The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries.

Restrictions of cross-border mobility are typically used to prevent an emerging disease from entering a country in order to slow down its spread. However, such interventions can come with a significant societal cost and should thus be based on careful analysis and quantitative understanding on their effects. To this end, we model the influence of cross-border mobility on the spread of COVID-19 during 2020 in the neighbouring Nordic countries of Denmark, Finland, Norway and Sweden. We investigate the immediate impact of cross-border travel on disease spread and employ counterfactual scenarios to explore the cumulative effects of introducing additional infected individuals into a population during the ongoing epidemic. Our results indicate that the effect of inter-country mobility on epidemic growth is non-negligible essentially when there is sizeable mobility from a high prevalence country or countries to a low prevalence one. Our findings underscore the critical importance of accurate data and models on both epidemic progression and travel patterns in informing decisions related to inter-country mobility restrictions.

Non-Stokesian dynamics of magnetic helical nanoswimmers under confinement.

Electromagnetically propelled helical nanoswimmers offer great potential for nanorobotic applications. Here, the effect of confinement on their propulsion is characterized using lattice-Boltzmann simulations. Two principal mechanisms give rise to their forward motion under confinement: (i) pure swimming and (ii) the thrust created by the differential pressure due to confinement. Under strong confinement, they face greater rotational drag but display a faster propulsion for fixed driving frequency in agreement with experimental findings. This is due to the increased differential pressure created by the boundary walls when they are sufficiently close to each other and the particle. We have proposed two analytical relations (i) for predicting the swimming speed of an unconfined particle as a function of its angular speed and geometrical properties, and (ii) an empirical expression to accurately predict the propulsion speed of a confined swimmer as a function of the degree of confinement and its unconfined swimming speed. At low driving frequencies and degrees of confinement, the systems retain the expected linear behavior consistent with the predictions of the Stokes equation. However, as the driving frequency and/or the degree of confinement increase, their impact on propulsion leads to increasing deviations from the Stokesian regime and emergence of nonlinear behavior.

Nonmonotonic electrophoretic mobility of rodlike polyelectrolytes by multivalent coions in added salt.

It is well established that when multivalent counterions or salts are added to a solution of highly charged polyelectrolytes (PEs), correlation effects can cause charge inversion of the PE, leading to electrophoretic mobility (EM) reversal. In this work, we use coarse-grained molecular-dynamics simulations to unravel the less understood effect of coion valency on EM reversal for rigid DNA-like PEs. We find that EM reversal induced by multivalent counterions is suppressed with increasing coion valency in the salt added and eventually vanishes. Further, we find that EM is enhanced at fixed low salt concentrations for salts with monovalent counterions when multivalent coions with increasing valency are introduced. However, increasing the salt concentration causes a crossover that leads to EM reversal which is enhanced by increasing coion valency at high salt concentration. Remarkably, this multivalent coion-induced EM reversal persists even for low values of PE linear charge densities where multivalent counterions alone cannot induce EM reversal. These results facilitate tuning PE-PE interactions and self-assembly with both coion and counterion valencies.

Interactions between Rigid Polyelectrolytes Mediated by Ordering and Orientation of Multivalent Nonspherical Ions in Salt Solutions.

Multivalent ions in solutions with polyelectrolytes (PEs) induce electrostatic correlations that can drastically change ion distributions around the PEs and their mutual interactions. Using coarse-grained molecular dynamics simulations, we show how in addition to valency, ion shape and concentration can be harnessed as tools to control rigid like-charged PE-PE interactions. We demonstrate a correlation between the orientational ordering of aspherical ions and how they mediate the effective PE-PE attraction induced by multivalency. The interaction type, strength, and range can thus be externally controlled in ionic solutions. Our results can be used as generic guidelines to tune the self-assembly of like-charged polyelectrolytes by variation of the characteristics of the ions.

Theoretical and computational analysis of the electrophoretic polymer mobility inversion induced by charge correlations.

Electrophoretic (EP) mobility reversal is commonly observed for strongly charged macromolecules in multivalent salt solutions. This curious effect takes place, e.g., when a charged polymer, such as DNA, adsorbs excess counterions so that the counterion-dressed surface charge reverses its sign, leading to the inversion of the polymer drift driven by an external electric field. In order to characterize this seemingly counterintuitive phenomenon that cannot be captured by electrostatic mean-field theories, we adapt here a previously developed strong-coupling-dressed Poisson-Boltzmann approach to the cylindrical geometry of the polyelectrolyte-salt system. Within the framework of this formalism, we derive an analytical polymer mobility formula dressed by charge correlations. In qualitative agreement with polymer transport experiments, this mobility formula predicts that the increment of the monovalent salt, the decrease of the multivalent counterion valency, and the increase of the dielectric permittivity of the background solvent suppress charge correlations and increase the multivalent bulk counterion concentration required for EP mobility reversal. These results are corroborated by coarse-grained molecular dynamics simulations showing how multivalent counterions induce mobility inversion at dilute concentrations and suppress the inversion effect at large concentrations. This re-entrant behavior, previously observed in the aggregation of like-charged polymer solutions, calls for verification by polymer transport experiments.

