Article
Multidisciplinary Sciences
Andrei Hernandez-Robles, David Romeu, Arturo Ponce
Summary: The relative orientations of rotated graphene bi-layers (RGBs) deposited by chemical vapor deposition were measured, revealing spontaneously occurring preferred orientations. These special orientations result in simpler displacement fields and lead to the re-orientation of RGBs to simplify their strain fields.
Article
Engineering, Mechanical
Kun Wang, Jian S. Dai
Summary: This paper examines the variations and derivations of the dual Euler-Rodrigues formula and investigates their connections with matrices, Lie groups, and quaternions. By decomposing Chasles' motion and constructing screw matrices, the paper reveals the connection between the geometric and algebraic representations of rigid body transformations.
MECHANISM AND MACHINE THEORY
(2023)
Article
Astronomy & Astrophysics
M. K. Erdim, C. Ezer, O. Unver, F. Hazar, M. Hudaverdi
Summary: This study investigates the relative contribution of supernovae to the metal budget of the intracluster medium (ICM) of the Abell 1837 galaxy cluster at redshift z = 0.069. Utilizing theoretical nucleosynthesis models, the research finds that the distribution of SNIa contribution to the total supernovae in the cluster is uniform, supporting the early enrichment scenario where metal production processes begin in the early phase of cluster formation.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Nutrition & Dietetics
Marianthi Kalafati, Michael Lenz, Gokhan Ertaylan, Ilja C. W. Arts, Chris T. Evelo, Marleen M. J. van Greevenbroek, Ellen E. Blaak, Michiel Adriaens, Martina Kutmon
Summary: This study utilized publicly available datasets to analyze the impact of macrophage frequencies on gene expression in subcutaneous adipose tissue. It was found that individuals with high macrophage frequencies showed increased inflammation gene expression accompanied by decreased gene expression in pathways related to lipid metabolism and mitochondrial respiration in the adipose tissue.
FRONTIERS IN NUTRITION
(2021)
Article
Geosciences, Multidisciplinary
Sai Prabala Swetha Chittella, Pranab Deb, Jan Melchior van Wessem
Summary: We investigated the atmospheric drivers of extreme precipitation over the Amundsen Sea Embayment in West Antarctica. The study found that a coupled pattern consisting of an Amundsen Sea Low and a blocking high to the east is the main driver of extreme precipitation in this region.
GEOPHYSICAL RESEARCH LETTERS
(2022)
Article
Materials Science, Ceramics
Minghu Shen, Gaoyang Zhao, Li Lei, Hangkang Ji, Pengrong Ren
Summary: In this study, Bi2Sr2Ca1Cu2O8+sigma (Bi-2212) superconducting thin films were successfully prepared on LaAlO3 single crystal substrate using a sol-gel method. The thin films exhibited good epitaxial growth characteristics, with a critical transition temperature of 87 K, and showed the intrinsic Josephson effect.
CERAMICS INTERNATIONAL
(2021)
Article
Biotechnology & Applied Microbiology
N. K. Kadri, J. Zhang, C. Oget-Ebrad, Y. Wang, C. Couldrey, R. Spelman, C. Charlier, M. Georges, T. Druet
Summary: This study highlighted the significant contribution of the X-chromosome to individual recombination rate associated with testis in males. The study also suggests that the contribution of the X-chromosome to such a trait might be sex dependent.
Article
Virology
Guillaume Lafforgue, Thierry Michon, Justine Charon
Summary: Intrinsically disordered regions (IDRs) in the proteome of RNA viruses exhibit higher mutational robustness than highly structured regions (ORs). Substitutions in the ORs are constrained by physico-chemical properties, while substitutions in IDRs tend to be more random. IDRs may serve as a potential adaptive reservoir.
Article
Ecology
Thomas J. Loffler, Heike Lischke
Summary: This study examines the influence of intrinsic growth rates of species on community stability and finds that changes in the relative intrinsic growth rates of competing species have a strong effect on community stability.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Environmental Sciences
Danilo Candido Vieira, Fabiane Gallucci, Guilherme Nascimento Corte, Helio Herminio Checon, Antonia Cecilia Zacagnini Amaral, Gustavo Fonseca
Summary: The study examined the distribution of marine meiofaunal nematodes and macrofauna in relation to environmental limitations, finding that selection processes were the primary driver for both assemblages with rare species playing a significant role. It was also discovered that the total number of species explained by non-selection processes was 27% higher in nematodes compared to macrofauna, highlighting the importance of a species-level approach in determining the contribution of selection and non-selection assembly processes.
