Article
Neurosciences
Rosita Shishegar, Fabrizio Pizzagalli, Nellie Georgiou-Karistianis, Gary F. Egan, Neda Jahanshad, Leigh A. Johnston
Summary: This study introduces a new curvature-based local gyrification index (LB-GI) for accurate measurement of the complexity of patterns of cortical folding. The LB-GI method quantifies gyrification at each point on the cortical surface with reference to surrounding gyral points, overcoming limitations of traditional methods and providing detailed insights into patterns of cortical folding.
Article
Mathematics
Yanlin Li, Erhan Guler
Summary: This article examines twisted hypersurfaces x with a specific rotating axis in a five-dimensional Euclidean space E-5 and calculates their fundamental forms, Gauss map, and shape operator. The curvatures of the hypersurfaces x are obtained using the Cayley-Hamilton theorem in E-5. The solutions to the differential equations of the hypersurfaces' curvatures remain open problems, and the umbilically and minimality conditions of x's curvatures are determined. Additionally, the Laplace-Beltrami operator relation of x is provided.
Article
Mathematics
Yanlin Li, Erhan Guler
Summary: This article presents a family of hypersurfaces of revolution in the five-dimensional pseudo-Euclidean space E-2(5), distinguished by four parameters. The matrices corresponding to the fundamental form, Gauss map, and shape operator of this family are computed. Using the Cayley-Hamilton theorem, the curvatures of the specific family are determined. Furthermore, the criteria for maximality within this framework are established, along with the relationship between the Laplace-Beltrami operator of the family and a 5x5 matrix.
Article
Mathematics, Applied
Yanlin Li, Erhan Guler
Summary: In this study, a family of hypersurfaces of revolution characterized by six parameters in seven-dimensional pseudo-Euclidean space is introduced. The authors analyze the geometric properties of these hypersurfaces by calculating corresponding matrices and determining curvatures using matrix algebra techniques. Furthermore, equations describing the relationship between mean curvature and Gauss-Kronecker curvature are established, and the relation between the Laplace-Beltrami operator and a specific matrix is investigated.
Article
Mathematics, Applied
Sujuan Long, Qiqi Zhang, Guijuan Lin, Conghui Shen
Summary: In this paper, we estimate the first eigenvalue λ1(&UDelta;g) of the Laplace-Beltrami operator &UDelta;g associated with the Bergman metric g on the Cartan classical domains of type III and IV, denoted as RA.
Article
Mathematics
Shahroud Azami
Summary: This paper derives the evolution equation for the first eigenvalue of the Witten-Laplace operator on a closed oriented manifold, and shows some interesting monotonic quantities under the mean curvature flow.
INDIAN JOURNAL OF PURE & APPLIED MATHEMATICS
(2022)
Article
Mathematics
Zhuochao Tang, Zhuojia Fu, Sergiy Reutskiy
Summary: This paper presents an extrinsic approach based on physics-informed neural networks (PINNs) for solving partial differential equations on high-dimensional surfaces. By incorporating the surface differential operators into the loss function, this approach achieves higher accuracy and efficiency in solving surface problems compared to embedding methods based on PINNs. Furthermore, the strong nonlinear mapping ability of neural networks ensures robustness in solving time-dependent nonlinear problems on complex surfaces.
Article
Computer Science, Software Engineering
Ahmad Nasikun, Klaus Hildebrandt
Summary: Sparse eigenproblems are crucial in computer graphics, and this article introduces a novel solver called the Hierarchical Subspace Iteration Method (HSIM) that operates on a hierarchy of nested vector spaces. HSIM significantly reduces the number of iterations needed compared to non-hierarchical methods.
ACM TRANSACTIONS ON GRAPHICS
(2022)
Article
Mathematics
Mustafa Altin, Ahmet Kazan
Summary: This study focuses on rotational hypersurfaces in 4-dimensional Lorentz-Minkowski space, specifically about spacelike axes. Results are obtained based on Gaussian and mean curvatures, and the study also extends to rotational hypersurfaces about timelike and lightlike axes.
HACETTEPE JOURNAL OF MATHEMATICS AND STATISTICS
(2021)
Article
Multidisciplinary Sciences
Duluxan Sritharan, Shu Wang, Sahand Hormoz
Summary: The study examines two approaches from differential geometry to estimate the Riemannian curvature of low-dimensional manifolds, finding that the intrinsic approach fails to accurately estimate curvature while the extrinsic approach is able to handle more complex models even under practical constraints.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Interdisciplinary Applications
Jayaraman Thirumagal, Manjunatha Mahadevappa, Anup Sadhu, Pranab Kumar Dutta
Summary: Brain ventricle shape analysis using wave kernel signature algorithm shows promising results in distinguishing normal and atrophy subjects with high classification accuracy.
