Statistical mechanics of aggregation and crystallization for semiflexible polymers

Abstract

Abstract. -By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic beadstick model, where nonbonded monomers interact via Lennard-Jones forces. Aggregation turns out to be a process, in which the constituents experience strong structural fluctuations, similar to peptides in coupled folding-binding cluster formation processes. In contrast to a recently studied related proteinlike hydrophobic-polar heteropolymer model, aggregation and crystallization are separate processes for a homopolymer with the same small bending rigidity. Rather stiff semiflexible polymers form a liquid-crystal-like phase, as expected. In analogy to the heteropolymer study, we find that the first-order-like aggregation transition of the complexes is accompanied by strong system-size dependent hierarchical surface effects. In consequence, the polymer aggregation is a phase-separation process with entropy reduction.Cluster formation and crystallization of polymers are processes which are interesting for technological applications, e.g., for the design of new materials with certain mechanical properties or nanoelectronic organic devices and polymeric solar cells. From a biophysical point of view, the understanding of peptide oligomerization, but also the (de)fragmentation in semiflexible biopolymer systems like actin networks is of substantial relevance. This requires a systematic analysis of the basic properties of the polymeric cluster formation processes, in particular, for small polymer complexes on the nanoscale, where surface effects are competing noticeably with structure-formation processes in the interior of the aggregate.A further motivation for investigating the aggregation transition of semiflexible homopolymer chains derives from the intriguing results of our recent study of a similar aggregation process for peptides [1,2], which were modeled as heteropolymers with a sequence of two types of monomers, hydrophobic (A) and hydrophilic ones (B). By (a) E-mail: junghans@mpip-mainz.mpg.de (b) E-mail: m.bachmann@fz-juelich.de (c) E-mail: Wolfhard.Janke@itp.uni-leipzig.de specializing the previously employed heteropolymer model to the apparently simpler homopolymer case, we aim by comparison at isolating those properties which are mainly driven by the sequence properties of heteropolymers. In fact, while in both cases the aggregation transition is a phase-separation process, we will show below that for homopolymers the aggregation and crystallization (if any) are separate conformational transitions -unlike our study of heteropolymer aggregates where they were found to coincide [1,2]. The physical origin causing these differences will be explained within the microcanonical formalism [3,4], which proves [1,2] to be particularly suitable for this type of problem.We thus consider the same model as in [1,2], but here we assume that all monomers i µ = 1, . . . , N p-1

Aggregation of theta-polymers in spherical confinement

“…The influence of density on the aggregation a) zierenberg@itp.uni-leipzig.de b) mueller@itp.uni-leipzig.de c) schierz@itp.uni-leipzig.de d) marenz@itp.uni-leipzig.de e) janke@itp.uni-leipzig.de transition of two lattice proteins has been noticed recently 18 to be similar to that on an ideal gas. In this study we will extend this observation by investigating an off-lattice polymer model that has been successfully applied to peptide 19 and polymer aggregation 20,21 before. Focusing on the case of flexible homopolymers, we will provide entropic arguments for the density dependence and energetic arguments for finite-size effects which leads to a reasonable description of the density dependence in a spherical confinement.…”

Effect of grafting on the binding transition of two flexible polymers

“…This is in contrast to the directed or semiflexible approaches to study binding and allows one to compare to the uncorrelated motifs that originate within aggregation of flexible polymers [15]. We notice that there has been a somewhat equivalent use of the terms aggregation [23,24,25] and binding [7,8]. Here, we refer to binding as the process of two polymers attaching to each other, in our case even flexible polymers.…”

Accelerating atomic-level protein simulations by flat-histogram techniques

“…Compared to the canonical runs, we find that the tunneling frequency, on average, is a factor 2.8 higher in the 1/γ -ensemble simulations, where intermediate energies are not statistically suppressed. The tunneling frequency is a key figure when studying surface effects 16,42 and properties that strongly depend on the relative population of the coexisting states, such as the heat capacity.…”