Magnesium $\left(\mathrm{M}{\mathrm{g}}^{2+}\right)$ and calcium $\left(\mathrm{C}{\mathrm{a}}^{2+}\right)$ are of essential importance in biological activity, but the molecular understanding of their selectivity is still lacking. Here, based on density functional theory calculations and ab initio molecular dynamics simulations, we show that $\mathrm{M}{\mathrm{g}}^{2+}$ binds more tightly to phosphotyrosine (pTyr) and stabilizes the conformation of pTyr, while $\mathrm{C}{\mathrm{a}}^{2+}$ binds more flexibly to pTyr with less structural stability. The key for the selectivity is attributed to the cation-π interactions between the hydrated cations and the aromatic ring together with the synergic interaction between the cations and the side groups in pTyr to form a cation-binding pocket structure, which we refer as side-group-synergetic hydrated cation-π interaction. The existence and relative strength of the cation-π interactions in the pocket structures as well as their structural stability have been demonstrated experimentally with ultraviolet (UV) absorption spectra and ${}^1\mathrm{H}$ NMR spectra. The findings offer insight into understanding the selectivity of $\mathrm{M}{\mathrm{g}}^{2+}$ and $\mathrm{C}{\mathrm{a}}^{2+}$ in a variety of biochemical and physiological essential processes.

We propose a method for enumerating entanglements between long chained, linear polymers that is based on the Gaussian linking number. The linking number is calculated between closely approaching segments of the macromolecular chains. Topological features of an entanglement, i.e., the extent to which one open segment winds around another, are reflected by the linking number. We show that using this measure, we can track disentanglement events through a deformation history and gain insights into how large scale disentanglements lead to failure. Incorporating an additional step where the topological entanglements identified along each chain are optimally clustered using standard clustering algorithms, we can also obtain a measure of the average number of rheological constraints that exist along each chain in an ensemble. Comparisons with other methods of enumerating entanglements, especially the primitive path analysis, are also made. Our results indicate that the linking number between two entangled segments in the undeformed state is a good indicator of the strength of the entanglement. Also, disentanglements occurring overwhelmingly around chain ends are an important cause of failure when a triaxial stress state exists in the polymer.

The Soret effect, i.e., the flow of matter caused by a temperature gradient, is studied in a glass-forming binary Lennard-Jones (LJ) mixture, using nonequilibrium molecular dynamics computer simulation. The transport processes associated with this effect are thermal diffusion and interdiffusion. While interdiffusion processes exhibit a drastic slowing down when approaching the glass transition, thermal diffusion appears to be a fast process even in the glass. We show that the Soret effect becomes more pronounced in the vicinity of the glass transition, due to the decoupling between thermal diffusion and interdiffusion as well as the chemical ordering in the considered LJ mixture. This is reflected in the occurrence of large concentration gradients, nonlinear concentration profiles, and long-lived nonstationary structures.

We present results from Langevin dynamics simulations of a glassy active-passive mixture of soft-repulsive binary colloidal disks. Activity on the smaller particles is applied according to the quorum sensing scheme, in which a smaller particle will be active for a persistence time if its local nearest neighbors are equal to or greater than a certain threshold value. We start with a passive glassy state of the system and apply activity to the smaller particles, which shows a nonmonotonous glassy character of the active particles with the persistence time of the active force, from its passive limit (zero activity). On the other hand, passive particles of the active-passive mixture phase separate at the intermediate persistence time of the active force, resulting in the hexatic-liquid and solid-liquid phases. Thus, our system shows three regimes as active glass, phase separation, and active liquid, as the persistence time increases from its smaller values. We show that the solidlike and hexatic phases consisting of passive large particles are stable due to the smaller momentum transfer from active to passive particles, compared to the higher persistence time where the positional and orientational ordering vanishes. Our model is relevant to active biological systems, where glassy dynamics is present, e.g., bacterial cytoplasm, biological tissues, dense quorum sensing bacteria, and synthetic smart amorphous glasses.

