title: Magda - Manager for grid-based data

abstract:
  Magda is a distributed data manager prototype for grid-resident data. It
makes use of the MySQL open source relational database, Perl, Java and C++ to
provide file cataloging, retrieval and replication services. For data movement,
gridFTP, bbftp and scp can be chosen depending on available protocols. Third
party transfers are supported. Magda currently catalogs 321K files with total
size of 85.8 TB. It was successfully used in the Data Challenge 1 production
for the Atlas experiment. It has been used to replicate more than 7 TB of data
between BNL and CERN mass stores. We present here the design and implementation
of Magda, and how it has been used as a file catalog and replication tool.


title: The acceleration and storage of radioactive ions for a neutrino factory

abstract:
  The term beta-beam has been coined for the production of a pure beam of
electron neutrinos or their antiparticles through the decay of radioactive ions
circulating in a storage ring. This concept requires radioactive ions to be
accelerated to a Lorentz gamma of 150 for 6He and 60 for 18Ne. The neutrino
source itself consists of a storage ring for this energy range, with long
straight sections in line with the experiment(s). Such a decay ring does not
exist at CERN today, nor does a high-intensity proton source for the production
of the radioactive ions. Nevertheless, the existing CERN accelerator
infrastructure could be used as this would still represent an important saving
for a beta-beam facility. This paper outlines the first study, while some of
the more speculative ideas will need further investigations.


title: The BTeV Software Tutorial Suite

abstract:
  The BTeV Collaboration is starting to develop its C++ based offline software
suite, an integral part of which is a series of tutorials. These tutorials are
targeted at a diverse audience, including new graduate students, experienced
physicists with little or no C++ experience, those with just enough C++ to be
dangerous, and experts who need only an overview of the available tools. The
tutorials must both teach C++ in general and the BTeV specific tools in
particular. Finally, they must teach physicists how to find and use the
detailed documentation. This report will review the status of the BTeV
experiment, give an overview of the plans for and the state of the software and
will then describe the plans for the tutorial suite.


title: TPC tracking and particle identification in high-density environment

abstract:
  Track finding and fitting algorithm in the ALICE Time projection chamber
(TPC) based on Kalman-filtering is presented. Implementation of particle
identification (PID) using d$E$/d$x$ measurement is discussed. Filtering and
PID algorithm is able to cope with non-Gaussian noise as well as with ambiguous
measurements in a high-density environment. The occupancy can reach up to 40%
and due to the overlaps, often the points along the track are lost and others
are significantly displaced. In the present algorithm, first, clusters are
found and the space points are reconstructed. The shape of a cluster provides
information about overlap factor. Fast spline unfolding algorithm is applied
for points with distorted shapes. Then, the expected space point error is
estimated using information about the cluster shape and track parameters.
Furthermore, available information about local track overlap is used. Tests are
performed on simulation data sets to validate the analysis and to gain
practical experience with the algorithm.


title: Securing a HENP Computing Facility

abstract:
  Traditionally, HENP computing facilities have been open facilities that are
accessed in many different ways by users that are both internal and external to
the facility. However, the need to protect the facility from cybersecurity
threats has made it difficult to maintain the openness of the facility to
off-site and on-site users.
  In this paper, we discuss the strategy we have used and the architecture we
have developed and deployed to increase the security the US ATLAS and RHIC
Computing Facilities, while trying to maintain the openness and accessibility
that our user community has come to expect. Included in this discussion are the
tools that we have used and the operational experience we have had with the
deployed architecture.


title: The PROOF Distributed Parallel Analysis Framework based on ROOT

abstract:
  The development of the Parallel ROOT Facility, PROOF, enables a physicist to
analyze and understand much larger data sets on a shorter time scale. It makes
use of the inherent parallelism in event data and implements an architecture
that optimizes I/O and CPU utilization in heterogeneous clusters with
distributed storage. The system provides transparent and interactive access to
gigabytes today. Being part of the ROOT framework PROOF inherits the benefits
of a performant object storage system and a wealth of statistical and
visualization tools. This paper describes the key principles of the PROOF
architecture and the implementation of the system. We will illustrate its
features using a simple example and present measurements of the scalability of
the system. Finally we will discuss how PROOF can be interfaced and make use of
the different Grid solutions.


title: HBT-Analyzer - Particle Correlations Analysis Toolkit

abstract:
  The HBT-Analyzer is an universal tool for particle correlations analysis
under the ROOT environment. It provides an efficient mixing mechanism, a wide
range of correlation and monitoring functions, and a set of cuts that are
applicable on different levels of analysis. Thanks to an object oriented design
it is very easily extensible for particular user needs. It also enables easy
resolution studies of Monte-Carlo simulated data. The general concept and
design is presented as well as example analysis results obtained within ALICE
experiment.


title: Commissioning the CDF Offline Software

abstract:
  CDF II is one of the two large collider experiments at Fermilab's Tevatron.
Over the past two years we have commissioned the offline computing system. A
task that has involved bringing up hundreds of computers and millions of lines
of C++ software. This paper reports on this experience, concentrating on the
software aspects of the project. We will highlight some of the successes as
well as describe some of the work still to do.


title:
Experience with multi-threaded C++ applications in the ATLAS DataFlow
  software

abstract:
  The DataFlow is sub-system of the ATLAS data acquisition responsible for the
reception, buffering and subsequent movement of partial and full event data to
the higher level triggers: Level 2 and Event Filter. The design of the software
is based on OO methodology and its implementation relies heavily on the use of
posix threads and the Standard Template Library. This article presents our
experience with Linux, posix threads and the Standard Template Library in the
real time environment of the ATLAS data flow.


title: LCIO - A persistency framework for linear collider simulation studies

abstract:
  Almost all groups involved in linear collider detector studies have their own
simulation software framework. Using a common persistency scheme would allow to
easily share results and compare reconstruction algorithms. We present such a
persistency framework, called LCIO (Linear Collider I/O). The framework has to
fulfill the requirements of the different groups today and be flexible enough
to be adapted to future needs. To that end we define an `abstract object
persistency layer' that will be used by the applications. A first
implementation, based on a sequential file format (SIO) is completely separated
from the interface, thus allowing to support additional formats if necessary.
The interface is defined with the AID (Abstract Interface Definition) tool from
freehep.org that allows creation of Java and C++ code synchronously. In order
to make use of legacy software a Fortran interface is also provided. We present
the design and implementation of LCIO.


title: Interfacing the JQMD and JAM Nuclear Reaction Codes to Geant4

abstract:
  Geant4 is a toolkit for the simulation of the passage of particles through
matter. It provides a comprehensive set of tools for geometry, tracking,
detector response, run, event and track management, visualization and user
interfaces. Geant4 also has an abundant set of physics models that handle the
diverse interactions of particles with matter across a wide energy range.
However, there are also many well-established reaction codes currently used in
the same fields where Geant4 is applied. In order to take advantage of these
codes, we began to investigate their use from within the framework of Geant4.
The first codes chosen for this investigation were the Jaeri Quantum Molecular
Dynamics (JQMD) and Jet AA Microscopic Transportation Model (JAM) codes. JQMD
is a QMD model code which is widely used to analyze various aspects of heavy
ion reactions. JAM is a hadronic cascade model code which explicitly treats all
established hadronic states, including resonances with explicit spin and
isospin, as well as their anti-particles. We successfully developed interfaces
between these codes and Geant4. These allow a user to construct a detector
using the powerful material and geometrical capabilities of Geant4, while at
the same time implementing nuclear reactions handled by the JQMD and JAM models
and the Hadronic framework of Geant4 proved its flexibility and expandability.


title: The RooFit toolkit for data modeling

abstract:
  RooFit is a library of C++ classes that facilitate data modeling in the ROOT
environment. Mathematical concepts such as variables, (probability density)
functions and integrals are represented as C++ objects. The package provides a
flexible framework for building complex fit models through classes that mimic
math operators, and is straightforward to extend. For all constructed models
RooFit provides a concise yet powerful interface for fitting (binned and
unbinned likelihood, chi^2), plotting and toy Monte Carlo generation as well as
sophisticated tools to manage large scale projects. RooFit has matured into an
industrial strength tool capable of running the BABAR experiment's most
complicated fits and is now available to all users on SourceForge.


title: A 3-D Track-Finding Processor for the CMS Level-1 Muon Trigger

abstract:
  We report on the design and test results of a prototype processor for the CMS
Level-1 trigger that performs 3-D track reconstruction and measurement from
data recorded by the cathode strip chambers of the endcap muon system. The
tracking algorithms are written in C++ using a class library we developed that
facilitates automatic conversion to Verilog. The code is synthesized into
firmware for field-programmable gate-arrays from the Xilinx Virtex-II series. A
second-generation prototype has been developed and is currently under test. It
performs regional track-finding in a 60 degree azimuthal sector and accepts 3
GB/s of input data synchronously with the 40 MHz beam crossing frequency. The
latency of the track-finding algorithms is expected to be 250 ns, including
geometrical alignment correction of incoming track segments and a final
momentum assignment based on the muon trajectory in the non-uniform magnetic
field in the CMS endcaps.


title:
On the origin of the deviation from the first order kinetics in
  inactivation of microbial cells by pulsed electric fields

abstract:
  A computer model was developed for estimation of the kinetics of microbial
inactivation by pulsed electric field. The model is based on the
electroporation theory of individual membrane damage, where spherical cell
geometry and distribution of cell sizes are assumed. The variation of microbial
cell sizes was assumed to follow a statistical probability distribution of the
Gaussian type. Surviving kinetics was approximated by Weibull equation. The
dependencies of two Weibull parameters (shape \textit{n} and time $\tau $,
respectively) versus electric field intensity E and width of cell diameters
distribution was studied.


title: A comment on W. Greiner's "Quantum Mechanics -- An Introduction"

abstract:
  It is pointed out that in Greiner's book, ``Quantum Mechanics --An
Introduction,'' there is a confusion between the wavelength spectral function
and the (angular) frequency spectral function in the derivation of the Wien's
displacement law.


