title:
Derivation of the Lorentz Force Law and the Magnetic Field Concept using
  an Invariant Formulation of the Lorentz Transformation

abstract:
  It is demonstrated how the right hand sides of the Lorentz Transformation
equations may be written, in a Lorentz invariant manner, as 4--vector scalar
products. The formalism is shown to provide a short derivation, in which the
4--vector electromagnetic potential plays a crucial role, of the Lorentz force
law of classical electrodynamics, and the conventional definition of the
magnetic field in terms spatial derivatives of the 4--vector potential. The
time component of the relativistic generalisation of the Lorentz force law is
discussed. An important physical distinction between the space-time and
energy-momentum 4--vectors is also pointed out.


title: Intercluster Correlation in Seismicity

abstract:
  Mega et al.(cond-mat/0212529) proposed to use the ``diffusion entropy'' (DE)
method to demonstrate that the distribution of time intervals between a large
earthquake (the mainshock of a given seismic sequence) and the next one does
not obey Poisson statistics. We have performed synthetic tests which show that
the DE is unable to detect correlations between clusters, thus negating the
claimed possibility of detecting an intercluster correlation. We also show that
the LR model, proposed by Mega et al. to reproduce inter-cluster correlation,
is insufficient to account for the correlation observed in the data.


title: The Intrinsic Time Scale of Transient Neuronal Responses

abstract:
  In a generic neuron model, we present the linear response theory for the
firing rate in response to both time dependent input currents and noise
amplitudes. In both cases the signal transmission is strongly attenuated for
frequencies above the stationary firing rate. For high frequencies both the
mean input and the noise transmission function decay as \omega^{-2},
independent of model details. Our results indicate that previously suggested
mechanisms for near instantaneous transmission of information are not
consistent with the spike generation mechanism of real neurons.


title: A Growth Model for Multicellular Tumor Spheroids

abstract:
  Most organisms grow according to simple laws, which in principle can be
derived from energy conservation and scaling arguments, critically dependent on
the relation between the metabolic rate B of energy flow and the organism mass
m. Although this relation is generally recognized to be of the form B(m) = mp,
the specific value of the exponent p is the object of an ongoing debate, with
many mechanisms being postulated to support different predictions. We propose
that multicellular tumor spheroids provide an ideal experimental model system
for testing these allometric growth theories, especially under controlled
conditions of malnourishment and applied mechanical stress.


title: Three dimensional imaging of short pulses

abstract:
  We exploit a slightly noncollinear second-harmonic cross-correlation scheme
to map the 3D space-time intensity distribution of an unknown complex-shaped
ultrashort optical pulse. We show the capability of the technique to
reconstruct both the amplitude and the phase of the field through the coherence
of the nonlinear interaction down to a resolution of 10 $\mu$m in space and 200
fs in time. This implies that the concept of second-harmonic holography can be
employed down to the sub-ps time scale, and used to discuss the features of the
technique in terms of the reconstructed fields.


title: Entropy Estimates from Insufficient Samplings

abstract:
  We present a detailed derivation of some estimators of Shannon entropy for
discrete distributions. They hold for finite samples of N points distributed
into M "boxes", with N and M -> oo, but N/M < oo. In the high sampling regime
(<< 1 points in each box) they have exponentially small biases. In the low
sampling regime the errors increase but are still much smaller than for most
other estimators. One advantage is that our main estimators are given
analytically, with explicitly known analytical formulas for the biases.


title: Braided nodal lines in wave superpositions

abstract:
  Nodal lines (phase singularities, optical vortices) are the generic
interference fringes of complex scalar waves. Here, an exact complex solution
of the time independent wave equation (Helmholtz equation) is considered,
possessing nodal lines which are braided in the form of a borromean, or
pig-tail braid. The braid field is a superposition of counterpropagating,
counterrotating, non-coaxial third order Bessel beams, and a plane wave whose
propagation is perpendicular to that of the beams. The construction is
structurally stable, and can be generalized to a limited class of other braids.


title: A Bound on Mixing Efficiency for the Advection-Diffusion Equation

abstract:
  An upper bound on the mixing efficiency is derived for a passive scalar under
the influence of advection and diffusion with a body source. For a given
stirring velocity field, the mixing efficiency is measured in terms of an
equivalent diffusivity, which is the molecular diffusivity that would be
required to achieve the same level of fluctuations in the scalar concentration
in the absence of stirring, for the same source distribution. The bound on the
equivalent diffusivity depends only on the functional "shape" of both the
source and the advecting field. Direct numerical simulations performed for a
simple advecting flow to test the bounds are reported.


title: Constrained-Hamiltonian Shallow-Water Dynamics on the Sphere

abstract:
  Salmon's nearly geostrophic model for rotating shallow-water flow is derived
in full spherical geometry. The model, which results upon constraining the
velocity field to the height field in Hamilton's principle for rotating
shallow-water dynamics, constitutes an important prototype of Hamiltonian
balanced models. Instead of Salmon's original approach, which consists in
taking variations of particle paths at fixed Lagrangian labels and time, Holm's
approach is considered here, namely variations are taken on Lagrangian particle
labels at fixed Eulerian positions and time. Unlike the classical
quasigeostrophic model, Salmon's is found to be sensitive to the differences
between geographic and geodesic coordinates. One consequence of this result is
that the $\beta $ plane approximation, which is included in Salmon's original
derivation, is not consistent for this class of model.


title: Deep ocean influence on upper ocean baroclinic instability saturation

abstract:
  In this paper we extend earlier results regarding the effects of the lower
layer of the ocean (below the thermocline) on the baroclinic instability within
the upper layer (above the thermocline). We confront quasigeostrophic
baroclinic instability properties of a 2.5-layer model with those of a 3-layer
model with a very thick deep layer, which has been shown to predict spectral
instability for basic state parameters for which the 2.5-layer model predicts
nonlinear stability. We compute and compare maximum normal-mode perturbation
growth rates, as well as rigorous upper bounds on the nonlinear growth of
perturbations to unstable basic states, paying particular attention to the
region of basic state parameters where the stability properties of the 2.5- and
3-layer model differ substantially. We found that normal-mode perturbation
growth rates in the 3-layer model tend to maximize in this region. We also
found that the size of state space available for eddy-amplitude growth tends to
minimize in this same region. Moreover, we found that for a large spread of
parameter values in this region the latter size reduces to only a small
fraction of the total enstrophy of the system, thereby allowing us to make
assessments of the significance of the instabilities.


title: Modeling Amyloid Beta Peptide Insertion into Lipid Bilayers

abstract:
  Inspired by recent suggestions that the Alzheimer's amyloid beta peptide (A
beta) can insert into cell membranes and form harmful ion channels, we model
insertion of the 40 and 42 residue forms of the peptide into cell membranes
using a Monte Carlo code which is specific at the amino acid level. We examine
insertion of the regular A-beta peptide as well as mutants causing familial
Alzheimer's disease, and find that all but one of the mutants change the
insertion behavior by causing the peptide to spend more simulation steps in
only one leaflet of the bilayer. We also find that A-beta 42, because of the
extra hydrophobic residues relative to A-beta 40, is more likely to adopt this
conformation than A-beta 40 in both wild-type and mutant forms. We argue
qualitatively why these effects happen. Here, we present our results and
develop the hypothesis that this partial insertion increases the probability of
harmful channel formation. This hypothesis can partly explain why these
mutations are neurotoxic simply due to peptide insertion behavior. We further
apply this model to various artificial A-beta mutants which have been examined
experimentally, and offer testable experimental predictions contrasting the
roles of aggregation and insertion with regard to toxicity of A-beta mutants.
These can be used through further experiments to test our hypothesis.

categories: physics.bio-ph physics.comp-ph physics.med-ph q-bio.BM


title: Light Propagation in Turbulent Media

abstract:
  First, we make a revision of the up-to-date Passive Scalar Fields properties:
also, the refractive index is among them. Afterwards, we formulated the
properties that make the family of `isotropic' fractional Brownian motion (with
parameter H) a good candidate to simulate the turbulent refractive index.
Moreover, we obtained its fractal dimension which matches the estimated by
Constantin for passive scalar, and thus the parameter H determines the state of
the turbulence.
  Next, using a path integral velocity representation, with the Markovian
model, to calculate the effects of the turbulence over a system of grids.
  Finally, with the tools of Stochastic Calculus for fractional Brownian
motions we studied the ray-equation coming from the Geometric Optics in the
turbulent case. Our analysis covers those cases where average temperature
gradients are relevant.

categories: physics.optics physics.ao-ph physics.data-an physics.flu-dyn


title: Classroom computer animations of relativistic objects

abstract:
  This is a short note to announce the availability of some movies that may be
useful in classroom discussions on the photographic appearance of objects
moving at relativistic speeds. The images are based on special relativity with
no account taken of (other than to ignore) the effects of doppler shifts,
intensity shifts or gravitational effects.


title: Defining Civilization utilizing Anthropic Reasoning

abstract:
  We utilize anthropic reasoning to demonstrate that we are typical observers
of our reference class under a self-sampling assumption by investigating the
definition of what a civilization is. With reference to the conflict between
such reasoning and the observational lack of extra-terrestrial intelligent
life, we conclude that a part of our theoretical understanding of the Universe
will be at fault.


title: A Cosmic Ray Measurement Facility for ATLAS Muon Chambers

abstract:
  Monitored Drift Tube (MDT) chambers will constitute the large majority of
precision detectors in the Muon Spectrometer of the ATLAS experiment at the
Large Hadron Collider at CERN. For commissioning and calibration of MDT
chambers, a Cosmic Ray Measurement Facility is in operation at Munich
University. The objectives of this facility are to test the chambers and
on-chamber electronics, to map the positions of the anode wires within the
chambers with the precision needed for standalone muon momentum measurement in
ATLAS, and to gain experience in the operation of the chambers and on-line
calibration procedures.
  Until the start of muon chamber installation in ATLAS, 88 chambers built at
the Max Planck Institute for Physics in Munich have to be commissioned and
calibrated. With a data taking period of one day individual wire positions can
be measured with an accuracy of 8.3 micrometers in the chamber plane and 27
micrometers in the direction perpendicular to that plane.


