Stationary states of activity-driven harmonic chains

We study the stationary state of a chain of harmonic oscillators driven by two active reservoirs at the two ends. These reservoirs exert correlated stochastic forces on the boundary oscillators which eventually leads to a nonequilibrium stationary state of the system. We consider three most well-known dynamics for the active force, namely, the active Ornstein-Uhlenbeck process, run-and-tumble process, and active Brownian process, all of which have exponentially decaying two-point temporal correlations but very different higher-order fluctuations. We show that, irrespective of the specific dynamics of the drive, the stationary velocity fluctuations are Gaussian in nature with a kinetic temperature which remains uniform in the bulk. Moreover, we find the emergence of an "equipartition of energy" in the bulk of the system-the bulk kinetic temperature equals the bulk potential temperature in the thermodynamic limit. We also calculate the stationary distribution of the instantaneous energy current in the bulk which always shows a logarithmic divergence near the origin and asymmetric exponential tails. The signatures of specific active driving become visible in the behavior of the oscillators near the boundary. This is most prominent for the RTP- and ABP-driven chains where the boundary velocity distributions become non-Gaussian and the current distribution has a finite cutoff.

Effect of Buffers with Multiple Binding Sites on Calcium Waves

The existence and properties of intracellular waves of increased free cytoplasmic calcium concentration (calcium waves) are strongly affected by the binding and unbinding of calcium ions to a multitude of different buffers in the cell. These buffers can be mobile or immobile and, in general, have multiple binding sites that are not independent. Previous theoretical studies have focused on the case when each buffer molecule binds a single calcium ion. In this study, we analyze how calcium waves are affected by calcium buffers with two non-independent binding sites, and show that the interactions between the calcium binding sites can result in the emergence of new behaviors. In particular, for certain combinations of kinetic parameters, the profiles of buffer molecules with one calcium ion bound can be non-monotone.

Energy diffusion in two-dimensional momentum-conserving nonlinear lattices: Lévy walk and renormalized phonon

The energy diffusion process in a few two-dimensional Fermi-Pasta-Ulam-type lattices is numerically simulated via the equilibrium local energy spatiotemporal correlation. Just as the nonlinear fluctuating hydrodynamic theory suggested, the diffusion propagator consists of a bell-shaped central heat mode and a sound mode extending with a constant speed. The profiles of the heat and sound modes satisfy the scaling properties from a random-walk-with-velocity-fluctuation process very well. An effective phonon approach is proposed, which expects the frequencies of renormalized phonons as well as the sound speed with quite good accuracy. Since many existing analytical and numerical studies indicate that heat conduction in such two-dimensional momentum-conserving lattices is divergent and the thermal conductivity κ increases logarithmically with lattice length, it is expected that the mean-square displacement of energy diffusion grows as tlnt. Discrepancies, however, are noticeably observed.

Universal Kardar-Parisi-Zhang transient diffusion in nonequilibrium anharmonic chains

The well known nonlinear fluctuating hydrodynamics theory has grouped diffusions in anharmonic chains into two universality classes: one is the Kardar-Parisi-Zhang (KPZ) class for chains with either asymmetric potential or nonzero static pressure and the other is the Gaussian class for chains with symmetric potential at zero static pressure, such as Fermi-Pasta-Ulam-Tsingou (FPUT)-β chains. However, little is known of the nonequilibrium transient diffusion in anharmonic chains. Here, we reveal that the KPZ class is the only universality class for nonequilibrium transient diffusion, manifested as the KPZ scaling of the side peaks of momentum correlation (corresponding to the sound modes correlation), which was completely unexpected in equilibrium FPUT-β chains. The underlying mechanism is that the nonequilibrium soliton dynamics cause nonzero transient pressure so that the sound modes satisfy approximately the noisy Burgers equation, in which the collisions of solitons was proved to yield the KPZ dynamic exponent of the soliton dispersion. Therefore, the unexpected KPZ universality class is obtained in the nonequilibrium transient diffusion in FPUT-β chains and the corresponding carriers of nonequilibrium transient diffusion are attributed to solitons.

