Article
Computer Science, Information Systems
Yonal Kirsal, Yoney Kirsal Ever, Glenford Mapp, Mohsin Raza
Summary: This article proposes a 3D analytical model and a problem-solving approach for sustainability evaluation of high-performance computing clusters, with an iterative method to obtain performance measurements and a multi-repairman approach for availability modeling and evaluation of master and computing nodes. The analysis results are in good agreement with the simulations.
IEEE TRANSACTIONS ON CLOUD COMPUTING
(2022)
Article
Biochemical Research Methods
Antony McCabe, Andrew R. Jones
Summary: Complex biological samples are often analyzed using mass spectrometry paired with liquid chromatography or gas chromatography in proteomics and metabolomics research. lcmsWorld is a new software that utilizes graphics hardware to quickly examine and compare LC-MS data, providing a more intuitive way to visualize the data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Automation & Control Systems
Joshua J. Maraj, Kevin P. T. Haughn, Daniel J. Inman, Stephen A. Sarles
Summary: This study explores the effects of sensory adaptation in reservoir computing. Monazomycin-based biomolecular synapse devices with two modes of response are studied in RC tasks. The results show that reservoirs with sensory adaptation achieve higher classification accuracy and reduce fitting error in time series.
ADVANCED INTELLIGENT SYSTEMS
(2023)
Article
Computer Science, Information Systems
Bingwei Chen, Haohuan Fu, Wayne Luk, Guangwen Yang
Summary: This study explores the potential of improving large-scale scientific simulations on reconfigurable FPGA devices through a complete fixed-point design. By analyzing the accuracy and representation range of earthquake simulations, a fixed-point design suitable for major variables is proposed, and the range is dynamically represented through a dynamic scaling scheme. The experimental results demonstrate significant improvements in both performance and power efficiency.
SCIENCE CHINA-INFORMATION SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Oleg Mikhailovskii, Yi Xue, Nikolai R. Skrynnikov
Summary: A new refinement procedure for crystallographic protein structures has been developed using the Amber program, which has shown superior performance compared to the industry-standard phenix.refine program. The new method has led to lower Rfree values and higher MolProbity scores in the refinement of protein structures. It is particularly effective in refining low-accuracy scrambled models and molecular-replacement models.
Article
Mathematical & Computational Biology
Sotirios Panagiotou, Harry Sidiropoulos, Dimitrios Soudris, Mario Negrello, Christos Strydis
Summary: This article introduces a neural simulator called EDEN, which achieves high model flexibility and high computational performance through innovative model analysis and code generation techniques. The simulator can run NeuroML-v2 models directly without users having to learn a specific model specification language. Experimental results demonstrate that EDEN outperforms the established NEURON simulator in terms of both functional correctness and computational performance.
FRONTIERS IN NEUROINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
P. M. Gurubasavaraja Swamy, Nahid Abbas, Prasad Sanjay Dhiwar, Ekta Singh, Abhishek Ghara, Arka Das
Summary: In this study, a 3D QSAR pharmacophore model was generated using substituted pyrimidine class of Aurora-A kinase inhibitors, revealing the crucial role of molecular features in inhibitory activity. Five potential compounds were identified through screening and docking, demonstrating their distinctive ability to inhibit Aurora-A kinase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Pharmacology & Pharmacy
Yuwei Wang, Yifan Guo, Shaojia Qiang, Ruyi Jin, Zhi Li, Yuping Tang, Elaine Lai Han Leung, Hui Guo, Xiaojun Yao
Summary: In this study, the structure-activity relationships and binding modes of a series of anthraquinone derivatives targeting PGAM1 were investigated using 3D-QSAR, molecular docking, and molecular dynamics simulations, which showed satisfactory predictive ability. Molecular dynamics simulations revealed key residues and dominant interactions, as well as stable hydrogen bond formations during the ligand binding process. Overall, the study provided theoretical guidance for the design of new anthraquinone derivatives as PGAM1 inhibitors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Engineering, Environmental
Tao Chen, Xiaoke Ku, Tian Li, Bodil S. A. Karlsson, Jonas Sjoblom, Henrik Strom
Summary: In this study, a new algorithm was developed to investigate the heat transfer and multiphase flow in high-temperature pyrolysis of biomass particles, as well as the influence of temperature gradient inside the particles on primary pyrolysis products. Simulation results showed that using the new tar decomposition model significantly improved the yields of light gas and tar, as well as provided more reasonable predictions of species yield histories.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Lukasz Kazmierczak, Joanna Szala-Rearick, Dorota Swiatla-Wojcik
Summary: Understanding the properties of the (OH)-O-center dot radical in aqueous environments is crucial for various fields including biochemistry, atmospheric chemistry, and green chemistry technologies. This study utilized classical molecular dynamics simulation and the Voronoi polyhedra construction technique to provide 3D characteristics of the aqueous hydroxyl radical ((OHaq)-O-center dot). Statistical distribution functions of solvation shells were analyzed for different thermodynamic states of water, revealing the significant influence of water density on the geometrical properties of the (OH)-O-center dot solvation shell. This research highlights the limitations of 1D analysis based on oxygen-oxygen radial distribution functions in accurately representing the solvation behavior of (OH)-O-center dot.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Information Systems
Alem Colakovic
Summary: The increase in IoT applications has resulted in a need to handle vast amounts of data. Integrating IoT with the Cloud presents challenges such as network delays, throughput, and energy consumption. This paper proposes new computing concepts to support emerging IoT applications and addresses the issue of selecting the best offloading system for performance optimization.
