title:
Bond breaking in vibrationally excited methane on transition metal
  catalysts

abstract:
  The role of vibrational excitation of a single mode in the scattering of
methane is studied by wave packet simulations of oriented CH4 and CD4 molecules
from a flat surface. All nine internal vibrations are included. In the
translational energy range from 32 up to 128 kJ/mol we find that initial
vibrational excitations enhance the transfer of translational energy towards
vibrational energy and increase the accessibility of the entrance channel for
dissociation. Our simulations predict that initial vibrational excitations of
the asymmetrical stretch (nu_3) and especially the symmetrical stretch (nu_1)
modes will give the highest enhancement of the dissociation probability of
methane.


title: Excitation of resonators by electron beams

abstract:
  In this paper the main consequences of the vector theory of excitation of
resonators by particle beams are presented. Some features of excitation of
broadband radiation in longitudinal modes of the enclosed and open resonators
are discussed.


title: Will the Population of Humanity in the Future be Stabilized?

abstract:
  A phenomenological theory of growth of the population of humankind is
proposed. The theory based on the assumption about a multifractal nature of the
set of number of people in temporal axis and contains control parameters. In
particular cases the theory coincide with known Kapitza, Foerster, Hoerner
phenomenological theories.


title:
Are the Laws of Thermodynamics Consequences of a Fractal Properties of
  Universe?

abstract:
  Why in our Universe the laws of thermodynamics are valid? In the paper is
demonstrated the reason of it: if the time and the space are multifractal and
the Universe is in an equilibrium state the laws of the thermodynamics are
consequences of it's multifractal structure.


title: Crystalizing the genetic code

abstract:
  New developments are presented in the framework of the model introduced by
the authors in refs. [1,2] and in which nucleotides as well as codons are
classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit
q -> 0. An operator which gives the correspondence between the amino-acids and
the codons is now obtained for any known genetic code. The free energy released
by base pairing of dinucleotides as well as the relative hydrophilicity and
hydrophobicity of the dinucleosides are also computed. For the vertebrate
series, a universal behaviour in the ratios of codon usage frequencies is put
in evidence and is shown to fit nicely in our model. Then a first attempt to
represent the mutations relative to the deletion of a pyrimidine by action of a
suitable crystal spinor operator is proposed. Finally recent theoretical
descriptions are reviewed and compared with our model.


title: The Force-Velocity Relation for Growing Biopolymers

abstract:
  The process of force generation by the growth of biopolymers is simulated via
a Langevin-dynamics approach. The interaction forces are taken to have simple
forms that favor the growth of straight fibers from solution. The
force-velocity relation is obtained from the simulations for two versions of
the monomer-monomer force field. It is found that the growth rate drops off
more rapidly with applied force than expected from the simplest theories based
on thermal motion of the obstacle. The discrepancies amount to a factor of
three or more when the applied force exceeds 2.5kT/a, where a is the step size
for the polymer growth. These results are explained on the basis of restricted
diffusion of monomers near the fiber tip. It is also found that the mobility of
the obstacle has little effect on the growth rate, over a broad range.


title:
A fully {\it ab initio} potential curve of near-spectroscopic quality
  for the OH^- anion: importance of connected quadruple excitations and scalar
  relativistic effects

abstract:
  A benchmark study has been carried out on the ground-state potential curve of
the hydroxyl anion, OH^{-}, including detailed calibration of both the
1-particle and n-particle basis sets. The CCSD(T) basis set limit overestimates
$\omega_e$ by about 10 cm^{-1}, which is only remedied by inclusion of
connected quadruple excitations in the coupled cluster expansion --- or,
equivalently, the inclusion of the $2\pi$ orbitals in the active space of a
multireference calculation. Upon inclusion of scalar relativistic effects (-3
cm^{-1} on $\omega_e$), a potential curve of spectroscopic quality (sub-cm^{-1}
accuracy) is obtained. Our best computed EA(OH), 1.828 eV, agrees to three
decimal places with the best available experimental value. Our best computed
dissociation energies, D_0(OH^-)=4.7796 eV and D_0(OH)=4.4124 eV, suggest that
the experimental D_0(OH)=4.392 eV may possibly be about 0.02 eV too low.

categories: physics.chem-ph physics.ao-ph physics.plasm-ph physics.space-ph


title:
Pulsed pump in optical displacement transducer for experiments with
  probe bodies

abstract:
  The sensitivity of the displacement transducer pumped with a train of
high-intensity laser pulses is estimated. Due to the multicomponent character
of the pump a consideration of transformations of the signal and the noises
between optical modes plays an important role in estimation of the potential
sensitivity. An expression for the minimal detectable external classical force
resembles those for the continuous wave pumping with substitution of the laser
power by a time averaged power of pulsed laser. Possible scheme for back action
noise compensation for such transducers is considered. For full suppression of
back action noise the field of local oscillator has to be pulsed with the same
time dependence as the pump field.

categories: physics.optics gr-qc physics.gen-ph quant-ph


title: h is classical

abstract:
  Regardless of number, standing wave modes are by definition noninteracting,
and therefore cannot thermalize by themselves. Doppler shifts due to thermal
motions of cavity walls provide necessary mixing, but also preserve the
amplitudes and phases. The lambda/2 intervals of the modes thus preserved must
have equal energy expectations, say <E>, in the resulting equilibrium. By
definition again, they can be exchanged between modes only in whole numbers and
hence only between harmonics. Each family of harmonic modes is thus
self-contained and is disjoint from other families in such exchanges, and
further, can have no more than one mode excited at any instant. The second
property identifies harmonic families of standing wave modes as the harmonic
oscillators of Planck's theory, since a family can only bear energy equal to
exactly one of E, 2E, 3E, etc These two properties further imply that the
energy expectation gets averaged only over an individual family, as the
equilibrium energy <E(f)> steadily available at a given mode would have
contributions from its entire harmonic family. Planck's equations reemerge, and
radiation quantization arises as a classical rule <E(f)> = <E>f, as a mode must
contain a whole number of exchangeable lambda/2 intervals, but it only concerns
equilibrium states. The result makes Planck constant h an analogue of
Boltzmann's constant k for the frequency domain, and points to postulate-free
explanations of all aspects of quantum and kinetic theories.

categories: physics.class-ph gr-qc physics.gen-ph quant-ph


title:
Electron correlation in C_(4N+2) carbon rings: aromatic vs. dimerized
  structures

abstract:
  The electronic structure of C_(4N+2) carbon rings exhibits competing
many-body effects of Huckel aromaticity, second-order Jahn-Teller and Peierls
instability at large sizes. This leads to possible ground state structures with
aromatic, bond angle or bond length alternated geometry. Highly accurate
quantum Monte Carlo results indicate the existence of a crossover between C_10
and C_14 from bond angle to bond length alternation. The aromatic isomer is
always a transition state. The driving mechanism is the second-order
Jahn-Teller effect which keeps the gap open at all sizes.


title:
Ground and excited states of the hydrogen negative ion in strong
  magnetic fields

abstract:
  The lowest bound states of the hydrogen negative ion and negative donor
systems in a homogeneous magnetic field are investigated theoretically via a
full configuration interaction approach with an anisotropic Gaussian basis set.
The broad magnetic field regime \gamma=0.0008 - 4000 is covered.
Nonrelativistic total energies, electron detachment energies and transition
wavelengths are presented assuming an infinite nuclear mass. The binding
mechanisms are discussed in detail. The accuracy for the energies is enhanced
significantly compared to previously published data.


title:
New Resonant Bivacuum Mediated Interaction, as a Possible Explanation of
  Psi Phenomena

abstract:
  This paper contains development of following theories and models, related to
Psi phenomena, based on our Unified concept of Bivacuum, particles duality,
fields and time: - Theory of Virtual Replica (VR) of material objects in
Bivacuum and VR Multiplication: VRM (r,t). The VR represents a
three-dimensional (3D) superposition of Bivacuum virtual pressure waves VPW and
spin waves VirSW, modulated by pulsation of elementary particles and
translational and librational de Broglie waves of molecules of macroscopic
object (http://arxiv.org/abs/physics/0207027). The infinitive multiplication of
primary VR in space in form of 3D packets of virtual standing waves: VRM(r), is
a result of interference of all pervading external coherent basic reference
waves: (VPW) and (VirSW) with similar kinds of waves, forming VR. This
phenomena may stands for remote vision; - Theory of nonlocal Virtual Guides
(VirG) of spin, momentum and energy, with properties of quasi one-dimensional
virtual Bose condensate of bivacuum dipoles. The bundles of VirG, connecting
coherent atoms of Sender (S) and Receiver (S), are responsible for nonlocal
weak interaction; - Theory of Bivacuum Mediated Interaction (BMI) responsible
for nonlocal interaction and different Psi-phenomena without contradictions
with fundamental laws of Nature.


title:
Elementary Act of Consciousness or Cycle of Mind, involving Distant and
  Nonlocal Interaction

abstract:
  Each macroscopic process can be subdivided on the quantum and classical
stages. Particularly, the quantum stages of Cycle of Mind involves:1) the
stimulation of dynamic correlation between water clusters in the same and
remote microtubules (MTs) in state of mesoscopic Bose condensation (mBC) by
phonons (acoustic waves) and by librational IR photons (electromagnetic-EM
waves) distant exchange; 2) the transition from distant EM interaction between
remote MTs to nonlocal quantum interaction, induced by IR photons exchange
between clusters, the clusters Virtual Replicas multiplication (VRM) and
virtual guides (VirG) formation between elementary particles of remote coherent
water molecules. This process represents transition from mesoscopic Bose
condensation to macroscopic nonuniform semi-virtual Bose condensation (VirBC)
(Kaivarainen, 2006, http://arxiv.org/abs/physics/0207027); 3) the collapsing of
corresponding macroscopic wave function, as a result of the optical bistability
of the entangled water clusters and their disassembly due to librational
photons pumping, shifting clusters to less stable state; 4) turning the
clusterphilic interaction between water clusters in the open state of cavities
between alpha and beta tubulins to hydrophobic one and the in-phase shift of
these cavities to the closed state due to clusters disassembly (Kaivarainen,
http://arxiv.org/abs/physics/0102086). The classical stages of our Hierarchic
model of elementary act of Cycle of Mind are analyzed in detail.


