scholarly journals First Steps towards Understanding the Non-Linear Impact of Mg on Calcite Solubility: A Molecular Dynamics Study

Minerals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 407
Author(s):  
Janou A. Koskamp ◽  
Sergio E. Ruiz Ruiz Hernandez ◽  
Nora H. De Leeuw ◽  
Mariette Wolthers
Keyword(s):  
Molecular Dynamics ◽  
Surface Deformation ◽  
Crystal Surface ◽  
Local Variation ◽  
Interfacial Water ◽  
Flat Surfaces ◽  
Energy Profiles ◽  
Wide Range ◽  
Non Linear ◽  
Local Dissolution

Magnesium (Mg2+) is one of the most common impurities in calcite and is known to have a non-linear impact on the solubility of magnesian calcites. Using molecular dynamics (MD), we observed that Mg2+ impacts overall surface energies, local free energy profiles, interfacial water density, structure and dynamics and, at higher concentrations, it also causes crystal surface deformation. Low Mg concentrations did not alter the overall crystal structure, but stabilised Ca2+ locally and tended to increase the etch pit nucleation energy. As a result, Ca-extraction energies over a wide range of 39 kJ/mol were observed. Calcite surfaces with an island were less stable compared to flat surfaces, and the incorporation of Mg2+ destabilised the island surface further, increasing the surface energy and the calcium extraction energies. In general, Ca2+ is less stable in islands of high Mg2+ concentrations. The local variation in free energies depends on the amount and distance to nearest Mg in addition to local disruption of interfacial water and the flexibility of surface carbonate ions to rotate. The result is a complex interplay of these characteristics that cause variability in local dissolution energies. Taken together, these results illustrate molecular scale processes behind the non-linear impact of Mg2+ concentration on the solubility of magnesium-bearing calcites.

2D Color-Intensity Representation of Ultrasonic Thickness Gauge Measurements

2020 ◽  
pp. 1192-1198
Author(s):  
M.S. Mohammad ◽  
Tibebe Tesfaye ◽  
Kim Ki-Seong
Keyword(s):  
Cost Effective ◽  
The Other ◽  
Thickness Gauge ◽  
Color Intensity ◽  
Digital Readout ◽  
Flat Surfaces ◽  
Video Cameras ◽  
Wide Range ◽  
Cost Effective Alternative ◽  
Ultrasonic Thickness

Ultrasonic thickness gauges are easy to operate and reliable, and can be used to measure a wide range of thicknesses and inspect all engineering materials. Supplementing the simple ultrasonic thickness gauges that present results in either a digital readout or as an A-scan with systems that enable correlating the measured values to their positions on the inspected surface to produce a two-dimensional (2D) thickness representation can extend their benefits and provide a cost-effective alternative to expensive advanced C-scan machines. In previous work, the authors introduced a system for the positioning and mapping of the values measured by the ultrasonic thickness gauges and flaw detectors (Tesfaye et al. 2019). The system is an alternative to the systems that use mechanical scanners, encoders, and sophisticated UT machines. It used a camera to record the probe’s movement and a projected laser grid obtained by a laser pattern generator to locate the probe on the inspected surface. In this paper, a novel system is proposed to be applied to flat surfaces, in addition to overcoming the other limitations posed due to the use of the laser projection. The proposed system uses two video cameras, one to monitor the probe’s movement on the inspected surface and the other to capture the corresponding digital readout of the thickness gauge. The acquired images of the probe’s position and thickness gauge readout are processed to plot the measured data in a 2D color-coded map. The system is meant to be simpler and more effective than the previous development.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

PREDICTION OF PEEK RESIN PROPERTIES FOR PROCESSING MODELING USING MOLECULAR DYNAMICS

2021 ◽  
Author(s):  
KHATEREH KASHMARI ◽  
PRATHAMESH DESHPANDE ◽  
SAGAR PATIL ◽  
SAGAR SHAH ◽  
MARIANNA MAIARU ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Residual Stresses ◽  
Crystallization Kinetics ◽  
Material Properties ◽  
Elevated Temperatures ◽  
Processing Parameters ◽  
Thermomechanical Properties ◽  
Volumetric Shrinkage ◽  
Processing Temperature ◽  
Wide Range

Polymer Matrix Composites (PMCs) have been the subject of many recent studies due to their outstanding characteristics. For the processing of PMCs, a wide range of elevated temperatures is typically applied to the material, leading to the development of internal residual stresses during the final cool-down step. These residual stresses may lead to net shape deformations or internal damage. Also, volumetric shrinkage, and thus additional residual stresses, could be created during crystallization of the semi-crystalline thermoplastic matrix. Furthermore, the thermomechanical properties of semi-crystalline polymers are susceptible to the crystallinity content, which is tightly controlled by the processing parameters (processing temperature, temperature holding time) and material properties (melting and crystallization temperatures). Hence, it is vital to have a precise understanding of crystallization kinetics and its impact on the final component's performance to accurately predict induced residual stresses during the processing of these materials. To enable multi-scale process modeling of thermoplastic composites, molecular-level material properties must be determined for a wide range of crystallinity levels. In this study, the thermomechanical properties and volumetric shrinkage of the thermoplastic Poly Ether Ether Ketone (PEEK) resin are predicted as a function of crystallinity content and temperature using molecular dynamics (MD) modeling. Using crystallization-kinetics models, the thermo-mechanical properties are directly related to processing time and temperature. This research can ultimately predict the residual stress evolution in PEEK composites as a function of processing parameters.

Elastohydrodynamic Lubrication of Soft-Layered Solids at Elliptical Contacts: Part 1: Elasticity Analysis

1994 ◽  
Vol 208 (1) ◽  
pp. 31-41 ◽  
Author(s):  
J Q Yao ◽  
D Dowson
Keyword(s):  
Aspect Ratio ◽  
Surface Deformation ◽  
Applied Pressure ◽  
Numerical Procedure ◽  
Elastohydrodynamic Lubrication ◽  
Thin Layers ◽  
Elasticity Analysis ◽  
Synovial Joint ◽  
Wide Range ◽  
Non Linear System

In this two-part paper we consider the elastohydrodynamic lubrication (EHL) of soft-layered solids representing elliptical contacts. The problem has not previously attracted much attention, partly due to the lack of an effective numerical procedure to solve the coupled non-linear system of equations, but it is essential to the proper design of bearings with soft elastomeric liners and the full understanding of synovial joint lubrication. In Part 1, the elasticity analysis for the surface deformation of a low elastic modulus layer on a hard-backing half-space under various forms of normal loadings is considered, by means of both the rigorous Hankel transform method and various simplifications. For layers of compressible materials (v ≤ 0.4), a generalized foundation model described by a second-order differential equation is proposed to represent the relationship between the surface deformation and the applied pressure. The empirical equation developed in this study is valid for a very wide range of the aspect ratio of the contact and provides an alternative way of modelling the elastic deformation without recourse to the often tedious integration in the numerical analysis of the EHL problem. The simplest form (constrained column model) of the equation, where the surface deformation is directly proportional to the local applied pressure, was found to be reasonably accurate for compressible thin layers (the aspect ratio 2b/ht ≥ 5 and Poisson's ratio v ≤ 0.4).

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

2002 ◽  
Vol 116 (11) ◽  
pp. 4389-4402 ◽  
Author(s):  
Lula Rosso ◽  
Peter Mináry ◽  
Zhongwei Zhu ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profiles ◽  
Free Energy Profiles
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