molecular dynamics

Computational Atomistic Fluid-dynamics & Engineering

Computational Atomistic Fluid-dynamics & Engineering

Our approach is a physical one, addressing problems in engineering and biology. In particular, we use molecular dynamics and multiscale simulations which address the various time and length scales typical of wetting, cavitation, and biophysical phenomena.

Torsional characteristics of carbon nanotubes: Micropolar elasticity models and molecular dynamics simulation

Efficient application of carbon nanotubes (CNTs) in nano-devices and nano-materials requires comprehensive understanding of their mechanical properties. As observations suggest size dependent behaviour, non-classical theories preserving the memory of body’s internal structure via additional material parameters offer great potential when a continuum modelling is to be preferred.

Self-recovery superhydrophobic surfaces: modular design

Superhydrophobicity, the enhanced hydrophobicity of surfaces decorated with textures of suitable size, is associated with a layer of gas trapped within surface roughness. The reduced liquid/solid contact makes superhydrophobicity attractive for many technological applications. This gas layer, however, can break down with the liquid completely wetting the surface. Experiments have shown that the recovery of the "suspended" superhydrophobic state from the wet one is difficult.

Pore morphology determines spontaneous liquid extrusion from nanopores

In this contribution we explore by means of experiments, theory, and molecular dynamics the effect of pore morphology on the spontaneous extrusion of nonwetting liquids from nanopores. Understanding and controlling this phenomenon is central for manipulating nanoconfined liquids, e.g., in nanofluidic applications, drug delivery, and oil extraction.

The interplay among gas, liquid and solid interactions determines the stability of surface nanobubbles

Surface nanobubbles are gaseous domains found at immersed substrates, whose remarkable persistence is still not fully understood. Recently, it has been observed that the formation of nanobubbles is often associated with a local high gas oversaturation at the liquid-solid interface. Tan, An and Ohl have postulated the existence of an effective potential attracting the dissolved gas to the substrate and producing a local oversaturation within 1 nm from it that can stabilize nanobubbles by preventing outgassing in the region where gas flow would be maximum.

Dynamical behavior of the human ferroportin homologue from Bdellovibrio bacteriovorus: Insight into the ligand recognition mechanism

Members of the major facilitator superfamily of transporters (MFS) play an essential role in many physiological processes such as development, neurotransmission, and signaling. Aberrant functions of MFS proteins are associated with several diseases, including cancer, schizophrenia, epilepsy, amyotrophic lateral sclerosis and Alzheimer’s disease. MFS transporters are also involved in multidrug resistance in bacteria and fungi. The structures of most MFS members, especially those of members with significant physiological relevance, are yet to be solved.

Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose:glycoprotein glucosyltransferase

UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2). CtUGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements.

Self-assembling of calcium salt of the new DNA base 5-carboxylcytosine

Supramolecular architectures involving DNA bases can have a strong impact in several fields such as nanomedicine and nanodevice manufacturing. To date, in addition to the four canonical nucleobases (adenine, thymine, guanine and cytosine), four other forms of cytosine modified at the 5 position have been identified in DNA. Among these four new cytosine derivatives, 5-carboxylcytosine has been recently discovered in mammalian stem cell DNA, and proposed as the final product of the oxidative epigenetic demethylation pathway on the 5 position of cytosine.

Isomerization patterns and proton transfer in ionic liquids constituents as probed by ab-initio computation

We have recently shown that some protic ionic liquids (PILs) are characterized by an unexpected complex dynamic of proton transfer (M. Campetella et al., Phys. Chem. Chem. Phys. 19, 11,869, (2017)). These liquids are based on a combination of cholinium cations and amino acid (AA) deprotonated anions. The side chain proton migration, can take place both within the same anion and between different anions. The intra-molecular proton transfer leads to a tautomerization of the AA anion that gives rise to the appearance of an anionic zwitterionic form.

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