title: Ortho-Para Conversion in CH3F. Self-Consistent Theoretical Model

abstract:
  A complete theoretical model of the nuclear spin conversion in 13CH3F induced
by intramolecular ortho-para state mixing is proposed. The model contains
parameters determined from the level-crossing spectra of the 13CH3F spin
conversion. This set of parameters includes the ortho-para decoherence rate,
the magnitude of the hyperfine spin-spin interaction between the molecular
nuclei and the energy gap between the mixed ortho and para states. These
parameters are found to be in a good agreement with their theoretical
estimates.


title: The Flotational Mechanism of Etobicoke Creek's Self-Purification

abstract:
  A flotational mechanism of Etobicoke Creek's self-purification has been
investigated. It is shown that the froth contains a high concentration of
polluting agents. Chemical analyses of the top layer of surface water in
comparison to both before and after froth collector in the course of a year are
provided. As a result, the concentrations of pollutants by utilizing the model
froth collector are decreased.


title: On the uniqueness of the surface sources of evoked potentials

abstract:
  The uniqueness of a surface density of sources localized inside a spatial
region $R$ and producing a given electric potential distribution in its
boundary $B_0$ is revisited. The situation in which $R$ is filled with various
metallic subregions, each one having a definite constant value for the electric
conductivity is considered. It is argued that the knowledge of the potential in
all $B_0$ fully determines the surface density of sources over a wide class of
surfaces supporting them. The class can be defined as a union of an arbitrary
but finite number of open or closed surfaces. The only restriction upon them is
that no one of the closed surfaces contains inside it another (nesting) of the
closed or open surfaces.


title: Ultrastable CO2 Laser Trapping of Lithium Fermions

abstract:
  We demonstrate an ultrastable CO2 laser trap that provides tight confinement
of neutral atoms with negligible optical scattering and minimal laser-noise-
induced heating. Using this method, fermionic 6Li atoms are stored in a 0.4 mK
deep well with a 1/e trap lifetime of 300 sec, consistent with a background
pressure of 10^(-11) Torr. To our knowledge, this is the longest storage time
ever achieved with an all-optical trap, comparable to the best reported
magnetic traps.


title: RF-induced evaporative cooling and BEC in a high magnetic field

abstract:
  We present the design of our iron-core electromagnet for BEC, and how to
solve the specific experimental problems raised by this technique. After
presenting the experimental set-up, we address the interruption of runaway
evaporative cooling when the Zeeman effect is not linear. We present the ways
to circumvent this problem, use of multiple RF frequencies, sympathetic cooling
and show some applications of these high magnetic fields (cavity coupling, high
confinement).


title: Symmetry breaking of vibrating interfaces: a mechanism for morphogenesis

abstract:
  We show that very small-amplitude oscillations of a highly symmetric, spheric
or cylindrical, interface (thin membrane) between two fluids can result in
inhomogeneous instability and breaking of the interface symmetry: the frequency
of the breathing vibration selects the spatial symmetry. This mechanism may
govern morphogenesis.


title:
Nature of Sonoluminescence: Noble Gas Radiation Excited by Hot Electrons
  in "Cold" Water

abstract:
  We show that strong electric fields occurring in water near the surface of
collapsing gas bubbles because of the flexoelectric effect can provoke dynamic
electric breakdown in a micron-size region near the bubble and consider the
scenario of the SBSL. The scenario is: (i) at the last stage of incomplete
collapse of the bubble the gradient of pressure in water near the bubble
surface has such a value and sign that the electric field arising from the
flexoelectric effect exceeds the threshold field of the dynamic electrical
breakdown of water and is directed to the bubble center; (ii) mobile electrons
are generated because of thermal ionization of water molecules near the bubble
surface; (iii) these electrons are accelerated in ''cold'' water by the strong
electric fields; (iv) these hot electrons transfer noble gas atoms dissolved in
water to high-energy excited states and optical transitions between these
states produce SBSL UV flashes in the trasparency window of water; (v) the
breakdown can be repeated several times and the power and duration of the UV
flash are determined by the multiplicity of the breakdowns. The SBSL spectrum
is found to resemble a black-body spectrum where temperature is given by the
effective temperature of the hot electrons. The pulse energy and some other
characteristics of the SBSL are found to be in agreement with the experimental
data when realistic estimations are made.


title: Radiation from a Superluminal Source

abstract:
  The sweep speed of an electron beam across the face of an oscilloscope can
exceed the velocity of light, although of course the velocity of the electrons
does not. Associated with this possibility there should be a kind of Cherenkov
radiation, as if the oscilloscope trace were due to a charge moving with
superluminal velocity.


title: A new volatility term in the theory of options with transaction costs

abstract:
  The introduction of transaction costs into the theory of option pricing could
lead not only to the change of return for options, but also to the change of
the volatility. On the base of assumption of the portfolio analysis, a new
equation for option pricing with transaction costs is derived. A new solution
for the option price is obtained for the time close to expiration date.


title:
Enhanced dielectronic recombination of lithium-like Ti19+ ions in
  external ExB fields

abstract:
  Dielectronic recombination(DR) of lithium-like Ti19+(1s2 2s) ions via 2s->2p
core excitations has been measured at the Heidelberg heavy ion storage ring
TSR. We find that not only external electric fields (0 <= Ey <= 280 V/cm) but
also crossed magnetic fields (30 mT <= Bz <= 80 mT) influence the DR via high-n
(2p_j nl)-Rydberg resonances. This result confirms our previous finding for
isoelectronic Cl14+ ions [Bartsch T et al, PRL 82, 3779 (1999)] that
experimentally established the sensitivity of DR to ExB fields. In the present
investigation the larger 2p_{1/2}-2p_{3/2} fine structure splitting of Ti19+
allowed us to study separately the influence of external fields via the two
series of Rydberg DR resonances attached to the 2s -> 2p_{1/2} and 2s ->
2p_{3/2} excitations of the Li-like core, extracting initial slopes and
saturation fields of the enhancement. We find that for Ey > 80 V/cm the field
induced enhancement is about 1.8 times stronger for the 2p_{3/2} series than
for the 2p_{1/2} series.


title: Axicon Gaussian Laser Beams

abstract:
  We deduce the simplest form for an axicon Gaussian laser beam, i.e., one with
radial polarization of the electric field.


title: Diffraction as a Consequence of Faraday's Law

abstract:
  We consider a linearly polarized electromagnetic wave incident on an opaque
screen with square aperture of edge a. An application of Faraday's law to a
loop parallel to the screen, on the side away from the source, shows that the
wave must have longitudinal components there. The ratio of the longitudinal to
transverse field is a measure of the diffraction angle.


title: Time-Reversed Diffraction

abstract:
  We show that a time-reversed formulation of Huygens-Kirchhoff diffraction can
be used to deduce the transverse and longitudinal fields of a Gaussian laser
beam, starting from a simple assumption of a Gaussian beam profile in the far
field. An attempt to apply this technique to the far fields of a Hertzian
dipole shows how the laws of diffraction do not permit a wave to be focused to
a volume smaller than a cubic wavelength in a charge-free region.


title: Classical "Dressing" of a Free Electron in a Plane Electromagnetic Wave

abstract:
  The energy and momentum densities of the fields of a free electron in a plane
electromagnetic wave include interference terms that are the classical version
of the ``dressing'' of the electron the arises in a quantum analysis. The
transverse mechanical momentum of the oscillating electron is balanced by the
field momentum resulting from the interference between the driving wave and the
static part of the electron's field. The interference between the wave and the
oscillating part of the electron's field leads to a longitudinal field momentum
and a negative field energy that compensate for the longitudinal momentum and
kinetic energy of the electron. The interference terms are dominated by the
near zone, so that as the wave passes the electron by the latter reverts to its
energy and momentum prior to the arrival of the wave.


title:
The Hawking-Unruh Temperature and Quantum Fluctuations in Particle
  Accelerators

abstract:
  We wish to draw attention to a novel view of the effect of the quantum
fluctuations during the radiation of accelerated particles, particularly those
in storage rings. This view is inspired by the remarkable insight of Hawking
that the effect of the strong gravitational field of a black hole on the
quantum fluctuations of the surrounding space is to cause the black hole to
radiate with a temperature T = hbar g / 2 pi c k, where g is the acceleration
due to gravity at the surface of the black hole, c is the speed of light, and k
is Boltzmann's constant. Shortly thereafter Unruh argued that an accelerated
observer should become excited by quantum fluctuations to a temperature T =
hbar a* / 2 pi c k, where a* is the acceleration of the observer in its
instantaneous rest frame. In a series of papers Bell and co-workers have noted
that electron storage rings provide a demonstration of the utility of the
Hawking-Unruh temperature, with emphasis on the question of the incomplete
polarization of the electrons due to quantum fluctuations of synchrotron
radiation. Here we expand slightly on the results of Bell et al., and encourage
the reader to consult the literature for more detailed understanding.


title: The Hawking-Unruh Temperature and Damping in a Linear Focusing Channel

abstract:
  The Hawking-Unruh effective temperature, hbar a* / 2 pi c k, due to quantum
fluctuations in the radiation of an accelerated charged-particle beam can be
used to show that transverse oscillations of the beam in a practical linear
focusing channel damp to the quantum-mechanical limit. A comparison is made
between this behavior and that of beams in a wiggler.


title:
Limits on the Applicability of Classical Electromagnetic Fields as
  Inferred from the Radiation Reaction

abstract:
  Can the wavelength of a classical electromagnetic field be arbitrarily small,
or its electric field strength be arbitrarily large? If we require that the
radiation-reaction force on a charged particle in response to an applied field
be smaller than the Lorentz force we find limits on the classical
electromagnetic field that herald the need for a better theory, i.e., one in
better accord with experiment. The classical limitations find ready
interpretation in quantum electrodynamics. The examples of Compton scattering
and the QED critical field strength are discussed. It is still open to
conjecture whether the present theory of QED is valid at field strengths beyond
the critical field revealed by a semiclassical argument.


title: Energy Balance in an Electrostatic Accelerator

abstract:
  The principle of an electrostatic accelerator is that when a charge e escapes
from a conducting plane that supports a uniform electric field of strength E_0,
then the charge gains energy e E_0 d as it moves distance d from the plane.
Where does this energy come from? We that the mechanical energy gain of the
electron is balanced by the decrease in the electrostatic field energy of the
system.


title: A bounded source cannot emit a unipolar electromagnetic wave

abstract:
  We show that a bounded source cannot produce a unipolar electromagnetic
pulse. As a consequence, there are no three-dimensional electromagnetic
solitons in vacuum.