Delocalization of interacting directed polymers on a periodic substrate: Localization length and critical exponents from non-Hermitian spectra

We study a classical model of thermally fluctuating polymers confined to two dimensions, experiencing a grooved periodic potential, and subject to pulling forces both along and transverse to the grooves. The equilibrium polymer conformations are described by a mapping to a quantum system with a non-Hermitian Hamiltonian and with fermionic statistics generated by noncrossing interactions among polymers. Using molecular dynamics simulations and analytical calculations, we identify a localized and a delocalized phase of the polymer conformations, separated by a delocalization transition which corresponds (in the quantum description) to the breakdown of a band insulator when driven by an imaginary vector potential. We calculate the average tilt of the many-body system, at arbitrary shear values and filling density of polymer chains, in terms of the complex-valued non-Hermitian band structure. We find the critical shear value, the localization length, and the critical exponent by which the shear modulus diverges in terms of the branch points (exceptional points) in the band structure at which the bandgap closes. We also investigate the combined effects of non-Hermitian delocalization and localization due to both periodicity and disorder, uncovering preliminary evidence that while disorder favors localization at high values, it encourages delocalization at lower values.

Revisited relativistic Dirac-Hartree-Fock X-ray scattering factors. I. Neutral atoms with Z = 2-118

In this first of a series of publications, the X-ray scattering factors for neutral atoms are revisited. Using the recently developed DBSR_HF program [Zatsarinny & Froese Fischer (2016). Comput. Phys. Comm. 202, 287-303] the fully relativistic Dirac-Hartree-Fock ground-state wavefunctions for all atoms with Z = 2-118 (He-Og) have been calculated using the extended average level scheme and including both the Breit interaction correction to the electronic motion due to magnetic and retardation effects, and the Fermi distribution function for the description of the nuclear charge density. The comparison of our wavefunctions with those obtained in several previous studies in terms of the total and orbital (spinor) electronic energies, and a number of local and integrated total and orbital properties, confirmed the quality of the generated wavefunctions. The employed dense radial grid combined with the DBSR_HF's B-spline representation of the relativistic one-electron orbitals allowed for a precise integration of the X-ray scattering factors using a newly developed Fortran program SF. Following the established procedure [Maslen et al. (2006). International Tables for Crystallography, Vol. C, Section 6.1.1, pp. 554-589], the resulting X-ray scattering factors have been interpolated in the 0 ≤ sin θ/λ ≤ 2 Å^-1 and 2 ≤ sin θ/λ ≤ 6 Å^-1 ranges using the recommended analytical functions with both the four- (which is a current convention) and five-term expansions. An exhaustive comparison of the newly generated X-ray scattering factors with the International Union of Crystallography recommended values and those from a number of previous studies showed an overall good agreement and allowed identification of a number of typos and inconsistencies in the recommended quantities. A detailed analysis of the results suggests that the newly derived values may represent an excellent compromise among all the previous studies. The determined conventional interpolating functions for the two sin θ/λ intervals show, on average, the same accuracy as the recommended parametrizations. However, an extension of each expansion by only a single term provides a significant improvement in the accuracy of the interpolated values for an overwhelming majority of the atoms. As such, an updated set of the fully relativistic X-ray scattering factors and the interpolating functions for neutral atoms with Z = 2-118 can be easily incorporated into the existing X-ray diffraction software with only minor modifications. The outcomes of the undertaken research should be of interest to members of the crystallographic community who push the boundaries of the accuracy and precision of X-ray diffraction studies.

The ensemble of gene regulatory networks at mutation-selection balance

The evolution of diverse phenotypes both involves and is constrained by molecular interaction networks. When these networks influence patterns of expression, we refer to them as gene regulatory networks (GRNs). Here, we develop a model of GRN evolution analogous to work from quasi-species theory, which is itself essentially the mutation-selection balance model from classical population genetics extended to multiple loci. With this GRN model, we prove that-across a broad spectrum of selection pressures-the dynamics converge to a stationary distribution over GRNs. Next, we show from first principles how the frequency of GRNs at equilibrium is related to the topology of the genotype network, in particular, via a specific network centrality measure termed the eigenvector centrality. Finally, we determine the structural characteristics of GRNs that are favoured in response to a range of selective environments and mutational constraints. Our work connects GRN evolution to quasi-species theory-and thus to classical populations genetics-providing a mechanistic explanation for the observed distribution of GRNs evolving in response to various evolutionary forces, and shows how complex fitness landscapes can emerge from simple evolutionary rules.

