Molecular Dynamics Simulation

Activated wetting of nanostructured surfaces: reaction coordinates, finite size effects, and simulation pitfalls

A liquid in contact with a textured surface can be found in two states, Wenzel and Cassie. In the Wenzel state the liquid completely wets the corrugations while in the Cassie state the liquid is suspended over the corrugations with air or vapor trapped below. The superhydrophobic properties of the Cassie state are exploited for self-cleaning, drag reduction, drug delivery, etc., while in the Wenzel state most of these properties are lost; it is therefore of great fundamental and technological interest to investigate the kinetics and mechanism of the Cassie–Wenzel transition.

The pathological Trento variant of alpha-1-antitrypsin (E75V) shows nonclassical behaviour during polymerization

Severe alpha?1?antitrypsin deficiency (AATD) is most frequently associated with the alpha?1?antitrypsin (AAT) Z variant (E342K). ZZ homozygotes exhibit accumulation of AAT as polymers in the endoplasmic reticulum of hepatocytes. This protein deposition can lead to liver disease, with the resulting low circulating levels of AAT predisposing to early?onset emphysema due to dysregulation of elastinolytic activity in the lungs. An increasing number of rare AAT alleles have been identified in patients with severe AATD, typically in combination with the Z allele.

Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study

Human aquaporin 4 has been studied using non-equilibrium molecular dynamics simulations in the absence and presence of pulses of external electric fields. The pulses were 100 ns in duration and 0.005-0.015 V/angstrom in intensity acting along the pores' axes. Water diffusivity and the dipolar response of various residues of interest within the pores have been studied. Results show relatively little change in levels of water permeability per se within aquaporin channels during axially oriented field impulses, although care must be taken with regard to statistical certainty.

Leveraging the cruzain S3 subsite to increase affinity for reversible covalent inhibitors

Cruzain is themajor cysteine protease of Trypanosoma cruzi, the etiological agent of Chagas disease. Reversible covalent cruzain inhibitors can block the steps of cell differentiation in the parasite and kill the organism. To this end, the description of how inhibitors modified at the P2/P3 positions lead to analogs with greater cruzain affinity to the S2/S3 subsites is of fundamental importance. Albeit many efforts are being employed in the characterization of the interaction processes with S2 subsite, little is known about the cruzain S3 subsite.

© Università degli Studi di Roma "La Sapienza" - Piazzale Aldo Moro 5, 00185 Roma