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At least 1,261 records · Page 70

Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback

Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations. Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Linked coupled cluster Monte Carlo

We consider a new formulation of the stochastic coupled cluster method in terms of the similarity transformed Hamiltonian. We show that improvement in the granularity with which the wavefunction is represented results in a reduction in the critical population required to correctly sample the wavefunction for a range of systems and excitation levels and hence leads to a substantial reduction in the computational cost. This development has the potential to substantially extend the range of the method, enabling it to be used to treat larger systems with excitation levels not easily accessible with conventional deterministic methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

External noise-induced transitions in a current-biased Josephson junction

We investigate noise-induced transitions in a current-biased and weakly damped Josephson junction in the presence of multiplicative noise. By using the stochastic averaging procedure, the averaged amplitude equation describing dynamic evolution near a constant phase difference is derived. Numerical results show that a stochastic Hopf bifurcation between an absorbing and an oscillatory state occurs. This means the external controllable noise triggers a transition into the non-zero junction voltage state. With the increase of noise intensity, the stationary probability distribution peak shifts and is characterised by increased width and reduced height. And the different transition rates are shown for large and small bias currents.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Using full configuration interaction quantum Monte Carlo in a seniority zero space to investigate the correlation energy equivalence of pair coupled cluster doubles and doubly occupied configuration interaction

Over the past few years, pair coupled cluster doubles (pCCD) has shown promise for the description of strong correlation. This promise is related to its apparent ability to match results from doubly occupied configuration interaction (DOCI), even though the latter method has exponential computational cost. Here, by modifying the full configuration interaction quantum Monte Carlo algorithm to sample only the seniority zero sector of Hilbert space, we show that the DOCI and pCCD energies are in agreement for a variety of 2D Hubbard models, including for systems well out of reach for conventional configuration interaction algorithms. Our calculations are aided by the sign problem being much reduced in the seniority zero space compared with the full space. We present evidence for this and then discuss the sign problem in terms of the wave function of the system which appears to have a simplified sign structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Statistical characteristic in time-domain of direct current corona-generated audible noise from conductor in corona cage

The corona-generated audible noise (AN) has become one of decisive factors in the design of high voltage direct current (HVDC) transmission lines. The AN from transmission lines can be attributed to sound pressure pulses which are generated by the multiple corona sources formed on the conductor, i.e., transmission lines. In this paper, a detailed time-domain characteristics of the sound pressure pulses, which are generated by the DC corona discharges formed over the surfaces of a stranded conductors, are investigated systematically in a laboratory settings using a corona cage structure. The amplitude of sound pressure pulse and its time intervals are extracted by observing a direct correlation between corona current pulses and corona-generated sound pressure pulses. Based on the statistical characteristics, a stochastic model is presented for simulating the sound pressure pulses due to DC corona discharges occurring on conductors. The proposed stochastic model is validated by comparing the calculated and measured A-weighted sound pressure level (SPL). The proposed model is then used to analyze the influence of the pulse amplitudes and pulse rate on the SPL. Furthermore, a mathematical relationship is found between the SPL and conductor diameter, electric field, and radial distance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Vlasov simulations of electron-ion collision effects on damping of electron plasma waves

Collisional effects can play an essential role in the dynamics of plasma waves by setting a minimum damping rate and by interfering with wave-particle resonances. Kinetic simulations of the effects of electron-ion pitch angle scattering on Electron Plasma Waves (EPWs) are presented here. In particular, the effects of such collisions on the frequency and damping of small-amplitude EPWs for a range of collision rates and wave phase velocities are computed and compared with theory. Both the Vlasov simulations and linear kinetic theory find the direct contribution of electron-ion collisions to wave damping significantly reduced from that obtained through linearized fluid theory. To our knowledge, this simple result has not been published before. Simulations have been carried out using a grid-based (Vlasov) approach, based on a high-order conservative finite difference method for discretizing the Fokker-Planck equation describing the evolution of the electron distribution function. Details of the implementation of the collision operator within this framework are presented. Such a grid-based approach, which is not subject to numerical noise, is of particular interest for the accurate measurements of the wave damping rates.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics

We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systems with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of a reconnection-driven runaway ion tail in a reversed field pinch plasma