title: Computing System for the Belle Experiment

abstract:
  We describe the offline computing system of the Belle experiment, consisting
of a computing farm with one thousand IA-32 CPUs. Up to now, the Belle
experiment has accumulated more than 120 fb$^{-1}$ of data, which is the world
largest $B\bar{B}$ sample at the $\Upsilon(4S)$ energy. The data have to be
processed with a single version of reconstruction software and calibration
constants to perform precise measurements of $B$ meson decays. In addition,
Monte Carlo samples three times larger than the real beam data are generated.
To fullfill our computing needs, we have constructed the computing system with
90(300) quad(dual) CPU PC servers from multiple vendors as a central processing
system. The details of this computing system and performance of data processing
with the current model are presented.


title: A theory of Plasma Membrane Calcium Pump stimulation and activity

abstract:
  The ATP-driven Plasma Membrane Calcium pump or Ca(2+)-ATPase (PMCA) is
characterized by a high affinity to calcium and a low transport rate compared
to other transmembrane calcium transport proteins. It plays a crucial role for
calcium extrusion from cells. Calmodulin is an intracellular calcium buffering
protein which is capable in its Ca(2+) liganded form of stimulating the PMCA by
increasing both the affinity to calcium and the maximum calcium transport rate.
We introduce a new model of this stimulation process and derive analytical
expressions for experimental observables in order to determine the model
parameters on the basis of specific experiments. We furthermore develop a model
for the pumping activity. The pumping description resolves the seeming
contradiction of the Ca(2+):ATP stoichiometry of 1:1 during a translocation
step and the observation that the pump binds two calcium ions at the
intracellular site. The combination of the calcium pumping and the stimulation
model correctly describes PMCA function. We find that the processes of
calmodulin-calcium complex attachment to the pump and of stimulation have to be
separated. Other PMCA properties are discussed in the framework of the model.
The presented model can serve as a tool for calcium dynamics simulations and
provides the possibility to characterize different pump isoforms by different
type-specific parameter sets.


title: Grid Based Monitoring on the Rutgers CDF Analysis Farm

abstract:
  Run II at the Fermilab Tevatron Collider started in March 2001, and it will
continue probing the high energy frontier in particle physics until the start
of the LHC at CERN. The CDF collaboration at Fermilab has already stored 260 TB
of data and expects to store 1PB of data in the next two years. The HEXCAF
computing farm is being set up at Rutgers University to provide the software
environment, computing resources, and access to data for physicists
participating in the Collaboration. Some job submission, detector data access
and storage of the output results are based on the SAM-GRID tools. To extend
monitoring for these jobs running on the farm a bridge was developed between
the SAM-GRID monitoring tools and the internal farm monitoring. This
presentation will describe the configuration and functionality of the HEXCAF
farm with the emphasis on the monitoring tools. Finally we summarize our
experience of installing and operating a GRID environment on a remote cluster
that is being used for real physics studies in the big running experiment.


title: Ionization of the Xenon Fluorides

abstract:
  The noble-gas atom xenon can bind fluorine atoms and form several stable
compounds. We study the electronic structure of the xenon fluorides (XeFn, n =
2,4,6) by calculating their ionization spectra using a Green's function method,
which allows to treat many-body effects at a high level. Our focus is on the
valence region and on the Xe 4d core hole. We observe a sensitive dependence of
the spectra on the number of fluorine ligands. Systematic line shifts are
uncovered and explained. In the Xe 5s and F 2s inner-valence regimes, from XeF2
to XeF6, the usefulness of the one-particle picture of ionization is found to
become progressively worse. Moreover, adding the electronegative fluorine
ligands seems to enhance--not suppress--the Auger decay of a Xe 4d core hole.


title: The new object oriented analysis framework for H1

abstract:
  During the years 2000 and 2001 the HERA machine and the H1 experiment
performed substantial luminosity upgrades. To cope with the increased demands
on data handling an effort was made to redesign and modernize the analysis
software. Main goals were to lower turn-around time for physics analysis by
providing a single framework for data storage, event selection, physics and
event display. The new object oriented analysis environment based on the RooT
framework provides a data access front-end for the new data storage scheme and
a new event display. The analysis data is stored in four different layers of
separate files. Each layer represents a different level of abstraction, i.e.
reconstruction output, physics particles, event summary information and user
specific information. Links between the layers allow correlating quantities of
different layers. Currently, this framework is used for data analyses of the
previous collected data and for standard data production of the currently
collected data.


title: The Autohumidification Polymer Electrolyte Membrane Fuel Cell

abstract:
  A PEM fuel cell was specially constructed to determine kinetics under
conditions of well-defined gas phase composition and cell temperature. Steady
state multiplicity was discovered in the autohumidification PEM fuel cell,
resulting from a balance between water production and water removal. Ignition
was observed in the PEM fuel cell for a critical water activity of about 0.1.
Ignition is a consequence of the exponential increase of proton conductivity
with water activity, which creates an autocatalytic feedback between the water
production and the proton conduction. The steady state current in the ignited
state decreases with increasing temperature between 50 to 105 deg C. At
temperatures greater than 70 deg C five steady states were observed in the PEM
fuel cell. The steady state performance has been followed with variable load
resistance and hysteresis loops have been mapped. The dynamics of transitions
between steady states are slow about 10^3 to 10^4 s. These slow dynamics are
suggested to result from a coupling of mechanical and chemical properties of
the membrane electrode assembly due to swelling of the membrane with water
absorption.


title:
Highly efficient crystal deflector for channeling extraction of a proton
  beam from accelerators

abstract:
  The design and performance of a novel crystal deflector for proton beams are
reported. A silicon crystal was used to channel and extract 70 GeV protons from
the U-70 accelerator in Protvino with an efficiency of 85%, as measured for a
beam of ~1e12 protons directed towards crystals of ~2 mm length in spills of ~2
s duration. Experimental data agree with the theoretically predicted Monte
Carlo results for channeling. The technique allows one to manufacture a very
short deflector along the beam direction (2 mm). Consequently, multiple
encounters of circulating particles with the crystal are possible with little
probability of multiple scattering and nuclear interactions per encounter.
Thus, drastic increase in efficiency for particle extraction out of the
accelerator was attained. We show the characteristics of the crystal- deflector
and the technology behind it. Such an achievement is important in devising a
more efficient use of the U-70 accelerator and provides crucial support for
implementing crystal-assisted slow extraction and collimation in other
machines, such as the Tevatron, RHIC, the AGS, the SNS, COSY, and the LHC.


title: Status of the physics validation studies using Geant4 in ATLAS

abstract:
  The new simulation for the ATLAS detector at LHC is performed using Geant4 in
a complete OO/C++ environment. In this framework the simulation of the various
test beams for the different ATLAS subdetectors offers an excellent opportunity
to perform physics validation studies over a wide range of physics domains: the
electromagnetic processes, the individual hadronic interactions, the
electromagnetic and hadronic signals in calorimeters. The simulation is
implemented by paying special attention to all details of the experimental
layout and by testing all possible physics processes which may be of relevance
to the specific detector under test: the resulting simulation programs are
often more detailed than the corresponding Geant3-based simulation suites. In
this paper we present relevant features of muon, electron and pion signals in
various ATLAS detectors. All remaining discrepancies between Geant4 and
test-beam data are currently being addressed and progress is continuous. This
work shows that Geant4 is becoming a mature and useful product for simulating
specific features of large-scale detector systems.


title: Non-local updates for quantum Monte Carlo simulations

abstract:
  We review the development of update schemes for quantum lattice models
simulated using world line quantum Monte Carlo algorithms. Starting from the
Suzuki-Trotter mapping we discuss limitations of local update algorithms and
highlight the main developments beyond Metropolis-style local updates: the
development of cluster algorithms, their generalization to continuous time, the
worm and directed-loop algorithms and finally a generalization of the flat
histogram method of Wang and Landau to quantum systems.


title: The LCG POOL Project, General Overview and Project Structure

abstract:
  The POOL project has been created to implement a common persistency framework
for the LHC Computing Grid (LCG) application area. POOL is tasked to store
experiment data and meta data in the multi Petabyte area in a distributed and
grid enabled way. First production use of new framework is expected for summer
2003. The project follows a hybrid approach combining C++ Object streaming
technology such as ROOT I/O for the bulk data with a transactionally safe
relational database (RDBMS) store such as MySQL. POOL is based a strict
component approach - as laid down in the LCG persistency and blue print RTAG
documents - providing navigational access to distributed data without exposing
details of the particular storage technology. This contribution describes the
project breakdown into work packages, the high level interaction between the
main pool components and summarizes current status and plans.


title: Photonic Crystal Laser Accelerator Structures

abstract:
  Photonic crystals have great potential for use as laser-driven accelerator
structures. A photonic crystal is a dielectric structure arranged in a periodic
geometry. Like a crystalline solid with its electronic band structure, the
modes of a photonic crystal lie in a set of allowed photonic bands. Similarly,
it is possible for a photonic crystal to exhibit one or more photonic band
gaps, with frequencies in the gap unable to propagate in the crystal. Thus
photonic crystals can confine an optical mode in an all-dielectric structure,
eliminating the need for metals and their characteristic losses at optical
frequencies.
  We discuss several geometries of photonic crystal accelerator structures.
Photonic crystal fibers (PCFs) are optical fibers which can confine a
speed-of-light optical mode in vacuum. Planar structures, both two- and
three-dimensional, can also confine such a mode, and have the additional
advantage that they can be manufactured using common microfabrication
techniques such as those used for integrated circuits. This allows for a
variety of possible materials, so that dielectrics with desirable optical and
radiation-hardness properties can be chosen. We discuss examples of simulated
photonic crystal structures to demonstrate the scaling laws and trade-offs
involved, and touch on potential fabrication processes.


