title: Two dimensional incompressible ideal flow around a small obstacle

abstract:
  In this article we study the asymptotic behavior of incompressible, ideal,
time-dependent two dimensional flow in the exterior of a single smooth obstacle
when the size of the obstacle becomes very small. Our main purpose is to
identify the equation satisfied by the limit flow. We will see that the
asymptotic behavior depends on $\gamma$, the circulation around the obstacle.
For smooth flow around a single obstacle, $\gamma$ is a conserved quantity
which is determined by the initial data. We will show that if $\gamma = 0$, the
limit flow satisfies the standard incompressible Euler equations in the full
plane but, if $\gamma \neq 0$, the limit equation acquires an additional
forcing term. We treat this problem by first constructing a sequence of
approximate solutions to the incompressible 2D Euler equation in the full plane
from the exact solutions obtained when solving the equation on the exterior of
each obstacle and then passing to the limit on the weak formulation of the
equation. We use an explicit treatment of the Green's function of the exterior
domain based on conformal maps, {\it a priori} estimates obtained by carefully
examining the limiting process and the Div-Curl Lemma, together with a standard
weak convergence treatment of the nonlinearity for the passage to the limit.


title: Topos-theoretic Model of the Deutsch multiverse

abstract:
  The Deutsch multiverse is collection of parallel universes. In this article a
formal theory and a topos-theoretic model of the Deutsch multiverse are given.
For this the Lawvere-Kock Synthetic Differential Geometry and topos models for
smooth infinitesimal analysis are used. Physical properties of multi-variant
and many-dimensional parallel universes are discussed. Quantum fluctuations of
universe geometry are considered. Photon ghosts in parallel universes are
found.


title: Vector- and tensor-valued descriptors for spatial patterns

abstract:
  Higher-rank Minkowski valuations are efficient means for describing the
geometry and connectivity of spatial patterns. We show how to extend the
framework of the scalar Minkowski valuations to vector- and tensor-valued
measures. The properties of these extensions are described in detail. We show
the versatility of these measures by using simple toy models as well as real
data. Our applications cover the morphology of galaxy clusters, the structure
of spiral galaxies, and the geometry of molecules. Furthermore, we consider a
physical ansatz closely related to higher-rank Minkowski valuations, the
Rosenfeld functional known from density functional theory.

categories: physics.data-an astro-ph cond-mat.stat-mech math.GM


title: Geometry of compact tubes and protein structures

abstract:
  Proteins form a very important class of polymers. In spite of major advances
in the understanding of polymer science, the protein problem has remained
largely unsolved. Here, we show that a polymer chain viewed as a tube not only
captures the well-known characteristics of polymers and their phases but also
provides a natural explanation for many of the key features of protein
behavior. There are two natural length scales associated with a tube subject to
compaction -- the thickness of the tube and the range of the attractive
interactions. For short tubes, when these length scales become comparable, one
obtains marginally compact structures, which are relatively few in number
compared to those in the generic compact phase of polymers. The motifs
associated with the structures in this new phase include helices, hairpins and
sheets. We suggest that Nature has selected this phase for the structures of
proteins because of its many advantages including the few candidate strucures,
the ability to squeeze the water out from the hydrophobic core and the
flexibility and versatility associated with being marginally compact. Our
results provide a framework for understanding the common features of all
proteins.

categories: physics.bio-ph cond-mat.soft cond-mat.stat-mech q-bio


title:
An improved unified solver for compressible and incompressible fluids
  involving free surfaces. II. Multi-time-step integration and applications

abstract:
  An improved numerical solver for the unified solution of compressible and
incompressible fluids involving interfaces is proposed. The present method is
based on the CIP-CUP (Cubic Interpolated Propagation / Combined, Unified
Procedure) method, which is a pressure-based semi-implicit solver for the Euler
equations of fluid flows. In Part I of this series of articles [M. Ida, Comput.
Phys. Commun. 132 (2000) 44], we proposed an improved scheme for the convection
terms in the equations, which allowed us discontinuous descriptions of the
density interface by replacing the cubic interpolation function used in the CIP
scheme with a quadratic extrapolation function only around the interface. In
this paper, as Part II of this series, the multi-time-step integration
technique is adapted to the CIP-CUP integration. Because the CIP-CUP treats
different-nature components in the fluid equations separately, the adaptation
of the technique is straightforward. This modification allows us flexible
determinations of the time interval, which results in an efficient and accurate
integration. Furthermore, some additional discussion on our methods is
presented. Finally, the application results to composite flow problems such as
compressible and incompressible Kelvin-Helmholtz instabilities and the dynamics
of two acoustically coupled deformable bubbles in a viscous liquid are
provided.


title: Fundamental constants in effective theory

abstract:
  There is a discussion between L. B. Okun, G. Veneziano and M. J. Duff,
concerning the number of fundamental dimensionful constants in physics
(physics/0110060). They advocated correspondingly 3, 2 and 0 fundamental
constants. Here we consider this problem on example of the effective
relativistic quantum field theory, which emerges in the low energy corner of
quantum liquids and which reproduces many features of our physics including
chiral fermions, gauge fields and dynamical gravity.

categories: physics.class-ph cond-mat gr-qc hep-ph physics.gen-ph


title: Words for Nobel prizes

abstract:
  We present the statistics of the significant nouns and adjectives of social
impact figuring in the nominations of the Nobel prizes in Physics and Chemistry
over the period of the awards from 1901 to 2001


title: Resonant nonlinear magneto-optical effects in atoms

abstract:
  In this article, we review the history, current status, physical mechanisms,
experimental methods, and applications of nonlinear magneto-optical effects in
atomic vapors. We begin by describing the pioneering work of Macaluso and
Corbino over a century ago on linear magneto-optical effects (in which the
properties of the medium do not depend on the light power) in the vicinity of
atomic resonances, and contrast these effects with various nonlinear
magneto-optical phenomena that have been studied both theoretically and
experimentally since the late 1960s. In recent years, the field of nonlinear
magneto-optics has experienced a revival of interest that has led to a number
of developments, including the observation of ultra-narrow (1-Hz)
magneto-optical resonances, applications in sensitive magnetometry, nonlinear
magneto-optical tomography, and the possibility of a search for parity- and
time-reversal-invariance violation in atoms.


title: Chirality in Bare and Passivated Gold Nanoclusters

abstract:
  Chiral structures have been found as the lowest-energy isomers of bare
(Au$_{28}$ and Au$_{55}) and thiol-passivated (Au$_{28}(SCH$_{3})$_{16}$ and
Au$_{38}(SCH_{3})_{24}) gold nanoclusters. The degree of chirality existing in
the chiral clusters was calculated using the Hausdorff chirality measure. We
found that the index of chirality is higher in the passivated clusters and
decreases with the cluster size. These results are consistent with the observed
chiroptical activity recently reported for glutahione-passivated gold
nanoclusters, and provide theoretical support for the existence of chirality in
these novel compounds.


title: A New Spin on the Dirac Electron

abstract:
  We re-examine the non Hermitian position coordinate of Dirac's equation, in
the light of his own insights and conclude that this, and the Dirac equation
itself is symptomatic of an underlying Noncommutative Geometry.


title: Comment: Anomalous Anisotropic Light Scattering in Ge-Doped Silica Glass

abstract:
  This is a comment on a paper by Kazansky et al. appeared in Phys. Rev. Lett.,
82, 2199 (1999). We demonstrate that the bremsstrahlung of photoelectrons,
which oscillate in the light field of an ultrashort laser pulse, accounts for
the anomalous anisotropic light scattering, the "propeller effect", described
in the paper of Kazansky et al. This mechanism of light emission could explain
some results of white-light continuum generation and dielectric breakdown
emission.


title: On the limits of spectral methods for frequency estimation

abstract:
  An algorithm is presented which generates pairs of oscillatory random time
series which have identical periodograms but differ in the number of
oscillations. This result indicate the intrinsic limitations of spectral
methods when it comes to the task of measuring frequencies. Other examples, one
from medicine and one from bifurcation theory, are given, which also exhibit
these limitations of spectral methods. For two methods of spectral estimation
it is verified that the particular way end points are treated, which is
specific to each method, is, for long enough time series, not relevant for the
main result.


title: Exact Optics: A unification of optical telescope design

abstract:
  A perfect focus telescope is one in which all rays parallel to the axis meet
at a point and give equal magnification there. It is shown that these two
conditions define the shapes of both primary and secondary mirrors. Apart from
scale, the solution depends upon two parameters, $s$, which gives the mirror
separation in terms of the effective focal length, and $K$, which gives the
relative position of the final focus in that unit. The two conditions ensure
that the optical systems have neither spherical aberration nor coma, no matter
how fast the $f$ ratio. All known coma--free systems emerge as approximate
special cases. In his classical paper, K. Schwarzschild studied all two mirror
systems whose profiles were conic sections. We make no such a priori shape
conditions but demand a perfect focus and solve for the mirrors' shapes.


title: Chaotic dynamics in a storage-ring Free Electron Laser

abstract:
  The temporal dynamics of a storage-ring Free Electron Laser is here
investigated with particular attention to the case in which an external
modulation is applied to the laser-electron beam detuning. The system is shown
to produce bifurcations, multi-furcations as well as chaotic regimes. The
peculiarities of this phenomenon with respect to the analogous behavior
displayed by conventional laser sources are pointed out. Theoretical results,
obtained by means of a phenomenological model reproducing the evolution of the
main statistical parameters of the system, are shown to be in a good agreement
with experiments carried out on the Super-ACO Free Electron Laser.


title:
On planewave remittances and Goos-Haenchen shifts of planar slabs with
  negative real permittivity and permeability

abstract:
  Two results about the planewave response of an isotropic,
dielectric--magnetic, homogeneous, planar slab are deduced when the real parts
of both the permittivity and the permeability are altered from positive to
negative. First, the reflection and the transmission coefficients suffer phase
reversals without change in their respective magnitudes. Second, the
Goos-Haenchen shifts experienced by beams on total reflection reverse their
directions.


title: Variational approach for walking solitons in birefringent fibres

abstract:
  We use the variational method to obtain approximate analytical expressions
for the stationary pulselike solutions in birefringent fibers when differences
in both phase velocities and group velocities between the two components and
rapidly oscillating terms are taken into account. After checking the validity
of the approximation we study how the soliton pulse shape depends on its
velocity and nonlinear propagation constant. By numerically solving the
propagation equation we have found that most of these stationary solutions are
stable.


