title: On size and growth of cells

abstract:
  Understanding how growth induces form is a longstanding biological question.
Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some
others have shown the importance of the mechanical properties of bacterial
walls and plant tissues in pattern formation. Here I sketch a simple physical
picture of cell growth. The study is focussed on isolated cells that have
walls. They are modeled as thin elastic shells containing a liquid, which
pressure drives the growth as generally admitted for bacteria or plant cells.
Requiring mechanical equilibrium leads to estimations of typical cell sizes, in
quantitative agreement with compiled data including bacteria, cochlear outer
hair, fungi, yeast, root hair and giant alga cells.


title: Intense pulsed helium droplet beams

abstract:
  Pulsed (30 - 100 microseconds) nozzle beams have been used to generate helium
droplets (<N> = 10^4-10^5). The dependence of the beam intensity and the mean
droplet size on the source stagnation pressure and temperature are studied via
mass spectroscopy and laser induced fluorescence of embedded phthalocyanine
molecules. In comparison to a cw beam the pulsed source for the same pressure
and temperature has a factor of 100 higher flux and the droplet sizes are an
order of a magnitude larger.


title: A model for mutation in bacterial populations

abstract:
  We describe the evolution of $E.coli$ populations through a Bak-Sneppen type
model which incorporates random mutations. We show that, for a value of the
mutation level which coincides with the one estimated from experiments, this
model reproduces the measures of mean fitness relative to that of a common
ancestor, performed for over 10,000 bacterial generations.

categories: physics.bio-ph cond-mat.soft hep-lat nlin.AO q-bio


title: Radiation-condensation instability in a highly ionized dusty plasma

abstract:
  The dynamics of linear perturbations in a radiatively cooling dusty plasma is
considered, with the charge of both dust ($Z_d$) and plasma ($Z_p$) components
being allowed to vary with their densities. It is shown that in the
long-wavelength limit corresponding to the characteristic cooling length, when
the plasma can be treated as quasineutral, the presence of dust particles
changes the criteria for radiation instability, regardless the charging process
of the dust particles. In particular, the condensation (isobaric) mode is shown
to be stabilized (destabilized) if in the equilibrium, the relation between
densities of the dust $n_d$ and plasma $n$ under the quasineutrality condition,
$(d\ln n_{d}/d \ln n)_{q}<1$ ($>1$) is satisfied, while the isentropic mode is
stabilized (destabilized) when the opposite inequalities take place; the
isochoric mode is unaltered. Numerical estimates show that these effects can be
important in hot phases ($T\sim 10^{6}$ K) of the interstellar plasma, and in
tokamak plasma near the walls.


title: NLC Luminosity as a Function of Beam Parameters

abstract:
  Realistic calculation of NLC luminosity has been performed using particle
tracking in DIMAD and beam-beam simulations in GUINEA-PIG code for various
values of beam emittance, energy and beta functions at the Interaction Point
(IP). Results of the simulations are compared with analytic luminosity
calculations. The optimum range of IP beta functions for high luminosity was
identified.


title:
Probabilistic Clustering of Sequences: Inferring new bacterial regulons
  by comparative genomics

abstract:
  Genome wide comparisons between enteric bacteria yield large sets of
conserved putative regulatory sites on a gene by gene basis that need to be
clustered into regulons. Using the assumption that regulatory sites can be
represented as samples from weight matrices we derive a unique probability
distribution for assignments of sites into clusters. Our algorithm, 'PROCSE'
(probabilistic clustering of sequences), uses Monte-Carlo sampling of this
distribution to partition and align thousands of short DNA sequences into
clusters. The algorithm internally determines the number of clusters from the
data, and assigns significance to the resulting clusters. We place theoretical
limits on the ability of any algorithm to correctly cluster sequences drawn
from weight matrices (WMs) when these WMs are unknown. Our analysis suggests
that the set of all putative sites for a single genome (e.g. E. coli) is
largely inadequate for clustering. When sites from different genomes are
combined and all the homologous sites from the various species are used as a
block, clustering becomes feasible. We predict 50-100 new regulons as well as
many new members of existing regulons, potentially doubling the number of known
regulatory sites in E. coli.

categories: physics.bio-ph physics.data-an q-bio.GN q-bio.QM


title:
Electromagnetic Influence on Gravitational Mass - Theory, Experiments,
  and Mechanism of the Solar Corona Heating

abstract:
  Based on the model of Expansive Nondecelerative Universe, the aim of the
present contribution is to contribute to the theoretical rationalization of
some experiments, in particular of those performed by Podkletnov and de Aquino
and devoted to the gravitational mass cessation, to offer a mechanistic
explanation of the Solar corona heating, and to propose an experiment to verify
the explanation of the heating in the Earth conditions.


title:
Energy levels and lifetimes of Gd IV and enhancement of the electron
  dipole moment

abstract:
  We have calculated energy levels and lifetimes of 4f7 and 4f6 5d
configurations of Gd IV using Hartree-Fock and configuration interaction
methods. This allows us to reduce significantly the uncertainty of the
theoretical determination of the electron electric dipole moment (EDM)
enhancement factor in this ion and, correspondingly, in gadolinium-containing
garnets for which such measurements were recently proposed. Our new value for
the EDM enhancement factor of Gd+3 is -2.2 +- 0.5. Calculations of energy
levels and lifetimes for Eu~III are used to control the accuracy.


title: Spontaneous emission rate of an excited atom placed near a nanofiber

abstract:
  The spontaneous decay rates of an excited atom placed near a dielectric
cylinder are investigated. A special attention is paid to the case when the
cylinder radius is small in comparison with radiation wavelength (nanofiber or
photonic wire). In this case, the analytical expressions of the transition
rates for different orientations of dipole are derived. It is shown that the
main contribution to decay rates is due to quasistatic interaction of atom
dipole momentum with nanofiber and the contributions of guided modes are
exponentially small. On the contrary, in the case when the radius of fiber is
only slightly less than radiation wavelength, the influence of guided modes can
be substantial. The results obtained are compared with the case of dielectric
nanospheroid and ideally conducting wire.


title: From Localization to Stochastics in BBGKY Collective Dynamics

abstract:
  Fast and efficient numerical-analytical approach is proposed for modeling
complex collective behaviour in accelerator/plasma physics models based on
BBGKY hierarchy of kinetic equations. Our calculations are based on variational
and multiresolution approaches in the bases of polynomial tensor algebras of
generalized coherent states/wavelets. We construct the representation for
hierarchy of reduced distribution functions via the multiscale decomposition in
high-localized eigenmodes. Numerical modeling shows the creation of different
internal coherent structures from localized modes, which are related to
stable/unstable type of behaviour and corresponding pattern (waveletons)
formation.


title:
Fast Calculation Methods in Collective Dynamical Models of Beam/Plasma
  Physics

abstract:
  We consider an application of modification of our variational-wavelet
approach to some nonlinear collective model of beam/plasma physics:
Vlasov/Boltzmann-like reduction from general BBGKY hierachy related to modeling
of propagation of intense charged particle beams in high-intensity accelerators
and transport systems. We use fast convergent multiscale variational-wavelet
representations for solutions which allow to consider polynomial and rational
type of nonlinearities. The solutions are represented via the multiscale
decomposition in nonlinear high-localized eigenmodes (waveletons). In contrast
with different approaches we do not use perturbation technique or linearization
procedures.


title: Multiscale Decomposition for Vlasov-Poisson Equations

abstract:
  We consider the applications of a numerical-analytical approach based on
multiscale variational wavelet technique to the systems with collective type
behaviour described by some forms of Vlasov-Poisson/Maxwell equations. We
calculate the exact fast convergent representations for solutions in
high-localized wavelet-like bases functions, which correspond to underlying
hidden (coherent) nonlinear eigenmodes. This helps to control
stability/unstability scenario of evolution in parameter space on pure
algebraical level.


title: RMS/Rate Dynamics via Localized Modes

abstract:
  We consider some reduction from nonlinear Vlasov-Maxwell equation to rms/rate
equations for second moments related quantities. Our analysis is based on
variational wavelet approach to rational (in dynamical variables)
approximation. It allows to control contribution from each scale of underlying
multiscales and represent solutions via multiscale exact nonlinear eigenmodes
(waveletons) expansions. Our approach provides the possibility to work with
well-localized bases in phase space and best convergence properties of the
corresponding expansions without perturbations or/and linearization procedures.


title: Nonlinear Localized Coherent Spectrum of Beam-Beam Interactions

abstract:
  We consider modeling for strong-strong beam-beam interactions beyond
preceding linearized/perturbative methods such as soft gaussian approximation
or FMM (HFMM) etc. In our approach discrete coherent modes, discovered before,
and possible incoherent oscillations appear as a result of
multiresolution/multiscale fast convergent decomposition in the bases of
high-localized exact nonlinear modes represented by wavelets or wavelet packets
functions. The constructed solutions represent the full multiscale spectrum in
all internal hidden scales from slow to fast oscillating eigenmodes. Underlying
variational method provides algebraical control of the spectrum.


title: Nonlinear Motion in Electromagnetic Fields via Multiscale Expansions

abstract:
  The consideration of dynamics of relativistic beams/particles is based on
variational approach to rational (in dynamical variables) approximation for
equations of motions. It allows to control contribution from each scale of
underlying multiscales and represent solutions via exact nonlinear eigenmodes
expansions. Our approach is based on methods provided possibility to work with
well-localized bases in phase space and good convergence properties of the
corresponding expansions.


title: Graph-driven features extraction from microarray data

abstract:
  Gene function prediction from microarray data is a first step toward better
understanding the machinery of the cell from relatively cheap and
easy-to-produce data. In this paper we investigate whether the knowledge of
many metabolic pathways and their catalyzing enzymes accumulated over the years
can help improve the performance of classifiers for this problem.
  The complex network of known biochemical reactions in the cell results in a
representation where genes are nodes of a graph. Formulating the problem as a
graph-driven features extraction problem, based on the simple idea that
relevant features are likely to exhibit correlation with respect to the
topology of the graph, we end up with an algorithm which involves encoding the
network and the set of expression profiles into kernel functions, and
performing a regularized form of canonical correlation analysis in the
corresponding reproducible kernel Hilbert spaces.
  Function prediction experiments for the genes of the yeast S. Cerevisiae
validate this approach by showing a consistent increase in performance when a
state-of-the-art classifier uses the vector of features instead of the original
expression profile to predict the functional class of a gene.


