Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short-range pairwise interatomic potentials. These algorithms are based on the Verlet table (VT) and linked-cell (LC) methods. It is widely believed that the VT is more efficient than the LC. The analysis of these methods shows that in case when the average number of interactions per particle is relatively large, or more specifically, the particle density ρ and skin radius r(skin) meet the condition (4π/6)ρr (skin)3/27 ≫ 1, which may be true for most simulations of liquids, the number of memory data load operations in the LC is much less than that in the VT. Because memory access on modern processors is a bottleneck, this advantage of the LC should be and was in fact used, and a code outperforming the VT by a factor of almost 2 was obtained. Some modifications of the VT were proposed to reduce its disadvantage concerning memory data loading. The key modifications included automated skin radius tuning during simulations and compression of the VT to minimize duplications of atom identifiers in its nearby rows. Although these modifications had improved the performance, the VT failed to regain the superiority over the LC. The methods were tested in the MOLKERN simulation software by using SIMD and multithreading.

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The signal transduction protein PII plays an important role in cellular nitrogen assimilation and regulation. The molecular characteristics of the Mycobacterium tuberculosis PII (Mtb PII) were investigated using biophysical experiments. The Mtb PII coding ORF Rv2919c was cloned and expressed in Escherichia coli. The binding characteristics of the purified protein with ATP and ADP were investigated using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Mtb PII binds to ATP strongly with K(d) in the range 1.93-6.44 microM. This binding strength was not significantly affected by the presence of 2-ketoglutarate even in molar concentrations of 66 (ITC) or 636 (SPR) fold excess of protein concentration. However, an additional enthalpy of 0.3 kcal/mol was released in presence of 2-ketoglutarate. Binding of Mtb PII to ADP was weaker by an order of magnitude. Binding of ATP and 2-ketoglutarate were analysed by docking studies on the Mtb PII crystal structure (PDB id 3BZQ). We observed that hydrogen bonds involving the gamma-phosphate of ATP contribute to enhanced binding of ATP compared with ADP. Glutaraldehyde crosslinking showed that Mtb PII exists in homotrimeric state which is consistent with other PII proteins. Phylogenetic analysis showed that Mtb PII consistently grouped with other actinobacterial PII proteins.

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