title: Covariant Lagrangian Methods of Relativistic Plasma Theory

abstract:
  We obtain a covariant decomposition of the motion of a relativistic charged
particle into parallel motion and perpendicular gyration, and transform to
guiding-center coordinates using Lie transforms. The natural guiding-center
Poisson bracket structure and Hamiltonian are derived. The guiding-center
equations of motion are presented to one order higher than the usual drifts,
and the correction to the gyromomentum is given. We then allow for eikonal wave
perturbations to the Lagrangian action. We develop a manifestly gauge-invariant
and covariant oscillation-center theory to arbitrarily high order, and thereby
derive the relativistic ponderomotive Hamiltonian.
  We sum the guiding-center action over a distribution and add the Maxwell
action to obtain the total action of a guiding-center plasma. Upon variation,
this yields self-consistent covariant relativistic kinetic and field equations;
from these we identify the guiding-center current density and the
guiding-center magnetization. Noether's theorem then yields covariant
conservation laws for the momentum-energy and the angular momentum of a
relativistic guiding-center plasma; from these we identify the guiding-center
stress-energy tensor and the guiding-center spin angular momentum tensor.
Repeating this calculation for guiding/oscillation centers, we find that
variation yields self-consistent relativistic kinetic and field equations for
the plasma in the wave field, including the wave dispersion relation; from
these we identify the wave magnetization and susceptibility. Noether's theorem
then yields conservation laws for the guiding-center plasma in the presence of
a wave field, including the wave contribution to the stress-energy and spin
angular momentum tensors.


title: Parameterized optimized effective potential for atoms

abstract:
  The optimized effective potential equations for atoms have been solved by
parameterizing the potential. The expansion is tailored to fulfill the known
asymptotic behavior of the effective potential at both short and long
distances. Both single configuration and multi configuration trial wave
functions are implemented. Applications to several atomic systems are presented
improving previous works. The results here obtained are very close to those
calculated in either the Hartree-Fock and the multi configurational
Hartree-Fock framework.


title: A novel view of plane wave expansion method in photonic crystals

abstract:
  We propose a method derived from the simple plane wave expansion that can
easily solve the interface problem between vacuum and a semi-infinite photonic
crystal. The method is designed to find the complete set of all the
eigenfunctions, propagating or evanescent, of the translation operators $\{{\bf
T_R} \}$, at a fixed frequency. With these eigenfunctions and their
eigenvalues, the transmitted and reflected waves can be determined. Two kinds
of applications are presented for 2D photonic crystals. The first is a
selection rule for determine the normal direction of the vacuum-photonic
crystal interface to achieve the highest attenuation effect at a gap frequency.
The second is to calculate the transmittance and reflectance for a light
incident from vacuum to an semi-infinite photonic crystal. As an example we
recalculate a system studied previously by K. Sakoda et al. and get results in
agreement with theirs.


title:
Positron plasma diagnostics and temperature control for antihydrogen
  production

abstract:
  Production of antihydrogen atoms by mixing antiprotons with a cold, confined,
positron plasma depends critically on parameters such as the plasma density and
temperature. We discuss non-destructive measurements, based on a novel,
real-time analysis of excited, low-order plasma modes, that provide
comprehensive characterization of the positron plasma in the ATHENA
antihydrogen apparatus. The plasma length, radius, density, and total particle
number are obtained. Measurement and control of plasma temperature variations,
and the application to antihydrogen production experiments are discussed.


title:
Position Sensing from Charge Dispersion in Micro-Pattern Gas Detectors
  with a Resistive Anode

abstract:
  Micro-pattern gas detectors, such as the Gas Electron Multiplier (GEM) and
the Micromegas need narrow high density anode readout elements to achieve good
spatial resolution. A high-density anode readout would require an unmanageable
number of electronics channels for certain potential micro-detector
applications such as the Time Projection Chamber. We describe below a new
technique to achieve good spatial resolution without increasing the electronics
channel count in a modified micro-detector outfitted with a high surface
resistivity anode readout structure. The concept and preliminary measurements
of spatial resolution from charge dispersion in a modified GEM detector with a
resistive anode are described below.


title: Effective equations for discrete systems: A time stepper based approach

abstract:
  We propose a computer-assisted approach to studying the effective continuum
behavior of spatially discrete evolution equations. The advantage of the
approach is that the "coarse model" (the continuum, effective equation) need
not be explicitly constructed. The method only uses a time-integration code for
the discrete problem and judicious choices of initial data and integration
times; our bifurcation computations are based on the so-called Recursive
Projection Method (RPM) with arc-length continuation (Shroff and Keller, 1993).
The technique is used to monitor features of the genuinely discrete problem
such as the pinning of coherent structures and its results are compared to
quasi-continuum approaches such as the ones based on Pade approximations.


title:
High nuclear polarization of helium-3 at low and high pressure by
  metastability exchange optical pumping at 1.5 Tesla

abstract:
  We perform metastability exchange optical pumping of helium-3 in a strong
magnetic field of 1.5 T. The achieved nuclear polarization, from 80% at 1.33
mbar to 25% at 67 mbar, shows a substantial improvement at high pressures with
respect to standard low-field optical pumping. The specific mechanisms of
metastability exchange optical pumping at high field are investigated,
advantages and intrinsic limitations are discussed. From a practical point of
view, our results open the way to alternative technological solutions for
polarized helium-3 applications and in particular for magnetic resonance
imaging of human lungs.


title: Synchronization of active mechanical oscillators by an inertial load

abstract:
  Motivated by the operation of myogenic (self-oscillatory) insect flight
muscle, we study a model consisting of a large number of identical oscillatory
contractile elements joined in a chain, whose end is attached to a damped
mass-spring oscillator. When the inertial load is small, the serial coupling
favors an antisynchronous state in which the extension of one oscillator is
compensated by the contraction of another, in order to preserve the total
length. However, a sufficiently massive load can sychronize the oscillators and
can even induce oscillation in situations where isolated elements would be
stable. The system has a complex phase diagram displaying quiescent,
synchronous and antisynchrononous phases, as well as an unsual asynchronous
phase in which the total length of the chain oscillates at a different
frequency from the individual active elements.


title:
Exploring the Harmony between Theory and Computation - Toward a unified
  electronic structure theory

abstract:
  The physical aspect of a general perturbation theory is explored. Its role as
a physical principle for understanding the interaction among the matters with
different levels of hierarchy is appreciated. It is shown that the general
perturbation theory can not only be used for understanding the various
electronic phenomena including the nature of chemical bonds but also serve as a
unified theme for constructing general electronic structure theories and
calculation schemes.


title: GPCALMA: a Grid Approach to Mammographic Screening

abstract:
  The next generation of High Energy Physics experiments requires a GRID
approach to a distributed computing system and the associated data management:
the key concept is the "Virtual Organisation" (VO), a group of geographycally
distributed users with a common goal and the will to share their resources. A
similar approach is being applied to a group of Hospitals which joined the
GPCALMA project (Grid Platform for Computer Assisted Library for MAmmography),
which will allow common screening programs for early diagnosis of breast and,
in the future, lung cancer. HEP techniques come into play in writing the
application code, which makes use of neural networks for the image analysis and
shows performances similar to radiologists in the diagnosis. GRID technologies
will allow remote image analysis and interactive online diagnosis, with a
relevant reduction of the delays presently associated to screening programs.


title:
Dramatic Shape Sensitivity of Directional Emission Patterns from
  Similarly Deformed Cylindrical Polymer Lasers

abstract:
  Recent experiments on similarly shaped polymer micro-cavity lasers show a
dramatic difference in the far-field emission patterns. We show for different
deformations of the ellipse, quadrupole and hexadecapole that the large
differences in the far-field emission patterns is explained by the differing
ray dynamics corresponding to each shape. Analyzing the differences in the
appropriate phase space for ray motion, it is shown that the differing
geometries of the unstable manifolds of periodic orbits are the decisive
factors in determining the far-field pattern. Surprisingly, we find that
strongly chaotic ray dynamics is compatible with highly directional emission in
the far-field.


title: Post glacial rebounds measure the viscosity of the lithosphere

abstract:
  The observed higher uplift rates before the end of deglaciation requires the
existence of a low viscosity channel or layer. The uplifts observed after the
end of deglaciation does not show any contribution from this low viscosity
channel and a homogeneous viscosity model fits very well to the observed
uplift. Most of the researchers therefore prefer the homogeneous model and
suggest that the higher uplift rate before the end of deglaciation is the
result of elastic contamination. It has been shown that the elastic deformation
of the lithosphere is far too small to be responsible for the observed extra
uplift; therefore, the homogeneous viscosity model should be discredited.
  The homogeneous viscosity of the postglacial period and the high uplift rate
of the late glacial period can be explained with a model which has an upper
layer determining the homogeneous viscosity and the layer below it which has a
low viscosity. The contribution to the uplift of this low viscosity layer is
indistinguishable from an instantaneous uplift.
  Current GPS deformation measurements indicating 10^21 Pas average viscosity
for the lithosphere, which is consistent with this model. The viscosity of the
low velocity zone should be between 10^18 Pas and 10^11 Pas. The lower
constrain on the viscosity of the low velocity zone can be deduced from seismic
observations. This viscosity model is consistent with post glacial rebounds and
further supported by the lack of the dynamic topography.


title: Biopolymer Elasticity

abstract:
  In recent years molecular elasticity has emerged as an active area of
research: there are experiments that probe mechanical properties of single
biomolecules such as DNA and Actin, with a view to understanding the role of
elasticity of these polymers in biological processes such as transcription and
protein-induced DNA bending. Single molecule elasticity has thus emerged as an
area where there is a rich cross-fertilization of ideas between biologists,
chemists and theoretical physicists. In this article we present a perspective
on this field of research.


title: Low-energy quadrupole modes in deformed clusters

abstract:
  Properties of low-energy (infra-red) quadrupole modes (LEQM) of multipolarity
$+AFw-lambda+AFw-mu =$20, 21 and 22 in deformed sodium clusters are studied
within the Kohn-Sham LDA RPA approach. Possible manifestations of LEQM in
stimulated Raman adiabatic passage (STIRAP) reaction are discussed. It is shown
that, in free light clusters, where the low-energy spectrum is delute, LEQM can
be unambiguously identified as particular electron-hole pairs. This gives a
chance to reconstruct the mean field level scheme near the Fermi surface.
Moreover, due to the connection with electric $+AFw-lambda+AFw-mu =$21 mode,
the scissors mode can be detected. In heavy (supported) oblate clusters, LEQM
are in general rather involved. Nevertheless, some interesting
$+AFw-lambda+AFw-mu =$21 and 22 structures determined by specific deformation
effects can be resolved. The origin of the structures is discussed in detail.