title:
Numerical simulations on the motion of atoms travelling through a
  standing-wave light field

abstract:
  The motion of metastable helium atoms travelling through a standing light
wave is investigated with a semi-classical numerical model. The results of a
calculation including the velocity dependence of the dipole force are compared
with those of the commonly used approach, which assumes a conservative dipole
force. The comparison is made for two atom guiding regimes that can be used for
the production of nanostructure arrays; a low power regime, where the atoms are
focused in a standing wave by the dipole force, and a higher power regime, in
which the atoms channel along the potential minima of the light field. In the
low power regime the differences between the two models are negligible and both
models show that, for lithography purposes, pattern widths of 150 nm can be
achieved. In the high power channelling regime the conservative force model,
predicting 100 nm features, is shown to break down. The model that incorporates
velocity dependence, resulting in a structure size of 40 nm, remains valid, as
demonstrated by a comparison with quantum Monte-Carlo wavefunction
calculations.


title:
General properties and analytical approximations of photorefractive
  solitons

abstract:
  We investigate general properties of spatial 1-dimensional bright
photorefractive solitons and suggest various analytical approximations for the
soliton profile and the half width, both depending on an intensity parameter r.


title:
Data compression using correlations and stochastic processes in the
  ALICE Time Projection chamber

abstract:
  In this paper lossless and a quasi lossless algorithms for the online
compression of the data generated by the Time Projection Chamber (TPC) detector
of the ALICE experiment at CERN are described. The first algorithm is based on
a lossless source code modelling technique, i.e. the original TPC signal
information can be reconstructed without errors at the decompression stage. The
source model exploits the temporal correlation that is present in the TPC data
to reduce the entropy of the source. The second algorithm is based on a lossy
source code modelling technique. In order to evaluate the consequences of the
error introduced by the lossy compression, the results of the trajectory
tracking algorithms that process data offline are analyzed, in particular, with
respect to the noise introduced by the compression. The offline analysis has
two steps: cluster finder and track finder. The results on how these algorithms
are affected by the lossy compression are reported. In both compression
technique entropy coding is applied to the set of events defined by the source
model to reduce the bit rate to the corresponding source entropy. Using TPC
simulated data, the lossless and the lossy compression achieve a data reduction
to 49.2% of the original data rate and respectively in the range of 35% down to
30% depending on the desired precision.In this study we have focused on methods
which are easy to implement in the frontend TPC electronics.


title:
The action as a differential n-form and the analytic deduction of the
  nuclear potentials

abstract:
  All the natural forces act through potential fields. Both, the
electromagnetic vector potential and the gravitational potential of the general
relativity are usually deduced starting from general analytic considerations.
However, the nuclear potentials of the weak and strong forces are calculated
experimentally, leading to what is known as phenomenological potentials. That
is to say, expressions requiring adjustments according to the experimental
results. This fact may change if we consider the action as a differential form.
In this case it is possible to deduct some potentials for the nuclear forces
departing from general analytic considerations.


title: Muon Cooling Research and Development

abstract:
  The MuCool R&D program is described. The aim of MuCool is to develop all key
pieces of hardware required for ionization cooling of a muon beam. This effort
will lead to a more detailed understanding of the construction and operating
costs of such hardware, as well as to optimized designs that can be used to
build a Neutrino Factory or Muon Collider. This work is being undertaken by a
broad collaboration including physicists and engineers from many national
laboratories and universities in the U.S. and abroad. The intended schedule of
work will lead to ionization cooling being well enough established that a
construction decision for a Neutrino Factory could be taken before the end of
this decade based on a solid technical foundation.


title: Ruchhardt Oscillator Decay- Thermodynamic basis for Hysteretic Damping

abstract:
  Using thermodynamic arguments based on the ideal gas law, it is shown that
hysteretic (also called structural) damping is the natural form of energy
dissipation for this classic oscillator that is used to measure the ratio of
heat capacities for a gas.


title:
Longitudinal wave instability in magnetized high correlation dusty
  plasma

abstract:
  Low frequency longitudinal wave instability in magnetized high correlation
dusty plasmas is investigated. The dust charging relaxation is taken into
account. It is found that the instablity of wave is determined significantly by
the frequency of wave, the dust charging relaxation, the shear viscosity and
viscoelastic relaxation time, the coupling parameter of high correlation of
dust as well the strength of magnetic field.


title: Asymmetric Systematic Errors

abstract:
  Asymmetric systematic errors arise when there is a non-linear dependence of a
result on a nuisance parameter. Their combination is traditionally done by
adding positive and negative deviations separately in quadrature. There is no
sound justification for this, and it is shown that indeed it is sometimes
clearly inappropriate. Consistent techniques are given for this combination of
errors, and also for evaluating $\chi^2$, and for forming weighted sums.


title: General exact theory of autoresonance in nonautonomous systems

abstract:
  A general exact theory of autoresonance (self-sustained resonance) in both
dissipative and Hamiltonian nonautonomous systems is presented. The equations
that together govern the autoresonance solutions and excitations are derived
with the aid of a variational principle concerning the power functional. The
theory is applied to Duffing oscillators to obtain exact analytical expressions
for autoresonance excitations and solutions which explain all the
phenomenological and approximate results arising from the previous approach to
autoresonance phenomena.


title: Island Resonances

abstract:
  Resonances driven by the error field multipoles in the magnets often show
themselves as islands in phase plots of the particle motion. In order to be
able to measure the strength of the island resonance, and then to correct it,
it is helpful to study how these resonances show themselves. In particular, one
can study how the presence of the island resonances distort the tune dependence
on the amplitude, and the emittance growth caused by the island resonance.
Islands in 4-dimensional phase space, unlike islands in 2-dimensional phase
space, are not easy to visualize. This study will show how to visualize the
islands in 4-dimensional phase space by studying the tune dependence on the
amplitude of the particle motion. These effects are to some extent measureable,
and can lead to a way to correct the resonance.


title:
Use of a Generic Identification Scheme Connecting Events and Detector
  Description in the ATLAS Experiment

abstract:
  High energy physics detectors can be described hierarchically from the
different subsystems to their divisions in r, phi, theta and to the individual
readout channels. An identification schema that follows the logical
decomposition of the ATLAS detector has been introduced allowing identification
of individual readout channels as well as other parts of the detector, in
particular detector elements. These identifiers provide a sort of ?glue?
allowing, for example, the connection of raw event data to their detector
description for position calculation or alignment corrections, as well as fast
access to subsets of the event data for event trigger selection. There are two
important requirements on the software to support such an identification
scheme. First is the possibility to formally specify these identifiers in terms
of their structure and allowed values. And second is to generate different
forms of the identifiers optimised in terms of access efficiency to information
content, compactness or search key efficiency. We present here the generic
toolkit developed in the context of the ATLAS experiment to primarily provide
the identification of the readout channels and detector elements. The
architecture of the toolkit is decomposed into three parts: an XML-based
dictionary containing the formal specification of a particular range of
identifiers, a set of various identifier classes (offering various level of
compaction), and finally a set of ?helper? classes, specific for each detector
system, which serve as intermediaries between the dictionary and the identifier
classes to create, manipulate and interpret the identifiers. This architecture
will be described as well as the various applications of this identification
scheme.


title: Nonconservative Lagrangian Mechanics: A generalized function approach

abstract:
  We reexamine the problem of having nonconservative equations of motion arise
from the use of a variational principle. In particular, a formalism is
developed that allows the inclusion of fractional derivatives. This is done
within the Lagrangian framework by treating the action as a Volterra series. It
is then possible to derive two equations of motion, one of these is an advanced
equation and the other is retarded.


title:
Coulomb repulsion and quantum-classical correspondence in laser-induced
  nonsequential double ionization

abstract:
  The influence of electron-electron Coulomb repulsion on nonsequential double
ionization of rare-gas atoms is investigated. Several variants of the
quantum-mechanical transition amplitude are evaluated that differ by the form
of the inelastic electron-ion rescattering and whether or not Coulomb repulsion
between the two electrons in the final state is included. For high laser
intensity, an entirely classical model is formulated that simulates the
rescattering scenario.


title: Variable Free Spectral Range Spherical Mirror Fabry-Perot Interferometer

abstract:
  A spherical Fabry-Perot interferometer with adjustable mirror spacing is used
to produce interference fringes with frequency separation (c/2L)/N, N=2-15. The
conditions for observation of these fringes are derived from the consideration
of the eigenmodes of the cavity with high transverse indices.


title: Macrostate Data Clustering

abstract:
  We develop an effective nonhierarchical data clustering method using an
analogy to the dynamic coarse graining of a stochastic system. Analyzing the
eigensystem of an interitem transition matrix identifies fuzzy clusters
corresponding to the metastable macroscopic states (macrostates) of a diffusive
system. A "minimum uncertainty criterion" determines the linear transformation
from eigenvectors to cluster-defining window functions. Eigenspectrum gap and
cluster certainty conditions identify the proper number of clusters. The
physically motivated fuzzy representation and associated uncertainty analysis
distinguishes macrostate clustering from spectral partitioning methods.
Macrostate data clustering solves a variety of test cases that challenge other
methods.


title:
The uniformly most powerful test of statistical significance for
  counting-type experiments with background

abstract:
  In this paper, after a discussion of general properties of statistical tests,
we present the construction of the most powerful hypothesis test for
determining the existence of a new phenomenon in counting-type experiments
where the observed Poisson process is subject to a Poisson distributed
background with unknown mean.


title: The Best Possible Unification for any Collection of Physical Theories

abstract:
  It is shown that the set of all finitary consequence operators defined on any
nonempty language is a join-complete lattice. This result is applied to various
collections of physical theories to obtain an unrestricted supremum
unification.


title: Physical origin of nonlinear phenomena in optics

abstract:
  The physical nature of numerous of the nonlinear phenomena in optics is
explained by inequality of forward and reversed optical transitions, that
corresponds to a principle of time invariance violation in electromagnetic
interactions. The direct and indirect experimental proofs of such inequality
and direction of the further researches are discussed.


