Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented. The SALCs are constructed with the use of projection operators for the irreducible representations, as well as subgroups for determining splitting fields for a canonical basis. The character tables for the point groups are auto generated, and the algorithm is described. Symmetrisation of molecules use a projection into the totally symmetric space, whereas for wavefunctions projection as well and partner function determination and averaging is used. The software has been released as a stand-alone, open source library under the MIT license and integrated into both computational and molecular modelling software.Graphical abstract.
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http://dx.doi.org/10.1186/s13321-017-0193-3 | DOI Listing |
Chaos
December 2024
Potsdam Institute for Climate Impact Research, Telegrafenberg, Potsdam 14473, Germany.
Adaptive dynamical networks are ubiquitous in real-world systems. This paper aims to explore the synchronization dynamics in networks of adaptive oscillators based on a paradigmatic system of adaptively coupled phase oscillators. Our numerical observations reveal the emergence of synchronization cluster bursting, characterized by periodic transitions between cluster synchronization and global synchronization.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, P.R. China.
The evolution of photosynthetic reaction centers (RCs) from anoxygenic bacteria to higher-order oxygenic cynobacteria and plants highlights a remarkable journey of structural and functional diversification as an adaptation to environmental conditions. The role of chirality in these centers is important, influencing the arrangement and function of key molecules involved in photosynthesis. Investigating the role of chirality may provide a deeper understanding of photosynthesis and the evolutionary history of life on Earth.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
In simulations, particles are traditionally treated as rigid platforms with variable sizes, shapes, and interaction parameters. While this representation is applicable for rigid core platforms, particles consisting of soft platforms (e.g.
View Article and Find Full Text PDFAdv Sci (Weinh)
December 2024
School of Engineering Mathematics and Technology & Bristol Robotics Laboratory, University of Bristol, Bristol, BS8 1UB, UK.
Sperm swimming is essential for reproduction, with movement strategies adapted to specific environments. Sperm navigate by modulating the symmetry of their flagellar beating, but how they swim forward with asymmetrical beats remains unclear. Current methods lack the ability to robustly detect the flagellar symmetry state in free-swimming spermatozoa, despite its importance in understanding sperm motility.
View Article and Find Full Text PDFKnee Surg Sports Traumatol Arthrosc
December 2024
Department of Sports Physical Therapy and Rehabilitation, Faculty of Physical Therapy and Rehabilitation, Hacettepe University, Ankara, Turkey.
Purpose: Recently, blood flow restriction (BFR) and cross education (CE) trainings are the options for quadriceps strength recovery after anterior cruciate ligament reconstruction (ACLR). The aim of this study was to investigate the effects of CE combined with BFR on quadriceps strength and thickness after ACLR.
Methods: Twenty-four male patients [(Age: 24.
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