Exact expressions for the partition function of the one-dimensional Ising model in the fixed-M ensemble.

We obtain exact closed-form expressions for the partition function of the one-dimensional Ising model in the fixed-M ensemble, for three commonly used boundary conditions: periodic, antiperiodic, and Dirichlet. These expressions allow for the determination of fluctuation-induced forces in the canonical ensemble, which we term Helmholtz forces. The thermodynamic expressions and the calculations flowing from them should provide insights into the nature and behavior of fluctuation-induced forces in interesting and as-yet unexplored regimes.

Spanning tree model and the assembly kinetics of RNA viruses.

Single-stranded RNA (ssRNA) viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules and it is not known whether this also can be understood by free energy minimization. We address this question using a simple mathematical model, the spanning tree model, that was recently proposed for the assembly of small ssRNA viruses. We present a statistical physics analysis of the properties of this model. RNA selection takes place via a kinetic mechanism that operates during the formation of the nucleation complex and that is related to Hopfield kinetic proofreading.

Endocytosis at extremes: Formation and internalization of giant clathrin-coated pits under elevated membrane tension.

Internalization of clathrin-coated vesicles from the plasma membrane constitutes the major endocytic route for receptors and their ligands. Dynamic and structural properties of endocytic clathrin coats are regulated by the mechanical properties of the plasma membrane. Here, we used conventional fluorescence imaging and multiple modes of structured illumination microscopy (SIM) to image formation of endocytic clathrin coats within live cells and tissues of developing fruit fly embryos. High resolution in both spatial and temporal domains allowed us to detect and characterize distinct classes of clathrin-coated structures. Aside from the clathrin pits and plaques detected in distinct embryonic tissues, we report, for the first time, formation of giant coated pits (GCPs) that can be up to two orders of magnitude larger than the canonical pits. In cultured cells, we show that GCP formation is induced by increased membrane tension. GCPs take longer to grow but their mechanism of curvature generation is the same as the canonical pits. We also demonstrate that GCPs split into smaller fragments during internalization. Considering the supporting roles played by actin filament dynamics under mechanically stringent conditions that slow down completion of clathrin coats, we suggest that local changes in the coat curvature driven by actin machinery can drive splitting and internalization of GCPs.

Packaging contests between viral RNA molecules and kinetic selectivity.

The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules by packaging signals during the nucleation stage of the assembly of small RNA viruses. The effects of the RNA secondary structure and folding geometry of the packaging signals on the assembly activation energy barrier are encoded by a pair of characteristics: the wrapping number and the maximum ladder distance. Kinetic selection is found to be optimal when assembly takes place under conditions of supersaturation and also when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. As a function of the height of the activation energy barrier, there is a form of order-disorder transition such that for sufficiently low activation energy barriers, kinetic selectivity is erased by entropic effects associated with the number of assembly pathways.

Invariant theory and orientational phase transitions.

The Landau theory of phase transitions has been productively applied to phase transitions that involve rotational symmetry breaking, such as the transition from an isotropic fluid to a nematic liquid crystal. It even can be applied to the orientational symmetry breaking of simple atomic or molecular clusters that are not true phase transitions. In this paper, we address fundamental problems that arise with the Landau theory when it is applied to rotational symmetry breaking transitions of more complex particle clusters that involve order parameters characterized by larger values of the l index of the dominant spherical harmonic that describes the broken symmetry state. The problems are twofold. First, one may encounter a thermodynamic instability of the expected ground state with respect to states with lower symmetry. A second problem concerns the proliferation of quartic invariants that may or may not be physical. We show that the combination of a geometrical method based on the analysis of the space of invariants, developed by Kim to study symmetry breaking of the Higgs potential, with modern visualization tools provides a resolution to these problems. The approach is applied to the outcome of numerical simulations of particle ordering on a spherical surface and to the ordering of protein shells.

Kirigami and the Caspar-Klug construction for viral shells with negative Gauss curvature.

