Preliminary multiscale studies of the montmorillonite, amylose and fatty acids for polymer-clay nanocomposite modeling

MRS Advances ◽  
2019 ◽  
Vol 4 (20) ◽  
pp. 1155-1160
Author(s):  
Felipe A. R. Silva ◽  
Maria J. A. Sales ◽  
Mohamed Ghoul ◽  
Latifa Chebil ◽  
Elaine R. Maia
Keyword(s):  
Vegetable Oil ◽  
Dissipative Particle Dynamics ◽  
Md Simulations ◽  
Theoretical Work ◽  
Molecular Systems ◽  
Polymer Clay Nanocomposite ◽  
Starting Point ◽  
Complex Models ◽  
Experimental Findings ◽  
Materials Studio

Abstract:This work presents the mesoscale step of a theoretical study of a Polymer-Clay Nanocomposite (PCN) composed by starch, pequi vegetable oil and montmorillonite (MMT), a phyllosilicate. In the present study, amylose oligomers, oleic, palmitic and stearic acids in the proportion found in that vegetable oil and MMT were studied, as a simplified model, in order to simulate in multiscale their structural and behavioral correlations. The calculations were carried out by Dissipative Particle Dynamics (DPD), at 363 K, using Materials StudioTM suite. The DPD model had its interaction parameters calculated from previous MD simulations. It was observed that the organic material concentrated near the MMT surfaces, which correlated with the MD results, implying in the validity of the model. The new knowledge acquired about those molecular systems, works as a starting point to build more complex models and, if the theoretical work converge with the experimental findings, encourages further studies in the design of PCNs with biopolymers.

scholarly journals Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis

2021 ◽  
Vol 22 (7) ◽  
pp. 3793
Author(s):  
Sophie Blinker ◽  
Jocelyne Vreede ◽  
Peter Setlow ◽  
Stanley Brul
Keyword(s):  
Bacillus Subtilis ◽  
Membrane Protein ◽  
Spore Germination ◽  
Structural Information ◽  
Transmembrane Protein ◽  
Homology Modelling ◽  
Water Channel ◽  
Md Simulations ◽  
Integral Membrane Protein ◽  
Starting Point

Bacillus subtilis forms dormant spores upon nutrient depletion. Germinant receptors (GRs) in spore’s inner membrane respond to ligands such as L-alanine, and trigger spore germination. In B. subtilis spores, GerA is the major GR, and has three subunits, GerAA, GerAB, and GerAC. L-Alanine activation of GerA requires all three subunits, but which binds L-alanine is unknown. To date, how GRs trigger germination is unknown, in particular due to lack of detailed structural information about B subunits. Using homology modelling with molecular dynamics (MD) simulations, we present structural predictions for the integral membrane protein GerAB. These predictions indicate that GerAB is an α-helical transmembrane protein containing a water channel. The MD simulations with free L-alanine show that alanine binds transiently to specific sites on GerAB. These results provide a starting point for unraveling the mechanism of L-alanine mediated signaling by GerAB, which may facilitate early events in spore germination.

scholarly journals Near-Surface Mounted Reinforcement of Sawn Timber Beams-FEM Approach

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2780
Author(s):  
Izabela Burawska-Kupniewska ◽  
Piotr Beer
Keyword(s):  
European Standard ◽  
Near Surface ◽  
Bending Tests ◽  
Starting Point ◽  
Structural Applications ◽  
Bending Stresses ◽  
Complex Models ◽  
Near Surface Mounted ◽  
Sawn Timber ◽  
Timber Beams

The demand for timber has increased significantly in recent years. Therefore, reliable tools are needed to predict the mechanical properties of sawn timber, especially for structural applications. Very complex models require a lot of input data for analysis, which cannot always be guaranteed, especially in industrial practice. Thus, a simplified model for material description was developed and assessed with experiments (static bending tests carried out in accordance with the guidelines suggested in the European standard EN 408) and an analytical approach (gamma method according to the guidelines given in the European standard EN 1995). The effective stiffness was calculated as a major parameter, which has an influence on the elements’ behavior. The model included a near-surface mounted (NSM) local reinforcement technique, with CFRP strips of Scots pine timber beams being subjected to bending stresses. It is anticipated that the developed model can be a starting point for the repair engineering field, contributing to decision-making regarding conservation technique selection and range. Next, improvements of the model will provide more and more realistic results for numerical analysis in terms of the obtained failure mechanisms for sawn timber elements.