title: Phase Space Cell in Nonextensive Classical Systems

abstract:
  We calculate the phase space volume $\Omega$ occupied by a nonextensive
system of $N$ classical particles described by an equilibrium (or steady-state,
or long-term stationary state of a nonequilibrium system) distribution
function, which slightly deviates from Maxwell-Boltzmann (MB) distribution in
the high energy tail. We explicitly require that the number of accessible
microstates does not change respect to the extensive MB case. We also derive,
within a classical scheme, an analytical expression of the elementary cell that
can be seen as a macrocell, different from the third power of Planck constant.
Thermodynamic quantities like entropy, chemical potential and free energy of a
classical ideal gas, depending on elementary cell, are evaluated. Considering
the fractional deviation from MB distribution we can deduce a physical meaning
of the nonextensive parameter $q$ of the Tsallis nonextensive thermostatistics
in terms of particle correlation functions (valid at least in the case,
discussed in this work, of small deviations from MB standard case). pacs:
05.20.-y, 05.70.-a keywords: Classical Statistical Mechanics, Thermodynamics


title: The CMS Event Builder

abstract:
  The data acquisition system of the CMS experiment at the Large Hadron
Collider will employ an event builder which will combine data from about 500
data sources into full events at an aggregate throughput of 100 GByte/s.
Several architectures and switch technologies have been evaluated for the DAQ
Technical Design Report by measurements with test benches and by simulation.
  This paper describes studies of an EVB test-bench based on 64 PCs acting as
data sources and data consumers and employing both Gigabit Ethernet and Myrinet
technologies as the interconnect. In the case of Ethernet, protocols based on
Layer-2 frames and on TCP/IP are evaluated. Results from ongoing studies,
including measurements on throughput and scaling are presented.
  The architecture of the baseline CMS event builder will be outlined. The
event builder is organised into two stages with intelligent buffers in between.
The first stage contains 64 switches performing a first level of data
concentration by building super-fragments from fragments of 8 data sources. The
second stage combines the 64 super-fragments into full events. This
architecture allows installation of the second stage of the event builder in
steps, with the overall throughput scaling linearly with the number of switches
in the second stage. Possible implementations of the components of the event
builder are discussed and the expected performance of the full event builder is
outlined.


title: A Geometrical Modeller for HEP

abstract:
  Geometrical modelling generally provides the geometrical description of a
special structure and a set of services to "navigate" through its structure.
HEP geometrical modellers are designed to handle high complexity detector
geometries and they are usually embedded within simulation MC frameworks. The
fact that these frameworks greatly depend on their specific geometrical tools
makes simulation applications hardly portable to MC's other than the one they
were designed for. The ALICE Off-line Project in collaboration with the ROOT
team is proposing a multi-purpose geometrical modeller for HEP that is
integrated within a virtual MC infrastructure. This tool has been optimised for
performance with the geometry setups of several HEP experiments and provides a
single representation for the geometry used by different applications such as
simulation, reconstruction or event display.


title: Crystal Undulator As A Novel Compact Source Of Radiation

abstract:
  A crystalline undulator (CU) with periodically deformed crystallographic
planes is capable of deflecting charged particles with the same strength as an
equivalent magnetic field of 1000 T and could provide quite a short period L in
the sub-millimeter range. We present an idea for creation of a CU and report
its first realization. One face of a silicon crystal was given periodic
micro-scratches (grooves), with a period of 1 mm, by means of a diamond blade.
The X-ray tests of the crystal deformation have shown that a sinusoidal-like
shape of crystalline planes goes through the bulk of the crystal. This opens up
the possibility for experiments with high-energy particles channeled in CU, a
novel compact source of radiation. The first experiment on photon emission in
CU has been started at LNF with 800 MeV positrons aiming to produce 50 keV
undulator photons.


title: The Pedagogy of the p-n Junction: Diffusion or Drift?

abstract:
  The majority of current textbooks on device physics at the undergraduate
level derive the diode equation based on the diffusion of injected minority
carriers. Generally the drift of the majority carriers, or the extent of drift,
is not discussed and the importance of drift in the presence of a field in the
neutral regions is almost totally ignored. The assumptions of zero field in the
neutral regions and conduction by minority carrier diffusion lead to a number
of pedagogical problems and paradoxes for the student. The purpose of this
paper is to address the pedagogical problems and paradoxes apparent in the
current treatment of conduction in the pn junction as it appears in the
majority of texts.


title:
From ab initio quantum chemistry to molecular dynamics: The delicate
  case of hydrogen bonding in ammonia

abstract:
  The ammonia dimer (NH3)2 has been investigated using high--level ab initio
quantum chemistry methods and density functional theory (DFT). The structure
and energetics of important isomers is obtained to unprecedented accuracy
without resorting to experiment. The global minimum of eclipsed C_s symmetry is
characterized by a significantly bent hydrogen bond which deviates from
linearity by about 20 degrees. In addition, the so-called cyclic C_{2h}
structure is extremely close in energy on an overall flat potential energy
surface. It is demonstrated that none of the currently available (GGA,
meta--GGA, and hybrid) density functionals satisfactorily describe the
structure and relative energies of this nonlinear hydrogen bond. We present a
novel density functional, HCTH/407+, designed to describe this sort of hydrogen
bond quantitatively on the level of the dimer, contrary to e.g. the widely used
BLYP functional. This improved functional is employed in Car-Parrinello ab
initio molecular dynamics simulations of liquid ammonia to judge its
performance in describing the associated liquid. Both the HCTH/407+ and BLYP
functionals describe the properties of the liquid well as judged by analysis of
radial distribution functions, hydrogen bonding structure and dynamics,
translational diffusion, and orientational relaxation processes. It is
demonstrated that the solvation shell of the ammonia molecule in the liquid
phase is dominated by steric packing effects and not so much by directional
hydrogen bonding interactions. In addition, the propensity of ammonia molecules
to form bifurcated and multifurcated hydrogen bonds in the liquid phase is
found to be negligibly small.

categories: physics.chem-ph physics.atm-clus physics.comp-ph physics.flu-dyn


title: An Optical Lattice of Ring Traps

abstract:
  A new geometry of optical lattice is proposed, namely a lattice made of a 1D
stack of ring traps. It is obtained though the interference pattern of two
counterpropagating beams: one of the beam is a standard gaussian beam, while
the other one is a hollow beam obtained through a setup with two conical
lenses. The resulting lattice is shown to have a high filling rate and a good
confinement, so that it could be loaded directly from a MOT with applications
in the domain of quantum computing, or with a Bose-Einstein condensate, which
would have in this case a 1D ring geometry.


title: Role of Polymer Loops in DNA Replication

abstract:
  Loop formation in long molecules occurs many places in nature, from solutions
of carbon nanotubes to polymers inside a cell. In this article, we review
theoretical studies of the static and dynamic properties of polymer loops. For
example, long polymers must search many configurations to find a "target"
binding site, while short polymers are stiff and resist bending. In between,
there is an optimal loop size, which balances the entropy of long loops against
the energetic cost of short loops. We show that such simple pictures of loop
formation can explain several long-standing observations in DNA replication,
quantitatively.


title: Electron gas oscillations in plasma. Theory and applications

abstract:
  We analyze the obtained solutions of the non-linear Shroedinger equation for
spherically and axially symmetrical electrons density oscillations in plasma.
The conditions of the oscillations process existence are examined. It is shown
that in the center or on the axis of symmetry of the systems the static density
of electrons enhances. This process results in the increasing of density and
pressure of the ion gas. We suggest that this mechanism could occur in nature
as rare phenomenon called the fireball and could be used in carrying out the
research concerning controlled fusion. The description of the experiments,
carried out for the purpose to generate long-lived spherical plasma structures,
is presented.


title:
Conditions for non-stationary discharge initiation into
  "burning-through" mode

abstract:
  The special form of an electric discharge - "burn-through" in regard to the
ball lightning problem has been considered. Having been carried out within
closed volume, this mode of erosive discharge has shown the series of clear
differences consisting in the high gas density, formation of the metal-polymer
aerogel, the percolating current and unusual features of plasma's exhaust. The
conditions for its stable origination and the main stages of the discharge
process have been ascertained.


title:
Fluctuation-dissipation theorems for viscoelastic fluids: consistency of
  extended thermodynamic theories

abstract:
  Fluctuation-Dissipation Relations (FDR) for a Maxwell fluid are computed via
the GENERIC formalism. This formalism is determined by four building blocks,
two ``potentials'' (total energy and entropy) and two ``matrices'' which
determine the dynamics, but the understanding of fluctuations in a given
non-equilibrium system is reduced to determining a single friction matrix. The
FDR exhibits interesting features, arising from the type of entropy used in the
formalism. We show explicitly this dependence FDR-Entropy, also we show that
GENERIC renders results consistent with irreversible linear thermodynamics
(TIL) \emph{only} if it is used the corresponding entropy. An inconsistent
result is provided by GENERIC when it is used a modified entropy .


title:
The Gasdynamics First Problem Solution. The Gas Stream Parameters,
  Structures, Metering Characteristics for Pipe, Nozzle

abstract:
  The development of the classical physics fundamentals with usage of
experience of the experimental and computational-analytical investigations has
allowed to create the valid conception of a fluid motion. The multidisciplinary
approach on a new basis has allowed to ensure the physical adequacy to a
mathematical model of the gas flow with allowance for essential nonlinearity of
change of the gas stream main parameters and the metering characteristics of
the flow elements of the type: pipe, pipeline, convergent nozzle and also with
allowance for the evolutional character of the gas flow structure before a
setting, in the itself flow element and in jet flowing out from one. The
example of the valid solution of the direct and inverse problems about a gas
flow through the flow element is given for the first time. The results of the
solution by amount, kind and precision of the obtained information are an
example of the satisfactory solution of the gas dynamics problem.