title: Cluster Analysis of Gene Expression Data

abstract:
  The expression levels of many thousands of genes can be measured
simultaneously by DNA microarrays (chips). This novel experimental tool has
revolutionized research in molecular biology and generated considerable
excitement. A typical experiment uses a few tens of such chips, each dedicated
to a single sample - such as tissue extracted from a particular tumor. The
results of such an experiment contain several hundred thousand numbers, that
come in the form of a table, of several thousand rows (one for each gene) and
50 - 100 columns (one for each sample). We developed a clustering methodology
to mine such data. In this review I provide a very basic introduction to the
subject, aimed at a physics audience with no prior knowledge of either gene
expression or clustering methods. I explain what genes are, what is gene
expression and how it is measured by DNA chips. Next I explain what is meant by
"clustering" and how we analyze the massive amounts of data from such
experiments, and present results obtained from analysis of data obtained from
colon cancer, brain tumors and breast cancer.


title: Maximum-likelihood absorption tomography

abstract:
  Maximum-likelihood methods are applied to the problem of absorption
tomography. The reconstruction is done with the help of an iterative algorithm.
We show how the statistics of the illuminating beam can be incorporated into
the reconstruction. The proposed reconstruction method can be considered as a
useful alternative in the extreme cases where the standard ill-posed
direct-inversion methods fail.


title: Ultra-low energy elastic scattering in a system of three He atoms

abstract:
  Differential Faddeev equations in total angular momentum representation are
used for the first time to investigate ultra-low energy elastic scattering of a
helium atom on a helium dimer. Six potential models of interatomic interaction
are investigated. The results improve and extend the Faddeev equations based
results known in literature. The employed method can be applied to
investigation of different elastic and inelastic processes in three- and
four-atomic weakly bounded systems below three-body threshold.


title: Aging in gaseous photodetectors

abstract:
  This paper describes the present status of the aging studies in various
photosensitive detectors. New experimental data are presented on aging of
trimethilamine (TMA) and ethilferrocene (EF) photosensitive vapors as well as
on CsI and SbCs photocathodes. A new explanation of the CsI photocathodes aging
process based on solid state physics theory is given. Finally, based on our
studies, a general conclusion was made that thin polymer depositions on the
detector=92s cathode due to the aging can provoke breakdowns through the
Malter-type mechanism (or more precisely- an explosive field emission
mechanism).


title:
Coupled Two-Way Clustering Analysis of Breast Cancer and Colon Cancer
  Gene Expression Data

abstract:
  We present and review Coupled Two Way Clustering, a method designed to mine
gene expression data. The method identifies submatrices of the total expression
matrix, whose clustering analysis reveals partitions of samples (and genes)
into biologically relevant classes. We demonstrate, on data from colon and
breast cancer, that we are able to identify partitions that elude standard
clustering analysis.


title: Fundamental Disagreement of Wave Mechanics with Relativity

abstract:
  A number of well-known difficulties in physics resulted from merging the
theory of relativity with the Compton-de Broglie wave mechanics. Two such
problems were the failure of Dirac's relativistic wave equation to predict the
correct velocity of the electron, and the fact that the measured yield from
nuclear fission was found to be substantially less than the theoretical yield.
It is shown that the origin of these and other problems stem from the
inconsistency of the relativistic mass-energy equivalence principle with the
fundamental assumptions of wave mechanics. An alternative view of the concept
of mass-energy equivalence that results in a very good agreement between theory
and experiment is demonstrated. The conclusions of this paper will be quite
important for ongoing research, such as the current problem of the neutrino's
mass.


title:
Relativistic many-body calculations of energies for core-excited states
  in sodiumlike ions

abstract:
  Energies of (2s2 2p5 3l3l') and (2s 2p6 3l3l') states for sodiumlike ions
with Z =14--100 are evaluated to second order in relativistic many-body
perturbation theory starting from a neonlike Dirac-Fock potential. Second-order
Coulomb and Breit interactions are included. Correction for the
frequency-dependence of the Breit interaction is taken into account in lowest
order. The Lamb shift correction to energies is also included in lowest order.
Intrinsic particle-particle-hole contributions to energies are found to be
20-30% of the sum of one- and two-body contributions. Comparisons are made with
available experimental data. These calculations are presented as a theoretical
benchmark for comparison with experiment and theory.


title: Radiation Reaction for a Charged Brownian Particle

abstract:
  As it is known a model of a charged particle with finite size is a good tool
to consider the effects of self- action and backreaction, caused by
electromagnetic radiation. In this work the "size" of a charged particle is
induced by its stochastic Brownian vibration. Appropriate equation of
particle's motion with radiation force is derived. It is shown that the
solutions of this equation correctly describe the effects of radiation
reaction.


title: Self Force of a Charge in a Real Current Environment

abstract:
  The analysis of the EM radiation from a single charge shows that the radiated
power depends on the retarded acceleration of the charge. Therefore, for
consistency, an accelerated charge, free from the influence of external forces,
should gradually lose its acceleration, until its total energy is radiated.
Calculations show that the self force of a charge, which compensates for its
radiation, is proportional to the derivative of the acceleration. However, when
using this self-force in the equation of motion of the charge, one gets a
diverging solution, for which the acceleration runs away to infinity. This
means that there is an inconsistency in the solution of the single charge
problem. However, in the construction of the conserved Maxwell charge density,
there is implicitly an integral over the corresponding world line which
corresponds to a collection of charged spacetime events. One may therefore
consistently think of the ``self force'' as the force on a charge due to
another charge at the retarded position. From this point of view, the energy is
evidently conserved and the radiation process appears as an absorbing
resistance to the feeding source. The purpose of this work is to learn about
the behavior of single charges from the behavior of a real current,
corresponding to the set of chargesa moving on a world line, and to study the
analog of the self force of a charge associated with the radiation resistance
of a continuum of charges.


title: Fluctuation of the ambipolar equilibrium in magnetic perturbations

abstract:
  We draw attention on the fast oscillatory deviations from the residual
non-ambipolarity in the case where electrons are driven by strong magnetic
perturbations.


title: Growth Patterns of Microscopic Brain Tumors

abstract:
  Highly malignant brain tumors such as Glioblastoma Multiforme (GBM) form
complex growth patterns in vitro in which invasive cells organize in tenuous
branches. Here, we formulate a chemotaxis model for this sort of growth. A key
element controlling the pattern is homotype attraction, i.e., the tendency for
invasive cells to follow pathways previously explored. We investigate this in
two ways: we show that there is an intrinsic instability in the model, which
leads to branch formation. We also give a discrete description for the
expansion of the invasive zone, and a continuum model for the nutrient supply.
The results indicate that both, strong heterotype chemotaxis and strong
homotype chemo-attraction are required for branch formation within the invasive
zone. Our model thus can give a way to assess the importance of the various
processes, and a way to explore and analyze transitions between different
growth regimes.


title: KANGA(ROO): Handling the micro-DST of the BaBar Experiment with ROOT

abstract:
  A system based on ROOT for handling the micro-DST of the BaBar experiment is
described. The purpose of the Kanga system is to have micro-DST data available
in a format well suited for data distribution within a world-wide collaboration
with many small sites. The design requirements, implementation and experience
in practice after three years of data taking by the BaBar experiment are
presented.


title: Tuning Knobs for the NLC Final Focus

abstract:
  Compensation of optics errors at the Interaction Point (IP) is essential for
maintaining maximum luminosity at the NLC. Several correction systems (knobs)
using the Final Focus sextupoles have been designed to provide orthogonal
compensation of linear and the second order optics aberrations at IP. Tuning
effects of these knobs on the 250 GeV beam were verified using tracking
simulations.


title:
Faddeev-Merkuriev equations for resonances in three-body Coulombic
  systems

abstract:
  We reconsider the homogeneous Faddeev-Merkuriev integral equations for
three-body Coulombic systems with attractive Coulomb interactions and point out
that the resonant solutions are contaminated with spurious resonances. The
spurious solutions are related to the splitting of the attractive Coulomb
potential into short- and long-range parts, which is inherent in the approach,
but arbitrary to some extent. By varying the parameters of the splitting the
spurious solutions can easily be ruled out. We solve the integral equations by
using the Coulomb-Sturmian separable expansion approach. This solution method
provides an exact description of the threshold phenomena. We have found several
new S-wave resonances in the e- e+ e- system in the vicinity of thresholds.


title: Electron release of rare gas atom clusters under an intense laser pulse

abstract:
  Calculating the energy absorption of atomic clusters as a function of the
laser pulse length $T$ we find a maximum for a critical $T^*$. We show that
$T^*$ can be linked to an optimal cluster radius $R^*$. The existence of this
radius can be attributed to the enhanced ionization mechanism originally
discovered for diatomic molecules. Our findings indicate that enhanced
ionization should be operative for a wide class of rare gas clusters. From a
simple Coulomb explosion ansatz, we derive an analytical expression relating
the maximum energy release to a suitably scaled expansion time which can be
expressed with the pulse length $T^*$.


title: Novel position-sensitive gaseous detectors with solid photo-cathodes

abstract:
  Currently a revolution is happening in the development of gaseous detectors
of photons and particles. Recently developed gaseous detectors with solid
photocathodes are now replacing photosensitive wire chambers, which dominated
for years in high energy and space flight experiments. We will review the main
developments in this field as well as their applications in high-energy
physics, medicine, industry and plasma diagnostics. New results on solid
photocathodes coupled with gaseous micropattern/wire detectors will also be
presented.


title: A chaotic 'turnstile' for atoms in periodic potentials

abstract:
  Using a new type of chaotic ratchet generated by pulsed standing waves of
light, we propose a mechanism which would allow packets of atoms travelling
through a pulsed optical lattice in one direction to pass almost undisturbed,
while strongly heating atoms drifting through in the opposite direction. An
analytical formula for the diffusive energy growth is derived and shown to give
good agreement with numerical calculations.


title: Chaotic Behavior of Positronium in a Magnetic Field

abstract:
  Classical motion of positronium embedded in a magnetic field is studied, and
computation shows the emergence of chaotic orbits. Recent work investigating
quantum behavior of this system predicts extremely long lifetimes. Chaos
assisted tunneling, however may lead to significant shortening of the lifetime
of this system.