Stocks and cryptocurrencies: Antifragile or robust? A novel antifragility measure of the stock and cryptocurrency markets

In contrast with robust systems that resist noise or fragile systems that break with noise, antifragility is defined as a property of complex systems that benefit from noise or disorder. Here we define and test a simple measure of antifragility for complex dynamical systems. In this work we use our antifragility measure to analyze real data from return prices in the stock and cryptocurrency markets. Our definition of antifragility is the product of the return price and a perturbation. We explore different types of perturbations that typically arise from within the system. Our results suggest that for both the stock market and the cryptocurrency market, the tendency among the 'top performers' is to be robust rather than antifragile. It would be important to explore other possible definitions of antifragility to understand its role in financial markets and in complex dynamical systems in general.

Vizaj-A free online interactive software for visualizing spatial networks

In many fields of science and technology we are confronted with complex networks. Making sense of these networks often require the ability to visualize and explore their intermingled structure consisting of nodes and links. To facilitate the identification of significant connectivity patterns, many methods have been developed based on the rearrangement of the nodes so as to avoid link criss-cross. However, real networks are often embedded in a geometrical space and the nodes code for an intrinsic physical feature of the system that one might want to preserve. For these spatial networks, it is therefore crucial to find alternative strategies operating on the links and not on the nodes. Here, we introduce Vizaj a javascript web application to render spatial networks based on optimized geometrical criteria that reshape the link profiles. While optimized for 3D networks, Vizaj can also be used for 2D networks and offers the possibility to interactively customize the visualization via several controlling parameters, including network filtering and the effect of internode distance on the link trajectories. Vizaj is further equipped with additional options allowing to improve the final aesthetics, such as the color/size of both nodes and links, zooming/rotating/translating, and superimposing external objects. Vizaj is an open-source software which can be freely downloaded and updated via a github repository. Here, we provide a detailed description of its main features and algorithms together with a guide on how to use it. Finally, we validate its potential on several synthetic and real spatial networks from infrastructural to biological systems. We hope that Vizaj will help scientists and practitioners to make sense of complex networks and provide aesthetic while informative visualizations.

Contrasting pseudocriticality in the classical two-dimensional Heisenberg and RP^{2} models: Zero-temperature phase transition versus finite-temperature crossover

Tensor-network methods are used to perform a comparative study of the two-dimensional classical Heisenberg and RP^{2} models. We demonstrate that uniform matrix product states (MPSs) with explicit SO(3) symmetry can probe correlation lengths up to O(10^{3}) sites accurately, and we study the scaling of entanglement entropy and universal features of MPS entanglement spectra. For the Heisenberg model, we find no signs of a finite-temperature phase transition, supporting the scenario of asymptotic freedom. For the RP^{2} model we observe an abrupt onset of scaling behavior, consistent with hints of a finite-temperature phase transition reported in previous studies. A careful analysis of the softening of the correlation length divergence, the scaling of the entanglement entropy, and the MPS entanglement spectra shows that our results are inconsistent with true criticality, but are rather in agreement with the scenario of a crossover to a pseudocritical region which exhibits strong signatures of nematic quasi-long-range order at length scales below the true correlation length. Our results reveal a fundamental difference in scaling behavior between the Heisenberg and RP^{2} models: Whereas the emergence of scaling in the former shifts to zero temperature if the bond dimension is increased, it occurs at a finite bond-dimension independent crossover temperature in the latter.

