1,721,018 research outputs found
MD simulation of water at imperfect platinum surfaces: Part 2 electrostatics
No full textThree-dimensional electrostatic potential distributions of a series of platinum\water interfaces were calculated from trajectories of molecular dynamics simulations. The electrostatic potential within the adsorbed layer shows periodic features reflecting the structure of water. It is negative at a point vacancy, due to the water molecule that occupies it. In Vacant adsorption sites the potential is close to zero, thus ion adsorption can take place there. The potential around platinum atoms at the step edge varies spatially between highly negative and positive values, therefore ion adsorption may not be possible there. However, the potential is generally close to zero near platinum atoms under the step edge, thus these atoms are open for adsorption. The corner platinum atoms of a monoatomic rectangular terrace are surrounded with highly negative and positive potentials along the steps, but they can be reached from the (011) direction because the potential is only slightly positive there. In a kink site the electrostatic potential is close to zero and the kinks are usually open towards the bulk, thus they can serve as starting points for adsorption processes or electrochemical reactions. (C) 1997 Elsevier Science S.A
MD simulation of water at imperfect platinum surfaces: Part I structure
No full textThe aim of our work was to study the water structure at surfaces that contain imperfections. A series of molecular dynamics simulations of water at Pt(100) walls were performed while systematically introducing different types of imperfections onto the surface. Point dislocations, monoatomic steps, kink sites and rectangular terraces were considered. It was found that imperfections can lead to vacant surface sites and can loosen the rigid hydrogen bonded structure of the adsorbed water layer. A vacancy is filled with a water molecule, whereas on the step edges, the water molecules sit on top sites. Some of them point their dipole moment vector and one of the OH vectors towards the surface. This new water configuration provides a further possibility for hydrogen bonding between molecules on the step edge and at the step side. The majority of the water molecules at the step sides are also on top positions on the next row of Pt-atoms of the basal plane. However, a number of water molecules are adsorbed to Pt- atoms within the step. Around the corner of a terrace water molecules occupy top sites. A kink site on the surface is empty, but there is a water molecule immediately next to the site, built into the step. The kink is also surrounded by two other water molecules sitting on top positions of the basal plane. This unique configuration serves as a structural evidence explaining the well known fact, that kink sites act as starting points for adsorption and metal deposition processes
Three-dimensional random walk simulation of diffusion controlled electrode processes: (II) Arrays of growing hemispheres
No full textA series of random walk simulations of diffusion controlled electrodeposition processes following instantaneous nucleation were performed to predict chronoamperometric current transients. At short times the current increases due to the growth of individual deposits, while at long times the current drops under the control of linear diffusion towards the surface. The current transient exhibits a maximum at intermediate times soon after the diffusion zones of the growing centres overlap. Relating the positions and heights of the peaks to simulation parameters we found that, apart from the chemical characteristics of the system, the current depends only on bulk concentration and nuclear number density. After rescaling the current transients according to these relations we were able to derive a simple analytical expression that characterises the whole process with sufficient accuracy. Comparing our results with existing analytical theories, we found certain conditions when they agree with our simulations. In this way, we were able to define the concentration range where these theories work satisfactorily
Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package
Full text linkCircular dichroism spectroscopy is a structural biology technique frequently applied to determine the secondary structure composition of soluble proteins. Our recently introduced computational analysis package SESCA aids the interpretation of protein circular dichroism spectra and enables the validation of proposed corresponding structural models. To further these aims, we present the implementation and characterization of a new Bayesian secondary structure estimation method in SESCA, termed SESCA_bayes. SESCA_bayes samples possible secondary structures using a Monte Carlo scheme, driven by the likelihood of estimated scaling errors and non-secondary-structure contributions of the measured spectrum. SESCA_bayes provides an estimated secondary structure composition and separate uncertainties on the fraction of residues in each secondary structure class. It also assists efficient model validation by providing a posterior secondary structure probability distribution based on the measured spectrum. Our presented study indicates that SESCA_bayes estimates the secondary structure composition with a significantly smaller uncertainty than its predecessor, SESCA_deconv, which is based on spectrum deconvolution. Further, the mean accuracy of the two methods in our analysis is comparable, but SESCA_bayes provides more accurate estimates for circular dichroism spectra that contain considerable non-SS contributions
Three-dimensional random walk simulations of diffusion controlled electrode processes: (I) A hemisphere, disc and growing hemisphere
No full textThe model presented in this article is based on a statistical approach where diffusion controlled electrode processes are simulated in terms of the random walk of an ensemble of particles. The algorithm simulates diffusion in three dimensions and yields data which are directly related to real world quantities. The validity of the model was tested by simulating diffusion controlled current and charge transients for a hemispherical electrode, disc electrode and for a growing hemispherical electrodeposit. In addition, the algorithm was used to generate concentration profiles. In all cases the results of the simulation were compared with analytical equations
How accurate is circular dichroism-based model validation?
