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The effect of solution temperature and the determination of the kinetic parameters of methylene blue (MB) adsorption onto cereal chaff were performed to understand the adsorption mechanism. The pseudo-second order kinetic model was fitted to the experimental data and found it was good to predict the adsorption behavior using nonlinear regressive method, suggesting that the mechanism may be a chemisorption...
The shape that organic molecules such as biopolymers form within organic systems largely determines the function said molecules perform. RNA is a biopolymer that plays a central part in several stages of protein synthesis, and also has structural, functional, and regulatory roles in the cell. In an ab initio case most common structure prediction techniques employ minimization of the free energy of...
Computational ribonucleomics of heavy metal stress tolerant Bacillus sp. strain SJ-101 16SrRNA gene has led to the identification of a novel small non-coding RNA (sRNA) and promoter-like sequences within 3' region of the gene. Using RNAz web server, a 123 bp long functional sRNA with significant thermodynamic stability (Energy contribution: -25.2) and evolutionary conservation (structure conservation...
A photochemical reaction is initiated by a charge separation process in the reaction center (RC) complex. Major research in this regard is to analyze the light driven electron transfer and to study the response of the molecule in which the RC is embedded, stabilizing the charge separation process in photosynthesis. In research related to artificial photosynthesis, modeling and simulation of highly...
A clear understanding of the complicated interactions among various key ingredients of flux will be very beneficial for developing future high performance solder pastes. In this work, the group contribution method was introduced to estimate and predict the properties of compound and their interactions, especially, the chemical interactions. Based on the assumption that the effects of the individual...
RNA has important structural, functional, and regulatory parts in the cell as well as a critical role in multiple stages of protein synthesis. An RNA molecule's shape largely determines its function in an organic system. Accordingly, computational RNA structural prediction methods are of significant interest. For ab initio cases where only an RNA sequence is known, structure prediction techniques...
The RNA secondary structure design (SSD) problem is a recently emerging research topic motivated by applications such as customized drug design and the self-assembly of RNA nano-objects. This paper presents a novel local search algorithm, rnaDesign for SSD solving. An evaluation of the algorithm performance in terms of sequence affinity and structure specificity is made through comparison with another...
A model to simulate the transport and fate of methane gas released in deepwater is presented. Methane gas when released in deepwater undergoes a series of physical chemical processes as it rises through the water column from the sea bed to the water surface. In the high pressure and low temperatures that are typical in the deepwater, methane gas is likely to be converted to hydrates. These hydrates...
Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper presents SARNA-Predict-pk, an algorithm for pseudoknotted RNA secondary structure prediction based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and incorporates a new thermodynamic model into the algorithm, effectively enabling it to predict pseudo-knotted...
RNA is central in several stages of protein synthesis, and also has structural, functional, and regulatory roles in the cell. The shape of organic molecules such as RNA largely determines their function within an organic system, thus methods for the computational prediction of structure are sought after. In the ab initio case where only the RNA sequence is known, the currently dominant structure prediction...
A release of methane gas in deepwater undergoes a series of physical chemical processes as it rises from the deep to shallow water in the form of a plume. A key process is the formation of methane hydrate in the deep and the eventual hydrate dissociation when the plume reaches shallower regions of lower pressure and higher temperatures. This paper presents a model to simulate the behavior of methane...
Two extensive analyzes on RnaPredict, an evolutionary algorithm for RNA folding, are presented here. The first study evaluates the performance of individual nearest neighbor (INN) and individual nearest neighbor-hydrogen bond (INN-HB), two stacking-energy thermodynamic models; the criteria for comparison is the correlation between the prediction accuracy and the free energy of predicted structures...
Recent experimental evidences have shown that ribonucleic acid (RNA) plays a greater role in the cell than previously thought. An ensemble of RNA sequences believed to contain signals at the structure level can be exploited to detect functional motifs common to all or a portion of those sequences. We present here a general framework for analyzing multiple RNA secondary structures. A family of related...
Carbon dioxide (CO2) is the largest contributor among greenhouse gases (GHGs) in terms of emissions. Capturing CO2 from industrial gas stream by aqueous alkanolamine solution is the most cost-effective technology available today. Monoethanolamine (MEA) has been commonly used in gas processing industry for decades. In recent years, a sterically hindered amine, 2-amino-2-methyl-1-propanol (AMP), has...
Two polymorphs of famotidine, forms A and B, were prepared. The raw material of famotidine used in this study was proved to be a form B. Each famotidine sample ground for different grinding times in a ceramic mortar was determined by differential scanning calorimetry (DSC), Raman and thermal Fourier transform infrared (FT-IR) microspectroscoies, respectively. The effect of grinding process on the...
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