title: Maximum Probability and Maximum Entropy methods: Bayesian interpretation

abstract:
  (Jaynes') Method of (Shannon-Kullback's) Relative Entropy Maximization (REM
or MaxEnt) can be - at least in the discrete case - according to the Maximum
Probability Theorem (MPT) viewed as an asymptotic instance of the Maximum
Probability method (MaxProb). A simple bayesian interpretation of MaxProb is
given here. MPT carries the interpretation over into REM.


title: Maximum Entropy method with non-linear moment constraints: challenges

abstract:
  Traditionally, the Method of (Shannon-Kullback's) Relative Entropy
Maximization (REM) is considered with linear moment constraints. In this work,
the method is studied under frequency moment constraints which are non-linear
in probabilities. The constraints challenge some justifications of REM since a)
axiomatic systems are developed for classical linear moment constraints, b) the
feasible set of distributions which is defined by frequency moment constraints
admits several entropy maximizing distributions (I-projections), hence
probabilistic justification of REM via Conditioned Weak Law of Large Numbers
cannot be invoked. However, REM is not left completely unjustified in this
setting, since Entropy Concentration Theorem and Maximum Probability Theorem
can be applied.
  Maximum Renyi-Tsallis' entropy method (maxTent) enters this work because of
non-linearity of X-frequency moment constraints which are used in Non-extensive
Thermodynamics. It is shown here that under X-frequency moment constraints
maxTent distribution can be unique and different than the I-projection. This
implies that maxTent does not choose the most probable distribution and that
the maxTent distribution is asymptotically conditionally improbable. What are
adherents of maxTent accomplishing when they maximize Renyi's or Tsallis'
entropy?


title: The pushing force of a propagating electromagnetic wave

abstract:
  The effect of the electrodynamic forces on a charged particle in a
propagating plane electromagnetic wave is investigated. First it is pointed out
that for constant fields fulfilling the radiation condition there will be an
acceleration in the direction of the Poynting vector. When oscillating fields
are considered the Lorentz force on the particle only causes a drift, with
constant average velocity, in the direction of propagation of the wave, i.e.\
the direction of the Poynting vector. Finally, when the radiative reaction
(radiation damping) force is added the result is again an acceleration in the
direction of wave propagation. PACS classification numbers: 03.50.De, 41.60.-m,
41.75.Jv


title: Second harmonic generation in suspensions of spherical particles

abstract:
  We study the second harmonic generation (SHG) in a suspension of small
spherical particles confined within a slab, assuming undepleted pump and
applying (i) single scattering approximation and (ii) diffusion approximation.
In the case (i), the angular diagram, the differential and total crossections
of the SHG process, as well as the average cosine of SH scattering angle are
calculated. In the case (ii), the average SH intensity is found to show no
explicit dependence on the linear scattering properties of the suspension. The
average intensity of SH wave scales as I_0 L / \Lambda_2 in both cases (i) and
(ii), where I_0 is the intensity of the incident wave, L is the slab thickness,
and \Lambda_2 is an intensity-dependent "SH scattering" length.


title:
Free ion yield observed in liquid isooctane irradiated by gamma rays.
  Comparison with the Onsager theory

abstract:
  We have analyzed data on the free ion yield observed in liquid isooctane
irradiated by Co60 gamma rays within the framework of the Onsager theory about
initial recombination. Several distribution functions describing the electron
thermalization distance have been used and compared with the experimental
results: a delta function, a Gaussian type function and an exponential
function.
  A linear dependence between free ion yield and external electric field has
been found at low electric field values (E<1.2 MV/m) in excellent agreement
with the Onsager theory. At higher electric field values we obtain a solution
in power series of the external field using the Onsager theory.


title:
First results from cryogenic avalanche detectors based on gas electron
  multipliers

abstract:
  We study the performance of gaseous and two-phase (liquid-gas) cryogenic
detectors of ionizing radiation, based on gas electron multipliers (GEMs). For
the first time, high gas gains, exceeding 10^4, were obtained in pure He, Ar
and Kr at low temperatures and the stable avalanche mode of operation was
observed in the two-phase cryogenic detector in Kr. The electron avalanching at
low temperatures, in the range of 120-300 K, is systematically studied.


title: Scale Invariance and Nonlinear Patterns of Human Activity

abstract:
  We investigate if known extrinsic and intrinsic factors fully account for the
complex features observed in recordings of human activity as measured from
forearm motion in subjects undergoing their regular daily routine. We
demonstrate that the apparently random forearm motion possesses previously
unrecognized dynamic patterns characterized by fractal and nonlinear dynamics.
These patterns are unaffected by changes in the average activity level, and
persist when the same subjects undergo time-isolation laboratory experiments
designed to account for the circadian phase and to control the known extrinsic
factors. We attribute these patterns to a novel intrinsic multi-scale dynamic
regulation of human activity.


title: Nonstandard picture of turbulence(the second revised)

abstract:
  The nonstandard picture of a turbulent field is presented in this article. By
the concepts of nonstandard mathematics, the picture describes the hierarchical
structure of turbulence and shows the mechanism of the fluctuation appearing in
a turbulent field. The uncertainty of measurement is pointed out. And the
fundamental equations of turbulence are given too. It is natural in this
picture that the reasonable closure methods can be obtained and seem to be
precise.


title: Quasi-1D Modeling of Polymer Melt Die Swell in Short Dies

abstract:
  This paper describes the isothermal die swell using our recent quasi-1D model
for fast (high Deborah number) contraction flows of polymers melts. Because the
model analyzes the flow in several flow regions as one continuous process, it
makes possible to evaluate the die swell as a qusi-1D extrudate flow in dies of
various lengths. Using the asymptotic matching condition for the change in flow
type at the die exit allowed us to find the swelling profile for extrudate
along the flow direction. The calculations in paper performed using a
multi-mode viscoelastic constitutive equation of differential type, are
compared with the experimental/direct numerical data including basic
rheological tests. The presented swelling model involves no fitting parameter
and is applicable for calculations using any viscoelastic constitutive
equation.


title:
On some numerical methods in application to low-Reynolds-number
  turbulence models

abstract:
  To study and develop wall-functions for low-Reynolds-number models, a model
linear equation is introduced. This equation simulates major mathematical
peculiarities of the low-Reynolds-number model including a near wall sub-layer
and transition region. Dirichlet and Newman boundary-value problems are
considered. The standard and analytical wall-functions are investigated on
different properties including the mesh sensitivity of a solution. A Robin-type
interpretation of wall functions as boundary conditions is suggested. It is
shown that solution of a problem is mesh independent and more accurate in this
case. General type analytical and numerical wall-functions are developed on the
basis of a boundary condition transfer. An effective numerical method of
decomposition is suggested. The method can be used in application to either
high-Reynolds-number models with the numerical wall-functions or
low-Reynolds-number models directly. Although a model equation is considered,
the formulas, methods and conclusions are valid and can be directly used for
real low-Reynolds-number equations.


title: Electroporation of Biological Cells Embedded in a Polycarbonate Filter

abstract:
  The electropermeabilization of biological cell membranes by the application
of an external field occurs whenever an applied field exceeds a threshold
value. For fields above this threshold value but less than another critical
value, the pores formed in the membrane are transient or reversible. Several
mechanisms have been proposed for the formation of these transient pores. Here
we examine the local electric fields generated for the configuration of cells
embedded in a polycarbonate filter, both in the region in and around the pore.
We consider the shear forces created in the membrane due to the gradient of the
field along the surface of the membrane, and the interaction of the charged
molecules in the membrane with this field. A relationship between the electric
field strength and the size of the pore formed is derived.


title: Modes of wave-chaotic dielectric resonators

abstract:
  Dielectric optical micro-resonators and micro-lasers represent a realization
of a wave-chaotic system, where the lack of symmetry in the resonator shape
leads to non-integrable ray dynamics. Modes of such resonators display a rich
spatial structure, and cannot be classified through mode indices which would
require additional constants of motion in the ray dynamics. Understanding and
controlling the emission properties of such resonators requires the
investigation of the correspondence between classical phase space structures of
the ray motion inside the resonator and resonant solutions of the wave
equations. We first discuss the breakdown of the conventional eikonal
approximation in the short wavelength limit, and motivate the use of
phase-space ray tracing and phase space distributions. Next, we introduce an
efficient numerical method to calculate the quasi-bound modes of dielectric
resonators, which requires only two diagonalizations per N states, where N is
approximately equal to the number of half-wavelengths along the perimeter. The
relationship between classical phase space structures and modes is displayed
via the Husimi projection technique. Observables related to the emission
pattern of the resonator are calculated with high efficiency.

categories: physics.optics cond-mat.mes-hall nlin.CD quant-ph


title: Quaternions in University-Level Physics Considering Special Relativity

abstract:
  As an expansion of complex numbers, the quaternions show close relations to
numerous physically fundamental concepts. In spite of that, the didactic
potential provided by quaternion interrelationships in formulating physical
laws are hardly regarded in the current physics curriculum. In particular, many
approaches emerge that are useful in conveying the unity of seemingly distinct
theories in a didactically convincing manner. This will be exemplified with the
help of special relativity. The diverse examples of spatial and space-time
rotations are merged into a didactic whole by introducing quaternion
transformations and comparing them to the representation using rotation
matrices common in physics books.


title:
A generic scheme for choosing models and characterizations of complex
  systems

abstract:
  It is argued that the two problems of choosing characterizations and models
of complex systems should not be considered independently. A particular
criterion for these choices, oriented on the potential usefulness of the
results, is considered, and a generic formalization applicable to realistic
experiments is developed. It is applied to Kuramoto-Sivashinsky chaos.


