We theoretically investigate self-oscillating waves of an active material, which were recently introduced as a nonsymmetric part of the elastic moduli, termed odd elasticity. Using Purcell's three-link swimmer model, we reveal that an odd-elastic filament at low Reynolds number can swim in a self-organized manner and that the time-periodic dynamics are characterized by a stable limit cycle generated by elastohydrodynamic interactions. Also, we consider a noisy shape gait and derive a swimming formula for a general elastic material in the Stokes regime with its elasticity modulus being represented by a nonsymmetric matrix, demonstrating that the odd elasticity produces biased net locomotion from random noise.

By means of discrete-element methods, we investigate the joint effects of the grain size distribution (GSD) and contact friction on the structure of three-dimensional samples composed of spherical grains. Specifically, we compress these systems isotropically until jamming and then analyze their structure in terms of density, connectivity, coefficients of uniformity and curvature, and parameters of grading entropy. Our study focuses on power-law GSDs and particularly on the Fuller and Thompson distribution, proposed over a century ago. First, we show that, among the set of GSDs investigated, this particular distribution produces the densest and best-connected systems, falsifying a conjecture recently posed in the literature. Second, we find that the jamming packing fraction can be accurately predicted as a function of simple descriptors of the GSD, but among these descriptors the granular entropy concept proves to be the most useful. This allows for an alternative interpretation of both jamming and grading entropy concepts. Finally, we compare the Fuller and Thompson distribution with two well-known GSDs: that of the Apollonian sphere packing and that towards which granular systems evolve after intensive grain fracturing. Surprisingly, we find that these three GSDs are practically coincident in the limit of large size spans, despite having been introduced or discovered in different scientific contexts (i.e., engineering, mathematics, and earth sciences, respectively).

In nonlinear Thomson scattering, a relativistic electron reradiates the photons of a laser pulse, converting optical light to x rays or beyond. While this extreme frequency conversion offers a promising source for probing high-energy-density materials and driving uncharted regimes of nonlinear quantum electrodynamics, conventional nonlinear Thomson scattering has inherent trade-offs in its scaling with laser intensity. Here we discover that the ponderomotive control afforded by spatiotemporal pulse shaping enables regimes of nonlinear Thomson scattering that substantially enhance the scaling of the radiated power, emission angle, and frequency with laser intensity. By appropriately setting the velocity of the intensity peak, a spatiotemporally shaped pulse can increase the power radiated by orders of magnitude. The enhanced scaling with laser intensity allows for operation at significantly lower electron energies or intensities.

In this study, we estimate the distribution of lattice model parameters based on Bayesian estimation using the dispersion relation spectral data of lattice vibration. The dispersion relation of lattice vibration is observed using inelastic scattering of neutrons or x rays and is used to analyze the speed of sound and interatomic force. However, the current analysis method of dispersion relation observation data in the field of experimental physics requires manually fitting parameters, so the analysis is costly and cannot effectively handle high-dimensional data and large amounts of data. Moreover, it is impossible to discuss the estimation accuracy with the conventional method. Therefore, we solve these problems by estimating the distribution of parameters using Bayesian inference. We propose a lattice model parameter estimation method that uses Bayesian inference with a physical observation stochastic process and determine the method's effectiveness using artificial data.

We present a path integral calculation of the probability distribution associated with the time-integrated moments of the Ornstein-Uhlenbeck process that includes the Gaussian prefactor in addition to the dominant path or instanton term obtained in the low-noise limit. The instanton term was obtained recently [D. Nickelsen and H. Touchette, Phys. Rev. Lett. 121, 090602 (2018)] and shows that the large deviations of the time-integrated moments are anomalous in the sense that the logarithm of their distribution scales nonlinearly with the integration time. The Gaussian prefactor gives a correction to the low-noise approximation and leads us to define an instanton variance giving some insights as to how anomalous large deviations are created in time. The results are compared with simulations based on importance sampling, extending our previous results based on direct Monte Carlo simulations. We conclude by explaining why many of the standard analytical and numerical methods of large deviation theory fail in the case of anomalous large deviations.

The present paper investigates amplitude death (AD) in delay-coupled oscillators on directed graphs, in which the connection delays among oscillators are heterogeneous. We reveal that a linear stability analysis of AD can be significantly simplified by focusing on directed cycles in the graph. First, it is proven that the characteristic function of a steady state can be factorized into several functions that can be analyzed independently. Second, we show that the number of connection parameters to be considered for the stability analysis can be reduced, because the stability depends on the sums of connection delays for directed cycles and is independent of the connection delays on edges that do not form directed cycles. The theoretical results are verified through numerical simulations.