title: Physical Chirality. It Feeds on Negative Entropy

abstract:
  Chirality is considered by many scientists to be mainly a geometric concept.
There exists also a physical aspect of chirality which is largely being
overlooked at. Two examples of mechanical devices are introduced here that
represent ``Physical Chirality''. These are a rotating water sprinkler and a
variant of Crookes' radiometer. When interacting with appropriate media, they
both choose only one mode of rotation out of two possible ones. Such a behavior
does not obey time-reversal invariance, which is regarded to be a rule in
classical mechanics. This is due to their chiral nature. Instead, they do obey
a space-time (ST) law of invariance, that is, what is rotating in the opposite
direction is the mirror-image of the given device. In a recent experiment of
Koumura et al. they discovered a similar behavior of a molecular rotor. The
possible biological significance of physical chirality is emphasized hereby,
and the conclusion is that chiral molecular systems do not reach readily
thermal equilibrium. In other words: ``Physical chirality does feed on negative
entropy'', and therefore, it may well be of crucial value to life.


title:
Sensitivity Analysis of Stoichiometric Networks: An Extension of
  Metabolic Control Analysis to Non-equilibrium Trajectories

abstract:
  A sensitivity analysis of general stoichiometric networks is considered. The
results are presented as a generalization of Metabolic Control Analysis, which
has been concerned primarily with system sensitivities at steady state. An
expression for time-varying sensitivity coefficients is given, and the
Summation and Connectivity Theorems are generalized. The results are compared
to previous treatments. The analysis is accompanied by a discussion of the
computation of the sensitivity coefficients and an application to a model of
phototransduction.


title: An Early History of Heavy Water

abstract:
  Since 1945 Canada has had a nuclear power industry based on reactor design
which uses natural uranium and heavy water. The tortuous and improbable
sequence of events which led to this situation is examined.


title:
Rotating Metal Band Target for Pion Production at Muon Colliders and
  Neutrino Factories

abstract:
  A conceptual design is presented for a high power pion production target for
muon colliders and neutrino factories that is based around a rotating metal
band.


title:
Metamorphosis of plasma turbulence-shear flow dynamics through a
  transcritical bifurcation

abstract:
  The structural properties of an economical model for a confined plasma
turbulence governor are investigated through bifurcation and stability
analyses. A close relationship is demonstrated between the underlying
bifurcation framework of the model and typical behavior associated with low- to
high-confinement transitions such as shear flow stabilization of turbulence and
oscillatory collective action. In particular, the analysis evinces two types of
discontinuous transition that are qualitatively distinct. One involves
classical hysteresis, governed by viscous dissipation. The other is
intrinsically oscillatory and non-hysteretic, and thus provides a model for the
so-called dithering transitions that are frequently observed. This
metamorphosis, or transformation, of the system dynamics is an important late
side-effect of symmetry-breaking, which manifests as an unusual non-symmetric
transcritical bifurcation induced by a significant shear flow drive.


title: Ionization of clusters in strong X-ray laser pulses

abstract:
  The effect of intense X-ray laser interaction on argon clusters is studied
theoretically with a mixed quantum/classical approach. In comparison to a
single atom we find that ionization of the cluster is suppressed, which is in
striking contrast to the observed behavior of rare-gas clusters in intense
optical laser pulses. We have identified two effects responsible for this
phenomenon: A high space charge of the cluster in combination with a small
quiver amplitude and delocalization of electrons in the cluster. We elucidate
their impact for different field strengths and cluster sizes.


title: Classifying ancient texts by inter-word spacing

abstract:
  We use the inter-word spacing technique, that Ortuno et al devised for
analyzing DNA.We develop this idea further for classifying ancient texts.


title:
Implementation of Liu's procedure in Mathematica for use in Relativistic
  Constitutive Theory

abstract:
  The aim of this article is to show, how computer algebra can be used when
applying Liu's procedure. Although Mathematica (a commercial product by Wolfram
Research Inc.) is used, it is possible to use other computer algebra systems as
well.


title: Physics of multi-GEM structures

abstract:
  We show that physics of multi-GEM structures is rather complex, regarding the
number of phenomena affecting detector performance. The high-pressure operation
in noble gases and the ion feedback are considered in more detail. It is
proposed that the dominant avalanche mechanism in He and Ne, at high pressures,
is the associative ionization. Ion feedback effects related to the dependence
on gas, pressure and gain and to possible avalanche extension outside the GEM
holes are discussed.


title: A Model of Two Dimensional Turbulence Using Random Matrix Theory

abstract:
  We derive a formula for the entropy of two dimensional incompressible
inviscid flow, by determining the volume of the space of vorticity
distributions with fixed values for the moments Q_k= \int_w(x)^k d^2 x. This
space is approximated by a sequence of spaces of finite volume, by using a
regularization of the system that is geometrically natural and connected with
the theory of random matrices. In taking the limit we get a simple formula for
the entropy of a vortex field. We predict vorticity distributions of maximum
entropy with given mean vorticity and enstrophy; also we predict the
cylindrically symmetric vortex field with maximum entropy. This could be an
approximate description of a hurricane.


title: Nucleosome repositioning via loop formation

abstract:
  Active (catalysed) and passive (intrinsic) nucleosome repositioning is known
to be a crucial event during the transcriptional activation of certain
eucaryotic genes. Here we consider theoretically the intrinsic mechanism and
study in detail the energetics and dynamics of DNA-loop-mediated nucleosome
repositioning, as previously proposed by Schiessel et al. (H. Schiessel, J.
Widom, R. F. Bruinsma, and W. M. Gelbart. 2001. {\it Phys. Rev. Lett.}
86:4414-4417). The surprising outcome of the present study is the inherent
nonlocality of nucleosome motion within this model -- being a direct physical
consequence of the loop mechanism. On long enough DNA templates the longer
jumps dominate over the previously predicted local motion, a fact that
contrasts simple diffusive mechanisms considered before. The possible
experimental outcome resulting from the considered mechanism is predicted,
discussed and compared to existing experimental findings.


title: Tidal theory of the thermal wind

abstract:
  The baroclinic instability problem is considered in the framework of
Laplacian tidal theory. The Hilbert space of the quasigeostrophic vorticity
budget is spanned by spheroidal functions. The fluid is linearly stable against
quasigeostrophic disturbances. As the essential source of irregular
ocean-atmosphere motions, baroclinic instability is ruled out by tidal theory.
The midlatitude beta-plane budget of vorticity fluxes is inconsistent with
basic laws of motion on the rotating spherical surface. Realistic numerical
simulations of global wave dynamics and dynamical circulation instabilities
require a covariant account of fluid motion on the spherical planet.

categories: physics.flu-dyn math.AP nlin.CD physics.ao-ph


title: Initial-amplitude dependence in weakly damped oscillators

abstract:
  A pedagogically instructive experimental procedure is suggested for
distinguishing between different damping terms in a weakly damped oscillator,
which highclights the connection between non-linear damping and
initial-amplitude dependence. The most common damping terms such as contact
friction, air resistance, viscous drag, and electromagnetic damping have
velocity dependences of the form constant, v, or v^2. The corresponding energy
dependences of the form \sqrt{E}, E, or E\sqrt{E} in the energy loss equation
give rise to characteristic dependence of the amplitude decay slope on the
initial amplitude.


title:
Etched distributed Bragg reflectors as three-dimensional photonic
  crystals: photonic bands and density of states

abstract:
  The photonic band dispersion and density of states (DOS) are calculated for
the three-dimensional (3D) hexagonal structure corresponding to a distributed
Bragg reflector patterned with a 2D triangular lattice of circular holes.
Results for the Si/SiO$_2$ and GaAs/AlGaAs systems determine the optimal
parameters for which a gap in the 2D plane occurs and overlaps the 1D gap of
the multilayer. The DOS is considerably reduced in correspondence with the
overlap of 2D and 1D gaps. Also, the local density of states (i.e., the DOS
weighted with the squared electric field at a given point) has strong
variations depending on the position. Both results imply substantial changes of
spontaneous emission rates and patterns for a local emitter embedded in the
structure and make this system attractive for the fabrication of a 3D photonic
crystal with controlled radiative properties.


title: Theory of High-Force DNA Stretching and Overstretching

abstract:
  Single molecule experiments on single- and double stranded DNA have sparked a
renewed interest in the force-extension of polymers. The extensible Freely
Jointed Chain (FJC) model is frequently invoked to explain the observed
behavior of single-stranded DNA. We demonstrate that this model does not
satisfactorily describe recent high-force stretching data. We instead propose a
model (the Discrete Persistent Chain, or ``DPC'') that borrows features from
both the FJC and the Wormlike Chain, and show that it resembles the data more
closely. We find that most of the high-force behavior previously attributed to
stretch elasticity is really a feature of the corrected entropic elasticity;
the true stretch compliance of single-stranded DNA is several times smaller
than that found by previous authors. Next we elaborate our model to allow
coexistence of two conformational states of DNA, each with its own stretch and
bend elastic constants. Our model is computationally simple, and gives an
excellent fit through the entire overstretching transition of nicked,
double-stranded DNA. The fit gives the first values for the elastic constants
of the stretched state. In particular we find the effective bend stiffness for
DNA in this state to be about 10 nm*kbt, a value quite different from either
B-form or single-stranded DNA


title:
Multi-Band Dipole And Multipole Wakefields In NLC Traveling Wave
  Accelerators Using A Wire Measurement Technique

abstract:
  Dipole wakefields in NLC (Next Linear Collider) structures have been measured
with ASSET [1] and well predicted by a circuit model [2]. However, the
experimental technique is both time-consuming and expensive. Here, we report on
kick factor and synchronous frequency determination for 1st and higher order
dipole bands for TW (Traveling Wave) accelerators via a wire measurement
technique. This stand-alone technique is relatively inexpensive and may lead to
an efficient determination of wakefield parameters. The perturbative effect of
the wire on the dipole band is pointed out and a two-wire scheme with a limited
perturbative effect is also discussed.
  [1] C. Adolphsen, 1997, SLAC-PUB-7519 [2] R.M. Jones et al, LINAC96,
SLAC-PUB-7287


title: Manifold Damping Of Wakefields In High Phase Advance Linacs For The NLC

abstract:
  Earlier RDDS (Rounded Damped Detuned Structures) [1,2], designed, fabricated
and tested at SLAC, in collaboration with KEK, have been shown to damp
wakefields successfully. However, electrical breakdown has been found to occur
in these structures and this makes them inoperable at the desired gradient.
Recent results [3] indicate that lowering the group velocity of the
accelerating mode reduces electrical breakdown events. In order to preserve the
filling time of each structure a high synchronous phase advance (150 degrees as
opposed to 120 used in previous NLC designs) has been chosen. Here, damping of
the wakefield is analyzed. Manifold damping and interleaving of structure cell
frequencies is discussed. These wakefields impose alignment tolerances on the
cells and on the structure as a whole. Tolerance calculations are performed and
these are compared with analytic estimations.