title: Atomistic Simulations of Nanotube Fracture

abstract:
  The fracture of carbon nanotubes is studied by atomistic simulations. The
fracture behavior is found to be almost independent of the separation energy
and to depend primarily on the inflection point in the interatomic potential.
The rangle of fracture strians compares well with experimental results, but
predicted range of fracture stresses is marketly higher than observed. Various
plausible small-scale defects do not suffice to bring the failure stresses into
agreement with available experimental results. As in the experiments, the
fracture of carbon nanotubes is predicted to be brittle. The results show
moderate dependence of fracture strength on chirality.


title: Recoiling DNA Molecule: Simulation & Experiment

abstract:
  Single molecule DNA experiments often generate data from force versus
extension measurements involving the tethering of a microsphere to one end of a
single DNA molecule while the other is attached to a substrate. We show that
the persistence length of single DNA molecules can also be measured based on
the recoil dynamics of these DNA-microsphere complexes if appropriate
corrections are made to the friction coefficient of the microsphere in the
vicinity of the substrate. Comparison between computer simulated recoil curves,
generated from the corresponding Langevin equation, and experimental recoils is
used to assure the validity of data analysis.


title: Traveling waves of infection in the Hantavirus epidemics

abstract:
  Traveling waves are analyzed in a model of the Hantavirus infection of deer
mice. The existence of two kinds of wave phenomena is predicted. An
environmental parameter governs a transition between two regimes of
propagation. In one of them the front of infection lags behind at a constant
rate. In the other, fronts of susceptible and infected mice travel at the same
speed, separated by a constant delay. The dependence of the delay on system
parameters is analyzed numerically and through a piecewise linearization.

categories: physics.bio-ph cond-mat.stat-mech nlin.PS q-bio.PE


title: Collisional dynamics of ultracold OH molecules in an electrostatic field

abstract:
  Ultracold collisions of polar OH molecules are considered in the presence of
an electrostatic field. The field exerts a strong influence on both elastic and
state-changing inelastic collision rate constants, leading to clear
experimental signatures that should help disentangle the theory of cold
molecule collisions. Based on the collision rates we discuss the prospects for
evaporative cooling of electrostatically trapped OH. We also find that the
scattering properties at ultralow temperatures prove to be remarkably
independent of the details of the short-range interaction, owing to avoided
crossings in the long-range adiabatic potential curves. The behavior of the
scattering rate constants is qualitatively understood in terms of a novel set
of long-range states of the [OH]$_2$ dimer.


title:
Single or combined location measurements of the same parameter without
  prior probability. (Altern. title, Parametric inference as useful illusion;
  Part 1)

abstract:
  Motivation. This version is based solely on the calculus of probability,
excluding any statistical principle. "Location measurement" means the pdf of
the error is known. When the datum is obtained, intuition suggests something
like a pdf for the parameter; here we attempt a critical examination of its
meaning.
  Summary. In default of prior probability the parameter is not defined as a
random variable, hence there can be no genuine prior-free parametric inference.
Nevertheless prior-free predictive inference regarding any future datum is
generated directly from the datum of a location measurement. Such inference
turns out as if obtained from a certain pdf ("fiducial") indirectly associated
with the parameter. This false pdf can expedite predictive inference, but is
inappropriate in the analysis of combined measurements (unless they all are
location measurements of the same parameter). Also it has the same distribution
as the ostensible Bayesian posterior from a uniform "prior". However, if any of
these spurious entities is admitted in the analysis, inconsistent results
follow. When we combine measurements, we find that the quantisation errors,
inevitable in data recording, must be taken into consideration. These errors
cannot be folded into predictive inference in an exact sense; that is, we
cannot render a predictive distribution of a future datum except as an
approximation.
  Keywords: location measurement; combination of observations; parametric
inference; predictive inference; prior-free inference; quantisation error;
digitisation; frequentist interpretation; the fiducial argument; fiducial
probability; pivotal inference; intuitive assessment; prior-free assessment


title:
Collective Properties of the Exactly Solvable Model of Ion-Channel
  Assemblies in a Biological Cell Membrane

abstract:
  The behaviour of a system of ion channels formed across the cell membrane is
presented. The infinite number of channels with an infinite coupling is
introduced first as a reference point for the detailed derivation of the
thermal-equilibrium probability distribution and the classification of the
phase transitions. Fluctuations in a finite system are discussed next. We
propose a new, step-like model of the ion channel switching, for which we
provide the analytical results. The relation of this model to experiment is
also provided. Finally, the master equation for the finite channel-number
membrane is analysed numerically with the help of an exact-diagonalization
technique. In particular, the decay-time of a metastable solution is estimated.
The results do not agree with those obtained perturbationally, the difference
is explained by the proposed frozen-diffusion approach.


title:
Class of self-limiting growth models in the presence of nonlinear
  diffusion

abstract:
  The source term in a reaction-diffusion system, in general, does not involve
explicit time dependence. A class of self-limiting growth models dealing with
animal and tumor growth and bacterial population in a culture, on the other
hand are described by kinetics with explicit functions of time. We analyze a
reaction-diffusion system to study the propagation of spatial front for these
models.


title: DNA Dynamics in A Water Drop

abstract:
  Due to its polyionic character the DNA double helix is stable and
biologically active only in salty aqueous media where its charge is compensated
by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment
and they are usually considered as the possible driving force of
sequence-dependent modulations of DNA structure that make it recognizable by
proteins. In an effort to directly examine this hypothesis, MD simulations of
DNA in a water drop surrounded by vacuum were carried out, which relieves the
requirement of charge neutrality. Surprisingly, with zero concentration of
counterions a dodecamer DNA duplex appears metastable and its structure remains
similar to that observed in experiments.


title: Weakly non-linear analysis of wind-driven gravity waves

abstract:
  We study the weakly non-linear development of shear-driven gravity waves, and
investigate the mixing properties of the finite amplitude solutions.
Calculations to date have been restricted to the linear theory, which predicts
that gravity waves are amplified by an influx of energy through the critical
layer, where the velocity of the wind equals the wave phase velocity. Because
of the presence of a critical layer, ordinary weakly non-linear methods fail;
in this paper, we use a rescaling at the critical layer and matched asymptotics
to derive an amplitude equation for the most unstable wave, under the
simplifying assumption that the physical domain is periodic. These amplitude
equations are solved numerically, in their quasi-steady limit, for the cases of
small density ratio (applicable to oceanography), and for arbitrary density
ratio but strong stratification (for more general physical/astrophysical
situations). In addition to the familiar asymptotic growth found in other
inviscid flow, we find that, for the air over water case (provided the maximum
wind velocity is in the range of $0.2\mpers \sim 1\mpers$), the single mode
transitions from exponential to algebraic growth when the amplitude of the wave
is as small as $h\sim 10^{-5}\lambda$; hence, it may be difficult to observe
the linear regime for this case in numerical simulations. We also find that the
weakly non-linear flow allows for super-diffusive particle transport with an
exponent $\sim 3/2$, consistent with Venkataramani's results.


title:
The role of intense line wings in the process of infrared
  multiple--photon excitation of polyatomic molecules

abstract:
  The results of experimental testing the existence of intense Lorentzian--like
wings with FWHM $\sim 4.5 cm^{-1}$ in the absorption spectra of polyatomic
molecules in a gas phase are presented. Two independent experimental methods
were used for evaluating the integral intensity of the line wings for a number
of substances. In the first case, the cross--section of the far wings of
absorption bands in a gas phase spectrum were measured. Then, these band wings
were extrapolated inside the contour of absorption band. In the second case,
the saturation degree of the linear spectrum of molecules was determined.
Radiation of a pulsed $CO_2$--laser was used at low gas pressure ($\sim 16$
mtorr) and averaged excitation level of molecules ${<n>}\sim 0.1$
quanta/molecule. The values obtained by these two independent methods coincide
for a variety of molecules. The average relative integral intensity of the line
wings varied from $\sim 0.6%$ for $SF_6$ and $SiF_4$ to $\sim 90%$ for
$(CF_3)_2O$ and $(CF_3)_2CO$.


title: An additional planet as a model for the Pleistocene Ice Age

abstract:
  We propose a model for the Pleistocene Ice Age, assuming the following
scenario: Between 3 Myr and 11.5 kyr BP a Mars-sized object existed which moved
in a highly eccentric orbit. Originating from this object, gas clouds with a
complex dynamics reduced Earth's insolation and caused a drop in the global
temperature. In a close encounter, 11.5 kyr ago, tidal forces deformed the
Earth. While the shape of the gyroscope Earth relaxed, the North Pole moved
geographically from Greenland to its present position. During this close
encounter, the object was torn to pieces, each of which subsequently evaporated
or plunged into the sun. These events terminated the Ice Age Epoch.


title: The Design Of Fiber Optic Sensors For Measuring Hydrodynamic Parameters

abstract:
  We present an approximate analytic model that has been developed for
examining hydrodynamic flow near the surface of a fiber optic sensor. An
analysis of the conservation of momentum, the continuity equation and the
Navier-Stokes equation for compressible flow was used to develop expressions
for the velocity and the density as a function of the distance along the flow
and above a two dimensional flat surface. When examining the flow near the
surface, these expressions can be used to estimate the sensitivity required to
perform direct optical measurements and to parameterize the shear force for
indirect optical measurements. The use of these results allows for direct
modeling of sensors using the optical properties of the flow field. Future work
includes analyzing the optical parametric design of fiber optic sensors,
modeling sensors to utilize those parameters for optimal measurements involving
different mixtures of fluid flow.


title:
Numerical estimation of entropy loss on dimerization: improved
  prediction of the quaternary structure of the GCN4 leucine zipper

abstract:
  A lattice based model of a protein is used to study the dimerization
equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to
determine the free energy of both the monomeric and dimeric forms as a function
of temperature. The method of coincidences is then introduced to explicitly
calculate the entropy loss associated with dimerization, and from it the free
energy difference between monomer and dimer, as well as the corresponding
equilibrium reaction constant. We find that the entropy loss of dimerization is
a strong function of energy (or temperature), and that it is much larger than
previously estimated, especially for high energy states. The results confirm
that it is possible to study the dimerization equilibrium of GCN4 at
physiological concentrations within the reduced representation of the protein
employed.


