A5055160771- Protein Structure and Dynamics
- Protein Tyrosine Phosphatases
- Machine Learning in Materials Science
- Biochemical and Molecular Research
- Block Copolymer Self-Assembly
- Electrostatics and Colloid Interactions
- Advanced machining processes and optimization
- PI3K/AKT/mTOR signaling in cancer
- Spectroscopy and Quantum Chemical Studies
- Industrial Vision Systems and Defect Detection
- Scientific Computing and Data Management
- RNA Research and Splicing
- Sarcoma Diagnosis and Treatment
- Nanopore and Nanochannel Transport Studies
- Metabolomics and Mass Spectrometry Studies
- Advanced NMR Techniques and Applications
- Testicular diseases and treatments
- Photosynthetic Processes and Mechanisms
- Electron Spin Resonance Studies
- Engineering Technology and Methodologies
- Synthesis and biological activity
- Endoplasmic Reticulum Stress and Disease
- Cancer Diagnosis and Treatment
- Gene expression and cancer classification
- Galectins and Cancer Biology
University of California, Irvine
2021-2025
First Affiliated Hospital of GuangXi Medical University
2024
Guangxi Medical University
2024
Shenzhen University
2024
Nanjing University of Science and Technology
2023
AmberTools is a free and open-source collection of programs used to set up, run, analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
Molecular dynamics (MD) simulations are essential for understanding molecular phenomena at the atomic level, with their accuracy largely dependent on both employed force field and sampling. Polarizable fields, which incorporate polarization effects, represent a significant advancement in simulation technology. The polarizable Gaussian multipole (pGM) model has been noted its accurate reproduction of ab initio electrostatic interactions. In this study, we document our effort to enhance...
The critical importance of water in sustaining life highlights the need for accurate models computer simulations, aiming to mimic biochemical processes experimentally. polarizable Gaussian multipole (pGM) model, recently introduced biomolecular improves handling complex interactions. As an integral part our initial exploration, we examined a minimalist fixed geometry three-center pGM model using ab initio quantum mechanical calculations oligomers. However, final development was based on...
Abstract Motivation Single-cell clustering plays a crucial role in distinguishing between cell types, facilitating the analysis of heterogeneity mechanisms. While many existing methods rely solely on gene expression data obtained from single-cell RNA sequencing techniques to identify clusters, information contained mono-omic is often limited, leading suboptimal performance. The emergence multi-omics technologies enables integration multiple omics for identifying but how integrate different...
Abstract Objective To develop an ultrasound-driven clinical deep learning radiomics (CDLR) model for stratifying the risk of testicular masses, aiming to guide individualized treatment and minimize unnecessary procedures. Methods We retrospectively analyzed 275 patients with confirmed lesions (January 2018 April 2023) from two hospitals, split into training (158 cases), validation (68 external test cohorts (49 cases). Radiomics (DL) features were extracted preoperative ultrasound images....
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression various human cancers neurodevelopmental disorders. Allosteric inhibitors have proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into open state, wherein catalytic cleft becomes fully exposed ligands. This study elucidates dynamical properties structures across different states, with focus on effects mutation two...
Accurate characterization of electrostatic interactions is crucial in molecular simulation. Various methods and programs have been developed to obtain parameters for additive or polarizable models replicate properties obtained from experimental measurements theoretical calculations. Electrostatic potentials (ESPs), a set physically well-defined observables quantum mechanical (QM) calculations, are well suited optimization efforts due the ease collecting large amount conformation-dependent...
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression various human cancers neurodevelopmental disorders. Allosteric inhibitors have proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into open state, wherein catalytic cleft becomes fully exposed ligands. This study elucidates dynamic properties structures across different states, with focus on effects mutation two known...
Liquid–liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells.
Liquid-Liquid Phase Separation (LLPS) plays pivotal roles in the organization and functionality of living cells. It is imperative to understand underlying driving forces behind LLPS control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool investigate systems comprising oligolysine adenosine triphosphate (ATP) under conditions various ionic concentrations lengths. Consistent with experimental observations, our CG captured formation upon addition...
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression various human cancers neurodevelopmental disorders. Allosteric inhibitors have proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into open state, wherein catalytic cleft becomes fully exposed ligands. This study elucidates dynamic properties structures across different states, with focus on effects mutation two known...
In computational biochemistry and biophysics, understanding the role of electrostatic interactions is crucial for elucidating structure, dynamics, function biomolecules. The Poisson-Boltzmann (PB) equation a foundational tool modeling these by describing potential in around charged molecules. However, solving PB presents significant challenges due to complexity biomolecular surfaces need account mobile ions. While traditional numerical methods are accurate, they computationally expensive...
Molecular surfaces play a pivotal role in elucidating the properties and functions of biological complexes. While various have been proposed for specific scenarios, their widespread adoption faces challenges due to limited efficiency stemming from hand-crafted modeling designs. In this work, we general framework that incorporates both point cloud concept neural networks. The use matrix multiplication enables efficient implementation across diverse platforms libraries. We applied develop...
Abstract γ-TiAl alloy is a typically difficult material to machine, and machining defects such as grain pull-out spalling are common during machining, resulting in component scrap. As result, it critical investigate the real-time monitoring method of surface roughness milling. A new model for predicting proposed this article. Based on idea deep learning, prediction problem turned into classification problem. The features force signal extracted using continuous wavelet transform,...
Liquid-Liquid Phase Separation (LLPS) plays pivotal roles in the organization and functionality of living cells. It is imperative to understand underlying driving forces behind LLPS control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool investigate systems comprising oligolysine adenosine triphosphate (ATP) under conditions various ionic concentrations lengths. Consistent with experimental observations, our CG captured formation upon addition...