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

scholarly journals Multivalent weak interactions enhance selectivity of interparticle binding

2020 ◽  
Vol 117 (37) ◽  
pp. 22690-22697 ◽  
Author(s):  
M. R. W. Scheepers ◽  
L. J. van IJzendoorn ◽  
M. W. J. Prins
Keyword(s):  
Targeted Drug Delivery ◽  
Colloidal Particles ◽  
High Selectivity ◽  
Weak Interactions ◽  
Theoretical Work ◽  
Coated Particles ◽  
Receptor Interactions ◽  
Two Factors ◽  
Experimental Findings

Targeted drug delivery critically depends on the binding selectivity of cargo-transporting colloidal particles. Extensive theoretical work has shown that two factors are necessary to achieve high selectivity for a threshold receptor density: multivalency and weak interactions. Here, we study a model system of DNA-coated particles with multivalent and weak interactions that mimics ligand–receptor interactions between particles and cells. Using an optomagnetic cluster experiment, particle aggregation rates are measured as a function of ligand and receptor densities. The measured aggregation rates show that the binding becomes more selective for shorter DNA ligand–receptor pairs, proving that multivalent weak interactions lead to enhanced selectivity in interparticle binding. Simulations confirm the experimental findings and show the role of ligand–receptor dissociation in the selectivity of the weak multivalent binding.

Thermodynamics of James Watt – Ignored or not Understood?

2021 ◽  
Vol 42 (3) ◽  
pp. 397
Author(s):  
Jovan Mitrovic
Keyword(s):  
Latent Heat ◽  
Heat Engine ◽  
Primary Source ◽  
Rankine Cycle ◽  
Theoretical Work ◽  
Steam Pressure ◽  
Steam Engine ◽  
Saturated Steam ◽  
Maximum Efficiency ◽  
Starting Point

In the analysis of the development of thermodynamics as a science, the theoretical work of Sadi Carnot, published in 1824, is generally considered to be the starting point. Carnot studied the cycle of an ideal heat engine and formulated the condition for its maximum efficiency. In this article we examine James Watt’s contributions to the formation of fundamental concepts of thermodynamics, made in the course of his work on improving the Newcomen engine and developing his own steam engine. It is shown that Watt was the first to characterize thermodynamic properties such as latent heat and vapor density. The authors prove Watt’s priority in the studies of the dependence of saturated steam pressure on temperature, in which a critical point was found when the latent heat disappears. These results of Watt anticipated by many decades the studies on the thermodynamic critical state by Th. Andrews and J. Thomson. The article also discusses Wattʼs research on thermodynamic cycles. It is shown that he was the first to study the Rankine cycle with superheated steam, known from the history of thermodynamics. Watt was also the first scientist to introduce the concept of a steam engine’ volumetric work as the product of pressure and volume, and developed a device, the steam pressure indicator, to measure its value. We show the results obtained by Watt with steam to be considerably ahead of Prescott Jouleʼs work on the cooling and condensation of gases during expansion. The article presents an interpretation of Watt’s 1769 patent that is very important as the primary source for a subsequent study and establishment of the principles of energy conversion. The factual material presented in this article suggests that Watt’s scientific research have not been properly understood or simply went unnoticed.