Anomalous finite-size scaling in higher-order processes with absorbing states

Here we study standard and higher-order birth-death processes on fully connected networks, within the perspective of large-deviation theory [also referred to as the Wentzel-Kramers-Brillouin (WKB) method in some contexts]. We obtain a general expression for the leading and next-to-leading terms of the stationary probability distribution of the fraction of "active" sites as a function of parameters and network size N. We reproduce several results from the literature and, in particular, we derive all the moments of the stationary distribution for the q-susceptible-infected-susceptible (q-SIS) model, i.e., a high-order epidemic model requiring q active ("infected") sites to activate an additional one. We uncover a very rich scenario for the fluctuations of the fraction of active sites, with nontrivial finite-size-scaling properties. In particular, we show that the variance-to-mean ratio diverges at criticality for [1≤q≤3], with a maximal variability at q=2, confirming that complex-contagion processes can exhibit peculiar scaling features including wild variability. Moreover, the leading order in a large-deviation approach does not suffice to describe them: next-to-leading terms are essential to capture the intrinsic singularity at the origin of systems with absorbing states. Some possible extensions of this work are also discussed.

Coherent correlation imaging for resolving fluctuating states of matter

Fluctuations and stochastic transitions are ubiquitous in nanometre-scale systems, especially in the presence of disorder. However, their direct observation has so far been impeded by a seemingly fundamental, signal-limited compromise between spatial and temporal resolution. Here we develop coherent correlation imaging (CCI) to overcome this dilemma. Our method begins by classifying recorded camera frames in Fourier space. Contrast and spatial resolution emerge by averaging selectively over same-state frames. Temporal resolution down to the acquisition time of a single frame arises independently from an exceptionally low misclassification rate, which we achieve by combining a correlation-based similarity metric^1,2 with a modified, iterative hierarchical clustering algorithm^3,4. We apply CCI to study previously inaccessible magnetic fluctuations in a highly degenerate magnetic stripe domain state with nanometre-scale resolution. We uncover an intricate network of transitions between more than 30 discrete states. Our spatiotemporal data enable us to reconstruct the pinning energy landscape and to thereby explain the dynamics observed on a microscopic level. CCI massively expands the potential of emerging high-coherence X-ray sources and paves the way for addressing large fundamental questions such as the contribution of pinning^5-8 and topology^9-12 in phase transitions and the role of spin and charge order fluctuations in high-temperature superconductivity^13,14.

Quasi-One-Dimensional van der Waals Transition Metal Trichalcogenides

The transition metal trichalcogenides (TMTCs) are quasi-one-dimensional (1D) MX3-type van der Waals layered semiconductors, where M is a transition metal element of groups IV and V, and X indicates chalcogen element. Due to the unique quasi-1D crystalline structures, they possess several novel electrical properties such as variable bandgaps, charge density waves, and superconductivity, and highly anisotropic optical, thermoelectric, and magnetic properties. The study of TMTCs plays an essential role in the 1D quantum materials field, enabling new opportunities in the material research dimension. Currently, tremendous progress in both materials and solid-state devices has been made, demonstrating promising applications in the realization of nanoelectronic devices. This review provides a comprehensive overview to survey the state of the art in materials, devices, and applications based on TMTCs. Firstly, the symbolic structure, current primary synthesis methods, and physical properties of TMTCs have been discussed. Secondly, examples of TMTC applications in various fields are presented, such as photodetectors, energy storage devices, catalysts, and sensors. Finally, we give an overview of the opportunities and future perspectives for the research of TMTCs, as well as the challenges in both basic research and practical applications.

Coarsening, condensates, and extremes in aggregation-fragmentation models

We use extreme value statistics to study the dynamics of coarsening in aggregation-fragmentation models which form condensates in the steady state. The dynamics is dominated by the formation of local condensates on a coarsening length scale which grows in time in both the zero range process and conserved mass aggregation model. The local condensate mass distribution exhibits scaling, which implies anomalously large fluctuations, with mean and standard deviation both proportional to the coarsening length. Remarkably, the state of the system during coarsening is governed not by the steady state, but rather a preasymptotic state in which the condensate mass fluctuates strongly.