title:
A Monte Carlo Calculation of the Pionium Break-up Probability with
  Different Sets of Pionium Target Cross Sections

abstract:
  Chiral Perturbation Theory predicts the lifetime of pionium, a hydrogen-like
$\pi^+ \pi^-$ atom, to better than 3% precision. The goal of the DIRAC
experiment at CERN is to obtain and check this value experimentally by
measuring the break-up probability of pionium in a target. In order to
accurately measure the lifetime one needs to know the relationship between the
break-up probability and lifetime to a 1% accuracy. We have obtained this
dependence by modeling the evolution of pionic atoms in the target using Monte
Carlo methods. The model relies on the computation of the pionium--target atom
interaction cross sections. Three different sets of pionium--target cross
sections with varying degrees of complexity were used: from the simplest first
order Born approximation involving only the electrostatic interaction to a more
advanced approach taking into account multi-photon exchanges and relativistic
effects. We conclude that in order to obtain the pionium lifetime to 1%
accuracy from the break-up probability, the pionium--target cross sections must
be known with the same accuracy for the low excited bound states of the pionic
atom. This result has been achieved, for low $Z$ targets, with the two most
precise cross section sets. For large $Z$ targets only the set accounting for
multiphoton exchange satisfies the condition.


title: The FLUKA code: present applications and future developments

abstract:
  The main features of the FLUKA Monte Carlo code, which can deal with
transport and interaction of electromagnetic and hadronic particles, are
summarised. The physical models embedded in FLUKA are mentioned, as well as
examples of benchmarking against experimental data. A short history of the code
is provided and the following examples of applications are discussed in detail:
prediction of calorimetric performances, atmospheric neutrino flux
calculations, dosimetry in atmosphere and radiobiology applications, including
hadrontherapy and space radiation protection. Finally a few lines are dedicated
to the FLUKA server, from which the code can be downloaded.


title:
Current Reversals in a inhomogeneous system with asymmetric unbiased
  fluctuations

abstract:
  We present a study of transport of a Brownian particle moving in periodic
symmetric potential in the presence of asymmetric unbiased fluctuations. The
particle is considered to move in a medium with periodic space dependent
friction. By tuning the parameters of the system, the direction of current
exhibit reversals, both as a function of temperature as well as the amplitude
of rocking force. We found that the mutual interplay between the opposite
driving factors is the necessary term for current reversals.


title: Virtual model of the differential pulse calorimeter

abstract:
  A new method of absolute heat capacity measurement was developed in the
Department of Biological Systems Physics at the E. Andronikashvili Institute of
Physics, Georgian Academy of Sciences. This is the method of absolute heat
capacity measurement of the differential calorimetric ampoule sample and
reference cell temperature difference registration while alternate transferring
of heat pulses to the cells occurs. The new method makes possible to determine
both the heat capacities of the sample and reference cells and the difference
of thereof. The method of cell temperature difference compensation is used in
order to decrease in the time of equilibrium establishment. The proposed method
of absolute heat capacity measurement was implemented in the model of the
virtual differential pulse calorimeter. The model allows to perform
calculations of the design of the differential ampoule - the main part of any
calorimeter.


title:
Influence of the bin-to-bin and inside bin correlations on measured
  quantities

abstract:
  A new method for measuring the quantities influenced by bin-to-bin and inside
bin correlations is presented. This method is essential for large multiplisity
and/or high density of particles in phase spase. The method was applied to the
two particle correation functions of e+e- -> W+W- events.


title: Theory of selective excitation in Stimulated Raman Scattering

abstract:
  A semiclassical model is used to investigate the possibility of selectively
exciting one of two closely spaced, uncoupled Raman transitions. The duration
of the intense pump pulse that creates the Raman coherence is shorter than the
vibrational period of a molecule (impulsive regime of interaction). Pulse
shapes are found that provide either enhancement or suppression of particular
vibrational excitations.


title: Coherent Control of Atomic Beam Diffraction by Standing Light

abstract:
  Quantum interference is shown to deliver a means of regulating the
diffraction pattern of a thermal atomic beam interacting with two standing wave
electric fields. Parameters have been identified to enhance the diffraction
probability of one momentum component over the others, with specific
application to Rb atoms.


title: Numerical path integration with Coulomb potential

abstract:
  A simple and efficient method for quantum Monte Carlo simulation is
presented, based on discretization of the action in the path integral, and a
Gaussian averaging of the potential, which works well e.g. with the Coulomb
potential.


title: The CDF Silicon Vertex Trigger

abstract:
  The CDF experiment's Silicon Vertex Trigger is a system of 150 custom 9U VME
boards that reconstructs axial tracks in the CDF silicon strip detector in a 15
microsecond pipeline. SVT's 35 micron impact parameter resolution enables CDF's
Level 2 trigger to distinguish primary and secondary particles, and hence to
collect large samples of hadronic bottom and charm decays. We review some of
SVT's key design features. Speed is achieved with custom VLSI pattern
recognition, linearized track fitting, pipelining, and parallel processing.
Testing and reliability are aided by built-in logic state analysis and
test-data sourcing at each board's input and output, a common inter-board data
link, and a universal "Merger" board for data fan-in/fan-out. Speed and
adaptability are enhanced by use of modern FPGAs.


title: Optimal Control of Quantum Dynamics : A New Theoretical Approach

abstract:
  A New theoretical formalism for the optimal quantum control has been
presented. The approach stems from the consideration of describing the
time-dependent quantum system in terms of the real physical observables, viz.,
the probability density rho(x,t) and the quantum current j(x,t) which is well
documented in the Bohm's hydrodynamical formulation of quantum mechanics. The
approach has been applied for manipulating the vibrational motion of HBr in its
ground electronic state under an external electric field.


title:
Estimation of Goodness-of-Fit in Multidimensional Analysis Using
  Distance to Nearest Neighbor

abstract:
  A new method for calculation of goodness of multidimensional fits in particle
physics experiments is proposed. This method finds the smallest and largest
clusters of nearest neighbors for observed data points. The cluster size is
used to estimate the goodness-of-fit and the cluster location provides clues
about possible problems with data modeling. The performance of the new method
is compared to that of the likelihood method and Kolmogorov-Smirnov test using
toy Monte Carlo studies. The new method is applied to estimate the
goodness-of-fit in a B->Kll analysis at BaBar.


title:
A new chiral electro-optic effect: Sum-frequency generation from
  optically active liquids in the presence of a dc electric field

abstract:
  We report the observation of sum-frequency signals that depend linearly on an
applied electrostatic field and that change sign with the handedness of an
optically active solution. This recently predicted chiral electro-optic effect
exists in the electric-dipole approximation. The static electric field gives
rise to an electric-field-induced sum-frequency signal (an achiral third-order
process) that interferes with the chirality-specific sum-frequency at
second-order. The cross-terms linear in the electrostatic field constitute the
effect and may be used to determine the absolute sign of second- and
third-order nonlinear optical susceptibilities in isotropic media.


title: Coherent Optimal Control of Multiphoton Molecular Excitation

abstract:
  We give a framework for molecular multiphoton excitation process induced by
an optimally designed electric field. The molecule is initially prepared in a
coherent superposition state of two of its eigenfunctions. The relative phase
of the two superposed eigenfunctions has been shown to control the optimally
designed electric field which triggers the multiphoton excitation in the
molecule. This brings forth flexibility in desiging the optimal field in the
laboratory by suitably tuning the molecular phase and hence by choosing the
most favorable interfering routes that the system follows to reach the target.
We follow the quantum fluid dynamical formulation for desiging the electric
field with application to HBr molecule.


title: X-ray image reconstruction from a diffraction pattern alone

abstract:
  A solution to the inversion problem of scattering would offer aberration-free
diffraction-limited 3D images without the resolution and depth-of-field
limitations of lens-based tomographic systems. Powerful algorithms are
increasingly being used to act as lenses to form such images. Current image
reconstruction methods, however, require the knowledge of the shape of the
object and the low spatial frequencies unavoidably lost in experiments.
Diffractive imaging has thus previously been used to increase the resolution of
images obtained by other means. We demonstrate experimentally here a new
inversion method, which reconstructs the image of the object without the need
for any such prior knowledge.


title: Efficiency and Current in a correlated ratchet

abstract:
  We present a detailed study of the transport and the efficiency of a ratchet
system in a periodic potential in the presence of correlated noises.
  The current and the efficiency of the system are investigated. It is found
that, when the potential is spatially symmetric, the correlation between the
two noises can induce a net transport. The efficiency shows many interesting
features as a function of the applied force, the noise intensity, the external
load, etc. The efficiency can be maximized as a function of noise intensity (or
temperature), which shows that the thermal fluctuation can facilitate the
efficiency of energy transformation.


title:
Exact magnetohydrodynamic equilibria with flow and effects on the
  Shafranov shift

abstract:
  Exact solutions of the equation governing the equilibrium magetohydrodynamic
states of an axisymmetric plasma with incompressible flows of arbitrary
direction [H. Tasso and G.N.Throumoulopoulos, Phys. Pasmas {\bf 5}, 2378
(1998)] are constructed for toroidal current density profiles peaked on the
magnetic axis in connection with the ansatz $S=-ku$, where $S=d/d u [\varrho
(d\Phi/du)^2]$ ($k$ is a parameter, $u$ labels the magnetic surfaces;
$\varrho(u)$ and $\Phi(u)$ are the density and the electrostatic potential,
respectively). They pertain to either unbounded plasmas of astrophysical
concern or bounded plasmas of arbitrary aspect ratio. For $k=0$, a case which
includes flows parallel to the magnetic field, the solutions are expressed in
terms of Kummer functions while for $k\neq 0$ in terms of Airy functions. On
the basis of a tokamak solution with $k\neq 0$ describing a plasma surrounded
by a perfectly conducted boundary of rectangular cross-section it turns out
that the Shafranov shift is a decreasing function which can vanish for a
positive value of $k$. This value is larger the smaller the aspect ratio of the
configuration.


title: Noise in an insect outbreak model

abstract:
  We study the steady state properties of an insect (spruce budworm) outbreak
model in the presence of Gaussian white noise. Based on the corresponding
Fokker-Planck equation the steady state solution of the probability
distribution function and its extrema have been investigated. It was found that
fluctuations of the insect birth rate reduces the population of the insects
while fluctuations of predation rate and the noise correlation can prevent the
population of the insects from going into extinction. Noise in the model can
induce a phase transition.


