The common structure of the space of pure states P of a classical or a quantum mechanical system is that of a Poisson space with a transition probability. This is a topological space equipped with a Poisson structure, as well as with a function p : P × P → [0, 1], with certain properties. The Poisson structure is connected with the transition probabilities through unitarity (in a specific formu...

The accurate prediction of ligand binding affinities to a protein remains a desirable goal of computational biochemistry. Many available methods use molecular mechanics (MM) to describe the system, however, MM force fields cannot fully describe the complex interactions involved in binding, specifically electron transfer and polarization. First principles approaches can fully account for these i...

Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecu...

Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity changes upon mutations in target is high interest as this can yield a better understanding into how such drive drug-resistance, especially when mutation question does not directly interfere with drug. The...

This paper investigates the lateral vibration of single-layered graphene sheets based on a new theory called doublet mechanics with a length scale parameter. After a brief reviewing of doublet mechanics fundamentals, a sixth order partial differential equation that governs the lateral vibration of single-layered graphene sheets is derived. Using doublet mechanics, the relation between natural f...

Objective(s): The novel 7-hydroxycoumarinyl gallates derivatives are detected in many pharmaceutical compounds like anticancer and antimicrobial agents. Whereas carbon nanotubes (CNTs) have been discussed for nanomedicine applications and in particular as drug delivery systems. The capability of armchair (5, 5) SWCNT -based drug delivery system in the therapy of anticancer has been investigated...

The fundamental problems in drug discovery are based on the process of molecular recognition by small molecules. The binding specificity of DNA-small molecule is identified mainly by studying the hydrogen bonding and polar interactions. Majority of the minor groove binders and their mechanism of action at the molecular level are not well studied. As these small molecules can act as effective th...

Protein kinase CK2, also known as casein kinase II, is related to various cellular events and is a potential target for numerous cancers. In this study, we attempted to gain more insight into the inhibition process of CK2 by a series of CX-4945 derivatives through an integrated computational study that combines molecular docking, molecular dynamics (MD) simulations, and binding free energy calc...