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  • 1. Agasthya, Lokahith
    et al.
    Picardo, Jason R.
    Sivaramakrishnan, Ravichandran
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Govindarajan, Rama
    Ray, Samriddhi Sankar
    Understanding droplet collisions through a model flow: Insights from a Burgers vortex2019In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 99, no 6, article id 063107Article in journal (Refereed)
    Abstract [en]

    We investigate the role of intense vortical structures, similar to those in a turbulent flow, in enhancing collisions (and coalescences) which lead to the formation of large aggregates in particle-laden flows. By using a Burgers vortex model, we show, in particular, that vortex stretching significantly enhances sharp inhomogeneities in spatial particle densities, related to the rapid ejection of particles from intense vortices. Furthermore our work shows how such spatial clustering leads to an enhancement of collision rates and extreme statistics of collisional velocities. We also study the role of polydisperse suspensions in this enhancement. Our work uncovers an important principle, which, if valid for realistic turbulent flows, may be a factor in how small nuclei water droplets in warm clouds can aggregate to sizes large enough to trigger rain.

  • 2.
    Agosta, Lorenzo
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Metere, Alfredo
    Dzugutov, Mikhail
    Hexatic smectic phase with algebraically decaying bond-orientational order2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 5, article id 052702Article in journal (Refereed)
    Abstract [en]

    The hexatic phase predicted by the theories of two-dimensional melting is characterized by the power-law decay of the orientational correlations, whereas the in-layer bond orientational order in all the hexatic smectic phases observed so far was found to be long range. We report a hexatic smectic phase where the in-layer bond orientational correlations decay algebraically, in quantitative agreement with the hexatic ordering predicted by the theory for two dimensions. The phase was formed in a molecular dynamics simulation of a one-component system of particles interacting via a spherically symmetric potential. The present results thus demonstrate that the theoretically predicted two-dimensional hexatic order can exist in a three-dimensional system.

  • 3. Argun, Aykut
    et al.
    Soni, Jalpa
    Dabelow, Lennart
    Bo, Stefano
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Pesce, Giuseppe
    Eichhorn, Ralf
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Volpe, Giovanni
    Experimental realization of a minimal microscopic heat engine2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 5, article id 052106Article in journal (Refereed)
    Abstract [en]

    Microscopic heat engines are microscale systems that convert energy flows between heat reservoirs into work or systematic motion. We have experimentally realized a minimal microscopic heat engine. It consists of a colloidal Brownian particle optically trapped in an elliptical potential well and simultaneously coupled to two heat baths at different temperatures acting along perpendicular directions. For a generic arrangement of the principal directions of the baths and the potential, the symmetry of the system is broken, such that the heat flow drives a systematic gyrating motion of the particle around the potential minimum. Using the experimentally measured trajectories, we quantify the gyrating motion of the particle, the resulting torque that it exerts on the potential, and the associated heat flow between the heat baths. We find excellent agreement between the experimental results and the theoretical predictions.

  • 4. Aurell, Erik
    et al.
    Bo, Stefano
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Steady diffusion in a drift field: A comparison of large-deviation techniques and multiple-scale analysis2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 3, article id 032140Article in journal (Refereed)
    Abstract [en]

    A particle with internal unobserved states diffusing in a force field will generally display effective advection-diffusion. The drift velocity is proportional to the mobility averaged over the internal states, or effective mobility, while the effective diffusion has two terms. One is of the equilibrium type and satisfies an Einstein relation with the effective mobility while the other is quadratic in the applied force. In this contribution we present two new methods to obtain these results, on the one hand using large deviation techniques and on the other by a multiple-scale analysis, and compare the two. We consider both systems with discrete internal states and continuous internal states. We show that the auxiliary equations in the multiple-scale analysis can also be derived in second-order perturbation theory in a large deviation theory of a generating function (discrete internal states) or generating functional (continuous internal states). We discuss that measuring the two components of the effective diffusion give a way to determine kinetic rates from only first and second moments of the displacement in steady state.

