Biomedical subjects

A Patkowski

Publications and source records attributed to A Patkowski.

At least 19 recordsLinked to original sources

PubMed2007

Isotropic Brillouin spectra of liquids having an internal degree of freedom.

Isotropic Brillouin spectra of the two chemically similar van der Waals glass forming liquids, 1,1(')-di(4-methoxy-5-methylphenyl)cyclohexane (BMMPC) and 1,1(')-bis(p-methoxy-phenyl)cyclohexane (BMPC) and ortho-terphenyl (OTP), were studied in a broad temperature and pressure range in order to characterize the effect of internal relaxations on the damping of longitudinal phonons. Such relaxations are present in BMPC, while in BMMPC and OTP they are strongly hindered. The authors show that in BMPC (with strong internal relaxations) the damping (broadening) of longitudinal phonons (Brillouin peaks) is much stronger than in BMMPC and OTP (with weaker internal relaxations). The contributions of the internal and structural relaxations to the phonon damping can be separated using high pressure, due to their very different pressure dependences. They show that internal relaxations strongly contribute to the damping of longitudinal phonons at all temperatures and should be taken into account in theoretical models describing the Brillouin spectra of supercooled liquids.

Journal Article↗

PubMed2006

Pressure effects on the alpha and alpha' relaxations in polymethylphenylsiloxane.

In some polymers, in addition to the usual structural alpha relaxation, a slower alpha' relaxation is observed with a non-Arrhenius temperature dependence. In order to understand better the molecular origin of this alpha' relaxation in poly(methylphenylsiloxane) (PMPS) we have studied, for the first time, the pressure dependence of its relaxation time, together with the usual temperature dependence, by means of dynamic light scattering (DLS). For the same material the alpha relaxation was also studied by means of DLS and dielectric spectroscopy (DS) in broad temperature and pressure ranges. We find that the temperature dependence of both alpha and alpha' relaxation times, at all pressures studied, can be described by a double Vogel-Fulcher-Tammann (VFT) law. The pressure dependence of the characteristic temperatures Tg (glass transition temperature) and T0 (Vogel temperature) as well as the activation volumes for both alpha and alpha' processes are very similar, indicating, that both relaxation processes originate from similar local molecular dynamics. Additionally, for both alpha and alpha' relaxations the combined temperature and pressure dependences of the relaxation times can be described using a parameter Gamma=rhon/T with the same value of the exponent n.

Computer Simulation↗

PubMed2006

Diffusion of spheres in isotropic and nematic suspensions of rods.

Diffusion of a small tracer sphere (apoferritin) in isotropic and nematic networks [of fd virus] is discussed. For a tracer sphere that is smaller than the mesh size of the network, screened hydrodynamic interactions between the sphere and the network determine its diffusion coefficient. A theory is developed for such interactions as well as their relation to the long-time self-diffusion coefficient. Fluorescence correlation spectroscopy measurements on mixtures of apoferritin and fd virus are presented. The long-time self-diffusion coefficient of apoferritin is measured as a function of the fd-virus concentration, both in the isotropic and nematic state, in directions parallel and perpendicular to the nematic director. The hydrodynamic screening length of the fd-virus network as a function of fd concentration is obtained by combining these experimental data with the theory. Surprisingly, the screening length increases with increasing concentration in nematic networks. This is due to the increase in the degree of alignment, which apparently leads to a strong increase of the screening length. Hydrodynamic screening is thus strongly diminished by alignment. A self-consistent calculation of the screening length does not work at higher concentrations, probably due to the strong variation of the typical incident flow fields over the contour of a rod.

Algorithms↗

PubMed2005

Diffusion and microstructural properties of solutions of charged nanosized proteins: experiment versus theory.

We have reanalyzed our former static small-angle x-ray scattering and photon correlation spectroscopy results on dense solutions of charged spherical apoferritin proteins using theories recently developed for studies of colloids. The static structure factors S(q), and the small-wave-number collective diffusion coefficient D(c) determined from those experiments are interpreted now in terms of a theoretical scheme based on a Derjaguin-Landau-Verwey-Overbeek-type continuum model of charged colloidal spheres. This scheme accounts, in an approximate way, for many-body hydrodynamic interactions. Stokesian dynamics computer simulations of the hydrodynamic function have been performed for the first time for dense charge-stabilized dispersions to assess the accuracy of the theoretical scheme. We show that the continuum model allows for a consistent description of all experimental results, and that the effective particle charge is dependent upon the protein concentration relative to the added salt concentration. In addition, we discuss the consequences of small ions dynamics for the collective protein diffusion within the framework of the coupled-mode theory.