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2021)
Article
Mathematics
Hans Volkmer
Summary: This study investigates the eigenvalues of the Laplace-Beltrami operator on a torus embedded in three-dimensional Euclidean space, which are determined by the eigenvalues of Sturm-Liouville problems with separated boundary conditions. The eigenvalues are approximated by those of generalized eigenvalue problems involving tridiagonal matrices, and a non-coexistence result is proved. The behavior of eigenvalues is studied as the ratio of inner and outer radius of the torus approaches zero or one.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2021)
Article
Mathematics, Applied
David B. Dunson, Hau-Tieng Wu, Nan Wu
Summary: In this study, a series of spectral convergence results are provided in the manifold setting, quantifying how the eigenvectors and eigenvalues of the graph Laplacian converge to the eigenfunctions and eigenvalues of the Laplace-Beltrami operator in the L-infinity sense. Based on these results, convergence of the proposed heat kernel approximation algorithm to the exact heat kernel is guaranteed, along with the convergence rate. This work is the first to explore spectral convergence in the L-infinity sense and provide a numerical heat kernel reconstruction with theoretical guarantees from a point cloud.
APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS
(2021)
Article
Mathematics, Applied
Mustafa Altin, Ahmet Kazan, Dae Won Yoon
Summary: This paper focuses on the Gaussian and mean curvatures, minimality, and Laplace-Beltrami operators of 2-ruled hypersurfaces in Euclidean 4-space.
JOURNAL OF GEOMETRY AND PHYSICS
(2021)
Article
Computer Science, Artificial Intelligence
Xu-Qian Fan, Wenyong Gong
Summary: The Laplace-Beltrami operator is essential for manifold analysis. This paper introduces a new SLBO operator in spatial Schwarzschild manifolds. Two global approximate schemes are derived and applied to robot path planning and tetrahedral mesh smoothing, demonstrating the effectiveness of the proposed methods using the SLBO.
SIAM JOURNAL ON IMAGING SCIENCES
(2023)
Article
Biophysics
Sebastian J. Mueller, Franziska Weigl, Carina Bezold, Christian Baecher, Krystyna Albrecht, Stephan Gekle
Summary: In this study, a numerical model is proposed to simulate the deformation of biological cells in arbitrary three-dimensional flows, calibrated using experimental data and validated through comparison to previous experiments on different types of cells and particles.
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
J. M. Lyu, Paul G. Chen, G. Boedec, M. Leonetti, M. Jaeger
Summary: This study presents an isogeometric computational framework combining finite element method (FEM) and boundary element method (BEM) for accurate prediction of deformation and motion of a single soft particle in microfluidic channels. The numerical method demonstrates second-order convergence in both time and space, and is validated by comparison with benchmark solutions for various examples in the literature.
COMPUTERS & FLUIDS
(2021)
Article
Mechanics
Katharina Graessel, Christian Baecher, Stephan Gekle
Summary: This study investigates the influence of anisotropy on the Rayleigh-Plateau instability mechanism under various surface tension conditions. It reveals the significant impact of anisotropy on the dominant wavelength of instability, as well as the formation of satellite droplets under anisotropic tension. The research combines analytical linear stability analysis with numerical simulations to explore the effects of different tension scenarios on instability behavior.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Mechanics
Sudip Das, Marc Jaeger, Marc Leonetti, Rochish M. Thaokar, Paul G. Chen
Summary: In this study, the deformation of deflated vesicles under different types of pulses was computationally investigated, revealing the sensitive dependence of intermediate shapes on pulse type. The research suggests that the transmembrane potential can be regulated using a bipolar pulsed-DC field, and the dynamics of vesicle shapes vary depending on whether the pulse is unipolar or bipolar. Parameters were suggested for potentially demonstrating simulation results in experiments.