Influential nodes identification in complex networks: a comprehensive literature review

Researchers have paid a lot of attention to complex networks in recent decades. Due to their rapid evolution, they turn into a major scientific and innovative field. Several studies on complex networks are carried out, and other subjects are evolving every day such as the challenge of detecting influential nodes. In this study, we provide a brief overview of complex networks, as well as several concepts key related to measurements, the structure of complex network and social influence, an important state of the art on complex networks including basic metrics on complex networks, the evolution of their topology over the years as well as the dynamic of networks. A detailed literature about influential finding approaches is also provided to indicate their strength and shortcomings. We aim that our contribution of literature can be an interesting base of information for beginners' scientists in this field. At the end of this paper, some conclusions are drawn and some future perspectives are mentioned to be studied as new directions in the future. More detailed references are provided to go further and deep in this area.

A few-layer covalent network of fullerenes

The two natural allotropes of carbon, diamond and graphite, are extended networks of sp³-hybridized and sp²-hybridized atoms, respectively¹. By mixing different hybridizations and geometries of carbon, one could conceptually construct countless synthetic allotropes. Here we introduce graphullerene, a two-dimensional crystalline polymer of C₆₀ that bridges the gulf between molecular and extended carbon materials. Its constituent fullerene subunits arrange hexagonally in a covalently interconnected molecular sheet. We report charge-neutral, purely carbon-based macroscopic crystals that are large enough to be mechanically exfoliated to produce molecularly thin flakes with clean interfaces-a critical requirement for the creation of heterostructures and optoelectronic devices². The synthesis entails growing single crystals of layered polymeric (Mg₄C₆₀)_∞ by chemical vapour transport and subsequently removing the magnesium with dilute acid. We explore the thermal conductivity of this material and find it to be much higher than that of molecular C₆₀, which is a consequence of the in-plane covalent bonding. Furthermore, imaging few-layer graphullerene flakes using transmission electron microscopy and near-field nano-photoluminescence spectroscopy reveals the existence of moiré-like superlattices³. More broadly, the synthesis of extended carbon structures by polymerization of molecular precursors charts a clear path to the systematic design of materials for the construction of two-dimensional heterostructures with tunable optoelectronic properties.

Frustrated ferromagnetic transition in AB-stacked honeycomb bilayer

In two-dimensional (2D) ferromagnets, anisotropy is essential for the magnetic ordering as dictated by the Mermin-Wagner theorem. But when competing anisotropies are present, the phase transition becomes nontrivial. Here, utilizing highly sensitive susceptometry of scanning superconducting quantum interference device microscopy, we probe the spin correlations of ABC-stacked CrBr₃ under zero magnetic field. We identify a plateau feature in susceptibility above the critical temperature (T_C) in thick samples. It signifies a crossover regime induced by the competition between easy-plane intralayer exchange anisotropy versus uniaxial interlayer anisotropy. The evolution of the critical behavior from the bulk to 2D shows that the competition between the anisotropies is magnified in the reduced dimension. It leads to a strongly frustrated ferromagnetic transition in the bilayer with fluctuation on the order of T_C, which is distinct from both the monolayer and the bulk. Our observation demonstrates unconventional 2D critical behavior on a honeycomb lattice.

An Introduction to Relativistic Theory as Implemented in GRASP

Computational atomic physics continues to play a crucial role in both increasing the understanding of fundamental physics (e.g., quantum electrodynamics and correlation) and producing atomic data for interpreting observations from large-scale research facilities ranging from fusion reactors to high-power laser systems, space-based telescopes and isotope separators. A number of different computational methods, each with their own strengths and weaknesses, is available to meet these tasks. Here, we review the relativistic multiconfiguration method as it applies to the General Relativistic Atomic Structure Package [grasp2018, C. Froese Fischer, G. Gaigalas, P. Jönsson, J. Bieroń, Comput. Phys. Commun. (2018). DOI: 10.1016/j.cpc.2018.10.032]. To illustrate the capacity of the package, examples of calculations of relevance for nuclear physics and astrophysics are presented.