Journal Article↗

PubMed2005

Hidden minima of the gibbs free energy revealed in a phase separation in polymer/surfactant/water mixture.

We observed a very unusual kinetic pathway in a separating C(12)E(6)/PEG/H(2)O ternary mixture. We let the mixture separate above the spinodal temperature (cloud point temperature) for some time and next cool it into a metastable region of a phase diagram, characterized by two minima of the Gibbs potential, one corresponding to the homogeneous mixture and one to the fully separated PEG-rich and C(12)E(6)-rich phases. Despite the fact that in the metastable region the thermodynamic equilibrium corresponds to the separated phases (global minimum of the Gibbs free energy), we observe perfect mixing of the initially separated phase. The homogeneous state, obtained in this way, does not separate, if left undisturbed. However, many cooling-heating cycles or full separation with visible meniscus above the cloud point temperature induce the phase separation in the metastable region. The metastable region can exist tens of degrees below the cloud point temperature. This effect is not observed in the binary mixture of C(12)E(6)/H(2)O.

Journal Article↗

PubMed2005

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.

Journal Article↗

PubMed2005

Diffusion of spheres in crowded suspensions of rods.

Translational tracer diffusion of spherical macromolecules in crowded suspensions of rodlike colloids is investigated. Experiments are done using several kinds of spherical tracers in fd-virus suspensions. A wide range of size ratios L/2a of the length L of the rods and the diameter 2a of the tracer sphere is covered by combining several experimental methods: fluorescence correlation spectroscopy for small tracer spheres, dynamic light scattering for intermediate sized spheres, and video microscopy for large spheres. Fluorescence correlation spectroscopy is shown to measure long-time diffusion only for relatively small tracer spheres. Scaling of diffusion coefficients with a/xi, predicted for static networks, is not found for our dynamical network of rods (with xi the mesh size of the network). Self-diffusion of tracer spheres in the dynamical network of freely suspended rods is thus fundamentally different as compared to cross-linked networks. A theory is developed for the rod-concentration dependence of the translational diffusion coefficient at low rod concentrations for freely suspended rods. The proposed theory is based on a variational solution of the appropriate Smoluchowski equation without hydrodynamic interactions. The theory can, in principle, be further developed to describe diffusion through dynamical networks at higher rod concentrations with the inclusion of hydrodynamic interactions. Quantitative agreement with the experiments is found for large tracer spheres, and qualitative agreement for smaller spheres. This is probably due to the increasing importance of hydrodynamic interactions as compared to direct interactions as the size of the tracer sphere decreases.

Journal Article↗

PubMed2004

Self-diffusion in solutions of a 20 base pair oligonucleotide: effects of concentration and ionic strength.

The long-time self-diffusion coefficients of a 20 base pair duplex oligonucleotide are measured as functions of 20-mer and added NaCl salt concentrations. The self-diffusion coefficients decrease monotonically with increasing 20-mer concentrations for the high-added salt sample and display non-monotonically decreasing 20-mer concentration dependences at lower added salt concentrations. The non-monotonic behavior is attributed to the opposing effects of the tendency to increase the interactions between 20-mers as the concentration is increased and to a decrease in the extent of the Coulomb forces as counterions from the 20-mer increasingly screen them. Attempts to account for the effect of the Coulomb forces on the self-diffusion coefficients by using effective dimensions in the hard rod theory give good agreement with experiment at the highest salt concentration studied. For the lower salt concentrations there appear to be two scaling regimes--one at low polyion concentration in which the high salt scaling of the rod dimensions by adding the Debye screening to the length and diameter of the rod is appropriate and one at high polyion concentrations where the scaling of the dimensions is the addition of 1/2 the Debye screening length. Estimates of the "overlap" concentration C*=1/L(eff) indicate that the non-monotonic decrease occurs at concentrations lower than C*. Finally, the fluorescence correlation spectroscopy self-diffusion coefficients measured here are compared with the mutual diffusion coefficients measured by dynamic light scattering.

Journal Article↗

PubMed2003

Photon correlation spectroscopy with high-energy coherent x rays.