We report measurements of $K$-shell fluorescence lines induced by fast electrons in ramp-compressed Co targets. The fluorescence emission was stimulated by fast electrons generated through short-pulse laser-solid interaction with an Al target layer. Compression up to $2.1\times$ solid density was achieved while maintaining temperatures well below the Fermi energy, effectively removing the thermal effects from consideration. We observed small but unambiguous redshifts in the $K\beta$ fluorescence line relative to unshifted Cu $K\alpha$. Redshifts up to 2.6 eV were found to increase with compression and to be consistent with predictions from self-consistent models based on density-functional theory.

Currently there is considerable interest in creating scalable laboratory plasmas to study the mechanisms behind the formation and evolution of astrophysical phenomena such as Herbig-Haro objects and supernova remnants. Laboratory-scaled experiments can provide a well diagnosed and repeatable supplement to direct observations of these extraterrestrial objects if they meet similarity criteria demonstrating that the same physics govern both systems. Here, we present a study on the role of collision and cooling rates on shock formation using colliding jets from opposed conical wire arrays on a compact pulsed-power driver. These diverse conditions were achieved by changing the wire material feeding the jets, since the ion-ion mean free path (${\lambda }_{\text{mfp-ii}}$) and radiative cooling rates ($P_{\mathrm{rad}}$) increase with atomic number. Low $Z$ carbon flows produced smooth, temporally stable shocks. Weakly collisional, moderately cooled aluminum flows produced strong shocks that developed signs of thermal condensation instabilities and turbulence. Weakly collisional, strongly cooled copper flows collided to form thin shocks that developed inconsistently and fragmented. Effectively collisionless, strongly cooled tungsten flows interpenetrated, producing long axial density perturbations.

In this paper, we develop a discrete unified gas kinetic scheme (DUGKS) for a general nonlinear convection-diffusion equation (NCDE) and show that the NCDE can be recovered correctly from the present model through the Chapman-Enskog analysis. We then test the present DUGKS through some classic convection-diffusion equations, and we find that the numerical results are in good agreement with analytical solutions and that the DUGKS model has a second-order convergence rate. Finally, as a finite-volume method, the DUGKS can also adopt the nonuniform mesh. Besides, we perform some comparisons among the DUGKS, the finite-volume lattice Boltzmann model (FV-LBM), the single-relaxation-time lattice Boltzmann model (SLBM), and the multiple-relaxation-time lattice Boltzmann model (MRT-LBM). The results show that the present DUGKS is more accurate than the FV-LBM, more stable than the SLBM, and almost has the same accuracy as the MRT-LBM. Moreover, the use of nonuniform mesh may make the DUGKS model more flexible.

We extend the step-balanced random walk [Y. Maruyama, Phys. Rev. E 96, 032135 (2017)], which was proposed for diffusion phenomena in three-dimensional discontinuous media, to systems that contain anisotropic phase zones with nonplane interfaces. What is key is threefold: For each interstep transition at discontinuous interfaces to be equilibrated by its reverse transition, incident and penetration steps are in one-to-one correspondence; at each incidence, penetration probability is determined by the normal components of an incident step and the corresponding penetration step with respect to an incident tangential plane, and for reflection, the reverse of an incident step, which satisfies the conditions for time reversibility at any interface, is used as a reflection step.

Many-body effective interactions are commonly used in a molecular dynamics simulation study of gel networks formed by colloidal particles. Here we report an interaction potential that can be used to investigate the mechanical response of colloidal gel networks under shear deformation. We then investigate the dependence of the numerical simulation results on the form of mathematical expression used to define the interparticle interactions. This work reveals insight into particle gel models by discussing the physical origins of their mechanical response.

A three-terminal refrigerator based on resonant-tunneling quantum wells is proposed. With the help of the Landauer formula, the expressions for the cooling rate and the coefficient of performance (COP) are derived. The working regions of the refrigerator are determined and the three-dimensional projection graphs of the cooling rate and the COP varying with the positions of the two energy levels are plotted. Moreover, the influence of the bias voltage, the asymmetric factor, and the temperature difference on the optimal performance parameters is analyzed in detail. Finally, the performance characteristics of the refrigerator in the case of negative temperature difference are discussed.