Discovery of two-dimensional binary nanoparticle superlattices using global Monte Carlo optimization

Binary nanoparticle (NP) superlattices exhibit distinct collective plasmonic, magnetic, optical, and electronic properties. Here, we computationally demonstrate how fluid-fluid interfaces could be used to self-assemble binary systems of NPs into 2D superlattices when the NP species exhibit different miscibility with the fluids forming the interface. We develop a basin-hopping Monte Carlo (BHMC) algorithm tailored for interface-trapped structures to rapidly determine the ground-state configuration of NPs, allowing us to explore the repertoire of binary NP architectures formed at the interface. By varying the NP size ratio, interparticle interaction strength, and difference in NP miscibility with the two fluids, we demonstrate the assembly of an array of exquisite 2D periodic architectures, including AB-, AB₂-, and AB₃-type monolayer superlattices as well as AB-, AB₂-, A₃B₅-, and A₄B₆-type bilayer superlattices. Our results suggest that the interfacial assembly approach could be a versatile platform for fabricating 2D colloidal superlattices with tunable structure and properties.

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.

Dissociation dynamics of a diatomic molecule in an optical cavity

We study the dissociation dynamics of a diatomic molecule, modeled as a Morse oscillator, coupled to an optical cavity. A marked suppression of the dissociation probability, both classical and quantum, is observed for cavity frequencies significantly below the fundamental transition frequency of the molecule. We show that the suppression in the probability is due to the nonlinearity of the dipole function. The effect can be rationalized entirely in terms of the structures in the classical phase space of the model system.

Universal scaling of extinction time in stochastic evolutionary dynamics

Evolutionary dynamics is well captured by the replicator equations when the population is infinite and well-mixed. However, the extinction dynamics is modified with finite and structured populations. Experiments on the non-transitive ecosystem containing three populations of bacteria found that the ecological stability sensitively depends on the spatial structure of the populations. Based on the Reference-Gamble-Birth algorithm, we use agent-based Monte Carlo simulations to investigate the extinction dynamics in the rock-paper-scissors ecosystem with finite and structured populations. On the fully-connected network, the extinction time in stable and unstable regimes falls into two universal functions when plotted with the rescaled variables. On the two dimensional grid, the spatial structure changes the transition boundary between stable and unstable regimes but doesn't change its extinction trend. The finding of universal scaling in extinction dynamics is unexpected, and may provide a powerful method to classify different evolutionary dynamics into universal classes.

Room-Temperature Semiconductor Gas Sensors: Challenges and Opportunities

Our demand for ubiquitous and reliable gas detection is spurring the design of intelligent and enabling gas sensors for the next-generation Internet of Things and Artificial Intelligence. The desire to introduce gas sensors everywhere is fueled by opportunities to create room-temperature semiconductor gas sensors with ultralow power consumption. In this Perspective, we provide an overview of the recent achievement of room-temperature gas sensors that have been translated from the advances in the design of the chemical and physical properties of low-dimensional semiconductor nanomaterials. The emergence of solution-processable nanomaterials opens up remarkable opportunities to integrate into high-performance and flexible room-temperature gas sensors by using low-temperature, large-area, solution-based methods instead of costly, high-vacuum, high-temperature device manufacturing processes. We review the fundamental factors which affect the receptor and transducer functions of semiconductor gas sensors. We also discuss challenges that must be addressed in the move to the continuous miniaturization and evolution of semiconductor gas sensors.

The Electronic Origin of the Zeta Potential is Supported by the Redox Mechanism on an Aqueous Dispersion of Exfoliated Graphite

Herein we have proposed that a redox mechanism can produce surface charges and negative zeta potential on an aqueous graphite dispersion. Graphite was kept in contact with a concentrated ammonia aqueous solution, washed, and exfoliated in water, resulting in a dispersion with lyophobic nature. Ammonia treatment did not provide functional groups or nitrogen doping to graphite. Moreover, this material was washed twice before sonication to remove most hydroxide. Therefore, neither functional groups, nitrogen atoms, nor hydroxide excess is responsible for the zeta potential. Kelvin probe force microscopy has shown that the ammonia-treated and exfoliated graphite has higher Fermi level than the water-treated material, indicating that the contact between ammonia and graphite promotes redox reactions that provide electrons to graphite. These electrons raise the Fermi level of graphite and generate the negative zeta potential, consequently, they account for the colloidal stability.