Temperature-resilient anapole modes associated with TE polarization in semiconductor nanowires.

Polarization-dependent scattering anisotropy of cylindrical nanowires has numerous potential applications in, for example, nanoantennas, photothermal therapy, thermophotovoltaics, catalysis, sensing, optical filters and switches. In all these applications, temperature-dependent material properties play an important role and often adversely impact performance depending on the dominance of either radiative or dissipative damping. Here, we employ numerical modeling based on Mie scattering theory to investigate and compare the temperature and polarization-dependent optical anisotropy of metallic (gold, Au) nanowires with indirect (silicon, Si) and direct (gallium arsenide, GaAs) bandgap semiconducting nanowires. Results indicate that plasmonic scattering resonances in semiconductors, within the absorption band, deteriorate with an increase in temperature whereas those occurring away from the absorption band strengthen as a result of the increase in phononic contribution. Indirect-bandgap thin ([Formula: see text]) Si nanowires present low absorption efficiencies for both the transverse electric (TE, [Formula: see text]) and magnetic (TM, [Formula: see text]) modes, and high scattering efficiencies for the TM mode at shorter wavelengths making them suitable as highly efficient scatterers. Temperature-resilient higher-order anapole modes with their characteristic high absorption and low scattering efficiencies are also observed in the semiconductor nanowires ([Formula: see text] nm) for the TE polarization. Herein, the GaAs nanowires present [Formula: see text] times greater absorption efficiencies compared to the Si nanowires making them especially suitable for temperature-resilient applications such as scanning near-field optical microscopy (SNOM), localized heating, non-invasive sensing or detection that require strong localization of energy in the near field.

Correction to "Structure and Pore Size Distribution in Nanoporous Carbon".

[This corrects the article DOI: 10.1021/acs.chemmater.1c03279.].

GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations.

We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in Fan et al. [Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package gpumd. We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach. We also detail our efficient implementation of the NEP approach in graphics processing units as well as our workflow for the construction of NEP models and demonstrate their application in large-scale atomistic simulations. By comparing to state-of-the-art MLPs, we show that the NEP approach not only achieves above-average accuracy but also is far more computationally efficient. These results demonstrate that the gpumd package is a promising tool for solving challenging problems requiring highly accurate, large-scale atomistic simulations. To enable the construction of MLPs using a minimal training set, we propose an active-learning scheme based on the latent space of a pre-trained NEP model. Finally, we introduce three separate Python packages, viz., gpyumd, calorine, and pynep, that enable the integration of gpumd into Python workflows.

Helical flow states in active nematics.

We show that confining extensile nematics in three-dimensional (3D) channels leads to the emergence of two self-organized flow states with nonzero helicity. The first is a pair of braided antiparallel streams-this double helix occurs when the activity is moderate, anchoring negligible, and reduced temperature high. The second consists of axially aligned counter-rotating vortices-this grinder train arises between spontaneous axial streaming and the vortex lattice. These two unanticipated helical flow states illustrate the potential of active fluids to break symmetries and form complex but organized spatiotemporal structures in 3D fluidic devices.

Interaction between two polyelectrolytes in monovalent aqueous salt solutions.

We use the recently developed soft-potential-enhanced Poisson-Boltzmann (SPB) theory to study the interaction between two parallel polyelectrolytes (PEs) in monovalent ionic solutions in the weak-coupling regime. The SPB theory is fitted to ion distributions from coarse-grained molecular dynamics (MD) simulations and benchmarked against all-atom MD modelling for poly(diallyldimethylammonium) (PDADMA). We show that the SPB theory is able to accurately capture the interactions between two PEs at distances beyond the PE radius. For PDADMA positional correlations between the charged groups lead to locally asymmetric PE charge and ion distributions. This gives rise to small deviations from the SPB prediction that appear as short-range oscillations in the potential of mean force. Our results suggest that the SPB theory can be an efficient way to model interactions in chemically specific complex PE systems.

Modified Poisson-Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions.

