scholarly journals Trimethylamine N-oxide (TMAO) resists the compression of water structure by magnesium perchlorate: terrestrial kosmotrope vs. Martian chaotrope

2020 ◽  
Vol 22 (9) ◽  
pp. 4924-4937
Author(s):  
Harrison Laurent ◽  
Alan K. Soper ◽  
Lorna Dougan
Keyword(s):  
Neutron Diffraction ◽  
Computational Modelling ◽  
Water Structure ◽  
Magnesium Perchlorate ◽  
Insight Into

Neutron diffraction and computational modelling provide insight into water structure.

scholarly journals Computational modelling of chromosome re-replication in mutant strains of fission yeast

2020 ◽  
Author(s):  
Béla Novák ◽  
John J Tyson
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Computational Modelling ◽  
Mitotic Cell ◽  
Cyclin Dependent Kinase ◽  
Slow Increase ◽  
Cell Cycles ◽  
Mitotic Cyclin ◽  
The Mathematical Model ◽  
Insight Into

AbstractTypically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized fashion (‘over-replication’) or by a systematic doubling of chromosome number (‘endoreplication’). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication licensing factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some over-replication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between over-replicating and endoreplicating cells. In case of induced over-production of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized over-replication, parallel to the slow increase of protein to very high levels.

scholarly journals Pathways towards true catalysts: computational modelling and structural transformations of Zn-polyoxotungstates

2019 ◽  
Vol 48 (35) ◽  
pp. 13293-13304 ◽  
Author(s):  
Lubin Ni ◽  
Robin Güttinger ◽  
C. A. Triana ◽  
Bernhard Spingler ◽  
Kim K. Baldridge ◽  
...  
Keyword(s):  
Noble Metal ◽  
Computational Modelling ◽  
Structural Transformations ◽  
Active Species ◽  
Oxidation Catalysts ◽  
Metal Free ◽  
Insight Into

Comprehensive computational modelling with advanced analytical investigations provides insight into mechanisms and active species of noble metal-free polyoxometalate oxidation catalysts.

Disorder in decagonal quasicrystals

2003 ◽  
Vol 218 (2) ◽  
Author(s):  
F. Frey ◽  
E. Weidner
Keyword(s):  
High Temperature ◽  
Neutron Diffraction ◽  
High Temperatures ◽  
Experimental Work ◽  
Diffuse Scattering ◽  
Diffuse Intensity ◽  
X Ray ◽  
Decagonal Quasicrystals ◽  
Ordered Alloys ◽  
Insight Into

AbstractComplementary neutron and x-ray diffuse scattering may provide insight into structural super-ordering and disordering of decagonal quasicrystals (d-phases), and, in consequence, into the formation and stability of aperiodically ordered alloys. Neutron diffraction makes a contrasting almost isoelectronic atomic species possible, as well as a separation of elastic and inelastic diffuse intensity contributions. Experimental work at high temperatures is comparatively unproblematic. The method suffers, however, from the difficulty in obtaining sufficiently sized mono-grain samples and a lack of dedicated neutron diffraction instruments. Recent results, with a main focus on high-temperature (<1000°C) investigations of disordered decagonal Al—Ni—Co phases are reported and some tentative models are discussed.

scholarly journals Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

2018 ◽  
Author(s):  
Michael Wall ◽  
Gaetano Calabró ◽  
Christopher I. Bayly ◽  
David Mobley ◽  
Gregory Warren
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Neutron Diffraction ◽  
Water Structure ◽  
Md Simulations ◽  
Neutron Density ◽  
Macromolecular Crystallography ◽  
Field Development ◽  
Biomolecular Solvation ◽  
Dynamics Simulations

In order to compare ordered water positions from experiment with those from molecular dynamics (MD) simulations, a number of MD models of water structure in crystalline endoglucanase were calculated. The starting MD model was derived from a joint X-ray and neutron diffraction crystal structure, enabling the use of experimentally assigned protonation states. Simulations were performed in the crystalline state, using a periodic 2x2x2 supercell with explicit solvent. Water electron and neutron density maps were computed from MD trajectories using standard macromolecular crystallography methods. In one set of simulations, harmonic restraints were applied to bias the protein structure toward the crystal structure. For these simulations, the recall of crystallographic waters using strong peaks in the MD water electron density was excellent, and there also was substantial visual agreement between the boomerang-like wings of the neutron density and the crystalline water hydrogen positions. An unrestrained simulation also was performed. For this simulation, the recall of crystallographic waters was much lower. The results demonstrate that it is now possible to recover crystallographic water structure using restrained MD simulations, but that it is not yet reasonable to expect unrestrained MD simulations to do the same. Further development and generalization of MD water models for force field development, macromolecular crystallography, and medicinal chemistry applications is now warranted. In particular, the combination of room-temperature crystallography, neutron diffraction, and crystalline MD simulations promises to substantially advance modeling of biomolecular solvation.

