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SSRN 2023年

作者： Injongkol, Yuwanda Zhang, Rui-Qin Montoya, Alejandro Rungrotmongkol, Thanyada Jungsuttiwong, Siriporn Center of Excellence in Biocatalyst and Sustainable Biotechnology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand City University of Hong Kong Hong Kong School of Chemical and Biomolecular Engineering The University of Sydney SydneyNSW2006 Australia Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand Department of Chemistry Faculty of Science Ubon Ratchathani University Ubon Ratchathani34190 Thailand

We employed Periodic Density Functional Theory (DFT) to investigate the catalytic activity of single and double dopant of boron (B), nitrogen (N), and phosphorous (P) anchored on diamond surfaces for the CO2 reduction reaction (CO2RR) by analyzing reaction energy profiles. Our findings show that the double-doped catalyst exhibits lower energy barriers in CO2RR compared to the single dopants. Specifically, when considering BB and NN configurations, there is a thermodynamic preference towards the formation of formic acid (HCOOH) with overpotentials of 0.40 and 0.09 V, respectively. The co-doped catalyst comprising B and N (BN) demonstrates a tendency towards the formation of HCOOH without requiring any applied overpotentials. Notably, BN outperforms other catalysts, occupying the top position on the volcano plot, indicating the lowest limiting potential (UL), remarkable thermal stability, and the ability to suppress the competing hydrogen evolution reaction (HER). This research provides valuable insights into the product differentiation in the electroreduction of CO2. © 2023, The Authors. All rights reserved.

关键词： Density functional theory

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Local and global measures of the shear moduli of jammed disk packings

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Physical Review E 2023年第5期107卷 054903-054903页

作者： Shiyun Zhang Weiwei Jin Dong Wang Ding Xu Jerry Zhang Mark D. Shattuck Corey S. O'Hern Department of Physics University of Science and Technology of China Hefei Anhui 230026 China Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Strain-controlled isotropic compression gives rise to jammed packings of repulsive, frictionless disks with either positive or negative global shear moduli. We carry out computational studies to understand the contributions of the negative shear moduli to the mechanical response of jammed disk packings. We first decompose the ensemble-averaged, global shear modulus as 〈G〉=(1−F−)〈G+〉+F−〈G−〉, where F− is the fraction of jammed packings with negative shear moduli and 〈G+〉 and 〈G−〉 are the average values from packings with positive and negative moduli, respectively. We show that 〈G+〉 and 〈|G−|〉 obey different power-law scaling relations above and below pN2∼1. For pN2>1, both 〈G+〉N and 〈|G−|〉N∼(pN2)β, where β∼0.5 for repulsive linear spring interactions. Despite this, 〈G〉N∼(pN2)β′ with β′≳0.5 due to the contributions from packings with negative shear moduli. We show further that the probability distribution of global shear moduli P(G) collapses at fixed pN2 and different values of p and N. We calculate analytically that P(G) is a Γ distribution in the pN2≪1 limit. As pN2 increases, the skewness of P(G) decreases and P(G) becomes a skew-normal distribution with negative skewness in the pN2≫1 limit. We also partition jammed disk packings into subsystems using Delaunay triangulation of the disk centers to calculate local shear moduli. We show that the local shear moduli defined from groups of adjacent triangles can be negative even when G>0. The spatial correlation function of local shear moduli C(r⃗) displays weak correlations for pnsub2<10−2, where nsub is the number of particles within each subsystem. However, C(r⃗) begins to develop long-ranged spatial correlations with fourfold angular symmetry for pnsub2≳10−2.

关键词： Jamming Packing & jamming problems Granular materials

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Void distributions reveal structural link between jammed packings and protein cores

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Physical Review E 2019年第2期99卷 022416-022416页

作者： John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

关键词： Jamming Protein structure Packing & jamming problems Proteins Crystal structures Finite-size scaling Molecular dynamics Percolation theory

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Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling

arXiv

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arXiv 2024年

作者： Liu, Zhuoyi Grigas, Alex T. Sumner, Jacob Knab, Edward Davis, Caitlin M. O’Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter-residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter-residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root-mean-square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter-residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs Nr that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, Nr/N 0.08, where N is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET-assisted MD simulations for atomic scale structural modeling of proteins in vivo. © 2024, CC BY.

