Biomedical subjects

Paul van der Schoot

Publications and source records attributed to Paul van der Schoot.

12 recordsLinked to original sources

PubMed2006

Dynamic heterogeneity in hydrogen-bonded polymers.

We report on neutron spin echo experiments on hydrogen-bonded polymers and compare the experimentally found dynamical structure factor with theoretical predictions. Surprisingly, we find that in the melt phase the expected scaling of the Rouse dynamics is not satisfied. We propose an explanation based upon the large spatial volume occupied by the connecting groups. When the effects of these bulky groups on the local friction are taken into account, the usual scaling behavior is restored.

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PubMed2006

Theory of the isotropic-nematic transition in dispersions of compressible rods.

We theoretically study the nematic ordering transition of rods that are able to elastically adjust their mutually excluded volumes. The model rods, which consist of a hard core surrounded by a deformable shell, mimic the structure of polymer-coated, rodlike fd virus particles that have recently been the object of experimental study [K. Purdy, Phys. Rev. Lett. 94, 057801 (2005)]. We find that fluids of such soft rods exhibit an isotropic-nematic phase transition at a density higher than that of the corresponding hard-rod system of identical diameter, and that at coexistence the order parameter of the nematic phase depends nonmonotonically on the elastic properties of the polymer coating. For binary mixtures of hard and soft rods, the topology of the phase diagram turns out to depend sensitively on the elasticity of a shell. The lower nematic-nematic critical point, discovered in mixtures of bare and polymer-coated fd virus particles, is not reproduced by the theory.

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PubMed2006

Probing the solvent-assisted nucleation pathway in chemical self-assembly.

Hierarchical self-assembly offers a powerful strategy for producing molecular nanostructures. Although widely used, the mechanistic details of self-assembly processes are poorly understood. We spectroscopically monitored a nucleation process in the self-assembly of p-conjugated molecules into helical supramolecular fibrillar structures. The data support a nucleation-growth pathway that gives rise to a remarkably high degree of cooperativity. Furthermore, we characterize a helical transition in the nucleating species before growth. The self-assembly process depends strongly on solvent structure, suggesting that an organized shell of solvent molecules plays an explicit role in rigidifying the aggregates and guiding them toward further assembly into bundles and/or gels.

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PubMed2006

Physical regulation of the self-assembly of tobacco mosaic virus coat protein.

We present a statistical mechanical model based on the principle of mass action that explains the main features of the in vitro aggregation behavior of the coat protein of tobacco mosaic virus (TMV). By comparing our model to experimentally obtained stability diagrams, titration experiments, and calorimetric data, we pin down three competing factors that regulate the transitions between the different kinds of aggregated state of the coat protein. These are hydrophobic interactions, electrostatic interactions, and the formation of so-called "Caspar" carboxylate pairs. We suggest that these factors could be universal and relevant to a large class of virus coat proteins.

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PubMed2006

Impact of steric interactions on the helical transition in assemblies of discotic molecules.

We investigate theoretically the effect of excluded-volume interactions on the helical configurational transition of supramolecular assemblies in solutions of chiral disklike molecules. To this end, we set up a second-virial theory within the context of the helical self-assembly of rodlike objects. We find that interaggregate interactions shift both the helical-transition point and the sharpness of the transition. For realistic values of the model parameters, the helical-transition temperature shifts by several degrees, and the more so the higher the concentration of assembling material. The mean aggregation number is also affected by the interactions, albeit only by a modest amount, unless the solution becomes very concentrated.

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PubMed2005

Classical nucleation theory of virus capsids.

A fundamental step in the replication of a viral particle is the self-assembly of its rigid shell (capsid) from its constituent proteins. Capsids play a vital role in genome replication and intercellular movement of viruses, and as such, understanding viral assembly has great potential in the development of new antiviral therapies and a systematic treatment of viral infection. In this article, we assume that nucleation is the underlying mechanism for self-assembly and combine the theoretical methods of the physics of equilibrium polymerization with those of the classical nucleation to develop a theory for the kinetics of virus self-assembly. We find expressions for the size of the critical capsid, the lag time, and the steady-state nucleation rate of capsids, and how they depend on both protein concentration and binding energy. The latter is a function of the acidity of the solution, the ionic strength, and the temperature, explaining why capsid nucleation is a sensitive function of the ambient conditions.

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PubMed2005

Geometry explains the large difference in the elastic properties of fcc and hcp crystals of hard spheres.

As is well known, hard-sphere crystals of the fcc and hcp type differ very little in their thermodynamic properties. Nonetheless, recent computer simulations by Pronk and Frenkel indicate that the elastic response to mechanical deformation of these two types of crystal are quite different [S. Pronk and D. Frenkel, Phys. Rev. Lett. 90, 255501 (2003)]. By invoking a geometrical argument put forward by Martin some time ago [R. M. Martin, Phys. Rev. B 6, 4546 (1972)], we suggest that this is largely due to the different symmetries of the fcc and hcp crystal structures. Indeed, we find that elastic constants of the fcc hard-sphere crystal can be mapped onto the equivalent ones of the hcp crystal to very high accuracy, as a comparison with the computer simulation data of Pronk and Frenkel shows. The same procedure applied to density functional theoretical predictions for the elastic properties of the fcc hard-sphere crystal also produces remarkably accurate predictions for those of the hcp hard-sphere crystal.