title:
Long-range Coulomb-like mode interaction in a coaxial waveguide filled
  with Faraday material

abstract:
  Nonlinear mode coupling in a coaxial waveguide filled with Faraday material
has been considered. The picture of mode interaction is shown to resemble
Coulomb interaction of charges: higher modes with nonzero angular momentum
interact like effective charges via exchange of zero angular momentum quanta of
the fundamental mode. Thus, at large distances this interaction becomes the
dominant mechanism of mode coupling. The developed model may be used in
designing coaxial photonic crystal fibers with strong tailored mode
interaction.


title: Production of Ultracold, Polar RbCs* Molecules via Photoassociation

abstract:
  We have produced ultracold, polar RbCs* molecules via photoassociation in a
laser-cooled mixture of Rb and Cs atoms. Using a model of the RbCs* molecular
interaction which reproduces the observed rovibrational structure, we infer
decay rates in our experiments into deeply bound singlet ground state RbCs
vibrational levels as high as 5 x 10^5 s^-1 per level. Population in such
deeply bound levels could be efficiently transferred to the vibrational ground
state using a single stimulated Raman transition, opening the possibility to
create large samples of stable, ultracold polar molecules.


title: Future Proof for Physics: Preserving the Record of SLAC

abstract:
  Paper provides a brief introduction to SLAC, discusses the origins of the
SLAC Archives and History Office, its present-day operations, and the present
and future challenges it faces in attempting to preserve an accurate historical
record of SLAC's activities.


title: Vacuum polarization calculations for hydrogenlike and alkalilike ions

abstract:
  Complete vacuum polarization calculations incorporating finite nuclear size
are presented for hydrogenic ions with principal quantum numbers n=1-5.
Lithiumlike, sodiumlike, and copperlike ions are also treated starting with
Kohn-Sham potentials, and including first-order screening corrections. In both
cases dominant Uehling terms are calculated with high accuracy, and smaller
Wichmann- Kroll terms are obtained using numerical electron Green's functions.


title:
Drifting diffusion on a circle as continuous limit of a multiurn
  Ehrenfest model

abstract:
  We study the continuous limit of a multibox Erhenfest urn model proposed
before by the authors. The evolution of the resulting continuous system is
governed by a differential equation, which describes a diffusion process on a
circle with a nonzero drifting velocity. The short time behavior of this
diffusion process is obtained directly by solving the equation, while the long
time behavior is derived using the Poisson summation formula. They reproduce
the previous results in the large $M$ (number of boxes) limit. We also discuss
the connection between this diffusion equation and the Schr$\ddot{\rm o}$dinger
equation of some quantum mechanical problems.


title: Route to nonlocality and observation of accessible solitons

abstract:
  We develop a general theory of spatial solitons in a liquid crystalline
medium exhibiting a nonlinearity with an arbitrary degree of effective
nonlocality. The model accounts the observability of "accessible solitons" and
establishes an important link with parametric solitons.


title: Generation of polarization squeezed light in PPNC

abstract:
  Theoretical analysis is presented on quantum state evolution of polarization
light waves at frequencies $\omega_{o}$ and $\omega_{e}$ in a periodically
poled nonlinear crystal (PPNC). It is shown that the variances of all the four
Stokes parameters can be squeezed.


title: Neutron halo, tritons and alpha clusters in the nucleus ${^8}He$

abstract:
  Recent experiments clearly demonstrate the importance of the excited state
$2^+$ at 1.8 MeV in the substruture ${^6}He$ for the ground state of the
nucleus ${^8}He$. It is shown here that this means that the ground state
structure of ${^8}He$ rather than being $\alpha$ + 4n is actually ${^3}H$ +
${^3}H$ +2n. As such the pair of tritons would form a compact core around which
the two valence neutrons provide a halo structure in ${^8}He$. Hence both
${^6}He$ and ${^8}He$ are two neutron halo nuclei but with cores of quite
different nature. All this demonstrates significance of triton clustering in
neutron rich nuclei.


title: What is spin?

abstract:
  This is a late answer to question #79 by R.I. Khrapko, "Does plane wave not
carry a spin?," Am. J. Phys. /69/, 405 (2001), and a complement (on gauge
invariance, massive spin 1 and 1/2, and massless spin 2 fields) to the paper by
H.C. Ohanian, "What is spin?," Am. J. Phys. /54/, 500--505 (1985). In
particular, it is confirmed that "spin" is a classical quantity which can be
calculated for any field using its definition, namely that it is just the
non-local part of the conserved angular momentum. This leads to explicit
expressions which are bilinear in the fields and which agree with their
standard "quantum" counterparts.


title:
Critical Behavior in a Cellular Automata Animal Disease Transmission
  Model

abstract:
  Using a cellular automata model, we simulate the British Government Policy
(BGP) in the 2001 foot and mouth epidemic in Great Britain. When clinical
symptoms of the disease appeared on a farm, there is mandatory slaughter
(culling) of all livestock on an infected premise (IP). Those farms that
neighbor an IP (contiguous premise, CP), are also culled, aka nearest neighbor
interaction. Farms where the disease may be prevalent from animal, human,
vehicle or airborne transmission (dangerous contact, DC), are additionally
culled, aka next-to-nearest neighbor iteractions and lightning factor. The
resulting mathematical model possesses a phase transition, whereupon if the
physical disease transmission kernel exceeds a critical value, catastrophic
loss of animals ensues. The non-local disease transport probability can be as
low as .01% per day and the disease can still be in the high mortality phase.
We show that the fundamental equation for sustainable disease transport is the
criticality equation for neutron fission cascade. Finally, we calculate that
the percentage of culled animals that are actually healthy is ~ 30%.


title:
NMR spectroscopy of hydrogen deuteride and magnetic moments of deuteron
  and triton

abstract:
  Magnetic moments of free and bound deuteron and triton are considered and new
results for their magnetic moments (in units of that of the proton) and their g
factors are presented. We report on a measurement with medium-pressure hydrogen
deuteride (HD) at 10 atm, which is to be compared with the previous measurement
done at 100 atm. We confirm that the high pressure used in former experiments
caused no systematic effects at a level of 10 ppb. We also reexamined a
theoretical uncertainty related to screening effects in HD and HT molecules and
found that previously it was underestimated. The medium-pressure result
obtained for the free deuteron mu_d/mu_p=0.307 012 206 5(28) with a fractional
uncertainty of 9.1 * 10^-9 is free of systematic effects related to former
high-pressure experiments. The reevaluated result for triton is mu_t/mu_p=1.066
639 908(10) with a fractional uncertainty of 9.3 * 10^-9.


title: Model of Morphogenesis

abstract:
  A new suggestion for pattern formation in biological systems is proposed. The
interaction of two signaling pathways provides complex patterning. The
interaction of two pathways involves few of the biochemical complexities of the
pathways. The 'Wnt' pathway is proposed to be one of these, in interaction with
others, one at a time, perhaps sequentially, such as Hunchback (Hh), Notch,
BMP, etc., those involved in development of metazoa. It is further shown how
such interactions can easily lead to such epithelial movements as gastrulation.
Numerical simulations of the model are given.


title:
Some Theoretical Estimations of Spatial Distribution of Compton
  Backscattered Laser Photons Beam

abstract:
  Spatial distribution of intensity, degree and direction of linear
polarization of tagged photon beam, which is obtained due to Compton
backscattering of laser light on high-energy electron beam, are calculated.
Effects of angular dispersion and spatial spread of electron beam are taken
into account. Calculations have been carried out for the example of LEGS
facility.


title: Friction as Basis for a Phonon Maser

abstract:
  Evidence is provided from experiment, for the hypothesis that defect
organization (internal friction) is a means for operation of a phonon maser.


title: Lorentz's theory and special relativity are completely identical

abstract:
  The main content of this paper has been moved into the new version of
physics/0308035.


title:
Plasma sheet structure in the magnetotail: kinetic simulation and
  comparison with satellite observations

abstract:
  We use the results of a three-dimensional kinetic simulation of an Harris
current sheet to propose an explanation and to reproduce the ISEE-1/2, Geotail,
and Cluster observations of the magnetotail current sheet structure. Current
sheet flapping, current density bifurcation, and reconnection are explained as
the results of the kink and tearing instabilities, which dominate the current
sheet evolution.


title:
Does special relativity theory tell us anything new about space and
  time?

abstract:
  It will be shown that, in comparison with the pre-relativistic
Galileo-invariant conceptions, special relativity tells us nothing new about
the geometry of spacetime. It simply calls something else "spacetime", and this
something else has different properties. All statements of special relativity
about those features of reality that correspond to the original meaning of the
terms "space" and "time" are identical with the corresponding traditional
pre-relativistic statements. It will be also argued that special relativity and
Lorentz theory are completely identical in both senses, as theories about
spacetime and as theories about the behavior of moving physical objects.


title: On the meaning of Lorentz covariance

abstract:
  In classical mechanics, Galilean covariance and the principle of relativity
are completely equivalent and hold for all possible dynamical processes. In
contrast, in relativistic physics the situation is much more complex. It will
be shown that Lorentz covariance and the principle of relativity are not
completely equivalent. The reason is that the principle of relativity actually
only holds for the equilibrium quantities that characterize the equilibrium
state of dissipative systems. In the light of this fact it will be argued that
Lorentz covariance should not be regarded as a fundamental symmetry of the laws
of physics.


title:
Retarded Interaction of Radiation Field and Symmetry Violation of Time
  Reversal in the High order Stimulated Radiation and Absorption Processes of
  Light

abstract:
  It is proved that when the retarded effect (or multiple moment effect) of
radiation fields is taken into account, the high order stimulated radiation and
stimulated absorption probabilities of light are not the same so that time
reversal symmetry would be violated, though the total Hamiltonian of
electromagnetic interaction is still unchanged under time reversal. The reason
to cause time reversal symmetry violation is that certain filial or partial
transitive processes of bounding state atoms are forbidden or can not be
achieved actually due to the law of energy conservation, the asymmetric actions
of effective transition operators before and after time reversal, as well as
the special states of atoms themselves. These restrictions would cause the
symmetry violation of time reversal of other filial or partial transition
processes which can be actualized really. The symmetry violation is also
relative to the initial state asymmetries of bounding atoms before and after
time reversal. For the electromagnetic interaction between non-bounding state
atoms and radiation field, there is no this kind of symmetry violation of time
reversal. In this way, the current formula of light stimulated radiation and
absorption parameters with time reversal symmetry should be revised. The
influence of time reversal symmetry violation on the foundational theory of
laser is also discussed and the phenomena of non-population inversion and
non-radiation transition can also be explained well. In this way, a more
reliable foundation can be established for the theories of laser and nonlinear
optics in which non-equilibrium processes are involved.