关键词： Conformations

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Phase transitions in the frustrated Ising ladder with stoquastic and nonstoquastic catalysts

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Physical Review Research 2021年第4期3卷 043013-043013页

作者： Kabuki Takada Shigetoshi Sota Seiji Yunoki Bibek Pokharel Hidetoshi Nishimori Daniel A. Lidar Department of Physics Tokyo Institute of Technology Yokohama Kanagawa 226-8503 Japan Computational Materials Science Research Team RIKEN Center for Computational Science (R-CCS) Kobe Hyogo 650-0047 Japan Computational Condensed Matter Physics Laboratory RIKEN Cluster for Pioneering Research (CPR) Wako Saitama 351-0198 Japan Computational Quantum Matter Research Team RIKEN Center for Emergent Matter Science (CEMS) Wako Saitama 351-0198 Japan Department of Physics University of Southern California Los Angeles California 90089 USA Center for Quantum Information Science & Technology University of Southern California Los Angeles California 90089 USA Institute of Innovative Research Tokyo Institute of Technology Yokohama Kanagawa 226-8503 Japan Graduate School of Information Sciences Tohoku University Sendai Miyagi 980-8579 Japan RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) Wako Saitama 351-0198 Japan Department of Electrical & Computer Engineering and Department of Chemistry University of Southern California Los Angeles California 90089 USA

The role of nonstoquasticity in the field of quantum annealing and adiabatic quantum computing is an actively debated topic. We study a strongly-frustrated quasi-one-dimensional quantum Ising model on a two-leg ladder to elucidate how a first-order phase transition with a topological origin is affected by interactions of the ±XX-type. Such interactions are sometimes known as stoquastic (negative sign) and nonstoquastic (positive sign) “catalysts”. Carrying out a symmetry-preserving real-space renormalization group analysis and extensive density-matrix renormalization group computations, we show that the phase diagrams obtained by these two methods are in qualitative agreement with each other and reveal that the first-order quantum phase transition of a topological nature remains stable against the introduction of both XX-type catalysts. This is the first study of the effects of nonstoquasticity on a first-order phase transition between topologically distinct phases. Our results indicate that nonstoquastic catalysts are generally insufficient for removing topological obstacles in quantum annealing and adiabatic quantum computing.

关键词： Adiabatic quantum optimization Phase transitions by order Quantum spin models Density matrix renormalization group Renormalization group

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Communicationmachine Learning-Based QSAR and LB-PaCS-MD Guided Design of SARs-CoV-2 Main Protease Inhibitors

SSRN

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SSRN 2024年

作者： Toopradab, Borwornlak Xie, Wanting Duan, Lian Hengphasatporn, Kowit Harada, Ryuhei Sinsulpsiri, Silpsiri Shigeta, Yasuteru Shi, Liyi Maitarad, Phornphimon Rungrotmongkol, Thanyada Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand Center of Excellence in Biocatalyst and Sustainable Biotechnology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand Research Center of Nano Science and Technology Department of Chemistry College of Science Shanghai University Shanghai200444 China University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8577 Japan Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki305–8571 Japan Emerging Industries Institute Shanghai University Zhejiang Jiaxing314006 China

The global outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus had led to profound respiratory health implications. This study focused on designing organoselenium-based inhibitors targeting the SARS-CoV-2 main protease (Mpro). The ligand-binding pathway sampling method based on parallel cascade selection molecular dynamics (LB-PaCS-MD) simulations was employed to elucidate plausible paths and conformations of ebselen, a synthetic organoselenium drug, within the Mpro catalytic site. Ebselen effectively engaged the active site, adopting proximity to H41 and interacting through the benzoisoselenazole ring in a π-π T-shaped arrangement, with an additional π-sulfur interaction with C145. In addition, the ligand-based drug design using the QSAR with GFA-MLR, RF, and ANN models were employed for biological activity prediction. The QSAR-ANN model showed robust statistical performance, with an R2training exceeding 0.98 and an RMSEtest of 0.21, indicating its suitability for predicting biological activities. Integration the ANN model with the LB-PaCS-MD insights enabled the rational design of novel compounds anchored in the ebselen core structure, identifying promising candidates with favorable predicted IC50 values. The designed compounds exhibited suitable drug-like characteristics and adopted an active conformation similar to ebselen, inhibiting Mpro function. These findings represent a synergistic approach merging ligand and structure-based drug design;with the potential to guide experimental synthesis and enzyme assay testing. © 2024, The Authors. All rights reserved.

