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1.
Phys Rev E ; 108(4-1): 044110, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37978655

ABSTRACT

We study a system of equal-size circular disks, each with an asymmetrically placed pivot at a fixed distance from the center. The pivots are fixed at the vertices of a regular triangular lattice. The disks can rotate freely about the pivots, with the constraint that no disks can overlap with each other. Our Monte Carlo simulations show that the one-point probability distribution of orientations has multiple cusplike singularities. We determine the exact positions and qualitative behavior of these singularities. In addition to these geometrical singularities, we also find that the system shows order-disorder transitions, with a disordered phase at large lattice spacings, a phase with spontaneously broken orientational lattice symmetry at small lattice spacings, and an intervening Berezinskii-Kosterlitz-Thouless phase in between.

2.
Phys Rev E ; 107(6-1): 064136, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37464626

ABSTRACT

We study the phase diagram of a lattice gas of 2×2×1 hard plates on the three-dimensional cubic lattice. Each plate covers an elementary plaquette of the cubic lattice, with the constraint that a site can belong to utmost one plate. We focus on the isotropic system, with equal fugacities for the three orientations of plates. We show, using grand canonical Monte Carlo simulations, that the system undergoes two phase transitions when the density of plates is increased: the first from a disordered fluid phase to a layered phase, and the second from the layered phase to a sublattice-ordered phase. In the layered phase, the system breaks up into disjoint slabs of thickness two along one spontaneously chosen Cartesian direction, corresponding to a twofold (Z_{2}) symmetry breaking of translation symmetry along the layering direction. Plates with normals perpendicular to this layering direction are preferentially contained entirely within these slabs, while plates straddling two adjacent slabs have a lower density, thus breaking the symmetry between the three types of plates. We show that the slabs exhibit two-dimensional power-law columnar order even in the presence of a nonzero density of vacancies. In contrast, interslab correlations of the two-dimensional columnar order parameter decay exponentially with the separation between the slabs. In the sublattice-ordered phase, there is twofold symmetry breaking of lattice translation symmetry along all three Cartesian directions. We present numerical evidence that the disordered to layered transition is continuous and consistent with universality class of the three-dimensional O(3) model with cubic anisotropy, while the layered to sublattice transition is first-order in nature.

3.
Phys Rev E ; 107(6-1): 064137, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37464694

ABSTRACT

We obtain the phase diagram of fully packed hard plates on the cubic lattice. Each plate covers an elementary plaquette of the cubic lattice and occupies its four vertices, with each vertex of the cubic lattice occupied by exactly one such plate. We consider the general case with fugacities s_{µ} for "µ plates," whose normal is the µ direction (µ=x,y,z). At and close to the isotropic point, we find, consistent with previous work, a phase with long-range sublattice order. When two of the fugacities s_{µ_{1}} and s_{µ_{2}} are comparable, and the third fugacity s_{µ_{3}} is much smaller, we find a spontaneously layered phase. In this phase, the system breaks up into disjoint slabs of width two stacked along the µ_{3} axis. µ_{1} and µ_{2} plates are preferentially contained entirely within these slabs, while plates straddling two successive slabs have a lower density. This corresponds to a twofold breaking of translation symmetry along the µ_{3} axis. In the opposite limit, with µ_{3}≫µ_{1}∼µ_{2}, we find a phase with long-range columnar order, corresponding to simultaneous twofold symmetry breaking of lattice translation symmetry in directions µ_{1} and µ_{2}. The spontaneously layered phases display critical behavior, with power-law decay of correlations in the µ_{1} and µ_{2} directions when the slabs are stacked in the µ_{3} direction, and represent examples of "floating phases" discussed earlier in the context of coupled Luttinger liquids and quasi-two-dimensional classical systems. We ascribe this remarkable behavior to the constrained motion of defects in this phase, and we sketch a coarse-grained effective field theoretical understanding of the stability of power-law order in this unusual three-dimensional floating phase.