title: The Grating Accelerator

abstract:
  In optics, a reflective grating is a conducting surface with a ripple. The
typical use of such a grating involves an incident electromagnetic wave with
wave vector k in the x-z plane, and interference effects lead to a discrete set
of reflected waves also with wave vectors in the x-z plane. Consider, instead,
an incident plane electromagnetic wave with wave vector in the y-z plane and
polarization in the x direction: We show that for small ripples, this leads to
a reflected wave plus two surface waves that are attenuated exponentially with
z. For certain values of the grating wavelength and the optical wavelength, the
component of the phase velocity of the surface waves is the speed of light c.
In this case, a charged particle moving with v_x ~ c could extract energy from
the wave, which is the principle of the "grating accelerator".


title: The Laser-Driven Vacuum Photodiode

abstract:
  A vacuum photodiode driven by a pulsed laser can sustain an average current
very similar to that of a continous diode, where the latter is described by
Child's law.


title: The Helical Wiggler

abstract:
  There is not a unique solution to the electro- or magnetostatic problem where
the "boundary condition" is merely a specification of the fields along a line.
As a practical example, we consider the case where it is desired to have a
magnetic field that that traces a helix about the z axis.


title:
Phase changes in 38 atom Lennard-Jones clusters. I: A parallel tempering
  study in the canonical ensemble

abstract:
  The heat capacity and isomer distributions of the 38 atom Lennard-Jones
cluster have been calculated in the canonical ensemble using parallel tempering
Monte Carlo methods. A distinct region of temperature is identified that
corresponds to equilibrium between the global minimum structure and the
icosahedral basin of structures. This region of temperatures occurs below the
melting peak of the heat capacity and is accompanied by a peak in the
derivative of the heat capacity with temperature. Parallel tempering is shown
to introduce correlations between results at different temperatures. A
discussion is given that compares parallel tempering with other related
approaches that ensure ergodic simulations.


title:
The Stern-Gerlach interaction between a traveling particle and a time
  varying magnetic field

abstract:
  The general expression of the Stern-Gerlach force is deduced for a charged
particle, endowed with a magnetic moment, which travels inside a time varying
magnetic field. Then, the energy integral of the Stern-Gerlach force is
evaluated in the case of a particle crossing a TE rf cavity with its magnetic
moment oriented in different ways with respect as the cavity axis. We shall
demonstrate that appropriate choices of the cavity characteristics and of the
spin orientation confirm the possibility of separating in energy the opposite
spin states of a fermion beam circulating in a storage ring and, in addition,
make feasible an absolute polarimeter provide that a parametric converter
acting between two coupled cavities is implemented


title:
Hierarchic theory of condensed matter and its interaction with light:
  new theories of light refraction, Brillouin scattering and Mossbauer effect

abstract:
  1: New approach to theory of light refraction 1.1. Refraction in gas; 1.2.
Light refraction in liquids and solids 2: Mesoscopic theory of Brillouin light
scattering 2.1. Traditional approach; 2.2. Fine structure of scattering; 2.3.
Mesoscopic approach; 2.4. Quantitative verification of hierarchic theory of
Brillouin scattering 3: Mesoscopic theory of Mossbauer effect 3.1. General
background; 3.2. Probability of elastic effects; 3.3. Doppler broadening in
spectra nuclear gamma-resonance (NGR) 3.4. Acceleration and forces, related to
thermal dynamics of molecules and ions.
  Vibro-gravitational interaction


title:
Hierarchic Theory of Complex Systems (biosystems, colloids):
  self-organization & osmos

abstract:
  1. Protein domain mesoscopic organization 2. Quantum background of lipid
domain organization in biomembranes 3. Hierarchic approach to theory of
solutions and colloid systems 4. Distant solvent-mediated interaction between
macromolecules 5. Spatial self-organization in the water-macromolecular systems
6. Properties of [bisolvent - polymer system] 7. Osmosis and solvent activity.
Traditional and mesoscopic approach


title:
Phase changes in 38 atom Lennard-Jones clusters. II: A parallel
  tempering study of equilibrium and dynamic properties in the molecular
  dynamics and microcanonical

abstract:
  We study the 38-atom Lennard-Jones cluster with parallel tempering Monte
Carlo methods in the microcanonical and molecular dynamics ensembles. A new
Monte Carlo algorithm is presented that samples rigorously the molecular
dynamics ensemble for a system at constant total energy, linear and angular
momenta. By combining the parallel tempering technique with molecular dynamics
methods, we develop a hybrid method to overcome quasi-ergodicity and to extract
both equilibrium and dynamical properties from Monte Carlo and molecular
dynamics simulations. Several thermodynamic, structural and dynamical
properties are investigated for LJ$_{38}$, including the caloric curve, the
diffusion constant and the largest Lyapunov exponent. The importance of
insuring ergodicity in molecular dynamics simulations is illustrated by
comparing the results of ergodic simulations with earlier molecular dynamics
simulations.


title:
Temporary Acceleration of Electrons While Inside an Intense
  Electromagnetic Pulse

abstract:
  A free electron can temporarily gain a very significant amount of energy if
it is overrun by an intense electromagnetic wave. In principle, this process
would permit large enhancements in the center-of-mass energy of
electron-electron, electron-positron and electron-photon interactions if these
take place in the presence of an intense laser beam. Practical considerations
severely limit the utility of this concept for contemporary lasers incident on
relativistic electrons. A more accessible laboratory phenomenon is
electron-positron production via an intense laser beam incident on a gas.
Intense electromagnetic pulses of astrophysical origin can lead to very
energetic photons via bremsstrahlung of temporarily accelerated electrons.


title:
Hierarchic Theory Of Condensed Matter: New state equation and
  Interrelation between mesoscopic and macroscopic properties

abstract:
  1. The state equation for real gas 2. New state equation for condensed matter
3.Vapor pressure 4. Surface tension 5. Mesoscopic theory of thermal
conductivity 6. Mesoscopic theory of viscosity for liquids and solids 7.
Brownian diffusion 8. Self-diffusion in liquids and solids 9. Mesoscopic
approach to proton conductivity in water, ice and other systems, containing
hydrogen bonds 10. Regulation of pH and shining of water by electromagnetic and
acoustic fields


title:
Very long storage times and evaporative cooling of cesium atoms in a
  quasi-electrostatic dipole trap

abstract:
  We have trapped cesium atoms over many minutes in the focus of a CO$_2$-laser
beam employing an extremely simple laser system. Collisional properties of the
unpolarized atoms in their electronic ground state are investigated. Inelastic
binary collisions changing the hyperfine state lead to trap loss which is
quantitatively analyzed. Elastic collisions result in evaporative cooling of
the trapped gas from 25 $\mu$K to 10 $\mu$K over a time scale of about 150 s.


title: Nonlinear Modes of Liquid Drops as Solitary Waves

abstract:
  The nolinear hydrodynamic equations of the surface of a liquid drop are shown
to be directly connected to Korteweg de Vries (KdV, MKdV) systems, giving
traveling solutions that are cnoidal waves. They generate multiscale patterns
ranging from small harmonic oscillations (linearized model), to nonlinear
oscillations, up through solitary waves. These non-axis-symmetric localized
shapes are also described by a KdV Hamiltonian system. Recently such ``rotons''
were observed experimentally when the shape oscillations of a droplet became
nonlinear. The results apply to drop-like systems from cluster formation to
stellar models, including hyperdeformed nuclei and fission.


title: Patterns on liquid surfaces: cnoidal waves, compactons and scaling

abstract:
  Localized patterns and nonlinear oscillation formation on the bounded free
surface of an ideal incompressible liquid are analytically investigated .
Cnoidal modes, solitons and compactons, as traveling non-axially symmetric
shapes are discused. A finite-difference differential generalized Korteweg-de
Vries equation is shown to describe the three-dimensional motion of the fluid
surface and the limit of long and shallow channels one reobtains the well known
KdV equation. A tentative expansion formula for the representation of the
general solution of a nonlinear equation, for given initial condition is
introduced on a graphical-algebraic basis. The model is useful in multilayer
fluid dynamics, cluster formation, and nuclear physics since, up to an overall
scale, these systems display liquid free surface behavior.


title:
A fast algorithm for generating a uniform distribution inside a
  high-dimensional polytope

abstract:
  We describe a uniformly fast algorithm for generating points \vec{x}
uniformly in a hypercube with the restriction that the difference between each
pair of coordinates is bounded. We discuss the quality of the algorithm in the
sense of its usage of pseudo-random source numbers, and present an interesting
result on the correlation between the coordinates.


title:
Emergence of intense jets and Jupiter Great Red Spot as maximum entropy
  structures

abstract:
  We explain the emergence and robustness of intense jets in highly turbulent
planetary atmospheres, like on Jupiter, by a general approach of statistical
mechanics of potential vorticity patches. The idea is that potential vorticity
mixing leads to the formation of a steady organized coarse grained flow,
corresponding to the statistical equilibrium state. Our starting point is the
quasi-geostrophic 1-1/2 layer model, and we consider the relevant limit of a
small Rossby radius of deformation. Then narrow jets are obtained, scaling like
the Rossby radius of deformation. These jets can be either zonal, or closed
into a ring bounding a vortex. Taking into account the effect of the beta
effect and a sublayer deep shear flow, we predict an organization of the
turbulent atmospheric layer into an oval-shaped vortex amidst a background
shear. Such an isolated vortex is centered over an extremum of the equivalent
topography (determined by the deep shear flow and beta-effect). This prediction
is in agreement with analysis of wind data in major Jovian vortices (Great Red
Spot and Oval BC).


title: Deformed Lorentz Symmetry and High-Energy Astrophysics (I)

abstract:
  An updated discussion of Lorentz symmetry violation in particle physics at
very high energy is presented, focusing on applications of models of deformed
Lorentz symmetry to high-energy astrophysics.


title: Theory of Complex Scattering Lengths

abstract:
  We derive a generalized Low equation for the T-matrix appropriate for complex
atom-molecule interaction. The properties of this new equation at very low
energies are studied and the complex scattering length and effective range are
derived.


title: The Induced Self-Purification of Creeks and Rivers

abstract:
  The clean-up of several Creeks and Rivers by induction of a self-purification
process was provided. The process took place at all the sites studied with the
up to 100% resulted removal of polluting agents depending on the site and
nature of the contaminant. The self-purification mechanism could be used for
drinking and technical water preparation.


title: Magnetic Geometry and the Confinement of Electrically Conducting Plasmas

abstract:
  We develop an effective field theory approach to inspect the electromagnetic
interactions in an electrically neutral plasma, with an equal number of
negative and positive charge carriers. We argue that the static equilibrium
configurations within the plasma are topologically stable solitons, that
describe knotted and linked fluxtubes of helical magnetic fields.

