The pH-driven opening and closure of beta-lactoglobulin EF loop, acting as a lid and closing the internal cavity of the protein, has been studied by molecular dynamics (MD) simulations and free energy calculations based on molecular mechanics/Poisson-Boltzmann (PB) solvent-accessible surface area (MM/PBSA) methodology. The forms above and below the transition pH differ presumably only in the pr...

Necessary and sufficient conditions for an existence of the Poisson brackets significantly simplify in the Liouville coordinates. The corresponding equations can be integrated. Thus, a description of local Hamiltonian structures is a first step in a description of integrable hydrodynamic chains. The concept of M Poisson bracket is introduced. Several new Poisson brackets are presented.

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are ...

We consider the link between fragility and elasticity that follows from analysis of data for a set soft colloid materials consisting deformable spheres reported by [Mattsson et al., Nature, 2009, 462, 83]. The present work makes quantitative through an explicit definition index m in terms density dependence, extending corresponding formula molecular systems temperature dependence. In addition, ...

To Vladimir Igorevich Arnol'd with admiration, on occasion of his 60 th birthday. Abstract Heisenberg motion equations in Quantum mechanics can be put into the Hamilton form. The difference between the commutator and its principal part, the Poisson bracket, can be accounted for exactly. Canonical transformations in Quantum mechanics are not, or at least not what they appear to be; their propert...

In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high-throughput screenings. Most scoring functions implemented in popular docking software packages were developed with many approximations for computational efficiency, which sacrifices the accuracy of prediction. With advanced technology and powerful computational hardware nowadays, it is feasibl...

The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess group of metalloproteins belonging to the MEROPS peptidase (M4) family, which main virulence factor these bacteria. In this work, we used previous results computational biochemistry protocol series ligands designed silico using...

We describe the ‘Lie algebra of classical mechanics’, modelled on the Lie algebra generated by kinetic and potential energy of a simple mechanical system with respect to the canonical Poisson bracket. It is a polynomially graded Lie algebra, a class we introduce. We describe these Lie algebras, give an algorithm to calculate the dimensions cn of the homogeneous subspaces of the Lie algebra of c...

where ρ is the mass density, S is the entropy density, and p is the pressure. It was shown in Morrison and Greene [1980] that this system, as well as its magnetohydrodynamic extension, admit a noncanonical Poisson formulation, that is, equation (1.1) can be written as ḟ = {f, h}, relative to a Hamiltonian function h. The study of the relativistic case was initiated in Bia lynicki-Birula, Hubbar...

On the local systems Hamiltonian in the weakly nonlocal Poisson brackets. Abstract We study in this work the important class of nonlocal Poisson Brackets (PB) which we call weakly nonlocal. They appeared recently in some investigations in the Soliton Theory. However there was no theory of such brackets except very special first order case. Even in this case the theory was not developed enough. ...