Article
Polymer Science
Sanwardhini Pantawane, Stephan Gekle
Summary: In this study, atomistic and coarse-grained molecular dynamics simulations were used to investigate the conformation of a single poly(3-hexylthiopene) chain at different temperatures. It was found that bundle and toroid structures were predominantly present, with bundles becoming more abundant at lower temperatures. A comparison of atomistic and Martini-based coarse-grained models showed excellent agreement. Furthermore, the temperature dependence of P3HT was linked to that of simple Lennard-Jones model polymers in a vacuum. The addition of solvent (THF) resulted in a prominent swelling of the molecular size at around 220 K, which correlated well with experimental observations of increased frequency of bundle structures.
Article
Chemistry, Multidisciplinary
Chen Liang, Jun Young Cheong, Gabriel Sitaru, Sabine Rosenfeldt, Anna S. Schenk, Stephan Gekle, II-Doo Kim, Andreas Greiner
Summary: The study shows that, for citrate and polyvinylpyrrolidone stabilized gold nanoparticles, the reactivity increases with increasing particle diameter in the size range of 10-58 nm when the total surface area is kept constant. Furthermore, internal structural parameters such as defect tendency also play a significant role in catalytic activity.
ADVANCED MATERIALS INTERFACES
(2022)
Article
Computer Science, Interdisciplinary Applications
Gabriel Sitaru, Stephan Gekle
Summary: Multistep catalytic reactions using chemically incompatible catalysts were studied by immobilizing the catalysts on fibrous membranes. The efficiency of the reactions was investigated using three different methods. The results showed that although the efficiency decreased with increased flow speed, the total production still increased. Additionally, the spatial proximity of the catalysts had a positive effect on the reaction efficiency.
COMPUTERS & FLUIDS
(2022)
Article
Polymer Science
Soren Schumacher, Sanwardhini Pantawane, Stephan Gekle, Seema Agarwal
Summary: This study presents the synthesis of four different monofunctional vinyl cyclopropane amides and investigates their photopolymerization behavior. It is found that all the amides can form hydrogen bonds, with one being the amide linkage and the other being the side chain. The number of additional hydrogen bonds is regulated by different side chains. The study demonstrates that hydrogen bonds can preorganize the monomers and lead to fast polymerization.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2022)
Article
Biology
Richard Gerum, Elham Mirzahossein, Mar Eroles, Jennifer Elsterer, Astrid Mainka, Andreas Bauer, Selina Sonntag, Alexander Winterl, Johannes Bartl, Lena Fischer, Shada Abuhattum, Ruchi Goswami, Salvatore Girardo, Jochen Guck, Stefan Schruefer, Nadine Stroehlein, Mojtaba Nosratlo, Harald Herrmann, Dorothea Schultheis, Felix Rico, Sebastian Johannes Mueller, Stephan Gekle, Ben Fabry
Summary: This study presents a high-throughput, simple, and low-cost microfluidic method to quantitatively measure the elastic and viscous moduli of individual cells. By measuring cell deformation and rotation frequency, the frequency-dependent viscoelastic properties of cells can be determined, revealing the influence of cell cycle and physical interactions between different cell structures.
Article
Physics, Applied
Sebastian J. Mueller, Ben Fabry, Stephan Gekle
Summary: Bioprinting of living cells can lead to shape deformations, affecting cell survival and functionality. Extensional stresses occurring when cells leave the nozzle have been ignored. Lattice Boltzmann simulations and a finite-element based cell model were used to study cell deformation inside the nozzle and at its exit. Two simple methods were developed to predict maximum cell stress and approximate cell strains based on printing parameters.
PHYSICAL REVIEW APPLIED
(2023)
Article
Physics, Fluids & Plasmas
Jinming Lyu, Paul G. Chen, Alexander Farutin, Marc Jaeger, Chaouqi Misbah, Marc Leonetti
Summary: We present a numerical study of vesicle dynamics in a microcirculation model, and identify spontaneous transitions from straight motion to swirling motion and from axisymmetric shape to a helical shape. Additionally, oscillatory motion of the mass center, called three-dimensional snaking, is observed. These oscillatory dynamics arise from pitch-fork bifurcation and Hopf bifurcation. We establish phase diagrams for different volume and confinement conditions, showing that oscillatory dynamics occur when the vesicle is sufficiently deflated. Stationary shapes and oscillatory dynamics are characterized by different limit cycles.