title: Tuning And Field Sensitivity Of Pi-Mode Standing Wave Linacs For The NLC

abstract:
  In order to mitigate the effects of electrical breakdown (which have been
found to occur in SLAC X-band traveling wave structures) standing wave
structures are being considered for the NLC linac. At SLAC, structures
consisting of 15 cells operating in the p accelerating mode are being tested
for their electrical breakdown characteristics. In this paper the tuning
requirement on the cavities is elucidated by utilizing a circuit model of the
structure. The sensitivity of the field to both random and systematic errors is
also discussed.


title: Coaxial Wire Measurements In NLC Accelerating Structures

abstract:
  The coaxial wire method provides an experimental way of measuring wake fields
without the need for a particle beam. A special setup has been designed and is
in the process of being fabricated at SLAC to measure the loss factors and
synchronous frequencies of dipole modes in both traveling and standing wave
structures for the Next Linear Collider (NLC). The method is described and
predictions based on electromagnetic field simulations are discussed


title: The quantum mechanical foundations of philosophy

abstract:
  Many of the most familiar features of our everyday environment, and some of
our basic notions about it, stem from Relativistic Quantum Field Theory (RQFT).
We argue in particular that the origin of common names, verbs, adjectives such
as full and empty, the concepts of identity, similarity, Plato's Universals,
natural numbers, and existence versus non-existence can be traced to the
space-time and gauge symmetries and quantum properties embodied in RQFT. These
basic tools of human thought cannot arise in a universe strictly described by
classical Physics based on Planck's constant being exactly equal to zero.


title: Large time behavior for vortex evolution in the half-plane

abstract:
  In this article we study the long-time behavior of incompressible ideal flow
in a half plane from the point of view of vortex scattering. Our main result is
that certain asymptotic states for half-plane vortex dynamics decompose
naturally into a nonlinear superposition of soliton-like states. Our approach
is to combine techniques developed in the study of vortex confinement with weak
convergence tools in order to study the asymptotic behavior of a self-similar
rescaling of a solution of the incompressible 2D Euler equations on a half
plane with compactly supported, nonnegative initial vorticity.


title: The Pendulum in the 21st Century--Relic or Trendsetter

abstract:
  When identifying instruments that have had great influence on the history of
physics, none comes to mind more quickly than the pendulum. Though 'birthed' by
Galileo in the 16th century, and in some respects nearly 'dead' by the middle
of the 20th century; the pendulum experienced 'rebirth' by becoming an
archetype of chaos. With the resulting acclaim for its surprising behavior at
large amplitudes, one might expect that there would already be widespread
interest in another of its significant nonlinearities. Such is not the case,
however, and the complex motions of small amplitude physical pendula are barely
known. The present paper shows that a simply-constructed metallic rod pendulum
is capable of demonstrating rich physics in a largely unstudied area.


title: Formation of atomic tritium clusters and condensates

abstract:
  We present an extensive study of the static and dynamic properties of systems
of spin-polarized tritium atoms. In particular, we calculate the two-body
|F,m_F>=|0,0> s-wave scattering length and show that it can be manipulated via
a Feshbach resonance at a field strength of about 870G. Such a resonance might
be exploited to make and control a Bose-Einstein condensate of tritium in the
|0,0> state. It is further shown that the quartet tritium trimer is the only
bound hydrogen isotope and that its single vibrational bound state is a
Borromean state. The ground state properties of larger spin-polarized tritium
clusters are also presented and compared with those of helium clusters.


title:
A Gaussian-optical Approach to Stable Periodic Orbit Resonances of
  Partially Chaotic Dielectric Micro-cavities

abstract:
  The quasi-bound modes localized on stable periodic ray orbits of dielectric
micro-cavities are constructed in the short-wavelength limit using the
parabolic equation method. These modes are shown to coexist with irregularly
spaced "chaotic" modes for the generic case. The wavevector quantization rule
for the quasi-bound modes is derived and given a simple physical interpretation
in terms of Fresnel reflection; quasi-bound modes are explictly constructed and
compared to numerical results. The effect of discrete symmetries of the
resonator is analyzed and shown to give rise to quasi-degenerate multiplets;
the average splitting of these multiplets is calculated by methods from quantum
chaos theory.


title:
Education Curricula of the Regional Centres for Space Science and
  Technology Education (Affiliated to the United Nations)

abstract:
  Since 1988, the United Nations, through the Programme on Space Applications,
is supporting the establishment and operation of regional Centres for Space
Science and Technology Education in Africa, Asia and the Pacific, Latin America
and the Caribbean, and Western Asia. Simultaneously, education curricula have
been developed for remote sensing and geographic information system, satellite
communications, satellite meteorology and global climate, and space and
atmospheric science. The paper reviews briefly these developments and
highlights the most recent updated education curricula in the four disciplines
that are made available in 2002, in the six official languages of the United
Nations, for implementation at the regional Centres and beyond.


title: Reaction Pathways Based on the Gradient of the Mean First-Passage Time

abstract:
  Finding representative reaction pathways is necessary for understanding
mechanisms of molecular processes, but is considered to be extremely
challenging. We propose a new method to construct reaction paths based on mean
first-passage times. This approach incorporates information of all possible
reaction events as well as the effect of temperature. The method is applied to
exemplary reactions in a continuous and in a discrete setting. The suggested
approach holds great promise for large reaction networks that are completely
characterized by the method through a pathway graph.


title: The Coupled Electronic-Ionic Monte Carlo Simulation Method

abstract:
  Quantum Monte Carlo (QMC) methods such as Variational Monte Carlo, Diffusion
Monte Carlo or Path Integral Monte Carlo are the most accurate and general
methods for computing total electronic energies. We will review methods we have
developed to perform QMC for the electrons coupled to a classical Monte Carlo
simulation of the ions. In this method, one estimates the Born-Oppenheimer
energy E(Z) where Z represents the ionic degrees of freedom. That estimate of
the energy is used in a Metropolis simulation of the ionic degrees of freedom.
Important aspects of this method are how to deal with the noise, which QMC
method and which trial function to use, how to deal with generalized boundary
conditions on the wave function so as to reduce the finite size effects. We
discuss some advantages of the CEIMC method concerning how the quantum effects
of the ionic degrees of freedom can be included and how the boundary conditions
can be integrated over. Using these methods, we have performed simulations of
liquid H2 and metallic H on a parallel computer.


title: A new vibrational level of the H$_2^+$ molecular ion

abstract:
  A new state of the H$_2^+$ molecular ion with binding energy of
1.09$\times10^{-9}$ a.u. below the first dissociation limit is predicted, using
highly accurate numerical nonrelativistic quantum calculations. It is the first
L=0 excited state, antisymmetric with respect to the exchange of the two
protons. It manifests itself as a huge p-H scattering length of $a=750\pm 5$
Bohr radii.

categories: physics.atom-ph astro-ph physics.atm-clus physics.comp-ph physics.gen-ph quant-ph


title: Key observational tests of the modern cosmology

abstract:
  Over the last decade, cosmological observations have attained a level of
precision which allows for detailed comparison with theoretical predictions. In
this paper, we briefly review some studies of the current and prospected
constraints imposed by measurements of the cosmic microwave background
radiation, of the mass and of the expansion of the Universe.


title:
Inference of entropies of discrete random variables with unknown
  cardinalities

abstract:
  We examine the recently introduced NSB estimator of entropies of severely
undersampled discrete variables and devise a procedure for calculating the
involved integrals. We discover that the output of the estimator has a well
defined limit for large cardinalities of the variables being studied. Thus one
can estimate entropies with no a priori assumptions about these cardinalities,
and a closed form solution for such estimates is given.


title: Analysis of Data from a Quantum Gravity Experiment

abstract:
  A new information-theoretic modelling of reality has given rise to a quantum-
foam description of space, relative to which absolute motion is meaningful. In
a previous paper (Cahill and Kitto) it was shown that in this new physics
Michelson interferometers show absolute motion effects when operated in
dielectric mode, as indeed all such experiments had indicated, and re-analysis
of the experimental data showed that the measured speeds were all in agreement
with the COBE CBR dipole-fit speed of 365 +/- 18 km/s. Here the new physics is
applied, using a different type of analysis, to the extensive data from
dielectric-mode interferometer observations by Miller (1933). Here the speed of
in-flow of the quantum foam towards the Sun is determined from Miller's data to
be 47 +/- 6km/s, compared to the theoretical value of 42 km/s. This observed
in-flow is a signature of a quantum gravity effect in the new physics.


title: Enhanced ionization in small rare gas clusters

abstract:
  A detailed theoretical investigation of rare gas atom clusters under intense
short laser pulses reveals that the mechanism of energy absorption is akin to
{\it enhanced ionization} first discovered for diatomic molecules. The
phenomenon is robust under changes of the atomic element (neon, argon, krypton,
xenon), the number of atoms in the cluster (16 to 30 atoms have been studied)
and the fluency of the laser pulse. In contrast to molecules it does not
dissappear for circular polarization. We develop an analytical model relating
the pulse length for maximum ionization to characteristic parameters of the
cluster.


title:
Schwinger's oscillator method, supersymmetric quantum mechanics and
  massless particles

abstract:
  We consider the Schwinger's method of angular momentum addition using the
SU(2) algebra with both a fermionic and a bosonic oscillator. We show that the
total spin states obtained are: one boson singlet state and an arbitrary number
of spin-1/2 states, the later ones are energy degenerate. It means that we have
in this case supersymmetric quantum mechanics and also the addition of angular
momentum for massless particles. We review too the cases of two bosonic and
fermionic oscillators.


