Search results for "Biomolecule"
showing 10 items of 666 documents
Algorithms for {K, s+1}-potent matrix constructions
2013
In this paper, we deal with {K, s + 1}-potent matrices. These matrices generalize all the following classes of matrices: k-potent matrices, periodic matrices, idempotent matrices, involutory matrices, centrosymmetric matrices, mirrorsymmetric matrices, circulant matrices, among others. Several applications of these classes of matrices can be found in the literature. We develop algorithms in order to compute {K, s + 1}-potent matrices and {K, s + 1}-potent linear combinations of {K, s + 1}-potent matrices. In addition, some examples are presented in order to show the numerical performance of the method. (C) 2012 Elsevier B.V. All rights reserved.
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
2016
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy
2018
Abstract Proteins have distinctive dynamical properties, characterized by the fluctuations of protein molecules among the different minima of their energy landscape. These fluctuations, progressively activated for temperature values larger than ~180 K, lead to a steep increase in the temperature dependence of all measurable dynamical properties. This phenomenon is known as Protein Dynamical Transition and, in spite of the intense studies due to its importance in protein function and to the relation with the fascinating fundamental thermodynamics of complex systems, many aspects of it are not yet clearly understood. Among these, the relationship with the properties of the external solvent an…
Vibrational spectroscopy of trans and cis deuterated formic acid (HCOOD): Anharmonic calculations and experiments in argon and neon matrices
2010
The absorption spectra of trans and cis conformers of deuterated formic acid (HCOOD) isolated in argon and neon matrices are analyzed in the mid-infrared and near-infrared spectral regions (7900–450 cm � 1 ). Vibrational excitation by narrow-band IR radiation is used to convert the lower-energy trans conformer to the higher-energy cis form. A large number of overtone and combination bands are identified. The results of anharmonic vibrational calculations (CC-VSCF) for both conformers are reported and compared to the experimental spectra.
Resistance to Nano-Based Antifungals Is Mediated by Biomolecule Coronas.
2018
Fungal infections are a growing global health and agricultural threat, and current chemical antifungals may induce various side-effects. Thus, nanoparticles are investigated as potential novel antifungals. We report that nanoparticles' antifungal activity strongly depends on their binding to fungal spores, focusing on the clinically important fungal pathogen Aspergillus fumigatus as well as common plant pathogens, such as Botrytis cinerea. We show that nanoparticle-spore complex formation was enhanced by the small nanoparticle size rather than the material, shape or charge, and could not be prevented by steric surface modifications. Fungal resistance to metal-based nanoparticles, such as Zn…
Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection
2013
Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic …
Biopolymer-Targeted Adsorption onto Halloysite Nanotubes in Aqueous Media.
2017
Studies on the adsorption of biopolymers onto halloysite nanotubes (HNTs) in water were conducted. Three polymers with different charges-anionic (pectin), neutral (hydroxypropyl cellulose), and cationic (chitosan)-were chosen. The thermodynamic parameters for the adsorption of polymers onto the HNT surface were determined by isothermal titration calorimetry (ITC). The experimental data were interpreted based on a Langmuir adsorption model. The standard variations in free energy, enthalpy, and entropy of the process were obtained and discussed. Turbidimetry was used to evaluate the stability of functionalized nanoparticles in water. The ζ-potential clarified the surface charge properties of …
Synthetic nanopores with fixed charges: An electrodiffusion model for ionic transport
2003
Synthetic nanopores with fixed charges exhibit ionic equilibrium and transport properties that resemble those displayed by biological ion channels. We present an electrodiffusion model based on the Nernst-Planck flux equations, which allows for a qualitative description of the steady state ionic transport through a nanopore when the membrane fixed charges and all mobile carriers (including the water ions) are properly taken into account. In particular, we study the current-voltage curve, the electrical conductance, the reversal potential (a measure of the nanopore ionic selectivity), as well as the flux inhibition by protons and divalent cations in the nanopore. The model clearly shows how …
Trapping of 27 bp–8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis
2006
Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip electrodes on the trapping efficiency have been investigated. Using finite element method simulations in conjunction with the analysis of the experimental data, the polarizabilities of the different size DNA fragments have been calculated for different frequencies. Also the immobilization of trapped hexanethiol- and DTPA-modified 140 nm long DNA to the end of gold nanoelectrodes was experimentally quantified and the observations were supported by density functiona…
Ultrastable, Uniform, Reproducible, and Highly Sensitive Bimetallic Nanoparticles as Reliable Large Scale SERS Substrates
2015
International audience; A strong interest exists in developing surface-enhanced Raman spectroscopy (SERS) substrates that uniformly enhance Raman signals of chemical and biological molecules over large scales while reaching the detection limit of trace concentrations. Even though the resonant excitation of localized surface plasmons of single or assembled metallic nanoparticles used in SERS substrates can induce large electromagnetic fields, these substrates display a SERS activity which suffers from poor reproducibility, uniformity, and stability, preventing them from being reliable for applications. In this work, we have developed self-supported large scale Ag/Au bimetallic SERS-active su…