Full text linkCircular dichroism (CD) spectroscopy is highly sensitive to the secondary structure (SS) composition of proteins. Several methods exist to either estimate the SS composition of a protein or to validate existing structural models using its CD spectrum. The accuracy and precision of these methods depend on the quality of both the measured CD spectrum and the used reference structure. Using a large reference protein set with high-quality CD spectra and synthetic data derived from this set, we quantified deviations from both ideal spectra and reference structures due to experimental limitations. We also determined the impact of these deviations on SS estimation, CD prediction, and SS validation methods of the SESCA analysis package. With regard to the CD spectra, our results suggest intensity scaling errors and non-SS contributions as the main causes of inaccuracies. These factors also can lead to overestimated model errors during validation. The errors of the used reference structures combine non-additively with errors caused by the CD spectrum, which increases the uncertainty of model validation. We have further shown that the effects of scaling errors in the CD spectrum can be nearly eliminated by appropriate re-scaling, and that the accuracy of model validation methods can be improved by accounting for typical non-SS contributions. These improvements have now been implemented within the SESCA package and are available at: https://www.mpibpc.mpg.de/sesca
MD simulation of water at imperfect platinum surfaces. III. Hydrogen bonding
No full textThe hydrogen bonding of interfacial water in the vicinity of different surface imperfections of Pt(100) surfaces was analysed from trajectories obtained from molecular dynamics simulations. Two alternative H-bond definitions-an energetic and a geometric-were used. We found that the number of hydrogen bonds for water molecules at different surface imperfections decreases as the number of neighbouring platinum atoms increases, although the number of neighbouring water molecules does not always decrease in a parallel way. Thus the effect of surface imperfections can be explained partly in terms of geometric reasons, but our analysis showed that the ordering effect of the platinum atoms also plays an important role. In certain positions at step edges there exist water pairs with stable configurations but with positive pair energies. Their existence is obviously due to the ordering effect of the platinum surface. These water pairs were found to have a very symmetrical arrangement pointing with their hydrogens almost towards each other
3-Nets realizing a diassociative loop in a projective plane
Full text linkA 3-net of order n is a finite incidence structure consisting of points and three pairwise disjoint classes of lines, each of size n, such that every point incident with two lines from distinct classes is incident with exactly one line from each of the three classes. The current interest around 3-nets (embedded) in a projective plane (Formula presented.) , defined over a field (Formula presented.) of characteristic p, arose from algebraic geometry; see Falk and Yuzvinsky (Compos Math 143:1069–1088, 2007), Miguel and Buzunáriz (Graphs Comb 25:469–488, 2009), Pereira and Yuzvinsky (Adv Math 219:672–688, 2008), Yuzvinsky (140:1614–1624, 2004), and Yuzvinsky (137:1641–1648, 2009). It is not difficult to find 3-nets in (Formula presented.) as far as (Formula presented.). However, only a few infinite families of 3-nets in (Formula presented.) are known to exist whenever (Formula presented.) , or (Formula presented.). Under this condition, the known families are characterized as the only 3-nets in (Formula presented.) which can be coordinatized by a group; see Korchmáros et al. (J Algebr Comb 39:939–966, 2014). In this paper we deal with 3-nets in (Formula presented.) which can be coordinatized by a diassociative loop G but not by a group. We prove two structural theorems on G. As a corollary, if G is commutative then every non-trivial element of G has the same order, and G has exponent 2 or 3 where the exponent of a finite diassociative loop is the maximum of the orders of its elements. We also discuss the existence problem for such 3-nets
Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models
Full text linkCircular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.Alexander von Humboldt-Stiftung https://doi.org/10.13039/100005156Max Plank Societ
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
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