Sedimentation path theory for mass-polydisperse colloidal systems

Both polydispersity and the presence of a gravitational field are inherent to essentially any colloidal experiment. While several theoretical works have focused on the effect of polydispersity on the bulk phase behavior of a colloidal system, little is known about the effect of a gravitational field on a polydisperse colloidal suspension. We extend here the sedimentation path theory to study sedimentation-diffusion-equilibrium of a mass-polydisperse colloidal system: the particles possess different buoyant masses but they are otherwise identical. The model helps to understand the interplay between gravity and polydispersity on sedimentation experiments. Since the theory can be applied to any parent distribution of buoyant masses, it can also be used to study the sedimentation of monodisperse colloidal systems. We find that mass-polydispersity has a strong influence in colloidal systems near density matching for which the bare density of the colloidal particles equals the solvent density. To illustrate the theory, we study crystallization in sedimentation-diffusion-equilibrium of a suspension of mass-polydisperse hard spheres.

First-principles superadiabatic theory for the dynamics of inhomogeneous fluids

For classical many-body systems subject to Brownian dynamics, we develop a superadiabatic dynamical density functional theory (DDFT) for the description of inhomogeneous fluids out-of-equilibrium. By explicitly incorporating the dynamics of the inhomogeneous two-body correlation functions, we obtain superadiabatic forces directly from the microscopic interparticle interactions. We demonstrate the importance of these nonequilibrium forces for an accurate description of the one-body density by numerical implementation of our theory for three-dimensional hard-spheres in a time-dependent planar potential. The relaxation of the one-body density in superadiabatic-DDFT is found to be slower than that predicted by standard adiabatic DDFT and significantly improves the agreement with Brownian dynamics simulation data. We attribute this improved performance to the correct treatment of structural relaxation within the superadiabatic-DDFT. Our approach provides fundamental insight into the underlying structure of dynamical density functional theories and makes possible the study of situations for which standard approaches fail.

Hidden symmetry of the flavivirus protein shell and pH-controlled reconstruction of the viral surface

Using recent Zika virus structural data we reveal a hidden symmetry of protein order in immature and mature flavivirus shells, violating the Caspar-Klug paradigmatic model of capsid structures. We show that proteins of the outer immature shell layer exhibit trihexagonal tiling, while proteins from inner and outer layers conjointly form a double-shelled close-packed structure, based on a common triangular spherical lattice. Within the proposed structural model, we furthermore rationalize the structural organization of misassembled non-infectious subviral particles that have no inner capsid. We consider a pH-controlled structural reconstruction of the outer shell from the trimeric to the dimeric state, and demonstrate that this transition, occurring during the virus maturation, can be induced by changes in protein charges at lower pH, leading to a decrease in the electrostatic interaction free energy. This transition could also be assisted by electrostatic attraction of shell proteins to the interposed lipid membrane substrate separating the shells.

Chain Confinement and Anomalous Diffusion in the Cross over Regime between Rouse and Reptation

By neutron spin echo (NSE) and pulsed field gradient (PFG) NMR, we study the dynamics of a polyethylene-oxide melt (PEO) with a molecular weight in the transition regime between Rouse and reptation dynamics. We analyze the data with a Rouse mode analysis allowing for reduced long wavelength Rouse modes amplitudes. For short times, subdiffusive center-of-mass mean square displacement ⟨r_com²(t)⟩ was allowed. This approach captures the NSE data well and provides accurate information on the topological constraints in a chain length regime, where the tube model is inapplicable. As predicted by reptation for the polymer ⟨r_com²(t)⟩, we experimentally found the subdiffusive regime with an exponent close to μ=12, which, however, crosses over to Fickian diffusion not at the Rouse time, but at a later time, when the ⟨r_com²(t)⟩ has covered a distance related to the tube diameter.

