Agnieszka M. Słowicka

Fibrinogen conformations and charge in electrolyte solutions derived from DLS and dynamic viscosity measurements

Hydrodynamic properties of fibrinogen molecules were theoretically calculated. Their shape was approximated by the bead model, considering the presence of flexible side chains of various length and orientation relative to the main body of the molecule. Using the bead model, and the precise many-multipole method of solving the Stokes equations, the mobility coefficients for the fibrinogen molecule were calculated for arbitrary orientations of the arms whose length was varied between 12 and 18 nm. Orientation averaged hydrodynamic radii and intrinsic viscosities were also calculated by considering interactions between the side arms and the core of the fibrinogen molecule. Whereas the hydrodynamic radii changed little with the interaction magnitude, the intrinsic viscosity exhibited considerable variation from 30 to 60 for attractive and repulsive interactions, respectively. These theoretical results were used for the interpretation of experimental data derived from sedimentation and diffusion coefficient measurements as well as dynamic viscosity measurements. Optimum dimensions of the fibrinogen molecule derived in this way were the following: the contour length 84.7 nm, the side arm length 18 nm, and the total volume 470 nm(3), which gives 16% hydration (by volume). Our calculations enabled one to distinguish various conformational states of the fibrinogen molecule, especially the expanded conformation, prevailing for pH<4 and lower ionic strength, characterized by high intrinsic viscosity of 50 and the hydrodynamic radius of 10.6 nm. On the other hand, for the physiological condition, that is, pH=7.4 and the ionic strength of 0.15M NaCl, the semi-collapsed conformation dominates. It is characterized by the average angle equal to =55°, intrinsic viscosity of 35, and the hydrodynamic radius of 10nm. Additionally, the interaction energy between the arms and the body of the molecule was predicted to be -4 kT units, confirming that they are oppositely charged than the central nodule. Results obtained in our work confirm an essential role of the side chains responsible for a highly anisotropic charge distribution in the fibrinogen molecule. These finding can be exploited to explain anomalous adsorption of fibrinogen on various surfaces.

Dynamics of fibers in a wide microchannel

Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the HYDROMULTIPOLE numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. Fibers, which are closer to a wall, more flexible (less stiff) or longer, deform more significantly and, for a wide range of the system parameters, they faster migrate towards the middle plane of the channel. For the considered systems, fiber velocity along the flow is only slightly smaller than (and can be well approximated by) the Poseuille flow velocity at the same position. In this way, the history of a fiber migration across the channel is sufficient to determine with a high accuracy its displacement along the flow.

Lateral migration of flexible fibers in Poiseuille flow between two parallel planar solid walls.

Dynamics of non-Brownian flexible fibers in Poiseuille flow between two parallel planar solid walls is evaluated from the Stokes equations which are solved numerically by the multipole method. Fibers migrate towards a critical distance from the wall zc, which depends significantly on the fiber length N and bending stiffness A. This effect can be used to sort fibers. Three types of accumulation are found, depending on a shear-to-bending parameter Γ. In the first type, stiff fibers deform only a little and accumulate close to the wall, where their tendency to drift away from the channel is balanced by the repulsive hydrodynamic interaction with the wall. In the second type, flexible fibers deform significantly and accumulate far from the wall. In both types, the fiber shapes at the accumulation positions are repeatable, while in the third type, they are very compact and non-repeatable. The difference between the second and third accumulation types is a special case of the difference between the regular and irregular modes for the dynamics of migrating fibers. At the regular mode, far from walls, the fiber tumbling frequency satisfies Jeffery’s expression, with the local shear rate and the aspect ratio close to N.Graphical abstract

Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte

Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water. These effects deviate significantly from simple proportionality of peptide tumbling time to solvent viscosity, leading to the investigation of microscopic preferential interaction behavior through molecular dynamics simulations. Examination of the interactions of denaturants and osmolyte with the peptide backbone uncovers the presence of strongest interaction with urea, intermediate with proline, and weakest with GdmCl. In contrast, the strongest preferential solvation of the peptide side chain is by the nonpolar part of the proline zwitterion, followed by urea, and GdmCl. Interestingly, the local density of urea around the side chain is higher, but the GdmCl distribution is more organized. Thus, the computed preferential solvation of the side chain by the denaturants and osmolyte can account for the trend in reorientation rates. Analysis of water structure and its dynamics uncovered underlying differences between urea, GdmCl, and proline. Urea exerted the smallest perturbation of water behavior. GdmCl had a larger effect on water, slowing kinetics and stabilizing interactions. Proline had the largest overall interactions, exhibiting a strong stabilizing effect on both water-water and water-peptide hydrogen bonds. The results for this elementary peptide system demonstrate significant differences in microscopic behavior of the examined solvent environments. For the commonly used denaturants, urea tends to form disorganized local aggregates around the peptide groups and has little influence on water, while GdmCl only forms specific interactions with the side chain and tends to destabilize water structure. The protective osmolyte proline has the strongest and most specific interactions with the tryptophan side chain, and also stabilizes both water-water and water-peptide hydrogen bonds. Our results strongly suggest protein or peptide denaturation triggered by urea occurs by direct interaction, whereas GdmCl interacts favorably with side chains and destabilizes peptide-water hydrogen bonds. The stabilization of biopolymers by an osmolyte such as proline is governed by favorable preferential interaction with the side chains and stabilization of water.

Structure of Shock Waves in Dense Media

The behaviour of shock waves propagating in a gas has been studied for more than a century, experimentally, theoretically and numerically. It was established, in particular, that the thickness of a shock wave (the layer, in which parameters of the medium vary rapidly in space) is of the order of several mean free paths of the gas molecules, provided that the shock is of moderate intensity. Distributions of the parameters of the medium inside the shock resemble the hyperbolic tangent function. The necessary condition for the above to be fulfilled is that the gas is dilute, which means that its molecules interact (collide) with only one neighbour at a time, and between collisions they move with constant speed along straight lines (concept of a mean free path – the average distance travelled this way). Duration of a single collision is negligibly short as compared to the time of free flight (mean free time). In dilute gas the mean free path of the molecules is much larger than the diameter of the molecule and larger than their average separation distance (Figure 1 – left).

Structure of the Plume Emitted during Laser Ablation of Materials

Laser ablation is a frequently used method of removing material from a solid surface by irradiating it with a powerful laser beam. It may be applied to machining materials, cleaning contaminated surfaces, deposition of thin coatings on surfaces etc. High energy, short duration laser pulse, focused on a small area of the target surface heats and evaporates it, forming eventually a plume which moves outwards from the target with high speed. The behaviour of the plume may influence the quality of the deposited layer, which is important if deposition is the goal of the process. This is particularly the case if the deposited material consists of disparate mass components. The light components move faster than the heavy ones and tend to spread on larger area of the substrate. In consequence the stoichiometry of the deposited material is not preserved. To improve the situation, the deposition process may be performed in the atmosphere of an ambient gas, which decelerates both the motion of the plume as a whole and its expansion. Deceleration is stronger for light components of the plume, which makes the expanding plume more uniform.

Structure and Expansion of a Plume Emitted During Laser Ablation of Multicomponent Materials

Pulsed laser deposition (PLD) is a technique frequently used for creating thin films of various materials on solid substrates. High-energy laser pulse causes evaporation of the target material, forming a plume which subsequently expands and moves with high speed from the target. Thin film of the evaporated material is deposited on the substrate placed at some distance in front of the target.

Similarity Parameters for Shock Waves in Dense Fluids

As it is well known, the shock wave is a layer in which parameters of the medium vary rapidly in space. The thickness of this layer is of the order of several mean free paths of the molecular motion (in a dilute gas) or several distances between the molecules (in a dense medium). The structure of the shock wave should therefore be properly described in terms of the molecular quantities.

Extinguishing Detonation in Pipelines—Optimization of the Process

The necessity of extinguishing detonation, which may occur in pipelines transporting gaseous fuels, creates nowadays a very important technological problem. The standard devices used for this purpose consist of matrices of very narrow channels. Cooling the gas by cold walls of such channels may extinguish the flame and stop detonation.

Structure of Shock Waves in Complex Molecular Liquids

The present paper is a continuation of our earlier work on the structure of shock waves in dense media. Simple, monoatomic gas, argon, was considered first [1]