COMPUTER SCIENCE REVIEW
(2023)
Article
Computer Science, Theory & Methods
Johannes de Fine Licht, Maciej Besta, Simon Meierhans, Torsten Hoefler
Summary: This study explores optimizing transformations for high-performance computing applications on spatial computing architectures, accelerating programmer productivity on these platforms and enhancing performance potential.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2021)
Article
Computer Science, Artificial Intelligence
Said Kerrache
Summary: The problem of link prediction involves determining the likelihood of a connection between two nodes in a network, which is enabled by the inherent topological structure in most real-life networks. Significant research has been devoted to developing link prediction algorithms, but existing implementations often use different languages and modalities, which hinders their effective utilization.
PEERJ COMPUTER SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Matthew Hancock, Thomas-Otavio Peulen, Benjamin Webb, Billy Poon, James S. Fraser, Paul Adams, Andrej Sali
Summary: This article discusses the challenge of integrating different software in integrative modeling, citing reasons such as software incompatibility, differing modeling logic, collaboration costs, and academic incentives. The author aims to formulate software standards to address the issue of modelers being unable to integrate tools from distinct software packages, thereby improving model quality and efficiency.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Andras Markus, Mate Biro, Karolj Skala, Zorislav Sojat, Attila Kertesz
Summary: Fog computing extends the functionality of the cloud to limited computing units closer to user devices, providing effective solutions. This study introduces a Dew computing model into the DISSECT-CF-Fog simulator, enabling cost-effective simulation of IoT-Dew-Fog systems, with a focus on service migration options for mobile devices and cases with temporary internet access limitations.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Kiyoshi Yagi, Suyong Re, Takaharu Mori, Yuji Sugita
Summary: Recent advances in atomistic molecular dynamics simulations have allowed us to explore the conformational spaces of biomolecules and observe transitions between distinct structures. Weight average approaches are used to analyze various experimental measurements and improve our understanding of molecular functions based on atomic structures.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Shingo Ito, Kiyoshi Yagi, Yuji Sugita
Summary: In this study, the allosteric regulation of TRPS was investigated using molecular dynamics simulations. The results revealed the effects of IGP binding on the conformation of the alpha and beta subunits, as well as the critical role of hydrogen bonds. These findings provide insights into the allosteric regulation of multidomain proteins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemical Research Methods
Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
Summary: Residue-level coarse-grained (CG) models play a crucial role in biomolecular simulations, enabling the study of large-scale biological phenomena with unified treatments of proteins and nucleic acids, as well as efficient parallel computations. The toolbox and methods introduced can help optimize the performance in CG MD simulations.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita
Summary: The Spike protein plays a crucial role in neutralization and vaccine development for SARS-CoV-2. Its inherent flexibility provides essential information for designing antiviral drugs and vaccines.
Article
Biophysics
Hisham M. Dokainish, Yuji Sugita
Summary: A single mutation (D614G) in the spike protein of SARS-CoV-2, which causes COVID-19, has become the dominant variant. This mutation enhances the virus's infectivity by inducing structural changes. Molecular dynamics simulations reveal that the mutation orders the structure, weakens local interactions, and alters global interactions, leading to conformational changes. Understanding this mutation is crucial as it is present in all variants of concern.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
Summary: gREST is an enhanced sampling algorithm used for proteins or other systems with rugged energy landscapes. It differs from the REMD method as the solvent temperatures are the same in all replicas, while solute temperatures are different and frequently exchanged between replicas to explore various solute structures. The gREST scheme is applied to large biological systems using a large number of processors, reducing communication time and performing energy evaluations on-the-fly during simulations. These advanced schemes in the GENESIS software provide new possibilities for studying large biomolecular complex systems with slow conformational dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Ryuta Uraki, Shun Iida, Peter J. Halfmann, Seiya Yamayoshi, Yuichiro Hirata, Kiyoko Iwatsuki-Horimoto, Maki Kiso, Mutsumi Ito, Yuri Furusawa, Hiroshi Ueki, Yuko Sakai-Tagawa, Makoto Kuroda, Tadashi Maemura, Taksoo Kim, Sohtaro Mine, Noriko Iwamoto, Rong Li, Yanan Liu, Deanna Larson, Shuetsu Fukushi, Shinji Watanabe, Ken Maeda, Zhongde Wang, Norio Ohmagari, James Theiler, Will Fischer, Bette Korber, Masaki Imai, Tadaki Suzuki, Yoshihiro Kawaoka
Summary: The Omicron subvariant BA.2.75 rapidly spread globally in India and Nepal during the summer of 2022. However, its virological features were largely unknown. In this study, BA.2.75 clinical isolates were evaluated in Syrian hamsters, and it was found that BA.2.75 had higher replicative ability in the lungs compared to BA.2 and BA.5. BA.2.75 also caused focal viral pneumonia in hamsters, unlike BA.5. These findings suggest that BA.2.75 may cause more severe respiratory disease and should be closely monitored.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, General & Internal
Lauren J. Beesley, Kelly R. Moran, Kshitij Wagh, Lauren A. Castro, James Theiler, Hyejin Yoon, Will Fischer, Nick W. Hengartner, Bette Korber, Sara Y. Del Valle
Summary: This paper retrospectively analyzes longitudinal sequencing data to characterize differences in the speed, calendar timing, and magnitude of 16 SARS-CoV-2 variant waves/transitions for 230 countries and sub-country regions. It also identifies groups of locations exhibiting similar variant transitions through clustering. The study finds associations between the behavior of an emerging variant and the number of co-circulating variants, as well as the demographic context of the population.