title:
A new insight into the negative-mass paradox of gravity and the
  accelerating universe

abstract:
  The discovery of acceleration of the universe expansion in recent
astrophysics research prompts the author to propose that the Newton's
gravitation law can be generalized to accommodate the antimatter: While the
force between matters(antimatters) is attractive, the force between matter and
antimatter is a repulsive one. A paradox of negative-mass in gravity versus a
basic symmetry (m-->-m) based on quantum mechanics is discussed in sufficient
detail so that the new postulate could be established quite naturally.
Corresponding modification of the theory of general relativity is also
suggested. If we believe in the symmetry of particle and antiparticle as well
as the antigravity between them, it might be possible to consider a new
scenario of the expansion of universe which might provide some new insight into
the interpretation of cosmological phenomena including the accelerating
universe observed.


title: A simple derivation of E = mc^2

abstract:
  Einstein's 1905 derivation of E = mc^2 has been criticized for being
circular. Although such criticisms have been challenged it is certainly true
that the reasoning in Einstein's original derivation is not at all obvious.
Einstein's original derivation could have been made clearer. This article
describes a clear way of doing so.


title: Application of Coarse Integration to Bacterial Chemotaxis

abstract:
  We have developed and implemented a numerical evolution scheme for a class of
stochastic problems in which the temporal evolution occurs on widely-separated
time scales, and for which the slow evolution can be described in terms of a
small number of moments of an underlying probability distribution. We
demonstrate this method via a numerical simulation of chemotaxis in a
population of motile, independent bacteria swimming in a prescribed gradient of
a chemoattractant. The microscopic stochastic model, which is simulated using a
Monte Carlo method, uses a simplified deterministic model for
excitation/adaptation in signal transduction, coupled to a realistic,
stochastic description of the flagellar motor. We show that projective time
integration of ``coarse'' variables can be carried out on time scales long
compared to that of the microscopic dynamics. Our coarse description is based
on the spatial cell density distribution. Thus we are assuming that the system
``closes'' on this variable so that it can be described on long time scales
solely by the spatial cell density. Computationally the variables are the
components of the density distribution expressed in terms of a few basis
functions, given by the singular vectors of the spatial density distribution
obtained from a sample Monte Carlo time evolution of the system. We present
numerical results and analysis of errors in support of the efficacy of this
time-integration scheme.


title: Ensembles of Protein Molecules as Statistical Analog Computers

abstract:
  A class of analog computers built from large numbers of microscopic
probabilistic machines is discussed. It is postulated that such computers are
implemented in biological systems as ensembles of protein molecules. The
formalism is based on an abstract computational model referred to as Protein
Molecule Machine (PMM). A PMM is a continuous-time first-order Markov system
with real input and output vectors, a finite set of discrete states, and the
input-dependent conditional probability densities of state transitions. The
output of a PMM is a function of its input and state. The components of input
vector, called generalized potentials, can be interpreted as membrane
potential, and concentrations of neurotransmitters. The components of output
vector, called generalized currents, can represent ion currents, and the flows
of second messengers. An Ensemble of PMMs (EPMM) is a set of independent
identical PMMs with the same input vector, and the output vector equal to the
sum of output vectors of individual PMMs. The paper suggests that biological
neurons have much more sophisticated computational resources than the presently
popular models of artificial neurons.

categories: physics.bio-ph cs.AI cs.NE physics.comp-ph physics.data-an q-bio.NC


title: "Quantum gravity": an oxymoron

abstract:
  I prove that "quantum" and "Einsteinian gravity" are incompatible concepts.
Accordingly, the graviton is a mere object of science fiction.


title:
Restricted equivalence of paired epsilon-negative and mu-negative layers
  to a negative phase-velocity material ({\em alias} left-handed material)

abstract:
  The time-harmonic electromagnetic responses of (a) a bilayer made of an
epsilon-negative layer and a mu-negative layer, and (b) a single layer of a
negative phase-velocity material are compared. Provided all layers are
electrically thin, a restricted equivalence between (a) and (b) exists. The
restricted equivalence depends on the linear polarization state and the
transverse wavenumber. Implications for perfect lenses and parallel-plate
waveguides are considered.


title: Stochastic Cooling Overview

abstract:
  The status of stochastic cooling and developments over the years are reviewed
with reference to much of the original work. Both theoretical and technological
subjects are considered.


title: Singular Sources of Maxwell Fields with Self-Quantized Electric Charge

abstract:
  Single- and multi-valued solutions of homogeneous Maxwell equations in vacuum
are considered, with ''sources'' formed by the (point- or string-like)
singularities of the field strengths and, generally, irreducible to any
delta-functions' distribution. Maxwell equations themselves are treated as
consequences (say, integrability conditions) of a primary ``superpotential''
field subject to some nonlinear and over-determined constraints (related, in
particular, to twistor structures). As the result, we obtain (in explicit or
implicit algebraic form) a distinguished class of Maxwell fields, with singular
sources necessarily carrying a ``self-quantized'' electric charge integer
multiple to a minimal ``elementary'' one. Particle-like singular objects are
subject to the dynamics consistent with homogeneous Maxwell equations and
undergo transmutations -- bifurcations of different types. The presented scheme
originates from the ``algebrodynamical'' approach developed by the author and
reviewed in the last section. Incidentally, fundamental equivalence relations
between the solutions of Maxwell equations, complex self-dual conditions and of
Weyl ``neutrino'' equations are established, and the problem of magnetic
monopole is briefly discussed.


title: Use of the likelihood for measuring the skill of probabilistic forecasts

abstract:
  We define the likelihood and give a number of justifications for its use as a
skill measure for probabilistic forecasts. We describe a number of different
scores based on the likelihood, and briefly investigate the relationships
between the likelihood, the mean square error and the ignorance.


title: A straw drift chamber spectrometer for studies of rare kaon decays

abstract:
  We describe the design, construction, readout, tests, and performance of
planar drift chambers, based on 5 mm diameter copperized Mylar and Kapton
straws, used in an experimental search for rare kaon decays. The experiment
took place in the high-intensity neutral beam at the Alternating Gradient
Synchrotron of Brookhaven National Laboratory, using a neutral beam stop, two
analyzing dipoles, and redundant particle identification to remove backgrounds.


title:
Criticality of the Grad-Shafranov equation: transport barriers and
  fragile equilibria

abstract:
  We review criticality theory as a prelude to consideration of criticality of
the Grad-Shafranov equation. Novel criticality conditions of ODEs and PDEs are
derived, easily evaluated. The possibility that transport barriers are
associated with characteristics of the equilibrium equation is explored. We
conjecture that equilibrium criticality permits the appearance of new solution
branches: the high confinement branch has high poloidal flux gradient in a
diamagnetic region of the plasma. Similarly, criticality may lead to loss of
solution, which could be related to MHD instability and/or island formation


title:
An application of interpolating scaling functions to wave packet
  propagation

abstract:
  Wave packet propagation in the basis of interpolating scaling functions (ISF)
is studied. The ISF are well known in the multiresolution analysis based on
spline biorthogonal wavelets. The ISF form a cardinal basis set corresponding
to an equidistantly spaced grid. They have compact support of the size
determined by the underlying interpolating polynomial that is used to generate
ISF. In this basis the potential energy matrix is diagonal and the kinetic
energy matrix is sparse and, in the 1D case, has a band-diagonal structure. An
important feature of the basis is that matrix elements of a Hamiltonian are
exactly computed by means of simple algebraic transformations efficiently
implemented numerically. Therefore the number of grid points and the order of
the underlying interpolating polynomial can easily be varied allowing one to
approach the accuracy of pseudospectral methods in a regular manner, similar to
high order finite difference methods. The results of numerical simulations of
an H+H_2 collinear collision show that the ISF provide one with an accurate and
efficient representation for use in the wave packet propagation method.

categories: physics.atom-ph math.NA physics.comp-ph quant-ph


title: Optimal rotations of deformable bodies and orbits in magnetic fields

abstract:
  Deformations can induce rotation with zero angular momentum where dissipation
is a natural ``cost function''. This gives rise to an optimization problem of
finding the most effective rotation with zero angular momentum. For certain
plastic and viscous media in two dimensions the optimal path is the orbit of a
charged particle on a surface of constant negative curvature with magnetic
field whose total flux is half a quantum unit.

categories: physics.class-ph math-ph math.MP physics.gen-ph


title: Matter X waves

abstract:
  We predict that an ultra-cold Bose gas in an optical lattice can give rise to
a new form of condensation, namely matter X waves. These are non-spreading 3D
wave-packets which reflect the symmetry of the Laplacian with a negative
effective mass along the lattice direction, and are allowed to exist in the
absence of any trapping potential even in the limit of non-interacting atoms.
This result has also strong implications for optical propagation in periodic
structures


title: Optically bound microscopic particles in one dimension

abstract:
  Counter-propagating light fields have the ability to create self-organized
one-dimensional optically bound arrays of microscopic particles, where the
light fields adapt to the particle locations and vice versa. We develop a
theoretical model to describe this situation and show good agreement with
recent experimental data (Phys. Rev. Lett. 89, 128301 (2002)) for two and three
particles, if the scattering force is assumed to dominate the axial trapping of
the particles. The extension of these ideas to two and three dimensional
optically bound states is also discussed.


title:
Dynamical Multiple-Timestepping Methods for Overcoming the Half-Period
  Time Step Barrier

abstract:
  Current molecular dynamic simulations of biomolecules using multiple time
steps to update the slowingly changing force are hampered by an instability
occuring at time step equal to half the period of the fastest vibrating mode.
This has became a critical barrier preventing the long time simulation of
biomolecular dynamics. Attemps to tame this instability by altering the slowly
changing force and efforts to damp out this instability by Langevin dynamics do
not address the fundamental cause of this instability. In this work, we trace
the instability to the non-analytic character of the underlying spectrum and
show that a correct splitting of the Hamiltonian, which render the spectrum
analytic, restores stability. The resulting Hamiltonian dictates that in
additional to updating the momentum due to the slowly changing force, one must
also update the position with a modified mass. Thus multiple-timestepping must
be done dynamically.


