Article
Chemistry, Physical
Takashi Tsuchimochi, Yoohee Ryo, Seiichiro L. Ten-no, Kazuki Sasasako
Summary: Quantum imaginary time evolution (QITE) is a hybrid algorithm that can guarantee reaching the lowest state of a system. This study improves upon QITE, specifically for molecular applications. The derivation of the QITE equation is analyzed step-by-step, and a theoretically well-founded modification is proposed. The results demonstrate the effectiveness of the derived equation, providing a better approximation for imaginary time propagation. Additionally, accurate estimation of the norm of an imaginary-time-evolved state is discussed and applied in excited state calculations using the quantum Lanczos algorithm. The folded-spectrum QITE scheme is also introduced as an extension for general excited-state simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Takashi Tsuchimochi, Yoohee Ryo, Seiichiro L. Ten-no, Kazuki Sasasako
Summary: In this study, several improvements are made to the Quantum Imaginary Time Evolution (QITE) algorithm, with a focus on molecular applications. By analyzing the derivation of the QITE equation and suggesting a theoretically grounded modification, our results demonstrate the soundness of the derived equation and its ability to better approximate imaginary time propagation. We also discuss accurately estimating the norm of an imaginary-time-evolved state and its application to excited state calculations. Additionally, the folded-spectrum QITE scheme is proposed as a straightforward extension for general excited-state simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Kevin Song, Raymond Park, Atanu Das, Dmitrii E. Makarov, Etienne Vouga
Summary: A milestone-based method for information-theoretical analysis of continuous trajectories is developed and shown to be useful in both Markov and non-Markov models and in trajectories obtained from molecular simulations.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Engineering, Electrical & Electronic
Milad R. Vahid, Bernard Hanzon, Raimund J. Ober
Summary: The advent of single molecule microscopy has revolutionized biological investigations by providing a powerful tool for studying protein molecule trafficking processes. However, the use of pixelated detectors in practice complicates the analysis of single molecule trajectories.
IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING
(2021)
Article
Computer Science, Software Engineering
Ryusuke Sugimoto, Terry Chen, Yiti Jiang, Christopher Batty, Toshiya Hachisuka
Summary: We introduce the walk-on-boundary (WoB) method, a grid-free Monte Carlo solver, for solving certain second order partial differential equations in computer graphics. Compared to the popular walk-on-spheres (WoS) method, WoB has additional advantages as it naturally supports various boundary conditions and is mathematically similar to light transport simulation in rendering. We demonstrate the advantages of WoB over WoS through numerical results, showing that WoB can estimate solutions precisely on the boundary without suffering from intrinsic bias.
ACM TRANSACTIONS ON GRAPHICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Ryan D. Schumm, Paul C. Bressloff
Summary: In this study, a Monte Carlo algorithm is developed to simulate diffusion across semi-permeable interfaces and solve diffusion problems with partially absorbing traps. The validation of the algorithm demonstrates its reliability and consistency with asymptotic results for similar problems.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Computer Science, Software Engineering
Rohan Sawhney, Bailey Miller, Ioannis Gkioulekas, Keenan Crane
Summary: Grid-free Monte Carlo methods based on the walk on spheres (WoS) algorithm can solve fundamental partial differential equations without discretizing the problem domain. We introduce the walk on stars (WoSt) algorithm, which can solve linear elliptic PDEs with arbitrary mixed Neumann and Dirichlet boundary conditions.
ACM TRANSACTIONS ON GRAPHICS
(2023)
Article
Computer Science, Software Engineering
Bailey Miller, Rohan Sawhney, Keenan Crane, Ioannis Gkioulekas
Summary: This paper proposes a fast caching strategy for solving elliptic partial differential equations by estimating solution values and derivatives at randomly sampled points along the boundary, and then using these cached values to evaluate the solution at interior points via a boundary integral formulation. Unlike classic methods, this caching scheme introduces zero statistical bias and does not require a dense global solve. It also handles imperfect geometry and detailed boundary/source terms without repairing or resampling the boundary representation. The approach is validated using test problems from visual and geometric computing.