The structures of many large bacteriophages, such as the P23-77 capsids, do not adhere strictly to the quasi-equivalence principle of viral architecture. Although the general architecture of the P23-77 capsids is classed as $T=28d$, it self-assembles from multiple copies of two types of coat protein subunits, and the resulting hexameric capsomers do not conform to the Caspar-Klug paradigm. There are two types of hexamers with distinct internal organization, that are located at specific positions in the capsid. It is an open problem which assembly mechanism can lead to such a complex capsid organization. Here we propose a simple set of local rules that can explain how such non-quasi-equivalent capsid structures can arise as a result of self-assembly.

A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination of tension and torque involves, in the framework of this method of analysis, the (thermal or mechanical) activation of a specific mix of statistically interacting particles carrying quanta of extension or contraction and quanta of twist or supercoiling. The methodology, which is elucidated in applications of increasing complexity, is capable of describing the conversion between twist chirality and plectonemic chirality in quasistatic processes. The control variables are force or extension and torque or linkage (a combination of twist and writhe). The versatility of this approach is demonstrated in two applications relevant and promising for double-stranded DNA under controlled tension and torque. One application describes conformational transformations between (native) B-DNA, (underwound) S-DNA, and (overwound) P-DNA in accord with experimental data. The other application describes how the conversion between a twisted chain and a supercoiled chain accommodates variations of linkage and excess length in a buckling transition.

We have elaborated a theoretical approach for the description of polar nematic phases observed by Nishikawa et al. [Adv. Mater. 29, 1702354 (2017)], their structures, and transitions between them. Specific symmetry contributions to the pair molecular potentials provide the molecular mechanisms responsible for the formation of proper and improper polarity on the macroscopic level. An improper antiferroelectric nematic M2 phase can arise between paraelectric nematic M1 and proper ferroelectric nematic MP in the temperature scale. The local polarization in M2 arises mostly due to the local splay deformation. The director distribution in M2 represents the conjugation of cylindrical waves with opposite splay and polarization signs. The director and polarization are parallel to the cylindrical domain axes in the middle of each cylinder but exhibit considerable (mostly radial) deformation on the periphery of each cylinder. Polarization vectors are mostly stacked antiparallel on the borders between the domains without the director disruption. The domain size decreases with the decreasing temperature, the percentage of the antiferroelectric decouplings increases, and M2 exhibits the first-order phase transition into proper ferroelectric MP. With the increasing temperature the domain size in the M2 phase increases, the domination of particular polar orientation of molecules reduces, and finally, the domain size diverges at particular temperature corresponding to the second-order phase transition from M2 to paraelectric M1. Variations of the polar and nonpolar orientational order parameters are estimated within each phase and between the phases. Our experimental and computer simulation results (also presented in the paper) fully support our theoretical findings.

In a noisy environment, oscillations lose their coherence, which can be characterized by a quality factor. We determine this quality factor for oscillations arising from a driven Fokker-Planck dynamics along a periodic one-dimensional potential analytically in the weak-noise limit. With this expression, we can prove for this continuum model the analog of an upper bound that has been conjectured for the coherence of oscillations in discrete Markov network models. We show that our approach can also be adapted to motion along a noisy two-dimensional limit cycle. Specifically, we apply our scheme to the noisy Stuart-Landau oscillator and the thermodynamically consistent Brusselator as a simple model for a chemical clock. Our approach thus complements the fairly sophisticated extant general framework based on techniques from Hamilton-Jacobi theory with which we compare our results numerically.

The dynamics of active matter driven by interacting molecular motors has a nonpotential structure at the local scale. However, we show that there exists a quasipotential effectively describing the collective self-organization of the motors propelling a cell at a continuum active gel level. Such a model allows us to understand cell motility as an active phase transition problem between the static and motile steady-state configurations that minimize the quasipotential. In particular, both configurations can coexist in a metastable fashion and a small stochastic disorder in the gel is sufficient to trigger an intermittent cell dynamics where either static or motile phases are more probable, depending on which state is the global minimum of the quasipotential.

Underneath its apparently simple architecture, the circular chromosome of Escherichia coli is known for displaying complex dynamics in its cytoplasm, with past investigations hinting at inherently diverse mobilities of chromosomal loci across the genome. To decipher its origin, we simulate the dynamics of genome-wide spectrum of E. coli chromosomal loci, via integrating its experimentally derived Hi-C interaction matrix within a polymer-based model. Our analysis demonstrates that, while the dynamics of the chromosome is subdiffusive in a viscoelastic media, the diffusion constants are strongly dependent of chromosomal loci coordinates and diffusive exponents ($\alpha$) are widely heterogenous with $\alpha \approx$ 0.36–0.60. The loci-dependent heterogeneous dynamics and mean first-passage times of interloci encounter were found to be modulated via genetically distant interloci communications and is robust even in the presence of active, ATP-dependent noises. Control investigations reveal that the absence of Hi-C-derived interactions in the model would have abolished the traits of heterogeneous loci diffusion, underscoring the key role of loci-specific genetically distant interaction in modulating the underlying heterogeneity of the loci diffusion.