title: The Nature of Space Time

abstract:
  We first examine the approximation involved in the conventional
differentiable spacetime manifold. We then analyse how, going beyond this
approximation, we reach the non commutative spacetime of recent approaches. It
is shown that this provides the rationale for El Naschie's transfinite
Cantorian spacetime. The nature and form of the consequent Generalized
Uncertainity Principle is also briefly investigated.


title: Effective area of photonic crystal fibers

abstract:
  We consider the effective area A_eff of photonic crystal fibers (PCFs) with a
triangular air-hole lattice in the cladding. It is first of all an important
quantity in the context of non-linearities, but it also has connections to
leakage loss, macro-bending loss, and numerical aperture. Single-mode versus
multi-mode operation in PCFs can also be studied by comparing effective areas
of the different modes. We report extensive numerical studies of PCFs with
varying air hole size. Our results can be scaled to a given pitch and thus
provide a general map of the effective area. We also use the concept of
effective area to calculate the "phase" boundary between the regimes with
single-mode and multi-mode operation.


title: Electrical Indicator of Imminent Freezing in Supercooled Water

abstract:
  Data is presented that demonstrate electrical activity and evidences of
dipole alignment in supercooled water and heavy water before and after the
onset of freezing. Voltage signals as high as 13 mV have been recorded. In some
cases up to 3 seconds before latent heat is released and freezing began. The
polarity of the voltage signals is suggestive of molecule dipole alignment
prior to freezing.


title: The Loss of Multifractality in Migraines

abstract:
  We study the middle cerebral artery blood flow velocity (MCAfv) in humans
using transcranial Doppler ultrasonography (TCD). The time series of the axial
flow velocity averaged over a cardiac beat interval is found to exhibit clear
multifractal properties for healthy subjects. We observe a loss of
multifractality for subjects with migraine.


title: Generalization of Boltzmann Equilibration Dynamics

abstract:
  We propose a novel approach in the study of transport phenomena in dense
systems or systems with long range interactions where multiple particle
interactions must be taken into consideration. Within Boltzmann's kinetic
formalism, we study the influence of other interacting particles in terms of a
random distortion of energy and momentum conservation occurring when
multi-particle interactions are considered as binary collisions. Energy and
momentum conservation still holds exactly but not in each model binary
collision. We show how this new system differs from the Boltzmann system and we
note that our approach naturally explains the emergence of Tsallis-like
equilibrium statistics in physically relevant systems in terms of the long
since neglected physics of interacting and dense systems.

categories: physics.class-ph cond-mat.stat-mech hep-ph nucl-th physics.gen-ph


title:
Stochastic Transition between Turbulent Branch and Thermodynamic Branch
  of an Inhomogeneous Plasma

abstract:
  Transition phenomena between thermodynamic branch and turbulent branch in
submarginal turbulent plasma are analyzed with statistical theory.
Time-development of turbulent fluctuation is obtained by numerical simulations
of Langevin equation which contains submarginal characteristics. Probability
density functions and transition rates between two states are analyzed.
Transition from turbulent branch to thermodynamic branch occurs in almost
entire region between subcritical bifurcation point and linear stability
boundary.


title: Light bullets and optical collapse in vacuum

abstract:
  In quantum electrodynamics, photon--photon scattering can be the result of
the exchange of virtual electron--positron pairs. Effectively, this gives rise
to self-interaction terms in Maxwell's equations, similar to the nonlinearities
due to polarization in nonlinear optics. These self-interaction terms vanish in
the limit of parallel propagating waves. However if the modes generated in
bounded regions are used, there will be a non-zero total effect. We show that
stationary two-dimensional light bullets can form in guiding structures, due to
the balancing effect of quantum electrodynamical vacuum nonlinearities on
dispersion and diffraction. These light bullets are unstable and exhibit the
possibility of self-focusing collapse. The consequences of our results are also
discussed.


title: Transition Probability to Turbulent Transport Regime

abstract:
  Transition phenomena between thermal noise state and turbulent state observed
in a submarginal turbulent plasma are analyzed with statistical theory.
Time-development of turbulent fluctuation is obtained by numerical simulations
of Langevin equation which contains hysteresis characteristics. Transition
rates between two states are analyzed. Transition from turbulent state to
thermal noise state occurs in entire region between subcritical bifurcation
point and linear stability boundary.


title: Fundamental parameters of QCD

abstract:
  The theory of strong interactions, QCD, is described in terms of a few
parameters, namely the strong coupling constant alpha_s and the quark masses.
We show how these parameters can be determined reliably using computer
simulations of QCD on a space-time lattice, and by employing a finite-size
scaling method, which allows to trace the energy dependence of alpha_s and
quark masses over several orders of magnitude. We also discuss methods designed
to reduce the effects of finite lattice spacing and address the issue of
computer resources required.

categories: physics.comp-ph hep-lat hep-ph physics.gen-ph


title:
Fiber-coupled Antennas for Ultrafast Coherent Terahertz Spectroscopy in
  Low Temperatures and High Magnetic Fields

abstract:
  For the purposes of measuring the high-frequency complex conductivity of
correlated-electron materials at low temperatures and high magnetic fields, a
method is introduced for performing coherent time-domain terahertz spectroscopy
directly in the cryogenic bore of existing dc and pulsed magnets. Miniature
fiber-coupled THz emitters and receivers are constructed and are demonstrated
to work down to 1.5 Kelvin and up to 17 Tesla, for eventual use in higher-field
magnets. Maintaining the sub-micron alignment between fiber and antenna during
thermal cycling, obtaining ultrafast (${<200}$~fs) optical gating pulses at the
end of long optical fibers, and designing highly efficient devices that work
well with low-power optical gating pulses constitute the major technical
challenges of this project. Data on a YBCO superconducting thin film and a high
mobility 2D electron gas is shown.


title: Complex space-localized fields interacting with electromagnetic fields

abstract:
  Several families of nonlinear field equations are known to possess space-
localized singularity-free solutions which describe fields with finite
Hermitian norms. This paper studies the interaction of such fields with given
electromagnetic potentials entering the field's equations through the covariant
derivative form. The main result is: the motion of a space-localized field, as
a whole, is essentially identical to that of a point charge moving in the same
electromagnetic potentials, if this field is a solution either to a nonlinear
Schrodinger or to a nonlinear Dirac equation, under some very general and
physically meaningful assumptions. Using an alternative method, similar result
is shown to hold for a very wide class of nonlinear field equations.


title: Shock wave surfing acceleration

abstract:
  Dynamics of a charged relativistic particle in a uniform magnetic field and
an obliquely propagating electrostatic shock wave is considered. The system is
reduced to a two degrees of freedom Hamiltonian system with slow and fast
variables. In this system, the phenomenon of capture into resonance can take
place. Under certain condition, a captured phase point stays captured forever.
This corresponds to unlimited surfing acceleration of the particle. The
preprint is a more detailed version of a comment on the paper by D.Ucer and
V.D.Shapiro (Phys.Rev.Lett., vol. 87, 075001, 2001), intended for the Comments
section of Physical Reviews Letters.


title: High-accuracy wavemeter based on a stabilized diode laser

abstract:
  We have built a high-accuracy wavelength meter for tunable lasers using a
scanning Michelson interferometer and a reference laser of known wavelength.
The reference laser is a frequency stabilized diode laser locked to an atomic
transition in Rb. The wavemeter has a statistical error per measurement of 5
parts in $10^7$ which can be reduced considerably by averaging. Using a second
stabilized diode laser, we have verified that systematic errors are below 4
parts in $10^8$.


title:
Direct measurement of the fine-structure interval in alkali atoms using
  diode lasers

abstract:
  We demonstrate a technique for directly measuring the fine-structure interval
in alkali atoms using two frequency-stabilized diode lasers. Each laser has a
linewidth of order 1 MHz and precise tunability: one laser is tuned to a
hyperfine transition in the D_1 line, and the other laser to a hyperfine
transition in the D_2 line. The outputs of the lasers are fed into a scanning
Michelson interferometer that measures the ratio of their wavelengths
accurately. To illustrate the technique, we measure the fine-structure interval
in Rb, and obtain a value of 237.6000(3)(5) cm^-1 for the hyperfine-free
5P_{3/2} - 5P_{1/2} interval.


title:
Observation of sub-natural linewidths for cold atoms in a magneto-optic
  trap

abstract:
  We have studied the absorption of a weak probe beam through cold rubidium
atoms in a magneto-optic trap. The absorption spectrum shows two peaks with the
smaller peak having linewidth as small as 28% of the natural linewidth. The
modification happens because the laser beams used for trapping also drive the
atoms coherently between the ground and excited states. This creates
``dressed'' states whose energies are shifted depending on the strength of the
drive. Linewidth narrowing occurs due to quantum coherence between the dressed
states. The separation of the states increases with laser intensity and
detuning, as expected from this model.


title: Loading of a Rb magneto-optic trap from a getter source

abstract:
  We study the properties of a Rb magneto-optic trap loaded from a commercial
getter source which provides a large flux of atoms for the trap along with the
capability of rapid turn-off necessary for obtaining long trap lifetimes. We
have studied the trap loading at two different values of background pressure to
determine the cross-section for Rb--N$_2$ collisions to be 3.5(4)x10^{-14} cm^2
and that for Rb--Rb collisions to be of order 3x10^{-13} cm^2. At a background
pressure of 1.3x10^{-9} torr, we load more than 10^8 atoms into the trap with a
time constant of 3.3 s. The 1/e lifetime of trapped atoms is 13 s limited only
by background collisions.


title: Sub-natural linewidth in room-temperature Rb vapor using a control laser

abstract:
  We demonstrate two ways of obtaining sub-natural linewidth for probe
absorption through room-temperature Rb vapor. Both techniques use a control
laser that drives the transition from a different ground state. The coherent
drive splits the excited state into two dressed states (Autler-Townes doublet),
which have asymmetric linewidths when the control laser is detuned from
resonance. In the first technique, the laser has a large detuning of 1.18 GHz
to reduce the linewidth to 5.1 MHz from the Doppler width of 560 MHz. In the
second technique, we use a counter-propagating pump beam to eliminate the
first-order Doppler effect. The unperturbed probe linewidth is about 13 MHz,
which is reduced below 3 MHz (0.5 \Gamma) at a detuning of 11.5 MHz.