While reconnection-driven ion heating is common in laboratory and astrophysical plasmas, the underlying mechanisms for converting magnetic to kinetic energy remain not fully understood. Reversed field pinch discharges are often characterized by rapid ion heating during impulsive reconnection, generating an ion distribution with an enhanced bulk temperature, mainly perpendicular to magnetic field. In the Madison Symmetric Torus, a subset of discharges with the strongest reconnection events develop a very anisotropic, high energy tail parallel to magnetic field in addition to bulk perpendicular heating, which produces a fusion neutron flux orders of magnitude higher than that expected from a Maxwellian distribution. Here, we demonstrate that two factors in addition to a perpendicular bulk heating mechanism must be considered to explain this distribution. First, ion runaway can occur in the strong parallel-to-B electric field induced by a rapid equilibrium change triggered by reconnection-based relaxation; this effect is particularly strong on perpendicularly heated ions which experience a reduced frictional drag relative to bulk ions. Second, the confinement of ions varies dramatically as a function of velocity. Whereas thermal ions are governed by stochastic diffusion along tearing-altered field lines (and radial diffusion increases with parallel speed), sufficiently energetic ions are well confined, only weakly affected by a stochastic magnetic field. High energy ions traveling mainly in the direction of toroidal plasma current are nearly classically confined, while counter-propagating ions experience an intermediate confinement, greater than that of thermal ions but significantly less than classical expectations. The details of ion confinement tend to reinforce the asymmetric drive of the parallel electric field, resulting in a very asymmetric, anisotropic distribution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Characterizing phonon dynamics using stochastic sampling

Predicting phonon relaxation time from molecular dynamics (MD) requires a long simulation time to compute the mode energy auto-correlation function. Here, we present an alternative approach to infer the phonon life-time from an approximate form of the energy auto-correlation function. The method requires as an input a set of sampled equilibrium configurations. A stochastic sampling method is used to generate the equilibrium configurations. We consider a truncated Taylor series expansion of the phonon energy auto-correlation function. The different terms in the truncated correlation function are obtained using the stochastic sampling approach. The expansion terms, thus, obtained are in good agreement with the corresponding values obtained using MD. We then use the approximate function to compute the phonon relaxation time. The relaxation time computed using this method is compared with that obtained from the exact correlation function. The two values are in agreement with each other.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stochastic responses of Van der Pol vibro-impact system with fractional derivative damping excited by Gaussian white noise

This paper focuses on the study of the stochastic Van der Pol vibro-impact system with fractional derivative damping under Gaussian white noise excitation. The equations of the original system are simplified by non-smooth transformation. For the simplified equation, the stochastic averaging approach is applied to solve it. Then, the fractional derivative damping term is facilitated by a numerical scheme, therewith the fourth-order Runge-Kutta method is used to obtain the numerical results. And the numerical simulation results fit the analytical solutions. Therefore, the proposed analytical means to study this system are proved to be feasible. In this context, the effects on the response stationary probability density functions (PDFs) caused by noise excitation, restitution condition, and fractional derivative damping are considered, in addition the stochastic P-bifurcation is also explored in this paper through varying the value of the coefficient of fractional derivative damping and the restitution coefficient. These system parameters not only influence the response PDFs of this system but also can cause the stochastic P-bifurcation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multipole electrodynamic ion trap geometries for microparticle confinement under standard ambient temperature and pressure conditions

Trapping of microparticles and aerosols is of great interest for physics and chemistry. We report microparticle trapping in case of multipole linear Paul trap geometries, operating under standard ambient temperature and pressure conditions. An 8- and 12-electrode linear trap geometries have been designed and tested with an aim to achieve trapping for larger number of particles and to study microparticle dynamical stability in electrodynamic fields. We report emergence of planar and volume ordered structures of microparticles, depending on the a.c. trapping frequency and particle specific charge ratio. The electric potential within the trap is mapped using the electrolytic tank method. Particle dynamics is simulated using a stochastic Langevin equation. We emphasize extended regions of stable trapping with respect to quadrupole traps, as well as good agreement between experiment and numerical simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The radiation protection principles model as a tool in the e-waste procedures

The electrical and electronic waste (e-waste) management is a global environmental problem dominated by the precautionary principle application, resulted to preliminary and ambiguous potential adverse effects, of extensive scientific uncertainty. In order to overcome the detected stochastic effects confusions in this field, we propose the inclusion of the principles of justification-optimization-limitation and of prudent avoidance. This model is already, established in radiation protection, so that toxicity as a result of the e-waste management would decrease, whilst the precious metals would be saved. We, further, resolve the classification of rejected items as reusable or as waste, so that the procedure of dismantling and recycling becomes easier, and the collecting-transporting-placement at an e-waste landfill would be safer. In conclusion, our proposing pattern in the e-waste management enforces the sustainable reducing-reusing-recycling, saves time/money and advances safety by including more sources of e-waste (military, medical etc) that were excluded previously.