title: Gravity and motion

abstract:
  Several arguments concerning the "vexatae quaestiones" of the gravity field
of a point mass and of the wavy gravity field.


title:
Influence of acoustic waves on Radiation Spectra of Argon Gas-discharge
  Plasma

abstract:
  It is shown that under the definite regime of interaction of the acoustic
waves with low-temperature, partially ionized plasma it is possible to change
the intensity of some spectral lines of atomic argon. It is shown also, that
the dependence of the intensities of these spectral lines on the intensity of
the acoustic wave has a hysteresis behavior.


title: Lagrangian Probability Distributions of Turbulent Flows

abstract:
  We outline a statistical theory of turbulence based on the Lagrangian
formulation of fluid motion. We derive a hierarchy of evolution equations for
Lagrangian N-point probability distributions as well as a functional equation
for a suitably defined probability functional which is the analog of Hopf's
functional equation. Furthermore, we adress the derivation of a generalized
Fokker-Plank equation for the joint velocity - position probability density of
N fluid particles.


title: The quadric metric as only possible metric for quantized spaces

abstract:
  It is shown, that the space quantum existence (SQE)non-ambigously determine
the metric form for the space without time, using weak condition of metrics
addivity. The hypotesis is proposed, Riemann metics is only possible for
quantized space classes. This statement probably can close the problem of
metrics form.


title:
Fourier Transform Model for All-Order PMD Compensation based on a
  Coupled-Mode Equation Solution using the First Born Approximation

abstract:
  We present a Fourier transform methodology for all-order polarization mode
dispersion (PMD) analysis, based on the first Born approximation to the
coupled-mode equation solution. Our method predicts wavelength-dependent PMD
effects and allows design of filters for their mitigation.


title:
On the remote interaction of biological objects with identical genetic
  structures

abstract:
  The paper puts forward an unusual prediction that cultivating a clone can
curtail the lifespan of the clone donor. Neither the arrangement of this
suggested empirical study nor the analyses of the anticipated outcomes rely on
the accompanying theoretical contemplations. This prediction has come from the
interpretation of the genome as a "barcode". The genome is considered as an
identification label rather than a repository of control information, so living
beings are portrayed as a community of users on the "Internet of the physical
Universe". Thus, biological objects with identical (or nearly identical) DNA
structures can interfere, and the surmised remote impact appears tangible. The
effect of clone-donor interaction leads to a decisive Experimentum Crucis that
can reject the common view on the organization of biological information
processing. Exploitation of this effect can be potentially dangerous.


title: $\frac{\lambda}{8}$-period optical potentials

abstract:
  A Raman configuration of counterpropagating traveling wave fields, one of
which is $lin\bot lin$ polarized and the other $lin\Vert lin$ polarized, is
shown to lead to optical potentials having $\frac{\lambda}{8}$ periodicity.
Such optical potentials may be used to construct optical lattices having $%
\frac{\lambda}{8}$ periodicity. Using numerical diagonalization, we obtain the
optical potentials for $^{\text{85}}$Rb atoms.


title: Buyer feedback as a filtering mechanism for reputable sellers

abstract:
  We propose a continuum model for the description of buyer and seller dynamics
in an Internet market. The relevant variables are the research effort of buyers
and the sellers' reputation building process. We show that, if a commercial
web-site gives consumers the possibility to rate credibly sellers they
bargained with, vendors are forced to be more honest. This leads to mutual
beneficial symbiosis between buyers and sellers; the overall enhanced volume of
transactions contributes ultimately to the web-site, which facilitates the
matchmaking service.

categories: physics.soc-ph cond-mat.stat-mech nlin.AO q-fin.GN


title:
Stochastic island generation and influence on the effective transport in
  stochastic magnetic fields

abstract:
  The transport of collisional particles in stochastic magnetic fields is
studied using the decorrelation trajectory method. The nonlinear effect of
stochastic generation of magnetic island by magnetic line trapping is
considered together with particle collisions. The running diffusion coefficient
is determined for arbitrary values of the statistical parameters of the
stochastic magnetic field and of the collisional velocity. The effect of the
stochastic magnetic islands is analysed.


title: The Energy-Entropy Principle

abstract:
  In this paper, through a criticism of what we call the paradigmatic view of
thermodynamics, we aim at showing a new perspective attained in this matter.
The generalization of heat as internal energy (generalization of the kinetic
energy concept of heat) permits the generalization of the Kelvin postulate: "It
is impossible, without another effect, to convert internal energy into work"
(no reference to heat or to heat reservoir).


title:
Data Compression and Entropy Estimates by Non-sequential Recursive Pair
  Substitution

abstract:
  We argue that Non-sequential Recursive Pair Substitution (NSRPS) as suggested
by Jim\'enez-Monta\~no and Ebeling can indeed be used as a basis for an optimal
data compression algorithm. In particular, we prove for Markov sequences that
NSRPS together with suitable codings of the substitutions and of the substitute
series does not lead to a code length increase, in the limit of infinite
sequence length. When applied to written English, NSRPS gives entropy estimates
which are very close to those obtained by other methods. Using ca. 135 GB of
input data from the project Gutenberg, we estimate the effective entropy to be
$\approx 1.82$ bit/character. Extrapolating to infinitely long input, the true
value of the entropy is estimated as $\approx 0.8$ bit/character.


title:
Clustering of SNPs along a chromosome: can the neutral model be
  rejected?

abstract:
  Single nucleotide polymorphisms (SNPs) often appear in clusters along the
length of a chromosome. This is due to variation in local coalescent times
caused by,for example, selection or recombination. Here we investigate whether
recombination alone (within a neutral model) can cause statistically
significant SNP clustering. We measure the extent of SNP clustering as the
ratio between the variance of SNPs found in bins of length $l$, and the mean
number of SNPs in such bins, $\sigma^2_l/\mu_l$. For a uniform SNP distribution
$\sigma^2_l/\mu_l=1$, for clustered SNPs $\sigma^2_l/\mu_l > 1$. Apart from the
bin length, three length scales are important when accounting for SNP
clustering: The mean distance between neighboring SNPs, $\Delta$, the mean
length of chromosome segments with constant time to the most recent common
ancestor, $\el$, and the total length of the chromosome, $L$. We show that SNP
clustering is observed if $\Delta < \el \ll L$. Moreover, if $l\ll \el \ll L$,
clustering becomes independent of the rate of recombination. We apply our
results to the analysis of SNP data sets from mice, and human chromosomes 6 and
X. Of the three data sets investigated, the human X chromosome displays the
most significant deviation from neutrality.


title: Application of Pad\'{e} interpolation to stationary state problems

abstract:
  If the small and large coupling behavior of a physical system can be computed
perturbatively and expressed respectively as power series in a coupling
parameter $g$ and $1/g$, a Pad\'{e} approximant embracing the two series can
interpolate between these two limits and provide an accurate estimate of the
system's behavior in the generally intractable intermediate coupling regime.
The methodology and validity of this approach are illustrated by considering
several stationary state problems in quantum mechanics.

categories: physics.comp-ph math-ph math.MP physics.ed-ph physics.gen-ph quant-ph


title: The Cyclic Universe: Some Historical Notes

abstract:
  The cyclic model of the universe has an old history in India. It has held the
preeminent position regarding the origins of the universe, and it is described
in astronomical texts, Puranic encyclopaedias, and philosophical literature.
Within the current cycle, which is supposed to have begun several billion years
ago, are smaller cycles of pole changes and extinctions on earth. Salient
features of the cyclic universe model are presented here.


title:
Unified Theory of Bivacuum, Particles Duality, Fields & Time. New
  Bivacuum Mediated Interaction, Overunity Devices, Cold Fusion &
  Nucleosynthesis

abstract:
  New concept of Bivacuum is introduced, as a dynamic matrix of the Universe,
composed from sub-quantum particles and antiparticles, forming vortical
structures. These structures are presented by continuum of dipoles, each dipole
containing a pair of correlated torus and antitorus: V(+) and V(-) of the
opposite energy/mass, spin, charge and magnetic moments, compensating each
other. The rest mass and charge of sub-elementary fermions or antifermions is a
result of Bivacuum dipoles opposite symmetry shifts. Their fusion to triplets
follows by elementary particles and antiparticles origination. The [corpuscle
(C) - wave (W)] duality is a result of correlated beats between the 'actual'
and 'complementary' states of sub-elementary fermions of triplets. It is shown,
that Principle of least action, the 2d and 3d laws of thermodynamics can be a
consequences of forced combinational resonance between positive and negative
virtual pressure waves (VPW+/-) of Bivacuum and [C-W] pulsation of elementary
particles. The quantum entanglement, mediated by virtual microtubules, composed
from Bivacuum dipoles, connecting remote particles, is a result of such
Bivacuum-matter interaction. The pace of time for any closed system is
determined by pace of kinetic energy change of this system. The proposed
mechanism of overunity devices can be provided by the electrons acceleration,
induced by their resonant interaction with high frequency positive and negative
VPW+/- in pull-in range conditions. The latter can be excited by pulsing
currents and fields. The mechanism of overheating and cold fusion in
electrolytic cells without violation of energy conservation is proposed also.


title:
Mixed configuration-interaction and many-body perturbation theory
  calculations of energies and oscillator strengths of J=1 odd states of neon

abstract:
  Ab-initio theory is developed for energies of J=1 particle-hole states of
neutral neon and for oscillator strengths of transitions from such states to
the J=0 ground state. Hole energies of low-Z neonlike ions are evaluated.


title:
Investigating Student Understanding of Quantum Mechanics: Spontaneous
  Models of Conductivity

abstract:
  Students are taught several models of conductivity, both at the introductory
and the advanced level. From early macroscopic models of current flow in
circuits, through the discussion of microscopic particle descriptions of
electrons flowing in an atomic lattice, to the development of microscopic
non-localized band diagram descriptions in advanced physics courses, they need
to be able to distinguish between commonly used, though sometimes
contradictory, physical models. In investigations of student reasoning about
models of conduction, we find that students often are unable to account for the
existence of free electrons in a conductor and create models that lead to
incorrect predictions and responses contradictory to expert descriptions of the
physics. We have used these findings as a guide to creating curriculum
materials that we show can be effective helping students to apply the different
conduction models more effectively.


