A5008188358- Polymer Surface Interaction Studies
- RNA and protein synthesis mechanisms
- Material Dynamics and Properties
- RNA modifications and cancer
- Polymer crystallization and properties
- DNA and Nucleic Acid Chemistry
- Block Copolymer Self-Assembly
- Nanopore and Nanochannel Transport Studies
- Polymer Nanocomposites and Properties
- RNA Research and Splicing
- Pickering emulsions and particle stabilization
- Surfactants and Colloidal Systems
- Force Microscopy Techniques and Applications
- Advanced Polymer Synthesis and Characterization
- Dendrimers and Hyperbranched Polymers
- Electrostatics and Colloid Interactions
- Protein Structure and Dynamics
- RNA Interference and Gene Delivery
- Computational Drug Discovery Methods
- Nonlinear Optical Materials Studies
- ATP Synthase and ATPases Research
- Statistical Methods and Bayesian Inference
- Adhesion, Friction, and Surface Interactions
- Cardiomyopathy and Myosin Studies
- Phase Equilibria and Thermodynamics
Zhejiang University
2012-2024
University of Missouri
2004-2024
Wenzhou University
2013
Jiaxing University
2013
Jiangsu University
2006
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
With rapid advances in computer algorithms and hardware, fast accurate virtual screening has led to a drastic acceleration selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions become an indispensable tool for RNA-targeted discovery. The current models RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking scoring should tackle four crucial problems: (1) conformational flexibility ligand, (2) RNA,...
The ability to accurately predict the binding site, pose, and affinity for ligand–RNA is important RNA-targeted drug design. Here, we describe a new computational method, RLDOCK, predicting site pose binding. By developing an energy-based scoring function, sample exhaustively all of possible sites with flexible ligand conformations pair based on geometric energetic scores. model distinguishes from other approaches in three notable features. First, enables exhaustive scanning sites, including...
Hypertrophic cardiomyopathy (HCM) is the most prominent cause of sudden cardiac death in young individuals. Due to heterogeneity clinical manifestations, conventional HCM drugs have limitations for mitochondrial hypertrophic cardiomyopathy. Discovering more effective compounds would be substantial benefit further elucidating pathogenic mechanisms and treating patients with this condition. We previously reported MT-RNR2 variant associated that results dysfunction. Here, we screened a...
Auditory neuropathy spectrum disorder (ANSD) is a hearing impairment caused by dysfunction of inner hair cells, ribbon synapses, spiral ganglion neurons and/or the auditory nerve itself. Approximately 1/7000 newborns have abnormal function, accounting for 10%-14% cases permanent loss in children. Although we previously identified AIFM1 c.1265 G > A variant to be associated with ANSD, mechanism which ANSD poorly understood. We generated induced pluripotent stem cells (iPSCs) from peripheral...
By employing molecular dynamics simulations, we explored the effective depletion zone for nanoparticles (NP) immersed in semiflexible polymer melts and calculated entropic interactions between a pair of NPs nanocomposite melts. The average volumes rely mainly on chain stiffness increase with increasing. In melts, are attractive anisotropic, Meanwhile, polymers can also affect strongly interactions. For athermal system, change from anisotropic to isotropic when NP/polymer increase. rodlike...
We investigate the dynamics of two-dimensional soft vesicles filled with chiral active particles by employing overdamped Langevin simulation. The unidirectional rotation is observed for vesicles, and rotational angular velocity depends mainly on area fraction (ρ) (ω) particles. There exists an optimal parameter ω at which vesicle takes its maximal value. Meanwhile, low concentration continuity curvature destroyed seriously particles, especially large ω, high cover almost uniformly. In...
By employing molecular dynamics simulations, we explored the conformation transition of nanoparticles (NPs) in semiflexible ring polymer nanocomposite melts. A novel aggregation-dispersion for NPs nanocomposites occurs when bending energy chains increases. The conformations flexible near are radial distribution, and entropic depletion interactions between a pair melts attractive, however, rod-like wrap around repulsive. induced by chain topology can provide new access to achieve miscibility...
Abstract The limited success of current targeted therapies for pancreatic cancer underscores an urgent demand novel treatment modalities. challenge in mitigating this malignancy can be attributed to the digestive organ expansion factor (DEF), a pivotal yet underexplored tumorigenesis. study uses blend vitro and vivo approaches, complemented by theoretical analyses, propose DEF as promising anti‐tumor target. Analysis clinical samples reveals that high expression is correlated with diminished...
