303 research outputs found
Scattering of Dirac particles from non-local separable potentials: the eigenchannel approach
An application of the new formulation of the eigenchannel method [R.
Szmytkowski, Ann. Phys. (N.Y.) {\bf 311}, 503 (2004)] to quantum scattering of
Dirac particles from non-local separable potentials is presented. Eigenchannel
vectors, related directly to eigenchannels, are defined as eigenvectors of a
certain weighted eigenvalue problem. Moreover, negative cotangents of
eigenphase-shifts are introduced as eigenvalues of that spectral problem.
Eigenchannel spinor as well as bispinor harmonics are expressed throughout the
eigenchannel vectors. Finally, the expressions for the bispinor as well as
matrix scattering amplitudes and total cross section are derived in terms of
eigenchannels and eigenphase-shifts. An illustrative example is also provided.Comment: Revtex, 9 pages, 4 figures, published versio
A review of size and geometrical factors influencing resonant frequencies in metamaterials
Although metamaterials and so-called left-handed media have originated from theoretical considerations, it is only by their practical fabrication and the measurement of their properties that they have gained credibility and can fulfil the potential of their predicted properties. In this review we consider some of the more generally applicable fabrication methods and changes in geometry as they have progressed, exhibiting resonant frequencies ranging from radio waves to the visible optical region
A renormalization group study of a class of reaction-diffusion model, with particles input
We study a class of reaction-diffusion model extrapolating continuously
between the pure coagulation-diffusion case () and the pure
annihilation-diffusion one () with particles input
() at a rate . For dimension , the dynamics
strongly depends on the fluctuations while, for , the behaviour is
mean-field like. The models are mapped onto a field theory which properties are
studied in a renormalization group approach. Simple relations are found between
the time-dependent correlation functions of the different models of the class.
For the pure coagulation-diffusion model the time-dependent density is found to
be of the form , where
is the diffusion constant. The critical exponent and are
computed to all orders in , where is the dimension of the
system, while the scaling function is computed to second order in
. For the one-dimensional case an exact analytical solution is
provided which predictions are compared with the results of the renormalization
group approach for .Comment: Ten pages, using Latex and IOP macro. Two latex figures. Submitted to
Journal of Physics A. Also available at
http://mykonos.unige.ch/~rey/publi.htm
Ligand-Receptor Interactions
The formation and dissociation of specific noncovalent interactions between a
variety of macromolecules play a crucial role in the function of biological
systems. During the last few years, three main lines of research led to a
dramatic improvement of our understanding of these important phenomena. First,
combination of genetic engineering and X ray cristallography made available a
simultaneous knowledg of the precise structure and affinity of series or
related ligand-receptor systems differing by a few well-defined atoms. Second,
improvement of computer power and simulation techniques allowed extended
exploration of the interaction of realistic macromolecules. Third, simultaneous
development of a variety of techniques based on atomic force microscopy,
hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or
flexible transducers yielded direct experimental information of the behavior of
single ligand receptor bonds. At the same time, investigation of well defined
cellular models raised the interest of biologists to the kinetic and mechanical
properties of cell membrane receptors. The aim of this review is to give a
description of these advances that benefitted from a largely multidisciplinar
approach
Absorption Enhancement in Lossy Transition Metal Elements of Plasmonic Nanosandwiches
Combination of catalytically active transition metals and surface plasmons offers a promising way to drive chemical reactions by converting incident visible light into energetic electron-hole pairs acting as a mediator. In such a reaction enhancement scheme, the conversion efficiency is dependent on light absorption in the metal. Hence, increasing absorption in the plasmonic structure is expected to increase generation of electron-hole pairs and, consequently, the reaction rate. Furthermore, the abundance of energetic electrons might facilitate new reaction pathways. In this work we discuss optical properties of homo- and heterometallic plasmonic nanosandwiches consisting of two parallel disks made of gold and palladium. We show how near-field coupling between the sandwich elements can be used to enhance absorption in one of them. The limits of this enhancement are investigated using finite-difference time-domain simulations. Physical insight is gained through a simple coupled dipole analysis of the nanostructure. For small palladium disks (compared to the gold disk), total absorption enhancement integrated over the near visible solar AM 1.5 spectrum is 8-fold, while for large palladium disks, similar in size to the gold one, it exceeds three
Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038−2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics methods. Although good results were reported by Mongan et al. on application of the standard method to the hen egg-white lysozyme (HEWL) system, residues which possess strong interactions with neighboring groups tend to converge slowly, resulting in the reported inconsistencies for predicted pKa values, as highlighted by the authors. The application of the coupled method described in this study to the HEWL system displays improvements over the standard version of the method, with the improved sampling leading to faster convergence and producing pKa values in closer agreement to those obtained experimentally for the more slowly converging residues
Redox Modulation at Work: Natural Phytoprotective Polysulfanes From Alliums Based on Redox-Active Sulfur
Purpose of review: This article provides a brief overview of natural phytoprotective products of allium with a special focus on the therapeutic potential of diallyl polysulfanes from garlic, their molecular targets and their fate in the living organisms. A comprehensive overview of antimicrobial and anticancer properties of published literature is presented for the reader to understand the effective concentrations of polysulfanes and their sensitivity towards different human pathogenic microbes, fungi, and cancer cell lines. Recent findings: The article finds polysulfanes potentials as new generation novel antibiotics and chemo preventive agent. The effective dose rates of polysulfanes for antimicrobial properties are in the range of 0.5–40 mg/L and for anticancer 20–100 μM. The molecular targets for these redox modulators are mainly cellular thiols as well as inhibition and/or activation of certain cellular proteins in cancer cell lines. Summary: Antimicrobial and anticancer activities of polysulfanes published in the literature indicate that with further development, they could be promising candidates for cancer prevention due to their selectivity towards abnormal cells
Mathematical modeling of the dynamic storage of iron in ferritin
<p>Abstract</p> <p>Background</p> <p>Iron is essential for the maintenance of basic cellular processes. In the regulation of its cellular levels, ferritin acts as the main intracellular iron storage protein. In this work we present a mathematical model for the dynamics of iron storage in ferritin during the process of intestinal iron absorption. A set of differential equations were established considering kinetic expressions for the main reactions and mass balances for ferritin, iron and a discrete population of ferritin species defined by their respective iron content.</p> <p>Results</p> <p>Simulation results showing the evolution of ferritin iron content following a pulse of iron were compared with experimental data for ferritin iron distribution obtained with purified ferritin incubated <it>in vitro </it>with different iron levels. Distinctive features observed experimentally were successfully captured by the model, namely the distribution pattern of iron into ferritin protein nanocages with different iron content and the role of ferritin as a controller of the cytosolic labile iron pool (cLIP). Ferritin stabilizes the cLIP for a wide range of total intracellular iron concentrations, but the model predicts an exponential increment of the cLIP at an iron content > 2,500 Fe/ferritin protein cage, when the storage capacity of ferritin is exceeded.</p> <p>Conclusions</p> <p>The results presented support the role of ferritin as an iron buffer in a cellular system. Moreover, the model predicts desirable characteristics for a buffer protein such as effective removal of excess iron, which keeps intracellular cLIP levels approximately constant even when large perturbations are introduced, and a freely available source of iron under iron starvation. In addition, the simulated dynamics of the iron removal process are extremely fast, with ferritin acting as a first defense against dangerous iron fluctuations and providing the time required by the cell to activate slower transcriptional regulation mechanisms and adapt to iron stress conditions. In summary, the model captures the complexity of the iron-ferritin equilibrium, and can be used for further theoretical exploration of the role of ferritin in the regulation of intracellular labile iron levels and, in particular, as a relevant regulator of transepithelial iron transport during the process of intestinal iron absorption.</p
Influence of the Escherichia coli oxyR gene function on λ prophage maintenance
In Escherichia coli hosts, hydrogen peroxide is one of the factors that may cause induction of λ prophage. Here, we demonstrate that H2O2-mediated λ prophage induction is significantly enhanced in the oxyR mutant host. The mRNA levels for cI gene expression were increased in a λ lysogen in the presence of H2O2. On the other hand, stimulation of the pM promoter by cI857 overproduced from a multicopy plasmid was decreased in the ΔoxyR mutant in the presence of H2O2 but not under normal growth conditions. The purified OxyR protein did bind specifically to the pM promoter region. This binding impaired efficiency of interaction of the cI protein with the OR3 site, while stimulating such a binding to OR2 and OR1 sites, in the regulatory region of the pM promoter. We propose that changes in cI gene expression, perhaps in combination with moderately induced SOS response, may be responsible for enhanced λ prophage induction by hydrogen peroxide in the oxyR mutant. Therefore, OxyR seems to be a factor stimulating λ prophage maintenance under conditions of oxidative stress. This proposal is discussed in the light of efficiency of induction of lambdoid prophages bearing genes coding for Shiga toxins
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