  • 5. Barfuss, Wolfram
    et al.
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Kurths, Jürgen
    Deterministic limit of temporal difference reinforcement learning for stochastic games2019In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 99, no 4, article id 043305Article in journal (Refereed)
    Abstract [en]

    Reinforcement learning in multiagent systems has been studied in the fields of economic game theory, artificial intelligence, and statistical physics by developing an analytical understanding of the learning dynamics (often in relation to the replicator dynamics of evolutionary game theory). However, the majority of these analytical studies focuses on repeated normal form games, which only have a single environmental state. Environmental dynamics, i.e., changes in the state of an environment affecting the agents' payoffs has received less attention, lacking a universal method to obtain deterministic equations from established multistate reinforcement learning algorithms. In this work we present a methodological extension, separating the interaction from the adaptation timescale, to derive the deterministic limit of a general class of reinforcement learning algorithms, called temporal difference learning. This form of learning is equipped to function in more realistic multistate environments by using the estimated value of future environmental states to adapt the agent's behavior. We demonstrate the potential of our method with the three well-established learning algorithms Q learning, SARSA learning, and actor-critic learning. Illustrations of their dynamics on two multiagent, multistate environments reveal a wide range of different dynamical regimes, such as convergence to fixed points, limit cycles, and even deterministic chaos.

  • 6.
    Bhatnagar, Akshay
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Indian Institute of Science, India.
    Gupta, Anupam
    Mitra, Dhrubaditya
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Pandit, Rahul
    Heavy inertial particles in turbulent flows gain energy slowly but lose it rapidly2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 3, article id 033102Article in journal (Refereed)
    Abstract [en]

    We present an extensive numerical study of the time irreversibility of the dynamics of heavy inertial particles in three-dimensional, statistically homogeneous, and isotropic turbulent flows. We show that the probability density function (PDF) of the increment, W(tau), of a particle's energy over a time scale tau is non-Gaussian, and skewed toward negative values. This implies that, on average, particles gain energy over a period of time that is longer than the duration over which they lose energy. We call this slow gain and fast loss. We find that the third moment of W(tau) scales as tau(3) for small values of tau. We show that the PDF of power-input p is negatively skewed too; we use this skewness Ir as a measure of the time irreversibility and we demonstrate that it increases sharply with the Stokes number St for small St; this increase slows down at St similar or equal to 1. Furthermore, we obtain the PDFs of t(+) and t(-), the times over which p has, respectively, positive or negative signs, i.e., the particle gains or loses energy. We obtain from these PDFs a direct and natural quantification of the slow gain and fast loss of the energy of the particles, because these PDFs possess exponential tails from which we infer the characteristic loss and gain times t(loss) and t(gain), respectively, and we obtain t(loss) < t(gain) for all the cases we have considered. Finally, we show that the fast loss of energy occurs with greater probability in the strain-dominated region than in the vortical one; in contrast, the slow gain in the energy of the particles is equally likely in vortical or strain-dominated regions of the flow.

  • 7.
    Bhatnagar, Akshay
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Indian Institute of Science, India.
    Gupta, Anupam
    Mitra, Dhrubaditya
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Perlekar, Prasad
    Wilkinson, Michael
    Pandit, Rahul
    Deviation-angle and trajectory statistics for inertial particles in turbulence2016In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 94, no 6, article id 063112Article in journal (Refereed)
    Abstract [en]

    Small particles in suspension in a turbulent fluid have trajectories that do not follow the pathlines of the flow exactly. We investigate the statistics of the angle of deviation phi between the particle and fluid velocities. We show that, when the effects of particle inertia are small, the probability distribution function (PDF) P-phi of this deviation angle shows a power-law region in which P-phi similar to phi(-4). We also find that the PDFs of the trajectory curvature. and modulus theta of the torsion theta have power-law tails that scale, respectively, as P-kappa similar to kappa (-5/2), as kappa -> infinity, and P-phi similar to phi(-3), as theta -> infinity: These exponents are in agreement with those previously observed for fluid pathlines. We propose a way to measure the complexity of heavy-particle trajectories by the number N-I(t, St) of points (up until time t) at which the torsion changes sign. We present numerical evidence that n(I)(St) lim(t ->infinity) N-I(t, St)/t similar to St(-Delta) for large St, with Lambda similar or equal to 0.5.

