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Surfaces: a software to quantify and visualize interactions within and between proteins and ligands.Bioinformatics (Oxford, England) Oct 2023Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and...
SUMMARY
Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here, we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics.
AVAILABILITY AND IMPLEMENTATION
All scripts are available at https://github.com/NRGLab/Surfaces. Surface's documentation is available at https://surfaces-tutorial.readthedocs.io/en/latest/index.html.
Topics: Software; Proteins; Molecular Dynamics Simulation; Documentation; Ligands
PubMed: 37788107
DOI: 10.1093/bioinformatics/btad608 -
The Journal of Physical Chemistry. A Nov 2023Amorphous silica (a-SiO) surfaces, when grafted with select metals on the active sites of the functionalized surfaces, can act as useful heterogeneous catalysts. From a...
Amorphous silica (a-SiO) surfaces, when grafted with select metals on the active sites of the functionalized surfaces, can act as useful heterogeneous catalysts. From a molecular modeling perspective, one challenge has been generating a-SiO slab models with controllable surface roughness to facilitate the study of the effect of surface morphology on the material properties. Previous computational methods either generate relatively flat surfaces or periodically corrugated surfaces that do not mimic the full range of potential surface roughness of the amorphous silica material. In this work, we present a new method, inspired by the capillary fluctuation theory of interfaces, in which rough silica slabs are generated by cleaving a bulk amorphous sample using a cleaving plane with Fourier components randomly generated from a Gaussian distribution. The width of this Gaussian distribution (and thus the degree of surface roughness) can be tuned by varying the surface roughness parameter α. Using the van Beest, Kramer, and van Santen (BKS) force field, we create a large number of silica slabs using cleaving surfaces of varying roughness (α) and using two different system sizes. These surfaces are then characterized to determine their roughness (mean-squared displacement), density profile, and ring size distribution. This analysis shows a higher concentration of surface defects (under-/overcoordinated atoms and strained rings) as the surface roughness increases. To examine the effect of the roughness on surface reactivity, we re-equilibriate a subset of these slabs using the reactive force field ReaxFF and then expose the slabs to water and observe the formation of surface silanols. We observe that the rougher surfaces exhibit higher silanol concentrations as well as bimodal acidity.
PubMed: 37938899
DOI: 10.1021/acs.jpca.3c04955 -
Materials (Basel, Switzerland) Dec 2022Surface topography in general is not easy to characterize due to a great number of different features that appear on it. It is still more challenging for machined...
Surface topography in general is not easy to characterize due to a great number of different features that appear on it. It is still more challenging for machined textured surfaces that are of high functional significance for tribological purposes. For practical reasons, there is a need to describe such surfaces using only a small number of parameters. Which of them represent surface details the best is still an open issue. To find out which parameters can be the most suitable in that case, three groups of machined textured surfaces were prepared. They were plateau-honed cylinder surfaces made of gray cast iron, steel, and bronze surfaces with isolated dimples and steel surfaces after abrasive blasting followed by lapping. All of them were measured by means of a white light interferometer. Different parameters and relationships were evaluated and based on them correlation and regression analyses were used. The basic description contained statistically independent parameters that can be used in production control, while the wider description in scientific research. In general, parameters of random surfaces were more intercorrelated than those of surfaces with isolated dimples. As was found for the basic description of random two-process surfaces, five parameters were enough while description of textured surfaces with isolated oil pockets needed six. In wider, scientific description, regardless the surface type seven parameters contained the necessary information about the surface. It was also proved that a pair of parameters, the emptiness coefficient Sp/Sz and Sq/Sa, can describe the shape of the ordinate distribution of machined textured surfaces better than, for example, skewness Ssk and kurtosis Sku, commonly used for that purpose.
PubMed: 36614502
DOI: 10.3390/ma16010163 -
Molecules (Basel, Switzerland) Dec 2021Solid wettability is especially important for biomaterials and implants in the context of microbial adhesion to their surfaces. This adhesion can be inhibited by changes...
Effect of Spontaneous and Water-Based Passivation on Components and Parameters of Ti6Al4V (ELI Grade) Surface Tension and Its Wettability by an Aqueous Solution of Sucrose Ester Surfactants.
