Investigation of structural, electronic and thermoelectric properties of two-dimensional graphdiyne/borophene monolayers and hetero-bilayers.

The integration of dissimilar 2D materials is important for nanoelectronic and thermoelectric applications. Among different polymorphs and different bond geometries, borophene and graphdiyne (GDY) are two promising candidates for these applications. In the present paper, we have studied hetero-bilayers comprising graphdiyne-borophene (GDY-BS) sheets.

Salt-induced effects on natural and inverse DPPC lipid membranes: Molecular dynamics simulation.

Molecular dynamics (MD) simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer and its neutral inverse-phosphocholine equivalent (DPCPe) were performed to find salt-induced effects on their surface structure and the nature of ion-lipid interactions. We found that the area per lipid is not considerably affected by the inversion, but the deuterium order parameter of carbon atoms in the region of carbonyl carbons changes dramatically. MD simulations indicate that Ca ions can bind to the surface of both DPPC and DPCPe membranes, but K ions do not bind to them.

Water transport and desalination through double-layer graphyne membranes.

Non-equilibrium molecular dynamics simulations of water-salt solutions driven through single and double-layer graphyne membranes by a pressure difference created by rigid pistons are carried out to determine the relative performance of the membranes as filters in a reverse osmosis desalination process. It is found that the flow rate of water through a graphyne-4 membrane is twice that of a graphyne-3 membrane for both single and double-layer membranes. Although the addition of a second layer to a single-layer membrane reduces the membrane permeability, the double-layer graphyne membranes are still two or three orders of magnitude more permeable than commercial reverse osmosis membranes.

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations.

To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center.

Study of procaine and tetracaine in the lipid bilayer using molecular dynamics simulation.

Despite available experimental results, the molecular mechanism of action of local anesthetics upon the nervous system and contribution of the cell membrane to the process are still controversial. In this work, molecular dynamics simulations were performed to investigate the effect of two clinically used local anesthetics, procaine and tetracaine, on the structure and dynamics of a fully hydrated dimyristoylphosphatidylcholine lipid bilayer. We focused on comparing the main effects of uncharged and charged drugs on various properties of the lipid membrane: mass density distribution, diffusion coefficient, order parameter, radial distribution function, hydrogen bonding, electrostatic potential, headgroup angle, and water dipole orientation.

Study of curcumin behavior in two different lipid bilayer models of liposomal curcumin using molecular dynamics simulation.

Liposomal formulation of curcumin is an important therapeutic agent for the treatment of various cancers. Despite extensive studies on the biological effects of this formulation in cancer treatment, much remains unknown about curcumin-liposome interactions. Understanding how different lipid bilayers respond to curcumin molecule may help us to design more effective liposomal curcumin.

Computational study of interaction of alkali metals with C3N nanotubes.

Interaction of the alkali metals (AMs) like lithium (Li), sodium (Na), and potassium (K) with defective and non-defective (8,0) C3N nanotubes (C3NNT) have been investigated using the first-principles study. In addition to structural properties, we have also studied the electronic properties, charge transfer, and work function of the AM-C3NNT complexes. AMs are adsorbed on hollow sites, regardless of the initial positions.

Free energy simulations of amylin I26P mutation in a lipid bilayer.

The amylin peptide in a dioleoylphosphatidylcholine (DOPC) bilayer is studied using united atom molecular dynamics (MD) simulations. Dynamics and transport properties of the peptide and the phospholipid bilayer are investigated. The lateral diffusion of DOPC is in the order of 10(-8) cm(2) s(-1), which is in agreement with the experimental results.

Effects of cholesterol concentration on the interaction of cytarabine with lipid membranes: a molecular dynamics simulation study.

Liposomal cytarabine, DepoCyt, is a chemotherapy agent which is used in cancer treatment. This form of cytarabine has more efficacy and fewer side effects relative to the other forms. Since DepoCyt contains the cytarabine encapsulated within phosphatidylcholine and the sterol molecules, we modeled dioleoylphosphatidylcholine (DOPC)/cholesterol bilayer membrane as a carrier for cytarabine to study drug-bilayer interactions.

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy.

Study of base pair mutations in proline-rich homeodomain (PRH)-DNA complexes using molecular dynamics.

Proline-rich homeodomain (PRH) is a regulatory protein controlling transcription and gene expression processes by binding to the specific sequence of DNA, especially to the sequence 5'-TAATNN-3'. The impact of base pair mutations on the binding between the PRH protein and DNA is investigated using molecular dynamics and free energy simulations to identify DNA sequences that form stable complexes with PRH. Three 20-ns molecular dynamics simulations (PRH-TAATTG, PRH-TAATTA and PRH-TAATGG complexes) in explicit solvent water were performed to investigate three complexes structurally.

Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

The proline-rich homeodomain (PRH)-DNA complex consists of a protein with 60 residues and a 13-base-pair DNA. The PRH protein is a transcription factor that plays a key role in the regulation of gene expression. PRH is a significant member of the Q50 class of homeodomain proteins.

Study of the Alzheimer's Aβ40 peptide in SDS micelles using molecular dynamics simulations.

The interaction of the Alzheimer's amyloid beta peptide, Aβ40, with sodium dodecyl sulfate (SDS) micelles, together with the self-assembly of SDS molecules around the peptide from an initial random distribution were studied using atomistic and coarse-grained (CG) molecular dynamics simulations. In atomistic simulations, the peptide structure in the micelle was characterized by two helical regions connected through a short hinge. The initial structure of the system was shown to affect the simulation results.