Anomalous Diffusion and Transport of Self Interacting Poly(Isopropylacrylamide) Setup

In this Ph.D. thesis I present three anomalous behaviors of systems that are based on polyisopropylacrylamide (pNIPAM). In all cases, the anomaly is related to a special character of pNIPAM - its willingness to form hydrogen bonds. Each of the thesis' experimental sections deals with a specific phenomenon that is related to either the law: < x2 > ∝ Dt, where < x2 > is the mean square displacement, D the diffusion constant and t the time, or the Einstein relation D ∝ r1, where r is the particle's radius. Taken as a whole, these results present a unique point of view on the relations between hydrogen binding and apparent measured diffusion.;The first experimental work deals with the influence of fluorescent quenching by pNIPAM on the measured diffusion constant in fluorescence correlation spectroscopy (FCS). It is traditionally accepted that in systems that exhibit diffusion and reaction, it is possible to extract the characteristic time scales of both processes using FCS. Here, I present FCS measurements of large polymers that appear as free dyes as a result of a quenching reaction. Changes in experimental conditions reveal the previously hidden fluctuations on the center of mass diffusion time scale of the autocorrelation function. The existence of the quenching reaction is established using other spectroscopic methods, including lifetime and quantum yield measurements. Substantial support is given to the identification of the quenching as an excited state hydrogen bonding. A specific atomic position on the dye is suggested as the location of the hydrogen bonding interaction. These measurements necessitate a revision in the theoretical framework of FCS and can influence the understanding of FCS measurements of non-conventional setups.;The second experimental work deals with diffusion of pNIPAM inside channels that are smaller than its radius of gyration, but interact with it attractively. Polymers can overcome an entropy barrier and enter attractive interacting pores. Using an adsorption assay, such conditions were identified for the interaction between pNIPAM and nanopores in polycarbonate membranes. Under these conditions the polymer translocates through the pores at a rate comparable to a test case solute that is ∼ 40 times smaller. However, its accumulation on the trans side follows a stretched exponential law rather than an exponential one as expected for ordinary diffusion inside the pores. Furthermore, pores coated with pNIPAM with a narrower cross section have hindered the diffusion of the test case solute, but had hardly any effect on pNIPAM translocation rate. It is suggested that stick-diffusion mechanism, due to transient hydrogen bonding, is responsible for the anomalous translocation behavior. Such a mechanism can be analyzed using the framework of fractional diffusion that predicts a trans side Mittag-Leffler accumulation behavior (a generalization of the exponential function behavior). The values of the anomalous diffusion exponent, as well as the diffusion coefficient, were extracted from a fit to the fractional diffusion model.;The third experimental work deals with facilitated diffusion of solutes inside a nanometer channel that interacts with the carrier molecule attractively. The anomalous behavior in this case is related to deviation from the Stokes-Einstein relation. The diffusion rate inside the channel is increased if a carrier particle binds a cargo-solute and expands its dimension. Theoretical considerations predict discrimination in translocation rates, if attractive interactions exist between the solutes and the channel walls. As a working hypothesis, it has been speculated that this effect can be large enough to compensate for the expanded dimensions. The validity of the working assumption was demonstrated by measuring the translocation rate of a test case solute - fluorescent tagged ssDNA - in polyisopropylacrylamide coated channels, using free pNIPAM as the carrier molecule. pNIPAM interactions via transient hydrogen bonds with the coated walls have resulted in an elevated translocation rate of the carrier-cargo complex over the bare cargo case. However, the translocation rate of the carrier-cargo complex was still smaller than that of ssDNA alone in uncoated channels. These results are related to some lately proposed models for the Nuclear Pore Complex in biological cells.