158 research outputs found
Increased optical pathlength through aqueous media for the infrared microanalysis of live cells
The study of live cells using Fourier transform infrared spectroscopy (FTIR) and FTIR microspectroscopy (FT-IRMS) intrinsically yields more information about cell metabolism than comparable experiments using dried or chemically fixed samples. There are, however, a number of barriers to obtaining high-quality vibrational spectra of live cells, including correction for the significant contributions of water bands to the spectra, and the physical stresses placed upon cells by compression in short pathlength sample holders. In this study, we present a water correction method that is able to result in good-quality cell spectra from water layers of 10 and 12 μm and demonstrate that sufficient biological detail is retained to separate spectra of live cells based upon their exposure to different novel anti-cancer agents. The IR brilliance of a synchrotron radiation (SR) source overcomes the problem of the strong water absorption and provides cell spectra with good signal-to-noise ratio for further analysis. Supervised multivariate analysis (MVA) and investigation of average spectra have shown significant separation between control cells and cells treated with the DNA cross-linker PL63 on the basis of phosphate and DNA-related signatures. Meanwhile, the same control cells can be significantly distinguished from cells treated with the protein kinase inhibitor YA1 based on changes in the amide II region. Each of these separations can be linked directly to the known biochemical mode of
action of each agent.
Keywords: Synchrotron radiation (SR), Fourier transform infrared spectroscopy (FTIR), Infrared microspectroscopy (IRMS), Cancer, Single cell, Drug-cell interaction
Open-flow mixing: Experimental evidence for strange eigenmodes
We investigate experimentally the mixing dynamics in a channel flow with a
finite stirring region undergoing chaotic advection. We study the
homogenization of dye in two variants of an eggbeater stirring protocol that
differ in the extent of their mixing region. In the first case, the mixing
region is separated from the side walls of the channel, while in the second it
extends to the walls. For the first case, we observe the onset of a permanent
concentration pattern that repeats over time with decaying intensity. A
quantitative analysis of the concentration field of dye confirms the
convergence to a self-similar pattern, akin to the strange eigenmodes
previously observed in closed flows. We model this phenomenon using an
idealized map, where an analysis of the mixing dynamics explains the
convergence to an eigenmode. In contrast, for the second case the presence of
no-slip walls and separation points on the frontier of the mixing region leads
to non-self-similar mixing dynamics.Comment: 12 pages, 8 figures
Boltzmann-Shannon Entropy: Generalization and Application
The paper deals with the generalization of both Boltzmann entropy and
distribution in the light of most-probable interpretation of statistical
equilibrium. The statistical analysis of the generalized entropy and
distribution leads to some new interesting results of significant physical
importance.Comment: 5 pages, Accepted in Mod.Phys.Lett.
Consistent thermodynamics for spin echoes
Spin-echo experiments are often said to constitute an instant of
anti-thermodynamic behavior in a concrete physical system that violates the
second law of thermodynamics. We argue that a proper thermodynamic treatment of
the effect should take into account the correlations between the spin and
translational degrees of freedom of the molecules. To this end, we construct an
entropy functional using Boltzmann macrostates that incorporates both spin and
translational degrees of freedom. With this definition there is nothing special
in the thermodynamics of spin echoes: dephasing corresponds to Hamiltonian
evolution and leaves the entropy unchanged; dissipation increases the entropy.