title:
Sub-Doppler spectroscopy of Rb atoms in a sub-micron vapor cell in the
  presence of a magnetic field

abstract:
  We report the first use of an extremely thin vapor cell (thickness ~ 400 nm)
to study the magnetic-field dependence of laser-induced-fluorescence excitation
spectra of alkali atoms. This thin cell allows for sub-Doppler resolution
without the complexity of atomic beam or laser cooling techniques. This
technique is used to study the laser-induced-fluorescence excitation spectra of
Rb in a 50 G magnetic field. At this field strength the electronic angular
momentum J and nuclear angular momentum I are only partially decoupled. As a
result of the mixing of wavefunctions of different hyperfine states, we observe
a nonlinear Zeeman effect for each sublevel, a substantial modification of the
transition probabilities between different magnetic sublevels, and the
appearance of transitions that are strictly forbidden in the absence of the
magnetic field. For the case of right- and left- handed circularly polarized
laser excitation, the fluorescence spectra differs qualitatively. Well
pronounced magnetic field induced circular dichroism is observed. These
observations are explained with a standard approach that describes the partial
decoupling of I and J states.


title:
Magnetic field-induced mixing of hyperfine states of Cs 6 2^P_{3/2}
  level observed with a sub-micron vapor cell

abstract:
  The fluorescence spectra of a sub-micron atomic cesium vapor layer observable
under resonant excitation on D2 line have been studied in the presence of an
external magnetic field. Substantial changes in amplitudes and frequency
positions of the individual (resolved) hyperfine transitions have been recorded
in moderate magnetic fields (up to ~ 50 Gauss). These features are caused by
mixing of the hyperfine states of the upper level resulting from comparable
values of the hyperfine splitting of the 62^P_{3/2} manifold and Larmor
frequencies of the magnetic sublevels. The results of simulation show a good
agreement with the experimental spectra. Possible application of the results
for high spatial resolution magnetometry is discussed.


title: Reference-State One-Particle Density-Matrix Theory

abstract:
  A density-matrix formalism is developed based on the one-particle
density-matrix of a single-determinantal reference-state. The v-representable
problem does not appear in the proposed method, nor the need to introduce
functionals defined by a constrained search. The correlation-energy functionals
are not universal; they depend on the external potential. Nevertheless, model
systems can still be used to derive universal energy-functionals. In addition,
the correlation-energy functionals can be partitioned into individual terms
that are -- to a varying degree -- universal; yielding, for example, an
electron gas approximation. Variational and non-variational energy functionals
are introduced that yield the target-state energy when the reference state --
or its corresponding one-particle density matrix -- is constructed from
Brueckner orbitals. Using many-body perturbation theory, diagrammatic
expansions are given for the non-variational energy-functionals, where the
individual diagrams explicitly depend on the one-particle density-matrix.
Non-variational energy-functionals yield generalized Hartree--Fock equations
involving a non-local correlation-potential and the Hartree--Fock exchange;
these equations are obtained by imposing the Brillouin--Brueckner condition.
The same equations -- for the most part -- are obtained from variational
energy-functionals using functional minimizations, yielding the (kernel of)
correlation potential as the functional derivative of correlation-energy
functionals. Approximations for the correlation-energy functions are
introduced, including a one-particle-density-matrix variant of the
local-density approximation (LDA) and a variant of the Lee--Yang--Parr (LYP)
functional.


title:
A New Framework for the Assessment and Calibration of Medium Range
  Ensemble Temperature Forecasts

abstract:
  We present a new framework for the assessment and calibration of medium range
ensemble temperature forecasts. The method is based on maximising the
likelihood of a simple parametric model for the temperature distribution, and
leads to some new insights into the predictability of uncertainty.


title: Geo-engineering Gone Awry: A New Partial Solution of Fermi's Paradox

abstract:
  Another partial solution of Fermi's famous paradox is proposed, based on our
increased understanding of geophysics, geo-engineering and climatology. It has
been claimed in the recent astrobiological literature (for instance, in the
recent controversial "rare Earth" theory of Ward and Brownlee), that geological
activity of a terrestrial planet is an important precondition for the emergence
of complex metazoan life forms. Technological civilizations arising on such
planets will be, at some point of their histories or another, tempted to embark
upon massive geo-engineering projects. If, for some reasons only very recently
understood, large-scale geo-engineering is in fact much more dangerous than
previously thought, the scenario in which at least some of the extraterrestrial
civilizations in the Milky Way self-destruct in this manner gains plausibility.
In addition, we speculate on possible reasons, both physical and
culturological, which could make such a threat even more pertinent on an
average Galactic terrestrial planet than on Earth.


title:
On Statistical Methods of Parameter Estimation for Deterministically
  Chaotic Time-Series

abstract:
  We discuss the possibility of applying some standard statistical methods (the
least square method, the maximum likelihood method, the method of statistical
moments for estimation of parameters) to deterministically chaotic
low-dimensional dynamic system (the logistic map) containing an observational
noise. A ``pure'' Maximum Likelihood (ML) method is suggested to estimate the
structural parameter of the logistic map along with the initial value $x_1$
considered as an additional unknown parameter. Comparisons with previously
proposed techniques on simulated numerical examples give favorable results (at
least, for the investigated combinations of sample size $N$ and noise level).
Besides, unlike some suggested techniques, our method does not require the a
priori knowledge of the noise variance. We also clarify the nature of the
inherent difficulties in the statistical analysis of deterministically chaotic
time series and the status of previously proposed Bayesian approaches. We note
the trade-off between the need of using a large number of data points in the ML
analysis to decrease the bias (to guarantee consistency of the estimation) and
the unstable nature of dynamical trajectories with exponentially fast loss of
memory of the initial condition. The method of statistical moments for the
estimation of the parameter of the logistic map is discussed. This method seems
to be the unique method whose consistency for deterministically chaotic time
series is proved so far theoretically (not only numerically).


title: The Free Electron Laser Klystron Amplifier Concept

abstract:
  The simplest high gain free electron laser (FEL) amplifier concept is
proposed. A klystron amplifier has the useful property that the various
electronic processes take place in separate portions of the amplifier, rather
than overlapping as in FEL amplifier with an uniform undulator. The klystron
consists of two fundamental parts: succession of 2-3 cascades (modulator), and
an output undulator (radiator) in which the modulated electron beam coherently
radiates. Each cascade consists of uniform undulator and dispersion section.
Unlike distributed optical klystrons, we have a high gain per cascade pass.
This has a few consequences. First, klystron gain does not depend on the bunch
compression in the injector linac, i.e. maximum gain per cascade pass at high
peak beam current is the same as at low peak beam current, without compression.
Conventional, short-wavelength FEL amplifier and distributed optical klystron
require electron beam peak current of a few kA. Second, there are no
requirements on the alignment of the cascade undulators and dispersion
sections, because, in our (high gain) case, there is no need for radiation
phase matching. There are applications, like XFELs, where the unique properties
of high gain klystron FEL amplifier are very desirable. Such a scheme allows
one to decrease the total length of the magnetic system. In this paper we
discuss also implementation of the proposed SASE FEL scheme for the frequency
multiplier, for femtosecond experiments, and multi-user soft X-ray facility.


title: Development of an elementary climate model: two-layer cellular case

abstract:
  A qualitative understanding of the greenhouse effect has long been available
through models based on globally- and time-averaged quantities. We examine here
a simple 864-cell climatological model that emphasizes vertical radiative
energy transport within each cell. It reproduces yearly average temperatures
obtained earlier from one of these global models and predicts a locally
distributed non-radiative flux when observed temperatures are employed as input
data. Vertical and lateral transport of latent heat do not appear explicitly in
this model. They are apparently handled well by one non-radiative flux
variable, SNR, which shows a strong latitude dependence. Only the Sahara desert
and Saudi Arabian regions appear to be complex. For those interested in
climatology and construction of climate models, our model provides constraints
upon specifying averaged non-radiative energy transport. The model is a useful
simplification for learning about radiative energy transfer into and out of
Earth?s atmosphere and for representing the results of more sophisticated
models.


title:
Foreign exchange market fluctuations as random walk in demarcated
  complex plane

abstract:
  We show that time-dependent fluctuations $\{\Delta x\}$ in foreign exchange
rates are accurately described by a random walk in a complex plane that is
demarcated into the gain (+) and loss (-) sectors. $\{\Delta x\}$ is the
outcome of $N$ random steps from the origin and $|\Delta x|$ is the square of
the Euclidean distance of the final $N$-th step position. Sign of $\{\Delta
x(t)\}$ is set by the $N$-th step location in the plane. The model explains not
only the exponential statistics of the probability density of $\{\Delta x\}$
for G7 markets but also its observed asymmetry, and power-law dependent
broadening with increasing time delay.


title: Sensitivity of searches for new signals and its optimization

abstract:
  A frequentist definition of sensitivity of a search for new phenomena is
discussed, that has several useful properties. It is based on completely
standard concepts, is generally applicable, and has a very clear
interpretation. It is particularly suitable for optimization, being independent
of a-priori expectations about the presence of a signal, thus allowing the
determination of a single set of cuts that is optimal both for setting limits
and for making a discovery. Simple approximate formulas are given for the
common problem of Poisson counts with background.


title: Coherent X-ray Diffractive Imaging; applications and limitations

abstract:
  The inversion of a diffraction pattern offers aberration-free
diffraction-limited 3D images without the resolution and depth-of-field
limitations of lens-based tomographic systems, the only limitation being
radiation damage. We review our experimental results, discuss the fundamental
limits of this technique and future plans.


title:
The Assessment and Calibration of Ensemble Seasonal Forecasts of
  Equatorial Pacific Ocean Temperature and the Predictability of Uncertainty

abstract:
  We evaluate the performance of two 44 year ensemble seasonal hindcast time
series for the Nino3 index produced as part of the DEMETER project. We show
that the ensemble mean carries useful information out to six months. The
ensemble spread, however, only carries useful information out to four months in
one of the models, and two months in the other.