title: A New Atom Trap: The Annular Shell Atom Trap (ASAT)

abstract:
  In the course of exploring some aspects of atom guiding in a hollow, optical
fiber, a small negative potential energy well was found just in front of the
repulsive or guiding barrier. This results from the optical dipole and the van
der Waals potentials. The ground state for atoms bound in this negative
potential well was determined by numerically solving the Schrodinger eq. and it
was found that this negative well could serve as an atom trap. This trap is
referred to as the Annular Shell Atom Trap or ASAT because of the geometry of
the trapped atoms which are located in the locus of points defining a very thin
annular shell just in front of the guiding barrier. A unique feature of the
ASAT is the compression of the atoms from the entire volume to the volume of
the annular shell resulting in a very high density of atoms in this trap. This
trap may have applications to very low temperatures using evaporative cooling
and possibly the formation of BEC. Finally, a scheme is discussed for taking
advantage of the de Broglie wavelength to store atoms in a bottle trap based on
the inability of long de Broglie wavelengths to escape through a selective de
Broglie wavelength filter in the atom bottle trap.


title:
Bound State Calculations for Three Atoms Without Explicit Partial Wave
  Decomposition

abstract:
  A method to calculate the bound states of three-atoms without resorting to an
explicit partial wave decomposition is presented. The differential form of the
Faddeev equations in the total angular momentum representation is used for this
purpose. The method utilizes Cartesian coordinates combined with the
tensor-trick preconditioning for large linear systems and Arnoldi's algorithm
for eigenanalysis. As an example, we consider the He$_3$ system in which the
interatomic force has a very strong repulsive core that makes the three-body
calculations with standard methods tedious and cumbersome requiring the
inclusion of a large number of partial waves. The results obtained compare
favorably with other results in the field.


title: Cold atom gas at very high densities in an optical surface microtrap

abstract:
  An optical microtrap is realized on a dielectric surface by crossing a
tightly focused laser beam with an horizontal evanescent-wave atom mirror. The
nondissipative trap is loaded with $\sim$$10^5$ cesium atoms through elastic
collisions from a cold reservoir provided by a large-volume optical surface
trap. With an observed 300-fold local increase of the atomic number density
approaching $10^{14}{\rm cm}^{-3}$, unprecedented conditions of cold atoms
close to a surface are realized.


title: Metal nanoplasmas as bright sources of hard x-ray pulses

abstract:
  We demonstrate a 13-fold increase in hard x-ray bremsstrahlung (10 - 200 keV)
emitted by a copper plasma created by 100 fs, 806 nm pulses at
$10^{14}-10^{15}$ Wcm$^{-2}$. This enhancement is achieved by roughening the
target surface with copper nanoparticles of ~15 nm size. A simple model that
invokes local field modifications by surface plasmon excitation and `lightning
rod' effects explains the observed enhancement quantitatively and provides
pointers to the design of structured surfaces for maximizing the emission.


title:
Constant-temperature molecular-dynamics algorithms for mixed
  hard-core/continuous potentials

abstract:
  We present a set of second-order, time-reversible algorithms for the
isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed
hard-core/continuous potentials. The methods are generated by combining
real-time Nose' thermostats with our previously developed Collision Verlet
algorithm [Mol. Phys. 98, 309 (1999)] for constant energy MD simulation of such
systems. In all we present 5 methods, one based on the Nose'-Hoover [Phys. Rev.
A 31, 1695 (1985)] equations of motion and four based on the Nose'-Poincare'
[J.Comp.Phys., 151 114 (1999)] real-time formulation of Nose' dynamics. The
methods are tested using a system of hard spheres with attractive tails and all
correctly reproduce a canonical distribution of instantaneous temperature. The
Nose'-Hoover based method and two of the Nose'-Poincare' methods are shown to
have good energy conservation in long simulations.


title: An Investigation of Time in Relativity

abstract:
  I added an Imaginary term by hand to the proper time in special theory of
relativity, and I wanted to see what will happen to it if I tried to get the
time dialation relationship. I found that this added imaginary term of time
does not have to be zero.


title: Hidden Vector 'Coordinates' in Particle Physics

abstract:
  Heretofore unrecognized (i.e., "hidden") Lorentz-invariant vector observables
in the fermion sector (i.e., flavor-defining fermion "coordinates") are shown
to indirectly explain most, if not all, of the so-called "accidental"
(internal) symmetries associated with fundamental fermions (quarks and
leptons), by explaining quark and lepton flavors, flavor doublets and families.
Moreover, these new fermion coordinates lead to quantitative constraints on
neutrino mixtures that are found to be in good agreement with current
experimental observations.


title:
Comments on "A gravitational shielding based upon ZnS:Ag phosphor" and
  "The gravitational mass at the superconducting state"

abstract:
  This is a discussion of two recent papers by De Aquino [physics/0112081
(2001) and physics/0201058 (2002)] that put forward an explanation of
observations of gravity shielding originally reported by Podkletnov and
Nieminen [Physica C 203 441 (1992)].


title: Using Self-Description to Handle Change in Systems

abstract:
  In the web age systems must be flexible, reconfigurable and adaptable in
addition to being quick to develop. As a consequence, designing systems to
cater for change is becoming not only desirable but required by industry.
Allowing systems to be self-describing or description-driven is one way to
enable these characteristics. To address the issue of evolvability in designing
self-describing systems, this paper proposes a pattern-based, object-oriented,
description-driven architecture. The proposed architecture embodies four
pillars - first, the adoption of a multi-layered meta-modeling architecture and
reflective meta-level architecture, second, the identification of four data
modeling relationships that must be made explicit such that they can be
examined and modified dynamically, third, the identification of five design
patterns which have emerged from practice and have proved essential in
providing reusable building blocks for data management, and fourth, the
encoding of the structural properties of the five design patterns by means of
one pattern, the Graph pattern. In this paper the fundamentals of the
description-driven architecture are described - the multi-layered architecture
and reflective meta-level architecture, remaining detail can be found in the
cited references. A practical example of this architecture is described,
demonstrating the use of description-driven data objects in handling system
evolution.


title: 1/f noise: a pedagogical review

abstract:
  This is a pedagogical review of the ubiquitous 1/f^\alpha noises. The
sections include the representation of 1/f^\alpha noise as a superposition of
many relaxation processes; a discussion of the infinitely large fluctuations in
the low frequency limit; 1/f^\alpha noise from diffusion processes; the
measured statistical properties of 1/f^\alpha noises; 1/f^\alpha noises in self
organized criticality; scaling laws in earthquake physics; 1/f noise in
deterministic dynamical systems; an example of noise in a biophysical system;
the numerical simulation of 1/f^\alpha noise; 1/f noise literature (including
online resources).


title: From Lorenz to Coulomb and other explicit gauge transformations

abstract:
  The main purposes of this paper are (i) to illustrate explicitly by a number
of examples the gauge functions chi(x, t) whose spatial and temporal
derivatives transform one set of electromagnetic potentials into another
equivalent set; and (ii) to show that, whatever propagation or non-propagation
characteristics are exhibited by the potentials in a particular gauge, the
electric and magnetic fields are always the same and display the experimentally
verified properties of causality and propagation at the speed of light. The
example of the transformation from the Lorenz gauge (retarded solutions for
both scalar and vector potential) to the Coulomb gauge (instantaneous,
action-at-a-distance, scalar potential) is treated in detail. A transparent
expression is obtained for the vector potential in the Coulomb gauge, with a
finite nonlocality in time replacing the expected spatial nonlocality of the
transverse current. A class of gauges (v-gauge) is described in which the
scalar potential propagates at an arbitrary speed v relative to the speed of
light. The Lorenz and Coulomb gauges are special cases of the v-gauge. The last
examples of gauges and explicit gauge transformation functions are the
Hamiltonian or temporal gauge, the nonrelativistic Poincare or multipolar
gauge, and the relativistic Fock-Schwinger gauge.


title:
A central partition of molecular conformational space. I. Basic
  structures

abstract:
  On the basis of empirical evidence from molecular dynamics simulations,
molecular conformational space can be described by means of a partition of
central conical regions characterized by the dominance relations between
cartesian coordinates. This work presents a geometric and combinatorial
description of this structure.


title: Nuclear spin conversion in polyatomic molecules

abstract:
  Except for ortho- and para-H2, very little is known about nuclear spin
isomers (or spin modifications) of molecules. The main reason is the lack of
practical enrichment techniques. Recently a few enrichment methods were
developed, which opened up new possibilities in the field. These methods are
briefly reviewed. Substantial progress in the field has been made by the
introduction of Light-Induced Drift as a gas-phase separation tool. This is
illustrated by extensive data on CH3F, which reveal that the gas-phase
ortho-para conversion is governed by intramolecular mixing of the nuclear spin
states. The role of ``direct'' ortho-para transitions is shown to be small.
Various aspects of the conversion were investigated in detail: pressure and
collision partner dependence, isotope effect, temperature dependence. The most
decisive information on the spin conversion mechanism is derived from the
observation of level-crossing resonances in an electric field and the Quantum
Zeno effect induced by collisions.


title:
Magnetic field of superconductive in-vacuo undulators in comparison with
  permanent magnet undulators

abstract:
  During the last few years superconductive undulators with a period length of
3.8 mm and 14 mm have been built. In this paper scaling laws for these novel
insertion devices are presented: a simple analytic formula is derived which
describes the achievable magnetic field of a superconcuctive undulator as a
function of gap-width and period length.


title:
Systematic observation of tunneling field-ionization in highly excited
  Rb Rydberg atoms

abstract:
  Pulsed field ionization of high-$n$ (90 $\leq n \leq$ 150) manifold states in
Rb Rydberg atoms has been investigated in high slew-rate regime. Two peaks in
the field ionization spectra were systematically observed for the investigated
$n$ region, where the field values at the lower peak do not almost depend on
the excitation energy in the manifold, while those at the higher peak increase
with increasing excitation energy. The fraction of the higher peak component to
the total ionization signals increases with increasing $n$, exceeding 80% at
$n$ = 147. Characteristic behavior of the peak component and the comparison
with theoretical predictions indicate that the higher peak component is due to
the tunneling process. The obtained results show for the first time that the
tunneling process plays increasingly the dominant role at such highly excited
nonhydrogenic Rydberg atoms.