In particular, there is no phase of entropy decrease in the echo. We also
discuss the definition of macrostates from the underlying quantum theory and we
show that the decay of net magnetization provides a faithful measure of entropy
change.Comment: 15 pages, 2 figs. Changed figures, version to appear in PR
Application of Information Theory in Nuclear Liquid Gas Phase Transition
Information entropy and Zipf's law in the field of information theory have
been used for studying the disassembly of nuclei in the framework of the
isospin dependent lattice gas model and molecular dynamical model. We found
that the information entropy in the event space is maximum at the phase
transition point and the mass of the cluster show exactly inversely to its
rank, i.e. Zipf's law appears. Both novel criteria are useful in searching the
nuclear liquid gas phase transition experimentally and theoretically.Comment: 5 pages, 5 figure
Deconvolving Smooth Residence Time Distributions from Raw Solute Transport Data
A residence time distribution (RTD) provides a complete model of longitudinal mixing effects that can be robustly derived from experimental solute transport data. Maximum entropy deconvolution has been shown to recover RTDs from preprocessed laboratory data. However, data preprocessing is time consuming and may introduce errors. Assuming data were recorded using sensors with a linear response, it should be possible to deconvolve raw data without preprocessing. This paper uses synthetically generated raw data to demonstrate that the quality of the deconvolved RTD remains satisfactory when preprocessing steps involving data cropping or calibration are skipped. Provided noise levels are relatively low, filtering steps may also be omitted. However, a rough subtraction of background concentration is recommended as a minimal preprocessing step. Deconvolved RTDs often include small-scale fluctuations that are inconsistent with a well-mixed fully turbulent system. These are believed to be associated with oversampling and/or unsuitable interpolation functions used in the maximum entropy deconvolution process. This paper describes a new interpolation function—linear interpolation with an automatic moving average (LAMA)—and demonstrates that, in combination with fewer sample points (e.g., 20), it enables smoother RTDs to be generated. The two improvements, to deconvolve raw data and to generate smoother RTDs, have been validated with experimental data. Raw solute transport traces collected from a river were deconvolved after background subtraction. The deconvolved RTDs compare favorably with those generated from the more traditional advection-dispersion equation (ADE) and aggregated dead zone (ADZ) models, but provide more detail of mixing processes. A laboratory manhole solute transport data set was deconvolved with and without preprocessing using 40 sample points and linear interpolation. The raw data were also deconvolved using 20 sample points and LAMA interpolation. The two sets of RTDs deconvolved from the raw data show the same mixing trends as those deconvolved from preprocessed data. However, those deconvolved with LAMA interpolation and 20 sample points are significantly smoother
Mobility Edge in Aperiodic Kronig-Penney Potentials with Correlated Disorder: Perturbative Approach
It is shown that a non-periodic Kronig-Penney model exhibits mobility edges
if the positions of the scatterers are correlated at long distances. An
analytical expression for the energy-dependent localization length is derived
for weak disorder in terms of the real-space correlators defining the
structural disorder in these systems. We also present an algorithm to construct
a non-periodic but correlated sequence exhibiting desired mobility edges. This
result could be used to construct window filters in electronic, acoustic, or
photonic non-periodic structures.Comment: RevTex, 4 pages including 2 Postscript figure
Isospin influences on particle emission and critical phenomenon in nuclear dissociation
Features of particle emission and critical point behavior are investigated as
functions of the isospin of disassembling sources and temperature at a moderate
freeze-out density for medium-size Xe isotopes in the framework of isospin
dependent lattice gas model. Multiplicities of emitted light particles,
isotopic and isobaric ratios of light particles show the strong dependence on
the isospin of the dissociation source, but double ratios of light isotope
pairs and the critical temperature determined by the extreme values of some
critical observables are insensitive to the isospin of the systems. Values of
the power law parameter of cluster mass distribution, mean multiplicity of
intermediate mass fragments (), information entropy () and Campi's
second moment () also show a minor dependence on the isospin of Xe
isotopes at the critical point. In addition, the slopes of the average
multiplicites of the neutrons (), protons (), charged particles
(), and IMFs (), slopes of the largest fragment mass number
(), and the excitation energy per nucleon of the disassembling source
() to temperature are investigated as well as variances of the
distributions of , , , , and . It
is found that they can be taken as additional judgements to the critical
phenomena.Comment: 9 Pages, 8 figure
NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates
This work reexamines seeded simulation results for NaCl nucleation from a supersaturated aqueous solution at 298.15 K and 1 bar pressure. We present a linear regression approach for analyzing seeded simulation data that provides both nucleation rates and uncertainty estimates. Our results show that rates obtained from seeded simulations rely critically on a precise driving force for the model system. The driving force vs. solute concentration curve need not exactly reproduce that of the real system, but it should accurately describe the thermodynamic properties of the model system. We also show that rate estimates depend strongly on the nucleus size metric. We show that the rate estimates systematically increase as more stringent local order parameters are used to count members of a cluster and provide tentative suggestions for appropriate clustering criteria
Near-LTE Linear Response Calculations with a Collisional-Radiative Model for He-like Al Ions
We investigate non-equilibrium atomic kinetics using a collisional- radiative model modified to include line absorption. Steady-state emission is calculated for He-like aluminum immersed in a specified radiation field having fixed deviations from a Planck spectrum. The calculated net emission is presented as a NLTE response matrix. In agreement with a rigorous general rule of non-equilibrium thermodynamics, the linear response is symmetric. We compute the response matrix for 1% and {+-} 50% changes in the photon temperature and find linear response over a surprisingly large range
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