title: A Model for Long Term Climate Change

abstract:
  In this paper we consider the well-known cyclical model for climate change,
for example from glaciation to the present day and back, and compare this with
a two-state model in Quantum Mechanics. We establish the full correspondence.


title: Exclusion regions and their power

abstract:
  The question of exclusion region construction in new phenomenon searches has
been causing considerable discussions for many years and yet no clear
mathematical definition of the problem has been stated so far. In this paper we
formulate the problem in mathematical terms and propose a solution to the
problem within the framework of statistical tests. The proposed solution avoids
problems of the currently used procedures.


title: Phase transition in the bounded one-dimensional multitrap system

abstract:
  We have previously discussed the diffusion limited problem of the bounded
one-dimensional multitrap system where no external fiel is included and pay
special attention to the transmission of the diffusing particles through the
system of imperfect traps. We discuss here the case in which an external field
is included to each trap and find not only the transmission but also the energy
associated with the diffusing particles in the presence and absence of such
fields. From the energy we find the specific heat $C_h$ and show that for
certain values of the parameters associated with the multitrap system it
behaves in a manner which is suggestive of phase transition. Moreover, this
phase transition is demonstrated not only through the conventional single peak
at which the specific heat function is undifferentiable but also through the
less frequent phenomenon of double peaks.


title: The spin of the mu-mesons

abstract:
  We can determine the intrinsic angular momentum of the mu-mesons from the sum
of the angular momentum vectors of the lattice oscillations and the sum of the
spin vectors of the neutrinos in the lattice and the spin vector of the
electric charge which the mu-mesons carry. We used this neutrino lattice before
to calculate the rest mass of the mu-mesons. Here we learn how the apparent
discrepancy between the concept of a point particle and the finite size of a
neutrino lattice is resolved. We also learn that the spin of the mu-mesons
originates exclusively from the spin of the electric charge of the mu(+,-)
mesons.


title: The self-organized multi-lattice Monte Carlo simulation

abstract:
  The self-organized Monte Carlo simulations of 2D Ising ferromagnet on the
square lattice are performed. The essence of devised simulation method is the
artificial dynamics consisting of the single-spin-flip algorithm of Metropolis
supplemented by the random walk in the temperature space. The walk is biased to
the critical region through the feedback equation utilizing the memory-based
filtering recursion instantly estimating the energy cumulants. The simulations
establish that the peak of the temperature probability density function is
located nearly the pseudocritical temperature pertaining to canonical
equilibrium. In order to eliminate the finite-size effects, the self-organized
approach is extended to multi-lattice systems, where feedback is constructed
from the pairs of the instantaneous running fourth-order cumulants of the
magnetization. The replica-based simulations indicate that several properly
chosen steady statistical distributions of the self-organized Monte Carlo
systems resemble characteristics of the standard self-organized critical
systems.


title:
New combined PIC-MCC approach for fast simulation of a radio frequency
  discharge at low gas pressure

abstract:
  A new combined PIC-MCC approach is developed for accurate and fast simulation
of a radio frequency discharge at low gas pressure and high density of plasma.
Test calculations of transition between different modes of electron heating in
a ccrf discharge in helium and argon show a good agreement with experimental
data.
  We demonstrate high efficiency of the combined PIC-MCC algorithm, especially
for the collisionless regime of electron heating.


title: Dispersion Relations for Thermally Excited Waves in Plasma Crystals

abstract:
  Thermally excited waves in a Plasma crystal were numerically simulated using
a Box_Tree code. The code is a Barnes_Hut tree code proven effective in
modeling systems composed of large numbers of particles. Interaction between
individual particles was assumed to conform to a Yukawa potential. Particle
charge, mass, density, Debye length and output data intervals are all
adjustable parameters in the code. Employing a Fourier transform on the output
data, dispersion relations for both longitudinal and transverse wave modes were
determined. These were compared with the dispersion relations obtained from
experiment as well as a theory based on a harmonic approximation to the
potential. They were found to agree over a range of 0.9<k<5, where k is the
shielding parameter, defined by the ratio between interparticle distance a and
dust Debye length lD. This is an improvement over experimental data as current
experiments can only verify the theory up to k = 1.5.


title: Dusty Plasma Correlation Function Experiment

abstract:
  Dust particles immersed within a plasma environment, such as those in
protostellar clouds, planetary rings or cometary environments, will acquire an
electric charge. If the ratio of the inter-particle potential energy to the
average kinetic energy is high enough the particles will form either a "liquid"
structure with short-range ordering or a crystalline structure with long range
ordering. Many experiments have been conducted over the past several years on
such colloidal plasmas to discover the nature of the crystals formed, but more
work is needed to fully understand these complex colloidal systems. Most
previous experiments have employed monodisperse spheres to form Coulomb
crystals. However, in nature (as well as in most plasma processing
environments) the distribution of particle sizes is more randomized and
disperse. This paper reports experiments which were carried out in a GEC rf
reference cell modified for use as a dusty plasma system, using varying sizes
of particles to determine the manner in which the correlation function depends
upon the overall dust grain size distribution. (The correlation function
determines the overall crystalline structure of the lattice.) Two dimensional
plasma crystals were formed of assorted glass spheres with specific size
distributions in an argon plasma. Using various optical techniques, the pair
correlation function was determined and compared to those calculated
numerically.


title: Finite Coulomb Crystal Formation

abstract:
  Dust particles immersed within a plasma environment, such as those found in
planetary rings or comets, will acquire an electric charge. If the ratio of the
inter-particle potential energy to average kinetic energy is large enough the
particles will form either a "liquid" structure with short-range ordering or a
crystalline structure with long-range ordering. Since their discovery in
laboratory environments in 1994, such crystals have been the subject of a
variety of experimental, theoretical and numerical investigations. Most
numerical and theoretical investigations have examined infinite systems
assuming periodic boundary conditions. Since experimentally observed crystals
can be comprised of a few hundred particles, this often leads to discrepancies
between predicted theoretical results and experimental data. In addition,
recent studies have concentrated on the importance of random charge variations
between individual dust particles, but very little on the importance of size
variations between the grains. Such size variations naturally lead to
inter-grain charge variations which can easily become more important than those
due to random charge fluctuations (which are typically less than one percent).
Although such size variations can be largely eliminated experimentally by
introducing mono-dispersive particles, many laboratory systems and all
astrophysical environments contain significant size distributions. This study
utilizes a program to find the equilibrium positions of a dusty plasma system
as well as a modified Barnes-Hut code to model the dynamic behavior of such
systems. It is shown that in terms of inter-particle spacing and ordering,
finite systems are significantly different than infinite ones, particularly for
the most-highly ordered states.


title: Dust Grain Orbital Behavior Around Ceres

abstract:
  Many asteroids show indications they have undergone impacts with meteoroid
particles having radii between 0.01 m and 1 m. During such impacts, small dust
grains will be ejected at the impact site. The possibility of these dust grains
(with radii greater than 2.2x10-6 m) forming a halo around a spherical asteroid
(such as Ceres) is investigated using standard numerical integration
techniques. The orbital elements, positions, and velocities are determined for
particles with varying radii taking into account both the influence of gravity,
radiation pressure, and the interplanetary magnetic field (for charged
particles). Under the influence of these forces it is found that dust grains
(under the appropriate conditions) can be injected into orbits with lifetimes
in excess of one year. The lifetime of the orbits is shown to be highly
dependent on the location of the ejection point as well as the angle between
the surface normal and the ejection path. It is also shown that only particles
ejected within 10 degrees relative to the surface tangential survive more than
a few hours and that the longest-lived particles originate along a line
perpendicular to the Ceres-Sun line.


title:
Nanolithography with metastable helium atoms in a high-power
  standing-wave light field

abstract:
  We have created periodic nanoscale structures in a gold substrate with a
lithography process using metastable triplet helium atoms that damage a
hydrofobic resist layer on top of the substrate. A beam of metastable helium
atoms is transversely cooled and guided through an intense standing-wave light
field. Compared to commonly used low-power optical masks, a high-power light
field (saturation parameter of 10E7) increases the confinement of the atoms in
the standing-wave considerably, and makes the alignment of the experimental
setup less critical. Due to the high internal energy of the metastable helium
atoms (20 eV), a dose of only one atom per resist molecule is required. With an
exposure time of only eight minutes, parallel lines with a separation of 542 nm
and a width of 100 nm (1/11th of the wavelength used for the optical mask) are
created.


title: Study of Friction at the Mesoscale using Nitinol Shape Memory Alloy

abstract:
  Elastic and dissipative properties of a NiTi shape memory alloy have been
studied in both the martensite and austenite phases, using the free-decay of a
vibrating Nitinol wire. The influence of air was estimated from a martensite
measurement in vacuum.


title:
Brane Worlds, the Subanthropic Principle and the Undetectability
  Conjecture

abstract:
  In the recent article `Conflict between anthropic reasoning and
observation'(gr-qc/0303070) Ken D. Olum, using some inflation-based ideas and
the anthropic premise that we should be typical among all intelligent observers
in the Universe, arrives at the puzzling conclusion that `we should find
ourselves in a large civilization (of galactic size) where most observers
should be, while in fact we do not'. In this note we discuss the intriguing
possibility whether we could be in fact immersed in a large civilization
without being aware of it. Our conclusion is that this possibility cannot be
ruled out provided two conditions are met, that we call the Subanthropic
Principle and the Undetectability Conjecture.
  -----
  En el reciente articulo `Conflicto entre razonamiento antropico y
observacion' Ken D. Olum, basandose en algunas ideas sobre la inflacion
cosmologica y en la premisa antropica de que tenemos que ser tipicos entre los
observadores inteligentes del Universo, llega a la sorprendente conclusion de
que `deberiamos encontrarnos en una civilizacion grande (de tamanio galactico)
al igual que la mayoria de los observadores, mientras que de hecho no lo
estamos'. En este articulo discutimos la posibilidad de que nuestra
civilizacion este de hecho inmersa en una civilizacion grande, sin que seamos
conscientes de ello. Nuestra conclusion es que esta posibilidad no puede
descartarse si se cumplen dos condiciones, que llamamos el Principio
Subantropico y la Conjetura de Indetectabilidad.