Abstract By employing molecular dynamics simulations, we explore the of NPs in semiflexible ring polymer nanocomposite melts. A novel glass transition is observed for melts as bending energy ( K b ) polymers increases. For flexible = 0), move classic diffusive behavior. However, with large energy, diffuse very slowly and exhibit glassy state which are all irreversibly caged be neighbouring polymers. This occurs well above classical temperature at microscopic mobility lost, topological...
The aggregation behaviors and phase separation of binary nanoparticles immersed in semiflexible polymer brushes are explored using molecular dynamics simulations. conformations the nanoparticle–brush mixtures very sensitive to size ratio q = σl/σs, where σl σs diameters for large small nanoparticles, respectively, attractive interactions εM between brushes. is observed at a relatively strong interaction under effects inter-nanoparticle depletion attractions provided by Furthermore,...
The self-assembly of diblock copolymer (DBCP)/diblock nanorod (DBNR) mixtures are studied by using a dissipative particle dynamics simulation method. microstructures DBCP/DBNR blends depend on the type DBCPs as well number DBNRs. For asymmetric A3B7, morphological transition from cylinder phase to lamellar is observed for DBNRs with suitable length and component. Meanwhile, symmetric A5B5, morphologies can always maintain during process adding except case component mismatch between On other...
Abstract Coarse‐grained molecular dynamics simulations are used to explore the spatial orientations and conformational transitions of nanorods (NRs) within semiflexible polymer brushes. The NR clusters controlled by competition between entropy cost for NRs infiltrated into brushes attractive energy By reducing grafting density or enhancing number NRs, cluster experiences an orientation transition from vertical direction horizontal direction. regarded as soft confinements can induce formation...
ABSTRACT The aggregation behavior and phase separation of nanorod (NR)/nanoparticle (NP) nanoinclusions immersed in semiflexible polymer brushes (PBs) are investigated by using molecular dynamics simulations. A variety phases formed varying the size ratio q = σ r /σ p , where diameters NR NPs, respectively, attractive interactions ε M between NR/NP PBs. Ordered structures NRs surrounded large NPs observed for small q, a dispersed mixture appears moderate at weak interaction. Meanwhile,...
The condensation of DNA induced by spermine is studied atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount multivalent cations added to the solutions different numbers steps, we find that process strongly depends on speed adding cations. That is, slower are added, aggregates. MD steered (SMD) results agree well with experimental results, data also show more steps there are, compact condensed structure will be. This...
Wrapping and unwrapping behaviors of double-stranded DNA around a positively charged nanosphere in solution are studied by using the coarse-grained molecular dynamics (CGMD) simulation method. When monovalent, divalent trivalent anions added to DNA-nanosphere complex solution, binds with owing strong electrostatic attraction. However, when tetravalent local charge inversion is observed for high anion concentration can be unwrapped from because near nanosphere. Moreover, helical structure...
The adsorption-desorption transition of DNA in DNA-dendrimer solutions is observed when high-valence anions, such as hexavalent are added to the solutions. In with low-valence dendrimers bind tightly V-shaped double-stranded DNA. When pentavalent or solutions, chains can be stretched straightly and released from chains. fact, adding anions change charge spatial distribution weaken electrostatic interactions between positively charged oppositely Adsorption-desorption induced by overcharging...
The growing interest in RNA-targeted drugs underscores the need for computational modeling of interactions between RNA molecules and small compounds. Having a reliable scoring function RNA-ligand is essential effective drug screening. An ideal should not only predict native pose ligand binding but also rank affinity different ligands. However, existing functions are primarily designed to modes given pair have been thoroughly assessed virtual screening purposes. In this paper, we introduce...
The self-assembly behaviors and phase transitions of binary nanoparticles (NPs) adsorbed on a soft elastic shell are investigated through molecular dynamics simulation. conformations NPs depend the bending energy Kb binding D0 between shell. ordered structures observed at moderate adhesive strength energy, in which small located near vertices regular pentagons as well large distributed along sides pentagons. shape can be adjusted by adding NPs, this investigation provide an effective way to...