The system of hard cut spheres (disk-shaped particles formed by symmetrically truncating the end caps of a sphere) exhibits an intriguing “cubatic” phase with cubic orientational symmetry. However, it is unclear whether this phase is metastable with respect to the columnar phase. We attempt to provide an answer to this question by carrying out free energy calculations by the expanded ensemble Monte Carlo method. We conclude that there may be a very small region of cubatic stability in the vicinity of the isotropic-cubatic phase transition, but that that transition would need to be determined more accurately to obtain a definitive answer. We also comment on the efficacy of the expanded ensemble method for these kinds of calculations.

Prefusion and postfusion states of the biological fusion process between lipid bilayer vesicle membranes are studied in this paper. Based on the Helfrich-type continuum theory, a diffuse interface model is developed which describes the phase changes on the deformable vesicles via a scalar phase field function, and incorporates the adhesion effect between the different phases of the vesicles through a nonlocal interaction potential. Various equilibrium configurations in the prefusion and postfusion states are examined. The effects of spontaneous curvatures, bending, and Gaussian rigidities on the fusion process are discussed. Instead of considering only the regions in close contact as in many previous studies, the present approach allows us to include the energetic contributions from all parts of the vesicles. By carrying out simulations based on the gradient flow of the associated energy functional, we are also able to elucidate the dynamic transitions between the prefusion and postfusion states.

Using numerical simulations of a simple sea-coast mechanical erosion model, we investigate the effect of spatial long-range correlations in the lithology of coastal landscapes on the fractal behavior of the corresponding coastlines. In the model, the resistance of a coast section to erosion depends on the local lithology configuration as well as on the number of neighboring sea sides. For weak sea forces, the sea is trapped by the coastline and the eroding process stops after some time. For strong sea forces erosion is perpetual. The transition between these two regimes takes place at a critical sea force, characterized by a fractal coastline front. For uncorrelated landscapes, we obtain, at the critical value, a fractal dimension $D=1.33$, which is consistent with the dimension of the accessible external perimeter of the spanning cluster in two-dimensional percolation. For sea forces above the critical value, our results indicate that the coastline is self-affine and belongs to the Kardar-Parisi-Zhang universality class. In the case of landscapes generated with power-law spatial long-range correlations, the coastline fractal dimension changes continuously with the Hurst exponent $H$, decreasing from $D=1.34$ to $1.04$, for $H=0$ and $1$, respectively. This nonuniversal behavior is compatible with the multitude of fractal dimensions found for real coastlines.

The cubic-quintic Swift-Hohenberg equation (SH35) provides a convenient order parameter description of several convective systems with reflection symmetry in the layer midplane, including binary fluid convection. We use SH35 with an additional quadratic term to determine the qualitative effects of breaking the midplane reflection symmetry on the properties of spatially localized structures in these systems. Our results describe how the snakes-and-ladders organization of localized structures in SH35 deforms with increasing symmetry breaking and show that the deformation ultimately generates the snakes-and-ladders structure familiar from the quadratic-cubic Swift-Hohenberg equation. Moreover, in nonvariational systems, such as convection, odd-parity convectons necessarily drift when the reflection symmetry is broken, permitting collisions among moving localized structures. Collisions between both identical and nonidentical traveling states are described.

Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants $D$ from molecular dynamics simulations. We find that $D$ for Coulomb crystals with relatively soft-core $1/r$ interactions may be larger than $D$ for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions “hop” in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter $\Gamma =175$ to Coulomb parameters up to $\Gamma =1750$, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.

Biomolecular simulations have become a major tool in understanding biomolecules and their complexes. However, one can typically only investigate a few mutants or scenarios due to the severe computational demands of such simulations, leading to a great interest in method development to overcome this restriction. One way to achieve this is to reduce the complexity of the systems by an approximation of the forces acting upon the constituents of the molecule. The harmonic approximation used in elastic network models simplifies the physical complexity to the most reduced dynamics of these molecular systems. The reduced polymer modeled this way is typically comprised of mass points representing coarse-grained versions of, e.g., amino acids. In this work, we show how the computation of free energy contributions of contacts between two residues within the molecule can be reduced to a simple lookup operation in a precomputable matrix. Being able to compute such contributions is of great importance: protein design or molecular evolution changes introduce perturbations to these pair interactions, so we need to understand their impact. Perturbation to the interactions occurs due to randomized and fixated changes (in molecular evolution) or designed modifications of the protein structures (in bioengineering). These perturbations are modifications in the topology and the strength of the interactions modeled by the elastic network models. We apply the new algorithm to (1) the bovine trypsin inhibitor, a well-known enzyme in biomedicine, and show the connection to folding properties and the hydrophobic collapse hypothesis and (2) the serine proteinase inhibitor CI-2 and show the correlation to $\Phi$ values to characterize folding importance. Furthermore, we discuss the computational complexity and show empirical results for the average case, sampled over a library of 77 structurally diverse proteins. We found a relative speedup of up to 10 000-fold for large proteins with respect to repeated application of the initial model.