54 ENVIRONMENTAL SCIENCES↗

Operational and biological effects zones from base stations of cellular telephony

The possible environmental impacts of cellular base stations are operational and biological. The operational effects comprise Εlectro-Μagnetic Interference (EMI), lightning alterations and aesthetic degradation. Both thermal and non-thermal biological effects depend on the absorption of UHF radiofrequencies used. We measured, calculated and estimated the impact zones. The results are: (a) The lightning lethal zone equal to the antenna height, (b) the EMI impact in a zone up to 40m and (c) the ICNIRP’s limits exceed to a zone of 8∼20m into the antenna’s radiation pattern (for 2G GSM and 3G UMTS station). Finally we conclude the adverse effects must not expected in a zone of more than 150m from the radiated antenna, whereas, there is possibility of stochastic effects in intermediate distances (20/40-150m).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dynamic response in a finite size composite multiferroic thin film

Composite multiferroics, heterostructures of ferromagnetic and ferroelectric materials, are characterized by a remarkable magnetoelectric effect at the interface. Previous work has supported the ferromagnetic structure with magnetic spins and the ferroelectric with pseudospins which act as electric dipoles in a microscopic model, coupled with a magnetoelectric interaction [Wang and Grimson, J. Appl. Phys. 118, 124109 (2015)]. In this work, by solving the stochastic Landau-Lifshitz-Gilbert equation, the electric-field-induced magnetization switching in a twisted boundary condition has been studied, and a behavior of domain wall in the ferromagnetic structure is discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Noisy homoclinic pulse dynamics

The effect of stochastic perturbations on nearly homoclinic pulse trains is considered for three model systems: a Duffing oscillator, the Lorenz-like Shimizu–Morioka model, and a co-dimension-three normal form. Using the Duffing model as an example, it is demonstrated that the main effect of noise does not originate from the neighbourhood of the fixed point, as is commonly assumed, but due to the perturbation of the trajectory outside that region. Singular perturbation theory is used to quantify this noise effect and is applied to construct maps of pulse spacing for the Shimizu–Morioka and normal form models. The dynamics of these stochastic maps is then explored to examine how noise influences the sequence of bifurcations that take place adjacent to homoclinic connections in Lorenz-like and Shilnikov-type flows.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Diagram of states and morphologies of flexible-semiflexible copolymer chains: A Monte Carlo simulation

A single copolymer chain consisting of multiple flexible (F) and semiflexible (S) blocks has been studied using a continuum bead-spring model by Stochastic Approximation Monte Carlo simulations, which determine the density of states of the model. The only difference between F and S blocks is the intramolecular bending potential, all non-bonded interactions are equal. The state diagrams for this class of models display multiple nematic phases in the collapsed state, characterized through a demixing of the blocks of different stiffness and orientational ordering of the stiff blocks. We observe dumbbell-like morphologies, lamellar phases, and for the larger block lengths also Saturn-like structures with a core of flexible segments and the stiff segments forming a ring around the core.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On effective temperature in network models of collective behavior

Collective behavior of self-propelled units is studied analytically within the Vectorial Network Model (VNM), a mean-field approximation of the well-known Vicsek model. We propose a dynamical systems framework to study the stochastic dynamics of the VNM in the presence of general additive noise. We establish that a single parameter, which is a linear function of the circular mean of the noise, controls the macroscopic phase of the system—ordered or disordered. By establishing a fluctuation–dissipation relation, we posit that this parameter can be regarded as an effective temperature of collective behavior. The exact critical temperature is obtained analytically for systems with small connectivity, equivalent to low-density ensembles of self-propelled units. Numerical simulations are conducted to demonstrate the applicability of this new notion of effective temperature to the Vicsek model. The identification of an effective temperature of collective behavior is an important step toward understanding order–disorder phase transitions, informing consistent coarse-graining techniques and explaining the physics underlying the emergence of collective phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Modulated heat pulse propagation and partial transport barriers in chaotic magnetic fields

Direct numerical simulations of the time dependent parallel heat transport equation modeling heat pulses driven by power modulation in three-dimensional chaotic magnetic fields are presented. The numerical method is based on the Fourier formulation of a Lagrangian-Green's function method that provides an accurate and efficient technique for the solution of the parallel heat transport equation in the presence of harmonic power modulation. The numerical results presented provide conclusive evidence that even in the absence of magnetic flux surfaces, chaotic magnetic field configurations with intermediate levels of stochasticity exhibit transport barriers to modulated heat pulse propagation. In particular, high-order islands and remnants of destroyed flux surfaces (Cantori) act as partial barriers that slow down or even stop the propagation of heat waves at places where the magnetic field connection length exhibits a strong gradient. Results on modulated heat pulse propagation in fully stochastic fields and across magnetic islands are also presented. In qualitative agreement with recent experiments in large helical device and DIII-D, it is shown that the elliptic (O) and hyperbolic (X) points of magnetic islands have a direct impact on the spatio-temporal dependence of the amplitude of modulated heat pulses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