Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase

The complex model of Thermus thermophilus xylose isomerase （TtXI） with D-xylose was constructed, and molecular dynamics （MD） simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration （Rg）, subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups： one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.

Molecular dynamics study of the ternary compound Li3AlB2O6

A new compound with the stone cheinical composition as Li3AlB2O6 but with a different x-ray powder diffraction pattern as reported before was synthesized and studied experimentally by M. He, Chen X Let al （J. Solid State Chem. 163, 369 （2002））, but there lacks first principles study on the structure of it. Using conjugant gradient （CG） molecule dynamics （MD） simulation with a full relaxation of the atomic positions and of the shape and size of the cell, the structure of Li3AlB2O6 is studied from first principles. For the density functional, the local density approximation （LDA） and the generalized gradient approximation （GGA） forms are used respectively. Both the LDA and GGA results support the experimental structure of M. He et al. The result of MD simulation using GGA agrees with the experimental result much better. The energy bands are also studied, the band gap given by LDA and GGA are 5.65 eV, 5.34eV, respectively.

Molecular dynamics study of ice structural evolution

Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of -1.0 GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H… O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80 K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.

DYNAMIC ASPECT OF THE INTERACTION OF DIATOMIC MOLECULES WITH METAL SURFACES

The dynamics of the scattering processes of diatomic molecules from metal surfaces has been studied with different theoretical approaches. Modified LEPS (London-Eyring-Polanyi-Sato) potential surfaces for several diatomie molecule-surface systems have been constructed and examined for the dynamic study. The surfaces are treated as rigid but corrugated. The potential parameters are adjusted to produce reliable potential hypersurfaces. Molecular dissociation, diffraction, adsorption and consequent desorption in the scattering processes have been observed through quasiclassieal trajectory calculations. The significance of the effective corrugation of the potential surfaces has been evaluated in calculating the dissociation and adsorption probabilities. Vibration-rotation-translation energy transfer in the inelastic scattering is investigated to understand the mechanism of selective adsorptions mediated through vibrational or rotational degrees of freedom. We have carried out quantum mechanical calculations to obtain the rotational and vibrational transition probabilities. Relative importance of rotational and vibrational transitions for each adsorbed state with respect to incidence energy has been carefully examined to determine the dominant factor which causes the adsorbed state. The results show that vibration mediation is an essential factor to the selective adsorption especially in the ease of higher incidence energies.

Molecular dynamics study of water molecules nucleation for fine particle removal:Effects of wettability and aggregation modes and comparison with experiment Author links open overlay panel

Water vapor nucleation on particle's surface plays an important role in dust removal,cloud formation,and particle measurement.However,the selectivity of nucleation sites and the nucleation characteristic of water molecule on the particle's surface are still unclear,especially for the aggregated particles.In this paper,the effects of particle wettability and aggregation modes on the selectivity of nucleation sites and the nucleation characteristics were investigated using molecular dynamics simulation.The results were compared with our earlier experimental findings.It illustrates how the contact angle of clusters,the growth velocity,and the growth duration are all influenced by the interaction coefficient between water and particles.Moreover,the nucleation sites of water molecules on the particle aggregation surface exhibit a definite selectivity.The primary indicator of this selectivity is the preferential nucleation of water molecules at the interfaces of linear chain aggregation particles,at the inner side of non-linear chain aggregation particles,and at the centers of ring aggregation.These results are in good agreement with our previous experimental findings.More significantly,additional research has revealed that subcritical-size clusters typically aggregate on two-particle surfaces spacing when the spacing smaller than the critical cluster size.

Phase Transition Temperature of HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene) from Molecule Dynamic Simulation

Molecule dynamics simulation was used on HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene), which is a discotic Liquid crystal. From analyzing the energy and displacement varying with the temperature, the phase transition temperature of PM6MPP can be predicted. The deviations of T-g, T-m and T-i due to the MD time scale are small enough that it should be possibly used to predict the material properties especially when more powerful computers are available.

Molecular Mechanisms of Intracellular Delivery of Nanoparticles Monitored by an Enzyme‑Induced Proximity Labeling

Achieving increasingly finely targeted drug delivery to organs,tissues,cells,and even to intracellular biomacromolecules is one of the core goals of nanomedicines.As the delivery destination is refined to cellular and subcellular targets,it is essential to explore the delivery of nanomedicines at the molecular level.However,due to the lack of technical methods,the molecular mechanism of the intracellular delivery of nanomedicines remains unclear to date.Here,we develop an enzyme-induced proximity labeling technology in nanoparticles(nano-EPL)for the real-time monitoring of proteins that interact with intracellular nanomedicines.Poly(lactic-co-glycolic acid)nanoparticles coupled with horseradish peroxidase(HRP)were fabricated as a model(HRP(+)-PNPs)to evaluate the molecular mechanism of nano delivery in macrophages.By adding the labeling probe biotin-phenol and the catalytic substrate H_(2)O_(2)at different time points in cellular delivery,nano-EPL technology was validated for the real-time in situ labeling of proteins interacting with nanoparticles.Nano-EPL achieves the dynamic molecular profiling of 740 proteins to map the intracellular delivery of HRP(+)-PNPs in macrophages over time.Based on dynamic clustering analysis of these proteins,we further discovered that different organelles,including endosomes,lysosomes,the endoplasmic reticulum,and the Golgi apparatus,are involved in delivery with distinct participation timelines.More importantly,the engagement of these organelles differentially affects the drug delivery efficiency,reflecting the spatial–temporal heterogeneity of nano delivery in cells.In summary,these findings highlight a significant methodological advance toward understanding the molecular mechanisms involved in the intracellular delivery of nanomedicines.

