scholarly journals Impact of Force Function Formulations on the Numerical Simulation of Centre-Based Models

2020 ◽  
Vol 82 (10) ◽  
Author(s):  
Sonja Mathias ◽  
Adrien Coulier ◽  
Anass Bouchnita ◽  
Andreas Hellander
Keyword(s):  
Cell Division ◽  
Open Source Software ◽  
Computational Study ◽  
Population Level ◽  
Biological Behaviour ◽  
Cancer Modelling ◽  
Software Implementations ◽  
Cell Trajectories ◽  
Cell Centre ◽  
Good Agreement

Abstract Centre-based or cell-centre models are a framework for the computational study of multicellular systems with widespread use in cancer modelling and computational developmental biology. At the core of these models are the numerical method used to update cell positions and the force functions that encode the pairwise mechanical interactions of cells. For the latter, there are multiple choices that could potentially affect both the biological behaviour captured, and the robustness and efficiency of simulation. For example, available open-source software implementations of centre-based models rely on different force functions for their default behaviour and it is not straightforward for a modeller to know if these are interchangeable. Our study addresses this problem and contributes to the understanding of the potential and limitations of three popular force functions from a numerical perspective. We show empirically that choosing the force parameters such that the relaxation time for two cells after cell division is consistent between different force functions results in good agreement of the population radius of a two-dimensional monolayer relaxing mechanically after intense cell proliferation. Furthermore, we report that numerical stability is not sufficient to prevent unphysical cell trajectories following cell division, and consequently, that too large time steps can cause geometrical differences at the population level.

scholarly journals Impact of force function formulations on the numerical simulation of centre-based models

2020 ◽  
Author(s):  
Sonja Mathias ◽  
Adrien Coulier ◽  
Anass Bouchnita ◽  
Andreas Hellander
Keyword(s):  
Cell Division ◽  
Open Source Software ◽  
Computational Study ◽  
Population Level ◽  
Biological Behaviour ◽  
Cancer Modelling ◽  
Software Implementations ◽  
Cell Trajectories ◽  
Cell Centre ◽  
Good Agreement

AbstractCentre-based, or cell-centre models are a framework for the computational study of multicellular systems with widespread use in cancer modelling and computational developmental biology. At the core of these models are the numerical method used to update cell positions and the force functions that encode the pairwise mechanical interactions of cells. For the latter there are multiple choices that could potentially affect both the biological behaviour captured, and the robustness and efficiency of simulation. For example, available open-source software implementations of centre-based models rely on different force functions for their default behaviour and it is not straightforward for a modeler to know if these are interchangeable. Our study addresses this problem and contributes to the understanding of the potential and limitations of three popular force functions from a numerical perspective. We show empirically that choosing the force parameters such that the relaxation time for two cells after cell division is consistent between different force functions results in good agreement of the population radius of a growing monolayer. Furthermore, we report that numerical stability is not sufficient to prevent unphysical cell trajectories following cell division, and consequently, that too large time steps can cause geometrical differences at the population level.

Explaining the magnetism of gold

2017 ◽  
Author(s):  
Robson de Farias
Keyword(s):  
Gas Phase ◽  
Computational Study ◽  
Formation Enthalpy ◽  
Gold Atom ◽  
Orbital Energy ◽  
Knudsen Effusion ◽  
Energy Diagram ◽  
Unpaired Electrons ◽  
The Difference ◽  
Good Agreement

<p>In the present work, a computational study is performed in order to clarify the possible magnetic nature of gold. For such purpose, gas phase Au<sub>2</sub> (zero charge) is modelled, in order to calculate its gas phase formation enthalpy. The calculated values were compared with the experimental value obtained by means of Knudsen effusion mass spectrometric studies [5]. Based on the obtained formation enthalpy values for Au<sub>2</sub>, the compound with two unpaired electrons is the most probable one. The calculated ionization energy of modelled Au<sub>2</sub> with two unpaired electrons is 8.94 eV and with zero unpaired electrons, 11.42 eV. The difference (11.42-8.94 = 2.48 eV = 239.29 kJmol<sup>-1</sup>), is in very good agreement with the experimental value of 226.2 ± 0.5 kJmol<sup>-1</sup> to the Au-Au bond<sup>7</sup>. So, as expected, in the specie with none unpaired electrons, the two 6s<sup>1</sup> (one of each gold atom) are paired, forming a chemical bond with bond order 1. On the other hand, in Au<sub>2</sub> with two unpaired electrons, the s-d hybridization prevails, because the relativistic contributions. A molecular orbital energy diagram for gas phase Au<sub>2</sub> is proposed, explaining its paramagnetism (and, by extension, the paramagnetism of gold clusters and nanoparticles).</p>