  • 8.
    Bhatnagar, Akshay
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Gustavsson, K.
    Mehlig, B.
    Mitra, Dhrubaditya
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Relative velocities in bidisperse turbulent aerosols: Simulations and theory2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 6, article id 063107Article in journal (Refereed)
    Abstract [en]

    We perform direct numerical simulations of a bidisperse suspension of heavy spherical particles in forced, homogeneous, and isotropic three-dimensional turbulence. We compute the joint distribution of relative particle distances and longitudinal relative velocities between particles of different inertia. For a pair of particles with small difference in their inertias we compare our results with recent theoretical predictions [Meibohm et al., Phys. Rev. E 96, 061102 (2017)] for the shape of this distribution. We also compute the moments of relative velocities as a function of particle separation and compare with the theoretical predictions. We observe good agreement. For a pair of particles that are very different from each other-one is heavy and the other one has negligible inertia-we give a theory to calculate their root-mean-square relative velocity. This theory also agrees well with the results of our simulations.

  • 9.
    Bhatnagar, Akshay
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Gustavsson, K.
    Mitra, Dhrubaditya
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Statistics of the relative velocity of particles in turbulent flows: Monodisperse particles2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 2, article id 023105Article in journal (Refereed)
    Abstract [en]

    We use direct numerical simulations to calculate the joint probability density function of the relative distance R and relative radial velocity component V-R for a pair of heavy inertial particles suspended in homogeneous and isotropic turbulent flows. At small scales the distribution is scale invariant, with a scaling exponent that is related to the particle-particle correlation dimension in phase space, D-2. It was argued [K. Gustavsson and B. Mehlig, Phys. Rev. E 84, 045304 (2011); J. Turbul. 15, 34 (2014)] that the scale invariant part of the distribution has two asymptotic regimes: (1) vertical bar V-R vertical bar << R, where the distribution depends solely on R, and (2) vertical bar V-R vertical bar >> R, where the distribution is a function of vertical bar V-R vertical bar alone. The probability distributions in these two regimes are matched along a straight line: vertical bar V-R vertical bar = z*R. Our simulations confirm that this is indeed correct. We further obtain D-2 and z* as a function of the Stokes number, St. The former depends nonmonotonically on St with aminimum at about St approximate to 0.7 and the latter has only a weak dependence on St.

  • 10.
    Bo, Stefano
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Schmidt, Falko
    Eichhorn, Ralf
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Volpe, Giovanni
    Measurement of anomalous diffusion using recurrent neural networks2019In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 100, no 1, article id 010102Article in journal (Refereed)
    Abstract [en]

    Anomalous diffusion occurs in many physical and biological phenomena, when the growth of the mean squared displacement (MSD) with time has an exponent different from one. We show that recurrent neural networks (RNNs) can efficiently characterize anomalous diffusion by determining the exponent from a single short trajectory, outperforming the standard estimation based on the MSD when the available data points are limited, as is often the case in experiments. Furthermore, the RNNs can handle more complex tasks where there are no standard approaches, such as determining the anomalous diffusion exponent from a trajectory sampled at irregular times, and estimating the switching time and anomalous diffusion exponents of an intermittent system that switches between different kinds of anomalous diffusion. We validate our method on experimental data obtained from subdiffusive colloids trapped in speckle light fields and superdiffusive microswimmers.

  • 11. Elperin, T.
    et al.
    Kleeorin, N.
    Liberman, Michael
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Lipatnikov, A. N.
    Rogachevskii, I.
    Yu, R.
    Turbulent diffusion of chemically reacting flows: Theory and numerical simulations2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 5, article id 053111Article in journal (Refereed)
    Abstract [en]

    The theory of turbulent diffusion of chemically reacting gaseous admixtures developed previously [T. Elperin et al., Phys. Rev. E 90, 053001 (2014)] is generalized for large yet finite Reynolds numbers and the dependence of turbulent diffusion coefficient on two parameters, the Reynolds number and Damkohler number (which characterizes a ratio of turbulent and reaction time scales), is obtained. Three-dimensional direct numerical simulations (DNSs) of a finite-thickness reaction wave for the first-order chemical reactions propagating in forced, homogeneous, isotropic, and incompressible turbulence are performed to validate the theoretically predicted effect of chemical reactions on turbulent diffusion. It is shown that the obtained DNS results are in good agreement with the developed theory.

