Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Influence of temperature and alloying elements on the threshold displacement energies in concentrated Ni–Fe–Cr alloys

Concentrated solid-solution alloys(CSAs) have demonstrated promising irradiation resistance depending on their compositions. Under irradiation, various defects can be produced. One of the most important parameters characterizing the defect production and the resulting defect number is the threshold displacement energies(E_d). In this work, we report the results of E_dvalues in a series of Ni–Fe–Cr concentrated solid solution alloys through molecular dynamics(MD)simulations. Based on several different empirical potentials, we show that the differences in the E_dvalues and its angular dependence are mainly due to the stiffness of the potential in the intermediate regime. The influences of different alloying elements and temperatures on E_dvalues in different CSAs are further evaluated by calculating the defect production probabilities. Our results suggest a limited influence of alloying elements and temperature on E_dvalues in concentrated alloys. Finally, we discuss the relationship between the primary damage and E_dvalues in different alloys. Overall, this work presents a thorough study on the E_dvalues in concentrated alloys, including the influence of empirical potentials,their angular dependence, temperature dependence, and effects on primary defect production.     

Experimental study on age and gender differences in microscopic movement characteristics of students

Campus security has aroused many concerns from the whole society. Stampede is one of the most frequent and influential accidents in campus. Studies on pedestrian dynamics especially focusing on students are essential for campus security, which are helpful to improve facility design and emergency evacuation strategy. In this paper, primary and middle school students were recruited to participate in the single-file experiments. The microscopic movement characteristics,including walking speed, headway, gait characteristics(step length, step frequency and swaying amplitude) and their relations were investigated. Age and gender differences in the headway-speed diagram and space requirements were analyzed by statistical tests. The results indicated that the impacts of age and gender were significant. There were three stages for the influence of gender on the headway-speed diagram for both age groups. The impacts on students' space requirements were consistent for different age and gender groups. But the impacts of age and gender on free-flow speed were affected by each other. Due to the connection of walking speed and gait characteristics, the comparisons of gait characteristics between different ages and genders were performed to understand the corresponding differences in speed more deeply. The results showed that differences in step length and swaying amplitude between males and females were significant for both age groups. The effect of gender on step frequency was significant for primary students. But for middle school students,whether gender had significant impact on step frequency was not clear here because of the large P-value. Besides, the influence of age on gait characteristics changed with gender.     

水化硅酸钙纳米压痕分子动力学模拟方法优化

针对水化硅酸钙纳米压痕模型忽视了压头与基底之间相互作用的问题，由尺寸差异引起的金刚石压头难以计算的问题，以及Wittmann模型无法得到实际接触面积的问题，提出了新的模型与计算方法．结合分子动力学方法，采用金刚石压头-Wittmann模型基底的组合方式构建无定形态水化硅酸钙纳米压痕试验模型．在建模阶段，考虑到压头模型与基底模型粒子间尺寸差异，提出了等比例替换模型，通过公式推导并就不同尺寸模拟结果验证了等比例替换模型的可行性．在计算阶段，提出了局部前处理的弛豫方法进行模拟．确定最大荷载位置处的接触面积为546 nm2，进而求出水化硅酸钙模型硬度H为0.84 GPa、折合模量Er为30.52 GPa．并通过纳米压痕试验，验证了模拟结果的准确性，证明了模型的科学性，对今后水化硅酸钙(C-S-H)纳米层面的模拟具有重要借鉴意义．     

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis₂ complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis₂ is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.     

Computational Insights into the Allosteric Effect and Dynamic Structural Features of the SARS-COV-2 Spike Protein

COVID-19 caused by SARS-COV-2 is continuing to surge globally. The spike (S) protein is the key protein of SARS-COV-2 that recognizes and binds to the host target ACE2. In this study, molecular dynamics simulation was used to elucidate the allosteric effect of the S protein. Binding of ACE2 caused a centripetal movement of the receptor-binding domain of the S protein. The dihedral changes in Phe329 and Phe515 played a key role in this process. Two potential cleavage sites S1/S2 and S2′ were exposed on the surface after the binding of ACE2. The binding affinity of SARS-COV-2 S protein and ACE2 was higher than that of SARS-COV. This was mainly due to the mutation of Asp480 in SARS-COV to Ser494 in SARS-COV-2, which greatly weakened the electrostatic repulsion. The result provides a theoretical basis for the SARS-COV-2 infection and aids the development of biosensors and detection reagents.     

Cycloparaphenylene and their radicals anchored to a metal−organic framework

Cycloparaphenylene (CPP) shows modulated photophysical and electronic properties due to its strained structure and radially oriented π-electron system. Incorporation of CPP into metal-organic frameworks (MOFs) could transfer its extensive properties in solution to porous solids. Moreover, with the unique arrangement of the macrocycles and their interactions with the framework, emerging characteristics are anticipated. As an example of “robust dynamics”, we synthesized the first MOF structure (FDM-1001) with CPP precisely anchored to the ordered framework by employing a [8]CPP-containing linear dicarboxylate linker. Metric relationship between the dynamic macrocycles and the robust backbone creates ideal π-π interactions between them, which leads to an essentially directional arrangement of [8]CPP in the three-dimensional space. Furthermore, the MOF with [8]CPP could be successfully oxidized to generate an infinite array of radicals that show enhanced air stability compared to its molecular analogue.     

Molecular dynamic study of dielectric polarization and ferroelectricity in a model polar polymer

Molecular dynamics simulations are used to explore the polarization response of a lamellar crystal consisting of folded chains of a highly simplified model polar polymer. The system is based on a united atom model of polyethylene with constrained bond lengths and bond angles, and it is endowed with artificial partial charges placed on the united atoms to give it a simple polar character. Simulations performed with various temperatures, electric field directions, and electric field application histories reveal a complicated sequence of reorientation processes, including pronounced ferroelectric behavior. The sequence includes a weak, temperature‐independent prompt response, and a slow‐rising delay regime with stretched exponential behavior and thermally‐activated reorientation parameters consistent with trans‐gauche (TG) barrier crossings in the amorphous phase. When the delay regime has progressed sufficiently, a primary large‐amplitude response due to organized rotation of large subsegments in the crystalline phase occurs in a rapid manner that requires relatively few TG barrier crossings. A final, extremely slow rise in residual polarization completes the sequence. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 740–759     

Composition-dependent melting behaviour of NaxK55–x core–shell nanoalloys

Molecular dynamics simulations at constant temperature are performed to investigate melting-like transition in Na₁₃K₄₂, Na₁₉K₃₆ and Na₂₆K₂₉ nanoalloys using a second-moment-approximation tight-binding analytic potential to calculate the forces on the constituent atoms. A weighted histogram analysis method is employed to remove non-ergodicity issues due to the complex potential energy surface of these nanoalloys. The heat capacity shows three distinctive steps in melting for Na₁₃K₄₂, while Na₂₆K₂₉ and Na₁₉K₃₆ have two-step and one-step melting transition, respectively. The steepest descent method is used to quench the configurations in a given interval during the simulation and also study the isomerisation processes occurring at different temperatures. Analysing the configuration energies of quenched structures for the entire nanoalloy and the core atoms separately gives more details about the melting mechanism. The Lindemann parameter is also calculated at several temperatures during the simulation which shows a gradual increase for Na₁₃K₄₂ and Na₂₆K₂₉ while a sharp change is observed for Na₁₉K₃₆. These findings are in agreement with the multi-step nature of the phase transition in Na₁₃K₄₂ and Na₂₆K₂₉ and one-step melting of the Na₁₉K₃₆ magic composition.