Computational Study on the Kinetics and Mechanisms of Unimolecular Reactions of (Z)-(Z)-N-(λ5-phosphanylidene) Formohydrazonic Formic Anhydride: Intramolecular aza-Wittig Reaction in Competition with Mumm Rearrangement

2020 ◽  
Vol 17 (11) ◽  
pp. 884-889
Author(s):  
Somayeh Mirdoraghi ◽  
Hamed Douroudgari ◽  
Farideh Piri ◽  
Morteza Vahedpour
Keyword(s):  
Rate Constants ◽  
Density Functional ◽  
Wittig Reaction ◽  
Computational Study ◽  
Single Step ◽  
Low Energy ◽  
Coupled Cluster ◽  
Unimolecular Reaction ◽  
Single Step Reaction ◽  
Good Agreement

For (Z)-(Z)-N-(λ5-phosphanylidene) formohydrazonic formic anhydride, Aza-Wittig reaction and Mumm rearrangement are studied using both density functional and coupled cluster theories. For this purpose, two different products starting from one substrate are considered that are competing with each other. The obtained products, P1 and P2, are thermodynamically favorable. The product of the aza-Wittig reaction, P1, is more stable than the product of Mumm rearrangement (P2). For the mentioned products, just one reliable pathway is separately proposed based on unimolecular reaction. Therefore, the rate constants based on RRKM theory in 300-600 K temperature range are calculated. Results show that the P1 generation pathway is a suitable path due to low energy barriers than the path P2. The first path has three steps with three transition states, TS1, TS2, and TS3. The P2 production path is a single-step reaction. In CCSD level, the computed barrier energies are 14.55, 2.196, and 10.67 kcal/mol for Aza-Wittig reaction and 42.41 kcal/mol for Mumm rearrangement in comparison with the corresponding complexes or reactants. For final products, the results of the computational study are in a good agreement with experimental predictions.

scholarly journals Combinatorial Library Designing and Virtual Screening of Cryptolepine Derivatives against Topoisomerase II by Molecular Docking

2020 ◽  
Author(s):  
Maria ◽  
Zahid Khan
Keyword(s):  
Molecular Docking ◽  
Cell Division ◽  
Binding Energy ◽  
Cancer Cells ◽  
Anticancer Agents ◽  
Combinatorial Library ◽  
Topoisomerase Ii ◽  
Computational Study ◽  
Binding Energies ◽  
Potential Inhibitors

AbstractComputational approaches have emerging role for designing potential inhibitors against topoisomerase 2 for treatment of cancer. TOP2A plays a key role in DNA replication before cell division and thus facilitates the growth of cells. This function of TOP2A can be suppressed by targeting with potential inhibitors in cancer cells to stop the uncontrolled cell division. Among potential inhibitors cryptolepine is more selective and has the ability to intercalate into DNA, effectively block TOP2A and cease cell division in cancer cells. However, cryptolepine is non-specific and have low affinity, therefore, a combinatorial library was designed and virtually screened for identification of its derivatives with greater TOP2A binding affinities.A combinatorial library of 31114 derivatives of cryptolepine was formed and the library was virtually screened by molecular docking to predict the molecular interactions between cryptolepine derivatives and TOP2A taking cryptolepine as standard. The overall screening and docking approach explored all the binding poses of cryptolepine for TOP2A to calculate binding energy. The compounds are given database number 8618, 907, 147, 16755, and 8186 scored lowest binding energies of −9.88kcal/mol, −9.76kcal/mol, −9.75kcal/mol, −9.73kcal/mol, and −9.72kcal/mol respectively and highest binding affinity while cryptolepine binding energy is −6.09kcal/mol. The good binding interactions of the derivatives showed that they can be used as potent TOP2A inhibitors and act as more effective anticancer agents than cryptolepine itself. The interactions of derivatives with different amino acid residues were also observed. A comprehensive understanding of the interactions of proposed derivatives with TOP2A helped for searching more novel and potent drug-like molecules for anticancer therapy. This Computational study suggests useful references to understand inhibition mechanisms that will help in the modification of TOP2A inhibitors.