We present a soft-potential-enhanced Poisson-Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based model for polyelectrolytes (PEs) in monovalent salt solutions as well as compared to a full atomistic molecular dynamics simulation with the explicit solvent. We demonstrate that our modification enables the SPB theory to accurately predict monovalent ion distributions around a rodlike PE in a wide range of ion and charge distribution conditions in the weak-coupling regime. These include excess salt concentrations up to 1M and ion sizes ranging from small ions, such as Na+ or Cl-, to softer and larger ions with a size comparable to the PE diameter. The work provides a simple way to implement an enhancement that effectively captures the influence of ion size and species into the PB theory in the context of PEs in aqueous salt solutions.

Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups.

We evaluate the efficiency of various heuristic strategies for allocating vaccines against COVID-19 and compare them to strategies found using optimal control theory. Our approach is based on a mathematical model which tracks the spread of disease among different age groups and across different geographical regions, and we introduce a method to combine age-specific contact data to geographical movement data. As a case study, we model the epidemic in the population of mainland Finland utilizing mobility data from a major telecom operator. Our approach allows to determine which geographical regions and age groups should be targeted first in order to minimize the number of deaths. In the scenarios that we test, we find that distributing vaccines demographically and in an age-descending order is not optimal for minimizing deaths and the burden of disease. Instead, more lives could be saved by using strategies which emphasize high-incidence regions and distribute vaccines in parallel to multiple age groups. The level of emphasis that high-incidence regions should be given depends on the overall transmission rate in the population. This observation highlights the importance of updating the vaccination strategy when the effective reproduction number changes due to the general contact patterns changing and new virus variants entering.

Multicore Assemblies from Three-Component Linear Homo-Copolymer Systems: A Coarse-Grained Modeling Study.

Multicore polymer micelles and aggregates are assemblies that contain several cores. The dual-length-scale compartmentalized solvophobic-solvophilic molecular environment makes them useful for, e.g., advanced drug delivery, high-precision synthesis platforms, confined catalysis, and sensor device applications. However, designing and regulating polymer systems that self-assemble to such morphologies remains a challenge. Using dissipative particle dynamics (DPD) simulations, we demonstrate how simple, three-component linear polymer systems consisting of free solvophilic and solvophobic homopolymers, and di-block copolymers, can self-assemble in solution to form well-defined multicore assemblies. We examine the polymer property range over which multicore assemblies can be expected and how the assemblies can be tuned both in terms of their morphology and structure. For a fixed degree of polymerization, a certain level of hydrophobicity is required for the solvophobic component to lead to formation of multicore assemblies. Additionally, the transition from single-core to multicore requires a relatively high solvophobicity difference between the solvophilic and solvophobic polymer components. Furthermore, if the solvophilic polymer is replaced by a solvophobic species, well-defined multicore-multicompartment aggregates can be obtained. The findings provide guidelines for multicore assemblies' formation from simple three-component systems and how to control polymer particle morphology and structure.

Self-assembly of binary solutions to complex structures.

Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionalities rise from their internal structure and molecular arrangement. The key microscopic features that control such assemblies remain poorly understood, nevertheless. Using classical density functional theory, we demonstrate how the intrinsic length scales and their interplay in terms of interspecies molecular interactions can be used to tune soft matter self-assembly. We apply our strategy to two different soft binary mixtures to create guidelines for tuning intermolecular interactions that lead to transitions from a fully miscible, liquid-like uniform state to formation of simple and core-shell aggregates and mixed aggregate structures. Furthermore, we demonstrate how the interspecies interactions and system composition can be used to control concentration gradients of component species within these assemblies. The insight generated by this work contributes toward understanding and controlling soft multi-component self-assembly systems. Additionally, our results aid in understanding complex biological assemblies and their function and provide tools to engineer molecular interactions in order to control polymeric and protein-based materials, pharmaceutical formulations, and nanoparticle assemblies.

Anomalous thermal conductivity enhancement in low dimensional resonant nanostructures due to imperfections.

Nanophononic metamaterials have broad applications in fields such as heat management, thermoelectric energy conversion, and nanoelectronics. Phonon resonance in pillared low-dimensional structures has been suggested to be a feasible approach to reduce thermal conductivity (TC). In this work, we study the effects of imperfections in pillared nanostructures based on graphene nanoribbons (GNR), using classical molecular dynamics simulations and harmonic lattice dynamics. The TC of perfect pillared GNR is only about 13% of that of pristine GNR due to the strong phonon resonant hybridization in pillared GNR. However, introducing imperfections such as vacancy defects and mass mismatch between the pillars and the base material, and alloy disorder in the pillars, can weaken the resonant hybridization and abnormally increase the TC. We show that both vacancy defects and mass mismatch can reduce the penetration of the resonant modes from the pillars into the base material, while the alloy disorder in the pillars can scatter the phonons inside them, which turns regular resonance into a random one with weaker hybridization. Our work provides useful insight into the phonon resonance mechanisms in experimentally relevant low dimensional nanostructures containing various imperfections.