ACM TRANSACTIONS ON GRAPHICS
(2023)
Article
Chemistry, Physical
Gaia Micca Longo, Domenico Giordano, Savino Longo
Summary: The ionization of the hydrogen atom confined in a spherical potential well and subjected to a static electric field is a stationary, gradual, and reversible process. The value of the electric field at the onset of ionization depends on the symmetry of the atomic wave function and on the confinement dimension. Decreasing the confinement sphere leads to pressure ionization of the atom. The off-center case is also studied, confirming the transition between field-induced and pressure-induced ionization.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Biochemical Research Methods
Ye Lin, Fatemeh Sharifi, Sean B. Andersson
Summary: The paper introduces a method based on SMC-EM technology that can simultaneously localize the position of biological macromolecules and estimate motion model parameters. The research results indicate that under low signal conditions, the SMC-EM method outperforms other methods, while at higher signal-to-background ratios, both SMC-EM and MLE-based methods perform equally well and are significantly better than fitting to the MSD.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Mathematics
Viacheslav V. Saenko, Vladislav N. Kovalnogov, Ruslan V. Fedorov, Dmitry A. Generalov, Ekaterina V. Tsvetova
Summary: This paper proposes a stochastic solution method for the anomalous diffusion equation with fractional derivatives in both time and coordinates. By considering the random walk process of particles and obtaining the master equation describing the particle distribution, it has been demonstrated that the process can be described by the equation of anomalous diffusion in the asymptotics of large times. The method allows for local estimation of the solution to the anomalous diffusion equation based on simulating random walk trajectories, providing the advantage of estimating the solution directly at a specific point and constructing it as a smooth function of the coordinate.
Article
Chemistry, Physical
Fenris Lu, Lixue Cheng, Ryan J. DiRisio, Jacob M. Finney, Mark A. Boyer, Pattarapon Moonkaen, Jiace Sun, Sebastian J. R. Lee, J. Emiliano Deustua, Thomas F. Miller, Anne B. McCoy
Summary: A machine-learning based approach is developed for evaluating potential energies of small molecules, allowing for quantum mechanical studies of their ground and excited vibrational states. The approach combines molecular-orbital-based machine learning and GPU-accelerated neural network potential energy surfaces to generate accurate electronic energies at a lower computational cost. The method is applied to variational calculations and diffusion Monte Carlo calculations of water, CH5+, and its deuterated analogues, yielding satisfactory results compared to potentials fit to larger sets of electronic energies.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Polymer Science
Zhiyong Yang, Linli He, Linxi Zhang
Summary: The conformations of a semiflexible polyelectrolyte chain with neutralizing charged counterions confined in a cylinder were investigated through off-lattice Monte Carlo simulations. The study found that at suitable parameter combinations, perfect helical structures can be observed, with larger cylindrical radius leading to a smaller range of the helix phase region.
Article
Optics
Gaia Micca Longo, Carla Maria Coppola, Domenico Giordano, Savino Longo
Summary: This study demonstrates how computational codes based on the diffusion Monte Carlo method can be applied to determine the quantum state of two-electron systems confined by external potentials, obtaining satisfactory results and adaptability to different types of confinement.
EUROPEAN PHYSICAL JOURNAL D
(2021)
Article
Genetics & Heredity
Bolin Chen, Jinlei Zhang, Teng Wang, Ci Shao, Lijun Miao, Shengli Zhang, Xuequn Shang
Summary: In this study, a method was proposed to discover the evolution between biological molecules and biological functions by investigating the multi-stage biological molecules of lung adenocarcinoma (LUAD). The study found 12 core modules and 11 core biological functions through evolutionary analyses, and explained their relationship with the disease as well as the functions that may serve as predictive signals.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Kumaresan Jayaraman, Anand K. Das, Dino Luethi, Daniel Szoellosi, Gerhard J. Schuetz, Maarten E. A. Reith, Harald H. Sitte, Thomas Stockner
Summary: Transporters of the SLC6 family mediate neurotransmitter reuptake, forming various quaternary structures that support the activity of release-type psychostimulants. Single molecule microscopy experiments have revealed differences in stoichiometry between individual members.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Boris Buchroithner, Sandra Mayr, Fabian Hauser, Eleni Priglinger, Herbert Stangl, Ana Raquel Santa-Maria, Maria A. Deli, Andras Der, Thomas A. Klar, Markus Axmann, Dmitry Sivun, Mario Mairhofer, Jaroslaw Jacak
Summary: This study demonstrates a microfluidic system that enables high-resolution imaging through horizontally separated channels and a cell-growth-promoting membrane. It successfully developed a coculture model of endothelial cells with pericytes to mimic the blood-brain barrier, and also achieved 3D imaging of the cytoskeleton and single-molecule-sensitive tracing of lipoprotein particles.