We performed x-ray photon correlation spectroscopy on a model suspension of colloidal particles using x rays of three different energies, namely, 8 keV, 13.5 keV, and 19 keV. The observed reduction in the degree of coherence with increasing x-ray energy, as measured by the contrast of the correlation functions, is consistent with theoretical estimates. We show that it is well possible and under certain circumstances even advantageous to perform experiments with coherent x rays at these higher energies. We argue that the reduced absorption may not only allow for thicker samples but also for longer acquisition times because of the reduced radiation damage, thus outweighing in many cases the effect of the reduced coherent flux. The use of higher energy x rays for photon correlation spectroscopy can therefore lead to a substantial increase in the signal-to-noise ratio and constitutes a promising option for future experiments on samples of polymeric or biological origin.

Models, Theoretical↗

PubMed2003

Effect of volume changes on segmental relaxation in siloxane polymers.

From dielectric relaxation and equation-of-state measurements on polymethylphenylsiloxane and polymethyltolylsiloxane, the relative contributions of volume and thermal energy to the temperature dependence of the segmental relaxation times are quantified. In both polymers, volume exerts a substantial effect, being almost as significant as thermal energy. A possible consequence of this prominent role of volume in governing the segmental dynamics is the finding that the relaxation times, measured for a series of temperature at various (fixed) pressures, can be expressed as a single function of the volume normalized by the volume at the glass transition temperature. A similar result is found for the (isothermal) relaxation times measured at various pressures.

Journal Article↗

PubMed2003

Temperature and pressure study of Brillouin transverse modes in the organic glass-forming liquid orthoterphenyl.

Transverse Brillouin spectra of orthoterphenyl are measured in the (250-305 K; 0.1-100 MPa) temperature-pressure range, which corresponds to the supercooled phase of this organic glass former. We show that the analysis of these spectra combined with an extrapolation of the reorientation times under pressure leads to an estimate of the static shear viscosity in a pressure range whose validity extends beyond the range of the Brillouin measurements. The relative contributions of temperature and of density to the change of this reorientation time measured along an isobar are extracted from our results in a large temperature range extending from the liquid to the low temperature supercooled state. They appear to be always of the same order of magnitude. It is also shown that in the range of the experiment, the orientational time is depending on a unique parameter built on temperature and density.

Journal Article↗

PubMed2003

Dynamics of supercooled liquids confined to the pores of sol-gel glass: a dynamic light scattering study.

Dynamics of low molecular weight and polymeric glass forming liquids in confined geometries has been studied by means of depolarized dynamic light scattering: photon correlation spectroscopy and Fabry-Perot interferometry. The pore size of the glassy matrix amounted to 2.5, 5.0, and 7.5 nm. The glass transition temperature T(g) of these liquids in confined geometries has been measured using differential scanning calorimetry. A systematic decrease of T(g) (up to 25 K) with decreasing pore size has been observed. The relaxation times of the alpha process at constant temperature were decreasing with decreasing pore size (up to 6 orders of magnitude at T(g)), while the width of their distribution was increasing. The change of the relaxation times can be assigned to the change of T(g) in confined geometries. After correcting the activation plots for the shift of T(g) a master curve was obtained for all pore sizes and the bulk material. The effect of chemical modification of the surface of the porous matrix on the dynamics of ortho-terphenyl has also been studied. These dramatic changes of the T(g) and the relaxation time of confined liquids can be explained by simple thermodynamic arguments. There is no indication that they are related to the change of the correlation length of cooperative dynamics.

Journal Article↗

PubMed2001

Apparent nonergodic behavior of supercooled liquids above the glass transition temperature.

A speckle pattern can be observed in the polarized component of light scattered from glass forming liquids far above their glass transition temperature. This speckle pattern fluctuates with characteristic time that corresponds to the relaxation time of the additional ultraslow component in the correlation function and is about seven orders of magnitude longer than the relaxation time of the alpha-process. This slow process is out of the experimental time window when the alpha-process is measured by means of the photon correlation spectroscopy and results in an apparent nonergodicity which can be seen as a baseline offset in the ensemble-averaged correlation function. In contrast, the time-averaged field correlation functions which have been measured in practically all light scattering studies always decay to zero. The slow process contributes a q-dependent excess intensity to the polarized component of scattered light. The values of the nonergodicity parameters obtained from the static and dynamic light scattering experiments are equal. Both the slow component and the excess intensity result from denser regions of fractal character which develop in glass-forming liquids on approaching the glass transition.