In this work we extend the Caspar-Klug construction to the archaeal viruses, which in recent years have captured the attention of many researchers for their ability to thrive in extreme environments. We assume that the shells of archaeal viruses are composed of hexamers and pentamers-as is true for icosahedral viruses-together with heptamers, necessary to introduce negative Gauss curvature. Following the original work of Caspar and Klug, we first construct models capable of reproducing the shape observed in electron microscopy images of archaeal viruses. Next, using the technique of kirigami, we present a systematic way to formulate archaeal virus templates from regular hexagonal lattices. Finally, we utilize the presented techniques to build finite element models of archaeal virus geometries and investigate their shapes as a function of material properties. In particular, using thin-shell elasticity theory, we describe a buckling transition as a function of a modified Föppl-von Kármán number γ^{★} and we show how changes in γ^{★} may initiate the tail formation in the Acidianus two-tailed archaeal virus.

Ground state instabilities of protein shells are eliminated by buckling.

We propose a hybrid discrete-continuum model to study the ground state of protein shells. The model allows for shape transformation of the shell and buckling transitions as well as the competition between states with different symmetries that characterize discrete particle models with radial pair potentials. Our main results are as follows. For large Föppl-von Kármán (FvK) numbers the shells have stable isometric ground states. As the FvK number is reduced, shells undergo a buckling transition resembling that of thin-shell elasticity theory. When the width of the pair potential is reduced below a critical value, then buckling coincides with the onset of structural instability triggered by over-stretched pair potentials. Chiral shells are found to be more prone to structural instability than achiral shells. It is argued that the well-width appropriate for protein shells lies below the structural instability threshold. This means that the self-assembly of protein shells with a well-defined, stable structure is possible only if the bending energy of the shell is sufficiently low so that the FvK number of the assembled shell is above the buckling threshold.

Orientational phase transitions and the assembly of viral capsids.

We present a Landau theory for large-l orientational phase transitions and apply it to the assembly of icosahedral viral capsids. The theory predicts two distinct types of ordering transitions. Transitions dominated by the l=6,10,12, and 18 icosahedral spherical harmonics resemble robust first-order phase transitions that are not significantly affected by chirality. The remaining transitions depend essentially on including mixed l states denoted as l=15+16 corresponding to a mixture of l=15 and l=16 spherical harmonics. The l=15+16 transition is either continuous or weakly first-order and it is strongly influenced by chirality, which suppresses spontaneous chiral symmetry breaking. The icosahedral state is in close competition with states that have tetrahedral, D_{5}, and octahedral symmetries. We present a group-theoretic method to analyze the competition between the different symmetries. The theory is applied to a variety of viral shells.

Manipulation and amplification of the Casimir force through surface fields using helicity.

We present both exact and numerical results for the behavior of the Casimir force in O(n) systems with a finite extension L in one direction when the system is subjected to surface fields that induce helicity in the order parameter. We show that for such systems, the Casimir force in certain temperature ranges is of the order of L^{-2}, both above and below the critical temperature, T_{c}, of the bulk system. An example of such a system would be one with chemically modulated bounding surfaces, in which the modulation couples directly to the system's order parameter. We demonstrate that, depending on the parameters of the system, the Casimir force can be either attractive or repulsive. The exact calculations presented are for the one-dimensional XY and Heisenberg models under twisted boundary conditions resulting from finite surface fields that differ in direction by a specified angle, and the three-dimensional Gaussian model with surface fields in the form of plane waves that are shifted in phase with respect to each other. Additionally, we present exact and numerical results for the mean-field version of the three-dimensional O(2) model with finite surface fields on the bounding surfaces. We find that all significant results are consistent with the expectations of finite-size scaling.

Protein viscoelastic dynamics: a model system.

