A5100364952- Protein Structure and Dynamics
- Lipid Membrane Structure and Behavior
- RNA Interference and Gene Delivery
- RNA and protein synthesis mechanisms
- Nanopore and Nanochannel Transport Studies
- Advanced biosensing and bioanalysis techniques
- Spectroscopy and Quantum Chemical Studies
- Plant biochemistry and biosynthesis
- DNA and Nucleic Acid Chemistry
- Enzyme Structure and Function
- Photosynthetic Processes and Mechanisms
- Mass Spectrometry Techniques and Applications
- Ion Transport and Channel Regulation
- Radiopharmaceutical Chemistry and Applications
- Receptor Mechanisms and Signaling
- Mitochondrial Function and Pathology
- Monoclonal and Polyclonal Antibodies Research
- Protein Kinase Regulation and GTPase Signaling
- Immune Response and Inflammation
- Membrane-based Ion Separation Techniques
- Advanced Chemical Physics Studies
- Force Microscopy Techniques and Applications
- NF-κB Signaling Pathways
- Photonic and Optical Devices
- Hydrogels: synthesis, properties, applications
Chinese University of Hong Kong
2016-2025
Beijing Proteome Research Center
2023-2024
Xi'an University of Technology
2024
Zhejiang University
2023
Tianjin University of Traditional Chinese Medicine
2023
Yangtze University
2023
South China Normal University
2023
University of Hong Kong
2004-2022
Chinese Academy of Sciences
2021-2022
Institute of Physics
2022
NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance petascale parallel supercomputers consisting hundreds thousands cores, as well inexpensive commodity clusters commonly found in academic environments. It is written C++ leans Charm++ optimal low-latency versatile, multipurpose code that gathers state-of-the-art algorithms to carry out apt thermodynamic ensembles,...
Predicting the rate of nonfacilitated permeation solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be estimated using molecular dynamics simulations combined with inhomogeneous solubility-diffusion model, which requires calculation potential mean force position-dependent diffusivity solute along transmembrane axis. In this paper, we assess efficiency accuracy several methods for permeability a model DMPC bilayer urea, benzoic acid, codeine....
Abstract 3D culture of cells in designer biomaterial matrices provides a biomimetic cellular microenvironment and can yield critical insights into behaviours not available from conventional 2D cultures. Hydrogels with dynamic properties, achieved by incorporating either degradable structural components or reversible crosslinks, enable efficient cell adaptation the matrix support associated functions. Herein we demonstrate that given similar equilibrium binding constants, hydrogels containing...
Achieving robust underwater adhesion by bioadhesives remains a challenge due to interfacial water. Herein coacervate-to-hydrogel strategy enhance water repulsion and bulk of is reported. The polyethyleneimine/thioctic acid (PEI/TA) coacervate deposited onto substrates, which can effectively repel completely spread into substrate surface irregularities its liquid water-immiscible nature. physical interactions between further adhesion. Furthermore, driven the spontaneous hydrophobic...
Abstract Effective and easy regulation of hydrogel surface properties without changing the overall chemical composition is important for their diverse applications but remains challenging to achieve. We report a generalizable strategy reconfigure networks based on hydrogel–substrate interface dynamics manipulation wettability bioadhesion. show that grafting hydrophobic yet flexible polymeric chains mold substrates can significantly elevate content polymer backbones reduce presence polar...
Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that provides efficient free energy calculations of biomolecules. Like the previous (aMD), GaMD allows for "unconstrained" without need to set predefined collective variables and so useful studying complex biomolecular conformational changes such as protein folding ligand binding. Furthermore, because boost potential constructed using harmonic function follows distribution in GaMD, cumulant...
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion lipids and limited time scale MD. In order to study mixing characterize distribution in converged mixtures, we report microsecond-long all-atom MD performed on special-purpose machine Anton. Two types mixed bilayers, POPE:POPG (3:1) POPC:cholesterol (2:1), as well a pure POPC bilayer, were each simulated for up 2 μs. These show that fully miscible at conditions, with final states bilayers...
