Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.     

Tetracyclines as a potential antiviral therapy against Crimean Congo hemorrhagic fever virus: Docking and molecular dynamic studies

Crimean-Congo Hemorrhagic Fever Virus (CCHFV) is one of the deadliest human diseases with mortality rate near 50%. Special attention should be paid to this virus since there is no approved treatment for it. On the other hand, the recent outbreak of Ebola virus which is a member of hemorrhagic fever viruses shows this group of viruses can be extremely dangerous. Previous studies have indicated that nucleoprotein of CCHFV, a pivotal protein in virus replication, is an appropriate target for antiviral drug development. The aim of this study is finding inhibitor(s) of this protein. Herein, a virtual screening procedure employing docking followed by molecular dynamic was used to identify small molecule inhibitors of the nucleoprotein from FDA-approved drugs. Regarding CCHFV, using in-silico method is a safe way to achieve its inhibitor(s) since this virus is categorized as a World Health Organization (WHO) biosafety level 4 pathogen and therefore investigation in general laboratories is restricted. In conclusion, considering docking and molecular dynamic results alongside with bioavailability of FDA-approved drugs, doxycycline and minocycline are proposed as potential inhibitors of CCHFV nucleoprotein. There is hope, this study encourage other research groups for in-vitro and in-vivo studies about the efficacy of those two medicines in CCHFV treatment.     

A Gibbs sampling method to determine biomarkers for asthma

PurposeTo identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling.MethodsThe molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0.6. Moreover, the differentially expressed genes (DEGs) and their correlated genes were screened and merged, called as co-expressed genes. Pathways enrichment analysis was implemented for the co-expressed genes.ResultsBased on the gene set more than 5, overall 396 MFs were determined. After Gibbs sampling, 5 differentially expressed MF were acquired according to alfa.pi > 0.6. Moreover, the genes in these 5 differentially expressed MF were merged, and 110 DEGs were identified. Subsequently, 338 co-expressed genes were gained. Based on the P value < 0.01, the co-expressed genes were significantly enriched in 6 pathways. Among these, ubiquitin mediated proteolysis contained the maximum numbers of 35 co-expressed genes, and cell cycle were enriched by the second largest number of 11 co-expressed genes, respectively.ConclusionsThe identified pathways such as ubiquitin mediated proteolysis and cell cycle might play important roles in the development of asthma and may be useful for developing the credible therapeutic approaches for diagnosis and treatment of asthma in future.     

Understanding Molecular Dynamics with Stochastic Processes via Real or Virtual Dynamics

Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation[J. Chem. Phys. 147 , 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme[J. Chem. Phys. 147 , 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation is proposed for understanding efficient stochastic thermostatting processes with molecular dynamics.     

计算材料科学中桥域多尺度方法的若干进展

材料科学中存在固有的多尺度特性,桥域多尺度方法是在宏观尺度(如连续介质力学)中引入不同的细微观尺度的计算区域,乃至纳米尺度的分子动力学、量子力学计算区域,将不同尺度的研究方法通过一定的数学模型耦合在一起。该方法既能节约计算成本,又能保证所研究问题的物理特性。本文对多尺度方法的基本概念、跨尺度桥域多尺度方法的发展、基本原理、耦合方法和离散方程进行了讨论,给出了几个应用算例,并在最后进行了总结,展望了今后的可能发展方向。     

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes (SWCNT’s) is established to describe the nonlinear stress-strain curve of SWCNT’s and to predict both the elastic properties and breaking strain of SWCNT’s during tensile deformation. An analysis based on the virtual internal bond (VIB) model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT’s. The project supported by the National Natural Science Foundation of China (10121202, 90305015 and 10328203), the Key Grant Project of Chinese Ministry of Education (0306) and the Research Grants Council of the Hong Kong Special Administrative Region, China (HKU 7195/04E).     

Harmonic behavior of silicon nanowire by molecular dynamics

Silicon nanowires (SiNW) have attracted increasing interests as potential core parts for nanoscale devices due to their distinguished mechanical and electrical properties. Using molecular dynamics (MD) method, we investigated the vibration behaviors of SiNW on the atomic scale, including the fundamental mode frequency and quality factor. The quality factor as low as 120 is attributed to the energy loss process coming from atomic friction and nonlinearity. We also found that the energy of lattice vibration (phonon energy) is much larger than the macroscale beam vibration energy. And both the energies are less than the surface relaxation energy of the beam. The comparison between MD and FEM has been made to discuss the validity of continuum approximation for the study of SiNW.     

Observability and topological dynamics

Using methods of topological dynamics, we study sufficiency conditions for observability of a given dynamical system (X, T) by a continuous output function. In particular, we show that ifX has either finite topological or covering dimension andT does not have infinitely many periodic points with same period, then (X, T) admits an observable. The paper also gives a partial survey of various related results and improves some of them.Dedicated to the memory of Douglas McMahon.     

Influence of Molecular Characteristics of a Substance on Detonation Phenomena

In the present study, the molecular-dynamics method has been used to examine the influence of the thermal effect of the chemical reaction on processes in a detonating molecular crystal (propagation velocity and structure of the detonation wave, delay time of the chemical reaction, and energy macrocharacteristics of the crystal in the disturbed region). Molecular-dynamics data are compared with predictions of the continuum theory of detonation; in particular, fulfillment of the Chapman–Jouguet condition is verified.     

5d过渡金属原子掺杂氮化铝纳米管电子结构、磁性性质的第一性原理计算

采用基于密度泛函理论(DFT)的第一性原理计算方法, 研究了5d过渡金属原子(Lu、Hf、Ta、W、Re、Os、Ir、Pt、Au、Hg)取代AlN纳米管(AlNNTs)中的铝原子或氮原子时体系的几何结构、电子结构和磁性性质; 并且以理想AlN纳米管(AlNNTs)、Al缺陷体系(VAl)和N缺陷体系(VN)的结果作为对比. 研究发现: 5d 原子取代Al(Al5d)时体系的局域对称性接近于C3v, 但是取代N(N5d)时体系的局域对称性偏离C3v对称性较大; 当掺杂的5d元素相同时, Al5d的成键能比N5d的成键能大; 当掺杂体系相同时(Al5d或N5d), 其成键能基本上随着5d原子的原子序数的增大而降低; 掺杂体系中出现了明显的杂质能级, 给出了态密度等结果; 不同掺杂情况的磁矩不同, 总磁矩呈现出较强的规律性. 利用C3v对称性和分子轨道理论解释了过渡金属原子取代Al时杂质能级的产生和体系磁性的变化规律.