categories: physics.plasm-ph cond-mat hep-lat hep-th


title:
Spatial-temporal correlations in the process to self-organized
  criticality

abstract:
  A new type of spatial-temporal correlation in the process approaching to the
self-organized criticality is investigated for the two simple models for
biological evolution. The change behaviors of the position with minimum barrier
are shown to be quantitatively different in the two models. Different results
of the correlation are given for the two models. We argue that the correlation
can be used, together with the power-law distributions, as criteria for
self-organized criticality.


title: Search for correlation effects in linear chains of trapped ions

abstract:
  We report a precise search for correlation effects in linear chains of 2 and
3 trapped Ca+ ions. Unexplained correlations in photon emission times within a
linear chain of trapped ions have been reported, which, if genuine, cast doubt
on the potential of an ion trap to realize quantum information processing. We
observe quantum jumps from the metastable 3d 2D_{5/2} level for several hours,
searching for correlations between the decay times of the different ions. We
find no evidence for correlations: the number of quantum jumps with separations
of less than 10 ms is consistent with statistics to within errors of 0.05%; the
lifetime of the metastable level derived from the data is consistent with that
derived from independent single-ion data at the level of the experimental
errors 1%; and no rank correlations between the decay times were found with
sensitivity to rank correlation coefficients at the level of |R| = 0.024.


title:
XAFS spectroscopy. I. Extracting the fine structure from the absorption
  spectra

abstract:
  Three independent techniques are used to separate fine structure from the
absorption spectra, the background function in which is approximated by (i)
smoothing spline. We propose a new reliable criterion for determination of
smoothing parameter and the method for raising of stability with respect to
k_min variation; (ii) interpolation spline with the varied knots; (iii) the
line obtained from bayesian smoothing. This methods considers various prior
information and includes a natural way to determine the errors of XAFS
extraction. Particular attention has been given to the estimation of
uncertainties in XAFS data. Experimental noise is shown to be essentially
smaller than the errors of the background approximation, and it is the latter
that determines the variances of structural parameters in subsequent fitting.


title: XAFS spectroscopy. II. Statistical evaluations in the fitting problems

abstract:
  The problem of error analysis is addressed in stages beginning with the case
of uncorrelated parameters and proceeding to the Bayesian problem that takes
into account all possible correlations when a great deal of prior information
about the accessible parametr space is available. The formulas for the standard
deviations and deviations with arbitrary confidence levels are derived.
Underestimation of the errors of XAFS-function extraction is shown to be a
source of unjustified optimistic errors of fitting parameters. The applications
of statistical chi^2- and F-tests to the fitting problems are also discussed.


title: Radiative recombination of bare Bi83+: Experiment versus theory

abstract:
  Electron-ion recombination of completely stripped Bi83+ was investigated at
the Experimental Storage Ring (ESR) of the GSI in Darmstadt. It was the first
experiment of this kind with a bare ion heavier than argon. Absolute
recombination rate coefficients have been measured for relative energies
between ions and electrons from 0 up to about 125 eV. In the energy range from
15 meV to 125 eV a very good agreement is found between the experimental result
and theory for radiative recombination (RR). However, below 15 meV the
experimental rate increasingly exceeds the RR calculation and at Erel = 0 eV it
is a factor of 5.2 above the expected value. For further investigation of this
enhancement phenomenon the electron density in the interaction region was set
to 1.6E6/cm3, 3.2E6/cm3 and 4.7E6/cm3. This variation had no significant
influence on the recombination rate. An additional variation of the magnetic
guiding field of the electrons from 70 mT to 150 mT in steps of 1 mT resulted
in periodic oscillations of the rate which are accompanied by considerable
changes of the transverse electron temperature.


title: Resistive axisymmetric equilibria with arbitrary flow

abstract:
  An analysis of axisymmetric equilibria with arbitrary incompressible flow and
finite resistivity is presented. It is shown that with large aspect ratio
approximation or vanishing poloidal current, a uniform conductivity profile is
consistent with equilibrium flows. Also a comment made on coexistence of both
toroidal and poloidal flows in an axisymmetric field-reversed configuration.


title:
Comparision of direct and Fourier space techniques in time-dependent
  density functional theory

abstract:
  Several techniques have appeared in the literatuare to solve the equations of
time-dependent density functional theory. We compare the efficiency of
different methods based on mesh representations of the wave function (direct
and Fourier space), taking as a test case the calculation of the surface
plasmon in the cluster Na_8. For smaller systems, the methods have comparable
efficiency. For large systems the direct time method has a decided advantage in
computer storage requirements. It is also more economical on arithmetic
operations, but is not as suited for parallel computing as the methods based on
a frequency representation.


title: A waveguide atom beamsplitter for laser-cooled neutral atoms

abstract:
  A laser-cooled neutral-atom beam from a low-velocity intense source is split
into two beams while guided by a magnetic-field potential. We generate our
multimode-beamsplitter potential with two current-carrying wires on a glass
substrate combined with an external transverse bias field. The atoms bend
around several curves over a $10$-cm distance. A maximum integrated flux of
$1.5\cdot10^{5} \mathrm{atoms/s}$ is achieved with a current density of
$5\cdot10^{4} \mathrm{Ampere/cm^{2}}$ in the 100-$\mathrm{\mu m}$ diameter
wires. The initial beam can be split into two beams with a 50/50 splitting
ratio.


title: Ultrahigh sensitivity of slow-light gyroscope

abstract:
  Slow light generated by Electromagnetically Induced Transparency is extremely
susceptible with respect to Doppler detuning. Consequently, slow-light
gyroscopes should have ultrahigh sensitivity.


title:
Hierarchic Theory of Condensed Matter: Role of water in protein
  dynamics, function and cancer emergency

abstract:
  1. Role of inter-domain water clusters in large-scale dynamics of proteins;
2. Description of large-scale dynamics of proteins based on generalized
Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand
complexes formation; 4. The life-time of quasiparticles and frequencies of
their excitation; 5. Mesoscopic mechanism of enzyme catalysis; 6. The mechanism
of ATP hydrolysis energy utilization in muscle contraction and protein
polymerization; 7. Water activity as a regulative factor in the intra- and
inter-cell processes; 8. Water and cancer.


title: Generalized Optimal Current Patterns and Electrical Safety in EIT

abstract:
  There are a number of constraints which limit the current and voltages which
can be applied on a multiple drive electrical imaging system. One obvious
constraint is to limit the maximum Ohmic power dissipated in the body. Current
patterns optimising distinguishability with respect to this constraint are
singular functions of the difference of transconductance matrices with respect
to the power norm. (the optimal currents of Isaacson). If one constrains the
total current ($L^1$ norm) the optimal patterns are pair drives. On the other
hand if one constrains the maximum current on each drive electrode (an
$L^\infty$ norm), the optimal patterns have each drive channel set to the
maximum source or sink current value. In this paper we consider appropriate
safety constraints and discuss how to find the optimal current patterns with
those constraints.


title: Variational-Wavelet Approach to RMS Envelope Equations

abstract:
  We present applications of variational-wavelet approach to nonlinear
(rational) rms envelope equations. We have the solution as a multiresolution
(multiscales) expansion in the base of compactly supported wavelet basis. We
give extension of our results to the cases of periodic beam motion and
arbitrary variable coefficients. Also we consider more flexible variational
method which is based on biorthogonal wavelet approach.

categories: physics.acc-ph math-ph math.MP nlin.CD physics.comp-ph


title: Classical Radiation Processes in the Weizsacker-Williams Approximation

abstract:
  The main features of radiation by relativistic electrons are well
approximated in the Weizsacker-Williams method of virtual quanta. This method
is best known for its application to radiation during elementary particle
collisions, but is equally useful in describing "classical" radiation emitted
during the interaction of a single relativistic electron with an extended
system, such as synchrotron radiation, undulator radiation, transition
radiation and Cerenkov radiation.


title:
Vector constants of motion for time-dependent Kepler and isotropic
  harmonic oscillator potentials

abstract:
  A method of obtaining vector constants of motion for time-independent as well
as time-dependent central fields is discussed. Some well-established results
are rederived in this alternative way and new ones obtained.


title: Tsallis' entropy maximization procedure revisited

abstract:
  The proper way of averaging is an important question with regards to Tsallis'
Thermostatistics. Three different procedures have been thus far employed in the
pertinent literature. The third one, i.e., the Tsallis-Mendes-Plastino (TMP)
normalization procedure, exhibits clear advantages with respect to earlier
ones. In this work, we advance a distinct (from the TMP-one) way of handling
the Lagrange multipliers involved in the extremization process that leads to
Tsallis' statistical operator. It is seen that the new approach considerably
simplifies the pertinent analysis without losing the beautiful properties of
the Tsallis-Mendes-Plastino formalism.


title:
Rapid acceleration of electrons in the magnetosphere by fast-mode MHD
  waves

abstract:
  During major megnetic storms, enhanced flux of relativistic electrons in the
inner magnetosphere have been observed to correleated with ULF waves. The
enhancements can take place over a period of several hours. In order to account
for such a rapid generation of relativistic electrons, we examine the mechanism
of transit-time acceleration of electrons by low-frequency fast-mode MHD waves,
here the assumed form of ULF waves. Calcaulations of the acceleration
timescales in the model show that fast-mode waves in the Pc4 to Pc5 frequency
range, with typically observed wave amplitudes 10--20 nT, can accelerate the
seed electrons to energies of order MeV in a period of a few hours.


title:
Auditory Sensitivity Provided by Self-tuned Critical Oscillations of
  Hair Cells

abstract:
  We introduce the concept of self-tuned criticality as a general mechanism for
signal detection in sensory systems. In the case of hearing, we argue that
active amplification of faint sounds is provided by a dynamical system which is
maintained at the threshold of an oscillatory instability. This concept can
account for the exquisite sensitivity of the auditory system and its wide
dynamic range, as well as its capacity to respond selectively to different
frequencies. A specific model of sound detection by the hair cells of the inner
ear is discussed. We show that a collection of motor proteins within a hair
bundle can generate oscillations at a frequency which depends on the elastic
properties of the bundle. Simple variation of bundle geometry gives rise to
hair cells with characteristic frequencies which span the range of audibility.
Tension-gated transduction channels, which primarily serve to detect the motion
of a hair bundle, also tune each cell by admitting ions which regulate the
motor protein activity. By controlling the bundle's propensity to oscillate,
this feedback automatically maintains the system in the operating regime where
it is most sensitive to sinusoidal stimuli. The model explains how hair cells
can detect sounds which carry less energy than the background noise.


