3-D maps and coupling numbers for protein sequences

Based on a five-letter model of the 20 amino acids, we propose a new 3-D graphical representation of protein sequence. Then we derive from the graphical representation, numerical indices called 3-D coupling numbers, to characterize protein sequences. The examination of the similarities/dissimilarities among the β-globin proteins of 15 species illustrates the utility of the approach.     

Electric Field-Induced Fluid Velocity Field Distribution in DNA Solution

We present an analytical solution for fluid velocity field distribution of polyelectrolyte DNA. Both the electric field force and the viscous force in the DNA solution are considered under a suitable boundary condition. The solution of electric potential is analytically obtained by using the linearized Poisson-Boltzmann equation. The fluid velocity along the electric field is dependent on the cylindrical radius and concentration. It is shown that the electric field-induced fluid velocity will be increased with the increasing cylindrical radius, whose distribution also varies with the concentration     

Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting

We propose a physics method to study the effect of laser field and mechanical force on the melting process of double-stranded deoxyribonucleic acid （DNA）. A two-dimensional lattice model is established for DNA molecules stuck on the surface, and the stretching energy of the hydrogen bond and stacking energy for each DNA molecule are calculated by using a nonlinear potential. A real-time algorithm is employed to deal with the dynamics process of DNA melting. Numerical results explain the experimental observations. The spatial distribution of the laser field determines the sequences of DNA melting. The simulation has shown the dependence of the final number of melted DNA on the laser field and mechanical force.     

Multifractal Analysis of Human Heartbeat in Sleep

We study the dynamical properties of heart rate variability （HRV） in sleep by analysing the scaling behaviour with the multifractal detrended fluctuation analysis method. It is well known that heart rate is regulated by the interaction of two branches of the autonomic nervous system： the parasympathetic and sympathetic nervous systems. By investigating the multifractal properties of light, deep, rapid-eye-movement （REM） sleep and wake stages, we firstly find an increasing multifractal behaviour during REM sleep which may be caused by augmented sympathetic activities relative to non-REM sleep. In addition, the investigation of long-range correlations of HRV in sleep with second order detrended fluctuation analysis presents irregular phenomena. These findings may be helpful to understand the underlying regulating mechanism of heart rate by autonomic nervous system during wake-sleep transitions.     

Ion acceleration by the space charge electric force arising from the radiation pressure in a magnetized electron–positron plasma

It is shown that ions can be accelerated by the space charge electric force arising from the separation of electrons and positrons due to the ponderomotive force of the magnetic field-aligned circularly polarized electromagnetic (CPEM) wave in a magnetized electron–positron–ion plasma. The ion acceleration critically depends on the external magnetic field strength. The result is useful in understanding differential ion acceleration in magnetized electron–positron–ion plasmas, such as those in magnetars and in some laboratory experiments that aim to mimic astrophysical environments.     

Nonlinear generation of zonal flows by ion-acoustic waves in a uniform magnetoplasma

It is shown that large-scale zonal flows (ZFs) can be excited by Reynolds stress of nonlinearly interacting random phase ion-acoustic waves (EIAWs) in a uniform magnetoplasma. Since ZFs are associated with poloidal sheared flows, they can tear apart short scale EIAW turbulence eddies, and hence contribute to the reduction of the cross-field turbulent transport in a magnetized plasma.     

Frequency Selectivity Behaviour in the Auditory Midbrain： Implications of Model Study

By numerical simulations on frequency dependence of the spiking threshold, i.e. on the critical amplitude of periodic stimulus, for a neuron to fire, we find that bushy cells in the cochlear nuclear exhibit frequency selec- tivity behaviour. However, the selective frequency band of a bushy cell is far away from that of the preferred spectral range in human and mammal auditory perception. The mechanism underlying this neural activity is also discussed. Further studies show that the ion channel densities have little impact on the selective frequency band of bushy cells. These findings suggest that the neuronal behaviour of frequency selectivity in bushy cells at both the single cell and population levels may be not functionally relevant to frequency discrimination. Our results may reveal a neural hint to the reconsideration on the busily cell functional role in auditory information processing of sound frequency.     