4.
Phys Rev E ; 107(4-1): 044112, 2023 Apr.
Article in English | MEDLINE | ID: mdl-37198813

ABSTRACT

We present a simple one-dimensional stochastic model with three control parameters and a surprisingly rich zoo of phase transitions. At each (discrete) site x and time t, an integer n(x,t) satisfies a linear interface equation with added random noise. Depending on the control parameters, this noise may or may not satisfy the detailed balance condition, so that the growing interfaces are in the Edwards-Wilkinson or in the Kardar-Parisi-Zhang universality class. In addition, there is also a constraint n(x,t)≥0. Points x where n>0 on one side and n=0 on the other are called "fronts." These fronts can be "pushed" or "pulled," depending on the control parameters. For pulled fronts, the lateral spreading is in the directed percolation (DP) universality class, while it is in a different universality class for pushed fronts, and another universality class in between. In the DP case, the activity at each active site can in general be arbitrarily large, in contrast to previous realizations of DP. Finally, we find two different types of transitions when the interface detaches from the line n=0 (with 〈n(x,t)〉→const on one side, and →∞ on the other), again with new universality classes. We also discuss a mapping of this model to the avalanche propagation in a directed Oslo rice pile model in specially prepared backgrounds.

5.
Phys Rev E ; 106(5): L052101, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36559425

ABSTRACT

In a system of interacting thin rigid rods of equal length 2ℓ on a two-dimensional grid of lattice spacing a, we show that there are multiple phase transitions as the coupling strength κ=ℓ/a and the temperature are varied. There are essentially two classes of transitions. One corresponds to the Ising-type spontaneous symmetry-breaking transition and the second belongs to less-studied phase transitions of geometrical origin. The latter class of transitions appears at fixed values of κ irrespective of the temperature, whereas the critical coupling for the spontaneous symmetry-breaking transition depends on it. By varying the temperature, the phase boundaries may cross each other, leading to a rich phase behavior with infinitely many phases. Our results are based on Monte Carlo simulations on the square lattice and a fixed-point analysis of a functional flow equation on a Bethe lattice.

6.
Phys Rev E ; 105(3-1): 034103, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35428120

ABSTRACT

A system of hard rigid rods of length k on hypercubic lattices is known to undergo two phase transitions when chemical potential is increased: from a low density isotropic phase to an intermediate density nematic phase, and on further increase to a high-density phase with no orientational order. In this paper, we argue that, for large k, the second phase transition is a first-order transition with a discontinuity in density in all dimensions greater than 1. We show that the chemical potential at the transition is ≈kln[k/lnk] for large k, and that the density of uncovered sites drops from a value ≈(lnk)/k^{2} to a value of order exp(-ak), where a is some constant, across the transition. We conjecture that these results are asymptotically exact, in all dimensions d≥2. We also present evidence of coexistence of nematic and disordered phases from Monte Carlo simulations for rods of length 9 on the square lattice.

7.
Phys Rev E ; 103(6-1): 062101, 2021 Jun.
Article in English | MEDLINE | ID: mdl-34271608

ABSTRACT

We study the distribution of lengths and other statistical properties of worms constructed by Monte Carlo worm algorithms in the power-law three-sublattice ordered phase of frustrated triangular and kagome lattice Ising antiferromagnets. Viewing each step of the worm construction as a position increment (step) of a random walker, we demonstrate that the persistence exponent θ and the dynamical exponent z of this random walk depend only on the universal power-law exponents of the underlying critical phase and not on the details of the worm algorithm or the microscopic Hamiltonian. Further, we argue that the detailed balance condition obeyed by such worm algorithms and the power-law correlations of the underlying equilibrium system together give rise to two related properties of this random walk: First, the steps of the walk are expected to be power-law correlated in time. Second, the position distribution of the walker relative to its starting point is given by the equilibrium position distribution of a particle in an attractive logarithmic central potential of strength η_{m}, where η_{m} is the universal power-law exponent of the equilibrium defect-antidefect correlation function of the underlying spin system. We derive a scaling relation, z=(2-η_{m})/(1-θ), that allows us to express the dynamical exponent z(η_{m}) of this process in terms of its persistence exponent θ(η_{m}). Our measurements of z(η_{m}) and θ(η_{m}) are consistent with this relation over a range of values of the universal equilibrium exponent η_{m} and yield subdiffusive (z>2) values of z in the entire range. Thus, we demonstrate that the worms represent a discrete-time realization of a fractional Brownian motion characterized by these properties.