Article
Chemistry, Multidisciplinary
Cheng Tan, Ai Niitsu, Yuji Sugita
Summary: In this study, the interactions between Hero11 protein and TDP-43-LCD protein were investigated using multiscale molecular dynamics simulations. Three possible regulatory mechanisms of Hero11 were proposed based on the simulation results. It was found that Hero11 can permeate into TDP-43-LCD condensates and induce changes in their conformation, intermolecular interactions, and dynamics. These mechanisms provide new insights into the regulation of biomolecular condensation under different conditions.
Article
Chemistry, Physical
Diego Ugarte La Torre, Shoji Takada, Yuji Sugita
Summary: iSoLF is a coarse-grained model used in molecular dynamics simulations of biological membranes with the implicit solvent approximation. By explicitly treating the electrostatic interactions and adding new particle types, the model can now simulate a wider range of lipid molecules. The improved model has been parameterized and validated, and it is also capable of simulating phase behaviors of lipid mixtures.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Immunology
Sam Turner, Arghavan Alisoltani, Debbie Bratt, Liel Cohen-Lavi, Bethany L. Dearlove, Christian Drosten, Will M. Fischer, Ron A. M. Fouchier, Ana Silvia Gonzalez-Reiche, Lukasz Jaroszewski, Zain Khalil, Eric LeGresley, Marc Johnson, Terry C. Jones, Barbara Muehlemann, David O'Connor, Mayya Sedova, Maulik Shukla, James Theiler, Zachary S. Wallace, Hyejin Yoon, Yun Zhang, Harm van Bakel, Marciela M. Degrace, Elodie Ghedin, Adam Godzik, Tomer Hertz, Bette Korber, Jacob Lemieux, Anna M. Niewiadomska, Diane J. Post, Morgane Rolland, Richard Scheuermann, Derek J. Smith
Summary: Since late 2020, SARS-CoV-2 variants with competitive and phenotypic differences have been regularly emerging, sometimes having the potential to escape immunity. The Early Detection group of the US National Institutes of Health uses bioinformatics to monitor and prioritize the most relevant variants for experimental characterization. Their success includes identifying major variants and providing updated information for phenotypic investigations.
EMERGING INFECTIOUS DISEASES
(2023)
Article
Medicine, Research & Experimental
Kristen W. Cohen, Andrew Fiore-Gartland, Stephen R. Walsh, Karina Yusim, Nicole Frahm, Marnie L. Elizaga, Janine Maenza, Hyman Scott, Kenneth H. Mayer, Paul A. Goepfert, Srilatha Edupuganti, Giuseppe Pantaleo, Julia Hutter, Daryl E. Morris, Stephen C. De Rosa, Daniel E. Geraghty, Merlin L. Robb, Nelson L. Michael, Will Fischer, Elena E. Giorgi, Harman Malhi, Michael N. Pensiero, Guido Ferrari, Georgia D. Tomaras, David C. Montefiori, Peter B. Gilbert, M. Juliana McElrath, Barton F. Haynes, Bette T. Korber, Lindsey R. Baden
Summary: This study found that vaccination with mosaic immunogens could induce more specific T cell responses and increase recognition of heterologous variants, suggesting that mosaic and consensus immunogens are promising approaches to address the global diversity of HIV-1.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Chemistry, Multidisciplinary
Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita
Summary: The rapid increase in computational power has enabled atomistic molecular dynamics simulations of biomolecules in large-scale biological systems. Spatial decomposition analysis (SPANA) reduces computational time and memory size by distributing analysis tasks to multiple CPU cores, opening new possibilities for detailed atomistic analyses of biomacromolecules and other molecules in MD simulation trajectories.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita
Summary: Proper balance between protein-protein and protein-water interactions is crucial for molecular dynamics simulations of proteins. Increasing the protein-water interactions helps optimize the balance and has significant effects on diffusive properties of proteins in crowded solutions.
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