categories: physics.pop-ph astro-ph gr-qc hep-ph hep-th


title:
Stable multiple-charged localized optical vortices in cubic-quintic
  nonlinear media

abstract:
  The stability of two-dimensional bright vortex solitons in a media with
focusing cubic and defocusing quintic nonlinearities is investigated
analytically and numerically. It is proved that above some critical beam powers
not only one- and two-charged but also multiple-charged stable vortex solitons
do exist. A vortex soliton occurs robust with respect to symmetry-breaking
modulational instability in the self-defocusing regime provided that its radial
profile becomes flattened, so that a self-trapped wave beam gets a pronounced
surface. It is demonstrated that the dynamics of a slightly perturbed stable
vortex soliton resembles an oscillation of a liquid stream having a surface
tension. Using the idea of sustaining effective surface tension for spatial
vortex soliton in a media with competing nonlinearities the explanation of a
suppression of the modulational instability is proposed.


title:
Building a 3.5 m prototype interferometer for the Q & A vacuum
  birefringence experiment and high precision ellipsometry

abstract:
  We have built and tested a 3.5 m high-finesse Fabry-Perot prototype
inteferometer with a precision ellipsometer for the QED test and axion search
(Q & A) experiment. We use X-pendulum-double-pendulum suspension designs and
automatic control schemes developed by the gravitational-wave detection
community. Verdet constant and Cotton-Mouton constant of the air are measured
as a test. Double modulation with polarization modulation 100 Hz and
magnetic-field modulation 0.05 Hz gives 10^{-7} rad phase noise for a 44-minute
integration.


title:
Convective instabilities in two superposed horizontal liquid layers
  heated laterally

abstract:
  This work is devoted to the theoretical study of the stability of two
superposed horizontal liquid layers bounded by two solid planes and subjected
to a horizontal temperature gradient.
  The liquids are supposed to be immiscible with a nondeformable interface.
  The forces acting on the system are buoyancy and interfacial tension. Four
different flow patterns and temperature profiles are found for the basic state.
A linear perturbative analysis with respect to two and three dimensional
perturbations reveals the existence of three kind of patterns. Depending on the
relative height of both liquids several situations are predicted: either wave
propagation from cold to the hot regions, or waves propagating in the opposite
direction or still stationary longitudinal rolls. The behavior of three
different pairs of liquids which have been used in experiments on bilayers
under vertical gradient by other authors have been examined. The instability
mechanisms are discussed and a qualitative interpretation of the different
behaviors exhibited by the system is provided. In some configurations it is
possible to find a codimension-two point created by the interaction of two Hopf
modes with different frequencies and wavenumbers. These results suggest to
consider two liquid layers as an interesting prototype for the study of
propagation and interaction of waves in the context of the B\'enard-Marangoni
problem.


title:
Spatial and Temporal Variability of the Gamma Radiation from Earth's
  Atmosphere during a Solar Cycle

abstract:
  The Solar Maximum Mission satellite's Gamma Ray Spectrometer observed Earth's
atmosphere for most of the period 1980-1989. Its 28deg orbit ensured that a
range of geomagnetic latitudes (geomagnetic cutoff rigidities) was sampled. We
measured the variation with time and rigidity of albedo gamma-ray lines at 1.6
MeV, 2.3 MeV and 4.4 MeV which are diagnostic of Galactic cosmic radiation
penetrating the cutoff and of the secondary neutrons produced in the
atmosphere. We found that the gamma-ray line intensities varied inversely with
solar activity and cutoff rigidity, as expected. The line ratio (1.6 MeV + 2.3
MeV)/4.4 MeV was remarkably constant (close to 0.39) at all times and
rigidities; the former two lines are produced by 5-10 MeV secondary neutrons
causing excitation and de-excitation of 14N, while the latter is produced by
more energetic (>20 MeV) neutrons inducing spallation. We infer that the shape
of the secondary neutron energy spectrum is virtually constant everywhere and
at all times. We also measured the intensity of the 0.511 MeV electron-positron
annihilation line. This line too varies with solar cycle and cutoff rigidity,
but its fall-off from low to high rigidity is less marked than that of the
nuclear lines. This results from the energy dependences of the cross sections
for positron production and for the hadronic processes which which produce
secondary neutrons.


title:
Dual kinetic balance approach to basis set expansions for the Dirac
  equation

abstract:
  A new approach to finite basis sets for the Dirac equation is developed. It
solves the problem of spurious states and, as a result, improves the
convergence properties of basis set calculations. The efficiency of the method
is demonstrated for finite basis sets constructed from B splines by calculating
the one-loop self-energy correction for a hydrogenlike ion.


title:
Using the local density approximation and the LYP, BLYP, and B3LYP
  functionals within Reference--State One--Particle Density--Matrix Theory

abstract:
  For closed-shell systems, the local density approximation (LDA) and the LYP,
BLYP, and B3LYP functionals are shown to be compatible with reference-state
one-particle density-matrix theory, where this recently introduced formalism is
based on Brueckner-orbital theory and an energy functional that includes exact
exchange and a non-universal correlation-energy functional. The method is
demonstrated to reduce to a density functional theory when the
exchange-correlation energy-functional has a simplified form, i.e., its
integrand contains only the coordinates of two electron, say r1 and r2, and it
has a Dirac delta function -- delta(r1 - r2) -- as a factor. Since Brueckner
and Hartree--Fock orbitals are often very similar, any local exchange
functional that works well with Hartree--Fock theory is a reasonable
approximation with reference-state one-particle density-matrix theory. The LDA
approximation is also a reasonable approximation. However, the Colle--Salvetti
correlation-energy functional, and the LYP variant, are not ideal for the
method, since these are universal functionals. Nevertheless, they appear to
provide reasonable approximations. The B3LYP functional is derived using a
linear combination of two functionals: One is the BLYP functional; the other
uses exact exchange and a correlation-energy functional from the LDA.


title:
Increased Concentration of Polyvalent Phospholipids in the Adsorption
  Domain of a Charged Protein

abstract:
  We studied the adsorption of a charged protein onto an oppositely charged
membrane, composed of mobile phospholipids of differing valence, using a
statistical-thermodynamical approach. A two-block model was employed, one block
corresponding to the protein-affected region on the membrane, referred to as
the adsorption domain, and the other to the unaffected remainder of the
membrane. We calculated the protein-induced lipid rearrangement in the
adsorption domain as arising from the interplay between the electrostatic
interactions in the system and the mixing entropy of the lipids. Equating the
electrochemical potentials of the lipids in the two blocks yields an expression
for the relations among the various lipid fractions in the adsorption domain,
indicating a sensitive dependence of lipid fraction on valence. This expression
is a result of the two-block picture but does not depend on further details of
the protein-membrane interaction. We subsequently calculated the lipid
fractions themselves using the Poisson-Boltzmann theory. We examined the
dependence of lipid enrichment, i.e., the ratio between the lipid fractions
inside and outside the adsorption domain, on various parameters such as ionic
strength and lipid valence. Maximum enrichment was found for lipid valence of
about (-3) to (-4) in physiological conditions. Our results are in qualitative
agreement with recent experimental studies on the interactions between peptides
having a domain of basic residues and membranes containing a small fraction of
the polyvalent phosphatidylinositol 4,5-bisphosphate (PIP2). This study
provides theoretical support for the suggestion that proteins adsorbed onto
membranes through a cluster of basic residues may sequester PIP2 and other
polyvalent lipids.


title: Remarks on statistical aspects of safety analysis of complex systems

abstract:
  We analyze safety problems of complex systems using the methods of
mathematical statistics for testing the output variables of a code simulating
the operation of the system under consideration when the input variables are
uncertain. We have defined a black box model of the code and derived formulas
to calculate the number of runs needed for a given confidence level to achieve
a preassigned measure of safety. In order to show the capabilities of different
statistical methods, firstly we have investigated one output variable with
unknown and known distribution functions. The general conclusion has been that
the different methods do not bring about large differences in the number of
runs needed to ensure a given level of safety. Analyzing the case of several
statistically dependent output variables we have arrived at the conclusion that
the testing of the variables separately may lead to false, safety related
decisions with unforseen consequences. We have advised two methods: the sign
test and the tolerance interval methods for testing more than one mutually
dependent output variables.


title: Multi-mode photonic crystal fibers for VCSEL based data transmission

abstract:
  Quasi error-free 10 Gbit/s data transmission is demonstrated over a novel
type of 50 micron core diameter photonic crystal fiber with as much as 100 m
length. Combined with 850$ nm VCSEL sources, this fiber is an attractive
alternative to graded-index multi-mode fibers for datacom applications. A
comparison to numerical simulations suggests that the high bit-rate may be
partly explained by inter-modal diffusion.


title:
Coulomb three-body systems and charge transfer collisions in a
  configuration-space approach

abstract:
  Some low-energy three-body muon- and electron-transfer processes are
considered within the Faddeev-Hahn formulation using two-, six-, and ten-state
close-coupling approximation. We test our approach in bound-state problems for
systems H$_2^+$ and ($\mu^-$dd)$^+$ within six- and ten-state schemes, where
$d$ is a deuteron and $\mu$ a muon. We present results in the six-state model
for muonium formation from hydrogen. We also present results for muon-transfer
rates from muonic hydrogen isotopes to bare nuclei S$^{16}$ and Ar$^{18}$ in
reasonable agreement with experiment. For these heavier targets a polarization
potential is included and Coulomb potentials are treated exactly without
approximation or cut off.


title: Spatial curvature effects on molecular transport by diffusion

abstract:
  For a substance diffusing on a curved surface, we obtain an explicit relation
valid for very small values of the time, between the local concentration, the
diffusion coefficient, the intrinsic spatial curvature and the time. We recover
the known solution of Fick's law of diffusion in the flat space limit. In the
biological context, this result would be useful in understanding the variations
in the diffusion rates of integral proteins and other molecules on membranes.


title:
Binding Energies and Scattering Observables in the ^3He^4He_2 Atomic
  System

abstract:
  The ^3He^4He_2 three-atomic system is studied on the basis of a hard-core
version of the Faddeev differential equations. The binding energy of the
^3He^4He_2 trimer, scattering phase shifts, and the scattering length of a ^3He
atom off a ^4He dimer are calculated using the LM2M2 and TTY He-He interatomic
potentials.