title: Laser-Generated Ultrashort Multi-Megagauss Magnetic Pulses in Plasmas

abstract:
  We demonstrate ultrashort (6 ps), multi-Megagauss (27 MG) magnetic pulses
generated upon interaction of an intense laser pulse (10^{16} Wcm^-2, 100 fs)
with a solid target. The temporal evolution of these giant fields generated
near the high density critical layer is obtained with the highest resolution
reported so far. Particle-in-cell simulations and phenomenological modeling is
used to explain the results. The first direct observations of anomalously rapid
damping of plasma shielding currents produced in response to the hot electron
currents penetrating the bulk plasma are presented.


title: Realistic interatomic potential for MD simulations

abstract:
  The coefficients of interatomic potential of simple form Exp-6 for neon are
obtained. Repulsive part is calculated ab-initio in the Hartree-Fock
approximation using the basis of atomic orbitals orthogonalized exactly on
different lattice sites. Attractive part is determined empirically using single
fitting parameter. The potential obtained describes well the equation of state
and elastic moduli of neon crystal in wide range of interatomic distances and
it is appropriate for molecular dynamic simulations of high temperature
properties and phenomena in crystals and liquids.


title: Fourier Synthesization of Optical Pulses and "Polar'' Light

abstract:
  It is shown that the direct Fourier synthesization of light beams allows one
to create polarity-asymmetric waves, which are able, in the process of
nonlinear interaction with a medium, to break its inversion symmetry. As a
result, these "polar" waves may show the effect of optical rectification in
nonlinear centrosymmetric media by generating light-induced dc electric
polarization. At the same time, the waves of this type, due to their unusual
symmetry properties, can be used for detecting the direction and sign of a dc
electric field applied to the medium. The prospects of application of polar
waves to data recording and processing are discussed.


title: Coloured conical emission via second-harmonic generation

abstract:
  We predict that the combination of space and time modulational instabilities
occuring via parametric wave-mixing in quadratic media leads to coloured
conical emission. This phenomenon should be observed under conditions usually
employed in second-harmonic generation experiments.


title: Superluminal Tunneling Devices

abstract:
  Photonic tunneling permits superluminal signal transmission. The principle of
causality is not violated but the time duration between cause and effect can be
shortened compared with an interaction exchange with velocity of light. This
outstanding property can be applied to speed-up photonic signal modulation and
transmission as well as to improve micro-electronic devices. Superluminal
photonic signal transmission have been presented at microwave and infrared
frequencies already. Presumably superluminal photonic and electronic devices
can become reality having in mind the experimental evidence of the universal
tunneling time of photons and of electrons.


title: Einstein's gravitational field

abstract:
  There exists some confusion, as evidenced in the literature, regarding the
nature of the gravitational field in Einstein's General Theory of Relativity.
It is argued here the this confusion is a result of a change in interpretation
of the gravitational field. Einstein identified the existence of gravity with
the inertial motion of accelerating bodies (i.e. bodies in free-fall) whereas
contemporary physicists identify the existence of gravity with space-time
curvature (i.e. tidal forces). The interpretation of gravity as a curvature in
space-time is an interpretation Einstein did not agree with.


title: Velocity and Pressure Fields Induced by Spheres in an Unbounded Fluid

abstract:
  We propose a procedure for the determination of the time-dependent velocity
and pressure fields of an unbounded incompressible viscous fluid in an external
force field induced by an arbitrary number of spheres moving and rotating in it
as well as the forces and torques exerted by the fluid on the particles. Within
the completely linearized scheme, we express the velocity and pressure fields
of the fluid in terms of induced surface force densities and derive the
explicit form for all quantities contained in these relations not imposing any
additional restrictions on the size of particles, distances between them, and
the frequency range. We show the incorrectness of similar results obtained
earlier by several authors because these results are expressed in terms of
nonexistent inverse tensors. We explain the reasons leading to this and propose
a procedure for the elimination of divergent quantities. In the stationary
case, using the proposed procedure, we obtained the translational, rotational,
and coupled friction and mobility tensors for a system containing an arbitrary
number of spheres up to, respectively, the second, forth, and third orders in
the dimensionless parameter equal to the ratio of a typical radius of a sphere
to a typical distance between two spheres. In various particular cases, the
results obtained in the present paper agree with the well-known results derived
by other methods.


title: New method for the Numerical Calculation of Hydrodynamics Shocks

abstract:
  The equations of hydrodynamics are rewritten in sense of functionals with
values in Non-Archimedean field of Laurent series or
$\mathbf{R}<\epsilon>$-distributions. A new ideology for understanding of
conservation laws is proposed. A set of nonlinear algebraic equations suitable
for the numerical work is given. The Newton iteration method are used for
calculation of microscopic shock profiles for the equations of compressible
flow.


title:
Proton Wires in an Electric Field: the Impact of Grotthuss Mechanism on
  Charge Translocation

abstract:
  We present the results of the modeling of proton translocation in finite
H-bonded chains in the framework of two-stage proton transport model. We
explore the influence of reorientation motion of protons, as well as the effect
of electric field and proton correlations on system dynamics. An increase of
the reorientation energy results in the transition of proton charge from the
surrounding to the inner water molecules in the chain. Proton migration along
the chain in an external electric field has a step-like character, proceeding
with the occurrence of electric field threshold-type effects and drastic
redistribution of proton charge. Electric field applied to correlated chains
induces first a formation of ordered dipole structures for lower field
strength, and than, with a further field strength increase, a stabilization of
states with Bjerrum D-defects. We analyze the main factors responsible for the
formation/annihilation of Bjerrum defects showing the strong influence of the
complex interplay between reorientation energy, electric field and temperature
in the dynamics of proton wire.


title:
Manipulating ionization path in a Stark map: Stringent schemes for the
  selective field ionization in highly excited Rb Rydberg atoms

abstract:
  We have developed a quite stringent method in selectivity to ionize the low
angular- momentum ($\ell$) states which lie below and above the adjacent
manifold in highly excited Rb Rydberg atoms. The method fully exploits the
pulsed field-ionization characteristics of the manifold states in high
slew-rate regime: Specifically the low $\ell$ state below (above) the adjacent
manifold is firstly transferred to the lowest (highest) state in the manifold
via the adiabatic transition at the first avoided crossing in low slew-rate
regime, and then the atoms are driven to a high electric field for ionization
in high slew-rate regime. These extreme states of the manifold are ionized at
quite different fields due to the tunneling process, resulting in thus the
stringent selectivity. Two manipulation schemes to realize this method actually
are demonstrated here experimentally.


title:
Further generalization and numerical implementation of pseudo-time
  Schroedinger equations for quantum scattering calculations

abstract:
  We review and further develop the recently introduced numerical approach for
scattering calculations based on a so called pseudo-time Schroedinger equation,
which is in turn a modification of the damped Chebyshev polynomial expansion
scheme.
  The method utilizes a special energy-dependent form for the absorbing
potential in the time-independent Schroedinger equation, in which the complex
energy spectrum E_k is mapped to u_k inside the unit disk, where u_k are the
eigenvalues of some explicitly known sparse matrix U.
  Most importantly for the numerical implementation, all the physical
eigenvalues u_k are extreme eigenvalues of U, which allows one to extract these
eigenvalues very efficiently by harmonic inversion of a pseudo-time
autocorrelation function using the filter diagonalization method. The
computation of 2T steps of the autocorrelation function requires only T sparse
real matrix-vector multiplications.
  We describe and compare different schemes, effectively corresponding to
different choices of the energy-dependent absorbing potential, and test them
numerically by calculating resonances of the HCO molecule. Our numerical tests
suggest an optimal scheme that provide accurate estimates for most resonance
states.


title: Soliton self-modulation of the turbulence amplitude and plasma rotation

abstract:
  The space-uniform amplitude envelope of the Ion Temperature Gradient driven
turbulence is unstable to small perturbations and evolves to nonuniform,
soliton-like modulated profiles. The induced poloidal asymmetry of the
transport fluxes can generate spontaneous poloidal spin-up of the tokamak
plasma.


title:
Analysis of the ellipticity and general scaling perturbation induced PMD
  in a transmitting fiber

abstract:
  Presented is an analysis of general scaling perturbations in a transmitting
fiber. For elliptical perturbations, under some conditions an intermode
dispersion parameter characterizing modal PMD is shown to be directly
proportional to the mode dispersion.


title: A lattice model for the kinetics of rupture of fluid bilayer membranes

abstract:
  We have constructed a model for the kinetics of rupture of membranes under
tension, applying physical principles relevant to lipid bilayers held together
by hydrophobic interactions. The membrane is characterized by the bulk
compressibility (for expansion), the thickness of the hydrophobic part of the
bilayer, the hydrophobicity and a parameter characterizing the tail rigidity of
the lipids. The model is a lattice model which incorporates strain relaxation,
and considers the nucleation of pores at constant area, constant temperature,
and constant particle number. The particle number is conserved by allowing
multiple occupancy of the sites. An equilibrium ``phase diagram'' is
constructed as a function of temperature and strain with the total pore surface
and distribution as the order parameters. A first order rupture line is found
with increasing tension, and a continuous increase in proto-pore concentration
with rising temperature till instability. The model explains current results on
saturated and unsaturated PC lipid bilayers and thicker artificial bilayers
made of diblock copolymers. Pore size distributions are presented for various
values of area expansion and temperature, and the fractal dimension of the pore
edge is evaluated.


title: Photonic quantum-corral ring laser: A fermionic phase transition

abstract:
  Extensive Bose-Einstein condensation research activities have recently led to
studies of fermionic atoms and optical confinements. Here we present a case of
micro-optical fermionic electron phase transition. Optically confined ordering
and phase transitions of a fermionic cloud in dynamic steady state are
associated with Rayleigh emissions from photonic quantum ring manifold which
are generated by nature without any ring lithography. The whispering gallery
modes, produced in a semiconductor Rayleigh-Fabry-Perot toroidal cavity at room
temperature, exhibit novel properties of ultralow thresholds open to
nano-ampere regime, thermal stabilities from square-root-T-dependent spectral
shift, and angularly varying intermode spacings. The photonic quantum ring
phenomena are associated with a photonic field-driven phase transition of
quantum-well-to-quantum-wire and hence the photonic (non-de Broglie) quantum
corral effect on the Rayleigh cavity-confined carriers in dynamic steady state.
Based upon the intra-cavity fermionic condensation we also offer a prospect for
an electrically driven few-quantum dot single photon source from the photonic
quantum ring laser for quantum information processors.