Due to antimicrobial resistance, the development of new drugs combat bacterial and fungal infections is an important area research. Nature uses short, charged, amphipathic peptides for defense, many which disrupt lipid membrane in addition other possible targets inside cell. Computer simulations have revealed atomistic details interactions cell-penetrating with bilayers. Strong between polar interface charged can induce bilayer deformations - including rupture peptide stabilization a...
Exchange of ATP and ADP across mitochondrial membrane replenishes the cytoplasm with newly synthesized provides mitochondria substrate for oxidative phosphorylation. The sole means this exchange is ADP/ATP carrier (AAC), a protein that suggested to cycle between two conformationally distinct states, cytosolic-open (c-state) matrix-open (m-state), thereby shuttling nucleotides inner membrane. However, c-state only structurally resolved state, binding site remains elusive. Here, we present...
Abstract Involvement of aquaporins in gas conduction across the membrane and physiological significance this process have attracted marked attention from both experimental theoretical studies. Previous work demonstrated that AQP1 is permeable to CO 2 O . Here we employ various simulation techniques examine permeability brain aquaporin AQP4 NO describe energetics pathways associated with these phenomena. The energy barrier permeation through central pore found be only ∼3 kcal mol −1 results...
Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist small proteins form hexameric units with semipermeable central pores containing binding sites for anions. This feature is thought to selectively allow access RuBisCO enzymes inside carboxysome by HCO3- (the dominant CO2 aqueous solution at pH 7.4) but not O2, which leads a nonproductive reaction. To test this hypothesis, here we use...
Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use manure fertilizer reduces application chemical fertilizers, main concern with regards to microbial pollution. Manure reservoir broad range populations, including pathogens, have potential cause contamination and pose risks public animal health. Despite widespread fertilizer, change diversity under various treatment processes still not well-understood. We hypothesize that population...
It is well established that epidermal growth factor (EGF) induces the cytoskeleton reorganization and cell migration through two major signaling cascades: phospholipase C-gamma1 (PLC-gamma1) Rho GTPases. However, little known about cross talk between PLC-gamma1 Here we showed forms a complex with Rac1 in response to EGF. This interaction direct mediated by Src homology 3 (SH3) domain (106)PNTP(109) motif. critical for EGF-induced activation vivo, SH3 actually potent specific guanine...
Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such generally require detailed knowledge the surface composition NP under investigation. Even for some well-characterized nanoparticles, however, this is not always available. An example nanodiamond, a nanoscale diamond particle dominated by oxygen-containing functional groups. In work, we explore using harmonic restraint method developed Venable et...
Voltage imaging with fluorescent dyes offers promise for interrogating the complex roles of membrane potential in coordinating activity neurons brain. Yet, low sensitivity often limits broad applicability optical voltage indicators. In this paper, we use molecular dynamics (MD) simulations to guide design new, ultrasensitive indicators that photoinduced electron transfer (PeT) as a voltage-sensing switch. MD predict an approximately 16% increase resulting purely from improved alignment dye...
Prediction of membrane permeability to small molecules represents an important aspect drug discovery. First-principles calculations this quantity require accurate description both the thermodynamics and kinetics that underlie translocation permeant across lipid bilayer. In contribution, three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA), hydrocortisone (HYL), are estimated in a pure 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) POPC:cholesterol...
Hybrid integration of two-dimensional (2D) materials holds great promise for realizing novel optoelectronic components on planar dielectric waveguides. Functional devices based 2D layered transition metal dichalcogenides (TMDs) offer the advantages low dark current and high speed. In this work, we propose experimentally demonstrate a high-speed hybrid integrated PtSe2 silicon nitride waveguide photodetector. The light is guided in channel by structure principle bound states continuum (BICs)....