关键词： Coronavirus

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Performance evaluation of LSTM neural networks for consumption prediction

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e-Prime - Advances in Electrical Engineering, Electronics and Energy 2022年 2卷

作者： da Silva, Davi Guimarães Geller, Marla Teresinha Barbosa Moura, Mauro Sérgio dos Santos Meneses, Anderson Alvarenga de Moura Federal University of Western Pará – Graduate Program in Society Nature and Development R. Vera Paz s/n Salé CEP 68.035-110 PA Santarém Brazil Federal Institute of Education Science and Technology of Pará Brazil Laboratory of Computational Intelligence Federal University of Western Pará Institute of Geosciences and Engineering Brazil

Energy consumption and energy efficiency are topics that have attracted the attention of researchers in recent years, in order to seek sustainable solutions for energy production and reduction of costs, aiming to provide a balance between development and protection of natural resources. One of the alternatives that have obtained satisfactory results is the use of technologies based on Internet of Things (IoT) and Deep Learning systems. Based on this, we assessed the performance of Long Short-Term Memory (LSTM) neural networks in time series electric energy consumption prediction, for a forecasting module of an IoT system. Three time series were used and we compared LSTM to the algorithms Extreme Boost Gradient and Random Forest. computational results indicate that the LSTM model showed a tendency of better RMSE performance in the first data set, and statistically significant better results in other two data sets, according to the Kruskal-Wallis test (p < 0.0001 in both cases). Thus, the proposed model was implemented and validated from experiments, presenting accurate prediction for monitoring and estimating power consumption, being applicable to Energy Efficiency and decision making. © 2022 The Authors

关键词： Deep learning Energy efficiency Internet of things Long short-term memory Monitoring and prediction Neural networks Prediction module

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Titania Nanosheets Generates Peroxynitrite for S-Nitrosylation and Enhanced p53 Function in Lung Cancer Cells

Research Square

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Research Square 2021年

作者： Soonnarong, Rapeepun Tungsukruthai, Sucharat Nutho, Bodee Rungrotmongkol, Thanyada Vinayanuwattikun, Chanida Maluangnont, Tosapol Chanvorachote, Pithi Interdisciplinary Program of Pharmacology Graduate School Chulalongkorn University Bangkok Thailand Cell-based Drug and Health Products Development Research Unit Chulalongkorn University Bangkok Thailand Departments of Pharmacology and Physiology Faculty of Pharmaceutical Sciences Bangkok Thailand Department of Pharmacology Faculty of Science Mahidol University Bangkok Thailand Biocatalyst and Environmental Biotechnology Reseach Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok Thailand Division of Medical Oncology Department of Medicine Chulalongkorn University Bangkok Thailand College of Materials Innovation and Technology King Mongkut’s Institute of Technology Ladkrabang Bangkok Thailand

