MM CALCULATIONS OF THE METAL-PROTEIN MODEL COMPLEXES Ⅰ.MOLECULAR FORCE FIELD FOR COBALT COMPEXES

Cobalt-protein complexes play an important role in biochemical processes.The structure of the model molecule,Co(H_2O)_3SO_4(phen) has been studied by molecular mechanics.The molecular force field (MM2) parameters have been developed for the particular class of the complexes.

Molecular force mechanism of hydrodynamics in clay nanopores

Nanopores are prevalent within various clay morphologies,and water flow in clay nanopores is significant for various engineering applications.In this study,we performed non-equilibrium molecular dynamics(NEMD)simulations to reveal the molecular force mechanisms of water flow in clay nanopores.The water dynamic viscosity,slip length,and average flow velocity were obtained to verify the NEMD models.Since the water confined in the nanopores maintained a dynamic mechanical equilibrium state,each water lamina can be regarded as a simply supported beam.The applied driving force,the force from clay crystal layers,the force from compensating sodium ions,and the force from other water laminae were further calculated to investigate the force mechanisms.The van der Wals barrier above the surface and hydraulic gradient lead to distribution differences in water oxygen atoms,which contribute to a net van der Waals resistance component of the force from clay crystal layers.Meanwhile,the water molecules tend to rotate to generate the electrostatic resistance component of the force from clay crystal layers and balance the increasing hydraulic gradient.Due to the velocity difference,the water molecules in the slower lamina have a higher tendency to lag and generate a net electrostatic resistance force as well as a net van der Waals driving force on the water molecules in the faster lamina,which together make up the viscous force.

Molecular simulation studies of hydrocarbon and carbon dioxide adsorption on coal

Sorption isotherms of hydrocarbon and carbon dioxide （CO2） provide crucial information for designing processes to sequester CO2 and recover natural gas from unmineable coal beds. Methane （CH4）, ethane （C2H6）, and CO2 adsorption isotherms on dry coal and the temperature effect on their maximum sorption capacity have been studied by performing combined Monte Carlo （MC） and molecular dynamics （MD） simulations at temperatures of 308 and 370 K （35 and 97 ~C） and at pressures up to 10 MPa. Simulation results demonstrate that absolute sorption （expressed as a mass basis） divided by bulk gas density has negligible temperature effect on CH4, C2H6, and CO2 sorption on dry coal when pressure is over 6 MPa. CO2 is more closely packed due to stronger interaction with coal and the stronger interaction between CO2 mole- cules compared, respectively, with the interactions between hydrocarbons and coal and between hydrocarbons. The results of this work suggest that the ＂a＂ constant （pro- portional to TcPc） in the Peng-Robinson equation of state is an important factor affecting the sorption behavior of hydrocarbons. CO2 injection pressures of lower than 8 MPa may be desirable for CH4 recovery and CO2 sequestration. This study provides a quantitative under- standing of the effects of temperature on coal sorptioncapacity for CH4, C2H6, and CO2 from a microscopic perspective.

NANOSCALE CUTTING OF MONOCRYSTALLINE SILICON USING MOLECULAR DYNAMICS SIMULATION

It has been found that the brittle material, monocrystalline silicon, can be machined in ductile mode in nanoscale cutting when the tool cutting edge radius is reduced to nanoscale and the undeformed chip thickness is smaller than the tool edge radius. In order to better understand the mechanism of ductile mode cutting of silicon, the molecular dynamics （MD） method is employed to simulate the nanoscale cutting of monocrystalline silicon. The simulated variation of the cutting forces with the tool cutting edge radius is compared with the cutting force results from experimental cutting tests and they show a good agreement. The results also indicate that there is silicon phase transformation from monocrystalline to amorphous in the chip formation zone that can be used to explain the cause of ductile mode cutting. Moreover, from the simulated stress results, the two necessary conditions of ductile mode cutting, the tool cutting edge radius are reduced to nanoscale and the undeformed chip thickness should be smaller than the tool cutting edge radius, have been explained.

Analyses of Conradin’s Becoming-animal in Saki’s Serdni Vashtar

Hector Hugo Munro(best known by his pen name Saki)is generally categorized as a master of short story who wrote witty and occasionally macabre stories that satirized hypocrisies and pretensions of Edwardian British society.However,one of the most prominent features of his short stories is that they are imbued with various animal characters,and his central positioning of the animal characters provides us a new perspective to interpret the relationship between animals and human beings.In Deleuze(and Guatari)’s philosophical thoughts and literary criticism,Becoming is of great importance.In Saki’s short story Serdni Vashtar,through Becoming-animal,the protagonist Conradin designed a beautiful line of flight and achieved his deterritorialization.Through his deterritorialization,he succeeded in getting rid of his cousin’s control and enhancing his molecular power to fight against the molar power of his cousin.Thus,the aim of this paper is to analyze the reasons and potential powers of Conradin’s becoming-animal,uncover the significance of Becoming in the current post-humanist context and explore a new form of relationship between human beings and animals from the perspective of Becoming-animal.