scholarly journals On the complexity of haplotyping a microbial community

2020 ◽  
Author(s):  
Samuel M Nicholls ◽  
Wayne Aubrey ◽  
Kurt De Grave ◽  
Leander Schietgat ◽  
Christopher J Creevey ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Sample ◽  
Population Level ◽  
Single Individual ◽  
Metagenomic Sample ◽  
Potential Benefits ◽  
Software Implementations ◽  
Occurrence Matrix ◽  
Number Of Individuals ◽  
Traversal Algorithm

Abstract Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes), but for an unknown number of individuals and haplotypes. Results The problem of single individual haplotyping (SIH) was first formalised by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of “haplotyping” metagenomic samples, with a new formalisation of Lancia et al’s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping (MIH) problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm. Availability and implementation Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) are open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively.

scholarly journals Benzamide Derivatives Targeting the Cell Division Protein FtsZ: Modifications of the Linker and the Benzodioxane Scaffold and Their Effects on Antimicrobial Activity

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 160 ◽  
Author(s):  
Valentina Straniero ◽  
Lorenzo Suigo ◽  
Andrea Casiraghi ◽  
Victor Sebastián-Pérez ◽  
Martina Hrast ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Cell Division ◽  
Single Molecule ◽  
Efflux Pump ◽  
Computational Study ◽  
Structural Features ◽  
Temperature Sensitive ◽  
Bacterial Cell Division ◽  
Gram Positive ◽  
Prokaryotic Protein

Filamentous temperature-sensitive Z (FtsZ) is a prokaryotic protein with an essential role in the bacterial cell division process. It is widely conserved and expressed in both Gram-positive and Gram-negative strains. In the last decade, several research groups have pointed out molecules able to target FtsZ in Staphylococcus aureus, Bacillus subtilis and other Gram-positive strains, with sub-micromolar Minimum Inhibitory Concentrations (MICs). Conversely, no promising derivatives active on Gram-negatives have been found up to now. Here, we report our results on a class of benzamide compounds, which showed comparable inhibitory activities on both S. aureus and Escherichia coli FtsZ, even though they proved to be substrates of E. coli efflux pump AcrAB, thus affecting the antimicrobial activity. These surprising results confirmed how a single molecule can target both species while maintaining potent antimicrobial activity. A further computational study helped us decipher the structural features necessary for broad spectrum activity and assess the drug-like profile and the on-target activity of this family of compounds.

scholarly journals Synthesis, characterization and theoretical calculations of Cu(I) complex of trithiocyanuric acid [Cu(ttc)3]

2018 ◽  
Vol 23 (2) ◽  
pp. 241-266 ◽  
Author(s):  
Ximena Verónica Jaramillo-Fierro ◽  
César Zambrano ◽  
Francisco Fernández ◽  
Regino Saenz-Puche ◽  
César Costa ◽  
...  
Keyword(s):  
Computational Study ◽  
Theoretical Calculations ◽  
Photophysical Properties ◽  
Vibrational Frequencies ◽  
Basis Sets ◽  
Vertical Excitation ◽  
Experimental Values ◽  
Homo Lumo ◽  
Perchlorate Hexahydrate ◽  
Good Agreement

A new Cu(I) complex constructed by reaction of trithiocyanuric acid (ttc) and copper (II) perchlorate hexahydrate has been successfully synthesized by a slow sedimentation method in a DMF solvent at room temperature. The molecular structure of the compound was elucidated by MALDI-TOFMS, UV Vis and FTIR spectroscopy, DSC-TGA analysis and magnetic susceptibility measurement. The proposed structure was corroborated by a computational study carried out with the Gaussian09 and AIMAII programs using the RB3LYP hybrid DFT functional with both 6-31G and Alhrich-TZV basis sets. The calculated vibrational frequencies values were compared with experimental FTIR values. Photophysical properties of the synthesized complex were evaluated by UV-Visible spectroscopy and compared with computed vertical excitation obtained from TDDFT. The theoretical vibrational frequencies and the UV Vis spectra are in good agreement with the experimental values. Additionally, the Frontier Molecular Orbitals (HOMO-LUMO) and the Molecular Electrostatic Potential of the complex was calculated using same theoretical approximation. The results showed the interaction between three coordinatedl igand atoms and the Cu(I) ion.