title: Physical Aspects of Axonemal Beating and Swimming

abstract:
  We discuss a two-dimensional model for the dynamics of axonemal deformations
driven by internally generated forces of molecular motors. Our model consists
of an elastic filament pair connected by active elements. We derive the dynamic
equations for this system in presence of internal forces. In the limit of small
deformations, a perturbative approach allows us to calculate filament shapes
and the tension profile. We demonstrate that periodic filament motion can be
generated via a self-organization of elastic filaments and molecular motors.
Oscillatory motion and the propagation of bending waves can occur for an
initially non-moving state via an instability termed Hopf bifurcation. Close to
this instability, the behavior of the system is shown to be independent of
microscopic details of the axoneme and the force-generating mechanism. The
oscillation frequency however does depend on properties of the molecular
motors. We calculate the oscillation frequency at the bifurcation point and
show that a large frequency range is accessible by varying the axonemal length
between 1 and 50$\mu$m. We calculate the velocity of swimming of a flagellum
and discuss the effects of boundary conditions and externally applied forces on
the axonemal oscillations.


title: Transition from the Couette-Taylor system to the plane Couette system

abstract:
  We discuss the flow between concentric rotating cylinders in the limit of
large radii where the system approaches plane Couette flow. We discuss how in
this limit the linear instability that leads to the formation of Taylor
vortices is lost and how the character of the transition approaches that of
planar shear flows. In particular, a parameter regime is identified where
fractal distributions of life times and spatiotemporal intermittency occur.
Experiments in this regime should allow to study the characteristics of shear
flow turbulence in a closed flow geometry.


title: Acoustic coupling between two air bubbles in water

abstract:
  The acoustic coupling between two air bubbles immersed in water is clearly
demonstrated. The system is acoustically forced, and its response is detected.
The experimental results confirm that both theoretically predicted eigenmodes,
respectively symmetrical and antisymmetrical, do exist. Their frequencies,
measured as a function of the bubbles spacing, follow theoretical estimations
within a 10% accuracy.


title: Novel approach for spin-flipping a stored polarized beam

abstract:
  The traditional method of spin-flipping a stored polarized beam is based on
slowly crossing an rf induced depolarizing resonance. This paper discusses a
novel approach where the polarization reversal is achieved by trapping the beam
polarization into a stable spin-flipping motion on top of the rf induced
resonance at a half-revolution frequency.


title: Noise-based switches and amplifiers for gene expression

abstract:
  The regulation of cellular function is often controlled at the level of gene
transcription. Such genetic regulation usually consists of interacting
networks, whereby gene products from a single network can act to control their
own expression or the production of protein in another network. Engineered
control of cellular function through the design and manipulation of such
networks lies within the constraints of current technology. Here we develop a
model describing the regulation of gene expression, and elucidate the effects
of noise on the formulation. We consider a single network derived from
bacteriophage $\lambda$, and construct a two-parameter deterministic model
describing the temporal evolution of the concentration of $\lambda$ repressor
protein. Bistability in the steady-state protein concentration arises
naturally, and we show how the bistable regime is enhanced with the addition of
the first operator site in the promotor region. We then show how additive and
multiplicative external noise can be used to regulate expression. In the
additive case, we demonstrate the utility of such control through the
construction of a protein switch, whereby protein production is turned ``on''
and ``off'' using short noise pulses. In the multiplicative case, we show that
small deviations in the transcription rate can lead to large fluctuations in
the production of protein, and describe how these fluctuations can be used to
amplify protein production significantly. These novel results suggest that an
external noise source could be used as a switch and/or amplifier for gene
expression. Such a development could have important implications for gene
therapy.


title: Elementary Quantum Mechanics

abstract:
  This is the first graduate course on elementary quantum mechanics in Internet
written in Romanian for the benefit of Romanian speaking students (Romania and
Moldova). It is a translation (with corrections) of the Spanish version of the
course (physics/9808031, English translation physics/0004072), which I did at
the request of students of physics in Bucharest. The topics included refer to
the postulates of quantum mechanics, one-dimensional barriers and wells,
angular momentum and spin, WKB method, harmonic oscillator, hydrogen atom,
quantum scattering, and partial waves


title:
Hierarchic Theory of Condensed Matter: Long relaxation, macroscopic
  oscillations and the effects of magnetic field

abstract:
  1. Theoretical background for macroscopic oscillations in condensed matter;
2. The hypothesis of [entropy - mass - time] interrelation; 3. The entropy -
information content of matter as a hierarchic system; 4. Experimentally
revealed macroscopic oscillations; 5. Phenomena in water and aqueous systems,
induced by magnetic field: Coherent radio-frequency oscillations in water,
revealed by C. Smith; 6. Influence of weak magnetic field on the properties of
solid bodies; 7. Possible mechanism of perturbations of nonmagnetic materials
under magnetic treatment.


title: Hierarchic Models of Turbulence, Superfluidity and Superconductivity

abstract:
  New models of Turbulence, Superfluidity and Superconductivity, based on new
Hierarchic theory, general for liquids and solids (physics/0102086), have been
proposed. CONTENTS: 1 Turbulence. General description; 2 Mesoscopic mechanism
of turbulence; 3 Superfluidity. General description; 4 Mesoscopic scenario of
fluidity; 5 Superfluidity as a hierarchic self-organization process; 6
Superfluidity in 3He; 7 Superconductivity: General properties of metals and
semiconductors; Plasma oscillations; Cyclotron resonance; Electroconductivity;
8. Microscopic theory of superconductivity (BCS); 9. Mesoscopic scenario of
superconductivity: Interpretation of experimental data in the framework of
mesoscopic model of superconductivity.


title: The ZEKE-effect in cold Rydberg gases

abstract:
  Cold, dense Rydberg gases produced in a cold-atom trap are investigated using
spectroscopic methods and time-resolved electron counting. On the discrete
Rydberg resonances we observe large trap losses and long lasting electron
emission from the Rydberg gas (>30ms). Our observations are explained by
quasi-elastic l-mixing collisions between Rydberg atoms and slow electrons that
lead to the population of long-lived high-angular-momentum Rydberg states.
These atoms thermally ionize slowly and with large probabilities, leading to
the observed effects.


title: The Fractal Universe

abstract: In this talk, we touch upon the chaotic and fractal aspects of the Universe.


title: A Brief note on Fluctuations and Interactions

abstract:
  In this brief note we re-emphasize the fact that an underpinning of
fluctuations characterizes the fundamental interactions in the light of El
Naschie's recent work.


title: Scaled Universe II

abstract:
  In an earlier paper we had pointed out that Quantum Mechanical type effects
are seen at different scales in the macro universe also. In this paper we
obtain a rationale for this, which lies in the picture of bound material
systems, spanning a Compton wavelength type extent, separated by much larger
and relatively much less dense distances.


title: Scale Dependent Dimensionality

abstract:
  We argue that dimensionality is not absolute, but that it depends on the
scale of resolution, from the Planck to the macro scale.


title: Lorentz-Covariant Hamiltonian Formalism

abstract:
  The dynamic of a classical system can be expressed by means of Poisson
brackets. In this paper we generalize the relation between the usual non
covariant Hamiltonian and the Poisson brackets to a covariant Hamiltonian and
new brackets in the frame of the Minkowski space. These brackets can be related
to those used by Feynman in his derivation of Maxwell's equations. The case of
curved space is also considered with the introduction of Christoffel symbols,
covariant derivatives, and curvature tensors.


title: Measurement of Carbon Disulfide Anion Diffusion in a TPC

abstract:
  A Negative Ion Time Projection Chamber was used to measure the field
dependence of lateral and longitudinal diffusion for CS$_2$ anions drifting in
mixtures of CS$_2$ and Ar at 40 Torr. Ion drift velocities and limits on the
capture distance for electrons as a function of field and gas mixture are also
reported.


title:
A microscopic derivation of Special Relativity: simple harmonic
  oscillations of a moving space-time lattice

abstract:
  The starting point of the theory of Special Relativity$^1$ is the Lorentz
transformation, which in essence describes the lack of absolute measurements of
space and time. These effects came about when one applies the Second Relativity
Postulate to inertial observers. Here I demonstrate that there is a very
elegant way of explaining how exactly nature enforces Special Relativity, which
compels us to conclude that Einstein's great theory has already revealed
quantization of space and time. The model proposes that microscopically the
structure of space-time is analogous to a crystal which consists of lattice
points or `tickmarks' (for measurements) connected by identical `elastic
springs'. When at rest the `springs' are at their natural states. When set in
motion and used to measure objects at rest, however, the lattice effectively
vibrates in a manner described by Einstein's theory of the heat capacity of
solids, with consequent widening of the `tickmarks' because the
root-mean-square separation now increases. I associate a vibration temperature
$T$ with the speed of motion $v$ via the fundamental postulate of this theory,
viz. the relation $\frac{v^2}{c^2} = e^{-\frac{\epsilon}{kT}}$ where $\epsilon$
is a quantum of energy of the lattice harmonic oscillator. A moving observer
who measures distances with such a vibrating lattice obtains results which are
precisely those given by the Lorentz transformation. Apart from its obvious
beauty, this approach provides many new prospects in understanding space and
time. For example, a consequence of the model is that space-time, like mass,
can in principle be converted to energy.


title: Dirac monopole with Feynman brackets

abstract:
  We introduce the magnetic angular momentum as a consequence of the structure
of the sO(3) Lie algebra defined by the Feynman brackets. The Poincare momentum
and Dirac magnetic monopole appears as a direct result of this framework.


title: Coupled Two-Way Clustering Analysis of Gene Microarray Data

abstract:
  We present a novel coupled two-way clustering approach to gene microarray
data analysis. The main idea is to identify subsets of the genes and samples,
such that when one of these is used to cluster the other, stable and
significant partitions emerge. The search for such subsets is a computationally
complex task: we present an algorithm, based on iterative clustering, which
performs such a search. This analysis is especially suitable for gene
microarray data, where the contributions of a variety of biological mechanisms
to the gene expression levels are entangled in a large body of experimental
data. The method was applied to two gene microarray data sets, on colon cancer
and leukemia. By identifying relevant subsets of the data and focusing on them
we were able to discover partitions and correlations that were masked and
hidden when the full dataset was used in the analysis. Some of these partitions
have clear biological interpretation; others can serve to identify possible
directions for future research.