8.
Phys Rev E ; 103(4-1): 042130, 2021 Apr.
Article in English | MEDLINE | ID: mdl-34005993

ABSTRACT

We determine the asymptotic behavior of the entropy of full coverings of a L×M square lattice by rods of size k×1 and 1×k, in the limit of large k. We show that full coverage is possible only if at least one of L and M is a multiple of k, and that all allowed configurations can be reached from a standard configuration of all rods being parallel, using only basic flip moves that replace a k×k square of parallel horizontal rods by vertical rods, and vice versa. In the limit of large k, we show that the entropy per site S_{2}(k) tends to Ak^{-2}lnk, with A=1. We conjecture, based on a perturbative series expansion, that this large-k behavior of entropy per site is superuniversal and continues to hold on all d-dimensional hypercubic lattices, with d≥2.

9.
Phys Rev E ; 103(3-1): 032122, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33862746

ABSTRACT

We study relaxation of long-wavelength density perturbations in a one-dimensional conserved Manna sandpile. Far from criticality where correlation length ξ is finite, relaxation of density profiles having wave numbers k→0 is diffusive, with relaxation time τ_{R}∼k^{-2}/D with D being the density-dependent bulk-diffusion coefficient. Near criticality with kξ≳1, the bulk diffusivity diverges and the transport becomes anomalous; accordingly, the relaxation time varies as τ_{R}∼k^{-z}, with the dynamical exponent z=2-(1-ß)/ν_{⊥}<2, where ß is the critical order-parameter exponent and ν_{⊥} is the critical correlation-length exponent. Relaxation of initially localized density profiles on an infinite critical background exhibits a self-similar structure. In this case, the asymptotic scaling form of the time-dependent density profile is analytically calculated: we find that, at long times t, the width σ of the density perturbation grows anomalously, σ∼t^{w}, with the growth exponent ω=1/(1+ß)>1/2. In all cases, theoretical predictions are in reasonably good agreement with simulations.

10.
J Mol Biol ; 431(19): 3814-3826, 2019 09 06.
Article in English | MEDLINE | ID: mdl-31330152

ABSTRACT

To obtain proper insight into how structure develops during a protein folding reaction, it is necessary to understand the nature and mechanism of the polypeptide chain collapse reaction, which marks the initiation of folding. Here, the time-resolved fluorescence resonance energy transfer technique, in which the decay of the fluorescence light intensity with time is used to determine the time evolution of the distribution of intra-molecular distances, has been utilized to study the folding of the small protein, monellin. It is seen that when folding begins, about one-third of the protein molecules collapse into a molten globule state (IMG), from which they relax by continuous further contraction to transit to the native state. The larger fraction gets trapped into a metastable misfolded state. Exit from this metastable state occurs via collapse to the lower free energy IMG state. This exit is slow, on a time scale of seconds, because of activation energy barriers. The trapped misfolded molecules as well as the IMG molecules contract continuously and slowly as structure develops. A phenomenological model of Markovian evolution of the polymer chain undergoing folding, incorporating these features, has been developed, which fits well the experimentally observed time evolution of distance distributions. The observation that the "wrong turn" to the misfolded state has not been eliminated by evolution belies the common belief that the folding of functional protein sequences is very different from that of a random heteropolymer, and the former have been selected by evolution to fold quickly.


Subject(s)
Plant Proteins/chemistry , Plant Proteins/metabolism , Protein Folding , Kinetics , Markov Chains , Molecular Dynamics Simulation , Peptides/chemistry , Peptides/metabolism , Probability , Protein Denaturation , Protein Stability
11.
Phys Rev E ; 99(5-1): 052129, 2019 May.
Article in English | MEDLINE | ID: mdl-31212423