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PubMed2005

End-evaporation dynamics revisited.

We present analytical results on the so-called end-evaporation kinetics in equilibrium polymeric systems following a temperature jump (T jump). A T jump prepares the system with a nonequilibrium length distribution, after which it relaxes back to its equilibrium state. Starting from a master equation, we develop a mean-field analytical theory based on a generating function approach, which allows explicit approximate expressions for the monomer and dimer concentrations to be derived in a discrete setting; the concentrations of the other chains as well as the average chain length were shown to be entirely expressible in terms of the monomer and dimer concentrations. We find that the calculated monomer and dimer concentrations as well as the average chain length are in good agreement with numerical simulation results and do not suffer from some of the defects of earlier continuum theories. Furthermore, the relaxation was shown to take place in three different stages. The first stage comprises the very fast relaxation of the monomers to almost their equilibrium concentration; the other polymer chains have hardly relaxed. During the second stage, which is highly nonlinear, a redistribution of material at practically constant monomer density takes place. Only in the final stage of the relaxation process the chain concentrations approach their true equilibrium values. In this stage there are only very small shifts in the concentrations of chains, which are governed by extremely slow "indirect" monomer-mediated processes.

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PubMed2005

Electrostatics and the assembly of an RNA virus.

Electrostatic interactions play a central role in the assembly of single-stranded RNA viruses. Under physiological conditions of salinity and acidity, virus capsid assembly requires the presence of genomic material that is oppositely charged to the core proteins. In this paper we apply basic polymer physics and statistical mechanics methods to the self-assembly of a synthetic virus encapsidating generic polyelectrolyte molecules. We find that (i) the mean concentration of the encapsidated polyelectrolyte material depends on the surface charge density, the radius of the capsid, and the linear charge density of the polymer but neither on the salt concentration nor the Kuhn length, and (ii) the total charge of the capsid interior is equal but opposite to that of the empty capsid, a form of charge reversal. Unlike natural viruses, synthetic viruses are predicted not to be under an osmotic swelling pressure. The design condition that self-assembly only produces filled capsids is shown to coincide with the condition that the capsid surface charge exceeds the desorption threshold of polymer surface adsorption. We compare our results with studies on the self-assembly of both synthetic and natural viruses.

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PubMed2005

Phase behavior and interfacial properties of nonadditive mixtures of Onsager rods.

Within a second virial theory, we study bulk phase diagrams as well as the free planar isotropic-nematic interface of binary mixtures of nonadditive thin and thick hard rods. For species of the same type, the excluded volume is determined only by the dimensions of the particles, whereas for dissimilar ones it is taken to be larger or smaller than that, giving rise to a nonadditivity that can be positive or negative. We argue that such a nonadditivity can result from modeling of soft interactions as effective hard-core interactions. The nonadditivity enhances or reduces the fractionation at isotropic-nematic (IN) coexistence and may induce or suppress a demixing of the high-density nematic phase into two nematic phases of different composition (N(1) and N(2)), depending on whether the nonadditivity is positive or negative. The interfacial tension between coexisting isotropic and nematic phases shows an increase with increasing fractionation at the IN interface, and complete wetting of the IN(2) interface by the N(1) phase upon approach of the triple-point coexistence. In all explored cases bulk and interfacial properties of the nonadditive mixtures exhibit a striking and quite unexpected similarity with the properties of additive mixtures of different diameter ratio.

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PubMed2004

Amplification of chirality in helical supramolecular polymers beyond the long-chain limit.

The optical activity of helical homopolymers devoid of chiral centers increases drastically when a small amount of homochiral monomers is incorporated into them. We study this so-called sergeants-and-soldiers effect of chirality amplification in solutions of helical supramolecular polymers with a theoretical model that bears a strong resemblance to a one-dimensional, two-component Ising model. In the limit of very long self-assembled helical polymers, the strength of the sergeants-and-soldiers effect depends strongly on the free energy of a helix reversal and less so on the concentration of aggregating material. Outside the long-chain limit, we find the reverse--that is, a strong concentration dependence and a weak dependence on the helix-reversal energy. Our treatment gives an excellent agreement with recently published circular-dichroism measurements on mixed aggregates of discotic molecules in the solvents water and n-butanol, at two different overall concentrations.

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PubMed2003

Shape and director-field transformation of tactoids.

Tactoids are droplets of a nematic phase that under suitable conditions form in dispersions of elongated colloidal particles. We theoretically study the shape and the director-field configuration of such droplets for the case where a planar anchoring of the director field to the interface is favored. A minimum of four regimes can be identified in which the droplets have a different structure. Large droplets tend to be nearly spherical with a director field that is bipolar if the surface tension is strongly anisotropic and homogeneous if this is not so. Small droplets can become very elongated and spindlelike if the surface tension is sufficiently anisotropic. Depending on the anchoring strength, the director field is then either homogeneous or bipolar. We find that the more elongated the tactoid, the more strongly it resists the crossing over from a homogeneous to a bipolar structure. This should have implications for the nucleation rate of the nematic phase. Our calculations qualitatively describe the size dependence of the aspect ratio of tactoids found in recent experiments.

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