MARINE ENVIRONMENTAL RESEARCH
(2021)
Article
Psychology, Multidisciplinary
Victoria I. Nicholls, Jan M. Wiener, Andrew Isaac Meso, Sebastien Miellet
Summary: As we age, many abilities decline, including executive functioning which affects older adults' decision-making when crossing the road. However, older adults with maintained executive functioning sample visual information and make road crossing decisions similar to younger adults. Environmental constraints and executive functioning abilities interact with aging to influence the performance of the road-crossing task.
FRONTIERS IN PSYCHOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sangwoo Park, Giovanni B. Brandani, Taekjip Ha, Gregory D. Bowman
Summary: Chromatin remodelers use a helicase-type ATPase motor to shift DNA and exhibit a sequence-dependent bias in nucleosome positioning, which is influenced by local DNA perturbations throughout the nucleosome footprint.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Environmental Studies
Qinghe Zhao, Shengyan Ding, Xiaoyu Ji, Zhendong Hong, Mengwen Lu, Peng Wang
Summary: This study quantifies the effects of climate change and human activities on runoff in the Yellow River basin, finding a decrease in annual and seasonal runoff over time due to the combined impacts of climate change and human activities. Human activities account for a large proportion of the runoff reduction, while climate change plays a smaller role in this decrease.
Article
Environmental Sciences
Zhendong Hong, Shengyan Ding, Qinghe Zhao, Zihan Geng, Pengwei Qiu, Jian Zhang, An Wang, Panpan Zhang
Summary: This study examines the contribution of multiple water sources to riparian wetlands in the lower Yellow River using hydrochemistry and isotopic methods. The results show that the Yellow River is the main water source for riparian wetlands, but its contribution varies spatially and temporally. Climate and hydrological variables, particularly suspended sediment content, have a significant impact on water recharge.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Materials Science, Multidisciplinary
D. A. Estyunin, T. P. Makarova, K. A. Kokh, O. E. Tereshchenko, A. M. Shikin, I. I. Klimovskikh
Summary: This paper experimentally investigates the gradual growth of a Pb thin film on the surface of Mn(Bi0.7Sb0.3)2Te4 and its effects on the topological properties of the material. The study shows that the shape of the Dirac cone state remains almost unchanged with the growth of the Pb film, indicating the preservation of the topological properties. The deposition of Pb atoms leads to surface modification and disorder in the layers closest to the surface, causing a shift in the localization of the Dirac cone state towards the bulk.
Article
Chemistry, Physical
Christoffer Lind, Poonam Pandey, Richard W. Pastor, Alexander D. MacKerell
Summary: The study utilized SILCS methodology to investigate the distribution of various chemical solutes in phospholipid bilayers, revealing differences in the distribution of aliphatic versus aromatic groups and variations in the distribution of different polar groups. The results provide insights into the energetics of functional groups in different regions of the bilayers and offer a method for calculating permeability of multifunctional drug-like molecules.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Anmol Kumar, Poonam Pandey, Payal Chatterjee, Alexander D. Jr Jr MacKerell
Summary: The Drude polarizable force field captures electronic polarization effects and is useful for simulating biomolecules and other molecules. Deep neural network models can accurately predict molecular dipole moments and polarizabilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell, Wonpil Im
Summary: The Drude Prepper tool has been developed in CHARMM-GUI to facilitate the use of polarizable FF based on the classic Drude oscillator model. It allows for easy construction of Drude FF-based PSF and generation of input for MD simulations using various simulation packages. The stability and effectiveness of the Drude Prepper protocol and inputs have been demonstrated through validation with a variety of heterogeneous systems.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Adam T. Green, Amanda J. Pickard, Rongzhong Li, Alexander D. MacKerell, Ulrich Bierbach, Samuel S. Cho
Summary: This study uses circular dichroism spectroscopy to show the parallel topologies of two putative ribosomal G-quadruplex sequences, and validates and refines the modeled structures using molecular dynamics simulations. The results provide a structural foundation for understanding G-quadruplex functions and designing novel chemotherapeutics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Review
Chemistry, Multidisciplinary
Himanshu Goel, Anthony Hazel, Wenbo Yu, Sunhwan Jo, Alexander D. MacKerell
Summary: SILCS utilizes molecular simulation to obtain functional group affinity patterns for drug discovery, allowing for identification of novel ligand binding pockets, prediction of protein-ligand binding affinities, and other applications in computer-aided drug design. It represents a comprehensive approach to improve drug development processes through accuracy and throughput enhancements.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Payal Chatterjee, Mert Y. Sengul, Anmol Kumar, Alexander D. MacKerell