scholarly journals Relevance of the Cell Neighborhood Size in Landscape Metrics Evaluation and Free or Open Source Software Implementations

2019 ◽  
Vol 8 (12) ◽  
pp. 586
Author(s):  
Paolo Zatelli ◽  
Stefano Gobbi ◽  
Clara Tattoni ◽  
Maria Giulia Cantiani ◽  
Nicola La Porta ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Landscape Metrics ◽  
Shape Index ◽  
Edge Density ◽  
Patch Area ◽  
Aggregation Index ◽  
Use Values ◽  
Software Implementations ◽  
Patch Density

Landscape metrics constitute one of the main tools for the study of the changes of the landscape and of the ecological structure of a region. The most popular software for landscape metrics evaluation is FRAGSTATS, which is free to use but does not have free or open source software (FOSS). Therefore, FOSS implementations, such as QGIS’s LecoS plugin and GRASS’ r.li modules suite, were developed. While metrics are defined in the same way, the “cell neighborhood” parameter, specifying the configuration of the moving window used for the analysis, is managed differently: FRAGSTATS can use values of 4 or 8 (8 is default), LecoS uses 8 and r.li 4. Tests were performed to evaluate the landscape metrics variability depending on the “cell neighborhood” values: some metrics, such as “edge density” and “landscape shape index”, do not change, other, for example “patch number”, “patch density”, and “mean patch area”, vary up to 100% for real maps and 500% for maps built to highlight this variation. A review of the scientific literature was carried out to check how often the value of the “cell neighborhood” parameter is explicitly declared. A method based on the “aggregation index” is proposed to estimate the effect of the uncertainty on the “cell neighborhood” parameter on landscape metrics for different maps.

Unsteady Hydrodynamic Forces due to Rotor-Stator Interaction on a Diffuser Pump With Identical Number of Vanes on the Impeller and Diffuser

2005 ◽  
Vol 127 (4) ◽  
pp. 743-751 ◽  
Author(s):  
M. Zhang ◽  
H. Tsukamoto
Keyword(s):  
Computational Study ◽  
Pressure Fluctuations ◽  
Vortex Method ◽  
Hydrodynamic Forces ◽  
Pump Impeller ◽  
Vaned Diffuser ◽  
Fluid Forces ◽  
Rotor Stator Interaction ◽  
Identical Number ◽  
Good Agreement

Experimental and computational study was developed for unsteady hydrodynamic forces on a diffuser pump impeller excited by the interaction between the impeller and the vaned diffuser with the same number of vanes as impeller. Unsteady flow calculations are made using commercially available CFD software, CFX-TASCflow, as well as the two-dimensional vortex method. Calculated pressure and fluid forces on the impeller show good agreement with measured ones. It has been demonstrated that the fluid forces on the impeller with the same number of vanes as the vaned diffuser are smaller compared with other combinations of vane numbers. However, the pressure fluctuations are found to be greater than other cases.

A Computational Study of the Overload Characteristic Curves of Projectile Penetrating Concrete

2011 ◽  
Vol 462-463 ◽  
pp. 582-586
Author(s):  
Qiong Deng ◽  
Yu Long Li ◽  
Q.J. Yu ◽  
Tao Suo ◽  
P. Xue
Keyword(s):  
Layer Thickness ◽  
Computational Study ◽  
Constitutive Models ◽  
Lagrange Method ◽  
Commercial Software ◽  
Concrete Material ◽  
Concrete Plate ◽  
Maximum Value ◽  
Good Agreement ◽  
Peak Value

In the present paper, a concrete material is taken as a studying object, both the No. 16 and the JHC constitutive models in LS-DYNA commercial software are used because the parameters of both models are comparatively easy to obtain. The results show that, computational maximum value and the width of the overload curves are good agreement with experimental curves by using these two models in the Lagrange method. With increasing penetrating depth, the ramp and down slopes of the overload curves by computing is increasingly agreement with experimental curves. The JHC model is better to compute overload curves in the Lagrange method. The Lagrange method is also used to compute the penetration of multilayer concrete plate. It is found that, the peak value of acceleration goes down with increasing penetrating layers; this decreasing peak value depends on layer thickness and the strength. Acceleration value between layers will go to zero; this trend is agreement with experiments.

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