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


title: Exact Topological Twistons in Crystalline Polyethylene

abstract:
  We investigate the presence of topological twistons in crystalline
polyethylene. We describe crystalline polyethylene with a model that couples
the torsional and longitudinal degrees of freedom of the polymeric chain by
means of a system of two real scalar fields. This model supports topological
twistons, which are described by exact and stable topological solutions that
appear when the interaction between torsional and longitudinal fields is
polynomial, containing up to the sixth power in the fields. We calculate the
energy of the topological twiston, and the result is in very good agreement
with the value obtained via molecular simulation.


title: Mechanism of Discordant Alternans in Spatially Homogeneous Tissue

abstract:
  Discordant alternans,the phenomenon of 2 separate cardiac tissue locations
exhibiting action potential duration (APD) alternans of opposite phase, appears
to be a potential mechanism for electrocardiographic T wave alternans, but its
initiation mechanism is unknown. We studied behavior of one- and two-
dimensional cardiac tissue spatially homogenous in all respects, including APD
restitution and conduction velocity restitution, using the Beeler Reuter ion
channel model. We found that discordant alternans was initiated when spatial
gradients of APD arose dynamically, such as from fixed rate pacing of a cable
end (sinus node scenario), or from fixed rate pacing at one site preceded by a
single excitation wavefront from another site (ectopic focus scenario). In the
sinus node scenario, conduction velocity restitution was necessary to initiate
discordant alternans. Alternating regimes of concordant and discordant
alternans arose along the length of the cable, with regimes delimited by nodes
of fixed APD. The number of observable nodes depended upon pacing rate and
tissue length. Differences in beat to beat conduction velocity values at steady
state were small. In the ectopic focus scenario, variable conduction velocity
was not required for induction of discrodant alternans. In both scenarios,
stability of node position was dependent upon electrotonic coupling. Other
mathematical models produced qualitatively similar results. We conclude that
spatial inhomogeneities of electrical restitution are not requiredd to produce
discordant alternans; rather, discordant alternans can arise dynamicaly from
interaction of APD and conduction veolocity resstitution with single site
pacing, or from APD restitution alone in two site pacing.

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


title:
Two Novel Special Relativistic Effects: Space Dilatation and Time
  Contraction

abstract:
  The conventional discussion of the observed distortions of space and time in
Special Relativity (the Lorentz-Fitzgerald Contraction and Time Dilatation) is
extended by considering observations, from a stationary frame, of : (i) objects
moving with constant velocity and uniformly illuminated during a short time
$\tau_L$ (their `Luminous Proper Time') in their rest frame; these may be
called `Transient Luminous Objects' and (ii) a moving, extended, array of
synchronised `equivalent clocks' in a common inertial frame. Application of the
Lorentz Transformation to (i) shows that such objects, observed from the
stationary frame with coarse time resolution in a direction perpendicular to
their direction of motion are seen to be at rest but {\it longer} in the
direction of the relative velocity $\vec{v}$ by a factor $1/\sqrt{1-(v/c)^2}$
(Space Dilatation) and to (ii) that the moving equivalent clock at any fixed
position in the rest frame of the stationary observer is seen to be running
{\it faster} than a similar clock at rest by the factor $1/\sqrt{1-(v/c)^2}$
(Time Contraction). All four space-time `effects' of Special Relativity are
simply classified in terms of the projective geometry of space-time, and the
close analogy of these effects to linear spatial perspective is pointed out.


title:
Efficient Methods for Handling Long-Range Forces in Particle-Particle
  Simulations

abstract:
  A number of problems arise when long-range forces, such as those governed by
Bessel functions, are used in particle-particle simulations. If a simple
cut-off for the interaction is used, the system may find an equilibrium
configuration at zero temperature that is not a regular lattice yet has an
energy lower than the theoretically predicted minimum for the physical system.
We demonstrate two methods to overcome these problems in Monte Carlo and
molecular dynamics simulations. The first uses a smoothed potential to truncate
the interaction in a single unit cell: this is appropriate for phenomenological
characterisations, but may be applied to any potential. The second is a new
method for summing the unmodified potential in an infinitely tiled periodic
system, which is in excess of 20,000 times faster than previous naive methods
which add periodic images in shells of increasing radius: this is suitable for
quantitative studies. Finally we show that numerical experiments which do not
handle the long-range force carefully may give misleading results: both of our
proposed methods overcome these problems.


title:
Ermakov-Lewis angles for one-parameter supersymmetric families of
  Newtonian free damping modes

abstract:
  We apply the Ermakov-Lewis procedure to the one-parameter damped modes
\tilde{y} recently introduced by Rosu and Reyes, which are related to the
common Newtonian free damping modes y by the general Riccati solution [H.C.
Rosu and M. Reyes, Phys. Rev. E 57, 4850 (1998), physics/9707019]. In
particular, we calculate and plot the angle quantities of this approach that
can help to distinguish these modes from the common y modes


title: Tumour Therapy with Particle Beams

abstract:
  Photons are exponentially attenuated in matter producing high doses close to
the surface. Therefore they are not well suited for the treatment of deep
seated tumours. Charged particles, in contrast, exhibit a sharp increase of
ionisation density close to the end of their range, the so-called Bragg-peak.
The depth of the Bragg-peak can be adjusted by varying the particle's energy.
In parallel with the large energy deposit the increase in biological
effectiveness for cell killing at the end of the range provides an ideal
scalpel for the surgeon effectively without touching the surface tissue.
Consequently proton therapy has gained a lot of ground for treating well
localized tumours. Even superior still are heavy ions, where the ionisation
pattern is increased by the square of their charge.


title:
Fast Algorithm for Finding the Eigenvalue Distribution of Very Large
  Matrices

abstract:
  A theoretical analysis is given of the equation of motion method, due to
Alben et al., to compute the eigenvalue distribution (density of states) of
very large matrices. The salient feature of this method is that for matrices of
the kind encountered in quantum physics the memory and CPU requirements of this
method scale linearly with the dimension of the matrix. We derive a rigorous
estimate of the statistical error, supporting earlier observations that the
computational efficiency of this approach increases with matrix size. We use
this method and an imaginary-time version of it to compute the energy and the
specific heat of three different, exactly solvable, spin-1/2 models and compare
with the exact results to study the dependence of the statistical errors on
sample and matrix size.


title:
Theory of acoustic analog of magneto-optic Kerr effect under
  magnon-phonon resonance

abstract:
  Theory of the acoustic analog of the polar Kerr effect is developed for an
inclined incidence of the p-type wave on the interface between isotropic
non-magnetic medium and ferromagnetic cubic crystal. Magnetic field dependences
of ellipticity and rotation of the polarization plane of the reflected wave
under magnon-phonon resonance are analysed in a weak-coupling approximation for
interaction of magnetic and elastic subsystems.


title:
Second-harmonic interferometric spectroscopy of the buried
  Si(111)-SiO$_2$ interface

abstract:
  The second-harmonic interferometric spectroscopy (SHIS) which combines both
amplitude (intensity) and phase spectra of the second-harmonic (SH) radiation
is proposed as a new spectroscopic technique being sensitive to the type of
critical points (CP's) of combined density of states at semiconductor surfaces.
The increased sensitivity of SHIS technique is demonstrated for the buried
Si(111)-SiO$_2$ interface for SH photon energies from 3.6 eV to 5 eV and allows
to separate the resonant contributions from $E^\prime_0/E_1$, $E_2$ and
$E^\prime_1$ CP's of silicon.


title: Signal Selection Based on Stochastic Resonance

abstract:
  Noise aids the encoding of continuous signals into pulse sequences by way of
stochastic resonance and endows the encoding device with a preferred frequency.
We study encoding by a threshold device based on the Ornstein-Uhlenbeck
process, equivalent to the leaky integrate-and-fire neuron model. Preferred
frequency, optimum noise intensity, and optimum signal-to-noise ratio are shown
to be linearly related to the AC amplitude of the input signal. The DC
component of the input tunes the device either into transmission (preferred
frequency nearly independent of signal amplitude) or selection mode (frequency
rising with amplitude). We argue that this behavior may facilitate selective
signal processing in neurons.


title:
CTMC calculations of electron capture and ionization in collisions of
  multiply charged ions with elliptical Rydberg atoms

abstract:
  We have performed classical trajectory Monte Carlo (CTMC) studies of electron
capture and ionization in multiply charged (Q=8) ion-Rydberg atom collisions at
intermediate impact velocities. Impact parallel to the minor and to the major
axis, respectively, of the initial Kepler electron ellipse has been
investigated. The important role of the initial electron momentum distribution
found for singly charged ion impact is strongly disminished for higher
projectile charge, while the initial spatial distribution remains important for
all values of Q studied.


title:
Influence of Random Irregularities on Quasi-Thermal Noise Spectrum of
  Plasma

abstract:
  The influence of random irregularities of electron density on quasi-thermal
noise spectra in plasma is considered in the paper. Quasi-thermal noise
spectrum of plasma in state near the thermal equilibrium is determined by
effective dielectric constant tensor. Presence of random irregularities change
dispersion law in plasma what cause the change in the shape of quasi-thermal
noise spectrum. Numerical estimation of noise spectra are fulfilled for both
conditions of ionospheric and solar wind plasma.


title: Dicluster Stopping in a Degenerate Electron Gas

abstract:
  In this paper we report on our theoretical studies of various aspects of the
correlated stopping power of two point-like ions (a dicluster) moving in close
but variable vicinity of each other in some metallic target materials the
latter being modelled by a degenerate electron gas with appropriate densities.
Within the linear response theory we have made a comprehensive investigation of
correlated stopping power, vicinage function and related quantities for a
diproton cluster in two metallic targets, aluminum and copper, and present
detailed and comparative results for three approximations to the electron gas
dielectric function, namely the plasmon-pole approximation without and with
dispersion as well as with the random phase approximation. The results are also
compared, wherever applicable, with those for an individual projectile.