Article
Multidisciplinary Sciences
Magdalena C. Schneider, Roger Telschow, Gwenael Mercier, Montserrat Lopez-Martinez, Otmar Scherzer, Gerhard J. Schuetz
Summary: Single molecule localization microscopy (SMLM) has the potential to resolve subcellular structures below the diffraction limit, with high localization precision. Sample fixation is necessary to prevent molecular motion during recording, but can affect the sample's ultrastructure. Performing SMLM at low temperatures can improve localization precision and enable reliable assignment of dye molecules.
Article
Cell Biology
Martin Foelser, Viktoria Motsch, Rene Platzer, Johannes B. Huppa, Gerhard J. Schuetz
Summary: This study presents a platform for simultaneous quantification of TCR distribution, intracellular calcium levels, and T-cell-exerted forces. The platform uses AFM cantilevers to bring single T-cells into contact with an activating surface, enabling the study of T-cell triggering via functionalized fluid-supported lipid bilayers.
Article
Multidisciplinary Sciences
Esteban Hoijman, Hanna-Maria Hakkinen, Queralt Tolosa-Ramon, Senda Jimenez-Delgado, Chris Wyatt, Marta Miret-Cuesta, Manuel Irimia, Andrew Callan-Jones, Stefan Wieser, Verena Ruprecht
Summary: Mechanical load-sharing enables the long-range cooperative uptake of apoptotic cells by multiple epithelial cells; and clearance of these apoptotic cells facilitates error correction, which is necessary for developmental robustness and survival of the embryo.
Article
Multidisciplinary Sciences
Janett Goehring, Florian Kellner, Lukas Schrangl, Rene Platzer, Enrico Klotzsch, Hannes Stockinger, Johannes B. Huppa, Gerhard J. Schuetz
Summary: This study introduces a FRET-based sensor that directly measures the magnitude and kinetics of forces imposed by TCR at the single molecule level. Results showed that when T cells were confronted with gel-phase SLBs, there was a single force peak of around 5pN prior and upon activation, with force loading rates around 1.5pN per second on the TCR; while facing fluid-phase SLBs, T cells exerted tensile forces prior to activation but not afterwards, although of reduced magnitude compared to gel-phase SLBs.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Joschka Hellmeier, Rene Platzer, Vanessa Muehlgrabner, Magdalena C. Schneider, Elke Kurz, Gerhard J. Schuetz, Johannes B. Huppa, Eva Sevcsik
Summary: DNA origami structures provide flexible scaffolds for organizing biomolecules with nanometer precision, but functionalizing them with proteins while maintaining stoichiometry and protein functionality remains challenging. This study systematically evaluated different strategies for site-specific decoration of DNA origami structures, with a focus on efficiency, stoichiometry, and protein functionality. The study found that using charge-neutral peptide nucleic acid emerged as the best strategy for achieving high yield and preserving protein functionality.
Article
Chemistry, Multidisciplinary
Lukas Velas, Mario Brameshuber, Johannes B. Huppa, Elke Kurz, Michael L. Dustin, Philipp Zelger, Alexander Jesacher, Gerhard J. Schuetz
Summary: This study utilized 3D-SMLM technique to accurately measure the three-dimensional topography of the immunological synapse, revealing the interface characteristics and cleft size between T-cells and antigen-presenting cells.