Pulling a folded polymer through a nanopore.

We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation theory for end-pulled polymer translocation to include the case of two segments of the folded polymer traversing simultaneously trough the pore. Our theory is extensively benchmarked with corresponding molecular dynamics (MD) simulations. The translocation process for a folded polymer can be divided into two main stages. In the first stage, both branches are traversing the pore and their dynamics is coupled. If the branches are not of equal length, there is a second stage where translocation of the shorter branch has been completed. Using the assumption of equal monomer flux of both branches confirmed by MD simulations, we analytically derive the equations of motion for both branches and characterize the translocation dynamics in detail from the average waiting time and its scaling form.

Kinetic roughening of the urban skyline.

We analyze the morphology of the modern urban skyline in terms of its roughness properties. This is facilitated by a database of 10^{7} building heights in cities throughout the Netherlands which allows us to compute the asymptotic height difference correlation function in each city. We find that in cities for which the height correlations display power-law scaling as a function of distance between the buildings, the corresponding roughness exponents are commensurate to the Edwards-Wilkinson and Kardar-Parisi-Zhang equations for kinetic roughening. Based on analogy to discrete deposition models, we argue that these two limiting classes emerge because of possible height restriction rules for buildings in some cities.

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics.

We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that in the realistic case of a single-stranded DNA molecule, dilute salt conditions characterized by weak charge screening, and a negatively charged membrane, the translocation dynamics is unexpectedly accelerated despite the presence of large repulsive electrostatic interactions between the polymer coil on the cis side and the charged membrane. This is due to the rapid release of the electrostatic potential energy of the coil during translocation, leading to an effectively attractive force that assists end-driven translocation. The speedup results in non-monotonic polymer length and membrane charge dependence of the exponent α characterizing the translocation time [Formula: see text] of the polymer with length N 0. In the regime of long polymers N 0 ≳ 500, the translocation exponent exceeds its upper limit α = 2 previously observed for the same system without electrostatic interactions.

A minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport properties.

Silicon is an important material and many empirical interatomic potentials have been developed for atomistic simulations of it. Among them, the Tersoff potential and its variants are the most popular ones. However, all the existing Tersoff-like potentials fail to reproduce the experimentally measured thermal conductivity of diamond silicon. Here we propose a modified Tersoff potential and develop an efficient open source code called GPUGA (graphics processing units genetic algorithm) based on the genetic algorithm and use it to fit the potential parameters against energy, virial and force data from quantum density functional theory calculations. This potential, which is implemented in the efficient open source GPUMD (graphics processing units molecular dynamics) code, gives significantly improved descriptions of the thermal conductivity and phonon dispersion of diamond silicon as compared to previous Tersoff potentials and at the same time well reproduces the elastic constants. Furthermore, we find that quantum effects on the thermal conductivity of diamond silicon at room temperature are non-negligible but small: using classical statistics underestimates the thermal conductivity by about 10% as compared to using quantum statistics.

Influence of thermostatting on nonequilibrium molecular dynamics simulations of heat conduction in solids.

Nonequilibrium molecular dynamics (NEMD) has been extensively used to study thermal transport at various length scales in many materials. In this method, two local thermostats at different temperatures are used to generate a nonequilibrium steady state with a constant heat flux. Conventionally, the thermal conductivity of a finite system is calculated as the ratio between the heat flux and the temperature gradient extracted from the linear part of the temperature profile away from the local thermostats. Here, we show that, with a proper choice of the thermostat, the nonlinear part of the temperature profile should actually not be excluded in thermal transport calculations. We compare NEMD results against those from the atomistic Green's function method in the ballistic regime and those from the homogeneous nonequilibrium molecular dynamics method in the ballistic-to-diffusive regime. These comparisons suggest that in all the transport regimes, one should directly calculate the thermal conductance from the temperature difference between the heat source and sink and, if needed, convert it into the thermal conductivity by multiplying it with the system length. Furthermore, we find that the Langevin thermostat outperforms the Nosé-Hoover (chain) thermostat in NEMD simulations because of its stochastic and local nature. We show that this is particularly important for studying asymmetric carbon-based nanostructures, for which the Nosé-Hoover thermostat can produce artifacts leading to unphysical thermal rectification.