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J. Briels, Soft Matter 5, 4401 (2009)1744-683X10.1039/b911310j] and the multichain slip-spring type models [T. Uneyama and Y. Masubuchi, J. Chem. Phys. 137, 154902 (2012)JCPSA60021-960610.1063/1.4758320]. As a demonstration, we apply our coarse-graining method with the LETP to a single particle dynamics in a supercooled liquid, and compare the results of the LETP with the molecular dynamics simulations and other coarse-graining models.The bulk of stochastic gene expression models in the literature do not have an explicit description of the age of a cell within a generation and hence they cannot capture events such as cell division and DNA replication. Instead, many models incorporate the cell cycle implicitly by assuming that dilution due to cell division can be described by an effective decay reaction with first-order kinetics. If it is further assumed that protein production occurs in bursts, then the stationary protein distribution is a negative binomial. Here we seek to understand how accurate these implicit models are when compared with more detailed models of stochastic gene expression. We derive the exact stationary solution of the chemical master equation describing bursty protein dynamics, binomial partitioning at mitosis, age-dependent transcription dynamics including replication, and random interdivision times sampled from Erlang or more general distributions; the solution is different for single lineage and population snapshot settings. We show that protein distributions are well approximated by the solution of implicit models (a negative binomial) when the mean number of mRNAs produced per cycle is low and the cell cycle length variability is large. When these conditions are not met, the distributions are either almost bimodal or else display very flat regions near the mode and cannot be described by implicit models. We also show that for genes with low transcription rates, the size of protein noise has a strong dependence on the replication time, it is almost independent of cell cycle variability for lineage measurements, and increases with cell cycle variability for population snapshot measurements. In contrast for large transcription rates, the size of protein noise is independent of replication time and increases with cell cycle variability for both lineage and population measurements.We study dipolarly coupled three-dimensional spin systems in both the microcanonical and the canonical ensembles by introducing appropriate numerical methods to determine the microcanonical temperature and by realizing a canonical model of heat bath. In the microcanonical ensemble, we show the existence of a branch of stable antiferromagnetic states in the low-energy region. Other metastable ferromagnetic states exist in this region by externally perturbing them, an effective negative specific heat is obtained. In the canonical ensemble, for low temperatures, the same metastable states are unstable and reach a new branch of more robust metastable states which is distinct from the stable one. Our statistical physics approach allows us to put some order in the complex structure of stable and metastable states of dipolar systems.We apply the homotopy analysis method to the motion of noninteracting active Brownian particles (ABPs) under a general situation such as in the presence of external fields, external torques, or even moving on non-Euclidean geometries. Within this framework, a general expression as a series solution in time for the probability density function (PDF) satisfying the Fokker-Planck (FP) equation is elucidated. Using the latter PDF, their respective mean values (first and second moments) are also found in general. Applications of the present technique are offered by solving classic ABP situations, namely free noninteracting ABPs, ABPs under a Poiseuille flow, and even ABPs confined to move on any Riemannian manifold. To improve the convergence of the obtained series solution for each situation, Padé approximants are incorporated. It is worth mentioning that the offered methodology may exactly be applied to other fields such as chemistry, biology, or econophysics where a FP equation governs the system.We use numerical simulations to study the flow of a bidisperse mixture of athermal, frictionless, soft-core two-dimensional spherocylinders driven by a uniform steady-state simple shear applied at a fixed volume and a fixed finite strain rate γ[over ̇]. Energy dissipation is via a viscous drag with respect to a uniformly sheared host fluid, giving a simple model for flow in a non-Brownian suspension with Newtonian rheology. Considering a range of packing fractions ϕ and particle asphericities α at small γ[over ̇], we study the angular rotation θ[over ̇]_i and the nematic orientational ordering S_2 of the particles induced by the shear flow, finding a nonmonotonic behavior as the packing ϕ is varied. Erlotinib in vitro We interpret this nonmonotonic behavior as a crossover from dilute systems at small ϕ, where single-particle-like behavior occurs, to dense systems at large ϕ, where the geometry of the dense packing dominates and a random Poisson-like process for particle rotations results. We also argue that the finite nematic ordering S_2 is a consequence of the shearing serving as an ordering field, rather than a result of long-range cooperative behavior among the particles. We arrive at these conclusions by consideration of (i) the distribution of waiting times for a particle to rotate by π, (ii) the behavior of the system under pure, as compared to simple, shearing, (iii) the relaxation of the nematic order parameter S_2 when perturbed away from the steady state, and (iv) by construction, a numerical mean-field model for the rotational motion of a particle. Our results also help to explain the singular behavior observed when taking the α→0 limit approaching circular disks.Random, uncorrelated displacements of particles on a lattice preserve the hyperuniformity of the original lattice, that is, normalized density fluctuations vanish in the limit of infinite wavelengths. In addition to a diffuse contribution, the scattering intensity from the the resulting point pattern typically inherits the Bragg peaks (long-range order) of the original lattice. Here we demonstrate how these Bragg peaks can be hidden in the effective diffraction pattern of independent and identically distributed perturbations. All Bragg peaks vanish if and only if the sum of all probability densities of the positions of the shifted lattice points is a constant at all positions. The underlying long-range order is then "cloaked" in the sense that it cannot be reconstructed from the pair correlation function alone. On the one hand, density fluctuations increase monotonically with the strength of perturbations a, as measured by the hyperuniformity order metric Λ[over ¯]. On the other hand, the disappearance and reemergence of long-range order, depending on whether the system is cloaked as the perturbation strength increases, is manifestly captured by the τ order metric.
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