A5058504410- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Nuclear physics research studies
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- Mass Spectrometry Techniques and Applications
- Force Microscopy Techniques and Applications
- Microtubule and mitosis dynamics
- Advanced NMR Techniques and Applications
- Spectroscopy and Quantum Chemical Studies
- Nuclear Physics and Applications
- Photosynthetic Processes and Mechanisms
- Machine Learning in Materials Science
- Nanopore and Nanochannel Transport Studies
- Cellular Mechanics and Interactions
- High-pressure geophysics and materials
- Asymmetric Synthesis and Catalysis
- Vehicle Dynamics and Control Systems
- Lipid Membrane Structure and Behavior
- Advanced Sensor and Control Systems
- DNA and Nucleic Acid Chemistry
- Glycosylation and Glycoproteins Research
- Metal-Organic Frameworks: Synthesis and Applications
Nanjing University
2016-2025
University of Chinese Academy of Sciences
2019-2025
Changchun University of Science and Technology
2019-2025
Shandong University
2012-2025
National Laboratory of Solid State Microstructures
2009-2025
Laboratoire de physique des Solides
2025
Anhui Agricultural University
2025
Peking University
2025
Collaborative Innovation Center of Advanced Microstructures
2014-2024
Zhejiang Lab
2022-2024
For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of one-particle-per-residue, CafeMol equips four structure-based protein models: (1) off-lattice Go model, (2) atomic interaction based CG model for native state folding dynamics, (3) multiple-basin conformational change (4) elastic network quasiharmonic fluctuations around structure. Ligands can be treated either...
Ligand binding modulates the energy landscape of proteins, thus altering their folding and allosteric conformational dynamics. To investigate such interplay, calmodulin has been a model protein. Despite much attention, fully resolved mechanisms folding/binding have not elucidated. Here, by constructing computational that can integrate folding, binding, motions, we studied in-depth isolated domains coupled with two calcium ions associated changes. First, mechanically pulled simulations...
Proteins have often evolved sequences so as to acquire the ability for regulation via allosteric conformational change. Here we investigate how dynamics is designed through with nonlinear interaction features. First, 71 proteins of which two, open and closed, structures are available, a statistical survey interactions using an all-atom model effective solvation shows that those residue contact specific one two states significantly weaker than shared by states. This feature indicates there...
While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow larger proteins, which recent suggested quite complex rich behaviors. Here, we address how the energy landscape theory can be applied to these reactions. Combining perfect-funnel approximation with a multiscale method, first extended our previous atomic-interaction based coarse grained (AICG) model take into account local flexibility protein molecules. Using...
Abstract Hydrogels capable of swift mechanical energy dissipation hold promise for a range applications including impact protection, shock absorption, and enhanced damage resistance. Traditional absorption in such materials typically relies on viscoelastic mechanisms, involving sacrificial bond breakage, yet often suffers from prolonged recovery times. Here, we introduce hydrogel designed friction-based damping. This features an internal structure that facilitates the motion chain walker...
Saccharides and peptides with markedly disparate stereochemical features serve as pivotal chiral molecular partners in living systems. The importance of glycosylation influencing glycopeptide self-assembly has been recognized. However, how different combinations saccharides influence the macroscopic hydrogel mechanics, fiber nanomechanics, asymmetric packing, thermodynamic changes during remains unknown. This study demonstrates that, following d-glycosylation peptides, resulting...
Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles life processes, depend on the binding of zinc ion for their proper folding. To computationally study zinc-coupled folding zinc-fingers, charge transfer metal induced protonation/deprotonation effects have to be considered. Here, by attempting implicitly account such classical molecular dynamics performing intensive simulations with explicit solvent peptides without binding, we investigate Cys2His2-type zinc-finger...
Quality assessment is essential for the computational prediction and design of RNA tertiary structures. To date, several knowledge-based statistical potentials have been proposed proved to be effective in identifying native near-native All these are based on inverse Boltzmann formula, while differing choice geometrical descriptor, reference state, training dataset. Via an approach that diverges completely from conventional potentials, our work explored power a 3D convolutional neural network...
Abstract Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation biological activities. Direct observation structures at high resolution native form however remains a challenge. The large vestibule and narrow constriction Mycobacterium smegmatis porin A (MspA) suggests sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering (siRNA), transfer (tRNA) 5 S ribosomal (rRNA). To...
Proteins perform their biological functions through motion. Although high throughput prediction of the three-dimensional static structures proteins has proved feasible using deep-learning-based methods, predicting conformational motions remains a challenge. Purely data-driven machine learning methods encounter difficulty for addressing such because available laboratory data on are still limited. In this work, we develop method generating protein allosteric by integrating physical energy...
The cell fate transition is a fundamental characteristic of living organisms. By introducing external perturbations, it possible to artificially intervene in and trigger reprogramming. Revealing the general principle underlying induced phenotypic reshaping populations remains central focus field biology. In this study, we investigate energetic dynamic features from differentiated somatic state pluripotent by constructing Boolean genetic network model. simulation experimental results...
Mechanosensitive (MS) channels are universal cellular membrane pores. Bacterial MS channels, as typified by channel of small conductance (MscS) from Escherichia coli ( Ec MscS), release osmolytes under hypoosmotic conditions. known to be ion selective different extents, but the underlying mechanism remains poorly understood. Here we identify an anion-selective MscS Thermoanaerobacter tengcongensis Tt MscS). The structure closely resembles that MscS, it lacks large cytoplasmic equatorial...
Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using principles nature, and peptides serve as promising building blocks to construct adaptable molecular architectures. Recently, series heptapeptides with alternative hydrophobic hydrophilic residues were reported form amyloid-like structures, which are capable catalyzing acyl ester hydrolysis remarkable efficiency. However, information remains elusive about atomic structures fibrils. What is origin...
Abstract Strictamine and rhazinoline are representative methanoquinolizidine‐containing akuammiline alkaloids that possess different stereochemistry at the C16 position. A unified approach to enantioselective total syntheses of these two molecules is described. The key steps in this synthesis include a photocatalytic intra/intermolecular type II radical cascade reaction, Tsuji–Trost allylation, palladium‐ or nickel‐mediated cyclization, late‐stage intramolecular N‐alkylation reaction.
Autonomous vehicles have been gaining increasing attentions, one key research interesting is stable path tracking for an advanced driver assistance system. This paper investigates Pure Pursuit, Stanley, Linear Quadratic Regulator (LQR) and Model Predictive Control (MPC) with Ackerman steering model these methods are tested on different shape paths in simulation experiments. It demonstrated that the performances of LQR MPC controllers better than those using Pursuit Stanley controllers. In...