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the model is a strongly overdamped oscillator described by a harmonic restoring force for small displacements that reversibly yields to stress under sufficiently large displacement. This simple dynamical system also reveals unexpectedly rich behavior-exhibiting a series of dynamical transitions and analogies with equilibrium thermodynamic phase transitions. The effects of noise and of inertia are briefly considered and described.

Reply to "Comment on 'Casimir force in the O(n→∞) model with free boundary conditions' ".

The preceding Comment raises a few points concerning our paper [Phys. Rev. E 89, 042116 (2014)]. In this Reply we stress that although Diehl et al. [Europhys. Lett. 100, 10004 (2012) and Phys. Rev. E 89, 062123 (2014)] use three different models to study the Casimir force for the O(n→∞) model with free boundary conditions we study a single model over the entire range of temperatures from above the bulk critical temperature T(c) to absolute temperatures down to T=0. The use of a single model renders more transparent the crossover from effects dominated by critical fluctuations in the vicinity of the bulk transition temperature to effects controlled by Goldstone modes at low temperatures. Contrary to the assertion in the Comment, we make no claim for the superiority of our model over any of those considered by Diehl et al. [Europhys. Lett. 100, 10004 (2012) and Phys. Rev. E 89, 062123 (2014)]. We also present additional evidence supporting our conclusion in Dantchev et al. [Phys. Rev. E 89, 042116 (2014)] that the temperature range in which our low-temperature analytical expansion for the Casimir force increases as L grows and remains accurate for values of the ratio T/T(c) that become closer and closer to unity, whereas T remains well outside of the critical region.

Casimir force in the O(n→∞) model with free boundary conditions.

We present results for the temperature behavior of the Casimir force for a system with a film geometry with thickness L subject to free boundary conditions and described by the n→∞ limit of the O(n) model. These results extend over all temperatures, including the critical regime near the bulk critical temperature Tc, where the critical fluctuations determine the behavior of the force, and temperatures well below it, where its behavior is dictated by the Goldstone mode contributions. The temperature behavior when the absolute temperature, T, is a finite distance below Tc, up to a logarithmic-in-L proximity of the bulk critical temperature, is obtained both analytically and numerically; the critical behavior follows from numerics. The results resemble-but do not duplicate-the experimental curve behavior for the force obtained for He4 films.

Shape transitions in soft spheres regulated by elasticity.

We study elasticity-driven morphological transitions of soft spherical core-shell structures in which the core can be treated as an isotropic elastic continuum and the surface or shell as a tensionless liquid layer, whose elastic response is dominated by bending. To generate the transitions, we consider the case where the surface area of the liquid layer is increased for a fixed amount of interior elastic material. We find that generically there is a critical excess surface area at which the isotropic sphere becomes unstable to buckling. At this point it adopts a lower symmetry wrinkled structure that can be described by a spherical harmonic deformation. We study the dependence of the buckled sphere and critical excess area of the transition on the elastic parameters and size of the system. We also relate our results to recent experiments on the wrinkling of gel-filled vesicles as their interior volume is reduced. The theory may have broader applications to a variety of related structures from the macroscopic to the microscopic, including the wrinkling of dried peas, raisins, as well as the cell nucleus.

Simplicity of the spherical spin-glass model.

We revisit an approach to the replica-based analysis of the spherical spin-glass model that makes use of a mapping of the problem onto a one-dimensional interacting charge system. A saddle point approximation leads to the conclusion that the interaction between charges is irrelevant in the thermodynamic limit, and as a consequence, that there is no nontrivial correlation between replicas for this model. This allows us to show that quenched and annealed disorder averages agree for the spherical spin glass. We demonstrate this result within two different mathematical frameworks, and we also relate our analysis to the conclusions that follow from the replica symmetry ansatz.

Physics of shell assembly: line tension, hole implosion, and closure catastrophe.