Explaining Ground Effect Aerodynamics via a Real-Life Reference Frame

2014 ◽  
Vol 553 ◽  
pp. 229-234
Author(s):  
Philip Close ◽  
Tracie J. Barber
Keyword(s):  
Reference Frame ◽  
Reference Frames ◽  
Computational Simulation ◽  
Real Life ◽  
Computational Modelling ◽  
Ground Effect ◽  
The Body ◽  
Moving Body ◽  
Set Up ◽  
Insight Into

The principle of relative motion as the cause of forces on a body submersedin a uid is foundational in the study of uid mechanics. In aerodynamics the wind tunnelis used as a convenient and safe method by which to test the aerodynamic performance ofbodies. This body-stationary convention has carried over into the computational world withthe development of CFD, though there is no practical reason why the moving body/stationaryuid set-up that corresponds to reality cannot be used for computational modelling. This pointbecomes particularly important as the concept of ground e ect is introduced. With an extraboundary nearby it becomes harder to appropriatel y match the experimental set-up with reality,and the extra boundary condition also adds complexity to computational simulation. A studywas undertaken to compare the body-stationary and body-moving reference frames in grounde ect. The moving reference frame velocity elds allowed new insight into the aerodynamics ofground e ect.

scholarly journals The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations

2019 ◽  
Vol 72 (8) ◽  
pp. 574 ◽  
Author(s):  
Nevena Todorova ◽  
Irene Yarovsky
Keyword(s):  
Amyloid Fibrils ◽  
Conformational Dynamics ◽  
Computational Modelling ◽  
Amyloid Β ◽  
Local Environment ◽  
Theoretical Modelling ◽  
Apolipoprotein C ◽  
Amyloidogenic Peptides ◽  
Insight Into ◽  
Aggregation Phenomena

Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.

Total neutron diffraction: a route to the correct local structure of disordered LaMo2O5 and its application to the model compound Zn2Mo3O8

1999 ◽  
Vol 55 (5) ◽  
pp. 683-697 ◽  
Author(s):  
Simon J. Hibble ◽  
Steven P. Cooper ◽  
Saban Patat ◽  
Alex. C. Hannon
Keyword(s):  
Neutron Diffraction ◽  
Local Structure ◽  
Model Compound ◽  
Group Symmetry ◽  
Total Neutron ◽  
Space Group Symmetry ◽  
Space Group ◽  
Average Structure ◽  
Local Structures ◽  
Insight Into

Analysis of Bragg diffraction is the normal route to the structure of crystalline materials. Here we demonstrate the use of total neutron diffraction in determining the local structure in the disordered lanthanum molybdate LaMo2O5. An average structure with space-group symmetry P63/mmc accounts for the Bragg scattering and shows that the compound contains the rare Mo6O18 cluster and a unique type of Mo—Mo bonded sheet. However, this gives an incomplete picture of the structure, since it does not reveal how the sites with fractional occupancy are occupied at a local level. Two models describing possible local structures are constructed by removing symmetry elements present in the average structure. Total correlation functions, T(r), calculated from these structures, with space-group symmetry P63 mc and P3¯m1, are compared with the experimental T(r) to show the validity of these local structures. The close relationship between the T(r)'s of the component structures gives an insight into why disorder occurs in LaMo2O5. The calculated and experimental T(r)'s for a model compound, Zn2Mo3O8, are compared to show the agreement expected from an ordered crystalline material. Remaining discrepancies between our model and the experimental T(r) give an insight into the origin of additional disorder in LaMo2O5.

scholarly journals Information Flow in Planar Polarity

2017 ◽  
Author(s):  
Katherine H Fisher ◽  
David Strutt ◽  
Alexander G Fletcher
Keyword(s):  
Information Flow ◽  
Double Mutant ◽  
Protein Complexes ◽  
Individual Cell ◽  
Cell Signalling ◽  
Computational Modelling ◽  
Planar Polarity ◽  
Signalling Models ◽  
Scale Properties ◽  
Insight Into

SummaryIn developing tissues, sheets of cells become planar polarised, enabling coordination of cell behaviours. It has been suggested that ‘signalling’ of polarity information between cells may occur either bidirectionally or monodirectionally between the molecules Frizzled (Fz) and Van Gogh (Vang). Using computational modelling we find that both bidirectional and monodirectional signalling models reproduce known non-autonomous phenotypes derived from patches of mutant tissue of key molecules, but predict different phenotypes from double mutant tissue, which have previously given conflicting experimental results. Consequently, we re-examine experimental phenotypes in the Drosophila wing, concluding that signalling is most likely bidirectional. Our modelling suggests that bidirectional signalling can be mediated either indirectly via bidirectional feedbacks between asymmetric intercellular protein complexes, or directly via different affinities for protein binding in intercellular complexes, suggesting future avenues for investigation. Our findings offer insight into mechanisms of juxtacrine cell signalling and how tissue-scale properties emerge from individual cell behaviours.

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