1,720,960 research outputs found
NuSol — Numerical solver for the 3D stationary nuclear Schrödinger equation
Full text linkAbstractThe classification of short hydrogen bonds depends on several factors including the shape and energy spacing between the nuclear eigenstates of the hydrogen.Here, we describe the NuSol program in which three classes of algorithms were implemented to solve the 1D, 2D and 3D time independent nuclear Schrödinger equation. The Schrödinger equation was solved using the finite differences based Numerov’s method which was extended to higher dimensions, the more accurate pseudo-spectral Chebyshev collocation method and the sinc discrete variable representation by Colbert and Miller. NuSol can be applied to solve the Schrödinger equation for arbitrary analytical or numerical potentials with focus on nuclei bound by the potential of their molecular environment. We validated the methods against literature values for the 2D Henon–Heiles potential, the 3D linearly coupled sextic oscillators and applied them to study hydrogen bonding in the malonaldehyde derivate 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione.With NuSol, the extent of nuclear delocalization in a given molecular potential can directly be calculated without relying on linear reaction coordinates in 3D molecular space.Program summaryProgram title: NuSolCatalogue identifier: AEXO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEXO_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GPL 3.0No. of lines in distributed program, including test data, etc.: 195332No. of bytes in distributed program, including test data, etc.: 4489808Distribution format: tar.gzProgramming language: Python 2.7, C.Computer: PC.Operating system: Linux.RAM: 0.1–40 GBClassification: 16.1.External routines: FEAST v2.1 [1][2] (included in the distribution file).Nature of problem: Solving the 3D nuclear Schrödinger EquationSolution method: Grid solver based on Numerov’s method, Chebyshev collocation and sinc() DVR for 1D/2D/3D potential gridsRunning time: System dependentReferences:[1]E. Polizzi, Density-Matrix-Based Algorithms for Solving Eigenvalue Problems, Phys. Rev. B. Vol. 79, 115112 (2009)[2]E. Polizzi, A High-Performance Numerical Library for Solving Eigenvalue Problems: FEAST solver User’s guide, arxiv.org/abs/1203.4031 (2012)
AMBER-DYES: Characterization of charge fluctuations and force field parameterization of fluorescent dyes for molecular dynamics simulations.
Full text linkRecent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized π-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories
Molecular dynamics simulations of alpha-synuclein ensemble FRET measurements from different force fields.
No full textThe Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution
Full text linkThere has been considerable debate on the existence of a low-barrier hydrogen bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. ( Proc. Natl. Acad. Sci., U. S. A., 2009, 106, 440−444) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased hydrogen bond length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large 1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 hydrogen bonds and crystal water positions for the protonated Arg52 residue in free MD simulations and predicted an Arg52 pKa upshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical 1H chemical shifts that agree with NMR solution data. We also calculated the effect of the Arg52 protonation state on the LBHB in 3D nuclear equilibrium density calculations. Only the charged crystal structure in vacuum supports a LBHB if Arg52 is neutral in PYP at the previously reported level of theory ( J. Am. Chem. Soc., 2014, 136, 3542−3552). We attribute the anomalies in the interpretation of the neutron data to a shift of the potential minimum, which does not involve nuclear quantum effects and is transferable beyond the Yamaguchi structure
Transient secondary and tertiary structure formation kinetics in the intrinsically disordered state of α-Synuclein from atomistic simulations.
Full text linkIn the absence of a stable fold, transient secondary structure kinetics define the native state of the prototypical and pharmacologically relevant intrinsically disordered protein (IDP) α-Synuclein (aS). Here, we investigate kinetics preventing ordering and possibly pathogenic β-sheet aggregation. Interestingly, transient β-sheets form frequently at sub μs time scales precisely at the positions observed in aS amyloid fibrils. The formation kinetics competes with rapid secondary structure dissociation rates, thus explaining the low secondary structure content. The fast secondary structure dissociation times are very similar to the dynamics of tertiary structure rearrangements. These findings suggest that the fast dissociation kinetics slows down conformational selection processes for aS aggregation, which may be a general mechanism controlling the aggregation kinetics of IDPs
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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