Studies on Single Chain Structure of Konjac Glucomannan

The simulation is carried out by employing the method of molecular dynamics with the single chain of konjac glucomannan （KGM） in vacuum as the structural model to discuss the factors that affect the single chain structure, the dynamic structure of the chain and the acting forces that maintain the chain structure. The results show that the shape and stability of the chain are affected by the degree of polymerization. As for the KGM with high degree of polymerization, its chain presents random coiling state and its stability declines. Both before and after deacetylation in the process of dynamic motion, the chain of KGM presents random coiling state with periodic variation of extension and coil and demonstrates favorable flexibility, indicating acetyl is not the main factor that affects the shape of chain, whereas dihedral angle and static actions are respectively the key bonding and nonbonding acting forces that influence the single chain conformations in vacuum.

Microscopic mechanism study and process optimization of dimethyl carbonate production coupled biomass chemical looping gasification system

Biomass chemical looping gasification technology is one of the essential ways to utilize abundant biomass resources.At the same time,dimethyl carbonate can replace phosgene as an environmentfriendly organic material for the synthesis of polycarbonate.In this paper,a novel system coupling biomass chemical looping gasification with dimethyl carbonate synthesis with methanol as an intermediate is designed through microscopic mechanism analysis and process optimization.Firstly,reactive force field molecular dynamics simulation is performed to explore the reaction mechanism of biomass chemical looping gasification to determine the optimal gasification temperature range.Secondly,steady-state simulations of the process based on molecular dynamics simulation results are carried out to investigate the effects of temperature,steam to biomass ratio,and oxygen carrier to biomass ratio on the syngas yield and compositions.In addition,the main energy indicators of biomass chemical looping gasification process including lower heating value and cold gas efficiency are analyzed based on the above optimum parameters.Then,two synthesis stages are simulated and optimized with the following results obtained:the optimal temperature and pressure of methanol synthesis stage are 150℃ and 4 MPa;the optimal temperature and pressure of dimethyl carbonate synthesis stage are 140℃ and 0.3 MPa.Finally,the pre-separation-extraction-decantation process separates the mixture of dimethyl carbonate and methanol generated in the synthesis stage with 99.11%purity of dimethyl carbonate.Above results verify the feasibility of producing dimethyl carbonate from the perspective of multi-scale simulation and realize the multi-level utilization of biomass resources.

Atomistic understanding of rough surface on the interfacial friction behavior during the chemical mechanical polishing process of diamond

The roughness of the contact surface exerts a vital role in rubbing.It is still a significant challenge to understand the microscopic contact of the rough surface at the atomic level.Herein,the rough surface with a special root mean square(RMS)value is constructed by multivariate Weierstrass–Mandelbrot(W–M)function and the rubbing process during that the chemical mechanical polishing(CMP)process of diamond is mimicked utilizing the reactive force field molecular dynamics(ReaxFF MD)simulation.It is found that the contact area A/A0 is positively related with the load,and the friction force F depends on the number of interfacial bridge bonds.Increasing the surface roughness will increase the friction force and friction coefficient.The model with low roughness and high lubrication has less friction force,and the presence of polishing liquid molecules can decrease the friction force and friction coefficient.The RMS value and the degree of damage show a functional relationship with the applied load and lubrication,i.e.,the RMS value decreases more under larger load and higher lubrication,and the diamond substrate occurs severer damage under larger load and lower lubrication.This work will generate fresh insight into the understanding of the microscopic contact of the rough surface at the atomic level.

Impact of lithium nitrate additives on the solid electrolyte interphase in lithium metal batteries

Lithium metal batteries(LMBs)represent a promising frontier in energy storage technology,offering high energy density but facing significant challenges.In this work,we address the critical challenge of lithium dendrite for-mation in LMBs,a key barrier to their efficiency and safety.Focusing on the potential of electrolyte additives,specifically lithium nitrate,to inhibit dendritic growth,we employ advanced multi-scale simulation techniques to explore the formation and properties of the solid electrolyte interphase(SEI)on the anode surface.Our study introduces a novel hybrid simulation methodology,HAIR(Hybrid ab initio and Reactive force field Molecular Dynamics),which combines ab initio molecular dynamics(AIMD)and reactive force field molecular dynamics(RMD).This approach allows for a more precise and reliable examination of the interaction mechanisms of nitrate additives within LMBs.Our findings demonstrate that lithium nitrate contributes to the formation of a stable and fast ionic conductor interface,effectively suppressing dendrite growth.These insights not only advance our un-derstanding of dendrite formation and mitigation strategies in lithium metal batteries,but also highlight the efficacy of HAIR as a pioneering tool for simulating complex chemical interactions in battery materials,offering significant implications for the broader field of energy storage technology.

3D-QSAR Studies on the Imidazopyrimidine Derivatives

Comparative molecular field analysis(CoMFA) and comparative molecular similarity indices analysis(CoMSIA) for imidazopyrimidine derivatives were performed to get the molecular active conformation selection, molecular alignment, as well as the establishment of corresponding 3 D-QSAR model. The model established by this method has good ability to predict such compounds. For CoMFA model, the cross-validated q2 and non-cross-validated r2 values are 0.665 and 0.872, respectively. The best q2 value for CoMSIA model is 0.632 and r2 value is 0.923. Using this information and the three-dimensional equipotential map for molecular design can theoretically obtain some new antibacterial drugs with higher activity. There are two newly designed molecules with activity values of 7.921 and 7.872, which are higher than that of the template molecule No. 12 with an activity value of 7.850, and the QSAR research results can provide a theoretical reference for the synthesis of new drugs.