The self-assembly of perfectly ordered closed shells is a challenging process involved in many biological and nanoscale systems. However, most of the aspects that determine their formation are still unknown. Here we investigate the growth of shells by simulating the assembly of spherical structures made of N identical subunits. Remarkably, we show that the formation and energetics of partially assembled shells are dominated by an effective line-tension that can be described in simple thermodynamic terms. In addition, we unveil two mechanisms that can prevent the correct formation of defect-free structures: "hole implosion," which leads to a premature closure of the shell; and "closure catastrophe," which causes a dramatic production of structural disorder during the later stages of the growth of big shells.

Casimir force in the rotor model with twisted boundary conditions.

We investigate the three-dimensional lattice XY model with nearest neighbor interaction. The vector order parameter of this system lies on the vertices of a cubic lattice, which is embedded in a system with a film geometry. The orientations of the vectors are fixed at the two opposite sides of the film. The angle between the vectors at the two boundaries is α where 0≤α≤π. We make use of the mean field approximation to study the mean length and orientation of the vector order parameter throughout the film--and the Casimir force it generates--as a function of the temperature T, the angle α, and the thickness L of the system. Among the results of that calculation are a Casimir force that depends in a continuous way on both the parameter α and the temperature and that can be attractive or repulsive. In particular, by varying α and/or T one controls both the sign and the magnitude of the Casimir force in a reversible way. Furthermore, for the case α=π, we discover an additional phase transition occurring only in the finite system associated with the variation of the orientations of the vectors.

Symmetries of interacting helices of charge.

We analytically examine the pair interaction for parallel discrete helices of charge. Symmetry arguments allow for the free energy to be decomposed into a sum of terms, each of which has an intuitive geometric interpretation. Truncated Fourier expansions of these terms are shown to provide effective free energy expressions that are valid under very general circumstances. These expressions are used to briefly examine and characterize the azimuthal interactions within F-actin and A-DNA aggregates.

Spherical spin-glass-Coulomb-gas duality: solution beyond mean-field theory.

We present an alternate solution of a Gaussian spin-glass model with infinite ranged interactions and a global spherical constraint at zero magnetic field. The replicated spin-glass Hamiltonian is mapped onto a Coulomb gas of logarithmically interacting particles confined by a logarithmic single particle potential. The precise free energy is obtained by analyzing the Painlevé τ{IV}[n] function in the n→0 limit. The large-N thermodynamics exactly recovers that of Kosterlitz, Thouless, and Jones [Phys. Rev. Lett. 36, 1217 (1976)10.1103/PhysRevLett.36.1217]. It is hoped that the approach here can be extended to apply to systems beyond the spherical model, particularly those in which destabilizing terms lead to replica symmetry breaking.

Boundary conditions and the critical Casimir force on an Ising model film: exact results in one and two dimensions.

Finite-size effects in certain critical systems can be understood as universal Casimir forces. Here, we compare the Casimir force for free, fixed, periodic, and antiperiodic boundary conditions in the exactly calculable case of the ferromagnetic Ising model in one and two dimensions. We employ a procedure which allows us to calculate the Casimir force with the aforementioned boundary conditions analytically in a transparent manner. Among other results, we find an attractive Casimir force for the case of periodic boundary conditions and a repulsive Casimir force in the antiperiodic case.

Finite-size effects in presence of gravity: the behavior of the susceptibility in 3He and 4He films near the liquid-vapor critical point.

We study critical-point finite-size effects on the behavior of susceptibility of a film placed in the Earth's gravitational field. The fluid-fluid and substrate-fluid interactions are characterized by van der Waals type power-law tails, and the boundary conditions are consistent with bounding surfaces that strongly prefer the liquid phase of the system. Specific predictions are made with respect to the behavior of 3He and 4He films in the vicinity of their respective liquid-gas critical points. We find that for all film thicknesses of current experimental interest the combination of van der Waals interactions and gravity leads to substantial deviations from the behavior predicted by models in which all interatomic forces are very short ranged and gravity is absent. In the case of a completely short-ranged system exact mean-field analytical expressions are derived, within the continuum approach, for the behavior of both the local and the total susceptibilities.