Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality

In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules-namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated.

Molecular Dynamics Simulation of the Thermal Behavior of Hydroxyapatite

Hydroxyapatite (HAP) is the main mineral component of bones and teeth. Due to its biocompatibility, HAP is widely used in medicine as a filler that replaces parts of lost bone and as an implant coating that promotes new bone growth. The modeling and calculations of the structure and properties of HAP showed that various structural defects have a significant effect on the properties of the material. By varying these structural heterogeneities, it is possible to increase the biocompatibility of HAP. An important role here is played by OH group vacancies, which are easily formed when these hydroxyl groups leave OH channels of HAP. In this case, the temperature dependence of the concentration of OH ions, which also determines the thermal behavior of HAP, is important. To study the evaporation of OH ions from HAP structures with increasing temperatures, molecular dynamics simulation (MDS) methods were used in this work. As a program for MDS modeling, we used the PUMA-CUDA software package. The initial structure of HAP, consisting of 4 × 4 × 2 = 32 unit cells of the hexagonal HAP phase, surrounded by a 15-Å layer of water was used in the modelling. Multiple and statistically processed MDS, running calculations in the range of 700-1400 K, showed that active evaporation of OH ions begins at the temperature of 1150 K. The analysis of the obtained results in comparison with those available in the literature data shows that these values are very close to the experiments. Thus, this MDS approach demonstrates its effective applicability and shows good results in the study of the thermal behavior of HAP.

Computational and experimental studies of size and shape related physical properties of hydroxyapatite nanoparticles

In this work, the properties of hydroxyapatite (HAP) nanoparticles (NPs) have been studied both theoretically and experimentally focusing on computational analysis. HAP is widely used to fabricate implants, for drug delivery, etc. The physical properties of the nanosized HAP particles play an important role in the interaction with cells in the human body and are of great interest. Computer simulation was employed to understand the properties of HAP clusters (Ca(5)(PO(4))(3)OH) including formation energies, dipole moments and polarization (surface charges) by molecular mechanics (MM + , OPLS) and mostly by quantum semi-empirical Hartree-Fock (PM3) methods. The size of the simulated cluster is found to affect its dipole moment, polarization, and, finally, the electron work function- ϕ. These parameters depend on the concentration of hydrogen atoms H (or protons) at the surface. Values of ϕ were experimentally estimated via photoelectron emission measurements. The magnitude of ϕ was demonstrated to have a positive correlation on sizes. The NPs demonstrated a capability to be gathered within conglomerates. This property is confirmed by the calculated data for various sizes. Their sizes have a positive correlation on ϕ by the native particles. The main results show that the distributions of dipole moments have very different space orientations (along the OX, OY and OZ axes, the OZ axis is oriented along the OH column) and change with the addition of hydrogen atoms, which saturate the broken hydrogen bonds. This electrical property of NP leads to different behaviors and motions with consequent aggregation: (1) for the case of NPs having dipole moment oriented preferably perpendicular to the OZ axis (with more hydrogen bonds saturated by added H)-the HAP NP aggregates with hexagonal orientation and forms a wider and more spherical shape (sphere-like or bundle-like); (2) for the case of NPs having dipole moment oriented along the OZ axis (as is the case in the absence of added protons or non-saturated hydrogen bonds)-the NPs firstly rotated and oriented along this axis to form the most elongated cylindrical shape (rod-like).

Impact of Hydrodynamics on Oral Biofilm Strength

Mechanical removal of oral biofilms is ubiquitously accepted as the best way to prevent caries and periodontal diseases. Removal effectiveness strongly depends on biofilm strength. To investigate the influence of hydrodynamics on oral biofilm strength, we grew single- and multi-species biofilms of Streptococcus oralis J22, Actinomyces naeslundii TV14-J1, and full dental plaque at shear rates ranging from 0.1 to 50 1/sec and measured their compressive strength. Subsequently, biofilm architecture was evaluated by confocal laser scanning microscopy. Multi-species biofilms were stronger than single-species biofilms, with strength values ranging from 6 to 51 Pa and from 5 to 17 Pa, respectively. In response to increased hydrodynamic shear, biofilm strength decreased, and architecture changed from uniform carpet-like to more “fluffy” with higher thickness. S. oralis biofilms grown under variable shear of 7 and 50 1/sec possessed properties intermediate of those measured at the respective single shears.

Low-load compression testing: a novel way of measuring biofilm thickness

Biofilms are complex and dynamic communities of microorganisms that are studied in many fields due to their abundance and economic impact. Biofilm thickness is an important parameter in biofilm characterization. Current methods of measuring biofilm thicknesses have several limitations, including application, availability, and costs. Here, we present low-load compression testing (LLCT) as a new method for measuring biofilm thickness. With LLCT, biofilm thicknesses are measured during compression by inducing small loads, up to 5 Pa, corresponding to 0.1% deformation, making LLCT essentially a nondestructive technique. Comparison of the thicknesses of various bacterial and yeasts biofilms obtained by LLCT and by using confocal laser scanning microscopy (CLSM) resulted in the conclusion that CLSM underestimates the biofilm thickness due to poor penetration of different fluorescent dyes, especially through the thicker biofilms, whereas LLCT does not suffer from this thickness limitation.

Measurement of biocolloid collision efficiencies for granular activated carbon by use of a two-layer filtration model

Point-of-use filters containing granular activated carbon (GAC) are an effective method for removing certain chemicals from water, but their ability to remove bacteria and viruses has been relatively untested. Collision efficiencies (alpha) were determined using clean-bed filtration theory for two bacteria (Raoutella terrigena 33257 and Escherichia coli 25922), a bacteriophage (MS2), and latex microspheres for four GAC samples. These GAC samples had particle size distributions that were bimodal, but only a single particle diameter can be used in the filtration equation. Therefore, consistent with previous reports, we used a particle diameter based on the smallest diameter of the particles (derived from the projected areas of 10% of the smallest particles). The bacterial collision efficiencies calculated using the filtration model were high (0.8 < or = alpha < or = 4.9), indicating that GAC was an effective capture material. Collision efficiencies greater than unity reflect an underestimation of the collision frequency, likely as a result of particle roughness and wide GAC size distributions. The collision efficiencies for microspheres (0.7 < or = alpha < or = 3.5) were similar to those obtained for bacteria, suggesting that the microspheres were a reasonable surrogate for the bacteria. The bacteriophage collision efficiencies ranged from > or = 0.2 to < or = 0.4. The predicted levels of removal for 1-cm-thick carbon beds ranged from 0.8 to 3 log for the bacteria and from 0.3 to 1.0 log for the phage. These tests demonstrated that GAC can be an effective material for removal of bacteria and phage and that GAC particle size is a more important factor than relative stickiness for effective particle removal.