Adam Patkowski

Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale.

We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length ξ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than ξ experienced matrix viscosity: η(matrix) ≈ 2.0 mPa·s for HeLa and 0.88 mPa·s for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, η(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Pa·s for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.

A high pressure photon correlation study of bulk poly(methylacrylate). Comparison with relaxation processes in poly(ethylacrylate) and related polymethacrylates

We report results of the photon correlation polarized light scattering study on the dynamics of bulk polymethylacrylate (PMA) in the temperature range of 7–76u2009°C and in the pressure range 1–2100 bar. A single relaxation process with a distribution of relaxation times represents the experimental photon correlation functions. The temperature and pressure dependence of the mean relaxation time are analyzed in terms of the VFT and WLF equations. The parameters obtained are discussed in terms of the rotational isomerization model and the free volume model. The results obtained in light scattering agree well with dielectric and mechanical relaxation data. In the case of polyethylmethacrylate (PEMA) and polybutylmethacrylate (PBMA), two overlapping relaxation modes are found. The values of the activation parameters and the relaxation time at the glass transition temperature (Tg) thus obtained characterizing the dynamics of a polymer melt above Tg are compared for PMA, PEA, PEMA, and PBMA.

Size and shape of micelles studied by means of SANS, PCS, and FCS.

The hexaethylene glycol monododecyl ether (C(12)E(6)) micelles at concentrations up to 10% have been studied in their isotropic phase (10-48 degrees C) by means of small angle neutron scattering (SANS) and photon correlation spectroscopy (PCS). The SANS data obtained at low temperatures could be unequivocally interpreted as a result of scattering from a suspension of compact globular micelles with the shape of a triaxial ellipsoid or a short end-capped elliptical rod. Different models have been applied to analyze the SANS data obtained at higher temperatures: (i) elongated rod-like micelles with purely sterical interactions, (ii) compact globular micelles with a weak attractive potential, and (iii) globular micelles influenced by the critical phenomena in the whole temperature range studied. The good quality of the experimental data indicated model (i) as the best fit for our data. The diffusion coefficients obtained from the PCS measurements have been compared to the diffusion coefficients calculated for the rod-like micelles--results of the SANS data analysis. A good agreement was achieved using the solvent viscosity, in agreement with the theoretical predictions for sterically interacting globular colloidal particles. Finally, the SANS results obtained at 24 degrees C were compared to the micelle self-diffusion coefficients previously measured by means of fluorescence correlation spectroscopy (FCS) at this temperature. The good agreement obtained after scaling the data with solution viscosity supports the validity of the generalized Stokes-Einstein relation in sterically interacting systems: the product of the colloidal particle self-diffusion coefficient and the macroscopic viscosity remains constant in a broad range of concentrations. It has been concluded that the FCS technique in combination with simple viscosity measurements might serve as a tool for estimating the micellar size and shape.

Solution Structure of Biopolymers: A New Method of Constructing a Bead Model

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma = 5.0 A was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (tau(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and tau(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger sigma = 5.7 A. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acids size. Experimental data of D(T) of small proteins were used to establish the optimum value of sigma = 4.5 A for amino acids. The lack of experimental data on tau(R) for proteins restricted the tests to the translational diffusion properties.

A comparison of relaxation processes in structurally related van der Waals glass formers: The role of internal degrees of freedom

Depolarized dynamic light scattering (DLS), dielectric relaxation (DS), and deuterium NMR studies of fragile van der Waals glass forming liquids phenylphthalein-dimethylether (PDE) and cresolphthalein-dimethylether (KDE) are presented. In PDE a new dielectric loss process was found, which can be attributed to the 180 degrees flip of the phenyl rings. The previous finding that the distribution of the structural relaxation times measured for PDE and KDE by DS is substantially narrower than that measured by DLS is explained by partial decoupling of the dynamics of the dipole moment from the structural relaxation of the sample. The dynamics of PDE and KDE is compared with the previous studies of two other structurally similar liquids: 1,1-di(4-methoxy-5-methylphenyl)cyclohexane (BMMPC) and 1,1-bis(p-methoxyphenyl)cyclohexane (BMPC) in order to relate dynamical features with the chemical structure of the material. The evidence for the intramolecular character of the secondary relaxations observed in BMPC and PDE is presented.