  • 12. Hertz, John
    et al.
    Tyrcha, Joanna
    Stockholm University, Faculty of Science, Department of Mathematics.
    Correales, Alvaro
    Stochastic activation in a genetic switch model2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 5, article id 052403Article in journal (Refereed)
    Abstract [en]

    We study a biological autoregulation process, involving a protein that enhances its own transcription, in a parameter region where bistability would be present in the absence of fluctuations. We calculate the rate of fluctuation-induced rare transitions between locally stable states using a path integral formulation and Master and Chapman-Kolmogorov equations. As in simpler models for rare transitions, the rate has the form of the exponential of a quantity S-0 (a barrier) multiplied by a prefactor eta. We calculate S-0 and eta first in the bursting limit (where the ratio gamma of the protein and mRNA lifetimes is very large). In this limit, the calculation can be done almost entirely analytically, and the results are in good agreement with simulations. For finite gamma numerical calculations are generally required. However, S-0 can be calculated analytically to first order in 1/gamma, and the result agrees well with the full numerical calculation for all gamma > 1. Employing a method used previously on other problems, we find we can account qualitatively for the way the prefactor eta varies with gamma, but its value is 15-20% higher than that inferred from simulations.

  • 13. Honkonen, J.
    et al.
    Lučivjanský, T.
    Škultéty, Viktor
    Stockholm University, Faculty of Science, Department of Physics.
    Influence of turbulent mixing on critical behavior of directed percolation process: Effect of compressibility2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 2, article id 022123Article in journal (Refereed)
    Abstract [en]

    Universal behavior is a typical emergent feature of critical systems. A paramount model of the nonequilibrium critical behavior is the directed bond percolation process that exhibits an active-to-absorbing state phase transition in the vicinity of a percolation threshold. Fluctuations of the ambient environment might affect or destroy the universality properties completely. In this work, we assume that the random environment can be described by means of compressible velocity fluctuations. Using field-theoretic models and renormalization group methods, we investigate large-scale and long-time behavior. Altogether, 11 universality classes are found, out of which 4 are stable in the infrared limit and thus macroscopically accessible. In contrast to the model without velocity fluctuations, a possible candidate for a realistic three-dimensional case, a regime with relevant short-range noise, is identified. Depending on the dimensionality of space and the structure of the turbulent flow, we calculate critical exponents of the directed percolation process. In the limit of the purely transversal random force, critical exponents comply with the incompressible results obtained by previous authors. We have found intriguing nonuniversal behavior related to the mutual effect of compressibility and advection.

  • 14. Jovanovic, Stojan
    et al.
    Hertz, John
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). University of Copenhagen, Denmark.
    Rotter, Stefan
    Cumulants of Hawkes point processes2015In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 91, no 4, article id 042802Article in journal (Refereed)
    Abstract [en]

    We derive explicit, closed-form expressions for the cumulant densities of a multivariate, self-exciting Hawkes point process, generalizing a result of Hawkes in his earlier work on the covariance density and Bartlett spectrum of such processes. To do this, we represent the Hawkes process in terms of a Poisson cluster process and show how the cumulant density formulas can be derived by enumerating all possible family trees, representing complex interactions between point events. We also consider the problem of computing the integrated cumulants, characterizing the average measure of correlated activity between events of different types, and derive the relevant equations.

  • 15. Klamser, Pascal P.
    et al.
    Wiedermann, Marc
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Donner, Reik V.
    Zealotry effects on opinion dynamics in the adaptive voter model2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 5, article id 052315Article in journal (Refereed)
    Abstract [en]

    The adaptive voter model has been widely studied as a conceptual model for opinion formation processes on time-evolving social networks. Past studies on the effect of zealots, i.e., nodes aiming to spread their fixed opinion throughout the system, only considered the voter model on a static network. Here we extend the study of zealotry to the case of an adaptive network topology co-evolving with the state of the nodes and investigate opinion spreading induced by zealots depending on their initial density and connectedness. Numerical simulations reveal that below the fragmentation threshold a low density of zealots is sufficient to spread their opinion to the whole network. Beyond the transition point, zealots must exhibit an increased degree as compared to ordinary nodes for an efficient spreading of their opinion. We verify the numerical findings using a mean-field approximation of the model yielding a low-dimensional set of coupled ordinary differential equations. Our results imply that the spreading of the zealots' opinion in the adaptive voter model is strongly dependent on the link rewiring probability and the average degree of normal nodes in comparison with that of the zealots. In order to avoid a complete dominance of the zealots' opinion, there are two possible strategies for the remaining nodes: adjusting the probability of rewiring and/or the number of connections with other nodes, respectively.