Solid wettability is especially important for biomaterials and implants in the context of microbial adhesion to their surfaces. This adhesion can be inhibited by changes in biomaterial surface roughness and/or its hydrophilic-hydrophobic balance. The surface hydrophilic-hydrophobic balance can be changed by the specifics of the surface treatment (proper conditions of surface preparation) or adsorption of different substances. From the practical point of view, in systems that include biomaterials and implants, the adsorption of compounds characterized by bacteriostatic or bactericidal properties is especially desirable. Substances that are able to change the surface properties of a given solid as a result of their adsorption and possess at least bacteriostatic properties include sucrose ester surfactants. Thus, in our studies the analysis of a specific surface treatment effect (proper passivation conditions) on a biomaterial alloy's (Ti6Al4V ELI, Grade 23) properties was performed based on measurements of the contact angles of water, formamide and diiodomethane. In addition, the changes in the studied solid surface's properties resulting from the sucrose monodecanoate (SMD) and sucrose monolaurate (SML) molecules' adsorption at the solid-water interface were also analyzed. For the analysis, the values of the contact angles of aqueous solutions of SMD and SML were measured at 293 K, and the surface tensions of the aqueous solutions of studied surfactants measured earlier were tested. From the above-mentioned tests, it was found that water environment significantly influences the components and parameters of Ti6Al4V ELI's surface tension. It also occurred that the addition of both SMD and SML to water (separately) caused a drop in the water contact angle on Ti6Al4V ELI's surface. However, the sucrose monolaurate surfactant is characterized by a slightly better tendency towards adsorption at the solid-water interface in the studied system compared to sucrose monodecanoate. Additionally, based on the components and parameters of Ti6Al4V ELI's surface tension calculated from the proper values of components and parameters of model liquids, it was possible to predict the wettability of Ti6Al4V ELI using the aqueous solutions of SMD and SML at various concentrations in the solution.
PubMed: 35011408
DOI: 10.3390/molecules27010179 -
Ortopedia, Traumatologia, Rehabilitacja Aug 2020Most cervical spine procedures in patients with degenerative disc disease involve discectomy and remo-val of osteophytes in posterior vertebral body surfaces followed by... (Review)
Review
BACKGROUND
Most cervical spine procedures in patients with degenerative disc disease involve discectomy and remo-val of osteophytes in posterior vertebral body surfaces followed by interbody stabilisation with an interbody implant. Interbody implants are made of a variety of materials, differing in structural design, shape and surface topography. Considering that fusion between the implant and host bone is crucial for long-term positive outcomes, the choice of an appropriate implant is significantly important clinically and continues to be an important area of study.
MATERIAL AND METHODS
Relevant published studies indexed by Medline were identified via PubMed and reviewed. The findings were combined with the authors' experiences. The database query was based on keywords related to implants in cervical spine surgery. This article presents the currently most popular types of implants by describing their properties and indicating their strengths and weaknesses as well as differences between different implant types.
RESULTS
Currently, the most popular interbody cages in cervical spine surgery are polyetheretherketone (PEEK) im-plants, titanium-coated PEEK implants and titanium implants. Besides the type of material used, the shape and surface structure of an implant appear to be of significant importance for a successful bony fusion.
CONCLUSIONS
1. 3D printing and the ability to produce 3-dimensional porous-surfaced implants opens up considerable pro-spects for this technique in the production of modern interbody implants. 2. Implants that facilitate the engagement (interlocking) of greater volumes of bone (e.g. porous implants) offer better implant fixation, with the type of material used being less important.
Topics: Adult; Aged; Aged, 80 and over; Cervical Vertebrae; Female; Humans; Intervertebral Disc Degeneration; Male; Middle Aged; Prostheses and Implants; Spinal Fusion
PubMed: 32986004
DOI: 10.5604/01.3001.0014.3457 -
ACS Biomaterials Science & Engineering Feb 2021The hemocompatibility of blood-contacting medical devices remains one of the major challenges in medical device development. A common tool for the analysis of adherent...
The hemocompatibility of blood-contacting medical devices remains one of the major challenges in medical device development. A common tool for the analysis of adherent and activated platelets on materials following in vitro tests is microscopy. Currently, most researchers develop their own routines, resulting in numerous different methods that are applied. The majority of those (semi-)manual methods analyze only a very small fraction of the material surface (<1%), which neglects the inhomogeneity of platelet distribution and makes results hardly comparable. Within this study, we examined the relation between the fraction of analyzed sample area and the platelet adhesion result. By means of image segmentation and machine learning algorithms, 103 100 microscopy images were analyzed automatically. We discovered a crucial impact of the analyzed surface fraction and thus a misrepresentation of a surface's platelet adhesion unless up to 40% of the sample surface is analyzed. These findings underline the necessity of standardization in the field of in vitro hemocompatibility tests and analyses in particular and provide a first basis to make future tests more reliable and comparable.
Topics: Biocompatible Materials; Blood Platelets; In Vitro Techniques; Materials Testing; Platelet Adhesiveness
PubMed: 33481566
DOI: 10.1021/acsbiomaterials.0c01589 -
The Journal of Physical Chemistry. B Oct 2022MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's...
Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface.
MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 10 particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and -29 or -34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid-base indicator dyes of various charge type, size, and structure. Their spectral and acid-base properties (p) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (p - p) in mV at 25 °C. The Ψ values were -50 and +10 mV, respectively, which indicate the "mosaic" way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.
Topics: Static Electricity; Molecular Probes; Hydrophobic and Hydrophilic Interactions; Levivirus; Nanoparticles; Coloring Agents; Surface Properties
PubMed: 36198175
DOI: 10.1021/acs.jpcb.2c04491 -
Physical Chemistry Chemical Physics :... Jul 2022The brightness of an emitter can be enhanced by metal-enhanced fluorescence, wherein the excitonic dipole couples with the electromagnetic field of the surface plasmon....