Uniqueness

1996 ◽  
Author(s):  
Craig M. Bethke
Keyword(s):  
Geochemical Modeling ◽  
Theoretical Work ◽  
Input Constraints ◽  
Governing Equations ◽  
Single Root ◽  
Rate Laws ◽  
Starting Point ◽  
The Subject ◽  
Geochemical Models ◽  
Practical Question

A practical question that arises in quantitative modeling is whether the results of a modeling study are unique. In other words, is it possible to arrive at results that differ, at least slightly, from the original ones but nonetheless satisfy the governing equations and honor the input constraints? In the broadest sense, of course, no model is unique (see, for example, Oreskes et al., 1994). A geochemical modeler could conceptualize the problem differently, choose a different compilation of thermodynamic data, include more or fewer species and minerals in the calculation, or employ a different method of estimating activity coefficients. The modeler might allow a mineral to form at equilibrium with the fluid or require it to precipitate according to any of a number of published kinetic rate laws and rate constants, and so on. Since a model is a simplified version of reality that is useful as a tool (Chapter 2), it follows that there is no“correct” model, only a model that is most useful for a given purpose. A more precise question (Bethke, 1992) is the subject of this chapter: in geochemical modeling is there but a single root to the set of governing equations that honors a given set of input constraints? We might call such a property mathematical uniqueness, to differentiate it from the broader aspects of uniqueness. The property of mathematical uniqueness is important because once the software has discovered a root to a problem, the modeler may abandon any search for further solutions. There is no concern that the choice of a starting point for iteration has affected the answer. In the absence of a demonstration of uniqueness, on the other hand, the modeler cannot be completely certain that another solution, perhaps a more realistic or useful one, remains undiscovered. Geochemists, following early theoretical work in other fields, have long considered the multicomponent equilibrium problem (as defined in Chapter 3) to be mathematically unique. In fact, however, this assumption is not correct. Although relatively uncommon, there are examples of geochemical models in which more than one root of the governing equations satisfy the modeling constraints equally well. In this chapter, we consider the question of uniqueness and pose three simple problems in geochemical modeling that have nonunique solutions.

scholarly journals Towards Building Blocks for Supramolecular Architectures Based on Azacryptates

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1733 ◽  
Author(s):  
Ana Miljkovic ◽  
Sonia La Cognata ◽  
Greta Bergamaschi ◽  
Mauro Freccero ◽  
Antonio Poggi ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Building Blocks ◽  
Water Mixture ◽  
Molecular Systems ◽  
Supramolecular Architectures ◽  
Starting Point ◽  
The Difference ◽  
Supramolecular Devices

In this work, we report the synthesis of a new bis(tris(2-aminoethyl)amine) azacryptand L with triphenyl spacers. The binding properties of its dicopper complex for aromatic dicarboxylate anions (as TBA salts) were investigated, with the aim to obtain potential building blocks for supramolecular structures like rotaxanes and pseudo-rotaxanes. As expected, UV-Vis and emission studies of [Cu2L]4+ in water/acetonitrile mixture (pH = 7) showed a high affinity for biphenyl-4,4′-dicarboxylate (dfc2−), with a binding constant of 5.46 log units, due to the best match of the anion bite with the Cu(II)-Cu(II) distance in the cage’s cavity. Compared to other similar bistren cages, the difference of the affinity of [Cu2L]4+ for the tested anions was not so pronounced: conformational changes of L seem to promote a good interaction with both long (e.g., dfc2−) and short anions (e.g., terephthalate). The good affinity of [Cu2L]4+ for these dicarboxylates, together with hydrophobic interactions within the cage’s cavity, may promote the self-assembly of a stable 1:1 complex in water mixture. These results represent a good starting point for the application of these molecular systems as building units for the design of new supramolecular architectures based on non-covalent interactions, which could be of interest in all fields related to supramolecular devices.

Intermediates in the Formation and Thermolysis of Peroxides from Oxidations with Singlet Oxygen

2014 ◽  
Vol 67 (3) ◽  
pp. 320 ◽  
Author(s):  
Werner Fudickar ◽  
Torsten Linker
Keyword(s):  
Singlet Oxygen ◽  
Theoretical Work ◽  
Ene Reaction ◽  
Experimental Findings ◽  
Zwitterionic Intermediate ◽  
Concerted Reaction