title:
Method for control gas diffusion and bubbles formation in liquid
  porosimetry

abstract:
  The main problem in liquid porosimetry, which prevents to see the pore sizes
smaller than 2 microns in diameter, is direct gas diffusion flow through a
micro-porous membrane. This diffusion causes bubbles formation below the
membrane and that spoils extrusion (intrusion) data, as one cannot distinguish
the volume of extrusion (intrusion) liquid from the volume of formatted
bubbles. The suggested below method cures the problem by creating the liquid
flow below the membrane. The flow washes out all of the small bubbles
preventing them to grow. That allows using the membrane at higher differential
pressures, even higher than minimum bubble point of the membrane, without
spoiling data.


title: Understanding and Affecting Student Reasoning About Sound Waves

abstract:
  Student learning of sound waves can be helped through the creation of
group-learning classroom materials whose development and design rely on
explicit investigations into student understanding. We describe reasoning in
terms of sets of resources, i.e. grouped building blocks of thinking that are
commonly used in many different settings. Students in our university physics
classes often used sets of resources that were different from the ones we wish
them to use. By designing curriculum materials that ask students to think about
the physics from a different view, we bring about improvement in student
understanding of sound waves. Our curriculum modifications are specific to our
own classes, but our description of student learning is more generally useful
for teachers. We describe how students can use multiple sets of resources in
their thinking, and raise questions that should be considered by both
instructors and researchers.


title:
Free-Electron Lasers Without Inversion: Design of Two-Magnet Drift
  Region

abstract:
  We propose a two-magnet design of a drift region for a free-electron laser
without inversion (FELWI). By performing direct calculations of the phase
shifts for electrons passing the drift region, we prove that the small-signal
gain integrated over the detuning is positive and is inversely proportional to
the energy spread of the ``hot'' electron beam. The dispersion and the geometry
of the drift region are specified, and the requirements to the electron beam
quality, including the transverse size and the angular spread, are found.


title: Photon sandwich detectors with WLS fiber readout

abstract:
  A photon detector for BNL experiment E949 is described. The detector consists
of lead/scintillator ``sandwich'' of 25 layers of 5 mm thick scintillator BC404
and 24 layers of 2 mm lead absorber. Readout is implemented with 30-60 cm long
WLS fibers (BCF99-29AA) glued into grooves in the BC404. Average yield was
measured with cosmic rays to be about 43 p.e./MeV. Extruded plastic
scintillation counters developed for sandwich detectors of photons for the
KOPIO experiment are also described. For a 7 mm thick counter with 4.3 m long
WLS fibers spaced at 7 mm a light yield of 18.7 p.e./MeV and time resolution of
0.71 ns were obtained. A prototype photon veto module consisting of 10 layers
of 7 mm thick extruded plastic slabs interleaved with 1 mm lead sheets was
tested.


title: Closed Description of Stationary Flames

abstract:
  The problem of non-perturbative description of stationary flames with
arbitrary gas expansion is considered. A general method for deriving equations
for the flame front position is developed. On the basis of the Thomson
circulation theorem an implicit integral of the flow equations is constructed.
With the help of this integral the flow structure near the flame front is
determined, and a closed system of equations for the flame front position and a
set of auxiliary quantities is obtained. This system is shown to be
quasi-local, and its transverse representation is found. This representation
allows reduction of the system to a single equation for the flame front
position. The developed approach is applied to the case of zero-thickness
flames.


title:
Interpolation formula for the electrical conductivity of nonideal
  plasmas

abstract:
  On the basis of a quantum-statistical approach to the electrical conductivity
of nonideal plasmas we derive analytical results in the classical low-density
regime, in the degenerate Born limit, and for the contribution of the
Debye-Onsager relaxation effect. These explicit results are used to construct
an improved interpolation formula of the electrical conductivity valid in a
wide range of temperature and density which allows to compare with available
experimental data of nonideal plasmas.


title:
Tollmien-Shlichting and sound waves interaction: general description and
  nonlinear resonances

abstract:
  The general hydro-thermodynamic system of equations in 2+1 dimensions with
arbitrary equations of state (Taylor series approximation) is split to eigen
modes: Tollmienn-Schlichting (TS) wave and two acoustic ones. A mode definition
is realized via local relation equations, extracted from the linearization of
the general system over boundary layer flow. Each such connection defines the
subspace and the corresponding projector. So the division is performed locally
and could help in initial (or boundary) problems formulation. The general
nonlinearity account determines the specific form of interaction between
acoustic and vortical boundary layer perturbation fields. After the next
projecting to a subspace of Orr-Sommerfeld equation solution for the TS wave
and the corresponding procedure for acoustics, the equations go to
one-dimensional system that describes evolution along the basic stream. A new
mechanism of nonlinear resonance excitation of the TS wave by sound is proposed
and modelled via four-wave interaction. Subjectclass: Primary 35Q30 ; Secondary
76F70, 35Q72; Keywords: keywords fluid mechanics, boundary layer, projector to
eigen modes, Tollmien-Schlichting waves, acoustic waves, nonlinear resonance,
N-wave system.


title: Body Motion in a Resistive Medium at Temperature T

abstract:
  We consider a macroscopic body propagating in a one-dimensional resistive
medium, consisting of an ideal gas at temperature $T$. For a whole family of
collisions with varying degree of inelasticity, we find an exact expression for
the effective force on the moving body as a function of the body's speed and
the value of the restitution coefficient. At low and high speeds it reduces to
the well-known Stoke's and Newton's law, respectively.


title: Is the Energy Balance Paradox Solved?

abstract:
  The question of what is the source of the energy carried by the radiation is
discussed. The case of a hyperbolic motion is analyzed, describing the
solutions suggested in the past for the "energy balance paradox". The solution
to the paradox is found in considerind the stress force created in the curved
electric field of the accelerated charge, that acts as a reaction force. The
work performed by the external force to overcome this stress force is the
source of the energy carried by the radiation. This stress force is the spatial
component of the four-vactor called "Schott term", that appears in Abraham
four-vector. This novel approach solves the "energy balance paradox".


title: Structure Space of Model Proteins --A Principle Component Analysis

abstract:
  We study the space of all compact structures on a two-dimensional square
lattice of size $N=6\times6$. Each structure is mapped onto a vector in
$N$-dimensions according to a hydrophobic model. Previous work has shown that
the designabilities of structures are closely related to the distribution of
the structure vectors in the $N$-dimensional space, with highly designable
structures predominantly found in low density regions. We use principal
component analysis to probe and characterize the distribution of structure
vectors, and find a non-uniform density with a single peak. Interestingly, the
principal axes of this peak are almost aligned with Fourier eigenvectors, and
the corresponding Fourier eigenvalues go to zero continuously at the
wave-number for alternating patterns ($q=\pi$). These observations provide a
stepping stone for an analytic description of the distribution of structural
points, and open the possibility of estimating designabilities of realistic
structures by simply Fourier transforming the hydrophobicities of the
corresponding sequences.


title: Reflectivity of Shock Compressed Xenon Plasma

abstract:
  Experimental results for the reflection coefficient of shock-compressed dense
Xenon plasmas at pressures of 1.6 - 17 GPa and temperatures around 30 000 K
using a laser beam with \lambda = 1.06 10^-6 m are compared with calculations
based on different theoretical approaches to the dynamical collision frequency.
It is found that a reasonable description can be given assuming a spatial
electron density profile corresponding to a finite width of the shock wave
front of about $2 10^-6 m.


title: Hausdorff moment problem via fractional moments

abstract:
  We outline an efficient method for the reconstruction of a probability
density function from the knowledge of its infinite sequence of ordinary
moments. The approximate density is obtained resorting to maximum entropy
technique, under the constraint of some fractional moments. The latter ones are
obtained explicitly in terms of the infinite sequence of given ordinary
moments. It is proved that the approximate density converges in entropy to the
underlying density, so that it demonstrates to be useful for calculating
expected values.


title:
The Object Coordination Class Applied to Wavepulses: Analysing Student
  Reasoning in Wave Physics

abstract:
  Detailed investigations of student reasoning show that students approach the
topic of wave physics using both event-like and object-like descriptions of
wavepulses, but primarily focus on object properties in their reasoning.
Student responses to interview and written questions are analysed using diSessa
and Sherin's coordination class model which suggests that student use of
specific reasoning resources is guided by possibly unconscious cues. Here, the
term reasoning resources is used in a general fashion to describe any of the
smaller grain size models of reasoning (p-prims, facets of knowledge, intuitive
rules, etc) rather than theoretically ambiguous (mis)conceptions. Student
applications of reasoning resources, including one previously undocumented, are
described. Though the coordination class model is extremely helpful in
organising the research data, problematic aspects of the model are also
discussed.


title: The Role of Astronomy in the History of Science

abstract:
  We discuss the extent to which the visibility of the heavens was a necessary
condition for the development of science, with particular reference to the
measurement of time. Our conclusion is that while astronomy had significant
importance, the growth of most areas of science was more heavily influenced by
the accuracy of scientific instruments, and hence by current technology.


title: The Asymptotic Number of Attractors in the Random Map Model

abstract:
  The random map model is a deterministic dynamical system in a finite phase
space with n points. The map that establishes the dynamics of the system is
constructed by randomly choosing, for every point, another one as being its
image. We derive here explicit formulas for the statistical distribution of the
number of attractors in the system. As in related results, the number of
operations involved by our formulas increases exponentially with n; therefore,
they are not directly applicable to study the behavior of systems where n is
large. However, our formulas lend themselves to derive useful asymptotic
expressions, as we show.


title:
Solid immersion lens-enhanced micro-photoluminescence: principle and
  applications

abstract:
  We demonstrate the combination of a hemispherical solid immersion lens with a
micro-photoluminescence setup. Two advantages introduced by the SIL, an
improved resolution of 0.4 times the wavelength in vacuum and a 5 times
enhancement of the collection efficiency, make it an ideal system for spatially
resolved spectroscopy applications. The influence of the air gap between the
SIL and the sample surface is investigated in detail. We confirm the tolerance
of the set--up to an air gap of several micrometers. Such a system is proven to
be ideal system in the studies of exciton transport and polarization dependent
single quantum dot spectroscopy.


