The goal of the present study was to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling time. For this purpose, we selected the 16-mer peptide BakBH3 as a model for study and carried out several samplings in explicit solvent. These samplings included an 8 μs trajectory (sampling S1); two 4 μs trajectories (sampling S2); four 2 μs trajectories (sampling S3); eight 1 μs trajectories (sampling S4); 16 0.5 μs trajectories (sampling S5), and 80 0.1 μs trajectories (sampling S6). Moreover, the 8 μs trajectory was further extended to 16 μs to have reference values of the diverse properties measured. The diverse samplings were compared qualitatively and quantitatively. Among the former, we carried out a comparison of the conformational profiles of the peptide using cluster analysis. Moreover, we also gained insight into the interchange among these structures along the sampling process. Among the latter, we computed the number of new conformational patterns sampled with time using strings defined from the conformations attained by each of the residues in the peptide. We also compared the locations and depths of the obtained minima on the free energy surface using principal component analysis. Finally, we also compared the helical profiles per residue at the end of the sampling process. The results suggest that a few short molecular dynamics trajectories may provide better sampling than one unique trajectory. Moreover, this procedure can also be advantageous to avoid getting trapped in a local minimum. However, caution should be exercised since short trajectories need to be long enough to overcome local barriers surrounding the starting point and the required sampling time depends on the number of degrees of freedom of the system under study. An effective way to gain insight into the minimum MD trajectory length is to monitor the convergence of different structural features, as shown in the present work.

No abstract

No abstract

The present study evaluates the technical and economical feasibility of the H2S elimination from an energy-rich gas using a full-scale biotrickling filter installed in a municipal waste water treatment plant. The study analyzes the continuous operation of a 4.5 months period, treating 80 m3 h-1 of biogas with an average H2S concentration of 3000 ppmv. The bioreactor was operated at a gas contact time of 180 seconds and maximum elimination capacities of 170 g H2S m-3 h-1 were obtained without any occurrence of neither biological nor mass transfer limitation. Elemental sulfur and sulfate were the main detected byproducts of the H2S treatment. The main drawback observed during the studied period was related to the air flow supply. This caused a removal efficiency decrease and an excess of sulfur production. A comparative cost-benefit analysis of the more applied chemical oxidation processes with the biological treatment was performed. Savings chemicals indicated that the payback time of the substitution treatment was about 4.5 years. Cost savings ranged between 11000€ per year, or 2.6€ per kg H2S treated. The results of this study have shown how to solve the main operational problems detected in the proposed system and the cost-benefit analysis suggests a significant benefit by replacing the current chemical treatment by the biological alternative not only from an environmental point of view, but also from an economical perspective.

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Graphical abstract Highlights The manuscript describes a computational study of the differential conformational behavior of the alanine dipeptide in diverse solvents including chloroform, methanol, DMSO, water and methyl formamide.  This study is important to understand the conformational behavior of peptides in diverse solvents, since the dialanine dipeptide is a model molecule to for peptides.  The manuscript discusses the role of inter-and intra-molecular interactions to understand the differential behavior of the molecule in the diverse solvents.2  This work aims to shed light into the controversy found in the literature between experimental and theoretical calculations of the dialanine dipeptide in water.  There has never been published a comparative computational study of the effect of the solvent on the molecule. AbstractIn general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra-and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents

Generalizing a property of isosceles trapezoids in the real plane, we obtain a characterization of inner product spaces (i.p.s.). The same property allows us to give a definition of a new orthogonality relation, which is studied in detail and generalizes many of the well-known orthogonalities, e.g. Pythagoras, Birkhoff and James. This orthogonality has the property of being empty for 2 dimensional spaces, but we give some examples of 3 dimensional spaces, not i.p.s., that admit couples of vectors relationed by our orthogonality.

New molecular descriptors, RED (Renyi entropy descriptors), based on the generalized entropies introduced by Renyi are presented. Topological descriptors based on molecular features have proven to be useful for describing molecular profiles. Renyi entropy is used as a variability measure to contract a feature-pair distribution composing the descriptor vector. The performance of RED descriptors was tested for the analysis of different sets of molecular distances, virtual screening, and pharmacological profiling. A free parameter of the Renyi entropy has been optimized for all the considered applications.

No abstract