We determine the complexity of several constraint-satisfaction problems using the heuristic algorithm WalkSAT. At large sizes $N$, the complexity increases exponentially with $N$ in all cases. Perhaps surprisingly, out of all the models studied, the hardest for WalkSAT is the one for which there is a polynomial time algorithm.

In a spatial evolutionary prisoner’s dilemma game (PDG), individuals interact with their neighbors and update their strategies according to some rules. As is well known, cooperators are destined to become extinct in a well-mixed population, whereas they could emerge and be sustained on a structured network. In this work, we introduce a simple model to investigate the crossover between a structured network and a well-mixed one in an evolutionary PDG. In the model, each link $j$ is designated a rewiring parameter ${\tau }_j$, which defines the time interval between two successive rewiring events for link $j$. By adjusting the rewiring parameter $\tau$ (the mean time interval for any link in the network), we could change a structured network into a well-mixed one. For the link rewiring events, three situations are considered: one synchronous situation and two asynchronous situations. Simulation results show that there are three regimes of $\tau$: large $\tau$ where the density of cooperators ${\rho }_c$ rises to ${\rho }_{c,\infty }$ (the value of ${\rho }_c$ for the case without link rewiring), small $\tau$ where the mean-field description for a well-mixed network is applicable, and moderate $\tau$ where the crossover between a structured network and a well-mixed one happens.

The continued fraction method (CFM) is used to solve the Fokker-Planck equation with arbitrary dc and ac fields. With an appropriate choice of basis functions, the Fokker-Planck equation is converted into a set of linear algebraic equations with short-ranged coupling and then CFM is implemented to obtain numerical solutions with high efficiency. Both a proposed perturbative CFM and the numerically exact matrix CFM are used to study the nonlinear response of driven systems, with their results compared to assess the validity regime of the perturbative approach. The proposed perturbative CFM approach needs scalar quantities only and hence is more efficient within its validity regime. Two nonlinear systems of different nature are used as examples: molecular dipole (rotational Brownian motion) and particle in a periodic potential (translational Brownian motion). The associated full dynamics is presented in the compact form of hysteresis loops. It is observed that as the strength of an AC driving field increases, pronounced nonlinear effects are manifested in the deformation of the hysteresis loops.

The response of an oscillating granular damper to an initial perturbation is studied using experiments performed in microgravity and granular dynamics simulations. High-speed video and image processing techniques are used to extract experimental data. An inelastic hard sphere model is developed to perform simulations and the results are in excellent agreement with the experiments. In line with previous work, a linear decay of the amplitude is observed. Although this behavior is typical for a friction-damped oscillator, through simulation it is shown that this effect is still present even when friction forces are absent. A simple expression is developed which predicts the optimal damping conditions for a given amplitude and is independent of the oscillation frequency and particle inelasticities.

We study the configurational structure of the point-island model for epitaxial growth in one dimension. In particular, we calculate the island gap and capture zone distributions. Our model is based on an approximate description of nucleation inside the gaps. Nucleation is described by the joint probability density $p_n^{\mathit{XY}}(x,y)$, which represents the probability density to have nucleation at position $x$ within a gap of size $y$. Our proposed functional form for $p_n^{\mathit{XY}}(x,y)$ describes excellently the statistical behavior of the system. We compare our analytical model with extensive numerical simulations. Our model retains the most relevant physical properties of the system.

Wetting of a single hexagonal boron nitride sheet by liquid water has been investigated by molecular dynamics simulations within a temperature range between 278 and 373 K. The wetting temperature was found to be $~$310 K, while the onset of prewetting happens around the much higher temperature of 354 K. The static (hydrogen-bond populations, density profiles, energy per molecule) and dynamic (diffusion coefficients) properties of water in the stable phases in this temperature range were also studied and compared to those of water on graphene. The results indicate that hydrophobicity of boron nitride is milder than that of graphene.

