Hamiltonian Lie-Poisson structures of the three-wave equations associated with the Lie algebras su(3) and su(2, 1) are derived and shown to be compatible. Poisson reduction is performed using the method of invariants and geometric phases associated with the reconstruction are calculated. These results can be applied to applications of nonlinear-waves in, for instance, nonlinear optics. Some of ...

We derive the Boltzmann principle SB=kB ln W based on classical mechanical models of thermodynamics. The argument is based on the heat theorem and can be traced back to the second half of the 19th century in the works of Helmholtz and Boltzmann. Despite its simplicity, this argument has remained almost unknown. We present it in a contemporary, self-contained, and accessible form. The approach c...

The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on ...

Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecu...

The successful application of high throughput molecular simulations to determine biochemical properties would be of great importance to the biomedical community if such simulations could be turned around in a clinically relevant timescale. An important example is the determination of antiretroviral inhibitor efficacy against varying strains of HIV through calculation of drug-protein binding aff...

Protein pKas and metalloprotein reduction potentials are studied with computational methodologies based on an ab initio quantum mechanics (QM) description of the protein and a linearized Poisson-Boltzmann Equation (LPBE) description of the solvent. The practical applicability of the QM/LPBE method is extended to proteins by using a QM description of the ionizable residue and a molecular mechani...

The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson]Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary el...

By considering the influence of volume exclusion on the solvent dielectric, a variable dielectric Poisson-Boltzmann (VDPB) model is explored for molecular solvation studies by using a dielectric as an explicit function of ionic sizes and concentrations. A finite element method is adopted and an iterative strategy is introduced to numerically solve the VDPB equation. According to our computation...