DNA and the origins of life in micaceous clay

Reproducible imaging of DNA by atomic force microscopy was a useful predecessor to Ned Seeman's DNA nanotechnology. Many of the products of DNA nanotechnology were imaged in the atomic force microscope. The mica substrate used in this atomic force microscopy research formed the inspiration for the hypothesis that micaceous clay was a likely habitat for the origins of life. Montmorillonite clay has been a successful substrate for the polymerization of amino acids and nucleotides into peptides and DNA oligomers in research on life's origins. Mica and montmorillonite have the same anionic lattice, with a hexagonal spacing of 0.5 nm. Micas are nonswelling clays, with potassium ions (K+) holding the crystal sheets together, providing a stable environment for the processes and molecular complexes needed for the emergence of living cells. Montmorillonite crystal sheets are held together by smaller sodium ions (Na+), which results in swelling and shrinking during wet-dry cycles, providing a less stable environment. Also, the cells in all types of living systems have high intracellular K+ concentrations, which makes mica a more likely habitat for the origins of life than montmorillonite. Finally, moving mica sheets provides mechanical energy at the split edges of the sheets in mica "books." This mechanical energy of mica sheets, moving open and shut, in response to fluid flow, may have preceded chemical energy at life's origins, powering early prebiotic processes, such as the formation of covalent bonds, the interactions of molecular complexes, and the budding off of protocells before the molecular mechanism of cell division had developed.

Fundamental features of AlCl4 --/AlCl4-graphite intercalation compounds of aluminum-ion-based battery cathodes

Up to now, many guest atoms/molecules/ions have been successfully synthesized into graphite to form various compounds. For example, alkali-atom graphite intercalation compounds are verified to reveal stage-n structures, including LiC_6n and LiM_8n [M = K, Rb, and Cs; n = 1, 2, 3; 4]. On the other side, AlCl₄ ^--ion/AlCl₄-molecule compounds are found to show stage-4 and stage-3 structures at room and lower temperatures, respectively. Stage-1 and stage-2 configurations, with the higher intercalant concentrations, cannot be synthesized in experimental laboratories. This might arise from the fact that it is quite difficult to build periodical arrangements along the longitudinal z and transverse directions simultaneously for large ions or molecules. Our work is mainly focused on stage-1 and stage-2 systems in terms of geometric and electronic properties. The critical features, being associated with the atom-dominated energy spectra and wave functions within the specific energy ranges, the active multi-orbital hybridization in distinct chemical bonds, and atom- & orbital-decomposed van Hove singularities, will be thoroughly clarified by the delicate simulations and analyses.

Torsional periodic lattice distortions and diffraction of twisted 2D materials

Twisted 2D materials form complex moiré structures that spontaneously reduce symmetry through picoscale deformation within a mesoscale lattice. We show twisted 2D materials contain a torsional displacement field comprised of three transverse periodic lattice distortions (PLD). The torsional PLD amplitude provides a single order parameter that concisely describes the structural complexity of twisted bilayer moirés. Moreover, the structure and amplitude of a torsional periodic lattice distortion is quantifiable using rudimentary electron diffraction methods sensitive to reciprocal space. In twisted bilayer graphene, the torsional PLD begins to form at angles below 3.89° and the amplitude reaches 8 pm around the magic angle of 1. 1°. At extremely low twist angles (e.g. below 0.25°) the amplitude increases and additional PLD harmonics arise to expand Bernal stacked domains separated by well defined solitonic boundaries. The torsional distortion field in twisted bilayer graphene is analytically described and has an upper bound of 22.6 pm. Similar torsional distortions are observed in twisted WS₂, CrI₃, and WSe₂/MoSe₂.

Dynamical fractal and anomalous noise in a clean magnetic crystal

Fractals-objects with noninteger dimensions-occur in manifold settings and length scales in nature. In this work, we identify an emergent dynamical fractal in a disorder-free, stoichiometric, and three-dimensional magnetic crystal in thermodynamic equilibrium. The phenomenon is born from constraints on the dynamics of the magnetic monopole excitations in spin ice, which restrict them to move on the fractal. This observation explains the anomalous exponent found in magnetic noise experiments in the spin ice compound Dy₂Ti₂O₇, and it resolves a long-standing puzzle about its rapidly diverging relaxation time. The capacity of spin ice to exhibit such notable phenomena suggests that there will be further unexpected discoveries in the cooperative dynamics of even simple topological many-body systems.