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

Multilayer metamaterial absorbers inspired by perfectly matched layers

We derive periodic multilayer absorbers with effective uniaxial properties similar to perfectly matched layers (PML). This approximate representation of PML is based on the effective medium theory and we call it an effective medium PML (EM-PML). We compare the spatial reflection spectrum of the layered absorbers to that of a PML material and demonstrate that after neglecting gain and magnetic properties, the absorber remains functional. This opens a route to create electromagnetic absorbers for real and not only numerical applications and as an example we introduce a layered absorber for the wavelength of $8$~$\mu$m made of SiO$_2$ and NaCl. We also show that similar cylindrical core-shell nanostructures derived from flat multilayers also exhibit very good absorptive and reflective properties despite the different geometry

Time-Resolved Thickness and Shape-Change Quantification using a Dual-Band Nanoplasmonic Ruler with Sub-Nanometer Resolution

Time-resolved measurements of changes in the size and shape of nanobiological objects and layers are crucial to understand their properties and optimize their performance. Optical sensing is particularly attractive with high throughput and sensitivity, and label-free operation. However, most state-of-the-art solutions require intricate modeling or multiparameter measurements to disentangle conformational or thickness changes of biomolecular layers from complex interfacial refractive index variations. Here, we present a dual-band nanoplasmonic ruler comprising mixed arrays of plasmonic nanoparticles with spectrally separated resonance peaks. As electrodynamic simulations and model experiments show, the ruler enables real-time simultaneous measurements of thickness and refractive index variations in uniform and heterogeneous layers with sub-nanometer resolution. Additionally, nanostructure shape changes can be tracked, as demonstrated by quantifying the degree of lipid vesicle deformation at the critical coverage prior to rupture and supported lipid bilayer formation. In a broader context, the presented nanofabrication approach constitutes a generic route for multimodal nanoplasmonic optical sensing

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 ($A+A\to A$) and the pure annihilation-diffusion one ($A+A\to\emptyset$) with particles input ($\emptyset\to A$) at a rate $J$. For dimension $d\leq 2$, the dynamics strongly depends on the fluctuations while, for $d >2$, 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 $c(t,J,D) = (J/D)^{1/\delta}{\cal F}[(J/D)^{\Delta} Dt]$, where $D$ is the diffusion constant. The critical exponent $\delta$ and $\Delta$ are computed to all orders in $\epsilon=2-d$, where $d$ is the dimension of the system, while the scaling function $\cal F$ is computed to second order in $\epsilon$. For the one-dimensional case an exact analytical solution is provided which predictions are compared with the results of the renormalization group approach for $\epsilon=1$.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

Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

We have studied the dependence of the chemical reaction mechanism of L-lactate dehydrogenase (LDH) on the protonation state of titratable residues and on the level of the quantum mechanical (QM) description by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods; this methodology has allowed clarification of the timing of the hydride transfer and proton transfer components that hitherto had not been possible to state definitively.Ferrer Castillo, Silvia, [email protected], Silla Santos, Estanislao, [email protected] ; Tuñon Garcia de Vicuña, Ignacio Nilo, [email protected]

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

Alkenyl group is responsible for the disruption of microtubule network formation in human colon cancer cell line HT-29 cells

Alk(en)yl trisulfides (R-SSS-R′) are organosulfur compounds produced by crushed garlic and other Allium vegetables. We found that these compounds exhibit potent anticancer effects through the reaction with microtubules, causing cell cycle arrest. Nine alk(en)yl trisulfides including dimethyl trisulfide, diethyl trisulfide, dipropyl trisulfide (DPTS), dibutyl trisulfide, dipentyl trisulfide, diallyl trisulfide (DATS), dibutenyl trisulfide, dipentenyl trisulfide and allyl methyl trisulfide were synthesized and added to cultures of HT-29 human colon cancer cells at a concentration of 10 μM. The trisulfides with alkenyl groups such as DATS, but not those with alkyl groups, induced rapid microtubule disassembly at 30–60 min as well as cell cycle arrest during the mitotic phase approximately at 4 h after the treatment. Both DATS-induced microtubule disassembly and the cell cycle arrest were cancelled by the simultaneous treatment of the cancer cells with 2 mM L-cysteine, glutathione (GSH) or N-acetyl-L-cysteine. Reciprocally, L-buthionine-(S,R)-sulfoximine (500 μM), an inhibitor of GSH synthesis, enhanced the power of DATS in inducing the cell cycle arrest. These results indicate that alk(en)yl trisulfide react with sulfhydryl groups in cysteine residues of cellular proteins such as microtubule proteins. Thus, the present study provides evidence that trisulfides with alkenyl groups have potent anticancer activities, at least in part, directed toward microtubules. These findings suggest that alkenyl trisulfides and their structurally related compounds may provide novel and effective anticancer agents

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