title: Noise in Genotype Selection Model

abstract:
  We study the steady state properties of a genotype selection model in
presence of correlated Gaussian white noise. The effect of the noise on the
genotype selection model is discussed. It is found that correlated noise can
break the balance of gene selection and induce the phase transition which can
makes us select one type gene haploid from a gene group.


title: Correlated noise in a logistic growth model

abstract:
  The logistic differential equation is used to analyze cancer cell population,
in the presence of a correlated Gaussian white noise. We study the steady state
properties of tumor cell growth and discuss the effects of the correlated
noise. It is found that the degree of correlation of the noise can cause tumor
cell extinction.


title:
Time and Space Variation of Fundamental Constants: Motivation and
  Laboratory Search

abstract:
  Fundamental physical constants play important role in modern physics. Studies
of their variation can open an interface to new physics. An overview of
different approaches to a search for such variations is presented as well as
possible reasons for the variations. Special attention is paid to laboratory
searches.


title:
Interpretation of heart rate variability via detrended fluctuation
  analysis and alpha-beta filter

abstract:
  Detrended fluctuation analysis (DFA), suitable for the analysis of
nonstationary time series, has confirmed the existence of persistent long-range
correlations in healthy heart rate variability data. In this paper, we present
the incorporation of the alpha-beta filter to DFA to determine patterns in the
power-law behaviour that can be found in these correlations. Well-known
simulated scenarios and real data involving normal and pathological
circumstances were used to evaluate this process. The results presented here
suggest the existence of evolving patterns, not always following a uniform
power-law behaviour, that cannot be described by scaling exponents estimated
using a linear procedure over two predefined ranges. Instead, the power law is
observed to have a continuous variation with segment length. We also show that
the study of these patterns, avoiding initial assumptions about the nature of
the data, may confer advantages to DFA by revealing more clearly abnormal
physiological conditions detected in congestive heart failure patients related
to the existence of dominant characteristic scales.


title: Metropolis Methods for Quantum Monte Carlo Simulations

abstract:
  Since its first description fifty years ago, the Metropolis Monte Carlo
method has been used in a variety of different ways for the simulation of
continuum quantum many-body systems. This paper will consider some of the
generalizations of the Metropolis algorithm employed in quantum Monte Carlo:
Variational Monte Carlo, dynamical methods for projector monte carlo ({\it
i.e.} diffusion Monte Carlo with rejection), multilevel sampling in path
integral Monte Carlo, the sampling of permutations, cluster methods for lattice
models, the penalty method for coupled electron-ionic systems and the Bayesian
analysis of imaginary time correlation functions.


title:
The fractional Brownian motion property of the turbulent refractive
  within Geometric Optics

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 refractive index properties, but they are not
differentiable. We overcome the apparent impossibility of their use within the
Ray Optics approximation introducing 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. In
particular, we analyze the dependence of the averaged solution against the
characteristic variables of a simple propagation problem.


title:
Phenotypic mixing and hiding may contribute to memory in viral
  quasispecies

abstract:
  Background. In a number of recent experiments with food-and-mouth disease
virus, a deleterious mutant, was found to avoid extinction and remain in the
population for long periods of time. This observation was called quasispecies
memory. The origin of quasispecies memory is not fully understood.
  Results. We propose and analyze a simple model of complementation between the
wild type virus and a mutant that has an impaired ability of cell entry. The
mutant will go extinct unless it is recreated from the wild type through
mutations. However, under phenotypic mixing-and-hiding as a mechanism of
complementation, the time to extinction in the absence of mutations increases
with increasing multiplicity of infection (m.o.i.). The mutant's frequency at
equilibrium under selection-mutation balance also increases with increasing
m.o.i. At high m.o.i., a large fraction of mutant genomes are encapsidated with
wild-type protein, which enables them to infect cells as efficiently as the
wild type virions, and thus increases their fitness to the wild-type level.
Moreover, even at low m.o.i. the equilibrium frequency of the mutant is higher
than predicted by the standard quasispecies model, because a fraction of mutant
virions generated from wild-type parents will also be encapsidated by wild-type
protein.
  Conclusions. Our model predicts that phenotypic hiding will strongly
influence the population dynamics of viruses, particularly at high m.o.i., and
will also have important effects on the mutation--selection balance at low
m.o.i. The delay in mutant extinction and increase in mutant frequencies at
equilibrium may, at least in part, explain memory in quasispecies populations.

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


title:
Fusion process of Lennard-Jones clusters: global minima and magic
  numbers formation

abstract:
  We present a new theoretical framework for modelling the fusion process of
Lennard-Jones (LJ) clusters. Starting from the initial tetrahedral cluster
configuration, adding new atoms to the system and absorbing its energy at each
step, we find cluster growing paths up to the cluster sizes of up to 150 atoms.
We demonstrate that in this way all known global minima structures of the
LJ-clusters can be found. Our method provides an efficient tool for the
calculation and analysis of atomic cluster structure. With its use we justify
the magic number sequence for the clusters of noble gas atoms and compare it
with experimental observations. We report the striking correspondence of the
peaks in the dependence on cluster size of the second derivative of the binding
energy per atom calculated for the chain of LJ-clusters based on the
icosahedral symmetry with the peaks in the abundance mass spectra
experimentally measured for the clusters of noble gas atoms. Our method serves
an efficient alternative to the global optimization techniques based on the
Monte-Carlo simulations and it can be applied for the solution of a broad
variety of problems in which atomic cluster structure is important.


title: Structure of A=6 Nuclei: ${^6}He$, ${^6}Li$ and ${^6}Be$

abstract:
  It is commonly believed that ($\alpha$-d) and (${^3}He$ - ${^3}H$) represent
equivalent states of ${^6}Li$. It is shown here that this is not correct. These
two are actually orthogonal to each other. It is shown here that these two with
very different shapes and forms actually co-exist for the ground state of
${^6}Li$. This shape co-existence is the same as similar phenomenon in heavy
nuclei. The puzzling anomaly of extremely small branching ratio for beta
delayed deuteron emission in ${^6}He$ is explained here. In addition the
anomalously large branching ratio for beta delayed triton emission in ${^8}He$
is explained. The cluster structure of the ground state and of the low-lying
states of ${^6}He$, ${^6}Li$ and ${^6}Be$ is clarified.


title: Thermal conductance through molecular wires

abstract:
  We consider phononic heat transport through molecular chains connecting two
thermal reservoirs. For relatively short molecules at normal temperatures heat
conduction is dominated by the harmonic part of the molecular force-field. We
develop a general theory for the heat conduction through harmonic chains in
3-dimensions. A Landauer-type expression for the heat conduction is obtained,
in agreement with other recent studies. We use this formalism to study the heat
conduction properties of alkanes. For relatively short (1-30 carbon atoms)
chains the length and temperature dependence of the molecular heat conduction
result from the balance of three factors: (i) The molecular frequency spectrum
in relation to the frequency cutoff of the thermal reservoirs, (ii) the degree
of localization of the molecular normal modes and (iii) the molecule-heat
reservoirs coupling. The fact that molecular modes at different frequency
regimes have different localization properties gives rise to intricate
dependence of the heat conduction on molecular length at different
temperatures. For example, the heat conduction increases with molecular length
for short molecular chains at low temperatures. Similar considerations apply
for isotopically substituted disordered chains. Finally, we compare the heat
conduction obtained from this microscopic calculation to that estimated by
considering the molecule as a cylinder characterized by a macroscopic heat
conduction typical to organic solids. We find that this classical model
overestimates the heat conduction of single alkane molecules by about an order
of magnitude at room temperature. Implications of the present study to the
problem of heating in electrically conducting molecular junctions are pointed
out.


title: Mapping a cloud of ultracold atoms onto a miniature storage ring

abstract:
  We describe how to realize magnetic and magneto-optical confinement of
ultracold atoms in a torus with adjustable diameter and how an elliptical cloud
of ultracold atoms can be adiabatically transformed to have a toroidal shape.
An experiment with cold 87Rb atoms demonstrates the feasibility of shape
transformations. These techniques can be used for atom interferometry and
quantum computation.


title: Standard and Embedded Solitons in Nematic Optical Fibers

abstract:
  A model for a non-Kerr cylindrical nematic fiber is presented. We use the
multiple scales method to show the possibility of constructing different kinds
of wavepackets of transverse magnetic (TM) modes propagating through the fiber.
This procedure allows us to generate different hierarchies of nonlinear partial
differential equations (PDEs) which describe the propagation of optical pulses
along the fiber. We go beyond the usual weakly nonlinear limit of a Kerr medium
and derive an extended Nonlinear Schrodinger equation (eNLS) with a third order
derivative nonlinearity, governing the dynamics for the amplitude of the
wavepacket. In this derivation the dispersion, self-focussing and diffraction
in the nematic are taken into account. Although the resulting nonlinear $PDE$
may be reduced to the modified Korteweg de Vries equation (mKdV), it also has
additional complex solutions which include two-parameter families of bright and
dark complex solitons. We show analytically that under certain conditions, the
bright solitons are actually double embedded solitons. We explain why these
solitons do not radiate at all, even though their wavenumbers are contained in
the linear spectrum of the system. Finally, we close the paper by making
comments on the advantages as well as the limitations of our approach, and on
further generalizations of the model and method presented.


title:
Einstein was Wrong: Newtonian Dynamics Can Disagree Completely with
  Relativistic Dynamics at Low Speed

abstract:
  According to Einstein, the trajectory of a particle that is predicted by
special relativistic mechanics is well approximated by the trajectory predicted
by Newtonian mechanics if the particle speed is low, i.e., much less than the
speed of light. However, in this paper, it is shown with a counterexample
Hamiltonian dynamical system that Newtonian dynamics can eventually disagree
completely with relativistic dynamics even though the particle speed is low.
After the breakdown of the agreement, either the Newtonian description is no
longer correct or the relativistic description is no longer correct or both
descriptions are no longer correct for the low speed motion.


