Search results for " Biophysics"
showing 10 items of 136 documents
Non-equilibrium Markov state modeling of periodically driven biomolecules
2019
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external p…
The role of network connectivity on epileptiform activity.
2021
AbstractA number of potentially important mechanisms have been identified as key players to generate epileptiform activity, such as genetic mutations, activity-dependent alteration of synaptic functions, and functional network reorganization at the macroscopic level. Here we study how network connectivity at cellular level can affect the onset of epileptiform activity, using computational model networks with different wiring properties. The model suggests that networks connected as in real brain circuits are more resistant to generate seizure-like activity. The results suggest new experimentally testable predictions on the cellular network connectivity in epileptic individuals, and highligh…
Application of model quality evaluation to systems biology
2008
Application of model quality evaluation to the quasispecies models is presented. These models are useful for the analysis of the DNA and RNA evolution and for the description of the population dynamics of viruses and bacteria. An estimate of the parameters together with their interval of variability is computed and the quality evaluation is tested on the basis of the model prediction error capability.
Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.
2012
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and …
Ab initio determination of the ionization potentials of DNA and RNA nucleobases
2006
Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra. Daniel.Roca@uv.es Mercedes.Rubio@uv.es Manuela.Merchan@uv.es Luis.Serrano@uv.es
Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage
2018
WOS:000452343100012; International audience; Background: Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn2+ protection of DNA repair enzymes. Methods: Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coif and DR. slip knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette. Results: DR1533 contains an N-terminal SRA…
Multi-objective optimization of nitinol stent design.
2017
Nitinol stents continuously experience loadings due to pulsatile pressure, thus a given stent design should possess an adequate fatigue strength and, at the same time, it should guarantee a sufficient vessel scaffolding. The present study proposes an optimization framework aiming at increasing the fatigue life reducing the maximum strut strain along the structure through a local modification of the strut profile.The adopted computational framework relies on nonlinear structural finite element analysis combined with a Multi Objective Genetic Algorithm, based on Kriging response surfaces. In particular, such an approach is used to investigate the design optimization of planar stent cell.The r…
Electrical characterization of deoxyribonucleic acid hybridization in metal-oxide-semiconductor-like structures
2012
In this work, metal-oxide-semiconductor (MOS)-like sensors in which deoxyribonucleic acid (DNA) strands are covalently immobilized either on Si oxide or on a gold surface were electrically characterized. Si oxide fabrication process allowed us to have a surface insensitive to the solution pH. A significant shift in the flat band voltage was measured after single strand DNA immobilization (+0.47 +/- 0.04 V) and after the complementary strand binding (+0.07 +/- 0.02 V). The results show that DNA sensing can be performed using a MOS structure which can be easily integrated in a more complex design, thus avoiding the problems related to the integration of micro-electrochemical cells.
Context-Aware Visual Exploration of Molecular Datab
2006
Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the res…
Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells
2006
Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual insp…