The brightness of an emitter can be enhanced by metal-enhanced fluorescence, wherein the excitonic dipole couples with the electromagnetic field of the surface plasmon. Herein, we experimentally map the landscape of photoluminescence enhancement (EF) of emitters in a plasmonic field as a function of the emitter-emitter separation, , and the emitter-plasmon distance, . We use Au nanoparticles overcoated with inert spacers as plasmonic systems and CdSe/ZnS quantum dots (QDs) as an emitter bearing opposite surface charges. The and are varied by changing the spacer thickness and number density of QDs on the plasmonic surface, respectively. The electrostatic binding of emitters on the plasmonic surface and their number density are established by following the variation of zeta-potential. EF is high, when is short and is large; nevertheless, it decreases when the emitter-emitter interaction dominates due to plasmon assisted nonradiative processes. In the absence of a plasmonic field, the enhancement observed is attributed to environmental effects and is independent of , confirming the role of the electric field. Indeed, the distance dependence of EF closely follows the decay of the plasmonic field upon dilution of the emitter concentration on nanoparticles' surface ( = 18 nm). The QD-plasmon system is visualized in the framework of the Thomson problem, and classical electrodynamics calculations give the trends in and dependence of the photoluminescence. Being the first report on the simultaneous dependence of and on plasmon-enhanced photoluminescence, the results presented herein will open newer opportunities in the design of hybrid systems with a high brightness.
PubMed: 35796601
DOI: 10.1039/d2cp01681h -
Journal of Pediatric Endocrinology &... Sep 2019Background/objective The olfactory bulb (OB) and pubertal development have a close relationship as they share a common ontogenetic origin. The aim of this study was to...
Background/objective The olfactory bulb (OB) and pubertal development have a close relationship as they share a common ontogenetic origin. The aim of this study was to analyze the potential relationship between precocious puberty (PP) in girls as a sign of early pubertal timing and their OB volume as an indicator of its functional activity. Design In the study group (n = 125), OB volume, pituitary height (PH), body mass index (BMI) and body surface (S) variables were retrospectively investigated in 49 girls included in the PP group and 76 healthy girls constituting the control group. Volumetric and length measurements were performed on a magnetic resonance imaging (MRI) scan by using manual segmentation of slices. Results The mean OB volume (73.41 ± 17.21 mm3) and PH (4.96 ± 1.01 mm) were significantly higher in the PP group (p = 0.001 and p = 0.001, respectively). The mean volume difference between the right and left bulbs (1.52 ± 1.87) was higher in the PP group (p = 0.03). The body surface (1.05 ± 0.16 m2) was larger in the PP group (p = 0.09). There was a high correlation between the OB volume and PH (r125 = 0.716). There was a moderate correlation between the body surface and OB volume (r125 = 654), and a weak correlation between the former (S) and the PH (r125 = 452). Conclusions This study showed that there is a strong correlation between increased OB volume and PH in cases with PP. It indicates that increased OB volume may be a strong clue that olfactory functions play a role in pubertal timing in humans, although it does not show definitive proof of a causal relationship.
Topics: Case-Control Studies; Child; Female; Follow-Up Studies; Humans; Nose; Olfactory Bulb; Organ Size; Prognosis; Puberty, Precocious; Retrospective Studies
PubMed: 31377742
DOI: 10.1515/jpem-2018-0534 -
Journal of Environmental Management Jul 2021The vast amount of oily wastewater released to the environment through industrialization has worsened the water quality in recent years, posing adverse impacts on... (Review)
Review
The vast amount of oily wastewater released to the environment through industrialization has worsened the water quality in recent years, posing adverse impacts on general human health. Oil emulsified in water is one of the most difficult mixtures to be treated, making it imperative for new technology to be explored to address this issue. The use of conventional water treatment such as flotation, coagulation, precipitation, adsorption, and chemical treatment have low separation efficiencies and high energy costs, and are not applicable to the separation of oil/water emulsions. Therefore, there is a demand for more efficient methods and materials for the separations of immiscible oil/water mixtures and emulsions. Superwetting materials that can repel oil, while letting water pass through have been widely explored to fit into this concern. These materials usually make use of simultaneous hydrophilic/oleophobic mechanisms to allow a solid surface to separate oily emulsion with little to no use of energy. Also, by integrating specific wettability concepts with appropriate pore scale, solid surfaces may achieve separation of multifarious oil/water mixtures namely immiscible oil/water blends and consolidated emulsions. In this review, materials used to impart superwetting in solid surfaces by focusing on superhydrophilic/superoleophobic wetting properties of the materials categorized into fluorinated and non-fluorinated surface modification are summarized. In each material, its background, mechanism, fabricating processes, and their effects on solid surface's wetting capability are elaborated in detail. The materials reviewed in this paper are mainly organic and green, suggesting the alternative material to replace the fluorine group that is widely used to achieve oleophobicity in oily wastewater treatment.
Topics: Humans; Hydrophobic and Hydrophilic Interactions; Oils; Wastewater; Water Purification; Wettability
PubMed: 33873023
DOI: 10.1016/j.jenvman.2021.112565