We report an experimental investigation of the drying of a deposited drop of whole blood. Flow motion, adhesion, gelation, and fracturation all occur during the evaporation of this complex matter, leading to a final typical pattern. Two distinct regimes of evaporation are highlighted: the first is driven by convection, diffusion, and gelation in a liquid phase, whereas the second, with a much slower rate of evaporation, is characterized by the mass transport of the liquid left over in the gellified biocomponent matter. A diffusion model of the drying process allows a prediction of the transition between these two regimes of evaporation. Moreover, the formation of cracks and other events occurring during the drying are examined and shown to be driven by critical solid mass concentrations.

We numerically analyze the scaling behavior of experimentally accessible dynamical relaxation forms for polymer networks modeled by a finite multihierarchical structure. In the framework of generalized Gaussian structures, by making use of the eigenvalue spectrum of the connectivity matrix, we determine the averaged monomer displacement under local external forces as well as the mechanical relaxation quantities (storage and loss moduli). Hence we generalize the known analysis for both classes of fractals to the case of multihierarchical structure, for which even though we have a mixed growth algorithm, the above cited observables still give information about the two different underlying topologies. For very large lattices, reached via an algebraic procedure that avoids the numerical diagonalizations of the corresponding connectivity matrices, we depict the scaling of both component fractals in the intermediate time (frequency) domain, which manifests two different slopes.

We investigate the orientational order transition of striped patterns in microphase structures of diblock copolymer-diblock copolymer mixtures in the presence of periodic oscillatory particles. Under certain conditions, although the macrophase separation of a system is almost isotropic, microphase separation of one diblock copolymer takes place and becomes anisotropic gradually. By changing the oscillatory frequency and amplitude, the orientational order transition of a striped microphase structure from the state parallel to the oscillatory direction to the state perpendicular to the oscillatory direction is observed. We also find that the order transition occurs when we change the initial composition ratio. Furthermore, we examine the domain size and the orientational order parameter of microstructure in the process of orientational order transition. The results may provide guidance for experimentalists. This model system can also give a simple way to realize orientational order transition of soft materials by changing the oscillatory field.

The decrease of the spectral radius, an important characterizer of network dynamics, by removing links is investigated. The minimization of the spectral radius by removing $m$ links is shown to be an NP-complete problem, which suggests considering heuristic strategies. Several greedy strategies are compared, and several bounds on the decrease of the spectral radius are derived. The strategy that removes that link $l=i~j$ with largest product $(x_1){}_i(x_1){}_j$ of the components of the eigenvector $x_1$ belonging to the largest adjacency eigenvalue is shown to be superior to other strategies in most cases. Furthermore, a scaling law where the decrease in spectral radius is inversely proportional to the number of nodes $N$ in the graph is deduced. Another sublinear scaling law of the decrease in spectral radius versus the number $m$ of removed links is conjectured.

We study the nontrivial clustering properties of extreme or recurrent events in the context of deterministic chaotic systems. We find that correlations between return times of such events can depend nonmonotonically on the threshold used to define the events, which leads to counterintuitive behavior. In particular, the distribution of the conditional return intervals can indicate clustering as well as repelling of extreme events for the same condition but different thresholds—in sharp contrast to what has been observed for stochastic processes with long-range correlations as well as for independent and identically distributed random variables. This has important implications for the time-dependent hazard assessment of extreme events, indicating that possible threshold dependencies should always be taken into account.

A fundamental relation exists between the statistical properties of the fluctuations of the energy-level spectrum of a Hamiltonian and the chaotic properties of the physical system it describes. This relationship has been addressed previously as a signature of chaos in quantum dynamical systems. In order to properly analyze these fluctuations, however, it is necessary to separate them from the general tendency, namely, its secular part. Unfortunately this process, called unfolding, is not trivial and can lead to erroneous conclusions about the chaoticity of a system. In this paper we propose a technique to improve the unfolding procedure for the purpose of minimizing the dependence on the particular procedure. This technique is based on detrending the fluctuations of the unfolded spectra through the empirical mode decomposition method.

We analyze the stochastic creation of a single bound state (BS) in a random potential with a compact support. We study both the Hermitian Schrödinger equation and non-Hermitian Zakharov-Shabat systems. These problems are of special interest in the inverse scattering method for Korteveg–de-Vries and the nonlinear Schrödinger equations since soliton solutions of these two equations correspond to the BSs of the two aforementioned linear eigenvalue problems. Analytical expressions for the average width of the potential required for the creation of the first BS are given in the approximation of delta-correlated Gaussian potential and additionally different scenarios of eigenvalue creation are discussed for the non-Hermitian case.