title:
Fixed exit DC-monochromator of general position for Side (or Top) Beam
  Line

abstract:
  We develop an idea of fixed exit double-crystal monochromator of general
position, in which the lines of entering and exit beams (both being fixed) do
not lie in one plane, i.e., are in general position.
  Both cases of identical and not identical crystals are considered, and exact
solutions are obtained describing valid positions and orientations of both
crystals. Special attention is paid to the case of small lattice mismatch
between the first and the second crystal (e.g. due to temperature difference)
and small angle of `skewness' (that is to say, an angle between skew lines of
entrance and exit beams is much less than unity).
  We derive also some useful formulations describing beam profile change after
two reflections (whose reflection planes are non-parallel). At last, possible
designing approach for such a skew DC-mono is briefly touched upon.


title: Sliding Mechanism for Actin Myosin System

abstract:
  Based on the Stochastic Inclined Rods Model (SIRM) proposed by H. Matsuura
and M. Nakano, we study the microscopic motion of actin myosin system including
the motion of the G-actin. Our model is composed of an inclined spring (rod), a
myosin head, a myosin filament and G-actins. We discuss the stochastic
resonance between the myosin head and random noise. The results of calculation
show that the model can convert the random motion to one directional motion,
and the myosin head works as a resonator of random noise which absorbs the
energy through the stochastic resonance. The intermolecular potential between
the myosin head and G-actin and the inclined rod play a key role for the
muscle's motion. The energy consumed by the motor is directly supplied from the
surroundings (i.e., the thermal motions of water molecules).


title: Intuitive Derivation of Reynolds Number

abstract:
  It is evident from the literature that many engineers describe the Reynolds
number qualitatively as ``the ratio of inertial forces to viscous forces''. Yet
it is not immediately obvious that the well known expression Re =
LV(rho)/(eta), which involves the size L of a solid object moving with speed V
relative to a fluid of density rho and viscosity eta--is in fact a ratio of
forces. It is hoped that the following treatment, which is based on an energy
rather than force perspective, will help to de-mystify the important parameter
given to us by Osborne Reynolds


title: Coupled-Bunch Beam Breakup due to Resistive-Wall Wake

abstract:
  The coupled-bunch beam breakup problem excited by the resistive wall wake is
formulated. An approximate analytic method of finding the asymptotic behavior
of the transverse bunch displacement is developed and solved.


title:
The DZERO DAQ/Online Monitoring System and Applications, Including an
  Active Auto-recovery Tool

abstract:
  The DZERO experiment, located at the Fermi National Accelerator Laboratory,
has recently started the Run 2 physics program. The detector upgrade included a
new Data Acquisition/Level 3 Trigger system. Part of the design for the
DAQ/Trigger system was a new monitoring infrastructure. The monitoring was
designed to satisfy real-time requirements with 1-second resolution as well as
non-real-time data. It was also designed to handle a large number of displays
without putting undue load on the sources of monitoring information. The
resulting protocol is based on XML, is easily extensible, and has spawned a
large number of displays, clients, and other applications. It is also one of
the few sources of detector performance available outside the Online System's
security wall. A tool, based on this system, which provides for auto-recovery
of DAQ errors, has been designed. This talk will include a description of the
DZERO DAQ/Online monitor server, based on the ACE framework, the protocol, the
auto-recovery tool, and several of the unique displays which include an
ORACLE-based archiver and numerous GUIs.


title: Absolute Motion and Gravitational Effects

abstract:
  The new Process Physics provides a new explanation of space as a quantum foam
system in which gravity is an inhomogeneous flow of the quantum foam into
matter. An analysis of various experiments demonstrates that absolute motion
relative to space has been observed experimentally by Michelson and Morley,
Miller, Illingworth, Torr and Kolen, and by DeWitte. The Dayton Miller and
Roland DeWitte data also reveal the in-flow of space into matter which
manifests as gravity. The in-flow also manifests turbulence and the
experimental data confirms this as well, which amounts to the observation of a
gravitational wave phenomena. The Einstein assumptions leading to the Special
and General Theory of Relativity are shown to be falsified by the extensive
experimental data. Contrary to the Einstein assumptions absolute motion is
consistent with relativistic effects, which are caused by actual dynamical
effects of absolute motion through the quantum foam, so that it is Lorentzian
relativity that is seen to be essentially correct.


title:
Study of Coherent and Incoherent Plasma Emissions: Role of Plasma Wave
  Excitation and Breaking

abstract:
  Here we experimentally map the dynamics of electron plasma waves in laser
solid interaction. We do time resolved measurements of second harmonic and hard
X-ray generation from interaction of intense ($10^{16} W cm^{-2}$, 100 fs,
800nm) laser with a pre-plasma generated on a solid surface. The parameter
space explored in this time resolved study includes variation of scale length,
laser polarization and laser intensity in conjunction. These measurements done
together brings novel features of strongly driven electron plasma wave
behavior, which have not been explored experimentally so far. We model the
results in terms of Resonance Absorption and Wave-Breaking mechanisms. The
Harmonic and X-ray emission show contrasting behaviour, which indicates
pitfalls in trying to increase harmonic efficiencies by brute force. However by
simple adjustments, we observe that hard X-rays can be enhanced or controlled
upto two orders of magnitude and second harmonic upto one order of magnitude
under optimum conditions. These results should help us understand the governing
mechanisms for short wavelength generation and fast particle generation to
develop more efficient sources for application purposes.


title:
A Computer Aided Detection system for mammographic images implemented on
  a GRID infrastructure

abstract:
  The use of an automatic system for the analysis of mammographic images has
proven to be very useful to radiologists in the investigation of breast cancer,
especially in the framework of mammographic-screening programs. A breast
neoplasia is often marked by the presence of microcalcification clusters and
massive lesions in the mammogram: hence the need for tools able to recognize
such lesions at an early stage. In the framework of the GPCALMA (GRID Platform
for Computer Assisted Library for MAmmography) project, the co-working of
italian physicists and radiologists built a large distributed database of
digitized mammographic images (about 5500 images corresponding to 1650
patients) and developed a CAD (Computer Aided Detection) system, able to make
an automatic search of massive lesions and microcalcification clusters. The CAD
is implemented in the GPCALMA integrated station, which can be used also for
digitization, as archive and to perform statistical analyses. Some GPCALMA
integrated stations have already been implemented and are currently on clinical
trial in some italian hospitals. The emerging GRID technology can been used to
connect the GPCALMA integrated stations operating in different medical centers.
The GRID approach will support an effective tele- and co-working between
radiologists, cancer specialists and epidemiology experts by allowing remote
image analysis and interactive online diagnosis.


title:
Characterization and diagnostics of combustion thermoacoustic
  instabilities using nonlinear dynamics and topological methods

abstract:
  The onset of thermoacoustic instabilities in lean-premixed gas-turbine
combustors is a crucial problem leading to degradation in engine and emissions
performance and shortened component life. The main aim of this study is to
propose a methodology based both on concepts of nonlinear dynamics and on
geometric-topological invariants, for the characterization of attractors
related to measurements based on the flame spontaneous light emission, like OH*
radical, in order to classify different phases of the combustion process and to
better recognize the transition mechanisms leading to the thermoacoustic
instabilities. Preliminary results, clearly show the powerfulness of the
approach to show the dynamical evolution of the flame and to evidence the onset
of the thermoacoustic instabilities: in particular the topological invariant
index (genus and related quantities) appear s as the best candidate for an
early indicator of the dynamical transition, characterized by the onset of a
more persistent, low entropy torus (quasi-periodic motion), as the related
thermoacoustic attractor.


title:
Folding of Cu, Zn superoxide dismutase and Familial Amyotrophic Lateral
  Sclerosis

abstract:
  Cu,Zn superoxide dismutase (SOD1) has been implicated in the familial form of
the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). It has been
suggested that mutant mediated SOD1 misfolding/aggregation is an integral part
of the pathology of ALS. We study the folding thermodynamics and kinetics of
SOD1 using a hybrid molecular dynamics approach. We reproduce the
experimentally observed SOD1 folding thermodynamics and find that the residues
which contribute the most to SOD1 thermal stability are also crucial for
apparent two-state folding kinetics. Surprisingly, we find that these residues
are located on the surface of the protein and not in the hydrophobic core.
Mutations in some of the identified residues are found in patients with the
disease. We argue that the identified residues may play an important role in
aggregation. To further characterize the folding of SOD1, we study the role of
cysteine residues in folding and find that non-native disulfide bond formation
may significantly alter SOD1 folding dynamics and aggregation propensity.


title: Scaling laws in the functional content of genomes

abstract:
  With the number of sequenced genomes now over one hundred, and the
availability of rough functional annotations for a substantial proportion of
their genes, it has become possible to study the statistics of gene content
across genomes. Here I show that, for many high-level functional categories,
the number of genes in the category scales as a power-law in the total number
of genes in the genome. The occurrence of such scaling laws can be explained
with a simple theoretical model, and this model suggests that the exponents of
the observed scaling laws correspond to universal constants of the evolutionary
process. I discuss some consequences of these scaling laws for our
understanding of organism design.


title: Pulse Shape Discrimination Techniques in Scintillating CsI(Tl) Crystals

abstract:
  There are recent interests with CsI(Tl) scintillating crystals for Dark
Matter experiments. The key merit is the capability to differentiate nuclear
recoil (nr) signatures from the background $\beta / \gamma$-events due to
ambient radioactivity on the basis of their different pulse shapes. One of the
major experimental challenges is to perform such pulse shape analysis in the
statistics-limited domain where the light output is close to the detection
threshold. Using data derived from measurements with low energy $\gamma$'s and
nuclear recoils due to neutron elastic scatterings, it was verified that the
pulse shapes between $\beta / \gamma$-events are different. Several methods of
pulse shape discrimination are studied, and their relative merits are compared.
Full digitization of the pulse shapes is crucial to achieve good
discrimination. Advanced software techniques with mean time, neural network and
likelihood ratios give rise to satisfactory performance, and are superior to
the conventional Double Charge method commonly applied at higher energies.
Pulse shape discrimination becomes effective starting at a light yield of about
20 photo-electrons. This corresponds to a detection threshold of about 5 keV
electron-equivalence energy, or 40$-$50 keV recoil kinetic energy, in realistic
experiments.