ABSTRACT

We study the phase diagram of a system of 2×2×2 hard cubes on a three-dimensional cubic lattice. Using Monte Carlo simulations, we show that the system exhibits four different phases as the density of cubes is increased: disordered, layered, sublattice ordered, and columnar ordered. In the layered phase, the system spontaneously breaks up into parallel slabs of size 2×L×L where only a very small fraction cubes do not lie wholly within a slab. Within each slab, the cubes are disordered; translation symmetry is thus broken along exactly one principal axis. In the solidlike sublattice-ordered phase, the hard cubes preferentially occupy one of eight sublattices of the cubic lattice, breaking translational symmetry along all three principal directions. In the columnar phase, the system spontaneously breaks up into weakly interacting parallel columns of size 2×2×L, where only a very small fraction cubes do not lie wholly within a column. Within each column, the system is disordered, and thus translational symmetry is broken only along two principal directions. Using finite-size scaling, we show that the disordered-layered phase transition is continuous, while the layered-sublattice and sublattice-columnar transitions are discontinuous. We construct a Landau theory written in terms of the layering and columnar order parameters which is able to describe the different phases that are observed in the simulations and the order of the transitions. Additionally, our results near the disordered-layered transition are consistent with the O(3) universality class perturbed by cubic anisotropy as predicted by the Landau theory.

12.
Phys Rev Lett ; 121(24): 240601, 2018 Dec 14.
Article in English | MEDLINE | ID: mdl-30608719

ABSTRACT

There is a misconception, widely shared among physicists, that the equilibrium free energy of a one-dimensional classical model with strictly finite-ranged interactions, and at nonzero temperatures, cannot show any singularities as a function of the coupling constants. In this Letter, we discuss an instructive counterexample. We consider thin rigid linear rods of equal length 2ℓ whose centers lie on a one-dimensional lattice, of lattice spacing a. The interaction between rods is a soft-core interaction, having a finite energy U per overlap of rods. We show that the equilibrium free energy per rod F[(ℓ/a),ß], at inverse temperature ß, has an infinite number of singularities, as a function of ℓ/a.

13.
Phys Rev E ; 96(2-1): 022215, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28950591

ABSTRACT

We consider the response of a memoryless nonlinear device that acts instantaneously, converting an input signal ξ(t) into an output η(t) at the same time t. For input Gaussian noise with power-spectrum 1/f^{α}, the nonlinearity can modify the spectral index of the output to give a spectrum that varies as 1/f^{α^{'}} with α^{'}≠α. We show that the value of α^{'} depends on the nonlinear transformation and can be tuned continuously. This provides a general mechanism for the ubiquitous 1/f noise found in nature.

14.
Phys Rev E ; 94(4-1): 042314, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27841652

ABSTRACT

We present simulations of the one-dimensional Oslo rice pile model in which the critical height at each site is randomly reset after each toppling. We use the fact that the stationary state of this sand-pile model is hyperuniform to reach system of sizes >10^{7}. Most previous simulations were seriously flawed by important finite-size corrections. We find that all critical exponents have values consistent with simple rationals: ν=4/3 for the correlation length exponent, D=9/4 for the fractal dimension of avalanche clusters, and z=10/7 for the dynamical exponent. In addition, we relate the hyperuniformity exponent to the correlation length exponent ν. Finally, we discuss the relationship with the quenched Edwards-Wilkinson model, where we find in particular that the local roughness exponent is α_{loc}=1.

15.
Phys Rev Lett ; 114(19): 190601, 2015 May 15.
Article in English | MEDLINE | ID: mdl-26024157

ABSTRACT

We show that critical exponents of the transition to columnar order in a mixture of 2×1 dimers and 2×2 hard squares on the square lattice depends on the composition of the mixture in exactly the manner predicted by the theory of Ashkin-Teller criticality, including in the hard-square limit. This result settles the question regarding the nature of the transition in the hard-square lattice gas. It also provides the first example of a polydisperse system whose critical properties depend on composition. Our ideas also lead to some interesting predictions for a class of frustrated quantum magnets that exhibit columnar ordering of the bond energies at low temperature.