title: Triple GEM operation in compressed He and Kr

abstract:
  We study the performance of the triple GEM (Gas Electron Multiplier) detector
in pure noble gases He and Kr at high pressures, varying from 1 to 15 atm. The
operation in these gases is compared to that recently studied in Ne, Ar and Xe.
It turned out that light noble gases, He and Ne, have superior performance: the
highest gain, approaching 10^5, and an unusual gain dependence on pressure. In
particular, the maximum gain in He and Ne does not decrease with pressure, in
contrast to Ar, Kr and Xe. These results are of high relevance for
understanding basic mechanisms of electron avalanching in noble gases and for
applications in cryogenic particle detectors, X-ray imaging and neutron
detectors.


title: Physical Properties of Iron in the Inner Core

abstract:
  The Earth's inner core plays a vital role in the dynamics of our planet and
is itself strongly exposed to dynamic processes as evidenced by a complex
pattern of elastic structure. To gain deeper insight into the nature of these
processes we rely on a characterization of the physical properties of the inner
core which are governed by the material physics of its main constituent, iron.
Here we review recent research on structure and dynamics of the inner core,
focusing on advances in mineral physics. We will discuss results on core
composition, crystalline structure, temperature,and various aspects of
elasticity. Based on recent computational results, we will show that aggregate
seismic properties of the inner core can be explained by temperature and
compression effects on the elasticity of pure iron, and use single crystal
anisotropy to develop a speculative textural model of the inner core that can
explain major aspects of inner core anisotropy.


title:
Fourth-order perturbative extension of the singles-doubles
  coupled-cluster method

abstract:
  Fourth-order many-body corrections to matrix elements for atoms with one
valence electron are derived. The obtained diagrams are classified using
coupled-cluster-inspired separation into contributions from n-particle
excitations from the lowest-order wavefunction. The complete set of
fourth-order diagrams involves only connected single, double, and triple
excitations and disconnected quadruple excitations. Approximately half of the
fourth-order diagrams are not accounted for by the popular coupled-cluster
method truncated at single and double excitations (CCSD). Explicit formulae are
tabulated for the entire set of fourth-order diagrams missed by the CCSD method
and its linearized version, i.e. contributions from connected triple and
disconnected quadruple excitations. A partial summation scheme of the derived
fourth-order contributions to all orders of perturbation theory is proposed.


title: Eddington & Uncertainty

abstract:
  Sir Arthur Eddington is considered one of the greatest astrophysicist of the
twentieth century and yet he gained a stigma when, in the 1930s, he embarked on
a quest to develop a unified theory of gravity and quantum mechanics. His
attempts ultimately proved fruitless and he was unfortunately partially shunned
by some physicists in the latter portion of his career. In addition some
historians have been less than kind to him regarding this portion of his work.
However, detailed analysis of how this work got started shows that Eddington's
theories were not as outlandish as they are often purported to be. His entire
theory rested on the use of quantum mechanical methods of uncertainty in the
reference frames of relativity. Though the work was ultimately not fruitful, in
hindsight it did foreshadow several later results in physics and his methods
were definitely rigorous. In addition, his philosophy regarding determinism and
uncertainty was actually fairly orthodox for his time. This work begins by
looking at Eddington's life and philosophy and uses this as a basis to explore
his work with uncertainty.


title:
Frequency locking of tunable diode lasers to a stabilized ring-cavity
  resonator

abstract:
  We demonstrate a technique for locking the frequency of a tunable diode laser
to a ring-cavity resonator. The resonator is stabilized to a diode laser which
is in turn locked to an atomic transition, thus giving it absolute frequency
calibration. The ring-cavity design has the principal advantage that there is
no feedback destabilization of the laser. The cavity has a free-spectral range
of 1.3 GHz and $Q$ of about 35, which gives robust locking of the laser. The
locked laser is able to track large scans of the cavity.


title:
Dispersive properties of quasi-phase-matched optical parametric
  amplifiers

abstract:
  The dispersive properties of non-degenerate optical parametric amplification
in quasi-phase-matched (QPM) nonlinear quadratic crystals with an arbitrary
grating profile are theoretically investigated in the no-pump-depletion limit.
The spectral group delay curve of the amplifier is shown to be univocally
determined by its spectral power gain curve through a Hilbert transform. Such a
constraint has important implications on the propagation of spectrally-narrow
optical pulses through the amplifier. In particular, it is shown that anomalous
transit times, corresponding to superluminal or even negative group velocities,
are possible near local minima of the spectral gain curve. A possible
experimental observation of such effects using a QPM Lithium-Niobate crystal is
suggested.


title: Flatness of the setting Sun

abstract:
  Atmospheric refraction is responsible for the bending of light-rays in the
atmosphere. It is a result of the continuous decrease in the refractive index
of the air as a function of altitude. A well-known consequence of this
phenomenon is the apparently elliptic shape of the setting or rising Sun (or
full-Moon). In the present paper we systematically investigate this phenomenon
in a standard atmosphere. Theoretical and numerical calculations are compared
with experimental data. The asymmetric rim of the Sun is computed as a function
of its inclination angle, observational height and meteorological conditions
characterized by pressure, temperature and lapse-rate. We reveal and illustrate
some extreme and highly unusual situations.


title: Problematic solutions to the Landau-Lifshitz equation

abstract:
  A critical look at the Landau-Lifshitz equation, which has been recently
advocated as an "exact" relativistic classical equation for the motion of a
point charge with radiation reaction, demonstrates that it generally does not
conserve energy-momentum. Its failure is dramatic in the one-dimensional case
of a stepped electric field, where it predicts discontinuous velocity and thus
infinite radiation. The Lorentz-Dirac equation, on the other hand, in spite of
its preacceleration over distances comparable to the classical electron radius,
does not display such problems.


title:
On the theoretical possibility of the electromagnetic scalar potential
  wave spreading with an arbitrary velocity in vacuum

abstract:
  In this work we revisit the process of constructing wave equations for the
scalar and vector potentials of an electromagnetic field, and show that a wave
equation with an arbitrary velocity (including a velocity higher than the
velocity of light in vacuum) for the scalar potential exists in the framework
of classical electrodynamics. Some consequences of this fact are considered. It
is shown (in the Appendix) at what point this work differs from works concerned
of the problem of the gauge invariance in the classical electrodynamics.


title:
Precise frequency measurements of the D-lines and fine-structure
  interval in K

abstract:
  We use a diode laser locked to a Rb transition as the frequency reference
along with a scanning Michelson interferometer to make precise measurements on
the $D_1$ and $D_2$ lines of potassium. The Rb reference frequency is known
with sub-MHz accuracy. We obtain the following values for the energy levels: 12
985.169 60(13)(15) cm$^{-1}$ for the $4P_{1/2}$ state ($D_1$ line); 13 042.875
95(14)(15) cm$^{-1}$ for the $4P_{3/2}$ state ($D_2$ line); and 57.706
35(19)(15) cm$^{-1}$ for the $4P_{3/2}-4P_{1/2}$ fine-structure interval. The
leading source of systematic error cancels in the determination of the
interval. The errors represent about an order of magnitude improvement over
tabulated values.


title:
Giant Magnetic Moments of Nitrogen Stabilized Mn Clusters and Their
  Relevance to Ferromagnetism in Mn Doped GaN

abstract:
  Using first principles calculations based on density functional theory, we
show that the stability and magnetic properties of small Mn clusters can be
fundamentally altered by the presence of nitrogen. Not only are their binding
energies substantially enhanced, but also the coupling between the magnetic
moments at Mn sites remains ferromagnetic irrespective of their size or shape.
In addition, these nitrogen stabilized Mn clusters carry giant magnetic moments
ranging from 4 Bohr magnetons in MnN to 22 Bohr magnetons in Mn_5N. It is
suggested that the giant magnetic moments of Mn_xN clusters may play a key role
in the ferromagnetism of Mn doped GaN which exhibit a wide range (10K - 940K)
of Curie temperatures.


title:
A Non-equilibrium Thermodynamic Framework for the Dynamics and Stability
  of Ecosystems

abstract:
  The population dynamics and stability of ecosystems of interacting species is
studied from the perspective of non-equilibrium thermodynamics by assuming that
species, through their biotic and abiotic interactions, are units of entropy
production and exchange in an open thermodynamic system with constant external
constraints. Within the context of the linear theory of irreversible
thermodynamics, such a system will naturally evolve towards a stable stationary
state in which the production of entropy within the ecosystem is at a local
minimum value. It is shown that this extremal condition leads to equations for
the stationary (steady) state population dynamics of interacting species, more
general than those of Lotka-Volterra, and to conditions on the parameters of
the community interaction matrix guaranteeing ecosystem stability. The
paradoxical stability of real complex ecosystems thus has a simple explanation
within the proposed framework. Furthermore, it is shown that the second law of
thermodynamics constrains the inter- and intra-species interaction coefficients
in the sense of maintaining stability during evolution from one stationary
state to another. A firm connection is thus established between the second law
of thermodynamics and natural selection.


title: Electromagnetic nonlinear X-waves

abstract:
  Nonlinear optical media that are normally dispersive, support a new type of
localized (nondiffractive and nondispersive) wavepackets that are X-shaped in
space and time and have slower than exponential decay. High-intensity X-waves,
unlike linear ones, can be formed spontaneously through a trigger mechanism of
conical emission, thus playing an important role in experiments.


title: The negative index of refraction demystified

abstract:
  We study electromagnetic wave propagation in mediums in which the effective
relative permittivity and the effective relative permeability are allowed to
take any value in the upper half of the complex plane. A general condition is
derived for the phase velocity to be oppositely directed to the power flow.
That extends the recently studied case of propagation in mediums for which the
relative permittivity and relative permeability are both simultaneously
negative, to include dissipation as well. An illustrative case study
demonstrates that in general the spectrum divides into five distinct regions.


