a synthetic or natural porous polymer. In this study, nanocomposite scaffolds made of gold nanotubes/nanowires incorporat- ed into biodegradable castor oil-based polyurethane were employed to make micro-porous scaffolds. H9C2 cardiomyocyte cells were cultured on the scaffolds for one day, and electrical stimulation was applied to improve cell communication and interaction in neighboring pores. Cells on scaffolds were examined by fluorescence microscopy and scanning electron microscopy, revealing that the combination of scaffold design and electrical stimulation significantly increased cell confluency of H9C2 cells on the scaffolds. Furthermore, we showed that the gene expression levels of Nkx2.5, atrial natriuretic peptide (ANF) and natriuretic peptide precursor B (NPPB), which are functional genes of the myocardium, were up-regulated by the incorporation of gold nanotubes/nanowires into the polyurethane scaffolds, in particular after electrical stimulation

In vivo anomalous diffusion and weak ergodicity breaking of lipid granules

Combining extensive single particle tracking microscopy data of endogenous lipid granules in living fission yeast cells with analytical results we show evidence for anomalous diffusion and weak ergodicity breaking. Namely we demonstrate that at short times the granules perform subdiffusion according to the laws of continuous time random walk theory. The associated violation of ergodicity leads to a characteristic turnover between two scaling regimes of the time averaged mean squared displacement. At longer times the granule motion is consistent with fractional Brownian motion.Comment: 4 pages, 4 figures, REVTeX. Supplementary Material. Physical Review Letters, at pres

Quantitative analysis of single particle trajectories: mean maximal excursion method

An increasing number of experimental studies employ single particle tracking to probe the physical environment in complex systems. We here propose and discuss new methods to analyze the time series of the particle traces, in particular, for subdiffusion phenomena. We discuss the statistical properties of mean maximal excursions, i.e., the maximal distance covered by a test particle up to time t. Compared to traditional methods focusing on the mean squared displacement we show that the mean maximal excursion analysis performs better in the determination of the anomalous diffusion exponent. We also demonstrate that combination of regular moments with moments of the mean maximal excursion method provides additional criteria to determine the exact physical nature of the underlying stochastic subdiffusion processes. We put the methods to test using experimental data as well as simulated time series from different models for normal and anomalous dynamics, such as diffusion on fractals, continuous time random walks, and fractional Brownian motion.Comment: 10 pages, 7 figures, 2 tables. NB: Supplementary material may be found in the downloadable source file