Background: Metal oxide nanomaterials are increasingly being exploited in cancer therapy thanks to their unique properties, which can enhance the efficacy of current cancer therapies. However, the nanotoxicity and mechanism of Ti0.8O2 nanosheets for specific site-targeting strategies in NSCLC have not yet been investigated. Methods: The effects of Ti0.8O2 nanosheets on cytotoxicity in NSCLC cells and normal cells were examined. The apoptosis characteristics, including condensed and fragmented nuclei, as assessed by positive staining with annexin V. The cellular uptake of the nanosheets and the induction of stress fiber were assessed via transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analyses, respectively. We also evaluated the expression of protein in death mechanism to identify the molecular mechanisms behind the toxicity of these cells. We investigated the relationship between S-nitrosylation and the increase in p53 stability by molecular dynamics. Results: Ti0.8O2 nanosheets caused cytotoxicity in several lung cancer cells, but not in normal cells. The nanosheets could enter lung cancer cells and exert an apoptosis induction. Results for protein analysis further indicated the activation of p53, increased Bax, decreased Bcl-2 and Mcl-1, and activation of caspase-3. The nanosheets also exhibited a substantial apoptosis effect in drug-resistant metastatic primary lung cancer cells, and it was found that the potency of the nanosheets was dramatically higher than that of cisplatin and etoposide. In terms of their mechanism of action, we found that the mode of apoptosis induction was through the generation of cellular ONOO− mediated the S-nitrosylation of p53 at C182. Molecular dynamics analysis further showed that the S-nitrosylation of one C182 stabilized the p53 dimer. Consequently, this nitrosylation of the protein led to an upregulation of p53 through its stabilization. Conclusions: Taking all the evidence together, we provided info

关键词： Molecular dynamics

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Dynamic ¹³C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin (vol 23, 100855, 2020)

引用

Iscience 2020年第12期23卷 100855页

作者： Quek, Lake-Ee Krycer, James R. Ohno, Satoshi Yugi, Katsuyuki Fazakerley, Daniel J. Scalzo, Richard Elkington, Sarah D. Dai, Ziwei Hirayama, Akiyoshi Ikeda, Satsuki Shoji, Futaba Suzuki, Kumi Locasale, Jason W. Soga, Tomoyoshi James, David E. Kuroda, Shinya Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia School of Mathematics and Statistics The University of Sydney Sydney NSW 2006 Australia Sydney Medical School The University of Sydney Sydney NSW 2006 Australia Department of Biological Sciences Graduate School of Science University of Tokyo Hongo 7-3-1 Bunkyo-ku Tokyo 113-0033 Japan School of Life and Environmental Sciences The University of Sydney Sydney NSW 2006 Australia Institute for Advanced Biosciences Keio University Tsuruoka Yamagata 997-0052 Japan YCI Laboratory for Trans-Omics Young Chief Investigator Program RIKEN Center for Integrative Medical Sciences 1-7-22 Suehiro-cho Tsurumi-ku Yokohama Kanagawa 230-0045 Japan Faculty of Engineering and Information Technologies The University of Sydney Sydney NSW 2006 Australia Department of Pharmacology and Cancer Biology Duke University School of Medicine Duke University Durham NC 27710 USA AMED-CREST AMED 1-7-1 Otemachi Chiyoda-Ku Tokyo 100-0004 Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan CREST Japan Science and Technology Agency Bunkyo-ku Tokyo 113-0033 Japan

Cellular metabolism is dynamic, but quantifying non-steady metabolic fluxes by stable isotope tracers presents unique computational challenges. Here, we developed an efficient 13 C-tracer dynamic metabolic flux analysis (13C-DMFA) framework for modeling central carbon fluxes that vary over time. We used B-splines to generalize the flux parameterization system and to improve the stability of the optimization algorithm. As proof of concept, we investigated how 3T3-L1 cultured adipocytes acutely metabolize glucose in response to insulin. Insulin rapidly stimulates glucose uptake, but intracellular pathways responded with differing speeds and magnitudes. Fluxes in lower glycolysis increased faster than those in upper glycolysis. Glycolysis fluxes rose disproportionally larger and faster than the tricarboxylic acid cycle, with lactate a primary glucose end product. The uncovered array of flux dynamics suggests that glucose catabolism is additionally regulated beyond uptake to help shunt glucose into appropriate pathways. This work demonstrates the value of using dynamic intracellular fluxes to understand metabolic function and pathway regulation.

关键词： Biological sciences Flux Data Metabolomics Metabolic Flux Analysis

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Random close packing in protein cores

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Physical Review E 2016年第3期93卷 032415-032415页

作者： Jennifer C. Gaines W. Wendell Smith Lynne Regan Corey S. O'Hern Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ≈0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ≈0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.

关键词： Protein structure Proteins

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