We explore the relation between active Brownian particles, a minimal particle-based model for active matter, and scalar field theories. Both show a liquid-gas-like phase transition toward stable coexistence of a dense liquid with a dilute active gas that terminates in a critical point. However, a comprehensive mapping between the particle-based model parameters and the effective coefficients governing the field theories has not been established yet. We discuss conflicting recent numerical results for the critical exponents of active Brownian particles in two dimensions. Starting from the intermediate effective hydrodynamic equations, we then present a construction for a scalar order parameter for active Brownian particles that yields the active model $\mathrm{B}+$. We argue that a crucial ingredient is the coupling between density and polarization in the particle current. The renormalization flow close to two dimensions exhibits a pair of perturbative fixed points that limit the attractive basin of the Wilson-Fisher fixed point, with the perspective that the critical behavior of active Brownian particles in two dimensions is governed by a strong-coupling fixed point different from Wilson-Fisher and not necessarily corresponding to Ising universality.

We study the adsorption of simple fluids at smoothly structured, completely wet walls and show that a meniscus osculation transition occurs when the Laplace and geometrical radii of curvature of locally parabolic regions coincide. Macroscopically, the osculation transition is of fractional, $\frac{7}{2}$, order and separates regimes in which the adsorption is microscopic, containing only a thin wetting layer, and mesoscopic, in which a meniscus exists. We develop a scaling theory for the rounding of the transition due to thin wetting layers and derive critical exponent relations that determine how the interfacial height scales with the geometrical radius of curvature. Connection with the general geometric construction proposed by Rascón and Parry is made. Our predictions are supported by a microscopic model density functional theory for drying at a sinusoidally shaped hard wall where we confirm the order of the transition and also an exact sum rule for the generalized contact theorem due to Upton. We show that as bulk coexistence is approached the adsorption isotherm separates into three regimes: A preosculation regime where it is microscopic, containing only a thin wetting layer; a mesoscopic regime, in which a meniscus sits within the troughs; and finally another microscopic regime where the liquid-gas interface unbinds from the crests of the substrate.

We develop a description of defect loops in three-dimensional active nematics based on a multipole expansion of the far-field director and show how this leads to a self-dynamics dependent on the loop's geometric type. The dipole term leads to active stresses that generate a global self-propulsion for splay and bend loops. The quadrupole moment is nonzero only for nonplanar loops and generates a net “active torque,” such that defect loops are both self-motile and self-orienting. Our analysis identifies right- and left-handed twist loops as the only force- and torque-free geometries, suggesting a mechanism for generating an excess of twist loops. Finally, we determine the Stokesian flows created by defect loops and describe qualitatively their hydrodynamics.

We present dynamical effects on conformation in a simple bead-spring model consisting of three beads connected by two stiff springs. The conformation defined by the bending angle between the two springs is determined not only by a given potential energy function depending on the bending angle, but also by fast motion of the springs which constructs the effective potential. A conformation corresponding with a local minimum of the effective potential is hence called the dynamically induced conformation. We develop a theory to derive the effective potential using multiple-scale analysis and the averaging method. A remarkable consequence is that the effective potential depends on the excited normal modes of the springs and amount of the spring energy. Efficiency of the obtained effective potential is numerically verified.

We use molecular dynamics simulation to probe the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed against a slit barrier. The flow-based compression gives rise to a packing of the chain against the channel end that possesses a striking organization, consisting of interweaving of folds and circular coils. For stiff chains at low flow, we find that the organization is dominated by repeated hairpin folds. For stiff chains at higher flow, we observe that circular coils arise along with the folds, with folding and coiling domains becoming interwoven at the highest flow speeds. Chain organization is retained even when the chain persistence length is on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coiled loops, arises from the minimization of the total chain free energy.

Employing a creation and annihilation operator formulation, we derive an approximate many-body master equation describing discrete hopping from the more general continuous description of Brownian motion on a deep-well nonequilibrium periodic potential. The many-body master equation describes interactions of arbitrary strength and range arising from a “top-hat” two-body interaction potential. We show that this master equation reduces to the well-known asymmetric simple exclusion process and the zero range process in certain regimes. We also use the creation and annihilation operator formalism to derive results for the steady-state drift and the number fluctuations in special cases, including the unexplored limit of weak interparticle interactions.