Effect of pressure and temperature on the dynamics of bulk polyethylacrylate and polyethylmethacrylate polymers studied by photon correlation spectroscopy

Photon correlation spectroscopy has been used to study relaxation processes in bulk polymers: PEA and PEMA, above the glass transition temperature under high pressure. In the case of PEA one relaxation process was observed over the whole pressure range of 1–2000 bar. This process is assigned to the localized backbone motion of the polymer chain. In PEMA two overlaping relaxation modes have been found. Quantitative characterization of these two modes was possible after their separation in the time domain, which was achieved by applying high pressure to the sample. It was found that an additionalα-methyl group in PEMA (in comparison with PEA) causes an appearance of an additional relaxation mode which can be assigned to the side group motion. Moreover, the localized backbone motion in PEMA is more cooperative because of a hindrance effect due to the presence of the additionalα-methyl side group. The obtained results are in a good agreement with the previous dielectric relaxations studies.

Successful FCS experiment in nonstandard conditions.

Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13-0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS.

Freezing lines of colloidal Yukawa spheres. I. A Rogers-Young integral equation study

Using the Rogers-Young (RY) integral equation scheme for the static structure factor combined with the one-phase Hansen-Verlet (HV) freezing rule, we study the equilibrium structure and two-parameter freezing lines of colloidal particles with Yukawa-type pair interactions representing charge-stabilized silica spheres suspended in dimethylformamide (DMF). Results are presented for a vast range of concentrations, salinities and effective charges covering particles with masked excluded-volume interactions. The freezing lines were obtained for the low-charge and high-charge solutions of the static structure factor, for various two-parameter sets of experimentally accessible system parameters. All RY-HV based freezing lines can be mapped on a universal fluid-solid coexistence line in good agreement with computer simulation predictions. The RY-HV calculations extend the freezing lines obtained in earlier simulations to a broader parameter range. The experimentally observed fluid-bcc-fluid reentrant transition of charged silica spheres in DMF can be explained using the freezing lines obtained in this work.

Size of Submicrometer Particles Measured by FCS: Correction of the Confocal Volume

When fluorescence correlation spectroscopy (FCS) in combination with a confocal microscope is used to determine the hydrodynamic radius a of particles comparable to or larger than the linear size σ of the confocal volume of the microscope, a correction must be used that depends on the a(2)/σ(2) ratio and the distribution of the dye within the particle. Here we present the experimental validation of the theoretically predicted approximate correction necessary for appropriate measurements of the size of uniformly fluorescently labeled spheres of radius comparable to the size of the confocal volume. We also test the approximate correction formula for different ranges of the a/σ ratio and propose a simple procedure to obtain the correct nanoparticle size from such a measurement.

Freezing lines of colloidal Yukawa spheres. II. Local structure and characteristic lengths.

Using the Rogers-Young (RY) integral equation scheme for the static pair correlation functions combined with the liquid-phase Hansen-Verlet freezing rule, we study the generic behavior of the radial distribution function and static structure factor of monodisperse charge-stabilized suspensions with Yukawa-type repulsive particle interactions at freezing. In a related article, labeled Paper I [J. Gapinski, G. Nägele, and A. Patkowski, J. Chem. Phys. 136, 024507 (2012)], this hybrid method was used to determine two-parameter freezing lines for experimentally controllable parameters, characteristic of suspensions of charged silica spheres in dimethylformamide. A universal scaling of the RY radial distribution function maximum is shown to apply to the liquid-bcc and liquid-fcc segments of the universal freezing line. A thorough analysis is made of the behavior of characteristic distances and wavenumbers, next-neighbor particle coordination numbers, osmotic compressibility factor, and the Ravaché-Mountain-Streett minimum-maximum radial distribution function ratio.