We consider the nonlinear classical dynamics of a diatomic molecule under the action of a laser field in the framework of the driven Morse oscillator model. We investigate the influence of the dipole function and the laser field on the deformations of the surviving, invariant tori. For intense and high-frequency fields, some invariant tori traverse the separatrix of motion, visiting both the bound and unbound regions of the interatomic potential. Based on this fact, we propose the use of appropriately designed laser pulses to induce dissociation of trajectories on such invariant tori. This mechanism constitutes a controlled nonchaotic route for dissociation, which is an alternative to chaotic multiphoton dissociation and to chirped pulse dissociation.

We analyze the onset of social-norm-violating behaviors when social punishment is present. To this aim, a compartmental model is introduced to illustrate the flows among the three possible states: honest, corrupt, and ostracism. With this simple model we attempt to capture some essential ingredients such as the contagion of corrupt behaviors to honest agents, the delation of corrupt individuals by honest ones, and the warning to wrongdoers (fear like that triggers the conversion of corrupt people into honesty). In nonequilibrium statistical physics terms, the former dynamics can be viewed as a non-Hamiltonian kinetic spin-1 Ising model. After developing in full detail its mean-field theory and comparing its predictions with simulations made on regular networks, we derive the conditions for the emergence of corrupt behaviors and, more importantly, illustrate the key role of the warning-to-wrongdoers mechanism in the latter.

We pose an engineering challenge of controlling an ensemble of energy devices via coordinated, implementation-light, and randomized on/off switching as a problem in nonequilibrium statistical mechanics. We show that mean-field control with nonlinear feedback on the cumulative consumption, assumed available to the aggregator via direct physical measurements of the energy flow, allows the ensemble to recover from its use in the demand response regime, i.e., transition to a statistical steady state, significantly faster than in the case of the fixed feedback. Moreover when the nonlinearity is sufficiently strong, one observes the phenomenon of “super-relaxation,” where the total instantaneous energy consumption of the ensemble transitions to the steady state much faster than the underlying probability distribution of the devices over their state space, while also leaving almost no devices outside of the comfort zone.

Starting from the stochastic thermodynamics description of two coupled underdamped Brownian particles, we showcase and compare three different coarse-graining schemes leading to an effective thermodynamic description for the first of the two particles: marginalization over one particle, bipartite structure with information flows, and the Hamiltonian of mean force formalism. In the limit of time-scale separation where the second particle with a fast relaxation time scale locally equilibrates with respect to the coordinates of the first slowly relaxing particle, the effective thermodynamics resulting from the first and third approach are shown to capture the full thermodynamics and to coincide with each other. In the bipartite approach, the slow part does not, in general, allow for an exact thermodynamic description as the entropic exchange between the particles is ignored. Physically, the second particle effectively becomes part of the heat reservoir. In the limit where the second particle becomes heavy and thus deterministic, the effective thermodynamics of the first two coarse-graining methods coincide with the full one. The Hamiltonian of mean force formalism, however, is shown to be incompatible with that limit. Physically, the second particle becomes a work source. These theoretical results are illustrated using an exactly solvable harmonic model.

The geomagnetic field's dipole undergoes polarity reversals in irregular time intervals. Particularly long periods without reversals (of the order of ${10}^7$ yr), called superchrons, have occurred at least three times in the Phanerozoic (since 541 million years ago). We provide observational evidence for high non-Gaussianity in the vicinity of a transition to and from a geomagnetic superchron, consisting of a sharp increase in high-order moments (skewness and kurtosis) of the dipole's distribution. Such an increase in the moments is a universal feature of crisis-induced intermittency in low-dimensional dynamical systems undergoing global bifurcations. This implies a temporal variation of the underlying parameters of the physical system. Through a low-dimensional system that models the geomagnetic reversals, we show that the increase in the high-order moments during transitions to geomagnetic superchrons is caused by the progressive destruction of global periodic orbits exhibiting both polarities as the system approaches a merging bifurcation. We argue that the non-Gaussianity in this system is caused by the redistribution of the attractor around local cycles as global ones are destroyed.