  • 16.
    Kleeorin, Nathan
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Ben-Gurion University of the Negev, Israel; University of Helsinki, Finland.
    Rogachevskii, Igor
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Ben-Gurion University of the Negev, Israel; University of Helsinki, Finland.
    Soustova, I. A.
    Troitskaya, Yu.
    Ermakova, O. S.
    Zilitinkevich, S.
    Internal gravity waves in the energy and flux budget turbulence-closure theory for shear-free stably stratified flows2019In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 99, no 6, article id 063106Article in journal (Refereed)
    Abstract [en]

    We have advanced the energy and flux budget turbulence closure theory that takes into account a two-way coupling between internal gravity waves (IGWs) and the shear-free stably stratified turbulence. This theory is based on the budget equation for the total (kinetic plus potential) energy of IGWs, the budget equations for the kinetic and potential energies of fluid turbulence, and turbulent fluxes of potential temperature for waves and fluid flow. The waves emitted at a certain level propagate upward, and the losses of wave energy cause the production of turbulence energy. We demonstrate that due to the nonlinear effects more intensive waves produce more strong turbulence, and this, in turn, results in strong damping of IGWs. As a result, the penetration length of more intensive waves is shorter than that of less intensive IGWs. The anisotropy of the turbulence produced by less intensive IGWs is stronger than that caused by more intensive waves. The low-amplitude IGWs produce turbulence consisting up to 90% of turbulent potential energy. This resembles the properties of the observed high-altitude tropospheric strongly anisotropic (nearly two-dimensional) turbulence.

  • 17.
    Liberman, Michael
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Kleeorin, Nathan
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Ben-Gurion University of the Negev, Israel.
    Rogachevskii, Igor
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Ben-Gurion University of the Negev, Israel.
    Haugen, Nils Erland L.
    Mechanism of unconfined dust explosions: Turbulent clustering and radiation-induced ignition2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 5, article id 051101Article in journal (Refereed)
    Abstract [en]

    It is known that unconfined dust explosions typically start off with a relatively weak primary flame followed by a severe secondary explosion. We show that clustering of dust particles in a temperature stratified turbulent flow ahead of the primary flame may give rise to a significant increase in the radiation penetration length. These particle clusters, even far ahead of the flame, are sufficiently exposed and heated by the radiation from the flame to become ignition kernels capable to ignite a large volume of fuel-air mixtures. This efficiently increases the total flame surface area and the effective combustion speed, defined as the rate of reactant consumption of a given volume. We show that this mechanism explains the high rate of combustion and overpressures required to account for the observed level of damage in unconfined dust explosions, e.g., at the 2005 Buncefield vapor-cloud explosion. The effect of the strong increase of radiation transparency due to turbulent clustering of particles goes beyond the state of the art of the application to dust explosions and has many implications in atmospheric physics and astrophysics.

  • 18. Liu, Jiaojiao
    et al.
    Dai, Jin
    He, Jianfeng
    Niemi, Antti J.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Uppsala University, Sweden; Beijing Institute of Technology, People’s Republic of China; Université de Tours, France; Far Eastern Federal University, Russia.
    Ilieva, Nevena
    Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 3, article id 032406Article in journal (Refereed)
    Abstract [en]

    We propose to combine a mean-field approach with all-atom molecular dynamics ( MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the C alpha backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the C alpha profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal alpha helix, some of which resemble a translating Davydov's Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

  • 19. Nasedkin, Alexandr
    et al.
    Davidsson, Jan
    Niemi, Antti J.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Chalmers University of Technology, Sweden; Uppsala University, Sweden; Université de Tours, France; Beijing Institute of Technology, China; Far Eastern Federal University, Russia.
    Peng, Xubiao
    Solution x-ray scattering and structure formation in protein dynamics2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 6, article id 062405Article in journal (Refereed)
    Abstract [en]