Journal Article↗

PubMed2001

Unusual features of long-range density fluctuations in glass-forming organic liquids: a Rayleigh and Rayleigh-Brillouin light scattering study.

A new feature of glass-forming liquids, i.e., long-range density fluctuations of the order of 100 nm, has been extensively characterized by means of static light scattering, photon correlation spectroscopy and Rayleigh-Brillouin spectroscopy in orthoterphenyl (OTP) and 1,1-di(4(')-methoxy-5(')methyl-phenyl)-cyclohexane (BMMPC). These long-range density fluctuations result in the following unusual features observed in a light scattering experiment, which are not described by the existing theories: (i) strong q-dependent isotropic excess Rayleigh intensity, (ii) additional slow component in the polarized photon correlation function, and (iii) high Landau-Placzek ratio. These unusual features are equilibrium properties of the glass-forming liquids and depend only on temperature, provided that the sample has been equilibrated long enough. The temperature-dependent equilibration times were measured for BMMPC and are about 11 orders of magnitude longer than the alpha process. It was found that the glass-forming liquid OTP may occur in two states: with and without long-range density fluctuations ("clusters"). We have characterized the two states by static and dynamic light scattering in the temperature range from T(g) to T(g)+200 K. The relaxation times of the alpha process as well as the parameters of the Brillouin line are identical in both OTP with and without clusters. The alpha process (density fluctuations) in OTP was characterized by measuring either the polarized (VV) or depolarized (VH) correlation function, which are practically identical and q-independent. This feature, which is commonly observed in glass-forming liquids, is not fully explained by the existing theories.

Journal Article↗

PubMed2000

Temperature and pressure scaling of the alpha relaxation process in fragile glass formers: A dynamic light scattering study

The dynamics of two fragile glass forming liquids was studied as a function of temperature and pressure using dynamic light scattering. On the basis of measured data we evaluated the pressure and temperature scaling of the alpha relaxation. All the isotherms can be superimposed and form a master curve when the reduced relaxation times are plotted versus reduced pressure. The Kohlrausch-Williams-Watts stretching parameter beta(KWW) is increasing with increasing temperature and decreasing pressure and plotted versus log follows a master curve at all temperatures and pressures studied.

Journal Article↗

PubMed2000

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 acid's 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.

DNA↗

PubMed2000

Long-range density fluctuations in orthoterphenyl as studied by means of ultrasmall-angle x-ray scattering.

The structure factor of a fragile glass-forming liquid orthoterphenyl was measured in the previously inaccessible intermediate q range between the conventional light scattering (LS) and small-angle x-ray scattering (SAXS) q ranges using the low-angle scattering beam line at the European Synchrotron Radiation Facility. At low q the structure factor exhibits an excess scattering and matches well the LS data. This excess scattering is due to long-range density fluctuations also observed in the isotropic component of scattered light. At high q the structure factor decays to a plateau corresponding to the isothermal compressibility in agreement with the conventional SAXS data. In the intermediate q range, the structure factor exhibits a power law q dependence which indicates that the excess scattering is due to fractal aggregates of denser domains.

Journal Article↗

PubMed1999

Light-scattering study of a supercooled epoxy resin.

The dynamics of the fragile glass-forming liquid diglycidyl ether of bisphenol-A was studied by depolarized Rayleigh-Brillouin light-scattering and photon correlation spectroscopy above the glass transition, in the temperature range from 261 to 473 K and in the frequency range from 1 Hz to 300 GHz. The structural (alpha-) relaxation process was revealed and no signature of the secondary relaxation previously evidenced by dielectric spectroscopy at about 0.1 GHz was observed. The characteristic time of the alpha process differs from that determined by dielectric spectroscopy of an amount, which increases with increasing temperature. The relaxation times were compared with viscosity data to test the predictions of the classic Stokes-Einstein-Debye model. The tau proportional, variant eta behavior was verified for dielectric data, while a fractional power law of viscosity tau proportional, variant eta(0.89) was obtained for light-scattering relaxation times, extending over more than seven decades in viscosity and time. This deviation of light scattering from viscosity data could be interpreted in terms of cooperative motion in the supercooled liquid with a characteristic length xi(a) proportional, variant(T-T0)(-v) where T(0)=229 K is the Vogel temperature and v is close to 2 / 3 which is consistent with the prediction of the fluctuation theory of glass transition.

Journal Article↗