title:
Strong Electromagnetic Waves Propagation in an Electron-Positron-Ion
  Plasma

abstract:
  The main purpose of this work is the investigation of the influence of
electron-positron-ion on the electrostatic wakefields that are driven by
intense, short electromagnetic wave packets in a three component unmagnetized
plasma. The equations that describes the driven electrostatic wakefield are
given in the form of system of nonlinear differential equations. The solution
of that system was carried out numerically and the results are displayed
graphically.


title: Where Did the Laws of Physics Come From?

abstract: This paper was withdrawn by the author.


title:
Aging vs crystallisation dynamics in hyperquenched glasses and a
  resolution of the water Tg controversy

abstract:
  The possibility of observing a glass transition in water before
crystallisation occurs has been debated vigorously but inconclusively over five
decades [1,2]. For two decades a glass transition at 136K [2,3] was accepted
but this transition has perplexing qualities [4]. Recently it has been
argued[2,5],that this assignment must be wrong. The re-assignment of Tg to
temperatures above the 150K crystallisation was vigorously contested [6]. Here
we use detailed anneal-and-scan studies of a hyperquenched inorganic glass,
which does not crystallize on heating, to interpret the perplexing aspects of
the 136K water phenomenon. We show that it is indeed linked to a glass
transition, though only via a cross-over phenomenon. The thermal history that
gives the same behaviour ("shadow" glass transition) in the inorganic glass is
linked by crossover to a "normal" glass transition 23% higher in temperature.
Thus a Tg is indeed unobservable for water, while the vitreous nature of
hyperquenched glassy water is strongly supported. The shadow Tg is reproducible
in the inorganic glass as it is in H2O. The observed aging dynamics are very
relevant to current glass theory, particularly to dynamical heterogeneity which
is seen to have an energy manifestation.


title:
Thermodynamic and Kinetic Analysis of Sensitivity Amplification in
  Biological Signal Transduction

abstract:
  Based on a thermodynamic analysis of the kinetic model for the protein
phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy
utilization of this ubiquitous biological signal transduction process. It is
shown that the free energy from hydrolysis inside cells, $\Delta G$
(phosphorylation potential), controls the amplification and sensitivity of the
switch-like cellular module; the response coefficient of the sensitivity
amplification approaches the optimal 1 and the Hill coefficient increases with
increasing $\Delta G$. We discover that zero-order ultrasensitivity is
mathematically equivalent to allosteric cooperativity. Furthermore, we show
that the high amplification in ultrasensitivity is mechanistically related to
the proofreading kinetics for protein biosynthesis. Both utilize multiple
kinetic cycles in time to gain temporal cooperativity, in contrast to
allosteric cooperativity that utilizes multiple subunits in a protein.


title:
Nuclear-polarization correction to the bound-electron g factor in heavy
  hydrogenlike ions

abstract:
  The influence of nuclear polarization on the bound-electron $g$ factor in
heavy hydrogenlike ions is investigated. Numerical calculations are performed
for the K- and L-shell electrons taking into account the dominant virtual
nuclear excitations. This determines the ultimate limit for tests of QED
utilizing measurements of the bound-electron $g$ factor in highly charged ions.


title: Enhancing science education in the elementary schools

abstract:
  This article describes some collaborative activities of the authors, aimed at
improving science education in elementary schools. These include curriculum
enhancement, development of new apparatus (a wind tunnel), science-education
web site contributions and production of a film about the physics of flight.
The output of these projects is intended to be generally accessible or
reproducible.


title:
Fringe Structure in the Phase-Space Dynamics of Atomic Stabilization in
  An Intense Field

abstract:
  An analytical expression of a Floquet operator, which describes the evolution
of a wave packet in combined atomic and an intense laser field,is obtained
approximately in the stabilization regime. Both the classical and quantum
versions of the Floquet operator are used to study the phase-space dynamics of
atomic stabilization, and the 'fringe structure' in the phase-space is clearly
demonstrated. Furthermore, we investigate the dynamical mechanism and
characters of this striking structure, and find that this structure is very
closely related to the classical invariant manifolds.


title:
Evaluation of the low-lying energy levels of two- and three-electron
  configurations for multi-charged ions

abstract:
  Accurate QED evaluations of the one- and two-photon interelectron interaction
for low lying two- and three-electron configurations for ions with nuclear
charge numbers $60\le Z \le 93$ are performed. The three-photon interaction is
also partly taken into account. The Coulomb gauge is employed. The results are
compared with available experimental data and with different calculations. A
detailed investigation of the behaviour of the energy levels of the
configurations $1s_{1/2}2s_{1/2} {}^1 S_0$, $1s_{1/2}2p_{1/2} {}^3 P_0$ near
the crossing points Z=64 and Z=92 is carried out. The crossing points are
important for the future experimental search for parity nonconserving (PNC)
effects in highly charged ions.


title:
Negative Thermal Expansion of ZrW2O8 and HfW2O8: Contradiction to a
  Thermodynamic Relation

abstract:
  It has been shown that the dependence of negative thermal expansion
coefficient of ZrW2O8 and HfW2O8 on the temperature found by many authors
contradicts to an important thermodynamic relation.


title: Elements of the System Theory of Time

abstract:
  In the paper, elements of the system theory of time are presented,
mathematical models for time are constructed, and various properties are
deduced from the main principles of the system theory of time. This theory is a
far-reaching development of the special relativity theory. One of the main
principles of the special relativity theory is that two physical systems that
are moving relative to each other have different times and it is necessary to
use a correspondence between clocks in these systems to coordinate their times.
Such correspondence is established by means of electromagnetic signals. In
accordance with this principle, it is postulated in the system theory of time
that each system has its own time. In some cases, two systems have the same
time. In other cases, times of systems are coordinated or correlated. However,
there are systems in which times are independent from one another.


title: An alternative interpretation for the Holm "alpha model"

abstract:
  By re-interpreting a recent successful closure procedure in terms of local
spatial averaging and the neglect of fluctuations about that average, it is
shown how the results of that closure scheme (the ''alpha model'') may be more
simply derived.


title: Kink-Based Path Integral Calculations of Atoms He-Ne

abstract:
  An adaptive, kink-based path integral formalism is used to calculate the
ground state energies of the atoms He-Ne. The method uses an adaptive scheme to
virtually eliminate the sign difficulties. This is done by using a Monte Carlo
scheme to identify states that contribute significantly to the canonical
partition function and then include them in the wavefunctions to calculate the
canonical averages. The calculations use the 6-31G basis set and obtain both
precision and accuracy.


title: Confidence Limits and their Robustness

abstract:
  Confidence limits are common place in physics analysis. Great care must be
taken in their calculation and use, especially in cases of limited statistics
when often one-sided limits are quoted. In order to estimate the stability of
the confidence levels to addition of more data and/or change of cuts, we argue
that the variance of their sampling distributions be calculated in addition to
the limit itself. The square root of the variance of their sampling
distribution can be thought of as a statistical error on the limit. We thus
introduce the concept of statistical errors of confidence limits and argue that
not only should limits be calculated but also their errors in order to
represent the results of the analysis to the fullest. We show that comparison
of two different limits from two different experiments becomes easier when
their errors are also quoted. Use of errors of confidence limits will lead to
abatement of the debate on which method is best suited to calculate confidence
limits.


title:
Hyperfine structure of antiprotonic helium revealed by a
  laser-microwave-laser resonance method

abstract:
  Using a newly developed laser-microwave-laser resonance method, we observed a
pair of microwave transitions between hyperfine levels of the $(n,L)=(37,35)$
state of antiprotonic helium. This experiment confirms the quadruplet hyperfine
structure due to the interaction of the antiproton orbital angular momentum,
the electron spin and the antiproton spin as predicted by Bakalov and Korobov.
The measured frequencies of $\nu_{\text HF}^+ =12.89596 \pm 0.00034$ GHz and
$\nu_{\text HF}^- =12.92467 \pm 0.00029$ GHz agree with recent theoretical
calculations on a level of $ 6 \times10^{-5}$.


title: Recognition of an organism from fragments of its complete genome

abstract:
  This paper considers the problem of matching fragment to organism using its
complete genome. Our method is based on the probability measure representation
of a genome. We first demonstrate that these probability measures can be
modelled as recurrent iterated function systems (RIFS) consisting of four
contractive similarities. Our hypothesis is that the multifractal
characteristic of the probability measure of a complete genome, as captured by
the RIFS, is preserved in its reasonably long fragments. We compute the RIFS of
fragments of various lengths and random starting points, and compare with that
of the original sequence for recognition using the Euclidean distance. A
demonstration on five randomly selected organisms supports the above
hypothesis.


title:
Resonance structures in the multichannel quantum defect theory for the
  photofragmentation processes involving one closed and many open channels

abstract:
  The transformation introduced by Giusti-Suzor and Fano and extended by
Lecomte and Ueda for the study of resonance structures in the multichannel
quantum defect theory (MQDT) is used to reformulate MQDT into the forms having
one-to-one correspondence with those in Fano's configuration mixing (CM) theory
of resonance for the photofragmentation processes involving one closed and many
open channels. The reformulation thus allows MQDT to have the full power of the
CM theory, still keeping its own strengths such as the fundamental description
of resonance phenomena without an assumption of the presence of a discrete
state as in CM.


title: A Novel Magnetometer

abstract:
  A magnetometer has been developed by a simple modification of the TEL-Atomic
Cavendish balance designed by the author. The usual tungsten wire fiber has
been replaced with a silk thread, and a rare earth magnet has been attached to
the boom near where the fiber connects. Because of the mechanical common mode
rejection feature of the instrument, pendulous noise is largely removed from
this compass-like magnetometer that is quite sensitive to direction changes in
the Earth's field.


title: Bistability of a Torsion Magnetometer

abstract:
  Low-level bistability has been observed in the output from a recently
developed novel magnetometer. It is not known whether this behavior is
associated with the torsion fiber of the instrument or with the Earth's
magnetic field. Whatever its cause, this form of complexity is not widely
known.


title: Dynamical investigation of macromolecular hybridization bioassays

abstract:
  A novel sensoric technique for the dynamical in situ investigation of a
hybridization bio assay is presented, which utilizes a metal bead labeling
method. Therein, hybridization results in an increased metal coverage on parts
of a substrate, where it takes place. Our sensing principle relies on the
measurement of the radio frequency impedance of the hybridization spots. We
propose several examples for sensor devices.