title: Gravity as Quantum Foam In-Flow

abstract:
  The new information-theoretic Process Physics provides an explanation of
space as a quantum foam system in which gravity is an inhomogeneous flow of the
quantum foam into matter. The older Newtonian and General Relativity theories
for gravity are analysed. It is shown that Newtonian gravity may be written in
the form of an in-flow. General Relativity is also analysed as an in-flow, for
those cases where it has been tested. An analysis of various experimental data
demonstrates that absolute motion relative to space has been observed by
Michelson and Morley, Miller, Illingworth, Jaseja et al, Torr and Kolen, and by
DeWitte. The Dayton Miller and Roland DeWitte data also reveal the in-flow of
space into matter which manifests as gravity. The experimental data suggests
that the in-flow is turbulent, which amounts to the observation of a
gravitational wave phenomena. A new in-flow theory of gravity is proposed which
passes all the tests that General Relativity was claimed to have passed, but as
well the new theory suggests that the so-called spiral galaxy rotation-velocity
anomaly may be explained without the need of `dark matter'. Various other
gravitational anomalies also appear to be explainable. Newtonian gravity
appears to be strictly valid only outside of spherically symmetric matter
systems.


title:
Advantages of axially aligned crystals used in positron production at
  future linear colliders

abstract:
  The characteristics of the electron-photon showers initiated by 2 to 10 GeV
electrons aligned along the <111>-axis of tungsten crystals are compared with
those for the amorphous tungsten . In this energy range, as known, the positron
yield at the optimal target thicknesses is larger in a crystal case only by
several percent. However, the amount of the energy deposition in a crystal
turns out to be considerably (by 20 - 50 %) lower than in an amorphous target
providing the same positron yield, while the peak energy-deposition density is
approximately of the same magnitude in the both cases.


title: On the Solutions of the Lorentz-Dirac Equation

abstract:
  We discuss the unstable character of the solutions of the Lorentz-Dirac
equation and stress the need of methods like order reduction to derive a
physically acceptable equation of motion. The discussion is illustrated with
the paradigmatic example of the non-relativistic harmonic oscillator with
radiation reaction. We also illustrate removal of the noncasual
pre-acceleration with the introduction of a small correction in the
Lorentz-Dirac equation.


title:
The Architecture of the ZEUS Micro Vertex Detector DAQ and Second Level
  Global Track Trigger

abstract:
  The architecture of the ZEUS Micro Vertex Detector data acquisition system
and the implementation of its second level trigger, the ZEUS Global Track
Trigger are described. Data from the vertex detectors HELIX read-out chips,
corresponding to 200k channels, are digitized by 3 crates of ADCs which perform
noise and pedestal subtraction, and data suppression and compaction. PowerPC
VME board computers push cluster data for second level trigger processing and
strip data for event building via Fast and Gigabit Ethernet network
connections. Additional tracking information from the central tracking chamber
and the forward straw tube tracker are interfaced into the 12 dual CPU PC farm
of the Global Track Trigger where track and vertex finding is performed. The
system is data driven at the ZEUS first level trigger rate (~500Hz) and must
generate a trigger result after a mean time of 10ms.


title:
Keynote Paper: Cell-Surface Adhesive Interactions in Microchannels and
  Microvessels

abstract:
  Adhesive interactions between white blood cells and the interior surface of
the blood vessels they contact is important in inflammation and in the
progression of heart disease. Parallel-plate microchannels have been useful in
characterizing the strength of these interactions, in conditions that are much
simplified over the complex environment these cells experience in the body.
Recent computational and experimental work by several laboratories have
attempted to bridge this gap between behavior observed in flow chamber
experiments, and cell-surface interactions observed in the microvessels of
anesthetized animals.


title: Thermodynamics in Density-Functional Theory and Force Theorems

abstract:
  The density-functional (DF) theory provides a simple method for calculating
the properties of an interacting system under an external potential by
associating it with a corresponding non-interacting system. Here, we find some
relations in this non-interacting system, which can enable us to set up the
thermodynamical relations for a neutral electron-nucleus mixture in terms of
quantities of the non-interacting system and the exchange-correlation effect.
In this way, Andersen's force theorems are clearly described and easily proved
in conjunction with other types of force theorems, Janak's theorem extended to
a finite-temperature system, pressure formulas and some thermodynamical
relations. For this purpose, the thermodynamics in the DF theory is presented
in a systematic and explicit way.


title:
Experimental investigation of cut-off phenomena in non-linear photonic
  crystal fibers

abstract:
  The modal cut-off is investigated experimentally in a series of high quality
non-linear photonic crystal fibers. We demonstrate a suitable measurement
technique to determine the cut-off wavelength and verify it by inspecting the
near field of the modes that may be excited below and above the cut-off. We
observe a double peak structure in the cut-off spectra, which is attributed to
a splitting of the higher order modes. The cut-off is measured for seven
different fiber geometries with different pitches and relative hole size, and a
very good agreement with recent theoretical work is found.


title: Modal cut-off and the V-parameter in photonic crystal fibers

abstract:
  We address the long-standing unresolved problem concerning the V-parameter in
a photonic crystal fiber (PCF). Formulate the parameter appropriate for a
core-defect in a periodic structure we argue that the multi-mode cut-off occurs
at a wavelength lambda* which satisfies V_PCF(lambda*)=pi. Comparing to
numerics and recent cut-off calculations we confirm this result.


title: Co-operation of two-state processes and 1/f noise

abstract:
  A general physical model is presented for 1/f noise. The main questions
raised by this type of noise can be solved if at the origin of the phenomenon
we consider many similar like RTN two-state processes in co-operation among
them to generate a Gaussian average process with 1/f power spectrum. Even if
the originating RTN processes have the same relaxation time, their co-operation
produces in short times secondary RTN processes with a distribution of
relaxation times which generates again 1/f noise. An extension of the model to
a single two-state process viewed in "series" reveals once more the appearance
of 1/f noise. Experimental results, found in the literature, agree with this
model under various aspects.


title:
Efficiency optimization in a correlation ratchet with asymmetric
  unbiased fluctuations

abstract:
  The efficiency of a Brownian particle moving in periodic potential in the
presence of asymmetric unbiased fluctuations is investigated. We found that
there is a regime where the efficiency can be a peaked function of temperature,
which proves that thermal fluctuations facilitate the efficiency of energy
transformation, contradicting the earlier findings (H. kamegawa et al. Phys.
Rev. Lett. 80 (1998) 5251). It is also found that the mutual interplay between
asymmetry of fluctuation and asymmetry of the potential may induce optimized
efficiency at finite temperature. The ratchet is not most efficiency when it
gives maximum current.


title: A Microscopic Mechanism for Muscle's Motion

abstract:
  The SIRM (Stochastic Inclined Rods Model) proposed by H. Matsuura and M.
Nakano can explain the muscle's motion perfectly, but the intermolecular
potential between myosin head and G-actin is too simple and only repulsive
potential is considered. In this paper we study the SIRM with different complex
potential and discuss the effect of the spring on the system. The calculation
results show that the spring, the effective radius of the G-actin and the
intermolecular potential play key roles in the motion. The sliding speed is
about $4.7\times10^{-6}m/s$ calculated from the model which well agrees with
the experimental data.


title: Internal Motility in Stiffening Actin-Myosin Networks

abstract:
  We present a study on filamentous actin solutions containing heavy meromyosin
subfragments of myosin II motor molecules. We focus on the viscoelastic phase
behavior and internal dynamics of such networks during ATP depletion. Upon
simultaneously using micro-rheology and fluorescence microscopy as
complementary experimental tools, we find a sol-gel transition accompanied by a
sudden onset of directed filament motion. We interpret the sol-gel transition
in terms of myosin II enzymology, and suggest a "zipping" mechanism to explain
the filament motion in the vicinity of the sol-gel transition.


title:
Revisiting the Jurassic Geomagnetic Reversal recorded in the Lesotho
  Basalt (Southern Africa)

abstract:
  We carried out a detailed and continuous paleomagnetic sampling of the
reversed to normal geomagnetic transition recorded by some 60 consecutive flow
units near the base of the Lesotho Basalt (183  1 Ma). After
alternating field or thermal cleaning the directions of remanence are generally
well clustered within flow units. In contrast, the thermal instability of the
samples did not allow to obtain reliable paleointensity determinations. The
geomagnetic transition is incompletely recorded due to a gap in volcanic
activity attested both by eolian deposits and a large angular distance between
the field directions of the flows underlying or overlying these deposits. The
transition path is noticeably different from that reported in the pioneer work
of van Zijl et al. (1962). The most transitional Virtual Geomagnetic Poles are
observed after the volcanic hiatus. Once continents are replaced in their
relative position 180 Ma ago, the post-hiatus VGP cluster over Russia. However,
two successive rebounds from that cluster are found, with VGP reaching
repeatedly Eastern Asia coast. Thus, the VGP path is not narrowly constrained
in paleolongitude. The decrease in intensity of magnetization as the field
deviates from the normal or reversed direction suggests that the decrease in
field magnitude during the reversal reached 80-90%. We conclude that although
the reversal is of a dipole of much weaker moment than that which existed on
average during Cenozoic time, the characteristics of the reversing geodynamo
seem to be basically similar.


title: Harmonic Oscillator Potential to describe Internal Dissipation

abstract:
  Assuming that a constant potential energy function has meaning for a
dissipated harmonic oscillator, then an important issue is the time dependence
of the turning points. Turning point studies demonstrate that the common model
of external (viscous) damping fails to properly describe those many systems
where structural (internal friction) damping is the most important source of
dissipation. For internal friction damping, the better model of potential
energy is one in which the function is not stationary.