16.
Phys Rev E Stat Nonlin Soft Matter Phys ; 86(3 Pt 1): 031135, 2012 Sep.
Article in English | MEDLINE | ID: mdl-23030894

ABSTRACT

We study a system of particles with nearest- and next-nearest-neighbor exclusion on the square lattice (hard squares). This system undergoes a transition from a fluid phase at low density to a columnar-ordered phase at high density. We develop a systematic high-activity perturbation expansion for the free energy per site about a state with perfect columnar order. We show that the different terms of the series can be regrouped to get a Mayer-like series for a polydisperse system of interacting vertical rods in which the nth term is of order z(-(n+1)/2), where z is the fugacity associated with each particle. We sum this series to get the exact expansion to order 1/z(3/2).

17.
Phys Rev Lett ; 108(24): 247216, 2012 Jun 15.
Article in English | MEDLINE | ID: mdl-23004328

ABSTRACT

We relate properties of nearest-neighbor resonating valence-bond (NNRVB) wave functions for SU(g) spin systems on two-dimensional bipartite lattices to those of fully packed interacting classical dimer models on the same lattice. The interaction energy can be expressed as a sum of n-body potentials V(n), which are recursively determined from the NNRVB wave function on finite subgraphs of the original lattice. The magnitude of the n-body interaction V(n) (n>1) is of order O(g(-(n-1))) for small g(-1). The leading term is a two-body nearest-neighbor interaction V2(g) favoring two parallel dimers on elementary plaquettes. For SU(2) spins, using our calculated value of V2(g=2), we find that the long-distance behavior of the bond-energy correlation function is dominated by an oscillatory term that decays as 1/|r|α with α≈1.22. This result is in remarkable quantitative agreement with earlier direct numerical studies of the corresponding wave function, which give α≈1.20.

18.
Phys Rev E Stat Nonlin Soft Matter Phys ; 85(6 Pt 1): 061114, 2012 Jun.
Article in English | MEDLINE | ID: mdl-23005058

ABSTRACT

We consider a directed Abelian sandpile on a strip of size 2×n, driven by adding a grain randomly at the left boundary after every T timesteps. We establish the exact equivalence of the problem of mass fluctuations in the steady state and the number of zeros in the ternary-base representation of the position of a random walker on a ring of size 3^{n}. We find that while the fluctuations of mass have a power spectrum that varies as 1/f for frequencies in the range 3^{-2n}≪f≪1/T, the activity fluctuations in the same frequency range have a power spectrum that is linear in f.


Subject(s)
Colloids/chemistry , Models, Chemical , Models, Statistical , Silicon Dioxide/chemistry , Computer Simulation
19.
Phys Rev E Stat Nonlin Soft Matter Phys ; 85(2 Pt 1): 021107, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22463153

ABSTRACT

We study the patterns formed by adding N sand grains at a single site on an initial periodic background in the Abelian sandpile models, and relaxing the configuration. When the heights at all sites in the initial background are low enough, one gets patterns showing proportionate growth, with the diameter of the pattern formed growing as N(1/d) for large N, in d dimensions. On the other hand, if sites with maximum stable height in the starting configuration form an infinite cluster, we get avalanches that do not stop. In this paper we describe our unexpected finding of an interesting class of backgrounds in two dimensions that show an intermediate behavior: For any N, the avalanches are finite, but the diameter of the pattern increases as N(α), for large N, with 1/2<α≤1. Different values of α can be realized on different backgrounds, and the patterns still show proportionate growth. The noncompact nature of growth simplifies their analysis significantly. We characterize the asymptotic pattern exactly for one illustrative example with α=1.


Subject(s)
Colloids/chemistry , Models, Chemical , Models, Molecular , Pattern Recognition, Automated/methods , Silicon Dioxide/chemistry , Computer Simulation
20.
Phys Rev E Stat Nonlin Soft Matter Phys ; 84(1 Pt 1): 011140, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21867146

ABSTRACT

We study a system of long rigid rods of fixed length k with only excluded volume interaction. We show that, contrary to the general expectation, the self-consistent field equations of the Bethe approximation do not give the exact solution of the problem on the Bethe lattice in this case. We construct a new lattice, called the random locally treelike layered lattice, which allows a dense packing of rods, and we show that the Bethe self-consistent equations are exact for this lattice. For a four-coordinated lattice, k-mers with k ≥ 4 undergo a continuous isotropic-nematic phase transition. For even coordination number q ≥ 6, the transition exists only for k ≥ k(min)(q), and is discontinuous.

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