MolSpin—Flexible and extensible general spin dynamics software

Nielsen, Claus; Solov’yov, Ilia A.

doi:10.1063/1.5125043

Cited by 16 publications

(19 citation statements)

References 47 publications

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“…This benefit is not obtained from a 2D visual illustration (additional steps are necessary to locate its position). The software helps teachers in problem solving and provides a variety of perspectives in solving problems (Nielsen & Solov'yov, 2019).…”

Section: Discussionmentioning

confidence: 99%

GeoGebra in Project-Based Learning (Geo-PJBL): A dynamic tool for analytical geometry course

Kholid

Pradana

Maharani

et al. 2022

J. Technol. Sci. Educ.

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The integration of learning models and software is a trend in mathematics courses. However, no existing learning model for geometry courses involves the students in the making of a tool or media project. The researchers noticed the potential of the project-based learning (PjBL) model and GeoGebra in analytical geometry courses. This study revealed differences in the influence of the Geo-PjBL and PjBL models on students’ achievement. The subjects consisted of 137 prospective mathematics teachers. The Basic Geometry Instrument (BGI) was used to measure the subjects’ initial ability in basic geometry, and the Geometry Analytic Instrument (GAI) was used to evaluate the model and prospective teachers’ performance. The Geo-PjBL and PjBL classroom activities lasted for 15 weeks. Both classrooms received the same content; the difference between the Geo-PjBL and PjBL classrooms was the tools used to present the problems and the project results. An analysis of covariance (ANCOVA) was conducted to analyze the data (α = 0.01). The Geo-PjBL model is more effective in applying analytical geometry subjects that require precision and accurate visual illustrations. Meanwhile, in the range of algebraic operations, the Geo-PjBL model is as effective as the PjBL model.

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Section: Discussionmentioning

confidence: 99%

GeoGebra in Project-Based Learning (Geo-PJBL): A dynamic tool for analytical geometry course

Kholid

Pradana

Maharani

et al. 2022

J. Technol. Sci. Educ.

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“…It was found in an earlier study that the dynamical behavior of ErCry4a and ClCry4a differs even though ErCry4a was constructed using ClCry4a as a homology template. , Molecular dynamics (MD) simulations provide a valuable tool to investigate the dynamics of biomolecules, , including local dynamical fluctuations of small molecules bound to proteins. − Here, MD simulations were performed to determine the relevant structural and dynamic properties of Trp •+ and FAD •– in the five RP states from which the most important hyperfine interactions were calculated using density functional theory (DFT). Finally, the magnetic sensitivity of AtCry1 and ErCry4a was compared using the time-averaged hyperfine interactions to simulate the quantum yields of the reaction products by means of the spin dynamics software package MolSpin …”

Section: Introductionmentioning

confidence: 99%

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

et al. 2022

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The magnetic compass of migratory birds is thought to rely on a radical pair reaction inside the blue-light photoreceptor protein cryptochrome. The sensitivity of such a sensor to weak external magnetic fields is determined by a variety of magnetic interactions, including electron-nuclear hyperfine interactions. Here, we investigate the implications of thermal motion, focusing on fluctuations in the dihedral and librational angles of flavin adenine dinucleotide (FAD) and tryptophan (Trp) radicals in cryptochrome 4a from European robin (Erithacus rubecula, ErCry4a) and pigeon (Columba livia, ClCry4a) and cryptochrome 1 from the plant Arabidopsis thaliana (AtCry1). Molecular dynamics simulations and density functional theory-derived hyperfine interactions are used to calculate the quantum yield of radical pair recombination dependent on the direction of the geomagnetic field. This quantity and various dynamical parameters are compared for [FAD •− Trp •+ ] in ErCry4a, ClCry4a, and AtCry1, with TrpC or TrpD being the third and fourth components of the tryptophan triad/tetrad in the respective proteins. We find that (i) differences in the average dihedral angles in the radical pairs are small, (ii) the librational motions of TrpC •+ in the avian cryptochromes are appreciably smaller than in AtCry1, (iii) the rapid vibrational motions of the radicals leading to strong fluctuations in the hyperfine couplings affect the spin dynamics depending on the usage of instantaneous or time-averaged interactions. Future investigations of radical pair compass sensitivity should therefore not be based on single snapshots of the protein structure but should include the ensemble properties of the hyperfine interactions.

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“…The radical pair dynamics task in VIKING relies on the MolSpin software, 53 which has been developed separately by the members of the VIKING development team. It is a dedicated spin dynamics software package, which is designed to be able to perform any kind of calculation on the spin systems of arbitrary complexity.…”

Section: Methodsmentioning

confidence: 99%

Introducing VIKING: A Novel Online Platform for Multiscale Modeling

et al. 2019

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Various biochemical and biophysical processes, occurring on multiple time and length scales, can nowadays be studied using specialized software packages on supercomputer clusters. The complexity of such simulations often requires application of different methods in a single study and strong computational expertise. We have developed VIKING, a convenient web platform for carrying out multiscale computations on supercomputers. VIKING allows combining methods in standardized workflows, making complex simulations accessible to a broader biochemical and biophysical society.

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MolSpin—Flexible and extensible general spin dynamics software

Abstract: Paper published as part of the special topic on Spin Chemistry Note: The paper is part of the JCP Special Topic on Spin Chemistry.

Cited by 16 publications

References 47 publications

GeoGebra in Project-Based Learning (Geo-PJBL): A dynamic tool for analytical geometry course

GeoGebra in Project-Based Learning (Geo-PJBL): A dynamic tool for analytical geometry course

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

Introducing VIKING: A Novel Online Platform for Multiscale Modeling

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