Polaron-assisted nonadiabatic dynamics in protonated TiO_(2) with surface water molecule

We investigated the polaron-assisted nonadiabatic dynamics in protonated TiO_(2),as well as the polaron-H_(2)O coupling and its effects on the relaxation of photogenerated electrons.We observed that different polaron hopping regimes result in varied nonadiabatic couplings and relaxations of excited electrons from the conduction band minimum to the gap states of protonated TiO_(2),with a weak dependence on the actual trapping site of the polaron.Surface-adsorbed H_(2)O molecules can attract polarons toward the adsorbed Ti sites,with the coupling between H_(2)O and the polaron being inversely proportional to their distance.Our findings suggest that the lifetime of the photogenerated charge carriers can be extended by reducing the polaron-H_(2)O distances,with expected benefits to the efficiency of the reduced TiO 2 samples for photocatalytic applications.

Submillimeter/millimeter observations of the high-mass star forming region IRAS 22506+5944

The mapping observations of CO J -- 2-1, CO J = 3- 2, 13CO J = 2-1 and 13CO J -- 3 - 2 lines in the direction of IRAS 22506＋5944 have been made. The results show that the cores in the J = 2 - i transition lines have a similar morphology to those in the J -- 3 - 2 transition lines. Bipolar molecular outflows are verified. The prior IRAS 22506＋5944 observations indicated that two IRAS sources and three H20 masers were located close to the peak position of the core. One of the IRAS sources may be the driving source of the outflows. In addition, the H20 masers may occur in relatively warm environments. The parameters of the dense core and outflow, obtained by the LTE method, indicate that IRAS 22506＋5944 is a high-mass star formation region.

A statistical study towards high-mass BGPS clumps with the MALT90 survey

In this work,we perform a statistical investigation towards 50 high-mass clumps using data from the Bolocam Galactic Plane Survey（BGPS）and Millimetre Astronomy Legacy Team 90-GHz survey（MALT90）.Eleven dense molecular lines（N2H^＋（1–0）,HNC（1–0）,HCO^＋（1–0）,HCN（1–0）,HN^（13）C（1–0）,H^（13）CO^＋（1–0）,C2H（1–0）,HC3N（10–9）,SiO（2–1）,^（13）CS（2–1）and HNCO（4（4,0）-3（0,3）））are detected.N2H^＋ and HNC are shown to be good tracers for clumps in various evolutionary stages since they are detected in all the fields.The detection rates of N-bearing molecules decrease as the clumps evolve,but those of O-bearing species increase with evolution.Furthermore,the abundance ratios[N2H^＋]/[HCO^＋]and log（[HC3N]/[HCO^＋]）decline with log（[HCO^＋]）as two linear functions,respectively.This suggests that N^＋2H^＋ and HC3N transform to HCOas the clumps evolve.We also find that C2H is the most abundant molecule with an order of magnitude 10^（-8）.In addition,three new infall candidates,G010.214–00.324,G011.121–00.128 and G012.215–00.118（a）,are discovered to have large-scale infall motions and infall rates with an order of magnitude 10^（-3）M⊙yr^（-1）.

High-strong-ductile magnesium alloys by interactions of nanoscale quasi-long period stacking order unit with twin

Magnesium alloys with high strength in combination of good ductility are especially desirable for applications in transportation,aerospace and bio-implants owing to their high stiffness,abundant raw materials,and environmental friendliness.However,the majority of traditional strengthening approaches including grain refining and precipitate strengthening can usually prohibit dislocation movement at the expense of ductility invariably.Herein,we report an effective strategy for simultaneously enhancing yield strength(205 MPa,2.41 times)and elongation(23%,1.54 times)in a Mg-0.2Zn-0.6Y(at.%)alloy at room temperature,based on the formation of a nanosized quasi-long period stacking order unit(QLPSO)-twin structure by ultrahigh-pressure treatment followed by annealing.The formation reason and strong-ductile mechanism of the unique QLPSO-twin structure have been clarified by transmission electron microscopy observations and molecule dynamics simulations.The improved strength is mainly associated with the presence of nanosized QLPSO and the modified∠86.3oQLPSO-twin boundary(TB)interface,effectively pinning dislocation movement.Comparatively,the enhanced ductility is related to the∠3.7oQLPSO-TB interface and micro-kinks of nanoscale QLPSO,providing some paths for plastic deformation.This strategy on the QLPSO-twin structure might provide an alternative perspective for designing innovative hexagonal close-packed structural materials with superior mechanical properties.

THE COLLAPSE OF POLYETHYLENE RINGS ON AN ATTRACTIVE SURFACE

Polymers exhibit extended structures at high temperatures or in good solvents and collapsed configurations at low temperatures or in poor solvents. This fundamental property is crucial to the design of materials, and indeed has been extensively studied in recent years. In this paper, the collapse of polyethylene rings on an attractive surface was investigated by using molecular dynamics simulations. It is found that the collapse of ring chains on the attractive surface is of distinct difference from their free counterparts, where the collapse becomes more continuous and a one-stage instead of two-stage collapse can be identified by the specific heat. Some hairpin-like crystal structures are found at low temperatures, which are induced by the adsorption interaction of polymer-surface. For a given chain length, the results were further compared with those of the adsorbed linear chains. Due to the topological constraint of ring chains, the number of hairpin structures is clearly less than that of the linear chains. These numerical simulations may provide some new insights into the folding of ring polymers under adsorption interactions.