Article
Multidisciplinary Sciences
Fabian Hinterer, Magdalena C. Schneider, Simon Hubmer, Montserrat Lopez-Martinez, Philipp Zelger, Alexander Jesacher, Ronny Ramlau, Gerhard J. Schuetz
Summary: Single molecule localization microscopy (SMLM) has the potential to resolve structural details of biological samples at the nanometer scale. By performing SMLM under cryogenic temperature, higher localization precision can be achieved. However, it is important to consider the anisotropic emission characteristics of dipole emitters with fixed orientation to fully exploit the resolution. This study demonstrates the use of astigmatic imaging and dipole orientation information to extract the position of dipole emitters without bias and reach a precision of 1 nm.
Review
Biochemistry & Molecular Biology
Markus Axmann, Birgit Plochberger, Mario Mikula, Florian Weber, Witta Monika Strobl, Herbert Stangl
Summary: Cholesterol transfer between lipoprotein particles and the plasma membrane is crucial for lipid supply in the human body. Different density lipoprotein particles deliver cholesterol to cells through redundant pathways, which can compensate for defects in one pathway but may lead to systemic diseases later on. Intracellular membrane-membrane contact sites and the plasma membrane itself play roles in cholesterol transfer.
Article
Biochemistry & Molecular Biology
Ingrid Hartl, Veronika Brumovska, Yasmin Striedner, Atena Yasari, Gerhard J. Schuetz, Eva Sevcsik, Irene Tiemann-Boege
Summary: This study utilized micropatterning to enrich FGFR3 in specific areas of the cell membrane, and quantified receptor activation by observing the recruitment of downstream signaling molecule GRB2 to FGFR3 micropatterns. The results showed that mutations in FGFR3 altered receptor activity, with increased activity in G380R and K650Q mutants upon ligand addition, while decreased activity in K650E mutant. These findings provide further insight into the functional effects of mutations to FGFR3.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Florian Weber, Markus Axmann, Andreas Horner, Bettina Schwarzinger, Julian Weghuber, Birgit Plochberger
Summary: This article focuses on the research of lipoprotein particles (LPs) in cardiovascular diseases, especially their transport functions and parameters such as class distribution, accumulation, site-specific delivery, cellular internalization, and escape. The aim is to load hydrophilic cargo into LPs, and insulin is used as an example for successful incorporation into high-density lipoprotein (HDL) particles. Atomic Force Microscopy (AFM) and Fluorescence Microscopy (FM) were used to study and verify the successful incorporation. Single-molecule-sensitive FM and confocal imaging visualized the membrane interaction of single, insulin-loaded HDL particles and the subsequent cellular translocation of glucose transporter type 4 (Glut4).
Article
Physics, Applied
Fabian Hinterer, Magdalena C. Schneider, Simon Hubmer, Montserrat Lopez-Martinez, Ronny Ramlau, Gerhard J. Schuetz
Summary: Single molecule localization microscopy relies on precise quantification of the positions of single dye emitters in a sample. The number of detected photons from each molecule determines the precision, which can be improved by recording at cryogenic temperatures to reduce photobleaching. However, long illuminations can cause image blur due to inevitable jitter or drift, which degrades localization precision. This paper demonstrates a method to largely eliminate drift effects by parallel recording fiducial marker beads and fitting the drift trajectory, applicable to drift magnitudes of several hundred nanometers per frame, and assuming fixed dipole orientations during each illumination.
APPLIED PHYSICS LETTERS
(2023)
Article
Cell Biology
Neus Sanfeliu-Cerdan, Frederic Catala-Castro, Borja Mateos, Carla Garcia-Cabau, Maria Ribera, Iris Ruider, Montserrat Porta-de-la-Riva, Adria Canals-Calderon, Stefan Wieser, Xavier Salvatella, Michael Krieg
Summary: This study reveals that the material properties of biomolecular condensates can change with time, and the MEC-2/stomatin condensates undergo a rigidity phase transition from fluid-like to solid-like, facilitating transport and mechanotransduction. This finding suggests that the rigidity phase transition has a physiological role in force transmission in mechanosensitive neurons.
NATURE CELL BIOLOGY
(2023)