    We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

  • 20. Pandey, Vikash
    et al.
    Perlekar, Prasad
    Mitra, Dhrubaditya
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Clustering and energy spectra in two-dimensional dusty gas turbulence2019In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 100, no 1, article id 013114Article in journal (Refereed)
    Abstract [en]

    We present direct numerical simulation of heavy inertial particles (dust) immersed in two-dimensional turbulent flow (gas). The dust particles are modeled as monodispersed heavy particles capable of modifying the flow through two-way coupling. By varying the Stokes number (St) and the mass-loading parameter (phi(m)), we study the clustering phenomenon and the gas phase kinetic energy spectra. We find that the dust-dust correlation dimension (d(2)) also depends on phi(m). In particular, clustering decreases as mass loading (phi(m)) is increased. In the kinetic energy spectra of gas we show (i) the emergence of a different scaling regime and that (ii) the scaling exponent in this regime is not universal but a function of both St and phi(m). Using a scale-by-scale enstrophy budget analysis we show that in this emerged scaling regime, which we call the dust-dissipative range, viscous dissipation due to the gas balances the back-reaction from the dust.

  • 21.
    Pramanik, Satyajit
    et al.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Wettlaufer, John S.
    Yale University, USA; University of Oxford, UK.
    Confinement effects in premelting dynamics2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 5, article id 052801Article in journal (Refereed)
    Abstract [en]

    We examine the effects of confinement on the dynamics of premelted films driven by thermomolecular pressure gradients. Our approach is to modify a well-studied setting in which the thermomolecular pressure gradient is driven by a temperature gradient parallel to an interfacially premelted elastic wall. The modification treats the increase in viscosity associated with the thinning of films, studied in a wide variety of materials, using a power law and we examine the consequent evolution of the confining elastic wall. We treat (1) a range of interactions that are known to underlie interfacial premelting and (2) a constant temperature gradient wherein the thermomolecular pressure gradient is a constant. The difference between the cases with and without the proximity effect arises in the volume flux of premelted liquid. The proximity effect increases the viscosity as the film thickness decreases thereby requiring the thermomolecular pressure driven flux to be accommodated at higher temperatures where the premelted film thickness is the largest. Implications for experiment and observations of frost heave are discussed.

  • 22. Schiulaz, Mauro
    et al.
    Laumann, Christopher R.
    Balatsky, Alexander V.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Institute for Materials Science, Los Alamos, USA.
    Spivak, Boris Z.
    Theory of combustion in disordered media2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 6, article id 062133Article in journal (Refereed)
    Abstract [en]

    The conventional theory of combustion describes systems where all of the parameters are spatially homogeneous. On the other hand, combustion in disordered explosives has long been known to occur after local regions of the material, called hot spots, are ignited. In this article we show that a system of randomly distributed hot spots exhibits a dynamic phase transition, which, depending on parameters of the system, can be either first or second order. These two regimes are separated by a tricritical point. We also show that on the qualitative level the phase diagram of the system is universal. It is valid in two and three dimensions, in the cases when the hot spots interact either by heat or sound waves, and in a broad range of microscopic disorder models.

  • 23. Schiulaz, Mauro
    et al.
    Laumann, Christopher R.
    Balatsky, Alexander V.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Institute for Materials Science, USA.
    Spivak, Boris Z.
    Theory of deflagration in disordered media2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 95, no 3, article id 032103Article in journal (Refereed)
    Abstract [en]

    The conventional theory of burning works well in the case of uniform media where all system parameters are spatially independent. We develop a theory of burning in disordered media. In this case, rare regions (hot spots) where the burning process is more effective than on average may control the heat propagation in an explosive sample. We show that most predictions of the theory of burning are quite different from the conventional case. In particular, we show that a system of randomly distributed hot spots exhibits a dynamic phase transition, which is similar to the percolation transition. Depending on parameters of the system the phase transition can be either first or second order. These two regimes are separated by a tricritical point. The above results may be applicable to dynamics of any overheated disordered system with a first order phase transition.