Collective decision making processes lie at the heart of many social, political, and economic challenges. The classical voter model is a well-established conceptual model to study such processes. In this work, we define a form of adaptive (or coevolutionary) voter model posed on a simplicial complex, i.e., on a certain class of hypernetworks or hypergraphs. We use the persuasion rule along edges of the classical voter model and the recently studied rewiring rule of edges towards like-minded nodes, and introduce a peer-pressure rule applied to three nodes connected via a 2-simplex. This simplicial adaptive voter model is studied via numerical simulation. We show that adding the effect of peer pressure to an adaptive voter model leaves its fragmentation transition, i.e., the transition upon varying the rewiring rate from a single majority state into a fragmented state of two different opinion subgraphs, intact. Yet, above and below the fragmentation transition, we observe that the peer pressure has substantial quantitative effects. It accelerates the transition to a single-opinion state below the transition and also speeds up the system dynamics towards fragmentation above the transition. Furthermore, we quantify that there is a multiscale hierarchy in the model leading to the depletion of 2-simplices, before the depletion of active edges. This leads to the conjecture that many other dynamic network models on simplicial complexes may show a similar behavior with respect to the sequential evolution of simplices of different dimensions.

Multiple scattering of waves arises in all fields of physics in either periodic or random media. For random media the organization of the microstructure (uniform or nonuniform statistical distribution of scatterers) has effects on the propagation of coherent waves. Using a recent exact resolution method and different homogenization theories, the effects of the microstructure on the effective wave number are investigated over a large frequency range ($ka$ between 0.1 and 13.4) and high concentrations. For uniform random media, increasing the configurational constraint makes the media more transparent for low frequencies and less for high frequencies. As a side but important result, we show that two of the homogenization models considered here appear to be very efficient at high frequency up to a concentration of 60% in the case of uniform media. For nonuniform media, for which clustered and periodic aggregates appear, the main effect is to reduce the magnitude of resonances and to make network effects appear. In this case, homogenization theories are not relevant to make a detailed analysis.

We explore the effects that quenched disorder has on discontinuous nonequilibrium phase transitions into absorbing states. We focus our analysis on the naming game model, a nonequilibrium low-dimensional system with different absorbing states. The results obtained by means of the finite-size scaling analysis and from the study of the temporal dynamics of the density of active sites near the transition point evidence that the spatial quenched disorder does not destroy the discontinuous transition.

We derive an integral fluctuation theorem (FT) in a general setup of cavity quantum electrodynamics systems. In the derivation, a key difficulty lies in a diverging behavior of entropy change arising from the zero-temperature limit of an external bath, which is required to describe the cavity loss. We solve this difficulty from the viewpoint of absolute irreversibility and find that two types of absolute irreversibility contribute to the integral FT. Furthermore, we show that, in a stationary and small cavity-loss condition, these contributions have simple relationships to the average number of photons emitted out of the cavity, and the integral FT yields an approximate form independent of the setup details. We illustrate the general results with a numerical simulation in a model of quantum heat engine.

Statistical thermodynamics of small systems shows dramatic differences from normal systems. Parallel to the recently presented steady-state thermodynamic formalism for master equation and Fokker-Planck equation, we show that a “thermodynamic” theory can also be developed based on Tsallis' generalized entropy $S^{\left(q\right)}={\sum }_{i=1}^N(p_i-p_i^q)/\left[q(q-1)\right]$ and Shiino's generalized free energy $F^{\left(q\right)}=[{\sum }_{i=1}^N{p}_i{(p_i/{\pi }_i)}^{q-1}-1]/\left[q(q-1)\right]$, where ${\pi }_i$ is the stationary distribution. $d{F}^{\left(q\right)}/dt=-f_d^{\left(q\right)}\le 0$ and it is zero if and only if the system is in its stationary state. $d{S}^{\left(q\right)}/dt-Q_{\text{ex}}^{\left(q\right)}=f_d^{\left(q\right)}$, where $Q_{\text{ex}}^{\left(q\right)}$ characterizes the heat exchange. For systems approaching equilibrium with detailed balance, $f_d^{\left(q\right)}$ is the product of Onsager's thermodynamic flux and force. However, it is discovered that the Onsager's force is nonlocal. This is a consequence of the particular transformation invariance for zero energy of Tsallis' statistics.