Cavitation refers to the formation of bubbles in a liquid flow leading to a two-phase mixture of liquid and vapor/gas, when the local pressure drops below the vapor pressure of the fluid. Fundamentally, the liquid to vapor transition can occur by heating the fluid at a constant pressure, known as boiling, or by decreasing the pressure at a constant temperature, which is known as cavitation. Sin...

Peptide binding to class II MHC protein is commonly viewed as a combination of discrete anchor residue preferences for pockets 1, 4, 6/7, and 9. However, previous studies have suggested cooperative effects during the peptide binding process. Investigation of the DRB1*0901 binding motif demonstrated a clear interaction between peptide binding pockets 6 and 9. In agreement with prior studies, poc...

Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a maj...

The shape of a protein is important for its functions. This includes the location and size of identiiable regions in its complement space. We formally deene pockets as regions in the complement with limited accessibility from the outside. Pockets can be eeciently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimension...

Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-pr...

Protein–ligand binding is a key biological process at the molecular level. The identification and characterization of small-molecule binding sites on therapeutically relevant proteins have tremendous implications for target evaluation and rational drug design. In this work, we used the recently developed level-set variational implicit-solvent model (VISM) with the Coulomb field approximation (C...

RNA-binding proteins play a significant role in pattern regulation of gene expression during developmental phases. Therefore in order to facilitate our understanding of organism development there is a continuous need to develop an extensive a priori method for the prediction of RNA-binding protein pockets. We present here a SVM (Support Vector Machine) based approach for successful prediction o...

We discuss new high-resolution (6.7 km/s) spectra of the associated absorption lines (AALs) in the radio-loud quasar 3C 191. The measured AALs have ionizations ranging from Mg I to N V, and multicomponent profiles that are blueshifted by ∼400 to ∼1400 km/s relative to the quasar’s broad emission lines. Excited-state absorption lines of Si II and C II imply volume densities of ∼300 cm and a nomi...

Giant bullae may be found in association with emphysema. They present as pockets of entrapped air which grow as the surrounding lung retracts away. As they do not take part in gas exchange and merely occupy space, their presence leads to severe impediment of mechanical ventilation in the adjacent lung parenchyma. Patients may present with dyspnoea, exercise intolerance and a feeling of pressure...

Isotopic signatures of nitrogen, argon, and xenon have been determined in separated millimeter-sized pockets of shock-melted glass in a recently identified lithology of the meteorite Zagami, a shergottite. The ratio of nitrogen-15 to nitrogen-14, which is at least 282 per mil larger than the terrestrial value, the ratio of xenon-129 to xenon-132 = 2.40, and the argon isotopic abundances match t...