PHYSICAL REVIEW FLUIDS
(2023)
Article
Physics, Fluids & Plasmas
Steffen M. Recktenwald, Katharina Graessel, Yazdan Rashidi, Jann Niklas Steuer, Thomas John, Stephan Gekle, Christian Wagner
Summary: Constricted blood vessels in the circulatory system can cause complications by affecting the organization of red blood cells. In this study, the dynamics of a cell-free layer (CFL) in a constricted microchannel under steady and time-dependent flow conditions were examined. A image-processing routine was developed to analyze the CFL evolution under various flow conditions. The results showed that the concentration of red blood cells and the amplitude of the pressure signal had dominant effects on the CFL dynamics.
PHYSICAL REVIEW FLUIDS
(2023)
Article
Physics, Fluids & Plasmas
Moritz Lehmann, Mathias J. Krause, Giorgio Amati, Marcello Sega, Jens Harting, Stephan Gekle
Summary: This study evaluates the feasibility of using different precision optimization algorithms in lattice Boltzmann method and finds that the accuracy difference between FP32 and 16-bit precision can be neglected in most cases.
Article
Mathematics, Interdisciplinary Applications
Moritz Lehmann, Stephan Gekle
Summary: The plane-cube intersection problem and its iterative solutions have been extensively studied in computational fluid dynamics simulation. This study proposes an improved analytic solution for all intersection cases and compares it with the previous solution from Scardovelli and Zaleski. The authors also evaluate the performance and accuracy of different solutions on different hardware platforms, and discuss the application of PLIC-curvature calculation in free surface fluid simulations.
Article
Biophysics
Steffen M. Recktenwald, Katharina Graessel, Felix M. Maurer, Thomas John, Stephan Gekle, Christian Wagner
Summary: The dynamics and shape transitions of single red blood cells (RBCs) under confined and unsteady flow conditions were investigated using microfluidic experiments and numerical simulations. It was found that the transition time from the symmetric croissant to the off-centered, nonsymmetric slipper shape was faster than the opposite shape transition. Simulations showed that these dynamics depend on the orientation of the RBC membrane in the channel during the time-dependent flow. The tank-treading movement of slipper-shaped RBCs combined with the narrow channel led to oscillations of the cell's center of mass.
BIOPHYSICAL JOURNAL
(2022)
Article
Computer Science, Interdisciplinary Applications
Usman Riaz, E. Seegyoung Seol, Robert Hager, Mark S. Shephard
Summary: The accurate representation and effective discretization of a problem domain into a mesh are crucial for achieving high-quality simulation results and computational efficiency. This work presents recent developments in extending an automated tokamak modeling and meshing infrastructure to better support the near flux field following meshing requirements of the XGC Gyro-kinetic Code.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Zhenglu Li, Gabriel Antonius, Yang-Hao Chan, Steven G. Louie
Summary: This article presents a workflow for practical calculations of electron-phonon coupling and includes the effect of many-electron correlations using GW perturbation theory. The workflow combines different software packages to enable accurate calculations at the level of quasiparticle band structures.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Akihiro Koide, Sara Rabouli, Pierre Le Meur, Sylvain Tricot, Philippe Schieffer, Didier Sebilleau, Calogero R. Natoli
Summary: We present the MsSpec Atomic Scattering Amplitude Package (MASAP), which includes a computation program and a graphical interface for generating atomic scattering amplitude (ASA). The study investigates the applicability of plane wave (PW) and curved spherical wave (SW) scattering in describing electron propagation. The results show that the imaginary part of the optical potential enhances the elastic scattering in the forward direction but causes damping effects in other directions.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
A. Bagci, Gustavo A. Aucar
Summary: The electron repulsion integrals over Slater-type orbitals with non-integer principal quantum numbers are investigated in this study. These integrals are important in calculations of many-electron systems. New relationships free from hyper-geometric functions are derived to simplify the calculations. With the use of auxiliary functions and straightforward recurrence relationships, these integrals can be efficiently computed, providing initial conditions for the evaluation of expectation values and potentials.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Andrzej Daniluk
Summary: RHEED_DIFF_2D is an open-source software for qualitative numerical simulations of RHEED oscillation intensity changes with layer deposition, used for interpreting heteroepitaxial structures under different scattering crystal potential models.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Niklas Kuehl, Hendrik Fischer, Michael Hinze, Thomas Rung
Summary: The article presents a strategy and algorithm for simulation-accompanying, incremental Singular Value Decomposition (SVD) for time-evolving, spatially parallel discrete data sets. The proposed method improves computational efficiency by introducing a bunch matrix, resulting in higher accuracy and practical applicability.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Jose M. Rodriguez-Borbon, Xian Wang, Adrian P. Dieguez, Khaled Z. Ibrahim, Bryan M. Wong