Herein we describe the recent mechanistic understandings of the singlet oxygen ene reaction to give hydroperoxides and the [4+2] cycloaddition affording endoperoxides. Both experimental findings and theoretical work conclude in the formation of intermediates structurally similar to perepoxides during the ene reaction. Such intermediates mainly control the regio- and stereoselectivities of this reaction class. For the [4+2] cycloaddition, both a synchronous concerted reaction (benzene, naphthalenes) and a stepwise reaction with a non-symmetric zwitterionic intermediate (larger acenes) have been found. The thermolysis of endoperoxides derived from acenes proceeds stepwise for anthracenes, but in a concerted manner for less stable adducts such as naphthalene.

scholarly journals QM/MM Molecular Dynamics Investigation of the Binding of Organic Phosphates to the 100 Diaspore Surface

2020 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Molecular Dynamics ◽  
Food System ◽  
Specific Binding ◽  
Md Simulations ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Molecular Systems ◽  
Organic Phosphates ◽  
Surface Plane

<div><div><div><p>The fate of phosphorus (P) in the eco-system is strongly affected by the interaction of phos- phates with soil components and especially reactive soil mineral surfaces. As a consequence, P immobilization could occur which eventually leads to P inefficiency and thus unavailability to plants with strong implications on the global food system. A molecular level understanding of the mechanisms of the P binding to soil mineral surfaces could be a key for the development of novel strategies for more efficient P application. Much experimental work has been done to understand P binding to several reactive and abundant minerals especially goethite (α-FeOOH). On the other hand, atomistic modeling of the P-mineral molecular systems using molecular dynamics (MD) simulations is emerging as a new tool which provides more detailed information regarding the mechanisms, nature, and strength of these binding processes. The present study characterize the binding of the most abundant organic phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), to the 100 diaspore (α-AlOOH) surface plane. Here, different molecular models have been introduced to simulate typical situations for the P-binding at the diaspore/water interface. For all models, quantum mechanics/molecular mechanics (QM/MM) based MD simulations have been performed to explore the diaspore–IHP/GP–water interactions. The results provide evidence for the formation of monodentate (M) and bidentate (B) motifs for GP and M and as well as two monodentate (2M) motifs for IHP with the surface. The calculated interaction energies suggest that GP and IHP prefer to form the B and 2M motif, respectively. Moreover, IHP exhibited stronger binding than GP with diaspore and water. Further, the role of water in controlling binding strengths via promoting of specific binding motifs, formation of H-bonds, adsorption and dissociation at the surface, as well as proton transfer processes is demonstrated. Finally, the P-binding at the 100 diaspore surface plane is weaker than that at the 010 plane highlighting the influential role of the coordination number of Al atoms at the top surface of diaspore.</p></div></div></div>

Computer-based techniques for lead identification and optimization I: Basics

2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Annalisa Maruca ◽  
Francesca Alessandra Ambrosio ◽  
Antonio Lupia ◽  
Isabella Romeo ◽  
Roberta Rocca ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lead Optimization ◽  
Computational Techniques ◽  
Starting Point ◽  
Lead Identification ◽  
Modeling Techniques ◽  
Computer Based ◽  
Identification Processes ◽  
Telomeric Rna

Abstract This chapter focuses on computational techniques for identifying and optimizing lead molecules, with a special emphasis on natural compounds. A number of case studies have been specifically discussed, such as the case of the naphthyridine scaffold, discovered through a structure-based virtual screening (SBVS) and proposed as the starting point for further lead optimization process, to enhance its telomeric RNA selectivity. Another example is the case of Liphagal, a tetracyclic meroterpenoid extracted from Aka coralliphaga, known as PI3Kα inhibitor, provide an evidence for the design of new active congeners against PI3Kα using molecular dynamics (MD) simulations. These are only two of the numerous examples of the computational techniques’ powerful in drug design and drug discovery fields. Finally, the design of drugs that can simultaneously interact with multiple targets as a promising approach for treating complicated diseases has been reported. An example of polypharmacological agents are the compounds extracted from mushrooms identified by means of molecular docking experiments. This chapter may be a useful manual of molecular modeling techniques used in the lead-optimization and lead identification processes.

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