Comparison of the energetic properties and the dynamical stability in a mathematical model of the stretch reflex

The previous studies on finite-time thermodynamic engines have shown that some of the parameters affecting their thermodynamic performance also affect their stability. Moreover, such parameters have to be tuned to reach an optimal trade-off between these two generic properties. In the present work we carry out a similar analysis on a mathematical model of the stretch reflex regulatory pathway, which is a simplified version of a previously published model. We show that the model has a unique stable fixed point in the absence of time delays. However, when the system inherent time delays are considered, they can destabilize the fixed point and engender a stable limit cycle. We further explore the parameter space to analyse the sensitivity of the system stability to variations in the parameter values. Particular attention is paid to the parameter here denoted as α, which has been shown to determine the muscle thermodynamic properties during steady-state contractions: larger values of α mean more powerful and less efficient muscles. Our results indicate that the stretch reflex pathway is less stable in the more powerful and less efficient muscles. We finally compare these observations with those obtained on thermal engines.     

Excitation of multiple wakefields by short laser pulses in quantum plasmas

We present a theoretical investigation of the excitation of multiple electrostatic wakefields by the ponderomotive force of a short electromagnetic pulse propagating through a dense plasma. It is found that the inclusion of the quantum statistical pressure and quantum electron tunneling effects can qualitatively change the classical behavior of the wakefield. In addition to the well-known plasma oscillation wakefield, with a wavelength of the order of the electron skin depth (λe=c/ωpe, which in a dense plasma is of the order of several nanometers, where c is the speed of light in vacuum and ωpe is the electron plasma frequency), wakefields in dense plasmas with a shorter wavelength (in comparison with λe) are also excited. The wakefields can trap electrons and accelerate them to extremely high energies over nanoscales.     

Sensitisation waves in a bidomain fire-diffuse-fire model of intracellular Ca dynamics

We present a bidomain threshold model of intracellular calcium (Ca²⁺) dynamics in which, as suggested by recent experiments, the cytosolic threshold for Ca²⁺ liberation is modulated by the Ca²⁺ concentration in the releasing compartment. We explicitly construct stationary fronts and determine their stability using an Evans function approach. Our results show that a biologically motivated choice of a dynamic threshold, as opposed to a constant threshold, can pin stationary fronts that would otherwise be unstable. This illustrates a novel mechanism to stabilise pinned interfaces in continuous excitable systems. Our framework also allows us to compute travelling pulse solutions in closed form and systematically probe the wave speed as a function of physiologically important parameters. We find that the existence of travelling wave solutions depends on the time scale of the threshold dynamics, and that facilitating release by lowering the cytosolic threshold increases the wave speed. The construction of the Evans function for a travelling pulse shows that of the co-existing fast and slow solutions the slow one is always unstable.     

Propagation and Interaction of Ion-Acoustic Solitary Waves in a Two-Dimensional Plasma Consisting of Isothermal Electrons and Hot Ions

We study the propagation and interaction of ion-acoustic solitary waves in a simple two-dimensional plasma by using the extended Poincare Lighthill-Kuo perturbation method. We consider the interaction between two ion-acoustic solitary waves with different propagation directions in such a system, and obtain two Korteweg-de Vries equations for small but finite amplitude solitary waves along both ξ and η trajectories. The effects of the ratio of ion temperature σ the ratio of heat capacity γ and the colliding angle a on the amplitude, the width of the new nonlinear wave created by the collision between two solitary waves are studied. The effects of these parameters on both the colliding solitary waves are examined as well. It is found that all the above-mentioned parameters have significant effects on the properties of these nonlinear waves.     

Dust-acoustic solitary waves in an adiabatic hot dusty plasma

An adiabatic hot dusty plasma (containing non-inertial adiabatic electron and ion fluids, and negatively charged inertial adiabatic dust fluid) is considered. The basic properties of arbitrary amplitude dust-acoustic (DA) solitary waves, which exist in such an adiabatic hot dusty plasma, are explicitly examined by the pseudo-potential approach. To compare the basic properties (critical Mach number, amplitude and width) of the DA solitary waves observed in a dusty plasma containing adiabatic electron, ion and dust fluids with those observed in a dusty plasma containing isothermal electron and ion fluids and adiabatic dust fluid, it has been found that the adiabatic effect of inertia-less electron and ion fluids has significantly modified the basic properties of the DA solitary waves, and that on the basic properties of the DA solitary waves, the adiabatic effect of electron and ion fluids is much more significant than that of the dust fluid.     

