The slowing down process of light charged subexcitation particles of finite size in a medium with time dispersion is considered. The theory developed is applied to the slowing down of the secondary electrons knocked out by another energetic particle. Total energy loss is made up from the Debye losses, excitation of intraand intermolecular vibrations and the mutual Coulomb attraction between par...

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) syste...

Long branch attraction is a problem that afflicts phylogenetic methods and a procedure to detect a data set suffering from this problem is the long branch extraction method[1]. This method has been well cited and used by many authors for their analysis but no strong validation has been performed as to its accuracy. We performed such an analysis by an extensive search of the branch length search...

MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F3CX···YLi···NCCN and F3CX···NCCN···LiY triads (X = Cl, Br; Y = CN, NC) which are connected via halogen and lithium bonds. Those complexes with the role of LiY as halogen acceptor and lithium donor show cooperativity with energy values ranging between -1.97 and -2.92 kJ mol...

In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crysta...

The electrostatic model, which is widely used to explain π-involved interactions, gives an intuitive picture of these intermolecular interactions and has successfully predicted many phenomena in recent decades. Still, this simple model faces problems in certain cases and it has come under fire in previous studies on π-π stacking interactions. Here, employing ab initio calculations, we have iden...

Carotenoids play the dual function of light harvesting and photoprotection in photosynthetic organisms. Despite their functional importance, the molecular basis for binding of carotenoids in the photosynthetic proteins is poorly understood. We have discovered that all carotenoids are surrounded either by aromatic residues or by chlorophylls in all known crystal structures of the photosynthetic ...

By modeling mass transfer phenomena, we simulate solids and liquids dissolving or changing to other substances. We also deal with the very small-scale phenomena that occur when a fluid spreads out at the interface of another fluid. We model the pressure at the interfaces between fluids with Darcy’s Law and represent the viscous fingering phenomenon in which a fluid interface spreads out with a ...

The many bystander macromolecules in the crowded cellular environments present both steric repulsion and weak attraction to proteins undergoing folding or binding and hence impact the thermodynamic and kinetic properties of these processes. The weak but nonrandom binding with bystander macromolecules may facilitate subcellular localization and biological function. Weak binding also leads to the...