  • 24. Sinelnikova, A.
    et al.
    Niemi, Antti J.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Uppsala University, Sweden; Far Eastern Federal University, Russia; Beijing Institute of Technology, People's Republic of China.
    Nilsson, Johan
    Ulybyshev, M.
    Multiple scales and phases in discrete chains with application to folded proteins2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 5, article id 052107Article in journal (Refereed)
    Abstract [en]

    Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein. Here we address this impending problem. We develop a methodology with the potential to systematically identify different length scales, in the general case of a linear polymer chain. For this we introduce and analyze the properties of an order parameter that can both reveal the presence of different length scales and can also probe the phase structure. We first develop our concepts in the case of chiral homopolymers. We introduce a variant of Kadanoff's block-spin transformation to coarse grain piecewise linear chains, such as the C alpha backbone of a protein. We derive analytically, and then verify numerically, a number of properties that the order parameter can display, in the case of a chiral polymer chain. In particular, we propose that in the case of a chiral heteropolymer the order parameter can reveal traits of several different phases, contingent on the length scale at which it is scrutinized. We confirm that this is the case with crystallographic protein structures in the Protein Data Bank. Thus our results suggest relations between the scales, the phases, and the complexity of folding pathways.

  • 25. Smith, Eric
    et al.
    Krishnamurthy, Supriya
    Stockholm University, Faculty of Science, Department of Physics.
    Flows, scaling, and the control of moment hierarchies for stochastic chemical reaction networks2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 6, article id 062102Article in journal (Refereed)
    Abstract [en]

    Stochastic chemical reaction networks (CRNs) are complex systems that combine the features of concurrent transformation of multiple variables in each elementary reaction event and nonlinear relations between states and their rates of change. Most general results concerning CRNs are limited to restricted cases where a topological characteristic known as deficiency takes a value 0 or 1, implying uniqueness and positivity of steady states and surprising, low-information forms for their associated probability distributions. Here we derive equations of motion for fluctuation moments at all orders for stochastic CRNs at general deficiency. We show, for the standard base case of proportional sampling without replacement (which underlies the mass-action rate law), that the generator of the stochastic process acts on the hierarchy of factorial moments with a finite representation. Whereas simulation of high-order moments for many-particle systems is costly, this representation reduces the solution of moment hierarchies to a complexity comparable to solving a heat equation. At steady states, moment hierarchies for finite CRNs interpolate between low-order and high-order scaling regimes, which may be approximated separately by distributions similar to those for deficiency-zero networks and connected through matched asymptotic expansions. In CRNs with multiple stable or metastable steady states, boundedness of high-order moments provides the starting condition for recursive solution downward to low-order moments, reversing the order usually used to solve moment hierarchies. A basis for a subset of network flows defined by having the same mean-regressing property as the flows in deficiency-zero networks gives the leading contribution to low-order moments in CRNs at general deficiency, in a 1/n expansion in large particle numbers. Our results give a physical picture of the different informational roles of mean-regressing and non-mean-regressing flows and clarify the dynamical meaning of deficiency not only for first-moment conditions but for all orders in fluctuations.

  • 26. Wiedermann, Marc
    et al.
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Kurths, Jürgen
    Donner, Reik V.
    Mapping and discrimination of networks in the complexity-entropy plane2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 4, article id 042304Article in journal (Refereed)
    Abstract [en]

    Complex networks are usually characterized in terms of their topological, spatial, or information-theoretic properties and combinations of the associated metrics are used to discriminate networks into different classes or categories. However, even with the present variety of characteristics at hand it still remains a subject of current research to appropriately quantify a network's complexity and correspondingly discriminate between different types of complex networks, like infrastructure or social networks, on such a basis. Here we explore the possibility to classify complex networks by means of a statistical complexity measure that has formerly been successfully applied to distinguish different types of chaotic and stochastic time series. It is composed of a network's averaged per-node entropic measure characterizing the network's information content and the associated Jenson-Shannon divergence as a measure of disequilibrium. We study 29 real-world networks and show that networks of the same category tend to cluster in distinct areas of the resulting complexity-entropy plane. We demonstrate that within our framework, connectome networks exhibit among the highest complexity while, e.g., transportation and infrastructure networks display significantly lower values. Furthermore, we demonstrate the utility of our framework by applying it to families of random scale-free and Watts-Strogatz model networks. We then show in a second application that the proposed framework is useful to objectively construct threshold-based networks, such as functional climate networks or recurrence networks, by choosing the threshold such that the statistical network complexity is maximized.

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