The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations ...

Hydrophobic free energy for protein folding is currently measured by liquid-liquid transfer, based on an analogy between the folding process and the transfer of a nonpolar solute from water into a reference solvent. The second part of the analogy (transfer into a nonaqueous solvent) is dubious and has been justified by arguing that transfer out of water probably contributes the major part of th...

Rotavirus and pathogenic free-living amoebae are causative agents of important health problems, especially for developing countries like Pakistan where the population has limited access to clean water supplies. Here, we evaluated the prevalence of rotavirus and free-living amoebae (Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri) in drinking water supplies of Karachi, Pakistan. Si...

We use thermodynamic integration (TI) and explicit solvent molecular dynamics (MD) simulation to estimate the absolute free energy of host-guest binding. In the unbound state, water molecules visit all of the internally accessible volume of the host, which is fully hydrated on all sides. Upon binding of an apolar guest, the toroidal host cavity is fully dehydrated; thus, during the intermediate...

Electron paramagnetic resonance (EPR) is a promising biodosimetric method, and fingernails are sensitive biomaterials to ionizing radiation. Therefore, kinetic energy released per unit mass (kerma) can be estimated by measuring the level of free radicals within fingernails, using EPR. However, to date this dosimetry has been deficient and insufficiently accurate. In the sampling processes and m...

background : we intend to study the inhibitory effect of sulfur compound in ramsar hot spring mineral on tumor-genesis ability of high natural background radiation. objective : the radioprotective effect of sulfur compounds was previously shown on radiation-induced chromosomal aberration, micronuclei in mouse bone marrow cells and human peripheral lymphocyte. ramsar is known for having the high...

Water saturation and cation exchange capacity are the most significant parameters used to calculate a hydrocarbon zone potential. In clean formations, by applying the famous Archie model, which assumes that in the formation the only electric conductor is the formation water, the water saturation can be calculated. Additionally, in shaly sand formations this assumption may not be true as the ion...

A mobile loop changes its conformation from "open" (free enzyme) to "closed" upon ligand binding. The difference in the Helmholtz free energy, ΔF(loop) between these states sheds light on the mechanism of binding. With our "hypothetical scanning molecular dynamics" (HSMD-TI) method ΔF(loop) = F(free) - F(bound) where F(free) and F(bound) are calculated from two MD samples of the free and bound ...

to survey the effects of nutritional and growth regulator components on adverse effects of recent consecutive droughts, an experiment was conducted on uniform grape trees (vitisviniferal.clv.'khalili') in bavanat and shiraz (akbar-abad) regions in 2010- 2011.trial was arranged in a randomized complete blockdesign (rcbd), with three replication and five trees per each plot. experimental treatmen...