Leaching Behavior of Unirradiated High Temperature Reactor (HTR) UO2-ThO2 Mixed Oxides Fuel Particles

2003 ◽  
Vol 807 ◽  
Author(s):  
Catherine Landesman ◽  
Sandra Delaunay ◽  
Bernd Grambow
Keyword(s):  
Control Mechanism ◽  
Mixed Oxides ◽  
Accessible Surface Area ◽  
Leaching Behavior ◽  
Precipitation Mechanism ◽  
High Temperature Reactor ◽  
Accessible Surface ◽  
Fuel Particles ◽  
Ph Range ◽  
Hydroxide Phase

ABSTRACTThe dissolution rate of small UO2, ThO2 and mixed UO2–ThO2 particles, representative of unirradiated HTR fuel, are investigated in the pH range 1.7 to 5.5 under oxic conditions. For UO2 particles, the dissolution is kinetically control while for ThO2 particles, a solubility control mechanism seems to prevail for pH > 2. In the mixed oxides UO2–ThO2 particles, a selective release of uranium is observed, which could be either the result of a dissolution/precipitation mechanism in which thorium reprecipitate as oxide or hydroxide phase, or a result of a higher accessible surface area. Under oxic conditions, uranium may be considered as a tracer for the other soluble elements. So, assuming constant conditions with time, one can estimate from these preliminary results that unirradiated thorium based fuel kernels seem to present intrinsic confinement properties for 15000 years relative to soluble elements.

Leaching behaviour of non-irradiated and irradiated HTR UO2-ThO2 fuel particles under reducing conditions

2006 ◽  
Vol 932 ◽  
Author(s):  
Cyrille Alliot ◽  
Bernd Grambow
Keyword(s):  
Continuous Flow ◽  
Accessible Surface Area ◽  
Fuel Particle ◽  
Reducing Conditions ◽  
Flow Through ◽  
Leaching Behaviour ◽  
Alpha Radiolysis ◽  
Accessible Surface ◽  
Fuel Particles ◽  
Irradiated Fuel

ABSTRACTThe dissolution of irradiated HTR UO2-ThO2 fuel particle under reducing conditions was studied using a continuous flow-through reactor and compared to the dissolution of unirradiated fuel particle in the same condition. The irradiated fuel particle was leached for more than eight months. A fast 137Cs release was observed, corresponding to a labile fraction (“instant release fraction”). Then, a congruent leaching of 137Cs and 90Sr was measured corresponding to a matrix dissolution rate equal to 1.7 mg/m2/d. A slower release of 238Pu probably due to sorption phenomena is observed. Dissolution rates are 100-2000 times higher than for unirradiated material. We can conclude that alpha-radiolysis is responsible for this increase due to local oxic conditions. However we cannot exclude that due to irradiation the accessible surface area has been increased as well.The coating of this irradiated particle was equally studied to determine the presence of different radionuclides and their leaching properties of leaching

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

scholarly journals An automated protocol for modelling peptide substrates to proteases

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rodrigo Ochoa ◽  
Mikhail Magnitov ◽  
Roman A. Laskowski ◽  
Pilar Cossio ◽  
Janet M. Thornton
Keyword(s):  
Substrate Recognition ◽  
Accessible Surface Area ◽  
Conformational Sampling ◽  
Structural Determinants ◽  
Peptide Substrates ◽  
The Family ◽  
Protease Substrate ◽  
Peptide Complexes ◽  
Accessible Surface ◽  
Automated Protocol

Abstract Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.

scholarly journals PAMAM dendrimer: a pH-controlled nanosponge

2017 ◽  
Vol 95 (9) ◽  
pp. 991-998 ◽  
Author(s):  
Prabal K. Maiti
Keyword(s):  
Accessible Surface Area ◽  
Pamam Dendrimer ◽  
Low Ph ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Water Molecules ◽  
Accessible Volume ◽  
Accessible Surface ◽  
Solvent Accessible Surface ◽  
Ph Controlled

Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).

PUTRACER: A NOVEL METHOD FOR IDENTIFICATION OF CONTINUOUS-DOMAINS IN MULTI-DOMAIN PROTEINS

2013 ◽  
Vol 11 (01) ◽  
pp. 1340012 ◽  
Author(s):  
SEYED SHAHRIAR ARAB ◽  
MOHAMMADBAGHER PARSA GHARAMALEKI ◽  
ZAIDDODINE PASHANDI ◽  
REZVAN MOBASSERI
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Computer Assisted ◽  
Correct Assignment ◽  
Critical Boundary ◽  
Novel Method ◽  
Accessible Surface ◽  
A Chain

Computer assisted assignment of protein domains is considered as an important issue in structural bioinformatics. The exponential increase in the number of known three dimensional protein structures and the significant role of proteins in biology, medicine and pharmacology illustrate the necessity of a reliable method to automatically detect structural domains as protein units. For this aim, we have developed a program based on the accessible surface area (ASA) and the hydrogen bonds energy in protein backbone (HBE). PUTracer (Protein Unit Tracer) is built on the features of a fast top-down approach to cut a chain into its domains (contiguous domains) with minimal change in ASA as well as HBE. Performance of the program was assessed by a comprehensive benchmark dataset of 124 protein chains, which is based on agreement among experts (e.g. CATH, SCOP) and was expanded to include structures with different types of domain combinations. Equal number of domains and at least 90% agreement in critical boundary accuracy were considered as correct assignment conditions. PUTracer assigned domains correctly in 81.45% of protein chains. Although low critical boundary accuracy in 18.55% of protein chains leads to the incorrect assignments, adjusting the scales causes to improve the performance up to 89.5%. We discuss here the success or failure of adjusting the scales with provided evidences. Availability: PUTracer is available at http://bioinf.modares.ac.ir/software/PUTracer/

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