On the chaotic aspects of three wave interaction in a magnetized plasma

Nonlinear processes in magnetized plasma are very much important for the proper understanding of many space and astrophysical events. One of the most important type of study has been done in the domain of Alfven waves. Here we show that a Galerkin type approximation of the DNLS (Derivative Nonlinear Schrödinger) equation describing such wave propagation leads to a new type of nonlinear dynamical systems, very much rich in chaotic properties. Starting with the detailed analysis of fixed points and stability zones we make an in depth study of the unstable periodic orbits, which span the whole attractor. Next the birth of a Hopf bifurcation is identified and normal form, limit cycle analyzed. In the course of our study the detailed structure of the attractor is analyzed. A possibility of internal crisis is also indicated. These results will help in the choice of the plasma parameters for the actual physical situation.     

Cascade generation of zonal flows by the drift wave turbulence

The purpose of this research is to investigate the formation of zonal flows that can lead to the enhanced confinement of plasma in tokamaks. We show that zonal flows can be effectively formed by resonance triad interactions in the process of the inverse cascade. We discuss what energy sources are more effective for the formation of zonal flows.     

Nonlinear Shock and Kink Waves with Complete Coriolis Force in Earth's Atmosphere

Nonlinear waves in a Boussinesq fluid model which includes both the vertical and horizontal components of Coriolis force are studied by using the semi-geostrophic approximation and the method of travelling-wave solution. Taylor series expansion has been employed to isolate the characteristics of the linear Rossby waves and to identify the nonlinear shock and kink waves. The KdV-Burgers and the compound KdV-Burgers equations are derived, their shock wave and kink wave solution are also obtained.     

Electrostatic solitons in unmagnetized hot electron-positron-ion plasmas

Linear and nonlinear electrostatic waves in unmagnetized electron-positron-ion (e-p-i) plasmas are studied. The electrons and positrons are assumed to be isothermal and dynamic while ions are considered to be stationary to neutralize the plasma background only. It is found that both upper (fast) and lower (slow) Langmuir waves can propagates in such a type of pair (e-p) plasma in the presence of ions. The small amplitude electrostatic Korteweg-de Vries (KdV) solitons are also obtained using reductive perturbation method. The electrostatic potential hump structures are found to exist when the temperature of the electrons is larger than the positrons, while the electrostatic potential dips are obtained in the reverse temperature conditions for electrons and positrons in e-p-i plasmas. The numerical results are also shown for illustration. The effects of different ion concentration and temperature ratios of electrons and positrons, on the formation of nonlinear electrostatic potential structures in e-p-i plasmas are also discussed.     

Effect of excavated trapped electron distributions on ion-acoustic solitary structures in an electron-positron-ion plasma

Fully nonlinear propagation of ion-acoustic solitary waves in an unmagnetized electron-positron-ion plasma is investigated. A more realistic situation is considered in which electrons interact with the wave potential during its evolution and, follow the vortex-like excavated trapped distribution. The basic properties of large amplitude solitary waves are studied by deriving an energy integral equation involving Sagdeev potential. It is shown that effects of such electron behavior and positron concentration change the maximum values of the Mach number and amplitude for which solitary waves can exist. The small amplitude limit is also investigated by expanding the Sagdeev potential to include third-order nonlinearity of electric potential. In this case, exact analytical solution is obtained which is related to the contribution of the resonant electron to the electron density. It is shown from both highly and weakly nonlinear analysis that the plasma system under consideration supports only compressive solitary waves.     

Kinetic theory of instabilities responsible for magnetic turbulence in laboratory rotating plasma

The problem of instabilities responsible for magnetic turbulence in collisionless laboratory rotating plasma is investigated. It is shown that the standard mechanism of driving the magnetorotational instability (MRI), due to negative rotation frequency gradient, disappears in such a plasma. Instead of it, a new driving mechanism due to plasma pressure gradient is predicted.     

Dynamics of a charged particle in a progressive plane wave

The dynamics of a charged particle in a relativistic strong electromagnetic plane wave propagating in a medium is studied. The problem is shown to be integrable when the wave propagates in vacuum. When it propagates in plasma, and when the full plasma response is considered, an exhaustive numerical work allows us to conclude that the problem is not integrable.