title: Reference spaces in Special Relativity Theory: an intrinsic approach

abstract:
  Starting from a suggestion of Einstein on the construction of the concept of
space, we elaborate an intrinsic method to obtain space and time
transformations between two inertial spaces of reference, mathematically
modeled as affine euclidean spaces. The principal device introduced for
relating the space readings in both spaces is the so-called tracer mapping,
which makes a snapshot of a space onto the other. The general form of the space
and time transformations is obtained as an affine--preserving mapping
compatible with the principle of relativity, a cylindrical symmetry around the
relative velocities between spaces and the group character of the
transformations. After having obtained Galileo and Lorentz transformations, the
same method has been applied to two classical problems: the Coriolis theorem of
Newtonian Mechanics and the geometry of a rotating disk in Special Relativity.
Even in the case of Newtonian Mechanics, the possibility of distinguishing the
spaces of reference is found useful.


title:
The Vocabulary of Introductory Physics and its Implications for Learning
  Physics

abstract:
  We investigate studnets' use of words used in everyday language as well as in
physics. We find students are more likely to identify and explain the meaning
of the word as it is used in physics when they have become familiar with the
associated physical variables.


title:
A More Rational and Perfect Scheme for C, P, T Transformations as well
  as C, T and CP Violations in the Regularization and Renormalization Processes
  of High Order Perturbations

abstract:
  Based on the original meanings of C, P, T transformations, a more perfect and
rational scheme is advanced. According to new scheme, the propagation function
of Femion would change a negative sign under C, T transformations, while that
of boson does not. When the C, P, T transformations of transition probabilities
are calculated, the results are similar to the current theory if the
renormalizations of high order processes are not considered. When mass
renormalizations are taken into account, for some high order perturbation
processes of electromagnetic interaction, C, T violations would be caused.
Meanwhile, the renormalization process of a single third order vertex angle of
electromagnetic interaction in momentum space also would violate P symmetry,
which leads to parity non-conservation for some high order electromagnetic
decays. But in the coordinate space for the sum of all third order vertex angle
processes, P symmetry still holds. Under the united CPT transformation, the
Hamiltonians of strong, weak and electromagnetic interactions in the coordinate
space are invariable with a completely symmetrical form. The Compton scattering
of positive electron is suggested to verify the existence of C violation in the
high order mass renormalization processes of electromagnetic interaction. The T
violation in renormalization process can be used to explain the reversibility
paradox in the non-equilibrium evolution processes of macro-systems. The CP
violation may also be used to explain the problem of positive and
anti-material's asymmetry in our university.


title: Melting of sodium clusters

abstract:
  Thermal stability properties and the melting-like transition of Na_n,
n=13-147, clusters are studied through microcanonical molecular dynamics
simulations. The metallic bonding in the sodium clusters is mimicked by a
many-body Gupta potential based on the second moment approximation of a
tight-binding Hamiltonian. The characteristics of the solid-to-liquid
transition in the sodium clusters are analyzed by calculating physical
quantities like caloric curves, heat capacities, and root-mean-square bond
length fluctuations using simulation times of several nanoseconds. Distinct
melting mechanisms are obtained for the sodium clusters in the size range
investigated. The calculated melting temperatures show an irregular variation
with the cluster size, in qualitative agreement with recent experimental
results. However, the calculated melting point for the Na_55 cluster is about
40 % lower than the experimental value.


title: Model Analysis: Assessing the dynamics of student learning

abstract:
  In this paper we present a method of modeling and analysis that permits the
extraction and quantitative display of detailed information about the effects
of instruction on a class's knowledge. The method relies on a congitive model
that represents student thinking in terms of mental models. Students frequently
fail to recognize relevant conditions that lead to appropriate uses of their
models. As a result they can use multiple models inconsistently. Once the most
common mental models have been determined by qualitative research, they can be
mapping onto a multiple choice test. Model analysis permits the interpretation
of such a situation. We illustrate the use of our method by analyzing results
from the FCI.


title:
Robustness and Optimality of Light Harvesting in Cyanobacterial
  Photosystem I

abstract:
  As most biological species, photosynthetic lifeforms have evolved to function
optimally, despite thermal disorder and with fault tolerance. It remains a
challenge to understand how this is achieved. To address this challenge the
function of the protein-pigment complex photosystem I (PSI) of the
cyanobacterium Synechococcus elongatus is investigated theoretically. The
recently obtained high resolution structure of this complex exhibits an
aggregate of 96 chlorophylls that are electronically coupled to function as a
light-harvesting antenna complex. This paper constructs an effective
Hamiltonian for the chlorophyll aggregate to describe excitation transfer
dynamics and spectral properties of PSI. For this purpose, a new kinetic
expansion method, the sojourn expansion, is introduced. Our study shows that at
room temperature fluctuations of site energies have little effect on the
calculated excitation lifetime and quantum yield, which compare favorably with
experimental results. The efficiency of the system is found to be robust
against `pruning' of individual chlorophylls. An optimality of the arrangement
of chlorophylls is identified through the quantum yield in comparison with an
ensemble of randomly oriented chlorophylls, though, the quantum yield is seen
to change only within a narrow interval in such an ensemble.


title: Wireless communications with diffuse waves

abstract:
  Diffuse, multiple-scattered waves can be very efficient for information
transfer through disordered media, provided that antenna arrays are used for
both transmission and reception of signals. Information capacity C of a
communication channel between two identical linear arrays of n equally-spaced
antennas, placed in a disordered medium with diffuse scattering, grows linearly
with n and can attain considerable values, if antenna spacing a > lambda/2,
where lambda is the wavelength. Decrease of a below lambda/2 makes the signals
received by different antennas partially correlated, thus introducing
redundancy and reducing capacity of the communication system. When the size of
antenna arrays is well below lambda/2, the scaling of C with n becomes
logarithmic and capacity is low.


title:
Contribution of forbidden orbits in the photoabsorption spectra of atoms
  and molecules in a magnetic field

abstract:
  In a previous work [Phys. Rev. A \textbf{66}, 0134XX (2002)] we noted a
partial disagreement between quantum R-matrix and semiclassical calculations of
photoabsorption spectra of molecules in a magnetic field. We show this
disagreement is due to a non-vanishing contribution of processes which are
forbidden according to the usual semiclassical formalism. Formulas to include
these processes are obtained by using a refined stationary phase approximation.
The resulting higher order in $\hbar$ contributions also account for previously
unexplained ``recurrences without closed-orbits''. Quantum and semiclassical
photoabsorption spectra for Rydberg atoms and molecules in a magnetic field are
calculated and compared to assess the validity of the first-order forbidden
orbit contributions.


title: The Adiabatic Piston and the Second Law of Thermodynamics

abstract:
  A detailed analysis of the adiabatic-piston problem reveals peculiar
dynamical features that challenge the general belief that isolated systems
necessarily reach a static equilibrium state. In particular, the fact that the
piston behaves like a perpetuum mobile, i.e., it never stops but keeps
wandering, undergoing sizable oscillations, around the position corresponding
to maximum entropy, has remarkable implications on the entropy variations of
the system and on the validity of the second law when dealing with systems of
mesoscopic dimensions.


title: Bose-Einstein Condensation and Intermediate State of the Photon Gas

abstract:
  Possibility of establishment of equilibrium between the photon and the dense
photon bunch is studied. In the case, when the density of plasma does not
change, the condition of production of the Bose-Einstein condensate is
obtained. It is shown that the inhomogeneity of density of photons leads to a
new intermediate state of the photon gas.

categories: physics.plasm-ph astro-ph physics.optics physics.space-ph


title: Signatures of quantum stability in a classically chaotic system

abstract:
  We experimentally and numerically investigate the quantum accelerator mode
dynamics of an atom optical realization of the quantum delta-kicked
accelerator, whose classical dynamics are chaotic. Using a Ramsey-type
experiment, we observe interference, demonstrating that quantum accelerator
modes are formed coherently. We construct a link between the behavior of the
evolution's fidelity and the phase space structure of a recently proposed
pseudoclassical map, and thus account for the observed interference
visibilities.


title:
The fractional Brownian motion property of the turbulent refractive
  index and the Fermat's Extremal Principle

abstract:
  We introduce fractional Brownian motion processes (fBm) as an alternative
model for the turbulent index of refraction. These processes allow to
reconstruct most of the index properties, but they are not differentiable. We
overcome the apparent impossibility of their use in the variational equation
coming from the Fermat's Principle with the introduction of a Stochastic
Calculus. Afterwards, we successfully provide a solution for the stochastic ray
equation; moreover, its implications in the statistical analysis of
experimental data is discussed.


title:
Epistemology mediating conceptual knowledge: Constraints on data
  accessible from interviews

abstract:
  A student's epistemological stance (be it knowledge as memorized information,
knowledge from authority, or knowledge as invented stuff) may constrain that
student from reasoning in productive ways while also shaping the inferences a
researcher can make about how that student reasons about a particular
phenomenon. We discuss both cases in the context of an individual student
interview on charge flow in wires. In the first part of the interview, her
focus on memorized knowledge prevents the researcher from learning about her
detailed reasoning about current. In the second part of the interview, her
focus on constructed knowledge provides the researcher with a picture of her
reasoning about the physical mechanisms of charge flow.


title: Structures generated by the Klein-like topology of space

abstract:
  We hypothesise that properties of space could underly some patterns observed
in nature. We explore the possibility that the observed variety of matter
particles and the pattern of their properties arise due to the
non-orientability of the manifold representing space.


title: Hamiltonian model for multidimensional epistasis

abstract:
  We propose and solve a Hamiltonian model for multidimensional epistastatic
interactions between beneficial mutations. The model is able to give rise
either to a phase transition between two equilibrium states, without any
coexistence, or exhibits a state where hybrid species can coexist, with gradual
passage from one wild type to another. The transition takes place as a function
of the "tolerance" of the environment, which we define as the amount of noise
in the system.


title:
The challenge of listening: The effect of researcher agenda on data
  collection and interpretation

abstract:
  Even in the relatively favorable circumstances of an individual interview,
accurate listening requires careful effort. Our research interests dictate
which student statements we attend to during the interview, and which we
consider to constitute data during later analysis. Explicit consideration of
possible research agendas can increase opportunity for productive research.