title: Inductive Logic: From Data Analysis to Experimental Design

abstract:
  In celebration of the work of Richard Threlkeld Cox, we explore inductive
logic and its role in science touching on both experimental design and analysis
of experimental results. In this exploration we demonstrate that the duality
between the logic of assertions and the logic of questions has important
consequences. We discuss the conjecture that the relevance or bearing, b, of a
question on an issue can be expressed in terms of the probabilities, p, of the
assertions that answer the question via the entropy.
  In its application to the scientific method, the logic of questions,
inductive inquiry, can be applied to design an experiment that most effectively
addresses a scientific issue. This is performed by maximizing the relevance of
the experimental question to the scientific issue to be resolved. It is shown
that these results are related to the mutual information between the experiment
and the scientific issue, and that experimental design is akin to designing a
communication channel that most efficiently communicates information relevant
to the scientific issue to the experimenter. Application of the logic of
assertions, inductive inference (Bayesian inference) completes the experimental
process by allowing the researcher to make inferences based on the information
obtained from the experiment.


title:
Electron-hydrogen scattering in Faddeev-Merkuriev integral equation
  approach

abstract:
  Electron-hydrogen scattering is studied in the Faddeev-Merkuriev integral
equation approach. The equations are solved by using the Coulomb-Sturmian
separable expansion technique. We present $S$- and $P$-wave scattering and
reactions cross sections up to the $H(n=4)$ threshold.


title: A Simple Model for the Evolution of Evolution

abstract:
  A simple model of macroevolution is proposed exhibiting both the property of
punctuated equilibrium and the dynamics of potentialities for different species
to evolve towards increasingly higher complexity. It is based on the phenomenon
of "fractal evolution" which has been shown to constitute a fundamental
property of nonlinear discretized systems with one memory- or random-based
feedback loop. The latter involves a basic "cognitive" function of each species
given by the power of distinction of states within some predefined resolution.
The introduction of a realistic background noise limiting the range of the
feedback operation yields a pattern signature in fitness space with a
distribution of temporal boost/mutation distances according to a randomized
devil's staircase function. Introducing a further level in the hierarchy of the
system's rules, the possibility of an adaptive evolutionary change of the
resolution itself is implemented, thereby providing a time-dependent measure of
the species' cognitive abilities: an additional feedback loop makes use of the
inevitable intrinsic fluctuations within the fitness landscape to direct the
temporal change of the resolution. Feeding back the small adaptive changes of
resolution into the essentially directionless variations of the patterns'
lifetimes in fitness space effectively leads to a clear tendency towards
increasing evolution potentials for each species ("hierarchically emergent
fractal evolution").


title: Un nouveau regard sur le monde physique

abstract:
  Dans ce colloque je discute la notion d'espace selon Descartes et Leibniz et
j'y oppose le point de vue de Samuel Clarke et Isaac Newton comme solution pour
comprendre la r\'ealit\'e du monde physique


title: Introduction \`a la Physique Quantique

abstract:
  En nous laissant guider par la notion de champ qui en fait domine toute la
physique nous d\'efinissons la nature physique d'un syst\`eme, ses
propri\'et\'es et ses \'etats possibles. Nous proposons alors un cadre tr\`es
g\'en\'erale permettant la description de tels syst\`emes et la construction de
mod\`eles consistants. Nous en donnons des exemples et pour illustrer les
concepts de notre th\'eorie nous d\'ecrivons diff\'erents types d'\'evolutions.
Pour terminer nous discutons en d\'etails un processus physique, les \'echos de
spins.


title: The Cosmology of Fluctuations

abstract:
  We review a cosmology in which particles are fluctuationally created from a
background Zero Point Field. This cosmology is consistent with recent
observations of an ever expanding and accelerating universe, as also the
recently confirmed evolution of the fine structure constant. All hitherto
mysterious and accidental, so called Large Number coincidences, infact follow
from the theory.


title:
Chaotic Temperatures vs Coefficients of Thermodynamic Activity: The
  Advantage of the Method of Chemical Dynamics

abstract:
  The article compares traditional coefficients of thermodynamic activity as a
parameter related to individual chemical species to newly introduced reduced
chaotic temperatures as system characteristics, both regarding their usage in
thermodynamic simulation of open chemical systems. Logical and mathematical
backgrounds of both approaches are discussed. It is shown that usage of reduced
chaotic temperatures and the Method of Chemical Dynamics to calculate chemical
and phase composition in open chemical systems is much less costly, easier to
perform and potentially leads to better precision.


title: Source separation as an exercise in logical induction

abstract:
  We examine the relationship between the Bayesian and information-theoretic
formulations of source separation algorithms. This work makes use of the
relationship between the work of Claude E. Shannon and the "Recent
Contributions" by Warren Weaver (Shannon & Weaver 1949) as clarified by Richard
T. Cox (1979) and expounded upon by Robert L. Fry (1996) as a duality between a
logic of assertions and a logic of questions. Working with the logic of
assertions requires the use of probability as a measure of degree of
implication. This leads to a Bayesian formulation of the problem. Whereas,
working with the logic of questions requires the use of entropy as a measure of
the bearing of a question on an issue leading to an information-theoretic
formulation of the problem.


title: Enhancement of the electron electric dipole moment in gadolinium 3+

abstract:
  There have been recent suggestions for searching for the electron electric
dipole moment, using solid state experiments with compounds containing Gd 3+
ions. These experiments could improve the sensitivity compared to present
atomic and molecular experiments by several orders of magnitude. The analysis
of the problem requires a calculation of the enhancement coefficient K for the
electron electric dipole moment in the Gd 3+ ion. In this work we perform this
calculation. The result is K = -4.9 +- 1.6. Limitations of the accuracy of the
calculation are mainly due to the lack of data on Gd 3+ excitation spectra. We
formulate which quantities have to be measured and/or calculated to improve the
accuracy.


title:
The possible role of Salam's effect in the fundamental interactions
  unification

abstract:
  The possibility of the fundamental interactions unification arises at the
consideration of the field equation of the energy conservation if one takes
into account Salam's effect. Such account results in the functional division
between gravitational, strong and electromagnetic interactions. The division
has the differential nature which is connected with an expansion of the
relativistic kinetic energy into McLoren's series. It is shown that the
existance of the angular momentum is connected with stationary features of the
series. The gauge transformations of the wave function and potential arise due
to the influence of the geometrization principle - variations of the
non-relativistic kinetic energy have to be equal to variations of the potential
energy on absolute value in the connected systems. The numerical quantities of
the elementary angular momentum, constant of the gravitational interaction and
the ratio of the rest masses of the proton and electron are coordinated with
corresponding experimental quantities.


title: An algorithm for calculating the Lorentz angle in silicon detectors

abstract:
  Future experiments will use silicon sensors in the harsh radiation
environment of the LHC (Large Hadron Collider) and high magnetic fields. The
drift direction of the charge carriers is affected by the Lorentz force due to
the high magnetic field. Also the resulting radiation damage changes the
properties of the drift.
  In this paper measurements of the Lorentz angle of electrons and holes before
and after irradiation are reviewed and compared with a simple algorithm to
compute the Lorentz angle.


title: Nonrelativistic ionization energy for the helium ground state

abstract:
  The helium ground state nonrelativistic energy with 24 significant digits is
presented. The calculations are based on variational expansion with randomly
chosen exponents. This data can be used as a benchmark for other approaches for
many electron and/or three-body systems.


title: Towards a sufficient criterion for collapse in 3D Euler equations

abstract:
  A sufficient integral criterion for a blow-up solution of the Hopf equations
(the Euler equations with zero pressure) is found. This criterion shows that a
certain positive integral quantity blows up in a finite time under specific
initial conditions. Blow-up of this quantity means that solution of the Hopf
equation in 3D can not be continued in the Sobolev space $H^2({\cal R}^3)$ for
infinite time.


title:
Manifestation of the Nuclear Anapole Moment in M1 Transitions in
  Thallium

abstract:
  We calculate nuclear spin-dependent parity non-conserving $E1$-amplitudes for
optical transition $6p_{1/2,F} -> 6p_{3/2,F'}$ and for hyperfine transition
$6p_{1/2,F} -> 6p_{1/2,F'}$ in Tl. Experimental limit on the former amplitude
placed by Vetter et al. [PRL, 74, 2658 (1995)] corresponds to the anapole
moment constant $\kappa_a = -0.26 \pm 0.27$. Experiment on the hyperfine
transition can give direct measurement of the spin-dependent amplitude, because
spin-independent amplitude turns to zero.


title:
Suppression of inhomogeneous broadening in rf spectroscopy of optically
  trapped atoms

abstract:
  We present a novel method for reducing the inhomogeneous frequency broadening
in the hyperfine splitting of the ground state of optically trapped atoms. This
reduction is achieved by the addition of a weak light field, spatially
mode-matched with the trapping field and whose frequency is tuned in-between
the two hyperfine levels. We experimentally demonstrate the new scheme with Rb
85 atoms, and report a 50-fold narrowing of the rf spectrum.


title: Field Theory Revisited

abstract:
  Following P. A. M. Dirac's critique in ``Lectures on Quantum Field Theory''
of the usual formalism, I will discuss the role of the time parameter to solve
R. Haag's no-go theorem on the non-equivalence of the conventional
Schr\"odinger picture and the Heisenberg picture. This is possible by first
defining in a correct way the concept of the vacuum state at a given time in
relativity. I will also discuss some consequences such as the spectral
condition.


title: Neutral Plasma Oscillations at Zero Temperature

abstract:
  We use cold plasma theory to calculate the response of an ultracold neutral
plasma to an applied rf field. The free oscillation of the system has a
continuous spectrum and an associated damped quasimode. We show that this
quasimode dominates the driven response. We use this model to simulate plasma
oscillations in an expanding ultracold neutral plasma, providing insights into
the assumptions used to interpret experimental data [Phys. Rev. Lett. 85, 318
(2000)].


title:
Separation of multiple evoked responses using differential amplitude and
  latency variability

abstract:
  In neuroelectrophysiology one records electric potentials or magnetic fields
generated by ensembles of synchronously active neurons in response to
externally presented stimuli. These evoked responses are often produced by
multiple generators in the presence of ongoing background activity. While
source localization techniques or current source density estimation are usually
used to identify generators, application of blind source separation techniques
to obtain independent components has become more popular.
  We approach this problem by applying the Bayesian methodology to a more
physiologically-realistic source model. As it is generally accepted that single
trials vary in amplitude and latency, we incorporate this variability into the
model. Rather than making the unrealistic assumption that these cortical
components are independent of one another, our algorithm utilizes the
differential amplitude and latency variability of the evoked waveforms to
identify the cortical components. The algorithm is applied to
intracortically-recorded local field potentials in monkeys performing a
visuomotor task.