title:
Restriction Condition of Gauge Transformation that Motion Equation of
  non-Abelian Gauge Field Must satisfy and Elimination of Higgs Mechanism

abstract:
  In the current theory of non-Abelian gauge field, we only claim the
invariability of Lagrangian, without claim the invariability of the motion
equation. This is inconsistent and irrational. It is proved that a restriction
relation between gauge potentials and group parameters must be satisfied in
order to ensure the gauge invariability of the motion equation of non-Abelian
gauge field, and the restriction relation is equivalent to the Faddeev--Popov
theory. The result leads to that the completely local gauge invariability is
violated but there still exists the incompletely local gauge invariability.
After the restriction relation is considered, the mass item of the non-Abelian
gauge fields can be added into the Lagrangian and motion equation directly
without violating gauge invariability. The corresponding W,T identity is
obtained and the theory is still renormalizable. In this way, the Higgs
mechanism becomes unnecessary. It means that we can reach a coincident theory
without the hypothesis of the Higgs particles again. The description of the
stander theory of particle physics can also be simplified greatly and the
problem of CP violation in strong interaction can also be solved thoroughly.


title: The role of acceleration and locality in the twin paradox

abstract:
  We study the role of acceleration in the twin paradox. From the coordinate
transformation that relates an accelerated and an inertial observer we find
that, from the point of view of the accelerated observer, the rate of the
differential lapses of time depends not only on the relative velocity, but also
on the product of the acceleration and the distance between the observers.
However, this result does not have a direct operational interpretation because
an observer at a certain position can measure only physical quantities that are
defined at the same position. For local measurements, the asymmetry between the
two observers can be attributed to the fact that noninertial coordinate
systems, contrary to inertial coordinate systems, can be correctly interpreted
only locally.


title:
Symmetry breaking and coarsening in spatially distributed evolutionary
  processes including sexual reproduction and disruptive selection

abstract:
  Sexual reproduction presents significant challenges to formal treatment of
evolutionary processes. A starting point for systematic treatments of
ecological and evolutionary phenomena has been provided by the gene centered
view of evolution which assigns effective fitness to each allele instead of
each organism. The gene centered view can be formalized as a dynamic mean field
approximation applied to genes in reproduction / selection dynamics. We show
that the gene centered view breaks down for symmetry breaking and pattern
formation within a population; and show that spatial distributions of organisms
with local mating neighborhoods in the presence of disruptive selection give
rise to such symmetry breaking and pattern formation in the genetic composition
of local populations. Global dynamics follows conventional coarsening of
systems with nonconserved order parameters. The results have significant
implications for the ecology of genetic diversity and species formation.


title:
Sommerfeld Particle in Static Magnetic Field: Tunneling and Delayed
  Untwisting in Cyclotron

abstract:
  Motion of a charged particle with finite size, described by Sommerfeld model,
in static magnetic field has two peculiar features: 1.) there is the effect of
tunneling - Sommerfeld particle overcomes the barrier and finds itself in the
forbidden, from classical point of view, area; 2.) the untwisting of trajectory
in cyclotron for Sommerfeld particle is strongly delayed compared to that of a
classical particle.


title:
What are the Hidden Quantum Processes In Einstein's Weak Principle of
  Equivalence?

abstract:
  We provide a quantum derivation of Einstein's Weak Equivalence Principle
(WEP) of general relativity using a new quantum gravity theory proposed by the
authors called Electro-Magnetic Quantum Gravity or EMQG (ref. 1). Newtonian
Inertia is a property of matter due to the strictly local electrical force
interactions contributed by each of the (electrically charged) elementary
particles of the mass with the surrounding (electrically charged) virtual
particles (virtual masseons) of the quantum vacuum. The sum of all the tiny
electrical forces (photon exchanges with the vacuum particles) originating in
each charged elementary particle of the accelerated mass is the source of the
total inertial force of a mass which opposes accelerated motion in Newton's law
'F = MA'. We found that gravity also involves the same 'inertial'
electromagnetic force component that exists in inertial mass. We propose that
Einstein's general relativistic Weak Equivalence Principle (WEP) originates
from common 'lower level' quantum vacuum processes occurring in both inertial
mass and gravitational mass, in accordance with the principles of quantum field
theory. Gravitational mass results from the quantum activities of both the
electrical force (photon exchanges) component and the pure gravitational force
(graviton exchanges) component, acting simultaneously on the elementary
particles that make up a mass.


title: Revitalization of an undergraduate physics program

abstract:
  This article describes the successful revitalization of an undergraduate
physics program. The areas of curriculum development, undergraduate research
experiences and advising and retention, to name a few, are emphasized in this
interconnecting and systematic approach whereby each and every effort combines
to get results. The program can be used by other physics departments wishing to
improve and expand undergraduate education in physics.


title: Lagrangians and Hamiltonians for High School Students

abstract:
  A discussion of Lagrangian and Hamiltonian dynamics is presented at a level
which should be suitable for advanced high school students. This is intended
for those who wish to explore a version of mechanics beyond the usual Newtonian
treatment in high schools, but yet who do not have advanced mathematical
skills.


title: An Underpinning for Space Time

abstract:
  We argue, that from a background pre space-time Zero Point Field, physical
space-time emerges on averaging over unphysical Compton scales.


title:
The rf control and detection system for PACO the parametric converter
  detector

abstract:
  In this technical note the rf control and detection system for a detector of
small harmonic displacements based on two coupled microwave cavities (PACO) is
presented. The basic idea underlying this detector is the principle of
parametric power conversion between two resonant modes of the system,
stimulated by the (small) harmonic modulation of one system parameter. In this
experiment we change the cavity length applying an harmonic voltage to a
piezo-electric crystal. The system can achieve a great sensitivity to small
harmonic displacements and can be an interesting candidate for the detection of
small, mechanically coupled, interactions (e.g. high frequency gravitational
waves).


title: Superheated drop as a neutron spectrometer

abstract:
  Superheated drops are known to vaporise when exposed to energetic nuclear
radiation since the discovery of bubble chamber. As the degree of superheat
increases in a given liquid, less and less energetic neutrons are required to
cause nucleation. This property of superheated liquids are being utilised to
develope the neutron spectromer. A new principle of neutron spectrometry using
Superheated liquid are developed and the developed principle has been tested by
Am-Be neutron source.


title: Efficiency of neutron detection of superheated drops of Freon-22

abstract:
  Neutron detection efficiency of superheated drops of Freon22 for neutrons
obtained from a 3Ci Am-Be neutron source has been reported in this paper.
Neutron detection efficiency of both F-22 and F-12 have been determined from
the measured nucleation rate using the volumetric method developed in our lab.
The result shows that the neutron detection efficiency of F-22 for the energy
spectrum obtained from Am-Be is almost double, while the life time is 58.6%
smaller than that of F-12, for a particular neutron flux of that source.


title:
On the Physical Cause and the Distance of Gamma Ray Bursts and Related
  Phenomena in the X-Rays and the Ultra-Violet

abstract:
  The modified Lorentz transformation of a distance-dependent special theory of
relativity - which will be briefly summarized - predicts the possibility of
superluminal velocity of very distantly moving material bodies to be connected
with the generation of Cerencov radiation off the quantum vacuum. It is shown
that vacuum Cerencov radiation due to the superluminal propagation of
extraterrestrial spaceprobes in the interstellar space would account for all
known properties of gamma ray bursts (GRBs) and the "afterglow" at lower
frequencies. Distances and other parameter prove to be calculable and the
theoretical results on these grounds to be in good accord with experiment.


title: Thermodynamic Equilibrium in Open Chemical Systems

abstract:
  The article presents new model of equilibrium in open chemical systems
suggesting a linear dependence of the reaction shift from equilibrium in
presence of the external thermodynamic force. Basic equation of this model
contains traditional logarithmic term and a non-traditional parabolic term. At
isolated equilibrium the non-traditional term equals to zero turning the whole
equation to the traditional form of constant equation. This term coincides with
the excessive thermodynamic function revealing linear relationship between
logarithm of the thermodynamic activity coefficient and reaction extent at open
equilibrium. Discovered relationship prompts us to use in many systems a
combination of the linearity coefficient and reaction shift from true
equilibrium rather then activity coefficients. The coefficient of linearity can
be found by thermodynamic computer simulation while the shift is an independent
variable defining the open equilibrium state. Numerical data obtained by
various simulation techniques proved premise of the method of chemical
dynamics.


title: Interstellar Hydrogen and Cosmic Background Radiation

abstract:
  It is shown that a collection of photons with nearly the same frequency
exhibits a "condensation" type of phenomenon corresponding to a peak intensity.
The observed cosmic background radiation can be explained from this standpoint
in terms of the radiation due to fluctuations in interstellar Hydrogen.


title: Coherent X-Ray Generation with Laser Driven Ions

abstract:
  Small parts of the electronic wavepacket of a multiple charged ion may still
tunnel through the high Coulomb barrier for a sufficiently intense laser field
of $10^{15}W/cm^2$ and higher. Solving numerically the corresponding
Schr\"odinger equation we find that the periodic recollisions of such a
wavepacket in the oscillating high power laser field will give rise to coherent
X-ray radiation in the multiple keV regime, i.e. substantially higher than
predicted or observed before.


title: Hyperfine spectra of CH3F nuclear spin conversion

abstract:
  A theoretical model of hyperfine spectra of nuclear spin conversion of
molecular isomers has been developed. The model takes into account the nuclear
spin-spin and spin-rotation interactions, as well as the saturation of
intramolecular mixing of molecular ortho and para states. The model has been
applied to hyperfine spectra of nuclear spin conversion in ^{13}CH3F molecules
subjected to an external electric field. Conditions under which the hyperfine
structure in the spectra can be resolved have been determined.


title: Quasispecies evolution on a fitness landscape with a fluctuating peak

abstract:
  A quasispecies evolving on a fitness landscape with a single peak of
fluctuating height is studied. In the approximation that back mutations can be
ignored, the rate equations can be solved analytically. It is shown that the
error threshold on this class of dynamic landscapes is defined by the time
average of the selection pressure. In the case of a periodically fluctuating
fitness peak we also study the phase-shift and response amplitude of the
previously documented low-pass filter effect. The special case of a small
harmonic fluctuation is treated analytically.


title: The Physical Origin of Intrinsic Bends in Double Helical DNA

abstract:
  The macroscopic curvature induced in the double helical B-DNA by regularly
repeated adenine tracts (A-tracts) is a long known, but still unexplained
phenomenon. This effect plays a key role in DNA studies because it is unique in
the amount and the variety of the available experimental information and,
therefore, is likely to serve as a gate to the unknown general mechanisms of
recognition and regulation of genome sequences. We report the results of
molecular dynamics simulations of a 25-mer B-DNA fragment with a sequence
including three A-tract phased with the helical screw. It represents the first
model system where properly directed static curvature emerges spontaneously in
conditions excluding any initial bias except the base pair sequence. The effect
has been reproduced in three independent MD trajectories of 10-20 ns with
important qualitative details suggesting that the final bent state is a strong
attractor of trajectories form a broad domain of the conformational space. The
ensemble of curved conformations, however, reveals significant microscopic
heterogeneity in contradiction to all existing theoretical models of bending.
Analysis of these unexpected observations leads to a new, significantly
different hypothesis of the possible mechanism of intrinsic bends in the double
helical DNA.


