Riboswitches are structured RNA regulatory elements located in the 5'-UTRs of mRNAs. Ligand-binding induces a structural rearrangement in these RNA elements, effecting events in downstream located coding sequences. Since they do not require proteins for their functions, they are ideally suited for computational analysis using the toolbox of RNA structure prediction methods. By their very defini...

The current study aimed at in vitro investigating the kinetic study and thermodynamic analysis of mebendazole drug released from electrospun cellulose nanofiber in which guar gum is used as a release controller. The nanofibers were fabricated by electrospinning technique. The fibers were boosted by different controller guar gum 10 at 50, 250, and 500 ppm concentrations. The drug releas...

Control of nonspecific protein adsorption is very important for the design of biocompatible and biomimetic materials as well as drug carriers. Grafted polymer layers can be used to prevent protein adsorption. We have studied the molecular factors that determine the equilibrium and kinetic control of protein adsorption by grafted polymer layers. We find that polymers that are not attracted to th...

We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated wi...

We develop a mesoscopic lattice Boltzmann model for liquid-vapor phase transition by handling the microscopic molecular interaction. The short-range interaction is incorporated recovering an equation of state dense gases, and long-range mimicked introducing pairwise force. Double distribution functions are employed, with density function mass momentum conservation laws innovative total kinetic ...

classical xerogels are robust, inexpensive and nontoxic materials with low-ordered nanoporous structures. in water streams where the ph is higher than the point of zero charge, the surface of classical xerogels such as tetraethoxy orthosilan (teos) xerogel is negatively charged. it was assumed that a xerogel can work as a strong adsorbent for metal ions without further modification. therefore, ...

Thermodynamic and kinetic aspects of interfacial decohesion are analyzed for a uniformly stressed interface in the presence of an embrittling impurity. During the interfacial separation, the impurity penetrates into the interface and reduces it cohesion. Rice (1976) and Hirth and Rice (1980) analyzed the thermodynamics of this process in great detail with emphasis on the limiting cases of infin...