Summary: This paper presents an open-source software package called TRAVOLTA for massively parallelized quantum optimal control calculations on GPUs. The TRAVOLTA package is an improvement on the previous NIC-CAGE algorithm and incorporates algorithmic improvements for faster convergence. Three different variants of GPU parallelization are examined to evaluate their performance in constructing optimal control fields in various quantum systems. The benchmarks show that the GPU-enhanced TRAVOLTA code produces the same results as previous CPU-based algorithms but with a speedup of more than ten times. The GPU enhancements and algorithmic improvements allow large quantum optimal control calculations to be efficiently executed on modern multi-core computational hardware.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Weijie Hua
Summary: This work introduces a program called MCNOX for computing and analyzing ultrafast nonlinear X-ray spectra. It is designed for cutting-edge applications in photochemistry/photophysics enabled by X-ray free-electron lasers and high harmonic generation light sources. The program can calculate steady-state X-ray absorption spectroscopy and three types of ultrafast nonlinear X-ray spectra, and it is capable of identifying major electronic transitions and providing physical and chemical insights from complex signals.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Leandro Benatto, Omar Mesquita, Lucimara S. Roman, Rodrigo B. Capaz, Graziani Candiotto, Marlus Koehler
Summary: Photoluminescence Quenching Simulator (PLQ-Sim) is a user-friendly software for studying the dynamics of photoexcited states at the interface between organic semiconductors. It provides important information on organic photovoltaic and photothermal devices and calculates transfer rates and quenching efficiency.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Dongming Li, James Kestyn, Eric Polizzi
Summary: This study introduces a practical and efficient approach to calculate the all-electron full potential band structure in real space using a finite element basis. Instead of the k-space method, this method solves the Kohn-Sham equation self-consistently within a larger finite system enclosing the unit-cell. Non-self-consistent calculations are then performed in the Brillouin zone to obtain the band structure results, which are found to be in excellent agreement with the pseudopotential k-space method. Furthermore, the study successfully observes the band bending of core electrons.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
R. Kleiber, M. Borchardt, R. Hatzky, A. Koenies, H. Leyh, A. Mishchenko, J. Riemann, C. Slaby, J. M. Garcia-Regana, E. Sanchez, M. Cole
Summary: This paper describes the current state of the EUTERPE code, focusing on the implemented models and their numerical implementation. The code is capable of solving the multi-species electromagnetic gyrokinetic equations in a three-dimensional domain. It utilizes noise reduction techniques and grid resolution transformation for efficient computation. Additionally, various hybrid models are implemented for comparison and the study of plasma-particle interactions. The code is parallelized for high scalability on multiple CPUs.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Pengliang Yang
Summary: This paper presents an open source software called SMIwiz, which combines seismic modelling, reverse time migration, and full waveform inversion into a unified computer implementation. SMIwiz supports both 2D and 3D simulations and provides various computational recipes for efficient calculation. Its independent processing and batchwise job scheduling ensure scalability, and its viability is demonstrated through applications on benchmark models.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Christian Tantardini, Miroslav Ilias, Matteo Giantomassi, Alexander G. Kvashnin, Valeria Pershina, Xavier Gonze
Summary: Material discovery has been an active research field, and this study focuses on developing pseudopotentials for actinides and super-heavy elements. These pseudopotentials are crucial for accurate first-principles calculations and simulations.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
S. Blanes, F. Casas, C. Gonzalez, M. Thalhammer
Summary: This paper explores the extension of modified potential operator splitting methods to specific classes of nonlinear evolution equations. Numerical experiments confirm the advantages of the proposed fourth-order modified operator splitting method over traditional splitting methods in dealing with Gross-Pitaevskii systems.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Siegfried Kaidisch, Thomas U. Hilger, Andreas Krassnigg, Wolfgang Lucha
Summary: Motivated by a use case in theoretical hadron physics, this paper revisits an application of a pole-sum fit to dressing functions of a confined quark propagator. Specifically, it investigates approaches to determine the number and positions of singularities closest to the origin for a function known numerically on a specific grid on the positive real axis. Comparing the efficiency of standard techniques to a pure artificial-neural-network approach and a combination of both, it finds that the combined approach is more efficient. This approach can be applied to similar situations where the positions of poles need to be estimated quickly and reliably from real-axis information alone.
COMPUTER PHYSICS COMMUNICATIONS
(2024)