title:
Structures and Stabilities of CaO and MgO Clusters and Cluster Ions: An
  alternative interpretation of the experimental mass spectra

abstract:
  The structures and relative stabilities of doubly-charged nonstoichiometric
(CaO)$_n$Ca$^{2+}$ (n=1--29) cluster ions and of neutral stoichiometric
(MgO)$_n$ and (CaO)$_n$ (n=3,6,9,12,15,18) clusters are studied through {\em ab
initio} Perturbed Ion plus polarization calculations. The large
coordination-dependent polarizabilities of oxide anions favor the formation of
surface sites, making the critical cluster size where anions with bulk
coordination first appear larger than that found in the related case of alkali
halides. Thus, we show that there are substantial structural differences
between alkali halide and alkaline-earth oxide cluster ions, contrary to what
is suggested by the similarities in the experimental mass spectra. An
alternative interpretation of the magic numbers for the case of oxides is
proposed, which involves an explicit consideration of isomer structures
different from the ground states. A comparison with the previously studied
(MgO)$_n$Mg$^{2+}$ cluster ions shows that the emergence of bulklike structural
properties with size is slower for calcium oxide. Nevertheless, the structures
of the doubly charged clusters are rather similar for the two materials. On the
contrary, the study of the neutrals reveals interesting structural differences
between MgO and CaO, similar to those found in the case of alkali halides.


title: Optimal Mutation Rates in Dynamic Environments

abstract:
  In this paper we study the evolution of the mutation rate for simple
organisms in dynamic environments. A model with multiple fitness coding loci
tracking a moving fitness peak is developed and an analytical expression for
the optimal mutation rate is derived. Surprisingly it turns out that the
optimal mutation rate per genome is approximately independent of genome length,
something that also has been observed in nature. Simulations confirm the
theoretical predictions. We also suggest an explanation for the difference in
mutation frequency between RNA and DNA based organisms.


title: Characterization of a high-power tapered semiconductor amplifier system

abstract:
  We have characterized a semiconductor amplifier laser system which provides
up to 200mW output after a single-mode optical fiber at 780nm wavelength. The
system is based on a tapered semiconductor gain element, which amplifies the
output of a narrow-linewidth diode laser. Gain and saturation are discussed as
a function of operating temperature and injection current. The spectral
properties of the amplifier are investigated with a grating spectrometer.
Amplified spontaneous emission (ASE) causes a spectral background with a width
of 4nm FWHM. The ASE background was suppressed to below our detection limit by
a proper choice of operating current and temperature, and by sending the light
through a single-mode optical fiber. The final ASE spectral density was less
than 0.1nW/MHz, i.e. less than 0.2 % of the optical power. Related to an
optical transition linewidth of $\Gamma/2\pi=6$ MHz for rubidium, this gives a
background suppression of better than -82dB. An indication of the beam quality
is provided by the fiber coupling efficiency up to 59 %. The application of the
amplifier system as a laser source for atom optical experiments is discussed.


title: Contraction of a Bundle of Actin Filaments: 50 years after Szent-Gyorgyi

abstract:
  Biological systems are among the most challenging subjects for theoretical
physicists, as well as experimentalists or simulationists. Physical principles
should have been both constraints and guide-lines for the evolution of living
systems over billions of years. One generally aims at clarifying what physical
principles, possibly new ones, are behind the phenomena of biological interest
and at understanding how they work within the entire biological world. In the
present talk we describe an example of such an effort.
  Since the discovery of `superprecipitation' by Szent-Gyorgyi's group in
1940's, it has been a long puzzle how an assemblage of actin filaments with
random orientation can contract in the presence of the two-headed myosin
molecules undergoing actin-activated ATP-hydrolysis reaction. It is widely
accepted that during the contraction the two-headed myosin mediates the
relative sliding of two actin filaments whose polarity directions are not
parallel but rather anti-parallel. But this fact solely does not account for
the shortening. We propose a dynamical model which, upon numerical simulation,
exhibits the shortening of an bundle of the actin filaments which are initially
dirstributed randomly both in space along a line and in polarity direction. In
the course of shortening several clusters of actins appears along the bundle.
The model also shows the sorting of the actin filaments according to their
polarity in the late stage. These findings are in accordance with the recent
experiment by Takiguchi.


title: High-harmonic generation from a confined atom

abstract:
  The order of high harmonics emitted by an atom in an intense laser field is
limited by the so-called cutoff frequency. Solving the time-dependent
Schr\"odinger equation, we show that this frequency can be increased
considerably by a parabolic confining potential, if the confinement parameters
are suitably chosen.
  Furthermore, due to confinement, the radiation intensity remains high
throughout the extended emission range. All features observed can be explained
with classical arguments.


title: Nonlinear, ground-state, pump-probe spectroscopy

abstract:
  A theory of pump-probe spectroscopy is developed in which optical fields
drive two-quantum, Raman-like transitions between ground state sublevels. Three
fields are incident on an ensemble of atoms. Two of the fields act as the pump
field for the two-quantum transitions. The absorption or gain of an additional
probe field is monitored as a function of its detuning from one of the fields
which constitutes the pump field. Although the probe absorption spectrum
displays features common to those found in pump-probe spectroscopy of
single-quantum transitions, new interference effects are found to modify the
spectrum. Many of these features can be explained within the context of a
dressed atom picture.


title: Informational interpretation of quantum mechanics

abstract:
  Ascribing to inanimate matter a possibility to receive, work on and transfer
information allows us to explain quantum-mechanical phenomena including
"delayed-choice"- and "Einstein-Podolsky-Rosen (EPR)"-type experiments adhering
to the basis of local realism, and to suggest essentially new experiments with
microparticles and atoms in which information plays the principal role.


title:
Excitation of nonlinear two-dimensional wake waves in
  radially-nonuniform plasma

abstract:
  It is shown that an undesirable curvature of the wave front of
two-dimensional nonlinear wake wave excited in uniform plasma by a relativistic
charged bunch or laser pulse may be compensated by radial change of the
equilibrium plasma density.


title:
Molecular Dynamics Studies of Sequence-directed Curvature in Bending
  Locus of Trypanosome Kinetoplast DNA

abstract:
  The macroscopic curvature induced in the double helical B-DNA by regularly
repeated adenine tracts (A-tracts) plays an exceptional role in structural
studies of DNA because this effect presents the most well-documented example of
sequence specific conformational modulations. Recently, a new hypothesis of its
physical origin has been put forward, based upon the results of molecular
dynamics simulations of a 25-mer fragment with three A-tracts phased with the
helical screw. Its sequence, however, had never been encountered in
experimental studies, but was constructed empirically so as to maximize the
magnitude of bending in specific computational conditions. Here we report the
results of a similar investigation of another 25-mer B-DNA fragment now with a
natural base pair sequence found in a bent locus of a minicircle DNA. It is
shown that the static curvature of a considerable magnitude and stable
direction towards the minor grooves of A-tracts emerges spontaneously in
conditions excluding any initial bias except the base pair sequence. Comparison
of the bending dynamics of these two DNA fragments reveals both qualitative
similarities and interesting differences. The results suggest that the A-tract
induced bending obtained in simulations reproduces the natural phenomenon and
validates the earlier conclusions concerning its possible mechanism.


title: A Brief Note on the Magnetic Effects of the Electron

abstract:
  In this paper it is shown that a recent formulation of the electron in terms
of a Kerr-Newman type metric, exhibits a short range magnetic effect, as indeed
has been observed at Cornell, and also an Aharonov-Bohm type of an effect.


title:
Equivalence of Descriptions of Gravity In Both Curved and Flat
  Space-time

abstract:
  It is proved in the manuscript that as long as the proper coordinate
transformation is introduced,, the equations of geodetic lines described in
curved space-time can be transformed into the dynamic equations in flat
space-time, that is to say, the Einstein theory of gravitation and other
theories based on the curved space-time can be identically transformed into
flat space-time to describe. As an example, the Schwarzschild solution of the
spherical symmetry gravitational field is transformed into flat space-time to
study. The results show that there exists no any singularity in the all
processes and the whole space-time including at the point r=0. So it seems more
rational to discuss the problems of gravitation in flat space-time.


title:
A Comment on the Roe-Woodroofe Construction of Poisson Confidence
  Intervals

abstract:
  We consider the Roe-Woodroofe construction of confidence intervals for the
case of a Poisson distributed variate where the mean is the sum of a known
background and an unknown non-negative signal. We point out that the intervals
do not have coverage in the usual sense but can be made to have such with a
modification that does not affect the believability and other desirable
features of this attractive construction. A similar modification can be used to
provide coverage to the construction recently proposed by Cousins for the
Gaussian-with-boundary problem.


title:
Analysis of the "Big Bang" and the Resulting Outward Cosmic Expansion:
  Hubble - Einstein Cosmology vs. The Universal Exponential Decay

abstract:
  There is general agreement that the universe began with an "explosion" of
matter and energy at a "singularity", the "Big Bang". This paper analyses the
mechanics of that beginning and two alternative theories related to it: - The
Hubble-Einstein theory that that beginning created space itself, expanding and
carrying the universe's matter and energy with it, and - The Universal Decay
theory that the length, (L), dimensional aspect of all quantities in the
universe is exponentially decaying while the material universe is expanding
outward within passive, static "space".
  The Hubble-Einstein theory has long been accepted by consensus.
  The Universal Decay theory first propounded in "The Origin and Its Meaning"
in 1996 has since been validated by the Pioneer 10 and 11 "anomalous
acceleration" as well as by the theory's success in accounting for "dark
matter" and "dark energy". The same centrally- directed, distance-independent
acceleration of (8.74 +/- 1.33) x 10^-8 cm/s^2 that is the Pioneer "anomalous
acceleration" supplies the "additional gravitation" that "dark matter" is
sought to supply.
  The mass of the universe is calculated and the its "Schwarzschild Radius"
evaluated. The velocities and distances of cosmic objects in general are
calculated and plotted from the end of the "inflation" to the present. It
develops that there is a theoretical limit on how far back into the past can be
observed regardless of the quality of our instrumentation.