Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation

In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics during the motion through channels with unprecedented spatial and temporal resolution. These striking experimental studies have stimulated many theoretical developments. In this short theory-experiment review, we discuss recent progress in this field with a strong focus on non-equilibrium aspects of polymer dynamics during the translocation process.Comment: 29 pages, 6 figures, 3 tables, to appear in J. Phys.: Condens. Matter as a Topical Revie

Modeling Primary Hemostasis

The physical properties of blood cells and blood flow are important for various biological functions of blood and for biomedical issues, ranging from blood diseases such as malaria to blood-related applications such as drug delivery. The main objective of this thesis is to study the very early stages of hemostasis, the process which stops bleeding after injury. The plasma protein von Willebrand factor (VWF) is a necessary component in primary hemostasis, especially at high shear rates, when platelets are not able to firmly adhere to an injured vessel wall on their own. A realistic model for this process is developed, in order to better understand how hemostasis occurs in the microvasculature. An important role in primary hemostasis is played by VWF concatemers with lengths of a few to tens of microns. Such large lengths make their size comparable to blood cells, i.e. they interact with blood cells as mesoscale objects in a different manner than the simple plasma. The dynamics of VWFs is studied here by mesoscale hydrodynamic simulations in simple shear and capillary flows, with and without blood cells. VWFs remain collapsed at low shear rates, due to intra-molecular attractions, while they stretch at shear rates beyond a critical value. The shielding of adhesive ligands of VWFs in the collapsed state makes these proteins shear-sensitive, so that VWFs adhere to vessel walls or platelets only when they are stretched. Thus, at high enough shear rates, VWFs and platelets form aggregates triggered by the shear sensitivity of VWFs for adhesion. Such aggregates are reversible and disappear at low shear rates. In blood flow, VWFs migrate toward the vessel walls through a process called margination. VWF margination is mediated by red blood cells since they migrate toward the center of the vessels and push VWFs to the walls. The presence of platelets and stretched VWFs near the vessel walls leads to their spontaneous aggregation. These aggregates are highly porous and deformable and eventually migrate to the center of a blood vessel due to a strong hydrodynamic lift force. Low shear rates at the center of a vessel lead to aggregate dissociation. This is a completely mechanical process which regulates the aggregation and restricts the formation of free-flowing large thrombi. In addition to the mechanical regulation of undesired aggregates, the concentration of large VWFs is controlled by the protease enzyme, ADAMTS13, which cleaves stretched VWFs. Modeling of this process shows that VWF polymers get cleaved gradually from their extruded ends, providing enough time for the hemostatic activity. The size distribution of VWFs obeys a power law according to the model predictions. The new model presented here for VWF and its aggregation with platelets captures detailed realistic behavior of VWFs and aggregates in flow. It allows the simulation of blood flow and coagulation on the cellular level for the first time, in order to interpret the causes of several VWF-related diseases, and find the possible treatment strategies. Also, the proposed models can be employed in more complex cases, like the blood vessel bifurcations, and blood discharge from the capillaries

Magnetic Hybrid-Materials

Externally tunable properties allow for new applications of suspensions of micro- and nanoparticles in sensors and actuators in technical and medical applications. By means of easy to generate and control magnetic fields, fluids inside of matrices are studied. This monnograph delivers the latest insigths into multi-scale modelling, manufacturing and application of those magnetic hybrid materials

Magnetic Hybrid-Materials

Externally tunable properties allow for new applications of suspensions of micro- and nanoparticles in sensors and actuators in technical and medical applications. By means of easy to generate and control magnetic fields, fluids inside of matrices are studied. This monnograph delivers the latest insigths into multi-scale modelling, manufacturing and application of those magnetic hybrid materials

Nonamphiphilic Assembly of Metal Carbonyl Complexes: Chemical Structure, Kinetics, and Hydrophobic Effect

Self-assembly is an effective approach for the synthesis of various nanostructures. Assembly of amphiphilic molecules has been well developed, which are mostly thermodynamic controlled. Although the importance of kinetics and hydrophobic effect in self-assembly of biological molecules, such as proteins, has been well recognized, it remains to be challenging to understand these factors at molecular level. We have investigated the assembling behaviour of a few hydrophobic metal carbonyl polymers P(FpP) (FpP: CpFe(CO)2(CH2)mPPh2, m = 3 or 6) and small molecules FpC6X (Fp head = (PPh3)(Cp)Fe(CO)(CO-); C6X = hydrocarbon tail) in water. As a result, we were able to kinetically control the assemblies resulting in stable colloids in water with narrow size distribution and also gained fundamental knowledge on the hydrophobic effect at molecular level. The background of self-assembly is introduced in Chapter 1. It concludes that the assembly of non-amphiphilic molecules is less studied, but crucial for the understanding of biological supramolecular systems. Chapter 2 discusses the kinetic behaviour of hydrophobic homopolymer P(FpP) in poor solvents. We find that the kinetic pathways for the precipitation of P(FpP) is altered depending on the solution conditions. Kinetically trapped nanospheres and nanowarms with narrow PDI were produced. In Chapter 3, the assembly of P(FpP) in water is discussed. It is found that the rigidity of the backbone is a parameter determining the assembling morphology. With increasing the flexibility, the macromolecules assemble into lamellae, vesicles and irregular aggregates. As discussed in chapter 4, the vesicles formed in water do not have traditional bilayer membrane structure, which can swell upon the addition of THF. The swollen vesicles are colloidal stable and their PDI remains narrow. In addition to P(FpP), Fp acyl derivatives with pyrene or azobenzene (FpC6Azobenzene and FpC6Pyrene) were synthesis for aqueous assembly. The assembly behaviour of FpC6Azobenzene, as influenced by the balance of aromatic interaction and hydrophobic effect of pyrene, is discussed in chapter 5. In DMSO/water or methanol/water systems, aromatic interactions are predominant and drive the assemble into lamellae, while in a THF/water system. hydrophobic effect drives the assembly into vesicles. The role of hydrophobic effect in solution behaviour of the assembled vesicles is discussed in Chapter 6. we find that the hydrophobic hydration of Fe in the MCsomes (aqueous vesicles of metal carbonyl complexes) can be detected by cyclic voltammetry and fluorescence quenching experiments. Moreover, the hydration can be adjusted by the chemical structures of tails as well as solution conditions, such as dilution and pH, which induces the hierarchical self-assembly of MCsomes. The research is summarized in Chapter 7

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that diffusion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarising their densely packed and heterogeneous structures. The most familiar phenomenon is a power-law increase of the MSD, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations, non-gaussian distributions of the displacements, heterogeneous diffusion, and immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarise some widely used theoretical models: gaussian models like FBM and Langevin equations for visco-elastic media, the CTRW model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Emphasis is put on the spatio-temporal properties of the transport in terms of 2-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even for identical MSDs. Then, we review the theory underlying common experimental techniques in the presence of anomalous transport: single-particle tracking, FCS, and FRAP. We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where model systems mimic physiological crowding conditions. Finally, computer simulations play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.Comment: review article, to appear in Rep. Prog. Phy