Identifying transitions in finite systems by means of partition function zeros and microcanonical inflection-point analysis: a comparison for elastic flexible polymers

Aggregation and crystallization of small alkanes

We present a computer simulation study of the aggregation and ordering of short alkane chains using a united atom model description. Our simulation approach allows us to determine the density of states of our systems and, from those, their thermodynamics for all temperatures. All systems show a first order aggregation transition followed by a low-temperature ordering transition. For a few chain aggregates of intermediate lengths (up to N = 40), we show that these ordering transitions resemble the quaternary structure formation in peptides. In an earlier publication, we have already shown that single alkane chains fold into low-temperature structures, best described as secondary and tertiary structure formation, thus completing this analogy here. The aggregation transition in the thermodynamic limit can be extrapolated in pressure to the ambient pressure for which it agrees well with experimentally known boiling points of short alkanes. Similarly, the chain length dependence of the crystallization transition agrees with known experimental results for alkanes. For small aggregates, for which volume and surface effects are not yet well separated, our method allows us to identify the crystallization in the core of the aggregate and at its surface, individually.

Transverse-size critical exponent of directed percolation from Yang-Lee zeros of survival probability

By using transfer-matrix method we compute survival probabilities for the directed percolation problem on strips of a square lattice, and get very precise estimates of their Yang-Lee zeros lying closest to the real axis in the complex plane of occupation probability. This allows us to get accurate values for transverse-size critical exponent and percolation threshold.

Diagrams of States of Single Flexible-Semiflexible Multi-Block Copolymer Chains: A Flat-Histogram Monte Carlo Study

The combination of flexibility and semiflexibility in a single molecule is a powerful design principle both in nature and in materials science. We present results on the conformational behavior of a single multiblock-copolymer chain, consisting of equal amounts of Flexible (F) and Semiflexible (S) blocks with different affinity to an implicit solvent. We consider a manifold of macrostates defined by two terms in the total energy: intermonomer interaction energy and stiffness energy. To obtain diagrams of states (pseudo-phase diagrams), we performed flat-histogram Monte Carlo simulations using the Stochastic Approximation Monte Carlo algorithm (SAMC). We have accumulated two-Dimensional Density of States (2D DoS) functions (defined on the 2D manifold of macrostates) for a SF-multiblock-copolymer chain of length N=64 with block lengths b = 4, 8, 16, and 32 in two different selective solvents. In an analysis of the canonical ensemble, we calculated the heat capacity and determined its maxima and the most probable morphologies in different regions of the state diagrams. These are rich in various, non-trivial morphologies, which are formed without any specific interactions, and depend on the block length and the type of solvent selectivity (preferring S or F blocks, respectively). We compared the diagrams with those for the non-selective solvent and reveal essential changes in some cases. Additionally, we implemented microcanonical analysis in the “conformational” microcanonical (NVU, where U is the potential energy) and the true microcanonical (NVE, where E is the total energy) ensembles with the aim to reveal and classify pseudo-phase transitions, occurring under the change of temperature.

The folding pathways and thermodynamics of semiflexible polymers

Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm. However, the population of the intermediates in the unfolding process is very low, insufficient to induce unfolding arm rollover. The total types of folding pathways from the coil state to the toroidal state for a semiflexible polymer chain remain unchanged by varying the solvent quality or temperature, whereas the kinetic partitioning into different folding events can be tuned significantly. In the process of knotting, three types of mechanisms, namely, plugging, slipknotting, and sliding, are discovered. Along the folding evolution, a semiflexible homopolymer chain can knot at any stage of folding upon leaving the extended coil state, and the probability to find a knot increases with chain compactness. In addition, we find rich types of knotted topologies during the folding of a semiflexible homopolymer chain. This study should be helpful in gaining insight into the general principles of biopolymer folding.

Partition function zeros of the p-state clock model in the complex temperature plane

We investigate the partition function zeros of the two-dimensional p-state clock model in the complex temperature plane by using the Wang-Landau method. For p=5, 6, 8, and 10, we propose a modified energy representation to enumerate exact irregular energy levels for the density of states without any binning artifacts. Comparing the leading zeros between different p's, we provide strong evidence that the upper transition at p=6 is indeed of the Berezinskii-Kosterlitz-Thouless (BKT) type in contrast to the claim of the previous Fisher zero study [Phys. Rev. E 80, 042103 (2009)10.1103/PhysRevE.80.042103]. We find that the leading zeros of p=6 at the upper transition collapse onto the zero trajectories of the larger p's including the XY limit while the finite-size behavior of p=5 differs from the converged behavior of p≥6 within the system sizes examined. In addition, we argue that the nondivergent specific heat in the BKT transition is responsible for the small partition function magnitude that decreases exponentially with increasing system size near the leading zero, fundamentally limiting access to large systems in search for zeros with an estimator under finite statistical fluctuations.

Subphase transitions in first-order aggregation processes

In this paper, we investigate the properties of aggregation transitions in the context of generic coarse-grained homopolymer systems. By means of parallel replica-exchange Monte Carlo methods, we perform extensive simulations of systems consisting of up to 20 individual oligomer chains with five monomers each. Using the tools of the versatile microcanonical inflection-point analysis, we show that the aggregation transition is a first-order process consisting of a sequence of subtransitions between intermediate structural phases. We unravel the properties of these intermediate phases by collecting and analyzing their individual contributions towards the density of states of the system. The central theme of this systematic study revolves around translational entropy and its role in the striking phenomena of missing intermediate phases. We conclude with a brief discussion of the scaling properties of the transition temperature and the latent heat.

Microcanonical analysis of a finite-size nonequilibrium system

Microcanonical analysis is a powerful method that can be used to generalize the concept of phase transitions to finite-size systems. However, microcanonical analysis has only been applied to equilibrium systems. I show that it is possible to conduct the microcanonical analysis of a finite-size nonequilibrium system by generalizing the concept of microcanonical entropy. A one-dimensional asymmetric diffusion process is studied as an example for which such a generalized entropy can be explicitly found, and the microcanonical method is used to define a generalized phase transition for the finite-size nonequilibrium system.

Confinement effects upon the separation of structural transitions in linear systems with restricted bond fluctuation ranges

By means of advanced parallel replica-exchange Monte Carlo methods we examine the influence of elasticity and confinement on the structural transitions of linear systems with restricted bonded interaction. For this purpose, we adopt a model for coarse-grained flexible polymers of finite length in the dilute regime. Hyperphase diagrams are constructed using energy-dependent canonical quantities to demonstrate the effects of the changes in the range of the confined interaction on the liquid and solid structural phases. With increasing bonded interaction range we observe the disappearance of the liquid phase and the fusion of the gas-liquid (or Θ) and the liquid-solid transitions. One of the most remarkable features, the liquid-gas transition, changes from second to first order if the confined interaction range exceeds a threshold that separates polymeric from nonpolymeric systems. The notoriously difficult sampling of the entropically suppressed conformations in the region of very strong first-order transitions is improved by using multiple Gaussian modified ensembles.