categories: physics.med-ph physics.bio-ph physics.data-an q-bio.NC


title: Negative index of refraction and distributed Bragg reflectors

abstract:
  The Bragg regime shifts when conventional materials in a multilayer
distributed Bragg reflector (DBR) are replaced by artificial materials with the
so-called negative index of refraction. This provides an avenue for
characterizing the latter class of materials.


title:
Local approximation for contour dynamics in effectively two-dimensional
  ideal electron-magnetohydrodynamic flows

abstract:
  The evolution of piecewise constant distributions of a conserved quantity
related to the frozen-in canonical vorticity in effectively two-dimensional
incompressible ideal EMHD flows is analytically investigated by the Hamiltonian
method. The study includes the case of axisymmetric flows with zero azimuthal
velocity component and also the case of flows with the helical symmetry of
vortex lines. For sufficiently large size of such a patch of the conserved
quantity, a local approximation in the dynamics of the patch boundary is
suggested, based on the possibility to represent the total energy as the sum of
area and boundary terms. Only the boundary energy produces deformation of the
shape with time. Stationary moving configurations are described.


title: On the nonlinear dynamics of topological solitons in DNA

abstract:
  Dynamics of topological solitons describing open states in the DNA double
helix are studied in the frameworks of the model which takes into account
asymmetry of the helix. It is shown that three types of topological solitons
can occur in the DNA double chain. Interaction between the solitons, their
interactions with the chain inhomogeneities and stability of the solitons with
respect to thermal oscillations are investigated.


title:
The finite-temperature Monte Carlo method and its application to
  superfluid helium clusters

abstract:
  We review the use of the path integral Monte Carlo (PIMC) methodology to the
study of finite-size quantum clusters, with particular emphasis on recent
applications to pure and impurity-doped He clusters. We describe the principles
of PIMC, the use of the multilevel Metropolis method for sampling particle
permutations, and the methods used to accurately incorporate anisotropic
molecule-helium interactions into the path integral scheme. Applications to
spectroscopic studies of embedded atoms and molecules are summarized, with
discussion of the new concepts of local and nanoscale superfluidity that have
been generated by recent PIMC studies of the impurity-doped He clusters.


title:
Transverse self-fields within an electron bunch moving in an arc of a
  circle

abstract:
  As a consequence of motions driven by external forces, self-fields (which are
different from the static case) originate within an electron bunch. In the case
of magnetic external forces acting on an ultrarelativistic beam, the
longitudinal self-interactions are responsible for CSR (Coherent Synchrotron
Radiation)-related phenomena, which have been studied extensively. On the other
hand, transverse self-interactions are present too. At the time being, existing
theoretical analysis of transverse self-forces deal with the case of a bunch
moving along a circular orbit only, without considering the situation of a
bending magnet with a finite length. In this paper we propose an
electrodynamical analysis of transverse self-fields which originate, at the
position of a test particle, from an ultrarelativistic electron bunch moving in
an arc of a circle. The problem will be first addressed within a two-particle
system. We then extend our consideration to a line bunch with a stepped density
distribution, a situation which can be easily generalized to the case of an
arbitrary density distribution. Our approach turns out to be also useful in
order to get a better insight in the physics involved in the case of simple
circular motion and in order to address the well known issue of the partial
compensation of transverse self-force.


title:
Evolving Networks with Multi-species Nodes and Spread in the Number of
  Initial Links

abstract:
  We consider models for growing networks incorporating two effects not
previously considered: (i) different species of nodes, with each species having
different properties (such as different attachment probabilities to other node
species); and (ii) when a new node is born, its number of links to old nodes is
random with a given probability distribution. Our numerical simulations show
good agreement with analytic solutions. As an application of our model, we
investigate the movie-actor network with movies considered as nodes and actors
as links.


title:
Determination of Functional Network Structure from Local Parameter
  Dependence Data

abstract:
  In many applications, such as those arising from the field of cellular
networks, it is often desired to determine the interaction (graph) structure of
a set of differential equations, using as data measured sensitivities. This
note proposes an approach to this problem.


title:
Decomposition of multicomponent mass spectra using Bayesian probability
  theory

abstract:
  We present a method for the decomposition of mass spectra of mixture gases
using Bayesian probability theory. The method works without any calibration
measurement and therefore applies also to the analysis of spectra containing
unstable species. For the example of mixtures of three different hydrocarbon
gases the algorithm provides concentrations and cracking coefficients of each
mixture component as well as their confidence intervals. The amount of
information needed to obtain reliable results and its relation to the accuracy
of our analysis are discussed.


title:
Simple Mechanical Equivalents of Stepping Rotary Dynamics in
  F$_1$-ATPase

abstract:
  Two simple (rotator and one-particle) mechanistic models are suggested to
describe simultaneously at a minimal level of sophistication two basic
functions of F$_1$-ATPase: a motor regime driven by ATP hydrolysis and its
inverted function as ATP synthesis. This description is consistent with the
so-called rotary binding-change mechanism, a milestone of functioning ATP
synthase, and uses a stepping (driving) function associated with two sequences
of time instants, at which hydrolysis and synthesis reactions occur. It is
useful to analyse experimental data and numerical simulations indeed predict
corresponding dynamic behavior.


title:
Fourier imaging study of efficient near-field optical coupling in solid
  immersion fluorescence microscopy

abstract:
  We measured images and Fourier images of fluorescence for 0.11- and
0.22-$\mu$m-diameter dye-doped polystyrene micro-sphere beads on a solid
immersion lens, and experimentally verified strongly-angle-dependent
fluorescence intensities due to efficient near-field optical coupling in solid
immersion fluorescence microscopy. The results are interpreted in comparison
with calculated emission patterns of an emission dipole placed near a solid
surface, which establish a basic model for high-collection efficiency in
solid-immersion fluorescence microscopy.


title: Energy Loss of a High Charge Bunched Electron Beam in Plasma

abstract:
  There has been much interest in the blowout regime of plasma wakefield
acceleration (PWFA), which features ultra-high fields and nonlinear plasma
motion. Using an exact analysis, we examine here a fundamental limit of
nonlinear PWFA excitation, by an infinitesimally short, relativistic electron
beam. The beam energy loss in this case is shown to be linear in charge even
for nonlinear plasma response, where a normalized, unitless charge exceeds
unity. The physical basis for this effect is discussed, as are deviations from
linear behavior observed in simulations with finite length beams.


title: Molecular gyroscopes and biological effects of weak ELF magnetic fields

abstract:
  Extremely-low-frequency magnetic fields are known to affect biological
systems. In many cases, biological effects display `windows' in biologically
effective parameters of the magnetic fields: most dramatic is the fact that
relatively intense magnetic fields sometimes do not cause appreciable effect,
while smaller fields of the order of 10--100 $\mu$T do. Linear resonant
physical processes do not explain frequency windows in this case. Amplitude
window phenomena suggest a nonlinear physical mechanism. Such a nonlinear
mechanism has been proposed recently to explain those `windows'. It considers
quantum-interference effects on protein-bound substrate ions. Magnetic fields
cause an interference of ion quantum states and change the probability of
ion-protein dissociation. This ion-interference mechanism predicts specific
magnetic-field frequency and amplitude windows within which biological effects
occur. It agrees with a lot of experiments. However, according to the
mechanism, the lifetime $\Gamma^{-1}$ of ion quantum states within a protein
cavity should be of unrealistic value, more than 0.01 s for frequency band
10--100 Hz. In this paper, a biophysical mechanism has been proposed that (i)
retains the attractive features of the ion interference mechanism and (ii) uses
the principles of gyroscopic motion and removes the necessity to postulate
large lifetimes. The mechanism considers dynamics of the density matrix of the
molecular groups, which are attached to the walls of protein cavities by two
covalent bonds, i.e., molecular gyroscopes. Numerical computations have shown
almost free rotations of the molecular gyros. The relaxation time due to van
der Waals forces was about 0.01 s for the cavity size of 28 angstr\"{o}ms.


title:
A Polarized Electron RF Photoinjector Using the Plane-Wave-Transformer
  (PWT) Design

abstract:
  Polarized electron beams are now in routine use in particle accelerators for
nuclear and high energy physics experiments. These beams are presently produced
by dc-biased photoelectron sources combined with rf chopping and bunching
systems with inherently high transverse emittances. Low emittances can be
produced with an rf gun, but the vacuum environment has until now been
considered too harsh to support a negative electron affinity GaAs photocathode.
We propose to significantly improve the vacuum conditions by adapting a PWT rf
photoinjector to achieve reasonable cathode emission rates and lifetimes. This
adaptation can also be combined with special optics that will result in a flat
beam with a normalized rms emittance in the narrow dimension that may be as low
as 10-8 m.


title: Computer simulations discussed in physical terms and terminology

abstract:
  As known, any numerical simulation is composed of two parts: (1) the initial
part of writing the relevant code and (2) the running of this code on the
computer screen. The second part of running the program is extensively
discussed theoretically and technically in the relevant literature. In this
work we pay special attention to the less discussed first part and show that it
may be discussed in a terminology and notation which describe physical
phenomena. As examples we discuss the two cases of simulating (1) the harmonic
oscillator and (2) the electron-photon interaction which results in the known
Lamb shift.


title: Motivations to modify special relativity

abstract:
  In the framework of special relativity, all particles are point-like or
string-like. This nature of particles has caused the divergence difficulties in
quantum field, string and superstring theories. In the framework of special
relativity, due to the non-uniformity of the m-space and phase space in the
usual inertial coordinate system, Boltzmann's hypothesis of the equality of the
probability of equal volume element is no longer appropriate. That makes it
very difficult to construct Lorentz-invariant statistical mechanics and
thermodynamics for many-particle systems. Besides, some observations on special
relativity itself and its experimental facts are also reported. The conclusions
from these observations are: Special relativity is not an ultimate theory; Some
modification is needed; Any modification must not violate the constancy of the
light speed and the local Lorentz invariance; It seems that we have to change
the assumption on local structures of gravity-free space and time in special
relativity.