Summary: The outcomes of computational chemistry and biology research are greatly influenced by the choice of forcefield used in molecular simulations. This study develops a deep learning-based framework for optimizing van der Waals interactions in molecular simulations. The resulting LJ parameters (interactions between atoms) are validated for their performance in reproducing condensed phase thermodynamic properties and demonstrate improved accuracy in reproducing solvent and crystal properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell
Summary: Generalized force fields (FFs) are extensions of biomolecular FFs used for organic molecules. However, their application to arbitrary molecules requires caution to ensure their integrity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Abhishek A. Kognole, Anthony Hazel, Alexander D. MacKerell
Summary: RNA molecules can be potential drug targets in various diseases due to their dysregulated expression or misfolding. Noncoding RNAs, which account for a large part of the human genome, have complex structures and can be targeted by small molecules. The SILCS computational approach, termed SILCS-RNA, was extended to target RNA in this study and evaluated against seven RNA targets. The method provides detailed functional group affinity patterns and facilitates the identification of new potential binding sites and ligand design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Wenbo Yu, David J. Weber, Alexander D. MacKerell
Summary: Covalent drug design plays a significant role in drug discovery by forming a covalent bond with targeted residues, leading to a more effective therapeutic approach. Computational methods can identify reactive residues, test potential reactivities, and predict noncovalent contributions to binding. SILCS, a functional group mapping approach, considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. SILCS-Covalent, an integrated workflow, can qualitatively and quantitatively inform covalent drug discovery.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor, Benoit Roux, Alexander D. MacKerell Jr, Jeffery B. Klauda
Summary: Accurate empirical force fields of lipid molecules are crucial for molecular dynamics simulations of various lipid systems and heterogeneous systems. The polarizable Drude force field has been optimized in this study to improve its accuracy in simulating pure bilayers and membranes. By using both experimental and quantum mechanical data, the optimized force field shows good agreement with a range of experimental observables. The polarizable Drude2023 force field is anticipated to advance our understanding of electronic polarization in lipid systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell Jr
Summary: In this study, the sampling efficiency of the GCMC method was improved by applying known cavity-bias and configurational-bias algorithms on GPU architecture. The method was parallelized using CUDA and OpenCL, resulting in simultaneous sampling of a large number of configurations during insertion attempts. The partitioning scheme allowed for simultaneous insertion attempts for large systems, significantly improving efficiency. The algorithm was shown to be useful in the application of the site-identification by ligand competitive saturation (SILCS) co-solvent sampling approach for the protein CDK2.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Asuka A. Orr, Aoxiang Tao, Olgun Guvench, Alexander D. MacKerell
Summary: Protein-based therapeutics often face challenges of protein aggregation and high solution viscosity due to high concentrations of active protein. The charge of a protein, affected by its environment, plays a significant role in these solution behaviors. This study presents a structure-based approach called SILCS-Biologics, which predicts the effective charge of proteins by considering the competition between ions and the presence of buffers.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: Metal ions, particularly Mg2+, play a role in stabilizing RNA's tertiary structures. However, the atomic-level mechanisms underlying this process are not fully understood. In this study, computational techniques were combined to investigate the specific interactions between Mg2+ ions and RNA, particularly in the pseudoknot structure of the Twister ribozyme.
Article
Chemistry, Multidisciplinary
Himanshu Goel, Wenbo Yu, Alexander D. MacKerell
Summary: This article presents the application of structure- and ligand-based approaches in simulating and predicting hERG drug liability. By combining the SILCS method with physicochemical properties, predictive models for hERG blockade were developed, resulting in improved predictability and aiding in rational drug design to minimize hERG risk.
CHEMISTRY-SWITZERLAND
(2022)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: The presence of polarizability in the force field improves the stability of RNA hairpin structures and leads to variations in dipole moments and ion distribution. Molecular dynamics simulations play a crucial role in modeling biomolecular systems, and the treatment of electrostatic interactions in the force field strongly affects simulation accuracy. In this study, the impact of polarization on structural properties, dipole moment distributions, and cation interactions in RNA hairpin systems is investigated using polarizable and non-polarizable nucleic acid force fields.
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY
(2022)